Applying bioinformatics to analyze auxinrelated genes in robusta coffee genome (Coffea canephora L.)

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Applying bioinformatics to analyze auxinrelated genes in robusta coffee genome (Coffea canephora L.)

Tác giả

Nguyễn Đình Sỹ

Tóm tắt



Coffea canephora, which belongs to the Rubiaceae family, is one of the most popular cultivated coffea worldwide. In this study, we identified and analyzed candidate genes that involved in auxinrelated gens in the C. canephora genome. The results showed that genome of C. canephora consists of 152 protein-coding genes related to auxin which are divided into 7 main groups depending on domain and motif: Auxin-induced protein; Auxin-binding protein; Auxin transporter-like protein; Auxin carrier component; Auxin response factor; Auxin-responsive protein; Auxin signaling protein. Using SMART software to analyze protein structure, the result indicated that there are some characteristic domains involved in auxin response such as EamA; AUX_IAA; Auxin inducible; Aldo_ket_red; Cupin; Aa_ trans; B3, Auxin_resp; Mem_trans; B561; GH3; and LRR domain. The study on candidate proteincoding genes relating to auxin is important for elucidating protein functions involved in various cellular processes, growth, development and climate change adaptation of C. canephora.




Article Details

Chuyên mục
Khoa học Tự nhiên & Công nghệ
Tiểu sử Tác giả

Nguyễn Đình Sỹ

Khoa Khoa học Tự nhiên và Công nghệ, Trường Đại học Tây Nguyên;
Tác giả liên hệ: Nguyễn Đình Sỹ; Tel: 0961367958; Email: ndsy@ttn.edu.vn.

Tài liệu tham khảo

  • Abel S, Nguyen MD, Theologis A. (1995). The PS-IAA4/5-like family of early auxin-inducible mRNAs in Arabidopsis thaliana. J Mol Biol. 1995 Aug 25;251(4):533-49. doi: 10.1006/jmbi.1995.0454. PMID: 7658471
  • Albuquerque, É. V. S. et al. (2015) 'Seed-Specific Stable Expression of the α-AI1 Inhibitor in Coffee Grains and the In Vivo Implications for the Development of the Coffee Berry Borer', Tropical Plant Biology, 8(3–4), pp. 98–107. doi: 10.1007/s12042-015-9153-0.
  • Barbosa, A. E. A. D. et al. (2010) 'α-Amylase inhibitor-1 gene from Phaseolus vulgaris expressed in Coffea arabica plants inhibits α-amylases from the coffee berry borer pest', BMC Biotechnology, 10(May 2014). doi: 10.1186/1472-6750-10-44.
  • Blakeslee JJ, Peer WA, Murphy AS. (2005). Auxin transport. Curr Opin Plant Biol. 2005 Oct;8(5):494-500. doi: 10.1016/j.pbi.2005.07.014. PMID: 16054428.
  • Bohren KM, Bullock B, Wermuth B, Gabbay KH. (1989). The aldo-keto reductase superfamily. cDNAs and deduced amino acid sequences of human aldehyde and aldose reductases. J Biol Chem. 1989 Jun 5;264(16):9547-51. PMID: 2498333.
  • Borhani DW, Harter TM, Petrash JM. (1992). The crystal structure of the aldose reductase.NADPH binary complex. J Biol Chem. 1992 Dec 5;267(34):24841-7. doi: 10.2210/pdb1abn/pdb. PMID: 1447221).
  • Bulgarelli, R. G. et al. (2016) 'Expression of metallothionein genes in coffee leaves in response to the absence or excess of Cu and Zn', Theoretical and Experimental Plant Physiology. Springer International Publishing, 28(4), pp. 371–383. doi: 10.1007/s40626-016-0075-5.
  • Denoeud, F. et al. (2014) 'The coffee genome provides insight into the convergent evolution of caffeine biosynthesis.', Science (New York, N.Y.), 345(6201), pp. 1181–1184. doi: 10.1126/ science.1255274.
  • Dinh, S. N. and Kang, H. (2017) 'An endoplasmic reticulum-localized Coffea arabica BURP domaincontaining protein affects the response of transgenic Arabidopsis plants to diverse abiotic stresses', Plant Cell Reports, 36(11), pp. 1829–1839. doi: 10.1007/s00299-017-2197-x.
  • Dunwell JM. (1998). Cupins: a new superfamily of functionally diverse proteins that include germins and plant storage proteins. Biotechnol Genet Eng Rev. 1998;15:1-32. doi: 10.1080/02648725.1998.10647950. PMID: 9573603.
  • Esteves Vieira, L. G. et al. (2006) 'Brazilian coffee genome project: An EST-based genomic resource', Brazilian Journal of Plant Physiology, 18(1), pp. 95–108. doi: 10.1590/S1677-04202006000100008.
  • Foreign Agricultural Service (FAS) (2024). https://fas.usda.gov/
  • Gil P, Green PJ. (1997). Regulatory activity exerted by the SAUR-AC1 promoter region in transgenic plants. Plant Mol Biol. 1997 Jul;34(5):803-8. doi: 10.1023/a:1005875300606. PMID: 9278170.
  • Gulbis JM, Zhou M, Mann S, MacKinnon R. (2000). Structure of the cytoplasmic beta subunit-T1 assembly of voltage-dependent K+ channels. Science. 2000 Jul 7;289(5476):123-7. doi: 10.1126/ science.289.5476.123. PMID: 10884227.
  • Hagen G, Guilfoyle TJ. (1985). Rapid induction of selective transcription by auxins. Mol Cell Biol. 1985 Jun;5(6):1197-203. doi: 10.1128/mcb.5.6.1197-1203.1985. PMID: 4041007; PMCID: PMC366846.
  • Jack DL, Yang NM, Saier MH Jr. The drug/metabolite transporter superfamily. Eur J Biochem. 2001 Jul; 268(13):3620-39. doi: 10.1046/j.1432-1327.2001.02265.x. PMID: 11432728
  • Kagaya Y, Ohmiya K, Hattori T. RAV1, a novel DNA-binding protein, binds to bipartite recognition sequence through two distinct DNA-binding domains uniquely found in higher plants. Nucleic Acids Res. 1999 Jan 15;27(2):470-8. doi: 10.1093/nar/27.2.470. PMID: 9862967; PMCID: PMC148202.).
  • Kramer EM. PIN and AUX/LAX proteins: their role in auxin accumulation. Trends Plant Sci. 2004 Dec;9(12):578-82. doi: 10.1016/j.tplants.2004.10.010. PMID: 15564124.).
  • Liscum E, Reed JW. Genetics of Aux/IAA and ARF action in plant growth and development. Plant Mol Biol. 2002 Jun-Jul;49(3-4):387-400. PMID: 12036262.
  • McCarthy, A. A. et al. (2007) 'Cloning, expression, crystallization and preliminary X-ray analysis of the XMT and DXMT N-methyltransferases from Coffea canephora (robusta)', Acta Crystallographica Section F: Structural Biology and Crystallization Communications. International Union of Crystallography, 63(4), pp. 304–307. doi: 10.1107/S1744309107009268.
  • McClure BA, Guilfoyle T. Characterization of a class of small auxin-inducible soybean polyadenylated RNAs. Plant Mol Biol. 1987 Nov;9(6):611-23. doi: 10.1007/BF00020537. PMID: 24277197
  • McIntire SL, Reimer RJ, Schuske K, Edwards RH, Jorgensen EM. Identification and characterization of the vesicular GABA transporter. Nature. 1997 Oct 23;389(6653):870-6. doi: 10.1038/39908. PMID: 9349821.
  • Mishra, M. K. and Slater, A. (2012) 'Recent Advances in the Genetic Transformation of Coffee', Biotechnology Research International, 2012, pp. 1–17. doi: 10.1155/2012/580857.
  • Nguyen Dinh, S. et al. (2016) 'Abiotic stresses affect differently the intron splicing and expression of chloroplast genes in coffee plants (Coffea arabica) and rice (Oryza sativa)', Journal of Plant Physiology. Elsevier GmbH., 201, pp. 85–94. doi: 10.1016/j.jplph.2016.07.004.
  • Okrent RA, Brooks MD, Wildermuth MC. Arabidopsis GH3.12 (PBS3) conjugates amino acids to 4-substituted benzoates and is inhibited by salicylate. J Biol Chem. 2009 Apr 10;284(15):9742-54. doi: 10.1074/jbc.M806662200. Epub 2009 Feb 2. PMID: 19189963; PMCID: PMC2665095.
  • Pallavicini, A. et al. (2005) Transcriptomics of resistance response in Coffea arabica L.
  • Perrois, C. et al. (2015) 'Differential regulation of caffeine metabolism in Coffea arabica (Arabica) and Coffea canephora (Robusta)', Planta, 241(1), pp. 179–191. doi: 10.1007/s00425-014-2170-7.
  • Privat, I. et al. (2011) 'The "PUCE CAFE" Project: The First 15K Coffee Microarray, a New Tool for Discovering Candidate Genes correlated to Agronomic and Quality Traits', BMC Genomics, 12. doi: 10.1186/1471-2164-12-5.
  • Rae GM, Uversky VN, David K, Wood M. DRM1 and DRM2 expression regulation: potential role of splice variants in response to stress and environmental factors in Arabidopsis. Mol Genet Genomics. 2014 Jun;289(3):317-32. doi: 10.1007/s00438-013-0804-2. Epub 2014 Jan 18. PMID: 24442277.
  • Raharimalala, N. et al. (2021) 'The absence of the caffeine synthase gene is involved in the naturally decaffeinated status of Coffea humblotiana, a wild species from Comoro archipelago', Scientific Reports. Nature Publishing Group UK, 11(1), pp. 1–14. doi: 10.1038/s41598-021-87419-0.
  • Schade SZ, Early SL, Williams TR, Kézdy FJ, Heinrikson RL, Grimshaw CE, Doughty CC. Sequence analysis of bovine lens aldose reductase. J Biol Chem. 1990 Mar 5;265(7):3628-35. PMID: 2105951.
  • Spartz AK, Ren H, Park MY, Grandt KN, Lee SH, Murphy AS, Sussman MR, Overvoorde PJ, Gray WM. SAUR Inhibition of PP2C-D Phosphatases Activates Plasma Membrane H+-ATPases to Promote Cell Expansion in Arabidopsis. Plant Cell. 2014 May;26(5):2129-2142. doi: 10.1105/ tpc.114.126037. Epub 2014 May 23. PMID: 24858935; PMCID: PMC4079373.
  • Stafstrom JP, Ripley BD, Devitt ML, Drake B. Dormancy-associated gene expression in pea axillary buds. Cloning and expression of PsDRM1 and PsDRM2. Planta. 1998 Aug;205(4):547-52. doi: 10.1007/s004250050354. PMID: 9684359.
  • Staswick PE, Serban B, Rowe M, Tiryaki I, Maldonado MT, Maldonado MC, Suza W. Characterization of an Arabidopsis enzyme family that conjugates amino acids to indole-3-acetic acid. Plant Cell. 2005 Feb;17(2):616-27. doi: 10.1105/tpc.104.026690. Epub 2005 Jan 19. PMID: 15659623; PMCID: PMC548830.
  • Torres, L. F. et al. (2019) 'Expression of DREB-Like Genes in Coffea canephora and C. arabica Subjected to Various Types of Abiotic Stress', Tropical Plant Biology, 12(2), pp. 98–116. doi: 10.1007/s12042-019-09223-5.
  • Vadivelu, J. (2013) 'Microbial Pathogens and Strategies for Combating them: Science, Technology and Education', in.
  • Verelst W, Asard H. A phylogenetic study of cytochrome b561 proteins. Genome Biol. 2003;4(6):R38. doi: 10.1186/gb-2003-4-6-r38. Epub 2003 May 28. PMID: 12801412; PMCID: PMC193617.
  • Wakuta S, Suzuki E, Saburi W, Matsuura H, Nabeta K, Imai R, Matsui H. OsJAR1 and OsJAR2 are jasmonyl-L-isoleucine synthases involved in wound- and pathogen-induced jasmonic acid signalling. Biochem Biophys Res Commun. 2011 Jun 17;409(4):634-9. doi: 10.1016/j. bbrc.2011.05.055. Epub 2011 May 17. PMID: 21619871.
  • Wilson DK, Bohren KM, Gabbay KH, Quiocho FA. An unlikely sugar substrate site in the 1.65 A structure of the human aldose reductase holoenzyme implicated in diabetic complications. Science. 1992 Jul 3;257(5066):81-4. doi: 10.1126/science.1621098. PMID: 1621098