Abstract

Info

Title:: Evolution Analysis of Abhydrolase_3 Gene Family in Soybean

Author(s):: WANG Jiao; ZHANG Pei-pei; CHENG Hao; YU De-yue; (Soybean Research Institute /National Center for Soybean Improvement/National Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China)

Keywords:: Soybean; Abhydrolase_3 gene family; Evolution; Function; Gene duplication

PACS:: -

DOI:: 10.11861/j.issn.1000-9841.2017.06.0842

Abstract:: Isoflavonoids are important secondary metabolites of soybean and involved in the interactions with pathogens. 2-hydroxyisoflavanone-dehydratase (HID) catalyzes the dehydration of 2-hydroxyisoflavanones to the formation of stable isoflavonoids. HID belongs to the Abhydrolase_3 gene family, which is involved in plenty of functions. To study the evolutionary patterns of Abhydrolase_3 gene family in soybean, 62 Abhydrolase_3 genes were identified from soybean genome. Tandem and segmental duplications are the primary duplicated patterns of this gene family. Based on the phylogenetic relationships, eight subfamilies were classified. Subfamily I contains the largest number of genes, in which several times of gene duplications occur. Genes in different subfamilies were characterized by distinct patterns of motif combinations. Genetic polymorphic analysis showed homologous genes in subfamilies I, III and V possess a higher level of nucleotide diversity, and experience a relaxed selection pressure. The expression analysis showed that genes in most subfamilies except II and IV show high levels of expression in different tissues, and the expression levels of genes in subfamilies I, III, IV, V and VI were induced by pathogens. The results showed that gene expansion and functional divergence exist in subfamily I, which contains HID, and that genes involved in the interaction with pathogens possess higher levels of genetic diversity and the expressions are induced by pathogens.

References:

［1］Pueppke S G. The genetic and biochemical basis for nodulation of legumes by rhizobia［J］. Critical Reviews in Biotechnology, 1996, 16(1):1-51.

［2］Dixon R A. Natural products and plant disease resistance［J］. Nature, 2001, 411(6839):843-847.

［3］Jung W, Yu O, Lau S M, et al. Identification and expression of isoflavone synthase, the key enzyme for biosynthesis of isoflavones in legumes［J］. Nature Biotechnology, 2000, 18(2):208-212.

［4］Akashi T, Aoki T, Ayabe S. Molecular and biochemical characterization of 2-hydroxyisoflavanone dehydratase. Involvement of carboxylesteraselike proteins in leguminous isoflavone biosynthesis［J］. Plant Physiology, 2005, 137(3):882-891.

［5］Lenfant N, Hotelier T, Velluet E, et al. ESTHER, the database of the alpha/beta-hydrolase fold superfamily of proteins: Tools to explore diversity of functions［J］. Nucleic Acids Research, 2013, 41(Database issue):D423-429.

［6］Ollis D L, Cheah E, Cygler M, et al. The alpha/beta hydrolase fold［J］. Protein Engineering, 1992, 5(3):197-211.

［7］Marshall S D, Putterill J J, Plummer K M, et al. The carboxylesterase gene family from Arabidopsis thaliana［J］. Journal of Molecular Evolution, 2003, 57(5):487-500.

［8］Nomura T, Murase T, Ogita S et al. Molecular identification of tuliposide B-converting enzyme: A lactone-forming carboxylesterase from the pollen of tulip［J］. The Plant Journal, 2015, 83(2):252-262.

［9］Lee S, Hwang S, Seo Y W, et al. Molecular characterization of the AtCXE8 gene, which promotes resistance to Botrytis cinerea-infection［J］. Plant Biotechnology Reports, 2012, 7(1):109-119.

［10］Gershater M C, Cummins I, Edwards R. Role of a carboxylesterase in herbicide bioactivation in Arabidopsis thaliana［J］. The Journal of Biological Chemistry, 2007, 282(29):21460-21466.

［11］Cummins I, Landrum M, Steel P G, et al. Structure activity studies with exnobiotic substrates using carboxylesterases isolated from Arabidopsis thaliana［J］. Phytochemistry, 2007, 68(6):811-818.

［12］Baudouin E, Charpenteau M, Roby D, et al. Functional expression of a tobacco gene related to the serine hydrolase family-esterase activity towards short-chain dinitrophenyl acylesters［J］. European Journal of Biochemistry, 1997, 248(3):700-706.

［13］Ko M K, Jeon W B, Kim K S, et al. A .Colletotrichum gloeosporioides-induced esterase gene of nonclimacteric pepper (Capsicum annuum) fruit during ripening plays a role in resistance against fungal infection［J］. Plant Molecular Biology, 2005, 58(4):529-541.

［14］Hirano K, Ueguchi-Tanaka M, Matsuoka M. GID1mediated gibberellin signaling in plants［J］. Trends in Plant Science, 2008, 13(4):192-199.

［15］Voegele A, Linkies A, Muller K, et al. Members of the gibberellin receptor gene family GID1 (GIBBERELLIN INSENSITIVE DWARF1) play distinct roles during Lepidium sativum and Arabidopsis thaliana seed germination［J］. Journal of Experimental Botany, 2011, 62(14):5131-5147.

［16］Huizinga D H, Omosegbon O, Omery B, et al. Isoprenylcysteine methylation and demethylation regulate abscisic acid signaling in Arabidopsis［J］. The Plant Cell, 2008, 20(10):2714-2728.

［17］Wang J, Chu S, Zhu Y, et al. Positive selection drives neofunctionalization of the UbiA prenyltransferase gene family［J］. Plant Molecular Biology, 2015, 87:383-394.

［18］Holub E B. The arms race is ancient history in Arabidopsis, the wildflower［J］. Nature Reviews Genetics, 2001, 2(7):516-527.

［19］Lee T H, Tang H, Wang X, et al. PGDD: A database of gene and genome duplication in plants［J］. Nucleic Acids Research, 2013, 41(Database issue):D1152-1158.

［20］Tamura K, Stecher G, Peterson D, et al. MEGA6: Molecular Evolutionary Genetics Analysis Version 6.0［J］. Molecular Biology and Evolution, 2013, 30(12):2725-2729.

［21］Thompson J D, Higgins D G, Gibson T J. CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, positionspecific gap penalties and weight matrix choice［J］. Nucleic Acids Research, 1994, 22(22):4673-4680.

［22］Lynch M, Crease T J. The analysis of population survey data on DNA sequence variation［J］. Molecular Biology and Evolution, 1990, 7(4):377-394.

［23］Nei M, Gojobori T. Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions［J］. Molecular Biology and Evolution, 1986, 3(5):418-426.

［24］Bailey T L, Boden M, Buske F A, et al. MEME SUITE: Tools for motif discovery and searching［J］. Nucleic Acids Research, 2009, 37(Web Server issue):W202-208.

［25］van de Mortel M, Recknor J C, Graham M A, et al. Distinct biphasic mRNA changes in response to Asian soybean rust infection［J］. Molecular Plant-microbe Interactions, 2007, 20(8):887-899.

［26］Wang Q, Wang J, Yang Y, et al. A genome-wide expression profile analysis reveals active genes and pathways coping with phosphate starvation in soybean［J］. BMC Genomics, 2016, 17(1):192.

［27］Schmutz J, Cannon S B, Schlueter J, et al. Genome sequence of the palaeopolyploid soybean［J］. Nature, 2010, 463(7278):178-183.

［28］Lan P, Li W, Wang H, et al. Characterization, sub-cellular localization and expression profiling of the isoprenylcysteine methylesterase gene family in Arabidopsis thaliana［J］. BMC Plant Biology, 2010, 10:212.

［29］Gershater M C, Edwards R. Regulating biological activity in plants with carboxylesterases［J］. Plant Science, 2007, 173(6):579-588.

［30］Nakajima M, Shimada A, Takashi Y, et al. Identification and characterization of Arabidopsis gibberellin receptors［J］. The Plant Journal, 2006, 46(5):880-889.

［31］Ueguchi-Tanaka M, Ashikari M, Nakajima M, et al. GIBBERELLIN INSENSITIVE DWARF1 encodes a soluble receptor for gibberellin［J］. Nature, 2005, 437(7059):693-698.

［32］Hirano K, Aya K, Matsuoka M, et al. Molecular determinants that convert hormone sensitive lipase into gibberellin receptor［J］. Protein and Peptide Letters, 2012, 19(2):180-185.

Evolution Analysis of Abhydrolase_3 Gene Family in Soybean(PDF)

《大豆科学》[ISSN:1000-9841/CN:23-1227/S]

Info

References:

Memo

Common functions

Navigate

Tools

Statistics