植物中微型反向重复转座元件(MITEs)研究进展及其在作物遗传研究中的应用

doi:10.11924/j.issn.1000-6850.casb16080112

摘要/Abstract

摘要： MITEs(Miniature Inverted-repeat Transposable Elements),是最近发现的几乎在所有生物基因组中广泛分布的一类非自主型DNA转座元件,具有典型的TIR(Terminal Invert Repeat)和TSD(Target Sequence Duplication)结构,长度较短。MITEs主要分布在常染色质区,并有大量的拷贝分布在基因编码区附近。MITEs可能来源于自主转座元件的内部缺失；转座酶通过对TIR的识别和结合,激活MITEs的转录活性,使其在基因组中进行扩增。MITEs在基因组中不同的分布模式,使物种中形成了大量的遗传多态性,为自然选择或驯化提供了基础,对基因的表达模式也有重要的影响。随着研究的深入,逐渐揭示出MTIEs与农艺性状间的联系,MITEs在作物遗传研究和育种中的应用价值也逐渐体现。本文对以上内容做了简单的综述,并对进一步的研究做出展望。

关键词: 青贮玉米, 青贮玉米, 不同器官, 产量, 品质

Abstract: MITE was first discovered in exon 11 of wx-B2 gene in the genome of Maize and be sorted to a novel non-autonomous DNA transposable elements which constitute a short DNA fragment (usually <600bp) with TIR and TSD. Since the TIRs complementing with each other, it tend to form a stem-loop in the secondary structure of MTEs. In the preliminary research stage, two super-families were mainly classified based on TSD sequences: Tourist-like (3-bp, TAA) and Stowaway-like (2-bp, TA). With explosion of genomic sequence inforamtion and development of analysis tools, later studies also find hAT-like (8bp TSD) and Mutator-like (9bp TSD) superfamilies. Subsequent researches reveal MITEs prevalence in almost all organism genomes, animals, plants and bacteria, ect. MITEs exist in genome with large amount of families and high copy numbers, and they become an important constituent of genomes.They distributed in genome widely, but not randomly, most copies prior to distribute in euchromatin regions and significant gene associated. Despite the short length limited proteins coding capacity of MITEs, part of their sequence can be transcript accompany with the neighboring genes. The novel transcripts deriving from MITEs provide sourse for new gene generation or serve as an alternative exon. Moreover, MITEs are the main contributor for siRNAs in plants, indicating the epigenetic regulation mechamism of MITEs induced gene expression. MITEs originate from internal deletion of autonomous transposable element, their activity and amplification induced by specific recognition and binding to the TIR region of transposase. Different profiles of MITEs insertion provide genetic diversity for natural selection and domestication. Recent results demonstrate that MITEs associated important agricultural traits through regulating the key genes expression about those traits. This paper mainly review progresses on the function and evolution of MITEs in recent years and propound perspective in crop genetic improvement.

中图分类号:

侯锦娜,刘永娟,安素妨,常丽,李保全. 植物中微型反向重复转座元件(MITEs)研究进展及其在作物遗传研究中的应用[J]. 中国农学通报, 2017, 33(26): 11-19.

李保全. Miniature Inverted-repeat Transposable Elements (MITEs) in Plants Applied in Crop Genetics Research[J]. Chinese Agricultural Science Bulletin, 2017, 33(26): 11-19.

参考文献

[1]Kazazian H H. Mobile DNA: Finding Treasure in Junk[M]. US,Financial Times Press, 2011.
[2]Parisod C,Alix K,Just J, et al. Impact of transposable elements on the organization and function of allopolyploid genomes[J].New Phytologist, 2010, 186(1):37-45.
[3]Rayan N A,Rosario R C H D,Prabhakar S. Massive contribution of transposable elements to mammalian regulatory sequences[M]. Seminars in Cell and Developmental Biology, 2016.
[4]Rebollo R,Romanish MT,Mager DL. Transposable elements: an abundant and natural source of regulatory sequences for host gene [J]. Annual Review of Genetics, 2012; 46:21-42.
[5]Rey O,Danchin E,Mirouze M, et al. Adaptation to Global Change: A Transposable Element-Epigenetics Perspective[J]. Trends in Ecology and Evolution, 2016, 31(7):514-526.
[6]Curcio MJ,Derbyshire KM. The outs and ins of transposition: from mu to kangaroo[J]. Nature Reviews Molecular Cell Biology, 2003, 4(11):865-877.
[7]Seberg O,Petersen G. A unified classification system for eukaryotic transposable elements should reflect their phylogeny[J]. Nature Reviews Genetics, 2009, 10(4):276.
[8]Wicker T,Sabot F,Hua-Van A, et al. A unified classification system for eukaryotic transposable elements[J]. Nature Reviews Genetics, 2007, 8(12):973-982.
[9]Bureau TE,Wessler SR. Tourist: a large family of small inverted repeat elements frequently associated with maize genes[J]. Plant Cell, 1992, 4(10):1283-1294.
[10]韩民锦. 家蚕MITE转座子的鉴定、进化和功能以及家蚕转座子的进化动力学研究[D].重庆：西南大学, 2013.
[11]Smit A F,Riggs A D. Tiggers and DNA transposon fossils in the human genome[J]. Proceedings of the National Academy of Sciences of the United States of America, 1996, 93(4):1443-8.
[12]Yeadon PJ,Catcheside DE. Guest: a 98 bp inverted repeat transposable element in Neurospora crassa[J]. Molecular and General Genetics, 1995, 247(1):105-109.
[13]Surzycki SA,Belknap WR. Characterization of repetitive DNA elements in Arabidopsis[J]. Journal of Molecular Evolution, 1999, 48(6):684-691.
[14]Garbus I,Romero J R,Valarik M, et al. Characterization of repetitive DNA landscape in wheat homeologous group 4 chromosomes[J]. BMC Genomics, 2015, 16(1):1-16.
[15]Lee S I,Kim N S. Transposable Elements and Genome Size Variations in Plants[J]. Genomics and Informatics, 2014, 12(3):87-97.
[16]Roffler S,Wicker T. Genome-wide comparison of Asian and African rice reveals high recent activity of DNA transposons[J]. Mobile DNA, 2015, 6(1):1-14.
[17]Bureau TE,Wessler SR. Stowaway: a new family of inverted repeat elements associated with the genes of both monocotyledonous and dicotyledonous plants[J]. Plant Cell, 1994, 6(6):907-916.
[18]Lu C,Chen J,Zhang Y, et al. Miniature inverted-repeat transposable elements (MITEs) have been accumulated through amplification bursts and play important roles in gene expression and species diversity in Oryza sativa[J]. Molecular Biology and Evolution, 2012, 29(3):1005-1017.
[19]Sampath P,Lee S C,Lee J, et al. Characterization of a new high copy Stowaway, family MITE, BRAMI -1 in Brassica, genome[J]. BMC Plant Biology, 2013, 13(2):1-13.
[20]Sampath P,Murukarthick J,Izzah NK, et al. Genome-wide comparative analysis of 20 miniature inverted-repeat transposable element families in Brassica rapa and B. oleracea[J]. PLoS One 2014, 9(4):e94499.
[21]Tu Z. Eight novel families of miniature inverted repeat transposable elements in the African malaria mosquito, Anopheles gambiae[J]. Proceedings of the National Academy of Sciences of the United States of America, 2001, 98(4):1699-1704.
[22]Chen Y,Zhou F,Li G, et al. MUST: a system for identification of miniature inverted-repeat transposable elements and applications to Anabaena variabilis and Haloquadratum walsbyi[J]. Gene, 2009, 436(1-2):1-7.
[23]Han Y,Wessler SR. MITE-Hunter: a program for discovering miniature inverted-repeat transposable elements from genomic sequences[J]. Nucleic Acids Research, 2010, 38(22):e199.
[24]Yang G. MITE Digger, an efficient and accurate algorithm for genome wide discovery of miniature inverted repeat transposable elements[J]. BMC Bioinformatics, 2013, 14:186.
[25]Tempel S,Giraud M,Lavenier D, et al. Domain organization within repeated DNA sequences: application to the study of a family of transposable elements[J]. Bioinformatics, 2006, 22(16):1948-1954.
[26]Waldmeier L,Hellmann I,Gutknecht CK, et al. Transpo-mAb display: Transposition-mediated B cell display and functional screening of full-length IgG antibody libraries[J]. MAbs, 2016, 8(4):726-740.
[27]Yang G,Hall TC. MAK, a computational tool kit for automated MITE analysis[J]. Nucleic Acids Research, 2003, 31(13):3659-3665.
[28]Ye C,Ji G,Liang C. detectMITE: A novel approach to detect miniature inverted repeat transposable elements in genomes[J]. Scientific Reports, 2016, 6:19688.
[29]Jurka J,Kapitonov VV,Pavlicek A, et al. Repbase Update, a database of eukaryotic repetitive elements[J]. Cytogenetics and Cell Genetics, 2005, 110(1-4):462-467.
[30]Chen J,Hu Q,Zhang Y, et al. P-MITE: a database for plant miniature inverted-repeat transposable elements[J]. Nucleic Acids Research, 2013, 42(Database issue):D1176-1181.
[31]Murukarthick J,Sampath P,Lee SC, et al. BrassicaTED — a public database for utilization of miniature transposable elements in Brassica species[J]. BMC Research Notes, 2014, 7:379.
[32]Hu TT, Pattyn P, Bakker EG, et al. The Arabidopsis lyrata genome sequence and the basis of rapid genome size change [J]. Nature Genetics, 2006, 43(5):476-481.
[33]Paterson AH, Bowers JE, Bruggmann R, et al. The Sorghum bicolor genome and the diversification of grasses[J]. Nature 2009, 457(7229):551-556.
[34]Santiago N, Herraiz C, Goni JR, et al. Genome-wide analysis of the Emigrant family of MITEs of Arabidopsis thaliana[J]. Molecular Biology and Evolution, 2002, 19(12):2285-2293.
[35]卢辰. 微小反向重复转座子(MITE)对水稻基因表达和基因组分化的作用及番茄特有miRNA基因的演化[D]. 武汉：华中农业大学,2013.
[36]Naito K, Monden Y, Yasuda K, et al. mPing: The bursting transposon [J]. Breeding Science, 2014, 64(2):109-114.
[37]Zerjal T, Joets J, Alix K, et al. Contrasting evolutionary patterns and target specificities among three Tourist-like MITE families in the maize genome [J]. Plant Molecular Biology, 2009, 71(1-2):99-114.
[38]Yaakov B, Ben-David S, Kashkush K. Genome-wide analysis of Stowaway-like MITEs in wheat reveals high sequence conservation, gene association, and genomic diversification [J]. Plant Physiology, 2012, 161(1):486-496.
[39]Macko-Podgorni A, Nowicka A, Grzebelus E, et al. DcSto: carrot Stowaway-like elements are abundant, diverse, and polymorphic [J]. Genetica, 2013, 141(4-6):255-267.
[40]Sarilar V, Marmagne A, Brabant P, et al. BraSto, a Stowaway MITE from Brassica: recently active copies preferentially accumulate in the gene space[J]. Plant Molecular Biology, 2011, 77(1-2):59-75.
[41]Shirasawa K, Hirakawa H, Tabata S, et al. Characterization of active miniature inverted-repeat transposable elements in the peanut genome [J]. Theoretical and Applied Genetics, 2012, 124(8):1429-1438.
[42]Benjak A, Boue S, Forneck A, et al. Recent amplification and impact of MITEs on the genome of grapevine (Vitis vinifera L.) [J]. Genome Biology and Evolution, 2009, 1:75-84.
[43]Dai S, Hou J, Long Y, et al. Widespread and evolutionary analysis of a MITE family Monkey King in Brassicaceae [J]. BMC Plant Biology, 2015, 15:149.
[44]Feschotte C, Mouches C. Evidence that a family of miniature inverted-repeat transposable elements (MITEs) from the Arabidopsis thaliana genome has arisen from a pogo-like DNA transposon [J]. Molecular Biology and Evolution, 2000, 17(5):730-737.
[45]Loot C, Santiago N, Sanz A, et al. The proteins encoded by the pogo-like Lemi1 element bind the TIRs and subterminal repeated motifs of the Arabidopsis Emigrant MITE: consequences for the transposition mechanism of MITEs [J]. Nucleic Acids Research, 2006, 34(18):5238-5246.
[46]Le QH, Wright S, Yu Z, et al. Transposon diversity in Arabidopsis thaliana [J]. Proceedings of the National Academy of Sciences of the United States of America, 2000, 97(13):7376-7381.
[47]Ade J, Belzile FJ. Hairpin elements, the first family of foldback transposons (FTs) in Arabidopsis thaliana [J]. Plant Journal, 1999, 19(5):591-597.
[48]Song WY, Pi LY, Bureau TE, et al. Identification and characterization of 14 transposon-like elements in the noncoding regions of members of the Xa21 family of disease resistance genes in rice [J]. Molecular Genetics and Genomics, 1998, 258(5):449-456.
[49]Jiang N, Bao Z, Zhang X, et al. An active DNA transposon family in rice [J]. Nature, 2003, 421(6919):163-167.
[50]Kikuchi K, Terauchi K, Wada M, et al. The plant MITE mPing is mobilized in anther culture [J]. Nature, 2003, 421(6919):167-170.
[51]Nakazaki T, Okumoto Y, Horibata A, et al. Mobilization of a transposon in the rice genome [J]. Nature, 2003, 421(6919):170-172.
[52]Naito K, Cho E, Yang G, et al. Dramatic amplification of a rice transposable element during recent domestication [J]. Proceedings of the National Academy of Sciences of the United States of America, 2006, 103(47):17620-17625.
[53]Jiang N, Feschotte C, Zhang X, et al. Using rice to understand the origin and amplification of miniature inverted repeat transposable elements (MITEs) [J]. Current Opinion in Plant Biology, 2004, 7(2):115-119.
[54]Teramoto S, Tsukiyama T, Okumoto Y, et al. Early embryogenesis-specific expression of the rice transposon Ping enhances amplification of the MITE mPing [J]. PLoS Genetics, 2014, 10(6):e1004396.
[55]Yang G, Nagel DH, Feschotte C, et al. Tuned for transposition: molecular determinants underlying the hyperactivity of a Stowaway MITE [J]. Science, 2009, 325(5946):1391-1394.
[56]Lorkovic ZJ, Wieczorek Kirk DA, Lambermon MH, et al. Pre-mRNA splicing in higher plants [J]. Trends in Plant Science, 2000, 5(4):160-167.
[57]Oki N, Yano K, Okumoto Y, et al. A genome-wide view of miniature inverted-repeat transposable elements (MITEs) in rice, Oryza sativa ssp. Japonica [J]. Genes and Genetic Systems, 2008, 83(4):321-329.
[58]Yano M, Katayose Y, Ashikari M, et al. Hd1, a major photoperiod sensitivity quantitative trait locus in rice, is closely related to the Arabidopsis flowering time gene CONSTANS [J]. Plant Cell, 2000, 12(12):2473-2484.
[59]Yang G, Lee YH, Jiang Y, et al. A two-edged role for the transposable element Kiddo in the rice ubiquitin2 promoter [J]. Plant Cell, 2005, 17(5):1559-1568.
[60]Casa AM, Brouwer C, Nagel A, et al. The MITE family heartbreaker (Hbr): molecular markers in maize [J]. Proceedings of the National Academy of Sciences of the United States of America, 2000, 97(18):10083-10089.
[61]Hou J, Long Y, Raman H, et al: A Tourist-like MITE insertion in the upstream region of the BnFLC.A10 gene is associated with vernalization requirement in rapeseed (Brassica napus L.) [J]. BMC Plant Biology, 2012, 12:238.
[62]Kuang H, Padmanabhan C, Li F, et al. Identification of miniature inverted-repeat transposable elements (MITEs) and biogenesis of their siRNAs in the Solanaceae: new functional implications for MITEs [J]. Genome Research, 2009, 19(1):42-56.
[63]Wei L, Gu L, Song X, et al. Dicer-like 3 produces transposable element-associated 24-nt siRNAs that control agricultural traits in rice [J]. Proceedings of the National Academy of Sciences of the United States of America, 2014, 111(10):3877-3882.
[64]侯锦娜. 甘蓝型油菜开花QTL-qFT10-4-的图位克隆及候选基因BnFLC.A10的表达调控研究[D]. 武汉：华中农业大学,2013.
[65]Monden Y, Naito K, Okumoto Y, et al. High potential of a transposon mPing as a marker system in japonica x japonica cross in rice [J]. DNA Research, 2009, 16(2):131-140.
[66]Nouroz F, Noreen S, Heslop-Harrison JS. Evolutionary genomics of miniature inverted-repeat transposable elements (MITEs) in Brassica [J]. Molecular Genetics ans Genomics, 2015, 290(6):2297-2312.
[67]Mao H, Wang H, Liu S, et al. A transposable element in a NAC gene is associated with drought tolerance in maize seedlings [J]. Nature Communication, 2015, 6:8326.
[68]Castelletti S, Tuberosa R, Pindo M, et al. A MITE transposon insertion is associated with differential methylation at the maize flowering time QTL Vgt1 [J]. G3 (Bethesda), 2014, 4(5):805-812.
[69]Yasuda K, Ito M, Sugita T, et al. Utilization of transposable element mPing as a novel genetic tool for modification of the stress response in rice [J]. Molecular Breeding, 2013, 32:505-516.
[70]Hancock CN, Zhang F, Floyd K, et al. The rice miniature inverted repeat transposable element mPing is an effective insertional mutagen in soybean [J]. Plant Physiology, 2011, 157(2):552-562.