Regulation of DNA methyltransferase gene expression by short peptides in nicotiana tabacum regenerants

Larisa I. Fedoreyeva; Boris F. Vanyushin; Larisa I. Fedoreyeva; Boris F. Vanyushin

doi:10.3934/biophy.2021005

AIMS Biophysics

2021, Volume 8, Issue 1: 66-79. doi: 10.3934/biophy.2021005

Previous Article Next Article

Research article Special Issues

Regulation of DNA methyltransferase gene expression by short peptides in nicotiana tabacum regenerants

Larisa I. Fedoreyeva ^{1
,
,},
Boris F. Vanyushin ^1,2

1.
All-Russian Research Institute of Agricultural Biotechnology RAS, 127550 Moscow, Timiryazevskaya 42, Russia
2.
A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119991 Moscow, Leninskie Gory1, Building 40, Russia

Received: 03 November 2020 Accepted: 17 December 2020 Published: 22 December 2020

Methylation of cytosine DNA residues is the most studied and stable of all epigenetic modifications. Methylation of eukaryotic DNA is carried out by DNA methyltransferases. DNA methylation is an active mechanism for controlling gene transcription and is usually associated with prolonged silencing of DNA. The effect of peptides AEDG and AEDL on the growth of calluses of tobacco (Nicotiana tabacum) at low concentrations (10⁻⁷ M) is similar to the effect of phytohormones, has a regulatory character, and is possibly epigenetic in nature. Peptides increase the expression of DNA methyltransferase genes. One of the possible mechanisms of regulation of DNA methyltransferase genes by AEDG and AEDL is their ability to bind to free DNA regions at certain CNG sites, which are also methylation sites of plant cytosine methyltransferases. The AEDG peptide preferably binds to the CAG site and the AEDL peptide to the CTG site. By binding to the same sites as DNA methyltransferase, peptides block methylation sites, thereby reducing the level of DNA methylation. The specific binding of peptides to different sites that we discovered can be of great importance in gene regulation, since peptides with different structures can block different DNA regions for methylation of certain genes, thereby activating or silencing their expression.

Keywords:

Citation: Larisa I. Fedoreyeva, Boris F. Vanyushin. Regulation of DNA methyltransferase gene expression by short peptides in nicotiana tabacum regenerants[J]. AIMS Biophysics, 2021, 8(1): 66-79. doi: 10.3934/biophy.2021005

Related Papers:

[1]	Longxing Qi, Shoujing Tian, Jing-an Cui, Tianping Wang . Multiple infection leads to backward bifurcation for a schistosomiasis model. Mathematical Biosciences and Engineering, 2019, 16(2): 701-712. doi: 10.3934/mbe.2019033
[2]	A. K. Misra, Jyoti Maurya, Mohammad Sajid . Modeling the effect of time delay in the increment of number of hospital beds to control an infectious disease. Mathematical Biosciences and Engineering, 2022, 19(11): 11628-11656. doi: 10.3934/mbe.2022541
[3]	Wahyudin Nur, Trisilowati, Agus Suryanto, Wuryansari Muharini Kusumawinahyu . Schistosomiasis model with treatment, habitat modification and biological control. Mathematical Biosciences and Engineering, 2022, 19(12): 13799-13828. doi: 10.3934/mbe.2022643
[4]	Jinhu Xu, Yicang Zhou . Bifurcation analysis of HIV-1 infection model with cell-to-cell transmission and immune response delay. Mathematical Biosciences and Engineering, 2016, 13(2): 343-367. doi: 10.3934/mbe.2015006
[5]	Shishi Wang, Yuting Ding, Hongfan Lu, Silin Gong . Stability and bifurcation analysis of $SIQR$ for the COVID-19 epidemic model with time delay. Mathematical Biosciences and Engineering, 2021, 18(5): 5505-5524. doi: 10.3934/mbe.2021278
[6]	Yu Yang, Gang Huang, Yueping Dong . Stability and Hopf bifurcation of an HIV infection model with two time delays. Mathematical Biosciences and Engineering, 2023, 20(2): 1938-1959. doi: 10.3934/mbe.2023089
[7]	Shunyi Li . Hopf bifurcation, stability switches and chaos in a prey-predator system with three stage structure and two time delays. Mathematical Biosciences and Engineering, 2019, 16(6): 6934-6961. doi: 10.3934/mbe.2019348
[8]	Hui Cao, Yicang Zhou, Zhien Ma . Bifurcation analysis of a discrete SIS model with bilinear incidence depending on new infection. Mathematical Biosciences and Engineering, 2013, 10(5&6): 1399-1417. doi: 10.3934/mbe.2013.10.1399
[9]	Kazeem Oare Okosun, Robert Smith? . Optimal control analysis of malaria-schistosomiasis co-infection dynamics. Mathematical Biosciences and Engineering, 2017, 14(2): 377-405. doi: 10.3934/mbe.2017024
[10]	Sarita Bugalia, Jai Prakash Tripathi, Hao Wang . Mathematical modeling of intervention and low medical resource availability with delays: Applications to COVID-19 outbreaks in Spain and Italy. Mathematical Biosciences and Engineering, 2021, 18(5): 5865-5920. doi: 10.3934/mbe.2021295

Abstract

Acknowledgments

The authors thank the Center of Scientific Equipment of the All-Russian Research Institute of Agricultural Biotechnology for technical support.
The study was performed in the framework of the Russian state assignment AAA-A1170912-8 and, partially, RFBR No. 18-016-00150.

Conflict of interest

All authors declare no conflicts of interest in this paper.

References

[1]	Haig D (2004) The (dual) origin of epigenetics. Cold Spring Harb Symp Quant Biol 69: 67-70. doi: 10.1101/sqb.2004.69.67
[2]	Luger K, Dechassa ML, Tremethick DJ (2012) New insights into nucleosome and chromatin structure: an ordered state or a disordered affair? Nat Rev Mol Cell Biol 13: 436-447. doi: 10.1038/nrm3382
[3]	Jaenisch R, Bird A (2003) Epigenetic regulation of gene expression: how the genome integrates intrinsic and environmental signals. Nat Genet 33: 245-254. doi: 10.1038/ng1089
[4]	Minard ME, Jain AK, Barton MC (2009) Analysis of epigenetic alterations to chromatin during development. Genesis 47: 559-572. doi: 10.1002/dvg.20534
[5]	Vanyushin BF, Ashapkin VV (2009) DNA Methylation in Plants New York: Nova Science Publishers Inc.
[6]	Vanyushin BF, Ashapkin VV (2007) Peculiarities of DNA methylation in plants. Progress in DNA Methylation Research New York: Nova Science Publishers Inc., 1-90.
[7]	Goll MG, Bestor TH (2005) Eukaryotic cytosine methyltransferases. Annu Rev Biochem 74: 481-514. doi: 10.1146/annurev.biochem.74.010904.153721
[8]	Lister R, Pelizzola M, Dowen RH, et al. (2009) Human DNA methylomes at base resolution show widespread epigenomic differences. Nature 462: 315-322. doi: 10.1038/nature08514
[9]	Lister R, Mukamel EA, Nery JR, et al. (2013) Global epigenomic reconfiguration during mammalian brain development. Science 341: 1237905. doi: 10.1126/science.1237905
[10]	Du J, Zhong X, Bernatavichute YV, et al. (2012) Dual binding of chromomethylase domains to H3K9me2-containing nucleosomes directs DNA methylation in plants. Cell 151: 167-180. doi: 10.1016/j.cell.2012.07.034
[11]	Law JA, Jacobsen SE (2010) Establishing, maintaining and modifying DNA methylation patterns in plants and animals. Nat Rev Genet 11: 204-220. doi: 10.1038/nrg2719
[12]	Chinnusamy V, Zhu JK (2009) RNA-directed DNA methylation and demethylation in plants. Sci China C Life Sci 52: 331-343. doi: 10.1007/s11427-009-0052-1
[13]	Jeddeloh JA, Stokes TL, Richards EJ (1999) Maintenance of genomic methylation requires a SWI2/SNF2-like protein. Nat Genet 22: 94-97. doi: 10.1038/8803
[14]	Lippman Z, Gendrel AV, Black M, et al. (2004) Role of transposable elements in heterochromatin and epigenetic control. Nature 430: 471-476. doi: 10.1038/nature02651
[15]	Ryan DP, Owen-Hughes T (2011) Snf2-family proteins: chromatin remodellers for any occasion. Curr Opin Chem Biol 15: 649-656. doi: 10.1016/j.cbpa.2011.07.022
[16]	Han YF, Dou K, Ma ZY, et al. (2014) SUVR2 is involved in transcriptional gene silencing by associating with SNF2-related chromatin—remodeling proteins in Arabidopsis. Cell Research 24: 1445-1465. doi: 10.1038/cr.2014.156
[17]	Tavormina P, De Coninck B, Nikonorova N, et al. (2015) The plant peptidome: an expanding repertoire of structural features and biological functions. Plant Cell 27: 2095-2118. doi: 10.1105/tpc.15.00440
[18]	Vanyushin BF, Ashapkin VV, Aleksandrushkina NI (2017) Regulation peptides in plants. Biochemistry 82: 89-94 (Moscow).
[19]	Wang G, Zhang G, Wu M (2016) CLE peptide signaling and crosstalk with phytohormones and environmental stimuli. Front Plant Sci 6: 1211.
[20]	Czyzewicz N, Yue K, Beeckman T, et al. (2013) Message in a bottle: small signalling peptide outputs during growth and development. J Exp Bot 64: 5281-5296. doi: 10.1093/jxb/ert283
[21]	Murphy E, Smith S, De Smet I (2012) Small signalinig peptides in Arabidopsis development: how cells communicate over a short distance. Plant Cell 24: 3198-3217. doi: 10.1105/tpc.112.099010
[22]	Motomitsu A, Sawa S, Ishida T (2015) Plant peptide hormone signaling. Essays Biochem 58: 115-131. doi: 10.1042/bse0580115
[23]	Fedoreyeva LI, Vanyushin BF, Baranova EN (2020) Peptide AEDL alters chromatin conformation via binding. AIMS Biophysics 7: 1-16. doi: 10.3934/biophy.2020001
[24]	Lakowicz JR, Weber G (1973) Quenching of fluorescence by oxygen. Probe for structural fluctuations in macromolecules. Biochemistry 12: 4161-4170. doi: 10.1021/bi00745a020
[25]	Favicchio R, Dragan AI, Kneale GG, et al. (2009) Fluorescence spectroscopy and anisotropy in the analysis of DNA-protein interactions. DNA-Protein Interactions Humana Press, 589-611. doi: 10.1007/978-1-60327-015-1_35
[26]	Kyte J, Doolittle RF (1982) A simple method for displaying the hydropathic character of a protein. J Mol Biol 157: 105-132. doi: 10.1016/0022-2836(82)90515-0
[27]	Vanyushin BF, Ashapkin VV (2011) DNA methylation in plants; past, present and future. BBA–Gene Regul Mech 1809: 360-368.
[28]	Malinin VV (2005) Gerontological aspects of genome peptide regulation Karger Medical and Scientific Publishers.

This article has been cited by:

M. A. Aziz-Alaoui, Jean M.-S. Lubuma, Berge Tsanou, Prevalence-based modeling approach of schistosomiasis: global stability analysis and integrated control assessment, 2021, 40, 2238-3603, 10.1007/s40314-021-01414-9

Reader Comments

Your name:*

Email:*
© 2021 the Author(s), licensee AIMS Press. This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0)