Citation: Sawako Takahashi, Ayana Takayanagi, Yurika Takahashi, Taku Oshima, Hiromi Nishida. Comparison of transcriptomes of enlarged spheroplasts of Erythrobacter litoralis and Lelliottia amnigena[J]. AIMS Microbiology, 2016, 2(2): 152-189. doi: 10.3934/microbiol.2016.2.152
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Enlarged spheroplasts are generated by spheroplast cultivation in a broth containing an inhibitor of peptidoglycan synthesis (for example, penicillin) and high salt concentration after lysozyme treatment of bacterial cells [1,2,3,4,5]. In presence of penicillin, spheroplasts do not divide but grow and enlarge with DNA replication in the marine broth, whereas they divide in the absence of penicillin [6,7]. The rate of DNA increase in the absence of penicillin is higher than that observed in the presence of penicillin [6,7].
Lelliottia amnigena(Enterobacter amnigenus) belongs to the family Enterobacteriaceae of Gram-negative bacteria [8]. Most enlarged spheroplasts of L. amnigena have quite different sizes of the inner and outer membrane vesicles [9]; the inner membrane shows a maximum size of approximately 15 μm in diameter, while the outer membrane has a maximum size of > 30 μm in diameter. Vacuole-like structures were formed in enlarged spheroplasts of L. amnigena. Based on the membrane specific protein distribution in Escherichia coli, the membrane of these vacuole-like structures is very similar but not identical to the inner membrane, which is completely different from the outer membrane [4].
Erythrobacter litoralisis an aerobic, anoxygenic, and photosynthetic marine bacterium, belonging to Alphaproteobacteria, which generates bacteriochlorophyll a and carotenoids [10]. The size of E. litoralis spheroplasts is limited to a diameter of 6-7 μm [7]. Continuous exposure to light was shown to inhibit their enlargement [7]. In addition, they lacked vacuole-like structures. We hypothesized that the difference of enlarged spheroplast size and the lack of vacuole-like structure may be related to the difference of general metabolism in bacterial cells. In contrast, the Gram-positive bacterium Bacillus subtilis and the Gram-negative bacterium E. coli are known to form vacuole-like structures and their cell size is approximately 15 μm in diameter [4,5]. Divergence between inner and outer membranes enlargements is not observed in E. litoralis enlarged spheroplasts.
Thus, the giant spheroplasts of E. litoralis and L. amnigena are structurally different. In order to elucidate this difference, we sequenced the RNAs expressed in the spheroplasts at the beginning of growth and in the enlarged spheroplasts. We then compared the changes in expression of the orthologous genes between the enlarged spheroplasts of E. litoralis andL. amnigena.
Cells of E. litoralis NBRC 102620 and L. amnigena (Enterobacter amnigenus) NBRC 105700 were grown on marine broth agar (Difco, Sparks, MD). The harvested cells (approximately 0.003 g) were suspended in a buffer (1 mL) consisting of 0.1 M Tris-HCl (pH 7.6) and 0.3 M sucrose. Lysozyme (200 μg/mL, Wako, Osaka) was added to the cell suspension and allowed to incubate at 25 °C (for E. litoralis) and 37 °C (for L. amnigena) for 15 min. After harvesting (centrifugation for 5 min at 3000 rpm) the suspension, the cells were suspended in marine broth (1 mL) containing 600 μg/mL penicillin G (Serva, München). The suspension was then diluted by adding 4 μL of suspension to marine broth (1 mL) containing penicillin G. The diluted suspension was then incubated at 25 °C in the dark. We used spheroplasts at two time points of growth: 0 h and 96 h for E. litoralis, and 0 h and 43 h for L. amnigena.
Fluorescence images of enlarged L. amnigena cells stained with DAPI were acquired. DAPI (final concentration, 0.25 μg/mL) was added to the cell suspension and incubated at room temperature for 1 h. Fluorescent micrographs were taken using Keyence BZ-X710.
Total RNA was isolated using the NucleoSpin RNA kit (Macherey-Nagel, Düren). After removal of rRNA with the RiboMinus Transcriptome Isolation Kit for bacteria (Thermo Fisher Science, Waltham, MA), the RNAs were purified and concentrated with the NucleoSpin RNA Clean-up XS kit (Macherey-Nagel, Düren).
Sequencing libraries were prepared from RiboMinus-treated RNAs by NEXTflex qRNA-Seq Kit (Bioo Scientific, Austin, TX). The resultant libraries were analyzed by TapeStation 2200 (Agilent, Waldbronn) equipped with a High Sensitivity D1000 tape (Agilent, Waldbronn). The concentration of each library was quantified with KAPA Library Quantification Kits. The four libraries were sequenced on a Miseq system (Illumina, San Diego, CA) with 2 × 75 base paired end sequencing.
FASTQ files were imported into the CLC Genomic Workbench (CLC bio, Germantown, MD) as paired-end reads, and read data were mapped on each genome by RNA-seq with the following parameters: Count paired reads as two = Yes, Auto-detect paired distances = No, Similarity fraction = 0.8, Length fraction = 0.5, Mismatch cost = 2, Insertion cost = 3, Deletion cost = 3.
We performed reciprocal best hits using BLASTp (E-value < 0.001) to select orthologous genes between E. litoralis and L. amnigena. For orthologous genes, we calculated the ratio of reads per kilobase of gene per million mapped sequence reads (RPMK) in the enlarged spheroplasts per the RPKM in spheroplasts at 0 h of growth and selected the ratio of > 2 for the upregulated genes and the ratio of < 0.5 for the downregulated genes. The difference in expression was estimated by Fisher's exact test [11]. Considering that the mapped number of E. litoralis spheroplasts was 3 times greater than that of spheroplasts at 0 h of growth, when the RPKM = 0 (the mapped number = 0) in E. litoralis spheroplasts at 0 h of growth, we did not consider the genes with the mapped number 1, 2, and 3 in E. litoralis enlarged spheroplasts but considered the genes with the mapped number > 3 in enlarged spheroplasts as upregulated genes.
In a previous study, it was observed that spheroplasts of L. amnigena elongated and divided in marine broth containing 3 μg/mL penicillin [9]. In contrast, in marine broth containing 300 μg/mL penicillin, they did not divide and became enlarged with differing sizes of the inner and outer membrane vesicles [9]. The fluorescence image of L. amnigena enlarged spheroplasts showed that the vacuole-like structures and the large periplasmic space were not stained with the DNA staining reagent DAPI (Figure 1). This indicates that the chromosomal DNA does not pass through the inner membrane of the enlarged spheroplasts or the membrane of the vacuole-like structures.
We obtained 78934 and 62870 reads from the spheroplasts of E. litoralis at the beginning (0 h) of growth and after enlargement, respectively. Excluding the RNA sequences that map to the ribosomal RNA genes (61767 reads at the beginning; 31412 reads after enlargement) and did not map to the genomic DNA (10565 reads at the beginning; 8902 reads after enlargement), 6602 and 22556 RNA sequences were mapped from the spheroplasts of E. litoralis at the beginning (0 h) of growth and after enlargement, respectively. On the other hand, we obtained 6921404 and 957576 reads from the spheroplasts of L. amnigena at the beginning (0 h) of growth and after enlargement, respectively. Excluding the RNA sequences that map to the ribosomal RNA genes (6532071 reads at the beginning; 701391 reads after enlargement) and did not map to the genomic DNA (330459 reads at the beginning; 174806 reads after enlargement), 58874 and 81379 RNA sequences were mapped at the beginning (0 h) of growth and after enlargement from the spheroplasts of L. amnigena. The RPKMs were then calculated and compared at the gene expression level.
The transcriptome data have been deposited in DDBJ under the accession number DRA004675.
We identified 1100 orthologous gene pairs between E. litoralis and L. amnigena. Among these 1100 orthologs, 347 and 213 genes were more than 2-fold upregulated in the enlarged spheroplasts of E. litoralis and L. amnigena, respectively; whereas 193 and 269 genes were less than 0.5-fold downregulated in those of E. litoralis and L. amnigena, respectively (Figure 2, Supplementary Table 1).
The 76 upregulated orthologous genes in both E. litoralis and L. amnigena enlarged spheroplasts are shown in Table 1. Of the 76 genes, 25 (32.9%) were homologous to membrane protein coding genes.
Protein ID of E. litoralis | RPKM in E. litoralis spheroplasts at the beginning of growth | RPKM in E. litoralis enlarged spheroplasts | Ratio of RPKMs of E. litoralis | Annotated function | Protein ID of L. amnigena | RPKM in L. amnigena spheroplasts at the beginning of growth | RPKM in L. amnigena enlarged spheroplasts | Ratio of RPKMs of L. amnigena | Annotated function |
Homologs of chaperone genes | |||||||||
KEO89606.1* | 0.00 | 623.74 | molecular chaperone GroES | KDM56993.1* | 347.00 | 1300.00 | 3.75 | chaperonin | |
KEO92782.1* | 0.00 | 4575.93 | phage shock protein | KDM46724.1* | 4670.00 | 27100.00 | 5.80 | phage shock protein A | |
KEO93197.1* | 0.00 | 2039.77 | ATP-dependent protease | KDM53259.1* | 178.00 | 608.00 | 3.42 | ATP-dependent protease ATPase subunit HslU | |
KEO93350.1* | 588.91 | 6885.08 | 11.69 | ATPase AAA | KDM51144.1* | 449.00 | 1660.00 | 3.70 | chaperone ClpB |
KEO98976.1* | 265.47 | 587.82 | 2.21 | molecular chaperone DnaJ | KDM57339.1* | 267.00 | 751.00 | 2.81 | chaperone dnaJ |
Homologs of DNA replication and repair-related genes | |||||||||
KEO92279.1* | 304.84 | 659.99 | 2.17 | ATPase AAA | KDM53654.1* | 0.00 | 8.08 | Mg chelatase-like protein | |
KEO92303.1* | 0.00 | 255.35 | chromosomal replication initiator protein DnaA | KDM52760.1* | 280.00 | 617.00 | 2.20 | chromosomal replication initiator protein dnaA | |
KEO92620.1* | 1142.64 | 8813.23 | 7.71 | recombinase RecA | KDM50414.1* | 401.00 | 893.00 | 2.23 | protein recA |
Homologs of lipopolysaccharide synthesis and transport-related genes | |||||||||
KEO89583.1* | 0.00 | 224.27 | ABC transporter ATP-binding protein | KDM54743.1* | 46.80 | 339.00 | 7.24 | lipopolysaccharide export system ATP-binding protein LptB | |
KEO90699.1* | 309.18 | 1369.19 | 4.43 | D-arabinose 5-phosphate | KDM54739.1* | 34.40 | 74.70 | 2.17 | arabinose 5-phosphate isomerase |
KEO92387.1* | 0.00 | 693.72 | permease | KDM54753.1* | 201.00 | 458.00 | 2.28 | lipopolysaccharide export system permease lptF | |
KEO96424.1* | 321.43 | 901.51 | 2.80 | ABC transporter | KDM55137.1* | 29.10 | 91.30 | 3.14 | lipid A export ATP-binding/permease MsbA |
KEO98632.1* | 0.00 | 130.74 | MFS transporter | KDM50532.1* | 0.00 | 10.30 | lysophospholipid transporter lplT | ||
Homologs of peptidoglycan synthesis-related genes | |||||||||
KEO92316.1* | 0.00 | 1429.28 | MltA | KDM50514.1* | 46.40 | 123.00 | 2.65 | membrane-bound lytic murein transglycosylase A | |
KEO93302.1* | 0.00 | 801.96 | peptidoglycan transglycosylase | KDM54749.1* | 0.00 | 16.90 | monofunctional biosynthetic peptidoglycan transglycosylase | ||
KEO93307.1* | 0.00 | 252.66 | N-acetylmuramoyl-L-alanine amidase | KDM55076.1* | 20.40 | 118.00 | 5.78 | N-acetylmuramoyl-L-alanine amidase AmiD | |
KEO93413.1* | 0.00 | 408.49 | peptidoglycan glycosyltransferase | KDM57390.1* | 115.00 | 452.00 | 3.93 | peptidoglycan synthase ftsI | |
KEO93417.1* | 0.00 | 193.99 | UDP-N-acetylmuramoylalanine--D-glutamate ligase | KDM57394.1* | 116.00 | 802.00 | 6.91 | UDP-N-acetylmuramoylalanine-D-glutamate ligase | |
Homologs of other membrane protein genes | |||||||||
KEO89306.1* | 1090.43 | 2253.52 | 2.07 | membrane protease subunit HflC | KDM56960.1* | 135.00 | 599.00 | 4.44 | protein HflC |
KEO89307.1* | 535.14 | 3554.84 | 6.64 | peptidase | KDM56961.1* | 431.00 | 1380.00 | 3.20 | protein HflK |
KEO89575.1* | 0.00 | 225.11 | flagellar biosynthesis protein FliR | KDM48637.1* | 0.00 | 31.30 | flagellar biosynthetic protein fliR | ||
KEO89580.1* | 0.00 | 221.23 | mechanosensitive ion channel protein MscS | KDM55515.1* | 68.20 | 188.00 | 2.76 | miniconductance mechanosensitive channel | |
KEO92762.1* | 0.00 | 194.41 | membrane protein | KDM51940.1* | 0.00 | 16.20 | hypothetical protein | ||
KEO93138.1* | 0.00 | 505.31 | ABC transporter | KDM55480.1* | 321.00 | 823.00 | 2.56 | hypothetical protein | |
KEO93143.1* | 0.00 | 301.81 | proline:sodium symporter PutP | KDM51759.1* | 495.00 | 1180.00 | 2.38 | sodium/proline symporter | |
KEO96616.1* | 0.00 | 211.59 | membrane protein | KDM48736.1* | 116.00 | 568.00 | 4.90 | hypothetical protein | |
KEO96782.1* | 0.00 | 281.12 | MarC family transcriptional regulator | KDM46654.1* | 0.00 | 37.90 | UPF0056 membrane protein yhcE | ||
KEO96802.1* | 0.00 | 526.58 | hypothetical protein | KDM51307.1* | 54.80 | 674.00 | 12.30 | manganese transporter mntH | |
KEO98444.1* | 159.95 | 613.91 | 3.84 | protoheme IX farnesyltransferase | KDM55407.1* | 612.00 | 1340.00 | 2.19 | protoheme IX farnesyltransferase |
KEO98495.1* | 0.00 | 1075.18 | hypothetical protein | KDM55130.1* | 24.50 | 70.90 | 2.89 | UPF0702 transmembrane protein ycaP | |
KEO98569.1* | 201.21 | 3148.42 | 15.65 | histidine kinase | KDM51863.1* | 0.00 | 16.80 | sensor protein phoQ | |
KEO98609.1* | 288.10 | 612.40 | 2.13 | membrane protein | KDM57482.1* | 316.00 | 742.00 | 2.35 | outer membrane protein assembly factor yaeT |
KEO99117.1* | 0.00 | 227.97 | membrane protein | KDM54035.1* | 14.10 | 51.10 | 3.62 | hypothetical protein | |
Others | |||||||||
KEO89324.1* | 0.00 | 339.26 | mannose-1-phosphate guanylyltransferase | KDM46222.1* | 118.00 | 1610.00 | 13.64 | mannose-1-phosphate guanylyltransferase | |
KEO89964.1* | 0.00 | 1086.92 | taurine dioxygenase | KDM57053.1* | 19.90 | 115.00 | 5.78 | alpha-ketoglutarate-dependent taurine dioxygenase | |
KEO89994.1* | 0.00 | 480.32 | aminomethyltransferase | KDM49721.1* | 264.00 | 696.00 | 2.64 | aminomethyltransferase | |
KEO90662.1* | 0.00 | 165.87 | phosphoribosylaminoimidazole carboxylase | KDM55484.1* | 0.00 | 138.00 | N5-carboxyaminoimidazole ribonucleotide synthase | ||
KEO90672.1* | 0.00 | 261.97 | succinyl-CoA synthetase subunit beta | KDM55689.1* | 480.00 | 1360.00 | 2.83 | succinyl-CoA ligase [ADP-forming] subunit beta | |
KEO91012.1* | 0.00 | 329.01 | glutamyl-tRNA synthetase | KDM57451.1* | 0.00 | 13.80 | glutamyl-Q tRNA(Asp) synthetase | ||
KEO92307.1* | 0.00 | 1173.54 | 2-octaprenylphenol hydroxylase | KDM52399.1* | 41.40 | 112.00 | 2.71 | 2-polyprenylphenol 6-hydroxylase | |
KEO92322.1* | 1243.70 | 5084.10 | 4.09 | alkyl hydroperoxide reductase | KDM55608.1* | 108.00 | 706.00 | 6.54 | alkyl hydroperoxide reductase subunit F |
KEO92357.1* | 0.00 | 486.82 | hypothetical protein | KDM55447.1* | 0.00 | 44.50 | maltose O-acetyltransferase | ||
KEO92389.1* | 0.00 | 1032.40 | Clp protease ClpS | KDM55108.1* | 212.00 | 689.00 | 3.25 | ATP-dependent Clp protease adapter protein ClpS | |
KEO92432.1* | 0.00 | 225.11 | acetyl-CoA acetyltransferase | KDM49670.1* | 0.00 | 10.40 | hypothetical protein | ||
KEO92626.1* | 0.00 | 371.92 | transcription elongation factor GreB | KDM53922.1* | 0.00 | 25.90 | transcription elongation factor greB | ||
KEO92766.1* | 0.00 | 499.00 | pseudouridine synthase | KDM54709.1* | 53.60 | 142.00 | 2.65 | tRNA pseudouridine synthase B | |
KEO92773.1* | 238.61 | 1937.27 | 8.12 | translation initiation factor IF-2 | KDM54711.1* | 645.00 | 1330.00 | 2.06 | translation initiation factor IF-2 |
KEO92898.1* | 0.00 | 183.68 | oxidoreductase | KDM50444.1* | 0.00 | 20.20 | formate hydrogenlyase subunit 2 | ||
KEO92901.1* | 0.00 | 211.59 | metallophosphoesterase | KDM54593.1* | 123.00 | 267.00 | 2.17 | protein icc | |
KEO93029.1* | 0.00 | 1061.69 | Fur family transcriptional regulator | KDM55662.1* | 494.00 | 1760.00 | 3.56 | ferric uptake regulation protein | |
KEO93118.1* | 0.00 | 351.20 | 4-hydroxythreonine-4-phosphate dehydrogenase | KDM57359.1* | 86.00 | 299.00 | 3.48 | 4-hydroxythreonine-4-phosphate dehydrogenase | |
KEO93158.1* | 0.00 | 513.67 | ubiquinone biosynthesis protein UbiH | KDM49723.1* | 43.20 | 93.80 | 2.17 | 2-octaprenyl-6-methoxyphenol hydroxylase | |
KEO93247.1* | 0.00 | 269.73 | TetR family transcriptional regulator | KDM55557.1* | 86.70 | 564.00 | 6.51 | HTH-type transcriptional regulator BetI | |
KEO93375.1* | 0.00 | 357.49 | 4-hydroxy-3-methylbut-2-enyl diphosphate reductase | KDM57347.1* | 53.60 | 142.00 | 2.65 | 4-hydroxy-3-methylbut-2-enyl diphosphate reductase | |
KEO93411.1* | 0.00 | 566.68 | 16S rRNA methyltransferase | KDM57388.1* | 162.00 | 1000.00 | 6.17 | ribosomal RNA small subunit methyltransferase H | |
KEO96480.1* | 303.62 | 627.48 | 2.07 | methionine sulfoxide reductase B | KDM51893.1* | 41.00 | 208.00 | 5.07 | peptide methionine sulfoxide reductase msrB |
KEO96529.1* | 0.00 | 210.35 | phosphoribosylamine--glycine ligase | KDM52454.1* | 92.00 | 380.00 | 4.13 | phosphoribosylamine-glycine ligase | |
KEO96539.1* | 0.00 | 696.27 | hypothetical protein | KDM51989.1* | 200.00 | 435.00 | 2.18 | FeS cluster assembly protein sufD | |
KEO96580.1* | 0.00 | 486.03 | PTS IIA-like nitrogen-regulatory protein PtsN | KDM54746.1* | 0.00 | 150.00 | nitrogen regulatory protein | ||
KEO96608.1* | 0.00 | 1394.71 | translation factor Sua5 | KDM53819.1* | 0.00 | 42.90 | tRNA threonylcarbamoyladenosine biosynthesis protein RimN | ||
KEO96752.1* | 97.51 | 359.85 | 3.69 | integrase | KDM51758.1* | 94.30 | 425.00 | 4.51 | putA protein |
KEO98470.1* | 0.00 | 124.49 | hypothetical protein | KDM51955.1* | 11.80 | 59.60 | 5.05 | UPF0061 protein ydiU | |
KEO98596.1* | 0.00 | 814.69 | LysR family transcriptional regulator | KDM57341.1* | 37.70 | 81.90 | 2.17 | transcriptional activator protein nhaR | |
KEO98607.1* | 0.00 | 192.91 | 1-deoxy-D-xylulose 5-phosphate reductoisomerase | KDM57478.1* | 42.50 | 1230.00 | 28.94 | 1-deoxy-D-xylulose 5-phosphate reductoisomerase | |
KEO98608.1* | 0.00 | 1552.72 | peptidase | KDM57481.1* | 264.00 | 854.00 | 3.23 | RIP metalloprotease RseP | |
KEO98641.1* | 0.00 | 1679.78 | LysR family transcriptional regulator | KDM53240.1* | 130.00 | 321.00 | 2.47 | hydrogen peroxide-inducible genes activator | |
KEO98759.1* | 0.00 | 157.99 | 3-dehydroquinate synthase | KDM53905.1* | 46.80 | 192.00 | 4.10 | 3-dehydroquinate synthase | |
KEO98794.1* | 0.00 | 345.72 | branched-chain alpha-keto acid dehydrogenase subunit E2 | KDM57421.1* | 744.00 | 6140.00 | 8.25 | dihydrolipoyllysine-residue acetyltransferase | |
KEO98866.1* | 0.00 | 196.33 | farnesyl-diphosphate synthase | KDM55391.1* | 75.50 | 519.00 | 6.87 | farnesyl diphosphate synthase | |
KEO98882.1* | 0.00 | 473.35 | rRNA methyltransferase | KDM51417.1* | 107.00 | 496.00 | 4.64 | tRNA (cytidine/uridine-2'-O-)-methyltransferase TrmJ | |
KEO98935.1* | 0.00 | 3161.33 | transcriptional regulator | KDM55471.1* | 0.00 | 120.00 | HTH-type transcriptional regulator CueR | ||
KEO98999.1* | 0.00 | 246.42 | nucleoside triphosphate hydrolase | KDM50489.1* | 85.80 | 233.00 | 2.72 | nucleoside triphosphate pyrophosphohydrolase | |
KEO99007.1* | 0.00 | 538.76 | 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase | KDM50467.1* | 70.80 | 154.00 | 2.18 | 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase | |
KEO99009.1* | 0.00 | 388.83 | cyclase | KDM51170.1* | 35.60 | 155.00 | 4.35 | hypothetical protein | |
KEO99027.1* | 0.00 | 95.59 | transketolase | KDM57420.1* | 1130.00 | 10900.00 | 9.65 | pyruvate dehydrogenase E1 component | |
KEO99055.1* | 0.00 | 1388.60 | hypothetical protein | KDM55136.1 | 0.00 | 5.43 | hypothetical protein | ||
*P-value < 0.05 |
Peptidoglycan synthesis-related homologous genes (for example, mltA homolog) were significantly (p < 0.05) upregulated in both E. litoralis and L. amnigena enlarged spheroplasts (Table 1). Penicillin causes cell wall stress which might lead to upregulation of peptidoglycan synthesis.
Chaperone homologous genes (for example, groES homolog) were also significantly upregulated in enlarged spheroplasts of both bacteria (Table 1), suggesting that a number of proteins may exist and be maintained in the enlarged spheroplasts. The expression of the phage shock protein homologous gene was very high in the enlarged spheroplasts (Table 1), suggesting that these cells were under stress.
Homologs of lipopolysaccharide synthesis and transport-related genes (for example, lptB and lptF homologs) were upregulated in both E. litoralis and L. amnigena enlarged spheroplasts (Table 1). It is strongly suggested that these genes may be required to maintain the enlarged inner and outer membranes of these bacteria [12].
Homologs of DNA replication initiator dnaA and recombinase recA genes were upregulated in both E. litoralis and L. amnigena enlarged spheroplasts (Table 1). DNA replication was not inhibited in the enlarged spheroplasts [6,7]. Thus, multiple chromosomal DNAs exist in a single cell. The DnaA and RecA homologs might function to maintain the multiple DNAs in the enlarged cells of both bacteria. The fact that enlarged spheroplasts have multiple copies of chromosome per cell supports the notion that chromosomal copy number is determined by the balance between DNA replication and cell division time [13].
The 51 downregulated genes in both the E. litoralis and L. amnigena enlarged spheroplasts are shown in Table 2. Of these 51 genes, 7 (13.7%) were homologous to inner and outer membrane protein coding genes, including 3 flagellar protein-encoding genes.
Protein ID of E. litoralis | RPKM in E. litoralis spheroplasts at the beginning of growth | RPKM in E. litoralis enlarged spheroplasts | Ratio of RPKMs of E. litoralis | Annotated function | Protein ID of L. amnigena | RPKM in L. amnigena spheroplasts at the beginning of growth | RPKM in L. amnigena enlarged spheroplasts | Ratio of RPKMs of L. amnigena | Annotated function |
Homologs of amino acid synthesis and metabolism-related genes | |||||||||
KEO88954.1* | 616.47 | 136.50 | 0.22 | L-asparaginase | KDM51897.1* | 33.40 | 0.00 | 0.00 | L-asparaginase 1 |
KEO89592.1* | 365.66 | 143.94 | 0.39 | S-adenosylmethionine synthetase | KDM49649.1* | 1070.00 | 255.00 | 0.24 | S-adenosylmethionine synthase |
KEO89916.1* | 363.48 | 0.00 | 0.00 | 2,3,4,5-tetrahydropyridine-2,6-carboxylate N-succinyltransferase | KDM57471.1* | 1050.00 | 432.00 | 0.41 | 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase |
KEO90596.1* | 298.26 | 88.06 | 0.30 | threonine aldolase | KDM55097.1* | 509.00 | 172.00 | 0.34 | low specificity L-threonine aldolase |
KEO92299.1* | 201.21 | 0.00 | 0.00 | 4-hydroxy-tetrahydrodipicolinate reductase | KDM57348.1* | 269.00 | 14.90 | 0.06 | dihydrodipicolinate reductase |
KEO92640.1* | 250.39 | 0.00 | 0.00 | argininosuccinate synthase | KDM54714.1* | 2220.00 | 219.00 | 0.10 | argininosuccinate synthase |
KEO92798.1* | 507.05 | 149.70 | 0.30 | 3-isopropylmalate dehydratase | KDM57378.1* | 196.00 | 60.80 | 0.31 | 3-isopropylmalate dehydratase small subunit |
KEO93106.1* | 831.23 | 245.41 | 0.30 | serine acetyltransferase | KDM52905.1* | 331.00 | 149.00 | 0.45 | serine acetyltransferase |
KEO93391.1* | 1078.83 | 318.51 | 0.30 | glutamine synthetase | KDM53324.1* | 385.00 | 174.00 | 0.45 | glutamine synthetase |
KEO93480.1* | 1248.41 | 595.39 | 0.48 | 3-phosphoglycerate dehydrogenase | KDM49615.1* | 964.00 | 369.00 | 0.38 | D-3-phosphoglycerate dehydrogenase |
KEO98853.1* | 596.53 | 0.00 | 0.00 | ketol-acid reductoisomerase | KDM53647.1* | 3330.00 | 450.00 | 0.14 | ketol-acid reductoisomerase |
KEO99046.1* | 292.53 | 0.00 | 0.00 | anthranilate synthase component I | KDM46686.1* | 1870.00 | 7.86 | 0.00 | anthranilate synthase component 1 |
KEO99050.1* | 459.56 | 45.23 | 0.10 | anthranilate phosphoribosyltransferase | KDM46685.1* | 2870.00 | 53.90 | 0.02 | anthranilate synthase component II |
Homologs of flagellar protein genes | |||||||||
KEO89561.1* | 22111.90 | 337.67 | 0.02 | flagellin | KDM48656.1* | 124.00 | 44.90 | 0.36 | hypothetical protein |
KEO90993.1* | 740.22 | 0.00 | 0.00 | flagellar basal body rod protein FlgC | KDM51808.1* | 41.90 | 0.00 | 0.00 | flagellar basal-body rod protein flgC |
KEO92484.1* | 806.97 | 79.42 | 0.10 | flagellar motor protein MotB | KDM51720.1* | 24600.00 | 1390.00 | 0.06 | outer membrane protein A |
Homologs of nucleotide synthesis and pentose phosphate pathway-related genes | |||||||||
KEO91063.1* | 325.03 | 95.96 | 0.30 | phosphoribosylpyrophosphate synthetase | KDM47000.1* | 985.00 | 298.00 | 0.30 | ribose-phosphate pyrophosphokinase |
KEO93239.1* | 414.76 | 61.23 | 0.15 | glucose-6-phosphate dehydrogenase | KDM48740.1* | 345.00 | 150.00 | 0.43 | glucose-6-phosphate 1-dehydrogenase |
KEO93278.1* | 293.09 | 0.00 | 0.00 | aspartate carbamoyltransferase catalytic subunit | KDM56880.1* | 1090.00 | 65.90 | 0.06 | aspartate carbamoyltransferase |
KEO96500.1* | 688.30 | 0.00 | 0.00 | ribulose-phosphate 3-epimerase | KDM53902.1* | 200.00 | 54.40 | 0.27 | ribulose-phosphate 3-epimerase |
KEO96518.1* | 349.69 | 103.24 | 0.30 | nicotinate-nucleotide pyrophosphorylase | KDM57413.1* | 57.00 | 27.50 | 0.48 | nicotinate-nucleotide pyrophosphorylase [carboxylating] |
KEO98799.1* | 610.90 | 45.09 | 0.07 | transketolase | KDM49630.1* | 844.00 | 278.00 | 0.33 | transketolase 1 |
Homologs of other membrane protein genes | |||||||||
KEO92879.1* | 12676.20 | 0.00 | 0.00 | membrane protein | KDM46678.1* | 80.50 | 0.00 | 0.00 | outer membrane protein W |
KEO93429.1* | 12522.20 | 4363.68 | 0.35 | membrane protein | KDM54978.1* | 216.00 | 86.80 | 0.40 | inner membrane protein YbhL |
KEO98493.1* | 726.95 | 268.28 | 0.37 | ABC transporter ATP-binding protein | KDM57319.1* | 479.00 | 192.00 | 0.40 | hypothetical protein |
KEO99262.1* | 1240.06 | 162.72 | 0.13 | hypothetical protein | KDM52093.1* | 131.00 | 11.80 | 0.09 | AI-2 transporter tqsA |
Others | |||||||||
KEO89629.1* | 824.47 | 121.71 | 0.15 | 3-demethylubiquinone-9 3-methyltransferase | KDM46348.1* | 116.00 | 16.90 | 0.15 | 3-demethylubiquinone-9 3-methyltransferase |
KEO90016.1* | 338.03 | 49.90 | 0.15 | hypothetical protein | KDM52077.1* | 18.60 | 0.00 | 0.00 | HTH-type transcriptional regulator AbgR |
KEO90690.1* | 737.52 | 0.00 | 0.00 | enoyl-ACP reductase | KDM46715.1* | 495.00 | 156.00 | 0.32 | enoyl-[acyl-carrier-protein] reductase [NADH] |
KEO92246.1* | 756.79 | 111.72 | 0.15 | glucose-1-phosphate thymidylyltransferase | KDM46209.1* | 58.80 | 28.30 | 0.48 | glucose-1-phosphate thymidylyltransferase 2 |
KEO92477.1* | 572.94 | 0.00 | 0.00 | molybdopterin biosynthesis protein B | KDM54974.1* | 232.00 | 47.90 | 0.21 | molybdenum cofactor biosynthesis protein B |
KEO92492.1* | 852.18 | 125.80 | 0.15 | oxidoreductase | KDM46695.1* | 312.00 | 80.60 | 0.26 | hypothetical protein |
KEO92638.1* | 479.48 | 0.00 | 0.00 | cyclopropane-fatty-acyl-phospholipid synthase | KDM52012.1* | 148.00 | 0.00 | 0.00 | cyclopropane-fatty-acyl-phospholipid synthase |
KEO92662.1* | 1438.43 | 212.34 | 0.15 | 50S ribosomal protein L17 | KDM53831.1* | 354.00 | 128.00 | 0.36 | 50S ribosomal protein L17 |
KEO92699.1* | 771.18 | 113.84 | 0.15 | LysR family transcriptional regulator | KDM50509.1* | 37.00 | 0.00 | 0.00 | glycine cleavage system transcriptional activator |
KEO93102.1* | 223.37 | 0.00 | 0.00 | bifunctional N-acetylglucosamine-1-phosphate uridyltransferase/glucosamine-1-phosphate acetyltransferase | KDM52744.1* | 372.00 | 108.00 | 0.29 | glmU protein |
KEO93190.1* | 831.23 | 409.01 | 0.49 | single-stranded DNA-binding protein | KDM56126.1* | 679.00 | 140.00 | 0.21 | single-stranded DNA-binding protein |
KEO93395.1* | 438.05 | 64.66 | 0.15 | cytosol aminopeptidase | KDM51408.1* | 158.00 | 47.70 | 0.30 | peptidase B |
KEO96463.1* | 111.07 | 32.79 | 0.30 | glutamate-ammonia-ligase adenylyltransferase | KDM54608.1* | 214.00 | 64.50 | 0.30 | glutamate-ammonia-ligase adenylyltransferase |
KEO96716.1* | 396.13 | 116.95 | 0.30 | GntR family transcriptional regulator | KDM52778.1* | 68.20 | 0.00 | 0.00 | hypothetical protein |
KEO96769.1* | 581.14 | 171.57 | 0.30 | ribonucleotide-diphosphate reductase subunit beta | KDM46350.1* | 481.00 | 130.00 | 0.27 | ribonucleoside-diphosphate reductase 1 subunit beta |
KEO98584.1* | 1114.39 | 0.00 | 0.00 | transcriptional regulator HU subunit alpha | KDM52452.1* | 2050.00 | 630.00 | 0.31 | DNA-binding protein HU-alpha |
KEO98612.1* | 1352.13 | 0.00 | 0.00 | 50S ribosomal protein L31 | KDM53254.1* | 159.00 | 0.00 | 0.00 | 50S ribosomal protein L31 |
KEO98687.1* | 228.14 | 84.19 | 0.37 | phosphoenolpyruvate carboxylase | KDM53245.1* | 621.00 | 236.00 | 0.38 | phosphoenolpyruvate carboxylase |
KEO98733.1* | 470.03 | 173.46 | 0.37 | DNA topoisomerase I | KDM46698.1* | 569.00 | 255.00 | 0.45 | DNA topoisomerase 1 |
KEO98800.1* | 603.63 | 0.00 | 0.00 | glyceraldehyde-3-phosphate dehydrogenase | KDM51892.1* | 2900.00 | 1360.00 | 0.47 | glyceraldehyde-3-phosphate dehydrogenase |
KEO98996.1* | 96.21 | 0.00 | 0.00 | methionine--tRNA ligase | KDM46274.1* | 576.00 | 115.00 | 0.20 | methionyl-tRNA synthetase |
KEO99011.1* | 473.88 | 139.91 | 0.30 | carbonate dehydratase | KDM52008.1* | 26.70 | 0.00 | 0.00 | hypothetical protein |
KEO99037.1* | 378.39 | 0.00 | 0.00 | inorganic polyphosphate kinase | KDM51166.1* | 96.60 | 0.00 | 0.00 | hypothetical protein |
KEO99041.1* | 4328.46 | 2008.15 | 0.46 | heat-shock protein | KDM52775.1* | 41.30 | 0.00 | 0.00 | small heat shock protein ibpA |
KEO99260.1* | 277.08 | 81.80 | 0.30 | aminotransferase | KDM51415.1* | 1540.00 | 637.00 | 0.41 | cysteine desulfurase |
*P-value < 0.05 |
Homologs of amino acid and nucleotide synthesis-related genes and pentose phosphate pathway genes were significantly downregulated in both E. litoralis and L. amnigena enlarged spheroplasts (Table 2). This indicated that amino acid and nucleotide synthesis were repressed in enlarged spheroplasts. Repression of nucleotide synthesis is consistent with the reduced speed of DNA replication [6,7]. In addition, homologs of flagellar protein genes were significantly downregulated in both E. litoralis and L. amnigena enlarged spheroplasts (Table 2), which is consistent with absence of motility in the spheroplasts of both bacteria.
The nucleoid protein HU homologous gene was significantly downregulated in both E. litoralis and L. amnigena enlarged spheroplasts (Table 2). Cross-talk between HU and topoisomerase I has been reported in E. coli [14]. Interestingly, topoisomerase I homologous gene was also significantly downregulated in both enlarged spheroplasts (Table 2). The downregulation of both HU and topoisomerase I homologous genes may be one of the characteristics of enlarged spheroplasts. Thus, in enlarged spheroplasts, recombination may be repressed in multiple copies of chromosomal DNAs.
The genes with differential expression between E. litoralis and L. amnigena enlarged spheroplasts are shown in Tables 3 and 4.
Protein ID of E. litoralis | RPKM in E. litoralis spheroplasts at the beginning of growth | RPKM in E. litoralis enlarged spheroplasts | Ratio of RPKMs of E. litoralis | Annotated function | Protein ID of L. amnigena | RPKM in L. amnigena spheroplasts at the beginning of growth | RPKM in L. amnigena enlarged spheroplasts | Ratio of RPKMs of L. amnigena | Annotated function |
Homologs of membrane protein genes | |||||||||
KEO89564.1* | 0.00 | 106.93 | hypothetical protein | KDM48649.1* | 40.40 | 14.60 | 0.36 | flagellar M-ring protein | |
KEO89607.1* | 0.00 | 129.05 | multidrug transporter | KDM52010.1* | 150.00 | 45.10 | 0.30 | multidrug resistance protein mdtK | |
KEO89895.1* | 0.00 | 634.32 | biopolymer transporter ExbB | KDM55699.1* | 564.00 | 177.00 | 0.31 | protein tolQ | |
KEO89973.1* | 0.00 | 184.81 | magnesium transporter CorA | KDM52382.1* | 661.00 | 168.00 | 0.25 | magnesium transporter CorA | |
KEO92632.1* | 0.00 | 146.76 | hypothetical protein | KDM46187.1* | 175.00 | 72.30 | 0.41 | inner membrane transporter YeeF | |
KEO92658.1* | 0.00 | 1301.72 | hypothetical protein | KDM57464.1* | 136.00 | 39.40 | 0.29 | UPF0126 inner membrane protein yadS | |
KEO92812.1* | 0.00 | 172.56 | type VI secretion protein | KDM54463.1* | 51.90 | 12.50 | 0.24 | hypothetical protein | |
KEO93024.1* | 262.72 | 2171.79 | 8.27 | iron transporter | KDM53929.1* | 413.00 | 171.00 | 0.41 | Fe/S biogenesis protein nfuA |
KEO93116.1* | 0.00 | 227.97 | organic solvent tolerance protein | KDM57361.1* | 483.00 | 224.00 | 0.46 | LPS-assembly protein lptD | |
KEO93384.1* | 352.12 | 1143.53 | 3.25 | MttB family protein | KDM52402.1* | 220.00 | 15.90 | 0.07 | sec-independent protein translocase tatC |
KEO98525.1* | 0.00 | 128.22 | hypothetical protein | KDM52772.1* | 118.00 | 38.00 | 0.32 | D-galactonate transporter | |
KEO98837.1* | 0.00 | 215.39 | phosphate ABC transporter permease | KDM52748.1* | 724.00 | 152.00 | 0.21 | phosphate transport system permease pstA | |
KEO98838.1* | 0.00 | 194.41 | phosphate ABC transporter permease | KDM52747.1* | 1310.00 | 230.00 | 0.18 | phosphate transport system permease pstC | |
KEO98907.1* | 243.77 | 539.78 | 2.21 | 3,4-dihydroxy-2-butanone 4-phosphate synthase | KDM54605.1* | 1220.00 | 432.00 | 0.35 | 3,4-dihydroxy-2-butanone 4-phosphate synthase |
Others | |||||||||
KEO88945.1* | 1061.88 | 3056.67 | 2.88 | peptide deformylase | KDM53823.1* | 699.00 | 313.00 | 0.45 | peptide deformylase |
KEO88946.1* | 0.00 | 300.90 | recombinase RecR | KDM55460.1* | 336.00 | 101.00 | 0.30 | recombination protein recR | |
KEO88958.1* | 0.00 | 546.11 | argininosuccinate lyase | KDM53241.1* | 1610.00 | 116.00 | 0.07 | argininosuccinate lyase | |
KEO88960.1* | 484.06 | 1822.10 | 3.76 | diaminopimelate decarboxylase | KDM50540.1* | 780.00 | 19.50 | 0.03 | diaminopimelate decarboxylase |
KEO89297.1* | 0.00 | 160.53 | histidinol-phosphate aminotransferase | KDM46192.1* | 240.00 | 92.60 | 0.39 | histidinol-phosphate aminotransferase | |
KEO89579.1* | 0.00 | 507.45 | tRNA (guanine-N7)-methyltransferase | KDM54472.1* | 802.00 | 154.00 | 0.19 | tRNA (guanine-N(7)-)-methyltransferase | |
KEO89635.1* | 0.00 | 207.20 | formyltetrahydrofolate deformylase | KDM46646.1* | 80.60 | 14.60 | 0.18 | formyltetrahydrofolate deformylase | |
KEO89998.1* | 0.00 | 437.71 | ArsR family transcriptional regulator | KDM55050.1* | 52.90 | 0.00 | 0.00 | hypothetical protein | |
KEO90041.1* | 0.00 | 118.57 | hypothetical protein | KDM48627.1* | 48.00 | 0.00 | 0.00 | DNA-cytosine methyltransferase | |
KEO90698.1* | 0.00 | 438.68 | 3-deoxy-manno-octulosonate cytidylyltransferase | KDM55141.1* | 91.00 | 0.00 | 0.00 | 3-deoxy-manno-octulosonate cytidylyltransferase | |
KEO91020.1* | 0.00 | 391.37 | molecular chaperone DnaK | KDM57452.1* | 5740.00 | 2210.00 | 0.39 | DnaK suppressor protein | |
KEO91036.1* | 0.00 | 883.47 | molecular chaperone Hsp33 | KDM53917.1* | 77.30 | 28.00 | 0.36 | chaperonin | |
KEO91037.1* | 0.00 | 191.92 | ornithine carbamoyltransferase | KDM56877.1* | 16.90 | 0.00 | 0.00 | ornithine carbamoyltransferase, catabolic | |
KEO92302.1* | 0.00 | 465.99 | molybdopterin biosynthesis protein MoeB | KDM52444.1* | 112.00 | 16.30 | 0.15 | sulfur carrier protein ThiS adenylyltransferase | |
KEO92334.1* | 113.82 | 285.62 | 2.51 | aconitate hydratase | KDM46701.1* | 305.00 | 152.00 | 0.50 | aconitate hydratase 1 |
KEO92372.1* | 0.00 | 272.18 | phosphomethylpyrimidine kinase | KDM46258.1* | 42.40 | 15.30 | 0.36 | hydroxymethylpyrimidine/phosphomethylpyrimidine kinase | |
KEO92402.1* | 0.00 | 190.30 | glutamyl-tRNA synthetase | KDM51312.1* | 216.00 | 86.80 | 0.40 | glutamyl-tRNA synthetase | |
KEO92434.1* | 0.00 | 266.53 | 2-hydroxyacid dehydrogenase | KDM52411.1* | 69.70 | 25.20 | 0.36 | glyoxylate/hydroxypyruvate reductase B | |
KEO92503.1* | 0.00 | 462.99 | inosine-5-monophosphate dehydrogenase | KDM51383.1* | 417.00 | 117.00 | 0.28 | inosine-5'-monophosphate dehydrogenase | |
KEO92549.1* | 0.00 | 490.81 | 30S ribosomal protein S6 | KDM56939.1* | 944.00 | 217.00 | 0.23 | 30S ribosomal protein S6 | |
KEO92597.1* | 0.00 | 368.72 | tryptophan synthase subunit beta | KDM46683.1* | 3260.00 | 134.00 | 0.04 | tryptophan synthase beta chain | |
KEO92634.1* | 0.00 | 460.61 | oxidoreductase | KDM52065.1* | 23.50 | 0.00 | 0.00 | dihydrofolate reductase folM | |
KEO92667.1* | 0.00 | 278.51 | adenylate kinase | KDM55462.1* | 1950.00 | 914.00 | 0.47 | adenylate kinase | |
KEO92711.1* | 0.00 | 424.08 | 3-isopropylmalate dehydrogenase | KDM57380.1* | 280.00 | 113.00 | 0.40 | 3-isopropylmalate dehydrogenase | |
KEO92758.1* | 0.00 | 1060.85 | DNA-binding protein | KDM51729.1* | 7260.00 | 966.00 | 0.13 | heat shock protein hspQ | |
KEO92776.1* | 0.00 | 1339.41 | ribosome maturation protein RimP | KDM54713.1* | 187.00 | 81.40 | 0.44 | ribosome maturation factor rimP | |
KEO92780.1* | 0.00 | 511.79 | ATPase AAA | KDM46723.1* | 52.10 | 25.10 | 0.48 | psp operon transcriptional activator | |
KEO92795.1* | 0.00 | 399.20 | thioesterase | KDM55422.1* | 298.00 | 61.60 | 0.21 | long-chain acyl-CoA thioesterase tesC | |
KEO92811.1* | 0.00 | 81.47 | polyphosphate kinase | KDM51368.1* | 437.00 | 107.00 | 0.24 | polyphosphate kinase | |
KEO93025.1* | 499.56 | 1179.89 | 2.36 | malonic semialdehyde reductase | KDM51751.1* | 57.50 | 20.80 | 0.36 | hypothetical protein |
KEO93125.1* | 0.00 | 144.29 | succinylarginine dihydrolase | KDM51916.1* | 89.70 | 27.80 | 0.31 | N-succinylarginine dihydrolase | |
KEO93177.1* | 0.00 | 687.39 | aromatic amino acid aminotransferase | KDM55151.1* | 385.00 | 124.00 | 0.32 | aspartate aminotransferase | |
KEO93181.1* | 0.00 | 286.50 | riboflavin synthase subunit alpha | KDM52011.1* | 317.00 | 76.60 | 0.24 | riboflavin synthase alpha chain | |
KEO93285.1* | 1214.49 | 3764.87 | 3.10 | bacterioferritin | KDM53859.1* | 463.00 | 77.30 | 0.17 | bacterioferritin |
KEO93379.1* | 0.00 | 350.17 | beta-hexosaminidase | KDM51842.1* | 248.00 | 71.90 | 0.29 | beta-hexosaminidase | |
KEO93387.1* | 0.00 | 283.79 | threonine dehydratase | KDM54671.1* | 51.50 | 0.00 | 0.00 | threonine dehydratase catabolic | |
KEO93441.1* | 0.00 | 293.53 | cystathionine beta-lyase | KDM54516.1* | 285.00 | 92.90 | 0.33 | cystathionine beta-lyase | |
KEO93476.1* | 0.00 | 3077.91 | hypothetical protein | KDM54633.1* | 68.60 | 24.80 | 0.36 | hypothetical protein | |
KEO96380.1* | 0.00 | 130.17 | protein-PII uridylyltransferase | KDM57472.1* | 108.00 | 32.10 | 0.30 | [protein-PII] uridylyltransferase | |
KEO96408.1* | 0.00 | 407.90 | GTP cyclohydrolase | KDM46702.1* | 287.00 | 104.00 | 0.36 | GTP cyclohydrolase-2 | |
KEO96434.1* | 131.11 | 377.39 | 2.88 | glutamate synthase | KDM54762.1* | 2310.00 | 320.00 | 0.14 | glutamate synthase [NADPH] large chain |
KEO96435.1* | 0.00 | 156.26 | glutamate synthase | KDM54763.1* | 1780.00 | 320.00 | 0.18 | glutamate synthase [NADPH] small chain | |
KEO96528.1* | 0.00 | 211.70 | exodeoxyribonuclease VII large subunit | KDM51384.1* | 74.20 | 0.00 | 0.00 | exodeoxyribonuclease 7 large subunit | |
KEO96545.1* | 0.00 | 814.69 | AsnC family transcriptional regulator | KDM51416.1* | 2800.00 | 150.00 | 0.05 | HTH-type transcriptional regulator iscR | |
KEO98460.1* | 0.00 | 1164.32 | 50S ribosomal protein L27 | KDM54727.1* | 1840.00 | 667.00 | 0.36 | 50S ribosomal protein L27 | |
KEO98556.1* | 0.00 | 200.94 | citrate lyase | KDM54480.1* | 19.40 | 0.00 | 0.00 | citrate lyase subunit beta | |
KEO98575.1* | 300.92 | 1066.10 | 3.54 | farnesyltranstransferase | KDM54729.1* | 175.00 | 25.30 | 0.14 | octaprenyl-diphosphate synthase |
KEO98712.1* | 0.00 | 412.01 | thioredoxin reductase | KDM55115.1* | 351.00 | 88.80 | 0.25 | thioredoxin reductase | |
KEO98796.1* | 0.00 | 1374.78 | 5-formyltetrahydrofolate cyclo-ligase | KDM49727.1* | 85.40 | 41.20 | 0.48 | 5-formyltetrahydrofolate cyclo-ligase | |
KEO98834.1* | 0.00 | 260.35 | chemotaxis protein CheY | KDM55825.1* | 2140.00 | 142.00 | 0.07 | phosphate regulon transcriptional regulatory protein phoB | |
KEO98839.1* | 0.00 | 180.36 | histidine kinase | KDM55824.1* | 380.00 | 47.40 | 0.12 | phosphate regulon sensor protein phoR | |
KEO98906.1* | 0.00 | 424.68 | 6,7-dimethyl-8-ribityllumazine synthase | KDM55386.1* | 325.00 | 157.00 | 0.48 | 6,7-dimethyl-8-ribityllumazine synthase | |
KEO98922.1* | 0.00 | 653.71 | 50S ribosomal protein L25 | KDM46330.1* | 477.00 | 129.00 | 0.27 | 50S ribosomal protein L25 | |
KEO98968.1* | 0.00 | 712.85 | nucleoside-triphosphate diphosphatase | KDM54467.1* | 57.20 | 0.00 | 0.00 | nucleoside-triphosphatase rdgB | |
KEO98978.1* | 0.00 | 229.80 | DNA repair protein RadA | KDM57315.1* | 282.00 | 106.00 | 0.38 | DNA repair protein radA | |
KEO99042.1* | 0.00 | 438.68 | CTP synthase | KDM50488.1* | 871.00 | 353.00 | 0.41 | CTP synthase | |
*P-value < 0.05 |
Protein ID of E. litoralis | RPKM in E. litoralis spheroplasts at the beginning of growth | RPKM in E. litoralis enlarged spheroplasts | Ratio of RPKMs of E. litoralis | Annotated function | Protein ID of L. amnigena | RPKM in L. amnigena spheroplasts at the beginning of growth | RPKM in L. amnigena enlarged spheroplasts | Ratio of RPKMs of L. amnigena | Annotated function |
Homologs of membrane protein genes | |||||||||
KEO89304.1* | 629.44 | 247.78 | 0.39 | penicillin-binding protein | KDM57456.1* | 296.00 | 1010.00 | 3.41 | penicillin-binding protein 1B |
KEO89573.1* | 405.64 | 59.88 | 0.15 | flagellar biosynthesis protein flip | KDM48639.1* | 0.00 | 16.70 | flagellar biosynthetic protein fliP | |
KEO90985.1* | 453.73 | 133.96 | 0.30 | hypothetical protein | KDM51816.1* | 0.00 | 22.50 | flagellar hook-associated protein 1 | |
KEO90987.1* | 2625.04 | 163.16 | 0.06 | flagellar P-ring protein FlgI | KDM51814.1* | 15.50 | 56.00 | 3.61 | flagellar P-ring protein |
KEO90994.1* | 859.40 | 0.00 | 0.00 | flagellar basal body rod protein FlgB | KDM51807.1* | 0.00 | 147.00 | flagellar basal-body rod protein flgB | |
KEO92489.1* | 458.87 | 135.47 | 0.30 | ABC transporter | KDM51852.1* | 72.60 | 175.00 | 2.41 | lipoprotein-releasing system ATP-binding protein LolD |
KEO92547.1* | 320.92 | 0.00 | 0.00 | ABC transporter | KDM48630.1* | 0.00 | 13.50 | inner membrane protein yedI | |
KEO92700.1* | 2204.56 | 0.00 | 0.00 | magnesium transporter ApaG | KDM57357.1* | 89.90 | 488.00 | 5.43 | protein ApaG |
KEO93367.1* | 2069.58 | 111.09 | 0.05 | secretion system protein | KDM53908.1* | 0.00 | 9.92 | hypothetical protein | |
KEO93416.1* | 284.06 | 0.00 | 0.00 | phospho-N-acetylmuramoyl-pentapeptide-transferase | KDM57393.1* | 204.00 | 817.00 | 4.00 | phospho-N-acetylmuramoyl-pentapeptide-transferase |
KEO93419.1* | 495.89 | 109.80 | 0.22 | UDP-diphospho-muramoylpentapeptide beta-N-acetylglucosaminyltransferase | KDM57396.1* | 79.70 | 415.00 | 5.21 | undecaprenyldiphospho-muramoylpentapeptide beta-N-acetylglucosaminyltransferase |
KEO93424.1* | 682.13 | 134.26 | 0.20 | cell division protein FtsA | KDM57400.1* | 865.00 | 2250.00 | 2.60 | cell division protein ftsA |
KEO98787.1* | 1321.30 | 373.84 | 0.28 | preprotein translocase subunit SecA | KDM57404.1* | 69.00 | 559.00 | 8.10 | protein translocase subunit secA |
KEO98980.1* | 184.72 | 54.53 | 0.30 | major facilitator transporter | KDM46178.1* | 64.50 | 159.00 | 2.47 | shikimate transporter |
Others | |||||||||
KEO89313.1* | 2157.65 | 0.00 | 0.00 | peptide methionine sulfoxide reductase | KDM56920.1* | 0.00 | 19.10 | peptide methionine sulfoxide reductase msrA | |
KEO89605.1* | 7190.86 | 2640.13 | 0.37 | molecular chaperone GroEL | KDM56992.1* | 1220.00 | 4660.00 | 3.82 | chaperonin |
KEO89995.1* | 402.88 | 33.98 | 0.08 | 5-methyltetrahydrofolate--homocysteine methyltransferase | KDM55766.1* | 111.00 | 223.00 | 2.01 | methionine synthase |
KEO90687.1* | 897.43 | 132.48 | 0.15 | pyridoxamine 5'-phosphate oxidase | KDM52037.1* | 0.00 | 37.40 | pyridoxine/pyridoxamine 5'-phosphate oxidase | |
KEO91004.1* | 607.24 | 0.00 | 0.00 | hypothetical protein | KDM49677.1* | 375.00 | 1380.00 | 3.68 | protein yciF |
KEO91044.1* | 382.68 | 0.00 | 0.00 | glucose-methanol-choline oxidoreductase | KDM55555.1* | 51.00 | 185.00 | 3.63 | choline dehydrogenase |
KEO91076.1* | 644.55 | 190.30 | 0.30 | phosphomannomutase | KDM46221.1* | 99.10 | 1120.00 | 11.30 | phosphomannomutase |
KEO92378.1* | 1931.61 | 855.42 | 0.44 | RNA polymerase sigma70 | KDM51449.1* | 2570.00 | 7420.00 | 2.89 | RNA polymerase sigma-E factor |
KEO92529.1* | 224.36 | 66.24 | 0.30 | hypothetical protein | KDM57043.1* | 0.00 | 6.34 | hypothetical protein | |
KEO92652.1* | 1365.79 | 554.44 | 0.41 | succinate--CoA ligase | KDM55690.1* | 566.00 | 1450.00 | 2.56 | succinyl-CoA ligase [ADP-forming] subunit alpha |
KEO92654.1* | 2162.76 | 141.89 | 0.07 | dihydrolipoamide succinyltransferase | KDM55688.1* | 415.00 | 1100.00 | 2.65 | hypothetical protein |
KEO92656.1* | 2572.76 | 822.87 | 0.32 | dihydrolipoamide dehydrogenase | KDM57422.1* | 775.00 | 3320.00 | 4.28 | dihydrolipoyl dehydrogenase |
KEO92681.1* | 1049.06 | 206.48 | 0.20 | 50S ribosomal protein L16 | KDM53849.1* | 537.00 | 2360.00 | 4.39 | 50S ribosomal protein L16 |
KEO93425.1* | 1877.96 | 607.24 | 0.32 | cell division protein FtsZ | KDM57401.1* | 1180.00 | 5490.00 | 4.65 | cell division protein ftsZ |
KEO93475.1* | 113.94 | 0.00 | 0.00 | ATPase AAA | KDM55119.1* | 88.50 | 311.00 | 3.51 | replication-associated recombination protein A |
KEO96455.1* | 712.48 | 35.06 | 0.05 | UDP-N-acetylglucosamine 1-carboxyvinyltransferase | KDM54731.1* | 162.00 | 351.00 | 2.17 | UDP-N-acetylglucosamine 1-carboxyvinyltransferase |
KEO96456.1* | 1034.79 | 101.84 | 0.10 | UTP--glucose-1-phosphate uridylyltransferase | KDM46650.1* | 206.00 | 678.00 | 3.29 | UTP-glucose-1-phosphate uridylyltransferase |
KEO96517.1* | 762.48 | 0.00 | 0.00 | chemotaxis protein CheY | KDM46276.1* | 0.00 | 68.30 | hypothetical protein | |
KEO96548.1* | 291.41 | 86.03 | 0.30 | dihydroorotate dehydrogenase | KDM51709.1* | 16.80 | 72.90 | 4.34 | dihydroorotate dehydrogenase |
KEO98611.1* | 618.35 | 0.00 | 0.00 | 3-hydroxyacyl-ACP dehydratase | KDM57485.1* | 74.50 | 350.00 | 4.70 | (3R)-hydroxymyristoyl-[acyl-carrier-protein] dehydratase |
KEO99053.1* | 249.16 | 73.56 | 0.30 | molybdopterin biosynthesis protein | KDM55029.1* | 68.90 | 149.00 | 2.16 | molybdopterin molybdenumtransferase |
KEO99263.1* | 1114.39 | 0.00 | 0.00 | glutamine amidotransferase | KDM54696.1* | 327.00 | 852.00 | 2.61 | protein yhbO |
*P-value < 0.05 |
As mentioned above, the recA homolog was upregulated in both enlarged spheroplasts (Table 1). However, the DNA recombinase radA homolog was upregulated in E. litoralis enlarged spheroplasts, but was downregulated in L. amnigena enlarged spheroplasts (Table 3). In the enlarged spheroplasts, the expression level of the E. litoralis recA homolog was much higher than that of L. amnigena, suggesting that higher requirement for DNA recombinase in E. litoralis. Although we should estimate the functional difference between RecA and RadA homologs [15], it is suggested that the RadA homolog might be needed in addition to the RecA homolog in E. litoralis enlarged spheroplasts.
The secA homolog was upregulated in L. amnigena enlarged spheroplasts but was downregulated in E. litoralis enlarged spheroplasts (Table 4). In a previous study [4], SecY, a major component of the Sec complex, was strongly detected in the vacuole-like structure membrane of E. coli. In our findings, the expression level of the secY homolog was upregulated (1.57-fold) in L. amnigena spheroplasts but was downregulated (0.84-fold) in E. litoralis enlarged spheroplasts (Supplementary Table 1). Thus, it is strongly suggested that the SecA homolog (and the SecY homolog) is associated with generation of the vacuole-like structure in L. amnigena.
The homologs of cell division-related genes ftsA and ftsZ were upregulated in L. amnigena enlarged spheroplasts but were downregulated in E. litoralis enlarged spheroplasts (Table 4), suggesting that these two genes may be also associated with the generation of vacuole-like structures.
Penicillin binding protein 1B homologous gene was upregulated in L. amnigena enlarged spheroplasts and was downregulated in E. litoralis (Table 4). E. coli spheroplasts resynthesize their cell wall and shape without penicillin [16], and the penicillin binding protein 1B was required for the shape recovery [16]. Upon transferring the enlarged spheroplasts to a penicillin-free broth, the shape recovery rate of L. amnigena may be higher than that of E. litoralis.
The Mg2+ transport system was contrasting between the E. litoralis and L. amnigena enlarged spheroplasts. The Mg2+ influx-related gene corA [17] was upregulated in E. litoralis enlarged spheroplasts but was downregulated in L. amnigena enlarged spheroplasts (Table 3). On the other hand, the Mg2+ efflux-related gene apaG (corD) [17] was downregulated in E. litoralis but was upregulated in L. amnigena (Table 4). These results strongly suggest that E. litoralis enlarged spheroplasts require Mg2+ but the L. amnigena enlarged spheroplasts discard it.
We showed that spheroplast enlargement varies between E. litoralis and L. amnigena. The changes in expression of the orthologous genes also vary between enlarged spheroplasts of the two bacteria. Based on the different gene expression pattern, the candidate genes related to the cell structural differences were extracted in this study.
We thank Dr. Shinji Kondo for his valuable comments and suggestion. This work was supported by grant from The Cannon Foundation.
The authors declare that there is no conflict of interest regarding the publication of this paper.
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3. | Haixia Tian, Jiao Wang, Jiayu Li, Yujie Wang, Megharaj Mallavarapu, Wenxiang He, Six New Families of Aerobic Arsenate Reducing Bacteria: Leclercia, Raoultella, Kosakonia, Lelliottia, Yokenella, and Kluyvera, 2019, 36, 0149-0451, 339, 10.1080/01490451.2018.1554726 | |
4. | Satoshi Kami, Rintaro Tsuchikado, Hiromi Nishida, DNA replication and cell enlargement of Enterococcus faecalis protoplasts, 2019, 5, 2471-1888, 347, 10.3934/microbiol.2019.4.347 | |
5. | Hiromi Nishida, Factors That Affect the Enlargement of Bacterial Protoplasts and Spheroplasts, 2020, 21, 1422-0067, 7131, 10.3390/ijms21197131 | |
6. | Sawako Takahashi, Hiromi Nishida, Comparison of gene expression among normally divided cells, elongated cells, spheroplasts at the beginning of growth, and enlarged spheroplasts at 43 h of growth in Lelliottia amnigena, 2017, 7, 24520144, 87, 10.1016/j.genrep.2017.02.005 | |
7. | Hikaru Nakamiya, Saeka Ijima, Hiromi Nishida, Changes in nucleosome formation at gene promoters in the archiascomycetous yeast Saitoella complicata, 2017, 3, 2471-1888, 136, 10.3934/microbiol.2017.2.136 | |
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9. | Koki Nishino, Hiromi Nishida, Calcium ion induces outer membrane fusion ofDeinococcus grandisspheroplasts to generate giant spheroplasts with multiple cytoplasms, 2019, 366, 1574-6968, 10.1093/femsle/fny282 | |
10. | Sawako Takahashi, Marin Mizuma, Satoshi Kami, Hiromi Nishida, Species-dependent protoplast enlargement involves different types of vacuole generation in bacteria, 2020, 10, 2045-2322, 10.1038/s41598-020-65759-7 | |
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12. | Sawako Takahashi, Hiromi Nishida, Effects of heterologous genome microinjection on the enlargement of Enterococcus faecalis protoplasts, 2022, 3, 26665174, 100104, 10.1016/j.crmicr.2022.100104 | |
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Protein ID of E. litoralis | RPKM in E. litoralis spheroplasts at the beginning of growth | RPKM in E. litoralis enlarged spheroplasts | Ratio of RPKMs of E. litoralis | Annotated function | Protein ID of L. amnigena | RPKM in L. amnigena spheroplasts at the beginning of growth | RPKM in L. amnigena enlarged spheroplasts | Ratio of RPKMs of L. amnigena | Annotated function |
Homologs of chaperone genes | |||||||||
KEO89606.1* | 0.00 | 623.74 | molecular chaperone GroES | KDM56993.1* | 347.00 | 1300.00 | 3.75 | chaperonin | |
KEO92782.1* | 0.00 | 4575.93 | phage shock protein | KDM46724.1* | 4670.00 | 27100.00 | 5.80 | phage shock protein A | |
KEO93197.1* | 0.00 | 2039.77 | ATP-dependent protease | KDM53259.1* | 178.00 | 608.00 | 3.42 | ATP-dependent protease ATPase subunit HslU | |
KEO93350.1* | 588.91 | 6885.08 | 11.69 | ATPase AAA | KDM51144.1* | 449.00 | 1660.00 | 3.70 | chaperone ClpB |
KEO98976.1* | 265.47 | 587.82 | 2.21 | molecular chaperone DnaJ | KDM57339.1* | 267.00 | 751.00 | 2.81 | chaperone dnaJ |
Homologs of DNA replication and repair-related genes | |||||||||
KEO92279.1* | 304.84 | 659.99 | 2.17 | ATPase AAA | KDM53654.1* | 0.00 | 8.08 | Mg chelatase-like protein | |
KEO92303.1* | 0.00 | 255.35 | chromosomal replication initiator protein DnaA | KDM52760.1* | 280.00 | 617.00 | 2.20 | chromosomal replication initiator protein dnaA | |
KEO92620.1* | 1142.64 | 8813.23 | 7.71 | recombinase RecA | KDM50414.1* | 401.00 | 893.00 | 2.23 | protein recA |
Homologs of lipopolysaccharide synthesis and transport-related genes | |||||||||
KEO89583.1* | 0.00 | 224.27 | ABC transporter ATP-binding protein | KDM54743.1* | 46.80 | 339.00 | 7.24 | lipopolysaccharide export system ATP-binding protein LptB | |
KEO90699.1* | 309.18 | 1369.19 | 4.43 | D-arabinose 5-phosphate | KDM54739.1* | 34.40 | 74.70 | 2.17 | arabinose 5-phosphate isomerase |
KEO92387.1* | 0.00 | 693.72 | permease | KDM54753.1* | 201.00 | 458.00 | 2.28 | lipopolysaccharide export system permease lptF | |
KEO96424.1* | 321.43 | 901.51 | 2.80 | ABC transporter | KDM55137.1* | 29.10 | 91.30 | 3.14 | lipid A export ATP-binding/permease MsbA |
KEO98632.1* | 0.00 | 130.74 | MFS transporter | KDM50532.1* | 0.00 | 10.30 | lysophospholipid transporter lplT | ||
Homologs of peptidoglycan synthesis-related genes | |||||||||
KEO92316.1* | 0.00 | 1429.28 | MltA | KDM50514.1* | 46.40 | 123.00 | 2.65 | membrane-bound lytic murein transglycosylase A | |
KEO93302.1* | 0.00 | 801.96 | peptidoglycan transglycosylase | KDM54749.1* | 0.00 | 16.90 | monofunctional biosynthetic peptidoglycan transglycosylase | ||
KEO93307.1* | 0.00 | 252.66 | N-acetylmuramoyl-L-alanine amidase | KDM55076.1* | 20.40 | 118.00 | 5.78 | N-acetylmuramoyl-L-alanine amidase AmiD | |
KEO93413.1* | 0.00 | 408.49 | peptidoglycan glycosyltransferase | KDM57390.1* | 115.00 | 452.00 | 3.93 | peptidoglycan synthase ftsI | |
KEO93417.1* | 0.00 | 193.99 | UDP-N-acetylmuramoylalanine--D-glutamate ligase | KDM57394.1* | 116.00 | 802.00 | 6.91 | UDP-N-acetylmuramoylalanine-D-glutamate ligase | |
Homologs of other membrane protein genes | |||||||||
KEO89306.1* | 1090.43 | 2253.52 | 2.07 | membrane protease subunit HflC | KDM56960.1* | 135.00 | 599.00 | 4.44 | protein HflC |
KEO89307.1* | 535.14 | 3554.84 | 6.64 | peptidase | KDM56961.1* | 431.00 | 1380.00 | 3.20 | protein HflK |
KEO89575.1* | 0.00 | 225.11 | flagellar biosynthesis protein FliR | KDM48637.1* | 0.00 | 31.30 | flagellar biosynthetic protein fliR | ||
KEO89580.1* | 0.00 | 221.23 | mechanosensitive ion channel protein MscS | KDM55515.1* | 68.20 | 188.00 | 2.76 | miniconductance mechanosensitive channel | |
KEO92762.1* | 0.00 | 194.41 | membrane protein | KDM51940.1* | 0.00 | 16.20 | hypothetical protein | ||
KEO93138.1* | 0.00 | 505.31 | ABC transporter | KDM55480.1* | 321.00 | 823.00 | 2.56 | hypothetical protein | |
KEO93143.1* | 0.00 | 301.81 | proline:sodium symporter PutP | KDM51759.1* | 495.00 | 1180.00 | 2.38 | sodium/proline symporter | |
KEO96616.1* | 0.00 | 211.59 | membrane protein | KDM48736.1* | 116.00 | 568.00 | 4.90 | hypothetical protein | |
KEO96782.1* | 0.00 | 281.12 | MarC family transcriptional regulator | KDM46654.1* | 0.00 | 37.90 | UPF0056 membrane protein yhcE | ||
KEO96802.1* | 0.00 | 526.58 | hypothetical protein | KDM51307.1* | 54.80 | 674.00 | 12.30 | manganese transporter mntH | |
KEO98444.1* | 159.95 | 613.91 | 3.84 | protoheme IX farnesyltransferase | KDM55407.1* | 612.00 | 1340.00 | 2.19 | protoheme IX farnesyltransferase |
KEO98495.1* | 0.00 | 1075.18 | hypothetical protein | KDM55130.1* | 24.50 | 70.90 | 2.89 | UPF0702 transmembrane protein ycaP | |
KEO98569.1* | 201.21 | 3148.42 | 15.65 | histidine kinase | KDM51863.1* | 0.00 | 16.80 | sensor protein phoQ | |
KEO98609.1* | 288.10 | 612.40 | 2.13 | membrane protein | KDM57482.1* | 316.00 | 742.00 | 2.35 | outer membrane protein assembly factor yaeT |
KEO99117.1* | 0.00 | 227.97 | membrane protein | KDM54035.1* | 14.10 | 51.10 | 3.62 | hypothetical protein | |
Others | |||||||||
KEO89324.1* | 0.00 | 339.26 | mannose-1-phosphate guanylyltransferase | KDM46222.1* | 118.00 | 1610.00 | 13.64 | mannose-1-phosphate guanylyltransferase | |
KEO89964.1* | 0.00 | 1086.92 | taurine dioxygenase | KDM57053.1* | 19.90 | 115.00 | 5.78 | alpha-ketoglutarate-dependent taurine dioxygenase | |
KEO89994.1* | 0.00 | 480.32 | aminomethyltransferase | KDM49721.1* | 264.00 | 696.00 | 2.64 | aminomethyltransferase | |
KEO90662.1* | 0.00 | 165.87 | phosphoribosylaminoimidazole carboxylase | KDM55484.1* | 0.00 | 138.00 | N5-carboxyaminoimidazole ribonucleotide synthase | ||
KEO90672.1* | 0.00 | 261.97 | succinyl-CoA synthetase subunit beta | KDM55689.1* | 480.00 | 1360.00 | 2.83 | succinyl-CoA ligase [ADP-forming] subunit beta | |
KEO91012.1* | 0.00 | 329.01 | glutamyl-tRNA synthetase | KDM57451.1* | 0.00 | 13.80 | glutamyl-Q tRNA(Asp) synthetase | ||
KEO92307.1* | 0.00 | 1173.54 | 2-octaprenylphenol hydroxylase | KDM52399.1* | 41.40 | 112.00 | 2.71 | 2-polyprenylphenol 6-hydroxylase | |
KEO92322.1* | 1243.70 | 5084.10 | 4.09 | alkyl hydroperoxide reductase | KDM55608.1* | 108.00 | 706.00 | 6.54 | alkyl hydroperoxide reductase subunit F |
KEO92357.1* | 0.00 | 486.82 | hypothetical protein | KDM55447.1* | 0.00 | 44.50 | maltose O-acetyltransferase | ||
KEO92389.1* | 0.00 | 1032.40 | Clp protease ClpS | KDM55108.1* | 212.00 | 689.00 | 3.25 | ATP-dependent Clp protease adapter protein ClpS | |
KEO92432.1* | 0.00 | 225.11 | acetyl-CoA acetyltransferase | KDM49670.1* | 0.00 | 10.40 | hypothetical protein | ||
KEO92626.1* | 0.00 | 371.92 | transcription elongation factor GreB | KDM53922.1* | 0.00 | 25.90 | transcription elongation factor greB | ||
KEO92766.1* | 0.00 | 499.00 | pseudouridine synthase | KDM54709.1* | 53.60 | 142.00 | 2.65 | tRNA pseudouridine synthase B | |
KEO92773.1* | 238.61 | 1937.27 | 8.12 | translation initiation factor IF-2 | KDM54711.1* | 645.00 | 1330.00 | 2.06 | translation initiation factor IF-2 |
KEO92898.1* | 0.00 | 183.68 | oxidoreductase | KDM50444.1* | 0.00 | 20.20 | formate hydrogenlyase subunit 2 | ||
KEO92901.1* | 0.00 | 211.59 | metallophosphoesterase | KDM54593.1* | 123.00 | 267.00 | 2.17 | protein icc | |
KEO93029.1* | 0.00 | 1061.69 | Fur family transcriptional regulator | KDM55662.1* | 494.00 | 1760.00 | 3.56 | ferric uptake regulation protein | |
KEO93118.1* | 0.00 | 351.20 | 4-hydroxythreonine-4-phosphate dehydrogenase | KDM57359.1* | 86.00 | 299.00 | 3.48 | 4-hydroxythreonine-4-phosphate dehydrogenase | |
KEO93158.1* | 0.00 | 513.67 | ubiquinone biosynthesis protein UbiH | KDM49723.1* | 43.20 | 93.80 | 2.17 | 2-octaprenyl-6-methoxyphenol hydroxylase | |
KEO93247.1* | 0.00 | 269.73 | TetR family transcriptional regulator | KDM55557.1* | 86.70 | 564.00 | 6.51 | HTH-type transcriptional regulator BetI | |
KEO93375.1* | 0.00 | 357.49 | 4-hydroxy-3-methylbut-2-enyl diphosphate reductase | KDM57347.1* | 53.60 | 142.00 | 2.65 | 4-hydroxy-3-methylbut-2-enyl diphosphate reductase | |
KEO93411.1* | 0.00 | 566.68 | 16S rRNA methyltransferase | KDM57388.1* | 162.00 | 1000.00 | 6.17 | ribosomal RNA small subunit methyltransferase H | |
KEO96480.1* | 303.62 | 627.48 | 2.07 | methionine sulfoxide reductase B | KDM51893.1* | 41.00 | 208.00 | 5.07 | peptide methionine sulfoxide reductase msrB |
KEO96529.1* | 0.00 | 210.35 | phosphoribosylamine--glycine ligase | KDM52454.1* | 92.00 | 380.00 | 4.13 | phosphoribosylamine-glycine ligase | |
KEO96539.1* | 0.00 | 696.27 | hypothetical protein | KDM51989.1* | 200.00 | 435.00 | 2.18 | FeS cluster assembly protein sufD | |
KEO96580.1* | 0.00 | 486.03 | PTS IIA-like nitrogen-regulatory protein PtsN | KDM54746.1* | 0.00 | 150.00 | nitrogen regulatory protein | ||
KEO96608.1* | 0.00 | 1394.71 | translation factor Sua5 | KDM53819.1* | 0.00 | 42.90 | tRNA threonylcarbamoyladenosine biosynthesis protein RimN | ||
KEO96752.1* | 97.51 | 359.85 | 3.69 | integrase | KDM51758.1* | 94.30 | 425.00 | 4.51 | putA protein |
KEO98470.1* | 0.00 | 124.49 | hypothetical protein | KDM51955.1* | 11.80 | 59.60 | 5.05 | UPF0061 protein ydiU | |
KEO98596.1* | 0.00 | 814.69 | LysR family transcriptional regulator | KDM57341.1* | 37.70 | 81.90 | 2.17 | transcriptional activator protein nhaR | |
KEO98607.1* | 0.00 | 192.91 | 1-deoxy-D-xylulose 5-phosphate reductoisomerase | KDM57478.1* | 42.50 | 1230.00 | 28.94 | 1-deoxy-D-xylulose 5-phosphate reductoisomerase | |
KEO98608.1* | 0.00 | 1552.72 | peptidase | KDM57481.1* | 264.00 | 854.00 | 3.23 | RIP metalloprotease RseP | |
KEO98641.1* | 0.00 | 1679.78 | LysR family transcriptional regulator | KDM53240.1* | 130.00 | 321.00 | 2.47 | hydrogen peroxide-inducible genes activator | |
KEO98759.1* | 0.00 | 157.99 | 3-dehydroquinate synthase | KDM53905.1* | 46.80 | 192.00 | 4.10 | 3-dehydroquinate synthase | |
KEO98794.1* | 0.00 | 345.72 | branched-chain alpha-keto acid dehydrogenase subunit E2 | KDM57421.1* | 744.00 | 6140.00 | 8.25 | dihydrolipoyllysine-residue acetyltransferase | |
KEO98866.1* | 0.00 | 196.33 | farnesyl-diphosphate synthase | KDM55391.1* | 75.50 | 519.00 | 6.87 | farnesyl diphosphate synthase | |
KEO98882.1* | 0.00 | 473.35 | rRNA methyltransferase | KDM51417.1* | 107.00 | 496.00 | 4.64 | tRNA (cytidine/uridine-2'-O-)-methyltransferase TrmJ | |
KEO98935.1* | 0.00 | 3161.33 | transcriptional regulator | KDM55471.1* | 0.00 | 120.00 | HTH-type transcriptional regulator CueR | ||
KEO98999.1* | 0.00 | 246.42 | nucleoside triphosphate hydrolase | KDM50489.1* | 85.80 | 233.00 | 2.72 | nucleoside triphosphate pyrophosphohydrolase | |
KEO99007.1* | 0.00 | 538.76 | 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase | KDM50467.1* | 70.80 | 154.00 | 2.18 | 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase | |
KEO99009.1* | 0.00 | 388.83 | cyclase | KDM51170.1* | 35.60 | 155.00 | 4.35 | hypothetical protein | |
KEO99027.1* | 0.00 | 95.59 | transketolase | KDM57420.1* | 1130.00 | 10900.00 | 9.65 | pyruvate dehydrogenase E1 component | |
KEO99055.1* | 0.00 | 1388.60 | hypothetical protein | KDM55136.1 | 0.00 | 5.43 | hypothetical protein | ||
*P-value < 0.05 |
Protein ID of E. litoralis | RPKM in E. litoralis spheroplasts at the beginning of growth | RPKM in E. litoralis enlarged spheroplasts | Ratio of RPKMs of E. litoralis | Annotated function | Protein ID of L. amnigena | RPKM in L. amnigena spheroplasts at the beginning of growth | RPKM in L. amnigena enlarged spheroplasts | Ratio of RPKMs of L. amnigena | Annotated function |
Homologs of amino acid synthesis and metabolism-related genes | |||||||||
KEO88954.1* | 616.47 | 136.50 | 0.22 | L-asparaginase | KDM51897.1* | 33.40 | 0.00 | 0.00 | L-asparaginase 1 |
KEO89592.1* | 365.66 | 143.94 | 0.39 | S-adenosylmethionine synthetase | KDM49649.1* | 1070.00 | 255.00 | 0.24 | S-adenosylmethionine synthase |
KEO89916.1* | 363.48 | 0.00 | 0.00 | 2,3,4,5-tetrahydropyridine-2,6-carboxylate N-succinyltransferase | KDM57471.1* | 1050.00 | 432.00 | 0.41 | 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase |
KEO90596.1* | 298.26 | 88.06 | 0.30 | threonine aldolase | KDM55097.1* | 509.00 | 172.00 | 0.34 | low specificity L-threonine aldolase |
KEO92299.1* | 201.21 | 0.00 | 0.00 | 4-hydroxy-tetrahydrodipicolinate reductase | KDM57348.1* | 269.00 | 14.90 | 0.06 | dihydrodipicolinate reductase |
KEO92640.1* | 250.39 | 0.00 | 0.00 | argininosuccinate synthase | KDM54714.1* | 2220.00 | 219.00 | 0.10 | argininosuccinate synthase |
KEO92798.1* | 507.05 | 149.70 | 0.30 | 3-isopropylmalate dehydratase | KDM57378.1* | 196.00 | 60.80 | 0.31 | 3-isopropylmalate dehydratase small subunit |
KEO93106.1* | 831.23 | 245.41 | 0.30 | serine acetyltransferase | KDM52905.1* | 331.00 | 149.00 | 0.45 | serine acetyltransferase |
KEO93391.1* | 1078.83 | 318.51 | 0.30 | glutamine synthetase | KDM53324.1* | 385.00 | 174.00 | 0.45 | glutamine synthetase |
KEO93480.1* | 1248.41 | 595.39 | 0.48 | 3-phosphoglycerate dehydrogenase | KDM49615.1* | 964.00 | 369.00 | 0.38 | D-3-phosphoglycerate dehydrogenase |
KEO98853.1* | 596.53 | 0.00 | 0.00 | ketol-acid reductoisomerase | KDM53647.1* | 3330.00 | 450.00 | 0.14 | ketol-acid reductoisomerase |
KEO99046.1* | 292.53 | 0.00 | 0.00 | anthranilate synthase component I | KDM46686.1* | 1870.00 | 7.86 | 0.00 | anthranilate synthase component 1 |
KEO99050.1* | 459.56 | 45.23 | 0.10 | anthranilate phosphoribosyltransferase | KDM46685.1* | 2870.00 | 53.90 | 0.02 | anthranilate synthase component II |
Homologs of flagellar protein genes | |||||||||
KEO89561.1* | 22111.90 | 337.67 | 0.02 | flagellin | KDM48656.1* | 124.00 | 44.90 | 0.36 | hypothetical protein |
KEO90993.1* | 740.22 | 0.00 | 0.00 | flagellar basal body rod protein FlgC | KDM51808.1* | 41.90 | 0.00 | 0.00 | flagellar basal-body rod protein flgC |
KEO92484.1* | 806.97 | 79.42 | 0.10 | flagellar motor protein MotB | KDM51720.1* | 24600.00 | 1390.00 | 0.06 | outer membrane protein A |
Homologs of nucleotide synthesis and pentose phosphate pathway-related genes | |||||||||
KEO91063.1* | 325.03 | 95.96 | 0.30 | phosphoribosylpyrophosphate synthetase | KDM47000.1* | 985.00 | 298.00 | 0.30 | ribose-phosphate pyrophosphokinase |
KEO93239.1* | 414.76 | 61.23 | 0.15 | glucose-6-phosphate dehydrogenase | KDM48740.1* | 345.00 | 150.00 | 0.43 | glucose-6-phosphate 1-dehydrogenase |
KEO93278.1* | 293.09 | 0.00 | 0.00 | aspartate carbamoyltransferase catalytic subunit | KDM56880.1* | 1090.00 | 65.90 | 0.06 | aspartate carbamoyltransferase |
KEO96500.1* | 688.30 | 0.00 | 0.00 | ribulose-phosphate 3-epimerase | KDM53902.1* | 200.00 | 54.40 | 0.27 | ribulose-phosphate 3-epimerase |
KEO96518.1* | 349.69 | 103.24 | 0.30 | nicotinate-nucleotide pyrophosphorylase | KDM57413.1* | 57.00 | 27.50 | 0.48 | nicotinate-nucleotide pyrophosphorylase [carboxylating] |
KEO98799.1* | 610.90 | 45.09 | 0.07 | transketolase | KDM49630.1* | 844.00 | 278.00 | 0.33 | transketolase 1 |
Homologs of other membrane protein genes | |||||||||
KEO92879.1* | 12676.20 | 0.00 | 0.00 | membrane protein | KDM46678.1* | 80.50 | 0.00 | 0.00 | outer membrane protein W |
KEO93429.1* | 12522.20 | 4363.68 | 0.35 | membrane protein | KDM54978.1* | 216.00 | 86.80 | 0.40 | inner membrane protein YbhL |
KEO98493.1* | 726.95 | 268.28 | 0.37 | ABC transporter ATP-binding protein | KDM57319.1* | 479.00 | 192.00 | 0.40 | hypothetical protein |
KEO99262.1* | 1240.06 | 162.72 | 0.13 | hypothetical protein | KDM52093.1* | 131.00 | 11.80 | 0.09 | AI-2 transporter tqsA |
Others | |||||||||
KEO89629.1* | 824.47 | 121.71 | 0.15 | 3-demethylubiquinone-9 3-methyltransferase | KDM46348.1* | 116.00 | 16.90 | 0.15 | 3-demethylubiquinone-9 3-methyltransferase |
KEO90016.1* | 338.03 | 49.90 | 0.15 | hypothetical protein | KDM52077.1* | 18.60 | 0.00 | 0.00 | HTH-type transcriptional regulator AbgR |
KEO90690.1* | 737.52 | 0.00 | 0.00 | enoyl-ACP reductase | KDM46715.1* | 495.00 | 156.00 | 0.32 | enoyl-[acyl-carrier-protein] reductase [NADH] |
KEO92246.1* | 756.79 | 111.72 | 0.15 | glucose-1-phosphate thymidylyltransferase | KDM46209.1* | 58.80 | 28.30 | 0.48 | glucose-1-phosphate thymidylyltransferase 2 |
KEO92477.1* | 572.94 | 0.00 | 0.00 | molybdopterin biosynthesis protein B | KDM54974.1* | 232.00 | 47.90 | 0.21 | molybdenum cofactor biosynthesis protein B |
KEO92492.1* | 852.18 | 125.80 | 0.15 | oxidoreductase | KDM46695.1* | 312.00 | 80.60 | 0.26 | hypothetical protein |
KEO92638.1* | 479.48 | 0.00 | 0.00 | cyclopropane-fatty-acyl-phospholipid synthase | KDM52012.1* | 148.00 | 0.00 | 0.00 | cyclopropane-fatty-acyl-phospholipid synthase |
KEO92662.1* | 1438.43 | 212.34 | 0.15 | 50S ribosomal protein L17 | KDM53831.1* | 354.00 | 128.00 | 0.36 | 50S ribosomal protein L17 |
KEO92699.1* | 771.18 | 113.84 | 0.15 | LysR family transcriptional regulator | KDM50509.1* | 37.00 | 0.00 | 0.00 | glycine cleavage system transcriptional activator |
KEO93102.1* | 223.37 | 0.00 | 0.00 | bifunctional N-acetylglucosamine-1-phosphate uridyltransferase/glucosamine-1-phosphate acetyltransferase | KDM52744.1* | 372.00 | 108.00 | 0.29 | glmU protein |
KEO93190.1* | 831.23 | 409.01 | 0.49 | single-stranded DNA-binding protein | KDM56126.1* | 679.00 | 140.00 | 0.21 | single-stranded DNA-binding protein |
KEO93395.1* | 438.05 | 64.66 | 0.15 | cytosol aminopeptidase | KDM51408.1* | 158.00 | 47.70 | 0.30 | peptidase B |
KEO96463.1* | 111.07 | 32.79 | 0.30 | glutamate-ammonia-ligase adenylyltransferase | KDM54608.1* | 214.00 | 64.50 | 0.30 | glutamate-ammonia-ligase adenylyltransferase |
KEO96716.1* | 396.13 | 116.95 | 0.30 | GntR family transcriptional regulator | KDM52778.1* | 68.20 | 0.00 | 0.00 | hypothetical protein |
KEO96769.1* | 581.14 | 171.57 | 0.30 | ribonucleotide-diphosphate reductase subunit beta | KDM46350.1* | 481.00 | 130.00 | 0.27 | ribonucleoside-diphosphate reductase 1 subunit beta |
KEO98584.1* | 1114.39 | 0.00 | 0.00 | transcriptional regulator HU subunit alpha | KDM52452.1* | 2050.00 | 630.00 | 0.31 | DNA-binding protein HU-alpha |
KEO98612.1* | 1352.13 | 0.00 | 0.00 | 50S ribosomal protein L31 | KDM53254.1* | 159.00 | 0.00 | 0.00 | 50S ribosomal protein L31 |
KEO98687.1* | 228.14 | 84.19 | 0.37 | phosphoenolpyruvate carboxylase | KDM53245.1* | 621.00 | 236.00 | 0.38 | phosphoenolpyruvate carboxylase |
KEO98733.1* | 470.03 | 173.46 | 0.37 | DNA topoisomerase I | KDM46698.1* | 569.00 | 255.00 | 0.45 | DNA topoisomerase 1 |
KEO98800.1* | 603.63 | 0.00 | 0.00 | glyceraldehyde-3-phosphate dehydrogenase | KDM51892.1* | 2900.00 | 1360.00 | 0.47 | glyceraldehyde-3-phosphate dehydrogenase |
KEO98996.1* | 96.21 | 0.00 | 0.00 | methionine--tRNA ligase | KDM46274.1* | 576.00 | 115.00 | 0.20 | methionyl-tRNA synthetase |
KEO99011.1* | 473.88 | 139.91 | 0.30 | carbonate dehydratase | KDM52008.1* | 26.70 | 0.00 | 0.00 | hypothetical protein |
KEO99037.1* | 378.39 | 0.00 | 0.00 | inorganic polyphosphate kinase | KDM51166.1* | 96.60 | 0.00 | 0.00 | hypothetical protein |
KEO99041.1* | 4328.46 | 2008.15 | 0.46 | heat-shock protein | KDM52775.1* | 41.30 | 0.00 | 0.00 | small heat shock protein ibpA |
KEO99260.1* | 277.08 | 81.80 | 0.30 | aminotransferase | KDM51415.1* | 1540.00 | 637.00 | 0.41 | cysteine desulfurase |
*P-value < 0.05 |
Protein ID of E. litoralis | RPKM in E. litoralis spheroplasts at the beginning of growth | RPKM in E. litoralis enlarged spheroplasts | Ratio of RPKMs of E. litoralis | Annotated function | Protein ID of L. amnigena | RPKM in L. amnigena spheroplasts at the beginning of growth | RPKM in L. amnigena enlarged spheroplasts | Ratio of RPKMs of L. amnigena | Annotated function |
Homologs of membrane protein genes | |||||||||
KEO89564.1* | 0.00 | 106.93 | hypothetical protein | KDM48649.1* | 40.40 | 14.60 | 0.36 | flagellar M-ring protein | |
KEO89607.1* | 0.00 | 129.05 | multidrug transporter | KDM52010.1* | 150.00 | 45.10 | 0.30 | multidrug resistance protein mdtK | |
KEO89895.1* | 0.00 | 634.32 | biopolymer transporter ExbB | KDM55699.1* | 564.00 | 177.00 | 0.31 | protein tolQ | |
KEO89973.1* | 0.00 | 184.81 | magnesium transporter CorA | KDM52382.1* | 661.00 | 168.00 | 0.25 | magnesium transporter CorA | |
KEO92632.1* | 0.00 | 146.76 | hypothetical protein | KDM46187.1* | 175.00 | 72.30 | 0.41 | inner membrane transporter YeeF | |
KEO92658.1* | 0.00 | 1301.72 | hypothetical protein | KDM57464.1* | 136.00 | 39.40 | 0.29 | UPF0126 inner membrane protein yadS | |
KEO92812.1* | 0.00 | 172.56 | type VI secretion protein | KDM54463.1* | 51.90 | 12.50 | 0.24 | hypothetical protein | |
KEO93024.1* | 262.72 | 2171.79 | 8.27 | iron transporter | KDM53929.1* | 413.00 | 171.00 | 0.41 | Fe/S biogenesis protein nfuA |
KEO93116.1* | 0.00 | 227.97 | organic solvent tolerance protein | KDM57361.1* | 483.00 | 224.00 | 0.46 | LPS-assembly protein lptD | |
KEO93384.1* | 352.12 | 1143.53 | 3.25 | MttB family protein | KDM52402.1* | 220.00 | 15.90 | 0.07 | sec-independent protein translocase tatC |
KEO98525.1* | 0.00 | 128.22 | hypothetical protein | KDM52772.1* | 118.00 | 38.00 | 0.32 | D-galactonate transporter | |
KEO98837.1* | 0.00 | 215.39 | phosphate ABC transporter permease | KDM52748.1* | 724.00 | 152.00 | 0.21 | phosphate transport system permease pstA | |
KEO98838.1* | 0.00 | 194.41 | phosphate ABC transporter permease | KDM52747.1* | 1310.00 | 230.00 | 0.18 | phosphate transport system permease pstC | |
KEO98907.1* | 243.77 | 539.78 | 2.21 | 3,4-dihydroxy-2-butanone 4-phosphate synthase | KDM54605.1* | 1220.00 | 432.00 | 0.35 | 3,4-dihydroxy-2-butanone 4-phosphate synthase |
Others | |||||||||
KEO88945.1* | 1061.88 | 3056.67 | 2.88 | peptide deformylase | KDM53823.1* | 699.00 | 313.00 | 0.45 | peptide deformylase |
KEO88946.1* | 0.00 | 300.90 | recombinase RecR | KDM55460.1* | 336.00 | 101.00 | 0.30 | recombination protein recR | |
KEO88958.1* | 0.00 | 546.11 | argininosuccinate lyase | KDM53241.1* | 1610.00 | 116.00 | 0.07 | argininosuccinate lyase | |
KEO88960.1* | 484.06 | 1822.10 | 3.76 | diaminopimelate decarboxylase | KDM50540.1* | 780.00 | 19.50 | 0.03 | diaminopimelate decarboxylase |
KEO89297.1* | 0.00 | 160.53 | histidinol-phosphate aminotransferase | KDM46192.1* | 240.00 | 92.60 | 0.39 | histidinol-phosphate aminotransferase | |
KEO89579.1* | 0.00 | 507.45 | tRNA (guanine-N7)-methyltransferase | KDM54472.1* | 802.00 | 154.00 | 0.19 | tRNA (guanine-N(7)-)-methyltransferase | |
KEO89635.1* | 0.00 | 207.20 | formyltetrahydrofolate deformylase | KDM46646.1* | 80.60 | 14.60 | 0.18 | formyltetrahydrofolate deformylase | |
KEO89998.1* | 0.00 | 437.71 | ArsR family transcriptional regulator | KDM55050.1* | 52.90 | 0.00 | 0.00 | hypothetical protein | |
KEO90041.1* | 0.00 | 118.57 | hypothetical protein | KDM48627.1* | 48.00 | 0.00 | 0.00 | DNA-cytosine methyltransferase | |
KEO90698.1* | 0.00 | 438.68 | 3-deoxy-manno-octulosonate cytidylyltransferase | KDM55141.1* | 91.00 | 0.00 | 0.00 | 3-deoxy-manno-octulosonate cytidylyltransferase | |
KEO91020.1* | 0.00 | 391.37 | molecular chaperone DnaK | KDM57452.1* | 5740.00 | 2210.00 | 0.39 | DnaK suppressor protein | |
KEO91036.1* | 0.00 | 883.47 | molecular chaperone Hsp33 | KDM53917.1* | 77.30 | 28.00 | 0.36 | chaperonin | |
KEO91037.1* | 0.00 | 191.92 | ornithine carbamoyltransferase | KDM56877.1* | 16.90 | 0.00 | 0.00 | ornithine carbamoyltransferase, catabolic | |
KEO92302.1* | 0.00 | 465.99 | molybdopterin biosynthesis protein MoeB | KDM52444.1* | 112.00 | 16.30 | 0.15 | sulfur carrier protein ThiS adenylyltransferase | |
KEO92334.1* | 113.82 | 285.62 | 2.51 | aconitate hydratase | KDM46701.1* | 305.00 | 152.00 | 0.50 | aconitate hydratase 1 |
KEO92372.1* | 0.00 | 272.18 | phosphomethylpyrimidine kinase | KDM46258.1* | 42.40 | 15.30 | 0.36 | hydroxymethylpyrimidine/phosphomethylpyrimidine kinase | |
KEO92402.1* | 0.00 | 190.30 | glutamyl-tRNA synthetase | KDM51312.1* | 216.00 | 86.80 | 0.40 | glutamyl-tRNA synthetase | |
KEO92434.1* | 0.00 | 266.53 | 2-hydroxyacid dehydrogenase | KDM52411.1* | 69.70 | 25.20 | 0.36 | glyoxylate/hydroxypyruvate reductase B | |
KEO92503.1* | 0.00 | 462.99 | inosine-5-monophosphate dehydrogenase | KDM51383.1* | 417.00 | 117.00 | 0.28 | inosine-5'-monophosphate dehydrogenase | |
KEO92549.1* | 0.00 | 490.81 | 30S ribosomal protein S6 | KDM56939.1* | 944.00 | 217.00 | 0.23 | 30S ribosomal protein S6 | |
KEO92597.1* | 0.00 | 368.72 | tryptophan synthase subunit beta | KDM46683.1* | 3260.00 | 134.00 | 0.04 | tryptophan synthase beta chain | |
KEO92634.1* | 0.00 | 460.61 | oxidoreductase | KDM52065.1* | 23.50 | 0.00 | 0.00 | dihydrofolate reductase folM | |
KEO92667.1* | 0.00 | 278.51 | adenylate kinase | KDM55462.1* | 1950.00 | 914.00 | 0.47 | adenylate kinase | |
KEO92711.1* | 0.00 | 424.08 | 3-isopropylmalate dehydrogenase | KDM57380.1* | 280.00 | 113.00 | 0.40 | 3-isopropylmalate dehydrogenase | |
KEO92758.1* | 0.00 | 1060.85 | DNA-binding protein | KDM51729.1* | 7260.00 | 966.00 | 0.13 | heat shock protein hspQ | |
KEO92776.1* | 0.00 | 1339.41 | ribosome maturation protein RimP | KDM54713.1* | 187.00 | 81.40 | 0.44 | ribosome maturation factor rimP | |
KEO92780.1* | 0.00 | 511.79 | ATPase AAA | KDM46723.1* | 52.10 | 25.10 | 0.48 | psp operon transcriptional activator | |
KEO92795.1* | 0.00 | 399.20 | thioesterase | KDM55422.1* | 298.00 | 61.60 | 0.21 | long-chain acyl-CoA thioesterase tesC | |
KEO92811.1* | 0.00 | 81.47 | polyphosphate kinase | KDM51368.1* | 437.00 | 107.00 | 0.24 | polyphosphate kinase | |
KEO93025.1* | 499.56 | 1179.89 | 2.36 | malonic semialdehyde reductase | KDM51751.1* | 57.50 | 20.80 | 0.36 | hypothetical protein |
KEO93125.1* | 0.00 | 144.29 | succinylarginine dihydrolase | KDM51916.1* | 89.70 | 27.80 | 0.31 | N-succinylarginine dihydrolase | |
KEO93177.1* | 0.00 | 687.39 | aromatic amino acid aminotransferase | KDM55151.1* | 385.00 | 124.00 | 0.32 | aspartate aminotransferase | |
KEO93181.1* | 0.00 | 286.50 | riboflavin synthase subunit alpha | KDM52011.1* | 317.00 | 76.60 | 0.24 | riboflavin synthase alpha chain | |
KEO93285.1* | 1214.49 | 3764.87 | 3.10 | bacterioferritin | KDM53859.1* | 463.00 | 77.30 | 0.17 | bacterioferritin |
KEO93379.1* | 0.00 | 350.17 | beta-hexosaminidase | KDM51842.1* | 248.00 | 71.90 | 0.29 | beta-hexosaminidase | |
KEO93387.1* | 0.00 | 283.79 | threonine dehydratase | KDM54671.1* | 51.50 | 0.00 | 0.00 | threonine dehydratase catabolic | |
KEO93441.1* | 0.00 | 293.53 | cystathionine beta-lyase | KDM54516.1* | 285.00 | 92.90 | 0.33 | cystathionine beta-lyase | |
KEO93476.1* | 0.00 | 3077.91 | hypothetical protein | KDM54633.1* | 68.60 | 24.80 | 0.36 | hypothetical protein | |
KEO96380.1* | 0.00 | 130.17 | protein-PII uridylyltransferase | KDM57472.1* | 108.00 | 32.10 | 0.30 | [protein-PII] uridylyltransferase | |
KEO96408.1* | 0.00 | 407.90 | GTP cyclohydrolase | KDM46702.1* | 287.00 | 104.00 | 0.36 | GTP cyclohydrolase-2 | |
KEO96434.1* | 131.11 | 377.39 | 2.88 | glutamate synthase | KDM54762.1* | 2310.00 | 320.00 | 0.14 | glutamate synthase [NADPH] large chain |
KEO96435.1* | 0.00 | 156.26 | glutamate synthase | KDM54763.1* | 1780.00 | 320.00 | 0.18 | glutamate synthase [NADPH] small chain | |
KEO96528.1* | 0.00 | 211.70 | exodeoxyribonuclease VII large subunit | KDM51384.1* | 74.20 | 0.00 | 0.00 | exodeoxyribonuclease 7 large subunit | |
KEO96545.1* | 0.00 | 814.69 | AsnC family transcriptional regulator | KDM51416.1* | 2800.00 | 150.00 | 0.05 | HTH-type transcriptional regulator iscR | |
KEO98460.1* | 0.00 | 1164.32 | 50S ribosomal protein L27 | KDM54727.1* | 1840.00 | 667.00 | 0.36 | 50S ribosomal protein L27 | |
KEO98556.1* | 0.00 | 200.94 | citrate lyase | KDM54480.1* | 19.40 | 0.00 | 0.00 | citrate lyase subunit beta | |
KEO98575.1* | 300.92 | 1066.10 | 3.54 | farnesyltranstransferase | KDM54729.1* | 175.00 | 25.30 | 0.14 | octaprenyl-diphosphate synthase |
KEO98712.1* | 0.00 | 412.01 | thioredoxin reductase | KDM55115.1* | 351.00 | 88.80 | 0.25 | thioredoxin reductase | |
KEO98796.1* | 0.00 | 1374.78 | 5-formyltetrahydrofolate cyclo-ligase | KDM49727.1* | 85.40 | 41.20 | 0.48 | 5-formyltetrahydrofolate cyclo-ligase | |
KEO98834.1* | 0.00 | 260.35 | chemotaxis protein CheY | KDM55825.1* | 2140.00 | 142.00 | 0.07 | phosphate regulon transcriptional regulatory protein phoB | |
KEO98839.1* | 0.00 | 180.36 | histidine kinase | KDM55824.1* | 380.00 | 47.40 | 0.12 | phosphate regulon sensor protein phoR | |
KEO98906.1* | 0.00 | 424.68 | 6,7-dimethyl-8-ribityllumazine synthase | KDM55386.1* | 325.00 | 157.00 | 0.48 | 6,7-dimethyl-8-ribityllumazine synthase | |
KEO98922.1* | 0.00 | 653.71 | 50S ribosomal protein L25 | KDM46330.1* | 477.00 | 129.00 | 0.27 | 50S ribosomal protein L25 | |
KEO98968.1* | 0.00 | 712.85 | nucleoside-triphosphate diphosphatase | KDM54467.1* | 57.20 | 0.00 | 0.00 | nucleoside-triphosphatase rdgB | |
KEO98978.1* | 0.00 | 229.80 | DNA repair protein RadA | KDM57315.1* | 282.00 | 106.00 | 0.38 | DNA repair protein radA | |
KEO99042.1* | 0.00 | 438.68 | CTP synthase | KDM50488.1* | 871.00 | 353.00 | 0.41 | CTP synthase | |
*P-value < 0.05 |
Protein ID of E. litoralis | RPKM in E. litoralis spheroplasts at the beginning of growth | RPKM in E. litoralis enlarged spheroplasts | Ratio of RPKMs of E. litoralis | Annotated function | Protein ID of L. amnigena | RPKM in L. amnigena spheroplasts at the beginning of growth | RPKM in L. amnigena enlarged spheroplasts | Ratio of RPKMs of L. amnigena | Annotated function |
Homologs of membrane protein genes | |||||||||
KEO89304.1* | 629.44 | 247.78 | 0.39 | penicillin-binding protein | KDM57456.1* | 296.00 | 1010.00 | 3.41 | penicillin-binding protein 1B |
KEO89573.1* | 405.64 | 59.88 | 0.15 | flagellar biosynthesis protein flip | KDM48639.1* | 0.00 | 16.70 | flagellar biosynthetic protein fliP | |
KEO90985.1* | 453.73 | 133.96 | 0.30 | hypothetical protein | KDM51816.1* | 0.00 | 22.50 | flagellar hook-associated protein 1 | |
KEO90987.1* | 2625.04 | 163.16 | 0.06 | flagellar P-ring protein FlgI | KDM51814.1* | 15.50 | 56.00 | 3.61 | flagellar P-ring protein |
KEO90994.1* | 859.40 | 0.00 | 0.00 | flagellar basal body rod protein FlgB | KDM51807.1* | 0.00 | 147.00 | flagellar basal-body rod protein flgB | |
KEO92489.1* | 458.87 | 135.47 | 0.30 | ABC transporter | KDM51852.1* | 72.60 | 175.00 | 2.41 | lipoprotein-releasing system ATP-binding protein LolD |
KEO92547.1* | 320.92 | 0.00 | 0.00 | ABC transporter | KDM48630.1* | 0.00 | 13.50 | inner membrane protein yedI | |
KEO92700.1* | 2204.56 | 0.00 | 0.00 | magnesium transporter ApaG | KDM57357.1* | 89.90 | 488.00 | 5.43 | protein ApaG |
KEO93367.1* | 2069.58 | 111.09 | 0.05 | secretion system protein | KDM53908.1* | 0.00 | 9.92 | hypothetical protein | |
KEO93416.1* | 284.06 | 0.00 | 0.00 | phospho-N-acetylmuramoyl-pentapeptide-transferase | KDM57393.1* | 204.00 | 817.00 | 4.00 | phospho-N-acetylmuramoyl-pentapeptide-transferase |
KEO93419.1* | 495.89 | 109.80 | 0.22 | UDP-diphospho-muramoylpentapeptide beta-N-acetylglucosaminyltransferase | KDM57396.1* | 79.70 | 415.00 | 5.21 | undecaprenyldiphospho-muramoylpentapeptide beta-N-acetylglucosaminyltransferase |
KEO93424.1* | 682.13 | 134.26 | 0.20 | cell division protein FtsA | KDM57400.1* | 865.00 | 2250.00 | 2.60 | cell division protein ftsA |
KEO98787.1* | 1321.30 | 373.84 | 0.28 | preprotein translocase subunit SecA | KDM57404.1* | 69.00 | 559.00 | 8.10 | protein translocase subunit secA |
KEO98980.1* | 184.72 | 54.53 | 0.30 | major facilitator transporter | KDM46178.1* | 64.50 | 159.00 | 2.47 | shikimate transporter |
Others | |||||||||
KEO89313.1* | 2157.65 | 0.00 | 0.00 | peptide methionine sulfoxide reductase | KDM56920.1* | 0.00 | 19.10 | peptide methionine sulfoxide reductase msrA | |
KEO89605.1* | 7190.86 | 2640.13 | 0.37 | molecular chaperone GroEL | KDM56992.1* | 1220.00 | 4660.00 | 3.82 | chaperonin |
KEO89995.1* | 402.88 | 33.98 | 0.08 | 5-methyltetrahydrofolate--homocysteine methyltransferase | KDM55766.1* | 111.00 | 223.00 | 2.01 | methionine synthase |
KEO90687.1* | 897.43 | 132.48 | 0.15 | pyridoxamine 5'-phosphate oxidase | KDM52037.1* | 0.00 | 37.40 | pyridoxine/pyridoxamine 5'-phosphate oxidase | |
KEO91004.1* | 607.24 | 0.00 | 0.00 | hypothetical protein | KDM49677.1* | 375.00 | 1380.00 | 3.68 | protein yciF |
KEO91044.1* | 382.68 | 0.00 | 0.00 | glucose-methanol-choline oxidoreductase | KDM55555.1* | 51.00 | 185.00 | 3.63 | choline dehydrogenase |
KEO91076.1* | 644.55 | 190.30 | 0.30 | phosphomannomutase | KDM46221.1* | 99.10 | 1120.00 | 11.30 | phosphomannomutase |
KEO92378.1* | 1931.61 | 855.42 | 0.44 | RNA polymerase sigma70 | KDM51449.1* | 2570.00 | 7420.00 | 2.89 | RNA polymerase sigma-E factor |
KEO92529.1* | 224.36 | 66.24 | 0.30 | hypothetical protein | KDM57043.1* | 0.00 | 6.34 | hypothetical protein | |
KEO92652.1* | 1365.79 | 554.44 | 0.41 | succinate--CoA ligase | KDM55690.1* | 566.00 | 1450.00 | 2.56 | succinyl-CoA ligase [ADP-forming] subunit alpha |
KEO92654.1* | 2162.76 | 141.89 | 0.07 | dihydrolipoamide succinyltransferase | KDM55688.1* | 415.00 | 1100.00 | 2.65 | hypothetical protein |
KEO92656.1* | 2572.76 | 822.87 | 0.32 | dihydrolipoamide dehydrogenase | KDM57422.1* | 775.00 | 3320.00 | 4.28 | dihydrolipoyl dehydrogenase |
KEO92681.1* | 1049.06 | 206.48 | 0.20 | 50S ribosomal protein L16 | KDM53849.1* | 537.00 | 2360.00 | 4.39 | 50S ribosomal protein L16 |
KEO93425.1* | 1877.96 | 607.24 | 0.32 | cell division protein FtsZ | KDM57401.1* | 1180.00 | 5490.00 | 4.65 | cell division protein ftsZ |
KEO93475.1* | 113.94 | 0.00 | 0.00 | ATPase AAA | KDM55119.1* | 88.50 | 311.00 | 3.51 | replication-associated recombination protein A |
KEO96455.1* | 712.48 | 35.06 | 0.05 | UDP-N-acetylglucosamine 1-carboxyvinyltransferase | KDM54731.1* | 162.00 | 351.00 | 2.17 | UDP-N-acetylglucosamine 1-carboxyvinyltransferase |
KEO96456.1* | 1034.79 | 101.84 | 0.10 | UTP--glucose-1-phosphate uridylyltransferase | KDM46650.1* | 206.00 | 678.00 | 3.29 | UTP-glucose-1-phosphate uridylyltransferase |
KEO96517.1* | 762.48 | 0.00 | 0.00 | chemotaxis protein CheY | KDM46276.1* | 0.00 | 68.30 | hypothetical protein | |
KEO96548.1* | 291.41 | 86.03 | 0.30 | dihydroorotate dehydrogenase | KDM51709.1* | 16.80 | 72.90 | 4.34 | dihydroorotate dehydrogenase |
KEO98611.1* | 618.35 | 0.00 | 0.00 | 3-hydroxyacyl-ACP dehydratase | KDM57485.1* | 74.50 | 350.00 | 4.70 | (3R)-hydroxymyristoyl-[acyl-carrier-protein] dehydratase |
KEO99053.1* | 249.16 | 73.56 | 0.30 | molybdopterin biosynthesis protein | KDM55029.1* | 68.90 | 149.00 | 2.16 | molybdopterin molybdenumtransferase |
KEO99263.1* | 1114.39 | 0.00 | 0.00 | glutamine amidotransferase | KDM54696.1* | 327.00 | 852.00 | 2.61 | protein yhbO |
*P-value < 0.05 |
Protein ID of E. litoralis | RPKM in E. litoralis spheroplasts at the beginning of growth | RPKM in E. litoralis enlarged spheroplasts | Ratio of RPKMs of E. litoralis | Annotated function | Protein ID of L. amnigena | RPKM in L. amnigena spheroplasts at the beginning of growth | RPKM in L. amnigena enlarged spheroplasts | Ratio of RPKMs of L. amnigena | Annotated function |
Homologs of chaperone genes | |||||||||
KEO89606.1* | 0.00 | 623.74 | molecular chaperone GroES | KDM56993.1* | 347.00 | 1300.00 | 3.75 | chaperonin | |
KEO92782.1* | 0.00 | 4575.93 | phage shock protein | KDM46724.1* | 4670.00 | 27100.00 | 5.80 | phage shock protein A | |
KEO93197.1* | 0.00 | 2039.77 | ATP-dependent protease | KDM53259.1* | 178.00 | 608.00 | 3.42 | ATP-dependent protease ATPase subunit HslU | |
KEO93350.1* | 588.91 | 6885.08 | 11.69 | ATPase AAA | KDM51144.1* | 449.00 | 1660.00 | 3.70 | chaperone ClpB |
KEO98976.1* | 265.47 | 587.82 | 2.21 | molecular chaperone DnaJ | KDM57339.1* | 267.00 | 751.00 | 2.81 | chaperone dnaJ |
Homologs of DNA replication and repair-related genes | |||||||||
KEO92279.1* | 304.84 | 659.99 | 2.17 | ATPase AAA | KDM53654.1* | 0.00 | 8.08 | Mg chelatase-like protein | |
KEO92303.1* | 0.00 | 255.35 | chromosomal replication initiator protein DnaA | KDM52760.1* | 280.00 | 617.00 | 2.20 | chromosomal replication initiator protein dnaA | |
KEO92620.1* | 1142.64 | 8813.23 | 7.71 | recombinase RecA | KDM50414.1* | 401.00 | 893.00 | 2.23 | protein recA |
Homologs of lipopolysaccharide synthesis and transport-related genes | |||||||||
KEO89583.1* | 0.00 | 224.27 | ABC transporter ATP-binding protein | KDM54743.1* | 46.80 | 339.00 | 7.24 | lipopolysaccharide export system ATP-binding protein LptB | |
KEO90699.1* | 309.18 | 1369.19 | 4.43 | D-arabinose 5-phosphate | KDM54739.1* | 34.40 | 74.70 | 2.17 | arabinose 5-phosphate isomerase |
KEO92387.1* | 0.00 | 693.72 | permease | KDM54753.1* | 201.00 | 458.00 | 2.28 | lipopolysaccharide export system permease lptF | |
KEO96424.1* | 321.43 | 901.51 | 2.80 | ABC transporter | KDM55137.1* | 29.10 | 91.30 | 3.14 | lipid A export ATP-binding/permease MsbA |
KEO98632.1* | 0.00 | 130.74 | MFS transporter | KDM50532.1* | 0.00 | 10.30 | lysophospholipid transporter lplT | ||
Homologs of peptidoglycan synthesis-related genes | |||||||||
KEO92316.1* | 0.00 | 1429.28 | MltA | KDM50514.1* | 46.40 | 123.00 | 2.65 | membrane-bound lytic murein transglycosylase A | |
KEO93302.1* | 0.00 | 801.96 | peptidoglycan transglycosylase | KDM54749.1* | 0.00 | 16.90 | monofunctional biosynthetic peptidoglycan transglycosylase | ||
KEO93307.1* | 0.00 | 252.66 | N-acetylmuramoyl-L-alanine amidase | KDM55076.1* | 20.40 | 118.00 | 5.78 | N-acetylmuramoyl-L-alanine amidase AmiD | |
KEO93413.1* | 0.00 | 408.49 | peptidoglycan glycosyltransferase | KDM57390.1* | 115.00 | 452.00 | 3.93 | peptidoglycan synthase ftsI | |
KEO93417.1* | 0.00 | 193.99 | UDP-N-acetylmuramoylalanine--D-glutamate ligase | KDM57394.1* | 116.00 | 802.00 | 6.91 | UDP-N-acetylmuramoylalanine-D-glutamate ligase | |
Homologs of other membrane protein genes | |||||||||
KEO89306.1* | 1090.43 | 2253.52 | 2.07 | membrane protease subunit HflC | KDM56960.1* | 135.00 | 599.00 | 4.44 | protein HflC |
KEO89307.1* | 535.14 | 3554.84 | 6.64 | peptidase | KDM56961.1* | 431.00 | 1380.00 | 3.20 | protein HflK |
KEO89575.1* | 0.00 | 225.11 | flagellar biosynthesis protein FliR | KDM48637.1* | 0.00 | 31.30 | flagellar biosynthetic protein fliR | ||
KEO89580.1* | 0.00 | 221.23 | mechanosensitive ion channel protein MscS | KDM55515.1* | 68.20 | 188.00 | 2.76 | miniconductance mechanosensitive channel | |
KEO92762.1* | 0.00 | 194.41 | membrane protein | KDM51940.1* | 0.00 | 16.20 | hypothetical protein | ||
KEO93138.1* | 0.00 | 505.31 | ABC transporter | KDM55480.1* | 321.00 | 823.00 | 2.56 | hypothetical protein | |
KEO93143.1* | 0.00 | 301.81 | proline:sodium symporter PutP | KDM51759.1* | 495.00 | 1180.00 | 2.38 | sodium/proline symporter | |
KEO96616.1* | 0.00 | 211.59 | membrane protein | KDM48736.1* | 116.00 | 568.00 | 4.90 | hypothetical protein | |
KEO96782.1* | 0.00 | 281.12 | MarC family transcriptional regulator | KDM46654.1* | 0.00 | 37.90 | UPF0056 membrane protein yhcE | ||
KEO96802.1* | 0.00 | 526.58 | hypothetical protein | KDM51307.1* | 54.80 | 674.00 | 12.30 | manganese transporter mntH | |
KEO98444.1* | 159.95 | 613.91 | 3.84 | protoheme IX farnesyltransferase | KDM55407.1* | 612.00 | 1340.00 | 2.19 | protoheme IX farnesyltransferase |
KEO98495.1* | 0.00 | 1075.18 | hypothetical protein | KDM55130.1* | 24.50 | 70.90 | 2.89 | UPF0702 transmembrane protein ycaP | |
KEO98569.1* | 201.21 | 3148.42 | 15.65 | histidine kinase | KDM51863.1* | 0.00 | 16.80 | sensor protein phoQ | |
KEO98609.1* | 288.10 | 612.40 | 2.13 | membrane protein | KDM57482.1* | 316.00 | 742.00 | 2.35 | outer membrane protein assembly factor yaeT |
KEO99117.1* | 0.00 | 227.97 | membrane protein | KDM54035.1* | 14.10 | 51.10 | 3.62 | hypothetical protein | |
Others | |||||||||
KEO89324.1* | 0.00 | 339.26 | mannose-1-phosphate guanylyltransferase | KDM46222.1* | 118.00 | 1610.00 | 13.64 | mannose-1-phosphate guanylyltransferase | |
KEO89964.1* | 0.00 | 1086.92 | taurine dioxygenase | KDM57053.1* | 19.90 | 115.00 | 5.78 | alpha-ketoglutarate-dependent taurine dioxygenase | |
KEO89994.1* | 0.00 | 480.32 | aminomethyltransferase | KDM49721.1* | 264.00 | 696.00 | 2.64 | aminomethyltransferase | |
KEO90662.1* | 0.00 | 165.87 | phosphoribosylaminoimidazole carboxylase | KDM55484.1* | 0.00 | 138.00 | N5-carboxyaminoimidazole ribonucleotide synthase | ||
KEO90672.1* | 0.00 | 261.97 | succinyl-CoA synthetase subunit beta | KDM55689.1* | 480.00 | 1360.00 | 2.83 | succinyl-CoA ligase [ADP-forming] subunit beta | |
KEO91012.1* | 0.00 | 329.01 | glutamyl-tRNA synthetase | KDM57451.1* | 0.00 | 13.80 | glutamyl-Q tRNA(Asp) synthetase | ||
KEO92307.1* | 0.00 | 1173.54 | 2-octaprenylphenol hydroxylase | KDM52399.1* | 41.40 | 112.00 | 2.71 | 2-polyprenylphenol 6-hydroxylase | |
KEO92322.1* | 1243.70 | 5084.10 | 4.09 | alkyl hydroperoxide reductase | KDM55608.1* | 108.00 | 706.00 | 6.54 | alkyl hydroperoxide reductase subunit F |
KEO92357.1* | 0.00 | 486.82 | hypothetical protein | KDM55447.1* | 0.00 | 44.50 | maltose O-acetyltransferase | ||
KEO92389.1* | 0.00 | 1032.40 | Clp protease ClpS | KDM55108.1* | 212.00 | 689.00 | 3.25 | ATP-dependent Clp protease adapter protein ClpS | |
KEO92432.1* | 0.00 | 225.11 | acetyl-CoA acetyltransferase | KDM49670.1* | 0.00 | 10.40 | hypothetical protein | ||
KEO92626.1* | 0.00 | 371.92 | transcription elongation factor GreB | KDM53922.1* | 0.00 | 25.90 | transcription elongation factor greB | ||
KEO92766.1* | 0.00 | 499.00 | pseudouridine synthase | KDM54709.1* | 53.60 | 142.00 | 2.65 | tRNA pseudouridine synthase B | |
KEO92773.1* | 238.61 | 1937.27 | 8.12 | translation initiation factor IF-2 | KDM54711.1* | 645.00 | 1330.00 | 2.06 | translation initiation factor IF-2 |
KEO92898.1* | 0.00 | 183.68 | oxidoreductase | KDM50444.1* | 0.00 | 20.20 | formate hydrogenlyase subunit 2 | ||
KEO92901.1* | 0.00 | 211.59 | metallophosphoesterase | KDM54593.1* | 123.00 | 267.00 | 2.17 | protein icc | |
KEO93029.1* | 0.00 | 1061.69 | Fur family transcriptional regulator | KDM55662.1* | 494.00 | 1760.00 | 3.56 | ferric uptake regulation protein | |
KEO93118.1* | 0.00 | 351.20 | 4-hydroxythreonine-4-phosphate dehydrogenase | KDM57359.1* | 86.00 | 299.00 | 3.48 | 4-hydroxythreonine-4-phosphate dehydrogenase | |
KEO93158.1* | 0.00 | 513.67 | ubiquinone biosynthesis protein UbiH | KDM49723.1* | 43.20 | 93.80 | 2.17 | 2-octaprenyl-6-methoxyphenol hydroxylase | |
KEO93247.1* | 0.00 | 269.73 | TetR family transcriptional regulator | KDM55557.1* | 86.70 | 564.00 | 6.51 | HTH-type transcriptional regulator BetI | |
KEO93375.1* | 0.00 | 357.49 | 4-hydroxy-3-methylbut-2-enyl diphosphate reductase | KDM57347.1* | 53.60 | 142.00 | 2.65 | 4-hydroxy-3-methylbut-2-enyl diphosphate reductase | |
KEO93411.1* | 0.00 | 566.68 | 16S rRNA methyltransferase | KDM57388.1* | 162.00 | 1000.00 | 6.17 | ribosomal RNA small subunit methyltransferase H | |
KEO96480.1* | 303.62 | 627.48 | 2.07 | methionine sulfoxide reductase B | KDM51893.1* | 41.00 | 208.00 | 5.07 | peptide methionine sulfoxide reductase msrB |
KEO96529.1* | 0.00 | 210.35 | phosphoribosylamine--glycine ligase | KDM52454.1* | 92.00 | 380.00 | 4.13 | phosphoribosylamine-glycine ligase | |
KEO96539.1* | 0.00 | 696.27 | hypothetical protein | KDM51989.1* | 200.00 | 435.00 | 2.18 | FeS cluster assembly protein sufD | |
KEO96580.1* | 0.00 | 486.03 | PTS IIA-like nitrogen-regulatory protein PtsN | KDM54746.1* | 0.00 | 150.00 | nitrogen regulatory protein | ||
KEO96608.1* | 0.00 | 1394.71 | translation factor Sua5 | KDM53819.1* | 0.00 | 42.90 | tRNA threonylcarbamoyladenosine biosynthesis protein RimN | ||
KEO96752.1* | 97.51 | 359.85 | 3.69 | integrase | KDM51758.1* | 94.30 | 425.00 | 4.51 | putA protein |
KEO98470.1* | 0.00 | 124.49 | hypothetical protein | KDM51955.1* | 11.80 | 59.60 | 5.05 | UPF0061 protein ydiU | |
KEO98596.1* | 0.00 | 814.69 | LysR family transcriptional regulator | KDM57341.1* | 37.70 | 81.90 | 2.17 | transcriptional activator protein nhaR | |
KEO98607.1* | 0.00 | 192.91 | 1-deoxy-D-xylulose 5-phosphate reductoisomerase | KDM57478.1* | 42.50 | 1230.00 | 28.94 | 1-deoxy-D-xylulose 5-phosphate reductoisomerase | |
KEO98608.1* | 0.00 | 1552.72 | peptidase | KDM57481.1* | 264.00 | 854.00 | 3.23 | RIP metalloprotease RseP | |
KEO98641.1* | 0.00 | 1679.78 | LysR family transcriptional regulator | KDM53240.1* | 130.00 | 321.00 | 2.47 | hydrogen peroxide-inducible genes activator | |
KEO98759.1* | 0.00 | 157.99 | 3-dehydroquinate synthase | KDM53905.1* | 46.80 | 192.00 | 4.10 | 3-dehydroquinate synthase | |
KEO98794.1* | 0.00 | 345.72 | branched-chain alpha-keto acid dehydrogenase subunit E2 | KDM57421.1* | 744.00 | 6140.00 | 8.25 | dihydrolipoyllysine-residue acetyltransferase | |
KEO98866.1* | 0.00 | 196.33 | farnesyl-diphosphate synthase | KDM55391.1* | 75.50 | 519.00 | 6.87 | farnesyl diphosphate synthase | |
KEO98882.1* | 0.00 | 473.35 | rRNA methyltransferase | KDM51417.1* | 107.00 | 496.00 | 4.64 | tRNA (cytidine/uridine-2'-O-)-methyltransferase TrmJ | |
KEO98935.1* | 0.00 | 3161.33 | transcriptional regulator | KDM55471.1* | 0.00 | 120.00 | HTH-type transcriptional regulator CueR | ||
KEO98999.1* | 0.00 | 246.42 | nucleoside triphosphate hydrolase | KDM50489.1* | 85.80 | 233.00 | 2.72 | nucleoside triphosphate pyrophosphohydrolase | |
KEO99007.1* | 0.00 | 538.76 | 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase | KDM50467.1* | 70.80 | 154.00 | 2.18 | 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase | |
KEO99009.1* | 0.00 | 388.83 | cyclase | KDM51170.1* | 35.60 | 155.00 | 4.35 | hypothetical protein | |
KEO99027.1* | 0.00 | 95.59 | transketolase | KDM57420.1* | 1130.00 | 10900.00 | 9.65 | pyruvate dehydrogenase E1 component | |
KEO99055.1* | 0.00 | 1388.60 | hypothetical protein | KDM55136.1 | 0.00 | 5.43 | hypothetical protein | ||
*P-value < 0.05 |
Protein ID of E. litoralis | RPKM in E. litoralis spheroplasts at the beginning of growth | RPKM in E. litoralis enlarged spheroplasts | Ratio of RPKMs of E. litoralis | Annotated function | Protein ID of L. amnigena | RPKM in L. amnigena spheroplasts at the beginning of growth | RPKM in L. amnigena enlarged spheroplasts | Ratio of RPKMs of L. amnigena | Annotated function |
Homologs of amino acid synthesis and metabolism-related genes | |||||||||
KEO88954.1* | 616.47 | 136.50 | 0.22 | L-asparaginase | KDM51897.1* | 33.40 | 0.00 | 0.00 | L-asparaginase 1 |
KEO89592.1* | 365.66 | 143.94 | 0.39 | S-adenosylmethionine synthetase | KDM49649.1* | 1070.00 | 255.00 | 0.24 | S-adenosylmethionine synthase |
KEO89916.1* | 363.48 | 0.00 | 0.00 | 2,3,4,5-tetrahydropyridine-2,6-carboxylate N-succinyltransferase | KDM57471.1* | 1050.00 | 432.00 | 0.41 | 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase |
KEO90596.1* | 298.26 | 88.06 | 0.30 | threonine aldolase | KDM55097.1* | 509.00 | 172.00 | 0.34 | low specificity L-threonine aldolase |
KEO92299.1* | 201.21 | 0.00 | 0.00 | 4-hydroxy-tetrahydrodipicolinate reductase | KDM57348.1* | 269.00 | 14.90 | 0.06 | dihydrodipicolinate reductase |
KEO92640.1* | 250.39 | 0.00 | 0.00 | argininosuccinate synthase | KDM54714.1* | 2220.00 | 219.00 | 0.10 | argininosuccinate synthase |
KEO92798.1* | 507.05 | 149.70 | 0.30 | 3-isopropylmalate dehydratase | KDM57378.1* | 196.00 | 60.80 | 0.31 | 3-isopropylmalate dehydratase small subunit |
KEO93106.1* | 831.23 | 245.41 | 0.30 | serine acetyltransferase | KDM52905.1* | 331.00 | 149.00 | 0.45 | serine acetyltransferase |
KEO93391.1* | 1078.83 | 318.51 | 0.30 | glutamine synthetase | KDM53324.1* | 385.00 | 174.00 | 0.45 | glutamine synthetase |
KEO93480.1* | 1248.41 | 595.39 | 0.48 | 3-phosphoglycerate dehydrogenase | KDM49615.1* | 964.00 | 369.00 | 0.38 | D-3-phosphoglycerate dehydrogenase |
KEO98853.1* | 596.53 | 0.00 | 0.00 | ketol-acid reductoisomerase | KDM53647.1* | 3330.00 | 450.00 | 0.14 | ketol-acid reductoisomerase |
KEO99046.1* | 292.53 | 0.00 | 0.00 | anthranilate synthase component I | KDM46686.1* | 1870.00 | 7.86 | 0.00 | anthranilate synthase component 1 |
KEO99050.1* | 459.56 | 45.23 | 0.10 | anthranilate phosphoribosyltransferase | KDM46685.1* | 2870.00 | 53.90 | 0.02 | anthranilate synthase component II |
Homologs of flagellar protein genes | |||||||||
KEO89561.1* | 22111.90 | 337.67 | 0.02 | flagellin | KDM48656.1* | 124.00 | 44.90 | 0.36 | hypothetical protein |
KEO90993.1* | 740.22 | 0.00 | 0.00 | flagellar basal body rod protein FlgC | KDM51808.1* | 41.90 | 0.00 | 0.00 | flagellar basal-body rod protein flgC |
KEO92484.1* | 806.97 | 79.42 | 0.10 | flagellar motor protein MotB | KDM51720.1* | 24600.00 | 1390.00 | 0.06 | outer membrane protein A |
Homologs of nucleotide synthesis and pentose phosphate pathway-related genes | |||||||||
KEO91063.1* | 325.03 | 95.96 | 0.30 | phosphoribosylpyrophosphate synthetase | KDM47000.1* | 985.00 | 298.00 | 0.30 | ribose-phosphate pyrophosphokinase |
KEO93239.1* | 414.76 | 61.23 | 0.15 | glucose-6-phosphate dehydrogenase | KDM48740.1* | 345.00 | 150.00 | 0.43 | glucose-6-phosphate 1-dehydrogenase |
KEO93278.1* | 293.09 | 0.00 | 0.00 | aspartate carbamoyltransferase catalytic subunit | KDM56880.1* | 1090.00 | 65.90 | 0.06 | aspartate carbamoyltransferase |
KEO96500.1* | 688.30 | 0.00 | 0.00 | ribulose-phosphate 3-epimerase | KDM53902.1* | 200.00 | 54.40 | 0.27 | ribulose-phosphate 3-epimerase |
KEO96518.1* | 349.69 | 103.24 | 0.30 | nicotinate-nucleotide pyrophosphorylase | KDM57413.1* | 57.00 | 27.50 | 0.48 | nicotinate-nucleotide pyrophosphorylase [carboxylating] |
KEO98799.1* | 610.90 | 45.09 | 0.07 | transketolase | KDM49630.1* | 844.00 | 278.00 | 0.33 | transketolase 1 |
Homologs of other membrane protein genes | |||||||||
KEO92879.1* | 12676.20 | 0.00 | 0.00 | membrane protein | KDM46678.1* | 80.50 | 0.00 | 0.00 | outer membrane protein W |
KEO93429.1* | 12522.20 | 4363.68 | 0.35 | membrane protein | KDM54978.1* | 216.00 | 86.80 | 0.40 | inner membrane protein YbhL |
KEO98493.1* | 726.95 | 268.28 | 0.37 | ABC transporter ATP-binding protein | KDM57319.1* | 479.00 | 192.00 | 0.40 | hypothetical protein |
KEO99262.1* | 1240.06 | 162.72 | 0.13 | hypothetical protein | KDM52093.1* | 131.00 | 11.80 | 0.09 | AI-2 transporter tqsA |
Others | |||||||||
KEO89629.1* | 824.47 | 121.71 | 0.15 | 3-demethylubiquinone-9 3-methyltransferase | KDM46348.1* | 116.00 | 16.90 | 0.15 | 3-demethylubiquinone-9 3-methyltransferase |
KEO90016.1* | 338.03 | 49.90 | 0.15 | hypothetical protein | KDM52077.1* | 18.60 | 0.00 | 0.00 | HTH-type transcriptional regulator AbgR |
KEO90690.1* | 737.52 | 0.00 | 0.00 | enoyl-ACP reductase | KDM46715.1* | 495.00 | 156.00 | 0.32 | enoyl-[acyl-carrier-protein] reductase [NADH] |
KEO92246.1* | 756.79 | 111.72 | 0.15 | glucose-1-phosphate thymidylyltransferase | KDM46209.1* | 58.80 | 28.30 | 0.48 | glucose-1-phosphate thymidylyltransferase 2 |
KEO92477.1* | 572.94 | 0.00 | 0.00 | molybdopterin biosynthesis protein B | KDM54974.1* | 232.00 | 47.90 | 0.21 | molybdenum cofactor biosynthesis protein B |
KEO92492.1* | 852.18 | 125.80 | 0.15 | oxidoreductase | KDM46695.1* | 312.00 | 80.60 | 0.26 | hypothetical protein |
KEO92638.1* | 479.48 | 0.00 | 0.00 | cyclopropane-fatty-acyl-phospholipid synthase | KDM52012.1* | 148.00 | 0.00 | 0.00 | cyclopropane-fatty-acyl-phospholipid synthase |
KEO92662.1* | 1438.43 | 212.34 | 0.15 | 50S ribosomal protein L17 | KDM53831.1* | 354.00 | 128.00 | 0.36 | 50S ribosomal protein L17 |
KEO92699.1* | 771.18 | 113.84 | 0.15 | LysR family transcriptional regulator | KDM50509.1* | 37.00 | 0.00 | 0.00 | glycine cleavage system transcriptional activator |
KEO93102.1* | 223.37 | 0.00 | 0.00 | bifunctional N-acetylglucosamine-1-phosphate uridyltransferase/glucosamine-1-phosphate acetyltransferase | KDM52744.1* | 372.00 | 108.00 | 0.29 | glmU protein |
KEO93190.1* | 831.23 | 409.01 | 0.49 | single-stranded DNA-binding protein | KDM56126.1* | 679.00 | 140.00 | 0.21 | single-stranded DNA-binding protein |
KEO93395.1* | 438.05 | 64.66 | 0.15 | cytosol aminopeptidase | KDM51408.1* | 158.00 | 47.70 | 0.30 | peptidase B |
KEO96463.1* | 111.07 | 32.79 | 0.30 | glutamate-ammonia-ligase adenylyltransferase | KDM54608.1* | 214.00 | 64.50 | 0.30 | glutamate-ammonia-ligase adenylyltransferase |
KEO96716.1* | 396.13 | 116.95 | 0.30 | GntR family transcriptional regulator | KDM52778.1* | 68.20 | 0.00 | 0.00 | hypothetical protein |
KEO96769.1* | 581.14 | 171.57 | 0.30 | ribonucleotide-diphosphate reductase subunit beta | KDM46350.1* | 481.00 | 130.00 | 0.27 | ribonucleoside-diphosphate reductase 1 subunit beta |
KEO98584.1* | 1114.39 | 0.00 | 0.00 | transcriptional regulator HU subunit alpha | KDM52452.1* | 2050.00 | 630.00 | 0.31 | DNA-binding protein HU-alpha |
KEO98612.1* | 1352.13 | 0.00 | 0.00 | 50S ribosomal protein L31 | KDM53254.1* | 159.00 | 0.00 | 0.00 | 50S ribosomal protein L31 |
KEO98687.1* | 228.14 | 84.19 | 0.37 | phosphoenolpyruvate carboxylase | KDM53245.1* | 621.00 | 236.00 | 0.38 | phosphoenolpyruvate carboxylase |
KEO98733.1* | 470.03 | 173.46 | 0.37 | DNA topoisomerase I | KDM46698.1* | 569.00 | 255.00 | 0.45 | DNA topoisomerase 1 |
KEO98800.1* | 603.63 | 0.00 | 0.00 | glyceraldehyde-3-phosphate dehydrogenase | KDM51892.1* | 2900.00 | 1360.00 | 0.47 | glyceraldehyde-3-phosphate dehydrogenase |
KEO98996.1* | 96.21 | 0.00 | 0.00 | methionine--tRNA ligase | KDM46274.1* | 576.00 | 115.00 | 0.20 | methionyl-tRNA synthetase |
KEO99011.1* | 473.88 | 139.91 | 0.30 | carbonate dehydratase | KDM52008.1* | 26.70 | 0.00 | 0.00 | hypothetical protein |
KEO99037.1* | 378.39 | 0.00 | 0.00 | inorganic polyphosphate kinase | KDM51166.1* | 96.60 | 0.00 | 0.00 | hypothetical protein |
KEO99041.1* | 4328.46 | 2008.15 | 0.46 | heat-shock protein | KDM52775.1* | 41.30 | 0.00 | 0.00 | small heat shock protein ibpA |
KEO99260.1* | 277.08 | 81.80 | 0.30 | aminotransferase | KDM51415.1* | 1540.00 | 637.00 | 0.41 | cysteine desulfurase |
*P-value < 0.05 |
Protein ID of E. litoralis | RPKM in E. litoralis spheroplasts at the beginning of growth | RPKM in E. litoralis enlarged spheroplasts | Ratio of RPKMs of E. litoralis | Annotated function | Protein ID of L. amnigena | RPKM in L. amnigena spheroplasts at the beginning of growth | RPKM in L. amnigena enlarged spheroplasts | Ratio of RPKMs of L. amnigena | Annotated function |
Homologs of membrane protein genes | |||||||||
KEO89564.1* | 0.00 | 106.93 | hypothetical protein | KDM48649.1* | 40.40 | 14.60 | 0.36 | flagellar M-ring protein | |
KEO89607.1* | 0.00 | 129.05 | multidrug transporter | KDM52010.1* | 150.00 | 45.10 | 0.30 | multidrug resistance protein mdtK | |
KEO89895.1* | 0.00 | 634.32 | biopolymer transporter ExbB | KDM55699.1* | 564.00 | 177.00 | 0.31 | protein tolQ | |
KEO89973.1* | 0.00 | 184.81 | magnesium transporter CorA | KDM52382.1* | 661.00 | 168.00 | 0.25 | magnesium transporter CorA | |
KEO92632.1* | 0.00 | 146.76 | hypothetical protein | KDM46187.1* | 175.00 | 72.30 | 0.41 | inner membrane transporter YeeF | |
KEO92658.1* | 0.00 | 1301.72 | hypothetical protein | KDM57464.1* | 136.00 | 39.40 | 0.29 | UPF0126 inner membrane protein yadS | |
KEO92812.1* | 0.00 | 172.56 | type VI secretion protein | KDM54463.1* | 51.90 | 12.50 | 0.24 | hypothetical protein | |
KEO93024.1* | 262.72 | 2171.79 | 8.27 | iron transporter | KDM53929.1* | 413.00 | 171.00 | 0.41 | Fe/S biogenesis protein nfuA |
KEO93116.1* | 0.00 | 227.97 | organic solvent tolerance protein | KDM57361.1* | 483.00 | 224.00 | 0.46 | LPS-assembly protein lptD | |
KEO93384.1* | 352.12 | 1143.53 | 3.25 | MttB family protein | KDM52402.1* | 220.00 | 15.90 | 0.07 | sec-independent protein translocase tatC |
KEO98525.1* | 0.00 | 128.22 | hypothetical protein | KDM52772.1* | 118.00 | 38.00 | 0.32 | D-galactonate transporter | |
KEO98837.1* | 0.00 | 215.39 | phosphate ABC transporter permease | KDM52748.1* | 724.00 | 152.00 | 0.21 | phosphate transport system permease pstA | |
KEO98838.1* | 0.00 | 194.41 | phosphate ABC transporter permease | KDM52747.1* | 1310.00 | 230.00 | 0.18 | phosphate transport system permease pstC | |
KEO98907.1* | 243.77 | 539.78 | 2.21 | 3,4-dihydroxy-2-butanone 4-phosphate synthase | KDM54605.1* | 1220.00 | 432.00 | 0.35 | 3,4-dihydroxy-2-butanone 4-phosphate synthase |
Others | |||||||||
KEO88945.1* | 1061.88 | 3056.67 | 2.88 | peptide deformylase | KDM53823.1* | 699.00 | 313.00 | 0.45 | peptide deformylase |
KEO88946.1* | 0.00 | 300.90 | recombinase RecR | KDM55460.1* | 336.00 | 101.00 | 0.30 | recombination protein recR | |
KEO88958.1* | 0.00 | 546.11 | argininosuccinate lyase | KDM53241.1* | 1610.00 | 116.00 | 0.07 | argininosuccinate lyase | |
KEO88960.1* | 484.06 | 1822.10 | 3.76 | diaminopimelate decarboxylase | KDM50540.1* | 780.00 | 19.50 | 0.03 | diaminopimelate decarboxylase |
KEO89297.1* | 0.00 | 160.53 | histidinol-phosphate aminotransferase | KDM46192.1* | 240.00 | 92.60 | 0.39 | histidinol-phosphate aminotransferase | |
KEO89579.1* | 0.00 | 507.45 | tRNA (guanine-N7)-methyltransferase | KDM54472.1* | 802.00 | 154.00 | 0.19 | tRNA (guanine-N(7)-)-methyltransferase | |
KEO89635.1* | 0.00 | 207.20 | formyltetrahydrofolate deformylase | KDM46646.1* | 80.60 | 14.60 | 0.18 | formyltetrahydrofolate deformylase | |
KEO89998.1* | 0.00 | 437.71 | ArsR family transcriptional regulator | KDM55050.1* | 52.90 | 0.00 | 0.00 | hypothetical protein | |
KEO90041.1* | 0.00 | 118.57 | hypothetical protein | KDM48627.1* | 48.00 | 0.00 | 0.00 | DNA-cytosine methyltransferase | |
KEO90698.1* | 0.00 | 438.68 | 3-deoxy-manno-octulosonate cytidylyltransferase | KDM55141.1* | 91.00 | 0.00 | 0.00 | 3-deoxy-manno-octulosonate cytidylyltransferase | |
KEO91020.1* | 0.00 | 391.37 | molecular chaperone DnaK | KDM57452.1* | 5740.00 | 2210.00 | 0.39 | DnaK suppressor protein | |
KEO91036.1* | 0.00 | 883.47 | molecular chaperone Hsp33 | KDM53917.1* | 77.30 | 28.00 | 0.36 | chaperonin | |
KEO91037.1* | 0.00 | 191.92 | ornithine carbamoyltransferase | KDM56877.1* | 16.90 | 0.00 | 0.00 | ornithine carbamoyltransferase, catabolic | |
KEO92302.1* | 0.00 | 465.99 | molybdopterin biosynthesis protein MoeB | KDM52444.1* | 112.00 | 16.30 | 0.15 | sulfur carrier protein ThiS adenylyltransferase | |
KEO92334.1* | 113.82 | 285.62 | 2.51 | aconitate hydratase | KDM46701.1* | 305.00 | 152.00 | 0.50 | aconitate hydratase 1 |
KEO92372.1* | 0.00 | 272.18 | phosphomethylpyrimidine kinase | KDM46258.1* | 42.40 | 15.30 | 0.36 | hydroxymethylpyrimidine/phosphomethylpyrimidine kinase | |
KEO92402.1* | 0.00 | 190.30 | glutamyl-tRNA synthetase | KDM51312.1* | 216.00 | 86.80 | 0.40 | glutamyl-tRNA synthetase | |
KEO92434.1* | 0.00 | 266.53 | 2-hydroxyacid dehydrogenase | KDM52411.1* | 69.70 | 25.20 | 0.36 | glyoxylate/hydroxypyruvate reductase B | |
KEO92503.1* | 0.00 | 462.99 | inosine-5-monophosphate dehydrogenase | KDM51383.1* | 417.00 | 117.00 | 0.28 | inosine-5'-monophosphate dehydrogenase | |
KEO92549.1* | 0.00 | 490.81 | 30S ribosomal protein S6 | KDM56939.1* | 944.00 | 217.00 | 0.23 | 30S ribosomal protein S6 | |
KEO92597.1* | 0.00 | 368.72 | tryptophan synthase subunit beta | KDM46683.1* | 3260.00 | 134.00 | 0.04 | tryptophan synthase beta chain | |
KEO92634.1* | 0.00 | 460.61 | oxidoreductase | KDM52065.1* | 23.50 | 0.00 | 0.00 | dihydrofolate reductase folM | |
KEO92667.1* | 0.00 | 278.51 | adenylate kinase | KDM55462.1* | 1950.00 | 914.00 | 0.47 | adenylate kinase | |
KEO92711.1* | 0.00 | 424.08 | 3-isopropylmalate dehydrogenase | KDM57380.1* | 280.00 | 113.00 | 0.40 | 3-isopropylmalate dehydrogenase | |
KEO92758.1* | 0.00 | 1060.85 | DNA-binding protein | KDM51729.1* | 7260.00 | 966.00 | 0.13 | heat shock protein hspQ | |
KEO92776.1* | 0.00 | 1339.41 | ribosome maturation protein RimP | KDM54713.1* | 187.00 | 81.40 | 0.44 | ribosome maturation factor rimP | |
KEO92780.1* | 0.00 | 511.79 | ATPase AAA | KDM46723.1* | 52.10 | 25.10 | 0.48 | psp operon transcriptional activator | |
KEO92795.1* | 0.00 | 399.20 | thioesterase | KDM55422.1* | 298.00 | 61.60 | 0.21 | long-chain acyl-CoA thioesterase tesC | |
KEO92811.1* | 0.00 | 81.47 | polyphosphate kinase | KDM51368.1* | 437.00 | 107.00 | 0.24 | polyphosphate kinase | |
KEO93025.1* | 499.56 | 1179.89 | 2.36 | malonic semialdehyde reductase | KDM51751.1* | 57.50 | 20.80 | 0.36 | hypothetical protein |
KEO93125.1* | 0.00 | 144.29 | succinylarginine dihydrolase | KDM51916.1* | 89.70 | 27.80 | 0.31 | N-succinylarginine dihydrolase | |
KEO93177.1* | 0.00 | 687.39 | aromatic amino acid aminotransferase | KDM55151.1* | 385.00 | 124.00 | 0.32 | aspartate aminotransferase | |
KEO93181.1* | 0.00 | 286.50 | riboflavin synthase subunit alpha | KDM52011.1* | 317.00 | 76.60 | 0.24 | riboflavin synthase alpha chain | |
KEO93285.1* | 1214.49 | 3764.87 | 3.10 | bacterioferritin | KDM53859.1* | 463.00 | 77.30 | 0.17 | bacterioferritin |
KEO93379.1* | 0.00 | 350.17 | beta-hexosaminidase | KDM51842.1* | 248.00 | 71.90 | 0.29 | beta-hexosaminidase | |
KEO93387.1* | 0.00 | 283.79 | threonine dehydratase | KDM54671.1* | 51.50 | 0.00 | 0.00 | threonine dehydratase catabolic | |
KEO93441.1* | 0.00 | 293.53 | cystathionine beta-lyase | KDM54516.1* | 285.00 | 92.90 | 0.33 | cystathionine beta-lyase | |
KEO93476.1* | 0.00 | 3077.91 | hypothetical protein | KDM54633.1* | 68.60 | 24.80 | 0.36 | hypothetical protein | |
KEO96380.1* | 0.00 | 130.17 | protein-PII uridylyltransferase | KDM57472.1* | 108.00 | 32.10 | 0.30 | [protein-PII] uridylyltransferase | |
KEO96408.1* | 0.00 | 407.90 | GTP cyclohydrolase | KDM46702.1* | 287.00 | 104.00 | 0.36 | GTP cyclohydrolase-2 | |
KEO96434.1* | 131.11 | 377.39 | 2.88 | glutamate synthase | KDM54762.1* | 2310.00 | 320.00 | 0.14 | glutamate synthase [NADPH] large chain |
KEO96435.1* | 0.00 | 156.26 | glutamate synthase | KDM54763.1* | 1780.00 | 320.00 | 0.18 | glutamate synthase [NADPH] small chain | |
KEO96528.1* | 0.00 | 211.70 | exodeoxyribonuclease VII large subunit | KDM51384.1* | 74.20 | 0.00 | 0.00 | exodeoxyribonuclease 7 large subunit | |
KEO96545.1* | 0.00 | 814.69 | AsnC family transcriptional regulator | KDM51416.1* | 2800.00 | 150.00 | 0.05 | HTH-type transcriptional regulator iscR | |
KEO98460.1* | 0.00 | 1164.32 | 50S ribosomal protein L27 | KDM54727.1* | 1840.00 | 667.00 | 0.36 | 50S ribosomal protein L27 | |
KEO98556.1* | 0.00 | 200.94 | citrate lyase | KDM54480.1* | 19.40 | 0.00 | 0.00 | citrate lyase subunit beta | |
KEO98575.1* | 300.92 | 1066.10 | 3.54 | farnesyltranstransferase | KDM54729.1* | 175.00 | 25.30 | 0.14 | octaprenyl-diphosphate synthase |
KEO98712.1* | 0.00 | 412.01 | thioredoxin reductase | KDM55115.1* | 351.00 | 88.80 | 0.25 | thioredoxin reductase | |
KEO98796.1* | 0.00 | 1374.78 | 5-formyltetrahydrofolate cyclo-ligase | KDM49727.1* | 85.40 | 41.20 | 0.48 | 5-formyltetrahydrofolate cyclo-ligase | |
KEO98834.1* | 0.00 | 260.35 | chemotaxis protein CheY | KDM55825.1* | 2140.00 | 142.00 | 0.07 | phosphate regulon transcriptional regulatory protein phoB | |
KEO98839.1* | 0.00 | 180.36 | histidine kinase | KDM55824.1* | 380.00 | 47.40 | 0.12 | phosphate regulon sensor protein phoR | |
KEO98906.1* | 0.00 | 424.68 | 6,7-dimethyl-8-ribityllumazine synthase | KDM55386.1* | 325.00 | 157.00 | 0.48 | 6,7-dimethyl-8-ribityllumazine synthase | |
KEO98922.1* | 0.00 | 653.71 | 50S ribosomal protein L25 | KDM46330.1* | 477.00 | 129.00 | 0.27 | 50S ribosomal protein L25 | |
KEO98968.1* | 0.00 | 712.85 | nucleoside-triphosphate diphosphatase | KDM54467.1* | 57.20 | 0.00 | 0.00 | nucleoside-triphosphatase rdgB | |
KEO98978.1* | 0.00 | 229.80 | DNA repair protein RadA | KDM57315.1* | 282.00 | 106.00 | 0.38 | DNA repair protein radA | |
KEO99042.1* | 0.00 | 438.68 | CTP synthase | KDM50488.1* | 871.00 | 353.00 | 0.41 | CTP synthase | |
*P-value < 0.05 |
Protein ID of E. litoralis | RPKM in E. litoralis spheroplasts at the beginning of growth | RPKM in E. litoralis enlarged spheroplasts | Ratio of RPKMs of E. litoralis | Annotated function | Protein ID of L. amnigena | RPKM in L. amnigena spheroplasts at the beginning of growth | RPKM in L. amnigena enlarged spheroplasts | Ratio of RPKMs of L. amnigena | Annotated function |
Homologs of membrane protein genes | |||||||||
KEO89304.1* | 629.44 | 247.78 | 0.39 | penicillin-binding protein | KDM57456.1* | 296.00 | 1010.00 | 3.41 | penicillin-binding protein 1B |
KEO89573.1* | 405.64 | 59.88 | 0.15 | flagellar biosynthesis protein flip | KDM48639.1* | 0.00 | 16.70 | flagellar biosynthetic protein fliP | |
KEO90985.1* | 453.73 | 133.96 | 0.30 | hypothetical protein | KDM51816.1* | 0.00 | 22.50 | flagellar hook-associated protein 1 | |
KEO90987.1* | 2625.04 | 163.16 | 0.06 | flagellar P-ring protein FlgI | KDM51814.1* | 15.50 | 56.00 | 3.61 | flagellar P-ring protein |
KEO90994.1* | 859.40 | 0.00 | 0.00 | flagellar basal body rod protein FlgB | KDM51807.1* | 0.00 | 147.00 | flagellar basal-body rod protein flgB | |
KEO92489.1* | 458.87 | 135.47 | 0.30 | ABC transporter | KDM51852.1* | 72.60 | 175.00 | 2.41 | lipoprotein-releasing system ATP-binding protein LolD |
KEO92547.1* | 320.92 | 0.00 | 0.00 | ABC transporter | KDM48630.1* | 0.00 | 13.50 | inner membrane protein yedI | |
KEO92700.1* | 2204.56 | 0.00 | 0.00 | magnesium transporter ApaG | KDM57357.1* | 89.90 | 488.00 | 5.43 | protein ApaG |
KEO93367.1* | 2069.58 | 111.09 | 0.05 | secretion system protein | KDM53908.1* | 0.00 | 9.92 | hypothetical protein | |
KEO93416.1* | 284.06 | 0.00 | 0.00 | phospho-N-acetylmuramoyl-pentapeptide-transferase | KDM57393.1* | 204.00 | 817.00 | 4.00 | phospho-N-acetylmuramoyl-pentapeptide-transferase |
KEO93419.1* | 495.89 | 109.80 | 0.22 | UDP-diphospho-muramoylpentapeptide beta-N-acetylglucosaminyltransferase | KDM57396.1* | 79.70 | 415.00 | 5.21 | undecaprenyldiphospho-muramoylpentapeptide beta-N-acetylglucosaminyltransferase |
KEO93424.1* | 682.13 | 134.26 | 0.20 | cell division protein FtsA | KDM57400.1* | 865.00 | 2250.00 | 2.60 | cell division protein ftsA |
KEO98787.1* | 1321.30 | 373.84 | 0.28 | preprotein translocase subunit SecA | KDM57404.1* | 69.00 | 559.00 | 8.10 | protein translocase subunit secA |
KEO98980.1* | 184.72 | 54.53 | 0.30 | major facilitator transporter | KDM46178.1* | 64.50 | 159.00 | 2.47 | shikimate transporter |
Others | |||||||||
KEO89313.1* | 2157.65 | 0.00 | 0.00 | peptide methionine sulfoxide reductase | KDM56920.1* | 0.00 | 19.10 | peptide methionine sulfoxide reductase msrA | |
KEO89605.1* | 7190.86 | 2640.13 | 0.37 | molecular chaperone GroEL | KDM56992.1* | 1220.00 | 4660.00 | 3.82 | chaperonin |
KEO89995.1* | 402.88 | 33.98 | 0.08 | 5-methyltetrahydrofolate--homocysteine methyltransferase | KDM55766.1* | 111.00 | 223.00 | 2.01 | methionine synthase |
KEO90687.1* | 897.43 | 132.48 | 0.15 | pyridoxamine 5'-phosphate oxidase | KDM52037.1* | 0.00 | 37.40 | pyridoxine/pyridoxamine 5'-phosphate oxidase | |
KEO91004.1* | 607.24 | 0.00 | 0.00 | hypothetical protein | KDM49677.1* | 375.00 | 1380.00 | 3.68 | protein yciF |
KEO91044.1* | 382.68 | 0.00 | 0.00 | glucose-methanol-choline oxidoreductase | KDM55555.1* | 51.00 | 185.00 | 3.63 | choline dehydrogenase |
KEO91076.1* | 644.55 | 190.30 | 0.30 | phosphomannomutase | KDM46221.1* | 99.10 | 1120.00 | 11.30 | phosphomannomutase |
KEO92378.1* | 1931.61 | 855.42 | 0.44 | RNA polymerase sigma70 | KDM51449.1* | 2570.00 | 7420.00 | 2.89 | RNA polymerase sigma-E factor |
KEO92529.1* | 224.36 | 66.24 | 0.30 | hypothetical protein | KDM57043.1* | 0.00 | 6.34 | hypothetical protein | |
KEO92652.1* | 1365.79 | 554.44 | 0.41 | succinate--CoA ligase | KDM55690.1* | 566.00 | 1450.00 | 2.56 | succinyl-CoA ligase [ADP-forming] subunit alpha |
KEO92654.1* | 2162.76 | 141.89 | 0.07 | dihydrolipoamide succinyltransferase | KDM55688.1* | 415.00 | 1100.00 | 2.65 | hypothetical protein |
KEO92656.1* | 2572.76 | 822.87 | 0.32 | dihydrolipoamide dehydrogenase | KDM57422.1* | 775.00 | 3320.00 | 4.28 | dihydrolipoyl dehydrogenase |
KEO92681.1* | 1049.06 | 206.48 | 0.20 | 50S ribosomal protein L16 | KDM53849.1* | 537.00 | 2360.00 | 4.39 | 50S ribosomal protein L16 |
KEO93425.1* | 1877.96 | 607.24 | 0.32 | cell division protein FtsZ | KDM57401.1* | 1180.00 | 5490.00 | 4.65 | cell division protein ftsZ |
KEO93475.1* | 113.94 | 0.00 | 0.00 | ATPase AAA | KDM55119.1* | 88.50 | 311.00 | 3.51 | replication-associated recombination protein A |
KEO96455.1* | 712.48 | 35.06 | 0.05 | UDP-N-acetylglucosamine 1-carboxyvinyltransferase | KDM54731.1* | 162.00 | 351.00 | 2.17 | UDP-N-acetylglucosamine 1-carboxyvinyltransferase |
KEO96456.1* | 1034.79 | 101.84 | 0.10 | UTP--glucose-1-phosphate uridylyltransferase | KDM46650.1* | 206.00 | 678.00 | 3.29 | UTP-glucose-1-phosphate uridylyltransferase |
KEO96517.1* | 762.48 | 0.00 | 0.00 | chemotaxis protein CheY | KDM46276.1* | 0.00 | 68.30 | hypothetical protein | |
KEO96548.1* | 291.41 | 86.03 | 0.30 | dihydroorotate dehydrogenase | KDM51709.1* | 16.80 | 72.90 | 4.34 | dihydroorotate dehydrogenase |
KEO98611.1* | 618.35 | 0.00 | 0.00 | 3-hydroxyacyl-ACP dehydratase | KDM57485.1* | 74.50 | 350.00 | 4.70 | (3R)-hydroxymyristoyl-[acyl-carrier-protein] dehydratase |
KEO99053.1* | 249.16 | 73.56 | 0.30 | molybdopterin biosynthesis protein | KDM55029.1* | 68.90 | 149.00 | 2.16 | molybdopterin molybdenumtransferase |
KEO99263.1* | 1114.39 | 0.00 | 0.00 | glutamine amidotransferase | KDM54696.1* | 327.00 | 852.00 | 2.61 | protein yhbO |
*P-value < 0.05 |