Export file:


  • RIS(for EndNote,Reference Manager,ProCite)
  • BibTex
  • Text


  • Citation Only
  • Citation and Abstract

Perspectives on the use of transcriptomics to advance biofuels

School of Biological Sciences, Department of Life Science, Ulsan National Institute of Science and Technology, Ulsan, 689-798, South Korea (R.O.K.)

Topical Section: Bioenergy and Biofuels

As a field within the energy research sector, bioenergy is continuously expanding. Although much has been achieved and the yields of both ethanol and butanol have been improved, many avenues of research to further increase these yields still remain. This review covers current research related with transcriptomics and the application of this high-throughput analytical tool to engineer both microbes and plants with the penultimate goal being better biofuel production and yields. The initial focus is given to the responses of fermentative microbes during the fermentative production of acids, such as butyric acid, and solvents, including ethanol and butanol. As plants offer the greatest natural renewable source of fermentable sugars within the form of lignocellulose, the second focus area is the transcriptional responses of microbes when exposed to plant hydrolysates and lignin-related compounds. This is of particular importance as the acid/base hydrolysis methods commonly employed to make the plant-based cellulose available for enzymatic hydrolysis to sugars also generates significant amounts of lignin-derivatives that are inhibitory to fermentative bacteria and microbes. The article then transitions to transcriptional analyses of lignin-degrading organisms, such as Phanerochaete chrysosporium, as an alternative to acid/base hydrolysis. The final portion of this article will discuss recent transcriptome analyses of plants and, in particular, the genes involved in lignin production. The rationale behind these studies is to eventually reduce the lignin content present within these plants and, consequently, the amount of inhibitors generated during the acid/base hydrolysis of the lignocelluloses. All four of these topics represent key areas where transcriptomic research is currently being conducted to identify microbial genes and their responses to products and inhibitors as well as those related with lignin degradation/formation.
  Article Metrics


1. Penuelas J, Carnicer J (2010) Climate change and peak oil: the urgent need for a transition to a non-carbon-emitting society. Ambio 39: 85-90.    

2. Kerr RA (2011) Energy supplies. Peak oil production may already be here. Science 331: 1510-1511.

3. Pauly M, Keegstra K (2008) Cell-wall carbohydrates and their modification as a resource for biofuels. Plant J 54: 559-568.    

4. Vanholme B, Desmet T, Ronsse F, et al. (2013) Towards a carbon-negative sustainable bio-based economy. Front Plant Sci 4: 174.

5. Kalluri UC, Keller M (2010) Bioenergy research: a new paradigm in multidisciplinary research. J R Soc Interface 7: 1391-1401.    

6. Chabannes M, Ruel K, Yoshinaga A, et al. (2001) In situ analysis of lignins in transgenic tobacco reveals a differential impact of individual transformations on the spatial patterns of lignin deposition at the cellular and subcellular levels. Plant J 28: 271-282.    

7. Ezeji T, Blaschek HP (2008) Fermentation of dried distillers' grains and solubles (DDGS) hydrolysates to solvents and value-added products by solventogenic clostridia. Bioresource Technol 99: 5232-5242.    

8. Ezeji T, Qureshi N, Blaschek HP (2007) Butanol production from agricultural residues: impact of degradation products on Clostridium beijerinckii growth and butanol fermentation. Biotechnol Bioeng 97: 1460-1469.    

9. Klinke HB, Thomsen AB, Ahring BK (2004) Inhibition of ethanol-producing yeast and bacteria by degradation products produced during pre-treatment of biomass. Appl Microbiol Biotechnol 66: 10-26.    

10. Lee S, Lee JH, Mitchell RJ (2015) Analysis of Clostridium beijerinckii NCIMB 8052's transcriptional response to ferulic acid and its application to enhance the strain tolerance. Biotechnol Bioeng 8: 68.

11. Palmqvist E, Hahn-Hagerdal B (2000) Fermentation of lignocellulosic hydrolysates. II: inhibitors and mechanisms of inhibition. Bioresource Technol 74: 25-33.

12. Persson P, Andersson J, Gorton L, et al. (2002) Effect of different forms of alkali treatment on specific fermentation inhibitors and on the fermentability of lignocellulose hydrolysates for production of fuel ethanol. J Agric Food Chem 50: 5318-5325.    

13. Martinez A, Rodriguez ME, York SW, et al. (2000) Effects of Ca(OH)(2) treatments (""overliming"") on the composition and toxicity of bagasse hemicellulose hydrolysates. Biotechnol Bioeng 69: 526-536.

14. Berson RE, Young JS, Hanley TR (2006) Reintroduced solids increase inhibitor levels in a pretreated corn stover hydrolysate. Appl Biochem Biotechnol 129-132: 612-620.

15. Guo X, Cavka A, Jonsson LJ, et al. (2013) Comparison of methods for detoxification of spruce hydrolysate for bacterial cellulose production. Microb Cell Fact 12: 93.    

16. Kumari R, Pramanik K (2013) Bioethanol production from Ipomoea carnea biomass using a potential hybrid yeast strain. Appl Biochem Biotechnol 171: 771-785.    

17. Kuhad RC, Gupta R, Khasa YP, et al. (2010) Bioethanol production from Lantana camara (red sage): Pretreatment, saccharification and fermentation. Bioresour Technol 101: 8348-8354.    

18. Nilvebrant NO, Reimann A, Larsson S, et al. (2001) Detoxification of lignocellulose hydrolysates with ion-exchange resins. Appl Biochem Biotechnol 91-93: 35-49.    

19. Hallsworth JE, Heim S, Timmis KN (2003) Chaotropic solutes cause water stress in Pseudomonas putida. Environ Microbiol 5: 1270-1280.    

20. Bhaganna P, Volkers RJ, Bell AN, et al. (2010) Hydrophobic substances induce water stress in microbial cells. Microb Biotechnol 3: 701-716.    

21. Hallsworth JE (1998) Ethanol-induced water stress in yeast. J Ferment Bioeng 85: 125-137.    

22. da Costa MS, Santos H, Galinski EA (1998) An overview of the role and diversity of compatible solutes in Bacteria and Archaea. Adv Biochem Eng Biotechnol 61: 117-153.

23. Mansure JJ, Panek AD, Crowe LM, et al. (1994) Trehalose inhibits ethanol effects on intact yeast cells and liposomes. Biochim Biophys Acta 1191: 309-316.    

24. Hallsworth JE, Prior BA, Nomura Y, et al. (2003) Compatible solutes protect against chaotrope (ethanol)-induced, nonosmotic water stress. Appl Environ Microbiol 69: 7032-7034.    

25. Cray JA, Stevenson A, Ball P, et al. (2015) Chaotropicity: a key factor in product tolerance of biofuel-producing microorganisms. Curr Opin Biotechnol 33: 228-259.    

26. Mitchell RJ, Gu MB (2004) An Escherichia coli biosensor capable of detecting both genotoxic and oxidative damage. Appl Microbiol Biot 64: 46-52.    

27. Choi SH, Gu MB (2002) A portable toxicity biosensor using freeze-dried recombinant bioluminescent bacteria. Biosens Bioelectron 17: 433-440.    

28. Choi SH, Gu MB (2003) Toxicity biomonitoring of degradation byproducts using freeze-dried recombinant bioluminescent bacteria. Anal Chim Acta 481: 229-238.    

29. Van Dyk TK, Smulski DR, Reed TR, et al. (1995) Responses to toxicants of an Escherichia coli strain carrying a uspA'::lux genetic fusion and an E. coli strain carrying a grpE'::lux fusion are similar. Appl Environ Microbiol 61: 4124-4127.

30. Mitchell RJ, Gu MB (2006) Characterization and optimization of two methods in the immobilization of 12 bioluminescent strains. Biosens Bioelectron 22: 192-199.    

31. Ahn J-M, Mitchell RJ, Gu MB (2004) Detection and classification of oxidative damaging stresses using recombinant bioluminescent bacteria harboring sodA∷, pqi∷, and katG∷ luxCDABE fusions. Enzyme Microb Tech 35: 540-544.    

32. Gao DH, Haarmeyer C, Balan V, et al. (2014) Lignin triggers irreversible cellulase loss during pretreated lignocellulosic biomass saccharification. Biotechnol Biofuels 7.

33. Kim HJ, Lee S, Kim J, et al. (2013) Environmentally friendly pretreatment of plant biomass by planetary and attrition milling. Bioresource Technol 144: 50-56.    

34. Oudshoorn A, van der Wielen LA, Straathof AJ (2009) Assessment of options for selective 1-butanol recovery from aqueous solution. Ind Eng Chem Res 48: 7325-7336.    

35. Jang Y-S, Lee JY, Lee J, et al. (2012) Enhanced butanol production obtained by reinforcing the direct butanol-forming route in Clostridium acetobutylicum. MBio 3: e00314-00312.

36. Tangney M, Mitchell WJ (2000) Analysis of a catabolic operon for sucrose transport and metabolism in Clostridium acetobutylicum ATCC 824. J Mol Microb Biotech 2: 71-80.

37. Wang L, Chen H (2011) Increased fermentability of enzymatically hydrolyzed steam-exploded corn stover for butanol production by removal of fermentation inhibitors. Process Biochem 46: 604-607.    

38. Servinsky MD, Kiel JT, Dupuy NF, et al. (2010) Transcriptional analysis of differential carbohydrate utilization by Clostridium acetobutylicum. Microbiology 156: 3478-3491.    

39. Ren C, Gu Y, Hu S, et al. (2010) Identification and inactivation of pleiotropic regulator CcpA to eliminate glucose repression of xylose utilization in Clostridium acetobutylicum. Metab Eng 12: 446-454.    

40. Tangney M, Galinier A, Deutscher J, et al. (2003) Analysis of the elements of catabolite repression in Clostridium acetobutylicum ATCC 824. J Mol Microb Biotech 6: 6-11.    

41. Grimmler C, Held C, Liebl W, et al. (2010) Transcriptional analysis of catabolite repression in Clostridium acetobutylicum growing on mixtures of d-glucose and d-xylose. J Biotechnol 150: 315-323.

42. Bayer EA, Belaich J-P, Shoham Y, et al. (2004) The cellulosomes: multienzyme machines for degradation of plant cell wall polysaccharides. Annu Rev Microbiol 58: 521-554.    

43. Stevenson DM, Weimer PJ (2005) Expression of 17 genes in Clostridium thermocellum ATCC 27405 during fermentation of cellulose or cellobiose in continuous culture. Appl Environ Microb 71: 4672-4678.    

44. Feinberg L, Foden J, Barrett T, et al. (2011) Complete genome sequence of the cellulolytic thermophile Clostridium thermocellum DSM1313. J Bacteriol 193: 2906-2907.    

45. Raman B, McKeown CK, Rodriguez M, et al. (2011) Transcriptomic analysis of Clostridium thermocellum ATCC 27405 cellulose fermentation. BMC Microbiol 11: 134.    

46. Riederer A, Takasuka TE, Makino S-i, et al. (2011) Global gene expression patterns in Clostridium thermocellum as determined by microarray analysis of chemostat cultures on cellulose or cellobiose. Appl Environ Microb 77: 1243-1253.    

47. Wang Y, Li X, Mao Y, et al. (2012) Genome-wide dynamic transcriptional profiling in Clostridium beijerinckii NCIMB 8052 using single-nucleotide resolution RNA-Seq. BMC Genomics 13: 102.    

48. Alsaker KV, Papoutsakis ET (2005) Transcriptional program of early sporulation and stationary-phase events in Clostridium acetobutylicum. J Bacteriol 187: 7103-7118.    

49. Grimmler C, Janssen H, Krauβe D, et al. (2011) Genome-wide gene expression analysis of the switch between acidogenesis and solventogenesis in continuous cultures of Clostridium acetobutylicum. J Mol Microb Biotech 20: 1-15.    

50. Shi Z, Blaschek HP (2008) Transcriptional analysis of Clostridium beijerinckii NCIMB 8052 and the hyper-butanol-producing mutant BA101 during the shift from acidogenesis to solventogenesis. Appl Environ Microb 74: 7709-7714.    

51. Hu S, Zheng H, Gu Y, et al. (2011) Comparative genomic and transcriptomic analysis revealed genetic characteristics related to solvent formation and xylose utilization in Clostridium acetobutylicum EA 2018. BMC Genomics 12: 93.    

52. Lütke-Eversloh T, Bahl H (2011) Metabolic engineering of Clostridium acetobutylicum: recent advances to improve butanol production. Curr Opin Biotech 22: 634-647.    

53. Knoshaug EP, Zhang M (2009) Butanol tolerance in a selection of microorganisms. Appl Biochem Biotech 153: 13-20.    

54. Atsumi S, Hanai T, Liao JC (2008) Non-fermentative pathways for synthesis of branched-chain higher alcohols as biofuels. Nature 451: 86-89.    

55. de Lima Alves F, Stevenson A, Baxter E, et al. (2015) Concomitant osmotic and chaotropicity-induced stresses in Aspergillus wentii: compatible solutes determine the biotic window. Curr Genet 61: 457-477.    

56. Tomas CA, Welker NE, Papoutsakis ET (2003) Overexpression of groESL in Clostridium acetobutylicum results in increased solvent production and tolerance, prolonged metabolism, and changes in the cell's transcriptional program. Appl Environ Microb 69: 4951-4965.    

57. Tomas CA, Beamish J, Papoutsakis ET (2004) Transcriptional analysis of butanol stress and tolerance in Clostridium acetobutylicum. J Bacteriol 186: 2006-2018.    

58. Alsaker KV, Spitzer TR, Papoutsakis ET (2004) Transcriptional analysis of spo0A overexpression in Clostridium acetobutylicum and its effect on the cell's response to butanol stress. J Bacteriol 186: 1959-1971.    

59. Janssen H, Grimmler C, Ehrenreich A, et al. (2012) A transcriptional study of acidogenic chemostat cells of Clostridium acetobutylicum—solvent stress caused by a transient n-butanol pulse. J Bacteriol 161: 354-365.

60. Schwarz KM, Kuit W, Grimmler C, et al. (2012) A transcriptional study of acidogenic chemostat cells of Clostridium acetobutylicum-Cellular behavior in adaptation to n-butanol. J Bacteriol 161: 366-377.

61. Winkler J, Kao KC (2011) Transcriptional analysis of Lactobacillus brevis to N-butanol and ferulic acid stress responses. PloS ONE 6: e21438.    

62. Santos J, Sousa MJ, Cardoso H, et al. (2008) Ethanol tolerance of sugar transport, and the rectification of stuck wine fermentations. Microbiology 154: 422-430.    

63. You KM, Rosenfield C-L, Knipple DC (2003) Ethanol tolerance in the yeast Saccharomyces cerevisiae is dependent on cellular oleic acid content. Appl Environ Microb 69: 1499-1503.    

64. Alexandre H, Ansanay-Galeote V, Dequin S, et al. (2001) Global gene expression during short-term ethanol stress in Saccharomyces cerevisiae. FEBS Lett 498: 98-103.    

65. Machado IM, Atsumi S (2012) Cyanobacterial biofuel production. J Biotechnol 162: 50-56.    

66. Lan EI, Liao JC (2011) Metabolic engineering of cyanobacteria for 1-butanol production from carbon dioxide. Metab Eng 13: 353-363.    

67. Anfelt J, Hallström B, Nielsen J, et al. (2013) Using transcriptomics to improve butanol tolerance of Synechocystis sp. strain PCC 6803. Appl Environ Microb 79: 7419-7427.

68. Rühl J, Schmid A, Blank LM (2009) Selected Pseudomonas putida strains able to grow in the presence of high butanol concentrations. Appl Environ Microb 75: 4653-4656.    

69. Fischer CR, Klein-Marcuschamer D, Stephanopoulos G (2008) Selection and optimization of microbial hosts for biofuels production. Metab Eng 10: 295-304.    

70. Yomano L, York S, Ingram L (1998) Isolation and characterization of ethanol-tolerant mutants of Escherichia coli KO11 for fuel ethanol production. J Ind Microbiol Biot 20: 132-138.    

71. López-Contreras AM, Claassen PA, Mooibroek H, et al. (2000) Utilisation of saccharides in extruded domestic organic waste by Clostridium acetobutylicum ATCC 824 for production of acetone, butanol and ethanol. Appl Environ Microb 54: 162-167.

72. Qureshi N, Saha BC, Dien B, et al. (2010) Production of butanol (a biofuel) from agricultural residues: Part I-Use of barley straw hydrolysate. Biomass Bioenerg 34: 559-565.    

73. Qureshi N, Saha BC, Hector RE, et al. (2010) Production of butanol (a biofuel) from agricultural residues: Part II-Use of corn stover and switchgrass hydrolysates. Biomass Bioenerg 34: 566-571.    

74. Mills TY, Sandoval NR, Gill RT (2009) Cellulosic hydrolysate toxicity and tolerance mechanisms in Escherichia coli. Biotechnol Biofuels 2: 26.    

75. Zaldivar J, Martinez A, Ingram LO (1999) Effect of selected aldehydes on the growth and fermentation of ethanologenic Escherichia coli. Biotechnol Bioeng 65: 24-33.

76. Fitzgerald D, Stratford M, Gasson M, et al. (2004) Mode of antimicrobial action of vanillin against Escherichia coli, Lactobacillus plantarum and Listeria innocua. J Appl Microbiol 97: 104-113.    

77. Cray JA, Stevenson A, Ball P, et al. (2015) Chaotropicity: a key factor in product tolerance of biofuel-producing microorganisms. Curr Opin Biotech 33: 228-259.    

78. Lee S, Monnappa AK, Mitchell RJ (2012) Biological activities of lignin hydrolysate-related compounds. BMB Rep 45: 265-274.    

79. Lee S, Nam D, Jung JY, et al. (2012) Identification of Escherichia coli biomarkers responsive to various lignin-hydrolysate compounds. Bioresource Technol 114: 450-456.    

80. Stead D (1993) The effect of hydroxycinnamic acids on the growth of wine‐spoilage lactic acid bacteria. J Appl Bacteriol 75: 135-141.    

81. Guo W, Jia W, Li Y, et al. (2010) Performances of Lactobacillus brevis for producing lactic acid from hydrolysate of lignocellulosics. Appl Biochem Biotech 161: 124-136.    

82. Lee S, Lee JH, Mitchell RJ (2015) Analysis of Clostridium beijerinckii NCIMB 8052's transcriptional response to ferulic acid and its application to enhance the strain tolerance. Biotechnol Biofuels 8: 68.    

83. Zhang Y, Ezeji TC (2013) Transcriptional analysis of Clostridium beijerinckii NCIMB 8052 to elucidate role of furfural stress during acetone butanol ethanol fermentation. Biotechnol Biofuels 6: 66.    

84. Wilson CM, Yang S, Rodriguez M, et al. (2013) Clostridium thermocellum transcriptomic profiles after exposure to furfural or heat stress. Biotechnol Biofuels 6: 131.    

85. Jin Y, Fang Y, Huang M, et al. (2015) Combination of RNA Sequencing and Metabolite Data to elucidate improved toxic compound tolerance and butanol fermentation of Clostridium acetobutylicum from wheat straw hydrolysate by supplying sodium sulfide. Bioresour Technol 198:77-86.    

86. Guo T, He A, Du T, et al. (2013) Butanol production from hemicellulosic hydrolysate of corn fiber by a Clostridium beijerinckii mutant with high inhibitor-tolerance. Bioresour Technol 135: 379-385.    

87. Yoon SH, Lee EG, Das A, et al. (2007) Enhanced vanillin production from recombinant E. coli using NTG mutagenesis and adsorbent resin. Biotechnol Progr 23: 1143-1148.

88. Larsson S, Nilvebrant N, Jönsson L (2001) Effect of overexpression of Saccharomyces cerevisiae Pad1p on the resistance to phenylacrylic acids and lignocellulose hydrolysates under aerobic and oxygen-limited conditions. Appl Microbiol Biot 57: 167-174.    

89. Corbisier P, van der Lelie D, Borremans B, et al. (1999) Whole cell-and protein-based biosensors for the detection of bioavailable heavy metals in environmental samples. Anal Chim Acta 387: 235-244.    

90. Mitchell RJ, Hong HN, Gu MB (2006) Induction of kanamycin resistance gene of plasmid pUCD615 by benzoic acid and phenols. J Microbiol Biotechn 16: 1175.

91. Mitchell RJ, Gu MB (2005) Construction and evaluation of nagR-nagAa:: lux fusion strains in biosensing for salicylic acid derivatives. Appl Biochem Biotech 120: 183-197.    

92. Monnappa AK, Lee S, Mitchell RJ (2013) Sensing of plant hydrolysate-related phenolics with an aaeXAB:: luxCDABE bioreporter strain of Escherichia coli. Bioresource Technol 127: 429-434.    

93. Lee S, Mitchell RJ (2012) Detection of toxic lignin hydrolysate-related compounds using an inaA:: luxCDABE fusion strain. J Biotechnol 157: 598-604.    

94. Monnappa AK, Lee JH, Mitchell RJ (2013) Detection of furfural and 5-hydroxymethylfurfural with a yhcN:: luxCDABE bioreporter strain. Int J Hydrogen Energ 38: 15738-15743.    

95. Prevot AR, Fischer G, Bizzini B, et al. (1954) [Studies on ligninolytic bacteria]. C R Hebd Seances Acad Sci 238: 743-745.

96. Raynaud M, Bizzini B, Fischer G, et al. (1955) [Studies on ligninolytic bacteria; first part]. Ann Inst Pasteur (Paris) 88: 454-465; contd.

97. Fischer G, Bizzini B, Raynaud M, et al. (1955) [Ligninolytic bacteria. II. Characters of ligninolytic bacteria isolated from the soil]. Ann Inst Pasteur (Paris) 88: 618-624.

98. Bandounas L, Wierckx NJP, de Winde JH, et al. (2011) Isolation and characterization of novel bacterial strains exhibiting ligninolytic potential. Bmc Biotechnol 11: 94.    

99. Raj A, Kumar S, Haq I, et al. (2014) Bioremediation and toxicity reduction in pulp and paper mill effluent by newly isolated ligninolytic Paenibacillus sp. Ecol Eng 71: 355-362.    

100. Hooda R, Bhardwaj NK, Singh P (2015) Screening and Identification of Ligninolytic Bacteria for the Treatment of Pulp and Paper Mill Effluent. Water Air Soil Poll 226: 305.    

101. Sahoo DK, Gupta R (2005) Evaluation of ligninolytic microorganisms for efficient decolorization of a small pulp and paper mill effluent. Process Biochem 40: 1573-1578.    

102. Chandra R, Singh S, Krishna Reddy MM, et al. (2008) Isolation and characterization of bacterial strains Paenibacillus sp. and Bacillus sp. for kraft lignin decolorization from pulp paper mill waste. J Gen Appl Microbiol 54: 399-407.

103. Chandra R, Bharagava RN (2013) Bacterial degradation of synthetic and kraft lignin by axenic and mixed culture and their metabolic products. J Environ Biol 34: 991-999.

104. Copley SD, Rokicki J, Turner P, et al. (2012) The whole genome sequence of Sphingobium chlorophenolicum L-1: insights into the evolution of the pentachlorophenol degradation pathway. Genome Biol Evol 4: 184-198.    

105. Deng Y, Fong SS (2011) Metabolic engineering of Thermobifida fusca for direct aerobic bioconversion of untreated lignocellulosic biomass to 1-propanol. Metab Eng 13: 570-577.    

106. Chen CY, Huang YC, Wei CM, et al. (2013) Properties of the newly isolated extracellular thermo-alkali-stable laccase from thermophilic actinomycetes, Thermobifida fusca and its application in dye intermediates oxidation. AMB Express 3: 49.    

107. Tian JH, Pourcher AM, Bouchez T, et al. (2014) Occurrence of lignin degradation genotypes and phenotypes among prokaryotes. Appl Microbiol Biotechnol 98: 9527-9544.    

108. Vanden Wymelenberg A, Gaskell J, Mozuch M, et al. (2009) Transcriptome and secretome analyses of Phanerochaete chrysosporium reveal complex patterns of gene expression. Appl Environ Microbiol 75: 4058-4068.    

109. Wong DW (2009) Structure and action mechanism of ligninolytic enzymes. Appl Biochem Biotechnol 157: 174-209.    

110. Gaskell J, Marty A, Mozuch M, et al. (2014) Influence of Populus genotype on gene expression by the wood decay fungus Phanerochaete chrysosporium. Appl Environ Microbiol 80: 5828-5835.    

111. Hori C, Ishida T, Igarashi K, et al. (2014) Analysis of the Phlebiopsis gigantea genome, transcriptome and secretome provides insight into its pioneer colonization strategies of wood. PLoS Genet 10: e1004759.    

112. MacDonald J, Doering M, Canam T, et al. (2011) Transcriptomic responses of the softwood-degrading white-rot fungus Phanerochaete carnosa during growth on coniferous and deciduous wood. Appl Environ Microbiol 77: 3211-3218.    

113. Macdonald J, Master ER (2012) Time-dependent profiles of transcripts encoding lignocellulose-modifying enzymes of the white rot fungus Phanerochaete carnosa grown on multiple wood substrates. Appl Environ Microbiol 78: 1596-1600.    

114. Garbelotto M, Guglielmo F, Mascheretti S, et al. (2013) Population genetic analyses provide insights on the introduction pathway and spread patterns of the North American forest pathogen Heterobasidion irregulare in Italy. Mol Ecol 22: 4855-4869.    

115. Zubieta C, Krishna SS, Kapoor M, et al. (2007) Crystal structures of two novel dye-decolorizing peroxidases reveal a beta-barrel fold with a conserved heme-binding motif. Proteins 69: 223-233.    

116. Chen F, Dixon RA (2007) Lignin modification improves fermentable sugar yields for biofuel production. Nat Biotechnol 25: 759-761.    

117. Van Acker R, Vanholme R, Storme V, et al. (2013) Lignin biosynthesis perturbations affect secondary cell wall composition and saccharification yield in Arabidopsis thaliana. Biotechnol Biofuels 6: 46.    

118. Pestana-Calsa MC, Pacheco CM, de Castro RC, et al. (2012) Cell wall, lignin and fatty acid-related transcriptome in soybean: Achieving gene expression patterns for bioenergy legume. Genet Mol Biol 35: 322-330.    

119. Vicentini R, Bottcher A, Brito Mdos S, et al. (2015) Large-Scale Transcriptome Analysis of Two Sugarcane Genotypes Contrasting for Lignin Content. PLoS ONE 10: e0134909.    

120. Van Acker R, Leple JC, Aerts D, et al. (2014) Improved saccharification and ethanol yield from field-grown transgenic poplar deficient in cinnamoyl-CoA reductase. Proc Natl Acad Sci U S A 111: 845-850.    

121. Weber AP, Weber KL, Carr K, et al. (2007) Sampling the Arabidopsis transcriptome with massively parallel pyrosequencing. Plant Physiol 144: 32-42.    

122. Cheung F, Haas BJ, Goldberg SM, et al. (2006) Sequencing Medicago truncatula expressed sequenced tags using 454 Life Sciences technology. BMC Genomics 7: 272.    

123. Barbazuk WB, Emrich SJ, Chen HD, et al. (2007) SNP discovery via 454 transcriptome sequencing. Plant J 51: 910-918.    

124. Wong MM, Cannon CH, Wickneswari R (2011) Identification of lignin genes and regulatory sequences involved in secondary cell wall formation in Acacia auriculiformis and Acacia mangium via de novo transcriptome sequencing. BMC Genomics 12: 342.    

Copyright Info: © 2015, Robert J. Mitchell, et al., licensee AIMS Press. This is an open access article distributed under the terms of the Creative Commons Attribution Licese (http://creativecommons.org/licenses/by/4.0)

Download full text in PDF

Export Citation

Article outline

Show full outline
Copyright © AIMS Press All Rights Reserved