Research Article | Volume: 4, Issue: 4, July-August, 2016
Genome-wide identification and expression analysis along the leaf developmental gradient of the sigma factor gene family in foxtail millet (Setaria italica)
Sigma factors are necessary for the initiation of transcription by RNA polymerase in bacteria and plastids of plants. In plants, a small family of nuclear genes is responsible for encoding the sigma factor proteins. In this study, a genome-wide identification and expression analysis of leaf gradient in millet (Setaria italica) were performed to characterize sigma factor genes and their proteins. By applying several bioinformatics tools, we identified chromosome locations of seven sigma factor genes in millet and their protein 3D structures. All these proteins contained three conserved domains of σ-70 family. These sigma factor genes have a closer phylogenetic relationship with their orthologs in maize than that in rice. The digital gene expression (DGE) analysis along the millet leaf developmental gradient indicated that Sisig1, Sisig5, Sisig6 showed extremely high expression levels in leaf middle and tip regions. Combining the conservation analysis of residues of each sigma factor protein with the DGE profiles of these proteins, it reveals that Sisig5 plays the housekeeping role compared with other Sisig proteins. Our study will facilitate the future research on crop evolution and the functional studies of sigma factor genes in millet.
Hongyun Liu, Jinjin Cheng, Siyuan Cheng, Hui Fan, Bo Wen, Zheng Liu., Genome-wide identification and expression analysis along the leaf developmentalgradient of the sigma factor gene family in foxtail millet (Setaria italica). J App Biol Biotech. 2016; 4 (04): 011-030. DOI: 10.7324/JABB.2016.40102
1. Borukhov S, Severinov K. Role of the RNA polymerase sigma subunit in transcription initiation. Res Microbiol. 2002; 153(9):557-562.
2. Lysenko EA. Analysis of the evolution of the family of the Sig genes encoding plant sigmafactors. Russ J Plant Physiol. 2006; 53(5):605-614.
3. Ishizaki Y, Tsunoyama Y, Hatano K, Ando K., Kato K, Shinmyo A, Kobori M, Takeba G, Nakahira Y, Shiina T. A nuclear-encoded sigma factor, Arabidopsis SIG6, recognizes sigma-70 type chloroplast promoters and regulates early chloroplast development in cotyledons. Plant J. 2005; 42(2):133-144.
4. Lerbs-Mache S. Function of plastid sigma factors in higher plants: regulation of gene expression or just preservation of constitutive transcription? Plant Mol Biol. 2011; 76(3-5):235-249.
5. Lysenko EA. Plant sigma factors and their role in plastid transcription. Plant Cell Rep. 2007; 26(26):845-859.
6. Hanaoka M, Kato M, Anma M, Tanaka K. SIG1, a sigma factor for the chloroplast RNA polymerase, differently associates with multiple DNA regions in the chloroplast chromosomes in vivo. Int J Mol Sci. 2012; 13(10):12182-12194.
7. Tozawa Y, Tanaka K, Takahashi H, Wakasa K. Nuclear encoding of a plastid σ factor in rice and its tissue- and light-dependent expression. Nucleic Acids Res. 1998; 26(2):415-419.
8. Kasai K, Kawagishi-Kobayashi M, Teraishi M, Ito Y, Ochi K, Wakasa K, Tozawa Y. Differential expression of three plastidial sigma factors, OsSIG1, OsSIG2A, and OsSIG2B, during leaf development in rice. Biosci Biotech Bioch. 2004; 68(4):973-977.
9. Kubota Y, Miyao A, Hirochika H, Tozawa Y, Yasuda H, Tsunoyama Y, Niwa Y, Imamura S, Shirai M, Asayama M. Two novel nuclear genes, OsSIG5 and OsSIG6, encoding potential plastid sigma factors of RNA polymerase in rice: tissue-speciï¬c and light-responsive gene expression. Plant Cell Physiol. 2007; 48(48):186-192.
10. Tozawa Y, Teraishi M, Sasaki T, Sonoike K, Nishiyama Y, Itaya M, Miyao A, Hirochika H. The plastid sigma factor SIG1 maintains photosystem I activity via regulated expression of the psaA operon in rice chloroplasts. Plant J. 2007; 52(1):124-132.
11. Tan S, Troxler RF. Characterization of two chloroplast RNA polymerase sigma factors from Zea mays: Photoregulation and differential expression. Proc Natl Acad Sci USA. 1999; 96(96):5316-5321.
12. Beardslee TA, Roy-Chowdhury S, Jaiswal P, Buhot L, Lerbs-Mache S, Stern DB, Allison LA. A nucleus-encoded maize protein with sigma factor activity accumulates in mitochondria and chloroplasts. Plant J. 2002; 31(2):199-209.
13. John CR, Smith-Unna RD, Woodfield H, Covshoff S, Hibberd JM. Evolutionary convergence of cell-speciï¬c gene expression in independent lineages of C4 grasses. Plant Physiol. 2014; 165(1):62-75.
14. Jia GQ, Huang XH, Zhi H, Zhao Y, Zhao Q, Li WJ, Chai Y, Yang LF, Liu KY, Lu HYet al. A haplotype map of genomic variations and genome-wide association studies of agronomic traits in foxtail millet (Setaria italica). Nat Genet. 2013; 45(8):957-961.
15. Yuan M, Qu LJ, Wang XJ, Qian Q, Yang WC, Wang T, Kong HZ, Jiang GM, Chong K. Research advances on plant science in China in 2013. Chinese Bulletin of Botany. 2014; 49:347-406.
16. Feng XL, Zhao ZH, Wang XM, Qiu FC, Song GL, Wang DQ, Su X, Zhang XL, Wang F. Recent Research Progress in Foxtail Millet (Setaria italica). Agr Sci & Technol. 2014; 15:564-570, 575.
17. Lin YX, Jiang HY, Chu ZX, Tang XL, Zhu SW, Cheng BJ. Genome-wide identification, classification and analysis of heat shock transcription factor family in maize. BMC Genomics. 2011; 12(1):76.
18. Guo AY, Zhu QH, Chen X, Luo JC. GSDS: a gene structure display server. Hereditas (Beijing). 2007; 29(8):1023-1026.
19. Wass MN, Kelley LA, Sternberg MJ. 3DLigandSite: predicting ligand-binding sites using similar structures. Nucleic Acids Res. 2010; 38 (Suppl.):W469-473.
20. Lovell SC, Davis IW, Arendall WB, de Bakker PIW, Word JM, Prisant MG, Richardson JS, Richardson DC. Structure validation by Cα geometry: Ï•, ψ and Cβ deviation. Proteins. 2003; 50:437-450.
21. Emanuelsson O, Nielsen H, von Heijne G. Predicting subcellular localization of proteins based on their N-terminal amino acid sequence. J Mol Biol. 2000; 300(4):1005-1016.
22. Tamura K, Dudley J, Nei M, Kumar S. MEGA4: molecular evolutionary genetics analysis (MEGA) software version 4.0. Mol Biol Evol. 2007; 24(8):1596-1599.
23. Zhang Q, Wang ZY, Ma XL, Nie LM, Wang HL, Wang JP. Comparative analysis of paleopolyploidy evolution in genomes of Setaria italica and Zea mays. J Henan Agric Sci. 2014; 43(6):10-15.
24. Schnable PS, Ware D, Fulton RS, Stein JC, Wei F, Pasternak S, Liang C, Zhang J, Fulton L, Graves TA, et al. The B37 maize genome: Complexity, diversity and dynamics. Science. 2009; 326(5956):1112-1115.
25. Bennetzen JL, Schmutz J, Wang H, Percifield R, Hawkins J, Pontaroli AC, Estep M, Feng L, Vaughn JN, Grimwood J, et al. Reference genome sequence of the model plant Setaria. Nat Biotechnol. 2012; 30(6):555-561.
26. Zhang GY, Liu X, Wang J. Genome sequence of foxtail millet (Setaria italica) provides insights into grass evolution and biofuel potential. Nat Biotechnol. 2012; 30(6):549-556.
27. Isono K, Shimizu M, Yoshimoto K, Niwa Y, Satoh K, Yokota A, Kobayashi H. Leaf-speciï¬cally expressed genes for polypeptides destined for chloroplasts with domains of σ70 factors of bacterial RNA polymerases in Arabidopsis thaliana. Proc Natl Acad Sci USA. 1997; 94(26):14948-14953.
28. Schweer J, Türkeri H, Kolpack A, Link G. Role and regulation of plastid sigma factors and their functional interactors during chloroplast transcription-Recent lessons from Arabidopsis thaliana. Eur J Cell Biol. 2010; 89(12):940-946.
29. Lahiri SD, Yao J, McCumbers C, Allison LA. Tissue-specific and light-dependent expression within a family of nuclear-encoded σ-like factors from Zea mays. Mol Cell Biol Res Commun. 1999; 1(1):14-20.
30. Lahiri SD, Allison LA. Complementary expression of two plastid-localized sigma-like factors in maize. Plant Physiol. 2000; 123(3): 883-894.
31. Yao J, Roy-Chowdhury S, Allison LA. AtSig5 is an essential nucleus-encoded Arabidopsis σ-like factor. Plant Physiol. 2003; 132(2):739-47.
32. Tsunoyama Y, Ishizaki Y, Morikawa K, Kobori M, Nakahira Y, Takeba G, Toyoshima Y, Shiina T. Blue light-induced transcription of plastid-encoded psbD gene is mediated by a nuclear-encoded transcription initiation factor, AtSig5. Proc Natl Acad Sci USA. 2004; 101(9):3304-3309.
33. Nagashima A, Hanaoka M, Shikanai T, Fujiwara M, Kanamaru K, Takahashi H, Tanaka K. The multiple-stress responsive plastid sigma factor, SIG5, directs activation of the psbD blue light-responsive promoter (BLRP) in Arabidopsis thaliana. Plant Cell Physiol. 2004; 45(4):357-368.
34. Favory JJ, Kobayahi M, Tanaka K, Peltier G, Kreis M, Valay JG, Lerbs-Mache S. Speciï¬c function of a plastid sigma factor for ndhF gene transcription. Nucleic Acids Res. 2005; 33(18):5991-5999.
35. Borsellino L. Influence of light and cytokinin on organellar phage-type RNA polymerase transcript levels and transcription of organellar genes in Arabidopsis thaliana. PhD thesis, Humboldt Universität zu Berlin. 2011.
36. Cortleven A, Schmülling T. Regulation of chloroplast development and function by cytokinin. J Exp Bot. 2015; 66(16):4999-5013.
37. Pick TR, Bräutigam A, Schlüter U, Denton AK, Colmsee C, Scholz U, Fahnenstich H, Pieruschka R, Rascher U, Sonnewald U, Weber AP. Systems analysis of a maize leaf developmental gradient redefines the current C4 model and provides candidates for regulation. Plant Cell. 2011; 23(12):4208-4220.
38. Wang L, Czedik-Eysenberg A, Mertz RA, Si Y, Tohge T, Nunes-Nesi A, Arrivault S, Dedow LK, Bryant DW, Zhou W, et al. Comparative analyses of C4 and C3 photosynthesis in developing leaves of maize and rice. Nat Biotechnol. 2014; 32(11):1158-1165.
39. Aubry S, Kelly S, Kumpers BMC, Smith-Unna RD, Hibberd JM. Deep evolutionary comparison of gene expression identifies parallel recruitment of trans-factors in two independent origins of C4 photosynthesis. PLOS Genet. 2014; 10(6):e1004365.
Year
Month