Identification, phylogeny and expression analysis of NAP-family histone chaperones in maize (Zea mays)

Abedi, Amin; Shirzadian-Khorramabad, Reza; Sohani, Mohammad Mehdi

Identification, phylogeny and expression analysis of NAP-family histone chaperones in maize (Zea mays)

Document Type : Research Paper

Authors

¹ Graduate Ph.D. Department of Agricultural Biotechnology, Faculty of Agricultural Sciences, University of Guilan, Rasht, Iran

² Assistant Professor, Department of Agricultural Biotechnology, Faculty of Agricultural Sciences, University of Guilan, Rasht, Iran

³ Associate Professor, Department of Agricultural Biotechnology, Faculty of Agricultural Sciences, University of Guilan, Rasht, Iran

Abstract

In eukaryotes cells, genomic DNA in combination with histone proteins is formed the chromatin. Histone chaperones affect the gene transcription via altering in DNA accessibility. In contrast to their animal and yeast counterparts, not much is known about plant histone chaperones. Nucleosome assembly protein (NAP) family histone chaperones are conserved throughout eukaryotic genomics. NAP is an integral component in the establishment, maintenance, and dynamics of eukaryotic chromatin. They transfer histones into the nucleus, assemble nucleosomes, and promote chromatin fluidity, thereby, affecting the transcription of many genes. In this study, by applying some bioinformatics analysis approaches, six putative NAP genes (ZmNAPL1–ZmNAPL6) were identified in maize (Zea mays) using the released maize genomic sequences. Phylogenetic analysis showed that these ZmNAPLs are classified into two subgroups as found in Arabidopsis and rice. Moreover, it was found that maize NAPL proteins are more closely related to rice. The ZmNAPL genes contained three to eleven introns and were distributed across 5 out of 20 chromosomes in maize. Microarray-based expression analysis of ZmNAPLs showed that there is a tight transcriptional regulation on ZmNAPL genes during the plant development in maize suggesting that they may play a role in genetic reprogramming in association with the developmental process. This study is the first report about NAPL gene family in maize and obtained results provide basic information for future research on the functions of NAPL genes in maize.

Keywords

20.1001.1.22520783.1396.7.18.3.2

Main Subjects

Bioinformatics

References

Artimo P, Jonnalagedda M, Arnold K, Baratin D, Csardi G, De Castro E, Duvaud S, Flegel V, Fortier A, Gasteiger E (2012) ExPASy: SIB bioinformatics resource portal. Nucleic Acids Res. 40: W957-W603.

Attia M, Förster A, Rachez C, Freemont P, Avner P, Rogner UC (2011) Interaction between nucleosome assembly protein 1-like family members. J. Mol. Biol. 407(5): 647-660.

Bailey TL, Williams N, Misleh C, Li WW (2006) MEME: discovering and analyzing DNA and protein sequence motifs. Nucleic Acids Res. 34: W369-W373.

Braun P, Aubourg S, Van Leene J, De Jaeger G, Lurin C (2013) Plant protein interactomes. Annu. Rev. Plant Biol. 64: 161-187.

Burgess RJ, Zhang Z (2013) Histone chaperones in nucleosome assembly and human disease. Nat. Struct. Mol. Biol. 20(1): 14-22.

Dash S, Van Hemert J, Hong L, Wise RP, Dickerson JA (2012) PLEXdb: gene expression resources for plants and plant pathogens. Nucleic Acids Res. 40: D1194-D1201.

De Koning L, Corpet A, Haber JE, Almouzni, G (2007) Histone chaperones: an escort network regulating histone traffic. Nat. Struct. Mol. Biol. 14(11): 997-1007.

Dennehey BK, Tyler J (2014) Histone chaperones in the assembly and disassembly of chromatin. In: Workman JA, Abmayr SM (Eds) Fundamentals of chromatin, Springer, New York, pp 29-67.

Eitoku M, Sato L, Senda T, Horikoshi M (2008) Histone chaperones: 30 years from isolation to elucidation of the mechanisms of nucleosome assembly and disassembly. Cell. Mol. Life Sci. 65(3): 414-444.

Felsenstein J (1985) Confidence limits on phylogenies: an approach using the bootstrap. Evolution. 39(4): 783-791.

Finn RD, Bateman A, Clements J, Coggill P, Eberhardt RY, Eddy SR, Heger A, Hetherington K, Holm L, Mistry J (2013) Pfam: the protein families database. Nucleic Acids Res. 42: D222-D230.

Frey FP, Urbany C, Hüttel B, Richard Reinhardt R, StichEmail B (2015) Genome-wide expression profiling and phenotypic evaluation of European maize inbreds at seedling stage in response to heat stress. BMC Genomics. 16:123.

Gamble MJ, Erdjument-Bromage H, Tempst P, Freedman LP, Fisher RP (2005) The histone chaperone TAF-I/SET/INHAT is required for transcription in vitro of chromatin templates. Mol. Cell. Biol. 25(2): 797-807.

Goodstein DM, Shu S, Howson R, Neupane R, Hayes RD, Fazo J, Mitros T, Dirks W, Hellsten U, Putnam N (2012) Phytozome: a comparative platform for green plant genomics. Nucleic Acids Res. 40: D1178-D1186.

Guo J, Wu J, Ji Q, Wang C, Luo L, Yuan Y, Wang Y, Wang J (2008) Genome-wide analysis of heat shock transcription factor families in rice and Arabidopsis. J. Genet. Genomics. 35(2): 105-118.

Hogeweg P (2011) The roots of bioinformatics in theoretical biology. PLoS Comput. Biol. 7: e1002021.

Hondele M, Ladurner AG (2011) The chaperone–histone partnership: for the greater good of histone traffic and chromatin plasticity. Curr. Opin. Struct. Biol. 21(6): 698-708.

Hu B, Jin J, Guo AY, Zhang H, Luo J, Gao G (2014) GSDS 2.0: an upgraded gene feature visualization server. Bioinformatics. 31(8):1296-1297.

Huang DW, Sherman BT, Lempicki RA (2009) Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat. Protoc. 4(1): 44-57.

Kawahara Y, de la Bastide M, Hamilton JP, Kanamori H, McCombie WR, Ouyang S, Schwartz DC, Tanaka T, Wu J, Zhou S, Childs KL, Davidson RM, Lin H, Quesada-Ocampo L, Vaillancourt B, Sakai H, Lee S S, Kim J, Numa H, Itoh T, Buell CR, Matsumoto T (2013) Improvement of the Oryza sativa Nipponbare reference genome using next generation sequence and optical map data. Rice. 6:4.

Kellogg DR, Murray AW (1995) NAP1 acts with Clb1 to perform mitotic functions and to suppress polar bud growth in budding yeast. J. Cell. Biol. 130(3): 675-685.

Kumar S, Stecher G, Tamura K (2016) MEGA7: Molecular Evolutionary Genetics Analysis version 7.0 for bigger datasets. Mol. Biol. Evol. 33(7):1870-1874.

Lamesch P, Berardini TZ, Li D, Swarbreck D, Wilks C, Sasidharan R, Muller R, Dreher K, Alexander DL, Garcia-Hernandez M, Karthikeyan AS, Lee CH, Nelson WD, Ploetz L, Singh S, Wensel A, Huala E (2012) The Arabidopsis Information Resource (TAIR): improved gene annotation and new tools. Nucleic Acids Res. 40: D1202-D1210.

Larkin MA, Blackshields G, Brown N, Chenna R, McGettigan PA, McWilliam H, Valentin F, Wallace IM, Wilm A, Lopez R (2007) Clustal W and Clustal X version 2.0. Bioinformatics. 23(21): 2947-2948.

Letunic I, Doerks T, Bork P (2012) SMART 7: recent updates to the protein domain annotation resource. Nucleic Acids Res. 40: D302-D305.

Liao Y, Liu S, Jiang Y, Hu C, Zhang X, Cao X, Xu Z, Gao X, Li L, Zhu J (2017) Genome-wide analysis and environmental response profiling of dirigent family genes in rice (Oryza sativa). Genes and Genomics. 39(1): 47-62.

Liu Z, Zhu Y, Gao J, Yu F, Dong A, Shen WH (2009) Molecular and reverse genetic characterization of NUCLEOSOME ASSEMBLY PROTEIN1 (NAP1) genes unravels their function in transcription and nucleotide excision repair in Arabidopsis thaliana. Plant J. 59(1): 27-38.

Marchler-Bauer A, Lu S, Anderson JB, Chitsaz F, Derbyshire MK, eWeese-Scott C, Fong JH, Geer LY, Geer RC, Gonzales NR, Gwadz M, Hurwitz DI, Jackson JD, Ke Z, Lanczycki CJ, Lu F, Marchler GH, Mullokandov M, Omelchenko MV, Robertson CL, Song JS, Thanki N, Yamashita RA, Zhang D, Zhang N, Zheng C, Bryant SH (2011) CDD: a Conserved Domain Database for the functional annotation of proteins. Nucleic Acids Res. 39: D225-D229.

Marheineke K, Krude T (1998) Nucleosome assembly activity and intracellular localization of human CAF-1 changes during the cell division cycle. J. Biol. Chem. 273(24): 15279-15286.

McGinnis S, Madden TL (2004) BLAST: at the core of a powerful and diverse set of sequence analysis tools. Nucleic Acids Res. 32: W20-W25.

Mosammaparast N, Ewart CS, Pemberton LF (2002) A role for nucleosome assembly protein 1 in the nuclear transport of histones H2A and H2B. EMBO J. 21(23): 6527-6538.

Park YJ, Luger K (2006) The structure of nucleosome assembly protein 1. Proc. Natl. Acad. Sci. U. S. A. 103(5): 1248-1253.

Sekhon RS, Lin H, Childs KL, Hansey CN, Buell CR, de Leon N, Kaeppler SM (2011) Genome-wide atlas of transcription during maize development. Plant J. 66(4): 553-563.

Sharp PA (1981). Speculations on RNA splicing (minireview). Cell. 23(3): 643-646.

Shimizu Y, Akashi T, Okuda A, Kikuchi A, Fukui K (2000) NBP1 (Nap1 binding protein 1), an essential gene for G2/M transition of Saccharomyces cerevisiae, encodes a protein of distinct sub-nuclear localization. Gene. 246(1-2): 395-404.

Singh AK, Kumar R, Tripathi AK, Gupta BK, Pareek A, Singla-Pareek SL (2015) Genome-wide investigation and expression analysis of Sodium/Calcium exchanger gene family in rice and Arabidopsis. Rice. 8: 21.

Singh AK, Sharma V, Pal AK, Acharya V, Ahuja PS (2013) Genome-wide organization and expression profiling of the NAC transcription factor family in potato (Solanum tuberosum L.). DNA Res. 20(4): 403-423.

Szklarczyk D, Morris JH, Cook H, Kuhn M, Wyder S, Simonovic M, Santos A, Doncheva NT, Roth A, Bork P (2016) The STRING database in 2017: quality-controlled protein–protein association networks, made broadly accessible. Nucleic Acids Res. 45(D1): D362-D368.

Tripathi AK, Pareek A, Singla-Pareek SL (2016) A NAP-Family histone chaperone functions in abiotic stress response and adaptation. Plant Physiol. 171(4): 2854-2868.

Tripathi AK, Singh K, Pareek A, Singla-Pareek SL (2015) Histone chaperones in Arabidopsis and rice: genome-wide identification, phylogeny, architecture and transcriptional regulation. BMC Plant Biol. 15: 42.

Valieva M, Feofanov A, Studitsky V (2016) Histone chaperones: Variety and functions. Moscow Univ. Biol.Sci. Bull. 71(3): 165-169.

Wei KF, Chen J, Chen YF, Wu LJ, Xie DX (2012) Molecular phylogenetic and expression analysis of the complete WRKY transcription factor family in maize. DNA Res. 19(2): 153-64.

Zhang Y, Gao M, Singer SD, Fei Z, Wang H, Wang X (2012) Genome-wide identification and analysis of the TIFY gene family in grape. PLoS One. 7(9): e44465.

Zhu P, Gu H, Jiao Y, Huang D, Chen M (2011) Computational identification of protein-protein interactions in rice based on the predicted rice interactome network. Genomics, proteomics and Bioinformatics. 9(4-5): 128-137.

Yu CS, Chen YC, Lu CH, Hwang JK (2006) Prediction of protein subcellular localization. Proteins. 64(3): 643-651.