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植物逆境相关长链非编码RNA的研究进展

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  摘要:植物长链非编码RNA(long non-coding RNA,lncRNA)是一类广泛存在的长度大于200 nt的非编码RNA调控分子,通过目标模拟、转录干扰、甲基化等机制调控真核生物基因表达。植物体内的许多lncRNA受外界胁迫的诱导或抑制,并作用于逆境相关基因,影响植物形态和生理生化进而产生对胁迫的应答。从植物lncRNA的合成、分子水平的作用方式、与植物生物和非生物胁迫逆境的响应机制等方面阐述了长链非编码RNA参与调控植物的抗逆机制,并提出了今后的研究方向,以期为植物逆境应对及抗逆新品种选育提供理论依据。
  关键词:lncRNA;植物形态;生物胁迫;非生物胁迫
  中图分类号: Q943.2文献标志码: A
  文章编号:1002-1302(2020)04-0019-04
  长链非编码RNA(long non-coding RNA,lncRNA)是一类非编码的内源RNA分子,在植物中普遍转录,成熟的lncRNA长度大于200 nt[1-2]。在对小鼠的测序分析中首次被提出[3]。目前在拟南芥、玉米、水稻、小麦等植物中已鉴定了大量lncRNA[4-5],随着植物lncRNA数量的增加,相关的数据库也增多,其中NONCODE数据库中提供了大量的植物lncRNA的详细信息[6]。相较于哺乳动物,植物lncRNAs方面的研究才刚刚起步,但已有研究发现,lncRNAs参与植物的生殖发育和环境胁迫响应。如低温胁迫诱导反义转录本COOLAIR表达量的增加,增加的COOLAIR会抑制FLC基因的表达,进而参与拟南芥的春化过程[7-8]。在干旱和盐分等逆境胁迫下拟南芥中的lncRNA表达量明显改变,进一步证实lncRNAs参与了环境胁迫的应答[9]。本文通过总结国内外植物lncRNAs的相关研究进展,以期通过lncRNA的作用机制来探索蔬菜抗逆的研究思路,以期为抗逆新品种选育和改良提供理论指导。
  1 lncRNA的合成与作用方式
  1.1 lncRNA的合成
  植物中lncRNAs主要由RNA聚合酶Ⅱ和聚合酶Ⅲ转录形成,还有一部分通过RNA聚合酶Ⅳ和聚合酶Ⅴ转录形成,主要定位在细胞核中[10]。大多数lncRNA具有5′帽子和3′poly(A)尾巴存在可变剪接位点[11-12],因此可用转录组测序(RNA-seq)技术来大量筛选lncRNA。除了以上lncRNA合成经典模式外,lncRNA还可以通过以下途径合成[13]:(1)在基因组中插入1个转座原件或通过编码蛋白基因插入1次框后与前一编码序列合并可以产生有功能的lncRNA;(2)外显子lncRNA可以在染色体重排后,由原来距离较远的非转录片段串联产生。目前这些非经典合成途径在动物中报道的较多,但也不排除植物中也有类似途径。然而,lncRNA选择合成途径的不同是否会导致与靶基因的协同表达模式的不同进而产生其他生物学意义还有待进一步研究。
  1.2 lncRNA的作用方式
  lncRNA广泛存在于真核生物中,其作用机制与功能多种多样。lncRNA可以作为诱饵分子结合miRNA,调控mRNA的表达;结合DNA发挥反式引导分子作用;也可以结合多个蛋白质发挥支架作用[14-15]。目前lncRNA在分子水平的作用机制可归纳为以下4种方式:(1)lncRNA通过抑制RNA聚合酶Ⅱ[16]或者结合mRNA后与Dicer酶共同作用[17]以及在蛋白编码基因上游区域进行转录等方式来影响基因的表达;(2)lncRNA可作为miRNA、siRNA等小RNA的生物合成前体;(3)通过影响mRNA产生不同的剪切形式来产生作用;(4)结合特定蛋白质调节其活性进而改变细胞质定位。
  2 植物lncRNAs与逆境响应
  植物在逆境下自身代谢、生理和生长会产生不同的变化进而来响应胁迫。植物lncRNAs在逆境胁迫中起调节因子的作用,通过模拟靶标、干扰转录和DNA甲基化等机制来影响基因表达。已有研究发现,拟南芥在低氧[18]、光[19]、高温[20]和低磷[21]的胁迫下,小麦在高温[22]逆境下,狐尾草[23]、香蕉[24]、白杨[25]和玉米[26]在干旱胁迫下,毛地黄[27]和土豆[28]在低温逆境以及苜蓿[29]在盐胁迫下,均有lncRNAs参与胁迫响应,表明植物中的lncRNA广泛参与非生物胁迫。在小麦感染白粉病和热胁迫下也发现了125个lncRNAs[22],说明植物lncRNAs在病原菌感染和胁迫中能够作出应答。然而生物互作的存在导致致病机制不清晰,使得lncRNA响应生物胁迫和病菌的研究结果相对较少。
  2.1 植物lncRNAs與非生物胁迫逆境
  植物在非生物胁迫下会启动一系列的信号通路来改变形态和生理生化。在逆境胁迫下,lncRNAs的表达可能比编码蛋白质的mRNA更加活跃[30-31]。在干旱和盐胁迫下,lncRNA表达量会迅速增加[31],调节植物适应不同环境。lncRNA IPS1和AT4在磷胁迫下诱导表达,通过影响miRNA399的活性,来调节磷酸含量的动态平衡[32]。
  拟南芥在干旱、低温和盐等胁迫处理后,有1 832 个lncRNAs的表达发生了明显变化[9]。lncRNA-At5NC056820过表达转入拟南芥中,转基因植株能够在一定程度上提高拟南芥的耐旱性[33]。通过高通量测序发现,苜蓿中存在大量的响应渗透、盐胁迫的lncRNAs,它们与蛋白质编码基因共同作用来调节逆境胁迫[34]。基于全基因组在木薯中鉴定到了响应低温和干旱胁迫的lncRNAs[35]。刘伟婳在野生蕉低温胁迫过程中获得了12 462条lncRNAs,同时发现在胁迫过程中lncRNAs对差异表达基因的调控起重要作用[36]。野生蕉lncRNAs与其靶基因之间存在复杂的调控关系,既有正调控,也有负调控。拟南芥中Npc536是一种天然反义转录物(NATs lncRNA),在干旱、盐和冷害等胁迫环境中会产生一系列的变化,如盐胁迫下过表达植株主根和侧根生长明显加快,在缺磷环境下,Npc536表达量会增加[37]。   2.2 植物lncRNAs与生物胁迫逆境
  植物lncRNAs不仅广泛参与非生物胁迫应答还参与生物胁迫的响应过程。高通量测序结果表明,植物体内大多数lncRNAs受到外界生物胁迫的诱导或抑制,如番茄中lncRNA16397可以通过减少活性氧的积累保护膜损伤进而来增强对疫霉病的抗性[38]。基于转录组数据分析土豆感病和抗病品种时发现,有559个长基因间非编码RNA(lincRNAs)对软腐病菌有响应[39]。已报道在甘蓝型油菜[40]和拟南芥中[41]分别发现响应核盘菌菌核病和响应尖孢镰刀菌的lncRNA。Wang等在猕猴桃研究中发现,lncRNAs可能会影响猕猴桃感染假单胞菌,推测在蛋白编码区域和非编码区域能够调控猕猴桃对假单胞菌的感染[42]。在感染小麦条锈病的小麦中鉴定出4个lncRNAs(Tal-ncRNA18、Tal-ncRNA73、Tal-ncRNA106、Tal-ncRNA108),通过表达分析发现它们可能在调整或沉默蛋白编码基因进入病原体防御反应中起作用[43];Zhang等通过沉默棉花中的GhlncNAT-ANX2和GhlncNAT-RLP7来增强植株对棉花黄萎病病菌和灰霉病病菌的抗性[44]。
  3 结语与展望
  随着高通量测序技术的快速发展,越来越多植物中的lncRNAs正在被发现。目前,在草本植物如向日葵[45]、草莓[46]、白菜[47]、豆科类[48]、黄瓜[49]等,以及木本植物如茶[50]、葡萄[51]、毛白杨[52]等植物中都进行了大量的lncRNAs鉴定和表达分析。然而,目前的研究大多集中在lncRNAs的初歩鉴定和功能方面,其转录调节机制方面的研究还未见报到。现已明确lncRNA具有保守性差、表达量低但组织特异性强的特点,如对茄科植物lncRNAs的序列分析发现,不同物种之间lncRNAs的序列保守性很低,如lncRNA-314在普通番茄和醋栗番茄中特异表达,而在潘那利番茄(Solanum pennellii)中则不表达[53]。在全基因组范围内进行水稻lncRNA的鉴定和分析发现,这些lncRNAs与哺乳动物的lncRNAs相比具有很高的组织特异或阶段特异表达性[5]。基于全基因组进行黄瓜lincRNAs研究,lincRNAs和mRNAs之间的共表达分析表明它们参与应激响应和多个生物学过程,分子进化的研究发现,至少有16个lincRNAs受自然选择作用,其中一部分受正选择和平衡选择作用[50]。由于lncRNAs表达水平低,为探索其在转录和转录后水平上的调控基因表达的作用机制可通过干扰lncRNAs的表达模式来进行[54-56]。
  lncRNAs在动物中表现出的多种功能使研究者更加重视lncRNAs的研究。近年来植物lncRNAs的相关研究也逐渐加快,已证实植物lncRNAs参与植物成花转变、花粉发育、逆境胁迫以及其他多个生物学过程,但与哺乳动物相比,研究者对lncRNAs参与植物生长发育全过程的转录调控和分子进化机制还知之甚少。通过梳理近年来研究过的植物lncRNAs发现,植物在结构、起源及分子功能上,都与动物具有一定的相似性,并逐渐显示出一些其特有的规律性[57]。目前植物lncRNAs的研究空间还很大,因此关于lncRNAs参与调控逆境机制的研究今后可以从以下2个方面入手:(1)利用现代较为成熟的高通量测序技术,基于全基因組,从转录组水平进行植物抗逆相关的lncRNAs大规模挖掘;(2)利用生物信息学分析技术对已获得的lncRNAs进行靴基因预测、与mRNAs的共表达分析及模拟miRNA内源伪靶基因的辨析,为深入的lncRNA功能性鉴定提供基础。
  参考文献:
  [1]Laurent S G,Wahlestedt C,Kapranov P. The landscape of long noncoding RNA classification[J]. Trends in Genetics,2015,31(5):239-251.
  [2]Kornienko A E,Guenzl P M,Barlow D P,et al. Gene regulation by the act of long non-coding RNA transcription[J]. BMC Biology,2013,11:59.
  [3]Okazaki Y,Furuno M,Kasukawa T,et al. Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs[J]. Nature,2002,420(6915):563-573.
  [4]Li L,Eichten S R,Shimizu R,et al. Genome-wide discovery and characterization of maize long non-coding RNAs[J]. Genome Biology,2014,15:R40.
  [5]Zhang Y C,Liao J Y,Li Z Y,et al. Genome-wide screening and functional analysis identify a large number of long noncoding RNAs involved in the sexual reproduction of rice[J]. Genome Biology,2014,15:512.
  [6]Zhao Y,Li H,Fang S S,et al. NONCODE 2016:an informative and valuable data source of long non-coding RNAs[J]. Nucleic Acids Research,2016,44(D1):D203-D208.   [7]Zhu Q Q,Li Z A,He Y X,et al. Research progress on epigenetic and flowering-time regulation[J]. Acta Horticulturae Sinica,2013,40(9):1787-1794.
  [8]Swiezewski S,Liu F Q,Magusin A,et al. Cold-induced silencing by long antisense transcripts of an Arabidopsis Polycomb target[J]. Nature,2009,462(7274):799-802.
  [9]Liu J,Jung C,Xu J,et al. Genome-wide analysis uncovers regulation of long intergenic noncoding RNAs in Arabidopsis[J]. Plant Cell,2012,24(11):4333-4345.
  [10]Rowley M J,Bhmdorfer G,Wierzbicki A T. Analysis of long non-coding RNAs produced by a specialized RNA polymerase in Arabidopsis thaliana[J]. Methods,2013,63(2):160-169.
  [11]Bardou F,Ariel F,Simpson C G,et al. Long noncoding RNA modulates alternative splicing regulators in Arabidopsis[J]. Developmental Cell,2014,30(2):166-176.
  [12]Plewka P,Thompson A,Szymanski M,et al. A stable tRNA-like molecule is generated from the long noncoding RNA GUT15 in Arabidopsis[J]. RNA Biology,2018,15(6):726-738.
  [13]Ponting C P,Oliver P L,Reik W. Evolution and functions of long noncoding RNAs[J]. Cell,2009,136(4):629-641.
  [14]Wang K C,Chang H Y. Molecular mechanisms of long noncoding RNAs[J]. Molecular Cell,2011,43(6):904-914.
  [15]Guttman M,Rinn J L. Modular regulatory principles of large non-coding RNAs[J]. Nature,2012,482(7385):339-346.
  [16]Novikova I V,Hennelly S P,Sanbonmatsu K Y. Structural architecture of the human long non-coding RNA,steroid receptor RNA activator[J]. Nucleic Acids Research,2012,40(11):5034-5051.
  [17]Yang J R,Zhang J. Human long noncoding RNAs are substantially less folded than messenger RNAs[J]. Molecular Biology and Evolution,2015,32(4):970-977.
  [18]Wu J,Okada T,Fukushima T,et al. A novel hypoxic stress-responsive long non-coding RNA transcribed by RNA polymerase Ⅲ in Arabidopsis[J]. RNA Biology,2012,9(3):302-313.
  [19]Wang H,Chung P J,Liu J,et al. Genome-wide identification of long noncoding natural antisense transcripts and their responses to light in Arabidopsis[J]. Genome Research,2014,24(3):444-453.
  [20]Wunderlich M,Gross-Hardt R,Schffl F. Heat shock factor HSFB2a involved in gametophyte development of Arabidopsis thaliana and its expression is controlled by a heat-inducible long non-coding antisense RNA[J]. Plant Molecular Biology,2014,85(6):541-550.
  [21]Yuan J P,Zhang Y,Dong J S,et al. Systematic characterization of novel lncRNAs responding to phosphate sarvation in Arabidopsis thaliana[J]. BMC Genomics,2016,17:655.   [22]Xin M M,Wang Y,Yao Y Y,et al. Identification and characterization of wheat long non-protein coding RNAs responsive to powdery mildew infection and heat stress by using microarray analysis and SBS sequencing[J]. BMC Plant Biology,2011,11:61.
  [23]Qi X,Xie S J,Liu Y W,et al. Genome-wide annotation of genes and noncoding RNAs of foxtail millet in response to simulated drought stress by deep sequencing[J]. Plant Molecular Biology,2013,83(4/5):459-473.
  [24]Muthusamy M,Uma S,Backiyarani S,et al. Genome-wide screening for novel,drought stress-responsive long non-coding RNAs in drought-stressed leaf transcriptome of drought-tolerant and -susceptible banana (Musa spp.) cultivars using Illuminahigh-throughput sequencing[J]. Plant Biotechnology Reports,2015,9(5):279-286.
  [25]Shuai P,Liang D,Tang S,et al. Genome-wide identification and functional prediction of novel and drought-responsive lincRNAs in Populus trichocarpa[J]. Journal of Experimental Botany,2014,65(17):4975-4983.
  [26]Zhang W,Han Z X,Guo Q L,et al. Identification of maize longnon-coding RNAs responsive to drought stress[J]. PLoS One,2014,9(6):e98958.
  [27]Wu B,Li Y,Yan H X,et al. Comprehensive transcriptome analysis reveals novel genes involved in cardiac glycoside biosynthesis and mlncRNAs associated with secondary metabolism and stress response in Digitalis purpurea[J]. BMC Genomics,2012,13:15.
  [28]Aversano R,Contaldi F,Ercolano M R,et al. The Solanum commersonii genome sequence provides insights into adaptation to stress conditions and genome evolution of wild potato relatives[J]. Plant Cell,2015,27(4):954-968.
  [29]Postnikova O A,Nemchinov L G. Natural antisense transcripts associated with salinity response in alfalfa[J]. The Plant Genome,2015,8(2):1-5.
  [30]Xu Q,Song Z H,Zhu C Y,et al. Systematic comparison of lncRNAs with protein coding mRNAs in population expression and their response to environmental change[J]. BMC Plant Biology,2017,17:42.
  [31]Qin T,Zhao H,Cui P,et al. A nucleus-localized long non-coding RNA enhances drought and salt strss tolerance[J]. Plant Physiology,2017,175(3):1321-1336.
  [32]Franco-Zorrilla J M,Valli A,Todesco M,et al. Target mimicry provides a new mechanism for regulation of microRNA activity[J]. Nature Genetics,2007,39(8):1033-1037.
  [33]毋若楠,王 紅,杨成成,等. 拟南芥lncRNA-At5NC056820过表达载体构建及其转基因植株的抗旱性研究[J]. 西北植物学报,2017,37(10):1904-1909.
  [34]Wang T Z,Liu M,Zhao M G,et al. Identification and characterization of long non-coding RNAs involved in osmotic and salt stress in Medicago truncatula,using genome-wide high-througput sequencing[J]. BMC Plant Biology,2015,15:131.   [35]Li S X,Yu X,Lei N,et al.Genome-wide identification and functional prediction of cold and/or drought- responsive lncRNAs in cassava[J]. Scientific Reports,2017,7:46795.
  [36]劉伟婳.基于全转录组学的野生蕉(Musa itinerans)低温胁迫响应机制研究[D]. 福州:福建农林大学,2018.
  [37]Ben Amor B,Wirth S,Merchan F,et al. Novel long non-protein coding RNAs involved in Arabidopsis differentiation and stress responses[J]. Genome Research,2009,19(1):57-69.
  [38]Cui J,Luan Y S,Jiang N,et al. Comparative transcriptome analysis between resistant and susceptible tomato allows the identification of lncRNA16397 conferring resistance to Phytophthora infestans byco-expressing glutaredoxin[J]. Plant Journal,2017,89(3):577-589.
  [39]Kwenda S,Brich P R J,Moleleki L N. Genome-wide identification of potato long intergenic noncoding RNAs responsive to Pectobacterium carotovorum subspecies brasiliense infection[J]. BMC Genomics,2016,17:614.
  [40]Joshi R K,Megha S,Basu U,et al. Genome wide identification and functional prediction of long non-coding RNAs responsive to Sclerotinia sclerotiorum infection in Brassica napus[J]. PLoS One,2016,11(7):e0158784.
  [41]Zhu Q H,Stephen S,Taylor J,et al. Long noncoding RNAs responsive to Fusarium oxysporum infection in Arabidopsis thaliana[J]. New Phytologist,2014,201(2):574-584.
  [42]Wang Z P,Liu Y F,Li L,et al. Whole transcriptome sequencing of Pseudomonas syringae pv. actinidiae-infected kiwifruit plants reveals species-specific interaction between long non-coding RNA and coding genes[J]. Scientific Reports,2017,7(1):4910.
  [43]Zhang H,Chen X E,Wang C Y,et al. Long non-coding genes implicated in response to stripe rust pathogen stress in wheat (Triticum aestivum L.)[J]. Molecular Biology Reports,2013,40(11):6245-6253.
  [44]Zhang L,Wang M J,Li N N,et al. Long noncoding RNAs involve in resistance to Verticillium dahliae,a fungal disease in cotton[J]. Plant Biotechnology Journal,2018,16(6):1172-1185.
  [45]Flórez-Zapata N M V,Reyes-Valdés M H,Martínez O. Longnon-coding RNAs are major contributors to transcriptome changes in sunflower meiocytes with different recombination rates[J]. BMC Genomics,2016,17:490.
  [46]Kang C Y,Liu Z C. Global identification and analysis of long non-coding RNAs in diploid strawberry Fragaria vesca during flower and fruit development[J]. BMC Genomics,2015,16:815.
  [47]Song X M,Liu G F,Huang Z N,et al. Temperature expression patterns of genes and their co-expression with LncRNAs revealed by RNA-Seq in non-heading Chinese cabbage[J]. BMC Genomics,2016,17:297.   [48]Kerr S C,Gaiti F,Beveridge C A,et al. De novo transcriptome assembly reveals high transcriptional complexity in Pisum sativum axillary buds and shows rapid changes in expression of diurnally regulated genes[J]. BMC Genomics,2017,18(1):221.
  [49]Hao Z Q,Fan C Y,Cheng T,et al. Genome-wide identification,characterization and evolutionary analysis of long intergenic noncoding RNAs in cucumber[J]. PLoS One,2015,10(3):e0121800.
  [50]Lin J K,Wilson I W,Ge G P,et al . Whole transcriptome analysis of three leaf stages in two cultivars and one of their F1 hybrid of Camellia sinensis L. with differing EGCG content[J]. Tree Genetics & Genomes,2017,13:13.
  [51]Vitulo N,Forcato C,Carpinelli E C,et al. A deep survey of alternative splicing in grape reveals changes in the splicing machinery related to tissue,stress condition and genotype[J]. BMC Plant Biology,2014,14:99.
  [52]Chen J H,Quan M Y,Zhang D Q. Genome-wide identification of novel long non-coding RNAs in Populus tomentosa tension wood,opposite wood and normal wood xylem by RNA-seq[J]. Planta,2015,241(1):125-143.
  [53]Wang X,Ai G,Zhang C L,et al. Expression and diversification analysis reveals transposable elements play important roles in the origin of Lycopersicon-specific lncRNAs in tomato[J]. New Phytologist,2016,209(4):1442-1455.
  [54]Mercer T R,Dinger M E,Mattick J S. Long non-coding RNAs:insights into functions[J]. Nature Reviews Genetics,2009,10(3):155-159.
  [55]Zhu Q H,Wang M B. Molecular functions of long non-coding RNAs in plants[J]. Genes,2012,3(1):176-190.
  [56]Rinn J L,Chang H Y. Genome regulation by long noncoding RNAs[J]. Annual Review of Biochemistry,2012,81:145-166.
  [57]Au P C,Zhu Q H,Dennis E S,et al. Long non-coding RNA-mediated mechanisms Independent of the RNAi pathway in animals and plants[J]. RNA Biology,2011,8(3):404-414.
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