|本期目录/Table of Contents|

[1]赵怡娇,唐为玲,李尊文,等.芥蓝AOP基因家族生物信息学分析[J].应用与环境生物学报,2021,27(06):1653-1661.[doi:10.19675/j.cnki.1006-687x.2020.07017]
　ZHAO Yijiao,TANG Weiling,LI Zunwen,et al.Bioinformatics analysis of the AOP gene family in Chinese kale[J].Chinese Journal of Applied & Environmental Biology,2021,27(06):1653-1661.[doi:10.19675/j.cnki.1006-687x.2020.07017]
点击复制

芥蓝AOP基因家族生物信息学分析()
分享到：

《应用与环境生物学报》[ISSN:1006-687X/CN:51-1482/Q]

卷:
27卷
期数:
2021年06期
页码:
1653-1661
栏目:
研究论文
出版日期:
2021-12-25

文章信息/Info

Title:
Bioinformatics analysis of the AOP gene family in Chinese kale
作者:
赵怡娇; 唐为玲; 李尊文; 赖钟雄; 郭容芳
1福建农林大学园艺植物生物工程研究所 福州 350002 2福建农林大学戴尔豪西大学联合实验室 福州 350002
Author(s):
ZHAO Yijiao1;  TANG Weiling1;  LI Zunwen1;  LAI Zhongxiong1 & GUO Rongfang1;  2?
1Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou 350002, China 2Joint FAFU-Dalhousie Lab, Fujian Agriculture and Forestry University, Fuzhou 350002, China
关键词:
芥蓝; AOP基因家族; 成员鉴定; 功能分析
Keywords:
Brassica alboglabra;  AOP gene family;  member identification;  functional analysis
DOI:
10.19675/j.cnki.1006-687x.2020.07017
摘要:
芥子油苷（GS）是一类植物次生代谢产物，其多样性是由特定氨基酸前体延伸和侧链修饰所致. 在侧链修饰过程中，AOP2和AOP3被证明可催化甲基亚磺酰基烷基GS分别形成烯基和羟烷基GS. 为了解芥蓝（Brassica alboglabra）AOP基因家族成员编码2-氧化戊二酸双加氧酶的生物学功能，利用鉴定的家族成员进行蛋白质理化性质、蛋白质保守结构、基因结构、染色体定位、共线性关系、系统进化树、启动子顺式作用元件以及编码蛋白互作预测的生物信息学分析. 结果显示芥蓝中有17个AOP基因家族成员，蛋白质分子量为34 106.15 - 51 346.77，属酸性非分泌蛋白质，分布在6条染色体上；系统进化树分析结果显示AOP基因家族可分为两大类；成员均包含DIOX_N和FE2OG_OXY结构域，Motif相对保守；成员启动子可能有多个转录起始位点，包含非生物胁迫应激响应元件及MYB结合位点，推测MYB可能通过调控AOP进而调控芥蓝GS代谢；AOP基因家族编码蛋白间不互作，与MYB、NDUF等蛋白互作；AOP家族成员间有3对共线性关系，与拟南芥基因组和芜菁基因组之间分别存在9对、20对共线性关系. 本研究表明芥蓝17个AOP基因家族成员在功能上存在差异，且该家族成员参与光、多种激素信号和MYB转录因子复杂的调控网络，结果可为今后人工调控芥蓝GS组分和含量提供理论依据. （图7 表1 参50）
Abstract:
Glucosinolates (GS) are a class of plant secondary metabolites whose diversity is driven by the elongation of specific amino acid precursors and side chain modifications. In the process of side chain modification, the AOP2 and AOP3 genes have been shown to catalyze the formation of alkenyl and hydroxyalkyl GS from methylsulfinyl alkyl GS, respectively. In this study, we aimed to use bioinformatics analysis to identify members of the AOP gene family in Chinese kale (Brassica alboglabra) and to understand the biological functions of 2-oxoglutarate dioxygenase encoded by members of the AOP gene family in Chinese kale. Bioinformatics analysis of protein physicochemical properties, protein conservative structure, gene structure, chromosomal localization, collinear relationships, phylogenetic trees, cis-acting promoter elements, and protein coding interactions were performed using the identified AOP gene family members. The results revealed 17 AOP genes in Chinese kale. The proteins, which were acidic, non-secreted proteins, were distributed on six chromosomes and had molecular weights ranging from 34 106.15 to 51 346.77. The phylogenetic tree analysis revealed that the genes could be divided into two subcategories, and all members contained the DIOX_N and FE2OG_OXY domains, with relatively conservative motifs. We suggest that the gene member promoter sequences may contain multiple transcription start sites, including abiotic stress response elements and MYB binding sites, and we hypothesize that MYB may change GS metabolism by regulating AOP. No interaction effects among AOP gene family encoding proteins were found; however, interaction effects between them and other proteins were found, namely MYB, NDUF, etc. Three pairs of collinearity were found among the AOP gene family members, while nine and 20 pairs of collinearity were found with the Arabidopsis and turnip genome, respectively. Ultimately, we show that functional differences are found among the 17 AOP gene family members in Chinese kale. In addition, the members of this gene family were shown to play a role in a complex regulatory network of light, multiple hormone signaling, and MYB transcription factors, which provides a theoretical basis for the artificial regulation of GS components and content of Chinese kale in the future.

参考文献/References:

1 Pfalz M, Mukhaimar M, Perreau F, Kirk J, Hansen CIC, Olsen CE, Agerbirk N, Kroymann J. Methyl transfer in glucosinolate biosynthesis mediated by indole glucosinolate O-methyltransferase 5 [J]. Plant Physiol, 2016, 172 (4): 2190-2203
2 Halkier BA, Gershenzon J. Biology and biochemistry of glucosinolates [J]. Annu Rev Plant biol, 2006, 57 (1): 303-333
3 Bla?evi? I, Montaut S, Bur?ul F, Olsen CE, Burow M, Rollin P, Agerbirk N. Glucosinolate structural diversity, identification, chemical synthesis and metabolism in plants [J]. Phytochemistry, 2020, 169: 112100
4 Fahey JW, Zhang YS, Talalay P. Broccoli sprouts: an exceptionally rich source of inducers of enzymes that protect against chemical carcinogens [J]. PNAS, 1997, 94 (19): 10367-10372
5 Wang JS, Yu HF, Zhao ZQ, Sheng XG, Shen Y, Gu, H. Natural variation of glucosinolates and their breakdown products in broccoli (Brassica oleracea var. italica) seeds [J]. J Agric Food Chem, 2019, 67 (45): 12528-12537
6 Zhang YY, Huai DX, Yang QY, Cheng Y, Ma M, Kliebenstein DJ, Zhou Y. Overexpression of three glucosinolate biosynthesis genes in Brassica napus identifies enhanced resistance to Sclerotinia sclerotiorum and Botrytis cinerea [J]. PLoS ONE, 2015, 10 (10): e140491
7 Sharma M, Mukhopadhyay A, Gupta V, Pental D, Pradhan AK. BjuB. CYP79F1 regulates synthesis of propyl fraction of aliphatic glucosinolates in oilseed mustard Brassica juncea: functional validation through genetic and transgenic approaches [J]. PLoS One, 2016, 11 (2): e150060
8 Ishida M, Hara M, Fukino N, Kakizaki T, Morimitsu Y. Glucosinolate metabolism, functionality and breeding for the improvement of Brassicaceae vegetables [J]. Breeding Sci, 2014, 64 (1): 48-59
9 Neal CS, Fredericks DP, Griffiths CA, Neale AD. The characterisation of AOP2: a gene associated with the biosynthesis of aliphatic alkenyl glucosinolates in Arabidopsis thaliana [J]. BMC Plant Biol, 2010, 10 (1): 170
10 Wang H, Wu J, Sun SL, Liu B, Cheng F, Sun RF, Wang XW. Glucosinolate biosynthetic genes in Brassica rapa [J]. Gene, 2011, 487 (2): 135-142
11 Augustine R, Bisht NC. Biofortification of oilseed Brassica juncea with the anti-cancer compound glucoraphanin by suppressing GSL-ALK gene family [J]. Sci Rep, 2015, 5 (1): 18005
12 刘志远, 张冀芳, 武剑, 梁建丽, 王晓武. 大白菜BrAOP2基因的遗传多样性及其与硫甙含量的相关性分析[J]. 中国蔬菜, 2013 (16): 14-21 [Liu ZY, Zhang YF, W J, Liang JL, Wang XW. Genetic diversity of BrAOP2 and analysis of its correlation with glucosinolate content in Chinese cabbage [J]. Chin Veg, 2013 (16): 14-21]
13 Guo RF, Huang ZK, Deng YP, Chen XD, XuHan X, Lai ZX. Comparative transcriptome analyses reveal a special glucosinolate metabolism mechanism in Brassica alboglabra sprouts [J]. Front Plant Sci, 2016, 7: 1497
14 Guo RF, Chen XD, Lin YL, XuHan X, Thu MK Lai ZX. Identification of novel and conserved miRNAs in leaves of in vitro grown Citrus reticulata “Lugan” plantlets by solexa sequencing [J]. Front Plant Sci, 2016, 6: 1212
15 Lei JJ, Chen GJ, Chen CM, Cao BH. Germplasm diversity of Chinese kale in China [J]. Hortic Plant J, 2017, 3 (3): 101-104
16 Guo RF, Wang XR, Han XY, Li WJ, Chen BX, Chen XD, Wang-Pruski G. Comparative transcriptome analyses revealed different heat stress responses in high- and low-GS Brassica alboglabra sprouts [J]. BMC Genomics, 2019, 20 (1): 269
17 Guo RF, Shen WS, Qian HM, Zhang M, Liu LH, Wang QM. Jasmonic acid and glucose synergistically modulate the accumulation of glucosinolates in Arabidopsis thaliana [J]. J Exp Bot, 2013, 64 (18): 5707-5719
18 Qian HM, Liu TY, Deng MD, Miao HY, Cai CX, Shen WS, Wang QM. Effects of light quality on main health-promoting compounds and antioxidant capacity of Chinese kale sprouts [J]. Food Chem, 2016, 196: 1232-1238
19 Gasteiger E, Gattiker A, Hoogland C, Lvanyi I, Appel RD, Bairoch A. ExPASy: the proteomics server for in-depth protein knowledge and analysis [J]. Nucleic Acids Res, 2003, 31 (13): 3784-3788
20 Hu B, Jin JP, Guo AY, Zhang H, Luo JC, Gao G. GSDS 2.0: an upgraded gene feature visualization server [J]. Bioinformatics, 2015, 31 (8): 1296-1297
21 Bailey TL, Boden M, Buske FA, Frith M,Grant CE, Clementi L, Ren JY, Li WW, Noble WS. MEME SUITE: tools for motif discovery and searching [J]. Nucleic Acids Res, 2009, 37 (Web server issue): W202-W208
22 Chen CJ, Chen H, Zhang Y, Thomas HR, Frank MH, He YH, Xia R. TBtools-an integrative toolkit developed for interactive analyses of big biological data [J]. Mol Plant, 2020, 13: 1194-1202
23 Wang YP, Tang HB, Debarry JD, Tan X, Li JP, Wang XY, Lee TH, Jin HZ, Marler B, Guo H. MCScanX: a toolkit for detection and evolutionary analysis of gene synteny and collinearity [J]. Nucleic Acids Res, 2012, 40 (7): e49
24 Kumar S, Stecher G, Tamura K. MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets [J]. Mol Biol Evol, 2016, 33 (7): 1870-1874
25 Pertea M, Pertea GM, Antonescu CM, Chang TC, Mendell JT, Salzberg SL. StringTie enables improved reconstruction of a transcriptome from RNA-seq reads [J]. Nat Biotechnol, 2015, 33 (3): 290-295
26 Liu SY, Liu YM, Yang XH, Tong CB, Edwards D, Parkin IAP, Zhao MX, Ma JX, Yu JY, Huang SM, Wang XY, Wang JY, Lu K, Fang ZY, Bancroft I, Yang TJ, Hu Q, Wang XF, Yue Z, Li HJ, Yang LF, Wu J, Zhou Q, Wang WX, King GJ, Pires JC, Lu CX, Wu ZY, Sampath P, Wang Z, Guo H, Pan SK, Yang LM, Min JM, Zhang D, Jin DC, Li WS, Belcram H, Tu JX,Guan M, Qi CK, Du DZ, Li JN, Jiang LC, Batley J, Sharpe AG, Park BS, Ruperao P, Cheng F, Waminal NE, Huang Y, Dong C, Wang L, Li JP, Hu ZY, Zhuang M, Huang Y, Huang JY, Shi JQ, Mei DS, Liu J, Lee TH, Wang JP, Jin HZ, Li ZY, Li X, Zhang JF, Xiao L, Zhou YM, Liu ZS, Liu XQ, Qin R, Tang X, Liu WB, Wang YP, Zhang YY, Lee J, Kim HH, Denoeud F, Xu X, Liang XM, Hua W, Wang XW, Wang J, Chalhoub B, Paterson AH. The Brassica oleracea genome reveals the asymmetrical evolution of polyploid genomes [J]. Nat Commum, 2014, 5 (1): 3930
27 Xu Z, Song J. The 2-oxoglutarate-dependent dioxygenase superfamily participates in tanshinone production in Salvia miltiorrhiza [J]. J Exp Bot, 2017, 68 (9): 2299-2308
28 徐小萍, 陈晓慧, 吕科良, 陈旭, 陈裕坤, 林玉玲, 赖钟雄. 龙眼漆酶家族成员全基因组结构与功能分析[J]. 应用与环境生物学报, 2018, 24 (4): 833-844 [X XP, Chen XH, Lv KL, Chen X, Chen YK, Lin YL, Lai ZX. Genome-wide identification and function analysis of the Laccase gene family in Dimocarpus longan Lour. [J]. Chin J Appl Environ Biol, 2018, 24 (4): 833-844]
29 Landis JB, Soltis DE, Li Z, Marx HE, Barker MS, Tank DC, Soltis PS. Impact of whole-genome duplication events on diversification rates in angiosperms [J]. Am J Bot, 2018, 105 (3): 348-363
30 Zhang JF, Liu ZY, Liang JL, Wu J, Cheng F, Wang XW. Three genes encoding AOP2, a protein involved in aliphatic glucosinolate biosynthesis, are differentially expressed in Brassica rapa [J]. J Exp Bot, 2015, 66 (20): 6205-6218
31 Jensen LM, Jepsen HS, Halkier BA, Kliebenstein DJ, Burow M. Natural variation in cross-talk between glucosinolates and onset of flowering in Arabidopsis [J]. Front Plant Sci, 2015, 6: 697
32 Kong WW, Li J, Yu QY, Cang W, Xu R, Wang Y, Ji W. Two novel flavin-containing monooxygenases involved in biosynthesis of aliphatic glucosinolates [J]. Front Plant Sci, 2016, 7: 1292
33 Brachi B, Meyer CG, Villoutreix R, Platt A, Morton TC, Roux F, Bergelson J. Coselected genes determine adaptive variation in herbivore resistance throughout the native range of Arabidopsis thaliana [J]. PNAS, 2015, 112 (13): 4032-4037
34 S?nderby IE, Geu-Flores F, Halkier BA. Biosynthesis of glucosinolates-gene discovery and beyond [J]. Trends Plant Sci, 2010, 15 (5): 283-290
35 Chan EKF, Rowe HC, Kliebenstein DJ. Understanding the evolution of defense metabolites in Arabidopsis thaliana using genome-wide association mapping [J]. Genetics, 2010, 185 (3): 991-1007
36 Kliebenstein DJ, Lambrix VM, Reichelt M, Gershenzon J, Mitchell-Olds M. Gene duplication in the diversification of secondary metabolism: tandem 2-oxoglutarate-dependent dioxygenases control glucosinolate biosynthesis in Arabidopsis [J]. Plant Cell, 2001, 13 (3): 681-693
37 Li G, Quiros CF. In planta side-chain glucosinolate modification in Arabidopsis by introduction of dioxygenase Brassica homolog BoGSL-ALK [J]. Theor Appl Genet, 2003, 106 (6): 1116-1121
38 Liu Z, Hirani AH, Mcvetty PBE, Dassyf F, Quiros CF, Li G. Reducing progoitrin and enriching glucoraphanin in Braasica napus seeds through silencing of the GSL-ALK gene family [J]. Plant Mol Biol, 2012, 79 (1): 179-189
39 Moreira-Rodriguez M, Nair V, Benavides J, Cisneros-Zevallos, Jacobo-Velazquez DA. UVA, UVB light, and methyl jasmonate, alone or combined, redirect the biosynthesis of glucosinolates, phenolics, carotenoids, and chlorophylls in broccoli sprouts [J]. Int J Mol Sci, 2017, 18 (11):
40 Araújo WL, Martins AO, Fernie AR, Tohge T. 2-Oxoglutarate: linking TCA cycle function with amino acid, glucosinolate, flavonoid, alkaloid, and gibberellin biosynthesis [J]. Front Plant Sci, 2014, 5: 552
41 黄忠凯. 光周期对芥蓝生长发育的影响及相关基因的表达分析[D]. 福州: 福建农林大学, 2017 [Huang ZK. Effecys of photoperiod on the growth and development of Chinese kale and analysis of related genes [D]. Fuzhou: Fujian Agriculture and Forestry University, 2017]
42 Wang QY, Chen XL, Chai XF, Xue DQ, Zheng W, Shi YY, Wang A. The involvement of jasmonic acid, ethylene, and salicylic acid in the signaling pathway of Clonostachys rosea-induced resistance to gray mold disease in tomato [J]. Phytopathology, 2019, 109 (7): 1102-1114
43 郭容芳. 化学调控对十字花科植物中芥子油苷代谢的影响及其机理[D]. 杭州: 浙江大学, 2013 [Guo RF. Effect of chemical regulations on glucosinolate metabolism and its possible mechanism in cruciferae plants [D]. Hangzhou: Zhejiang University, 2013]
44 Burow M, Atwell S, Francisco M, Kerwin RE, Halkier BA, Kliebenstein DJ. The glucosinolate biosynthetic gene AOP2 mediates feed-back regulation of jasmonic acid signaling in Arabidopsis [J]. Mol Plant, 2015, 8 (8): 1201-1212
45 Frerigmann H, Gigolashvili T. MYB34, MYB51, and MYB122 distinctly regulate indolic glucosinolate biosynthesis in Arabidopsis thaliana [J]. Mol Plant, 2014, 7 (5): 814-828
46 Yin L, Chen HC, Cao BH, Lei JJ, Chen GJ. Molecular characterization of MYB28 involved in aliphatic glucosinolate biosynthesis in Chinese kale (Brassica oleracea var. alboglabra Bailey) [J]. Front Plant Sci, 2017, 8: 1083
47 Guo LP, Zhu YL, Wang FW. Calcium sulfate treatment enhances bioactive compounds and antioxidant capacity in broccoli sprouts during growth and storage [J]. Postharv Biol Technol, 2018, 139: 12-19
48 Zuluaga DL, Graham NS, Klinder A, van Ommen Kloeke AE, Marcotrigiano AR,Wagstaff C, Verkerk R, Sonnante G, Aarts MGM. Overexpression of the MYB29 transcription factor affects aliphatic glucosinolate synthesis in Brassica oleracea [J]. Plant Mol Biol, 2019, 101 (1-2): 65-79
49 Gigolashvili T, Yatusevich R, Berger B, Müller C, Flügge UI. The R2R3-MYB transcription factor HAG1/MYB28 is a regulator of methionine-derived glucosinolate biosynthesis in Arabidopsis thaliana [J]. Plant J, 2007, 51 (2): 247-261
50 Li BH, Gaudinier A, Tang M, Taylor-Teeples M, Nham NT, Ghaffari C, Benson DS, Steinmann M, Gray JA, Brady SM, Kliebenstein DJ. Promoter-based integration in plant defense regulation [J]. Plant Physiol, 2014, 166 (4): 1803-1820

相似文献/References:

[1]陈家璇,陈泽源,赵怡娇,等.芥蓝MAM基因家族成员鉴定、分析及表达[J].应用与环境生物学报,2022,28(02):491.[doi:10.19675/j.cnki.1006-687x.2020.11023]
　CHEN Jiaxuan,CHEN Zeyuan,ZHAO Yijiao,et al.Bioinformatics analysis of MAM gene family in Chinese kale[J].Chinese Journal of Applied & Environmental Biology,2022,28(06):491.[doi:10.19675/j.cnki.1006-687x.2020.11023]

更新日期/Last Update: 2021-12-25