水稻瘤矮病毒广东分离物基因组第10组分的序列分析及原核表达

 应用RT-PCR技术克隆了水稻瘤矮病毒(Rice gall dwarf virus,RGDV)广东分离物基因组的第10片段,并测定了全序列。结果表明,RGDV广东分离物S10(登录号EF532325)全长1198bp,含有一个ORF,编码一条由320氨基酸组成、推测分子量约36kDa的多肽。与泰国分离物相应组分相比,基因结构基本一致,核苷酸和氨基酸序列同源性分别为96.2%和98.8%;S10编码多肽与水稻矮缩病毒(Rice dwarf virus,RDV)s9编码蛋白及伤瘤病毒(Wound tumor virus,WTV)S11编码蛋白也分别具有29%和33%的相似性。本研究还将S10cDNA克隆至原核表达载体pET28b(+)上,通过IPTG诱导在大肠杆菌BL21(DE3)中得到了高效表达,并利用His,Bind树脂纯化得到电泳纯级制品。本工作为进一步研究S10编码蛋白的结构与功能奠定了一定的基础。     

水稻黑条矮缩病毒(RBSDV)S3和S10基因组非编码区对翻译的调控作用

 水稻黑条矮缩病毒(Rice black-streaked dwarf virus, RBSDV)基因组含有5′帽子,无3′poly(A)尾巴,且不同基因组片段的5′和3′末端序列均十分保守。本研究以RBSDV S3和S10为对象,分析其非编码区对翻译的调控作用。研究发现S3和S10的5′UTR在有无帽子时均可以正向调控报告基因Fluc的翻译,具备核糖体内部进入位点(IRES)活性,且5′末端的基因组保守序列及邻近序列与IRES活性密切相关;而对应的3′UTR则抑制5′UTR对翻译的正调控效应,其分子基础是5′UTR和3′UTR之间的RNA-RNA互作,且该互作也抑制帽子依赖型翻译的效率。这是首次关于有帽子植物RNA病毒中IRES元件的报道,研究结果对了解植物双链RNA病毒基因组非编码区对翻译的调控作用具有重要科学意义。     

南方水稻黑条矮缩病毒一步双重RT-PCR 检测技术及其应用

 An one-step dual RT-PCR method was developed for Southern rice black-streaked dwarf virus (SRBSDV) detection from host plants and insect vector white-backed planthopper (Sogatella furcifera Horvath,Hemiptera: Delphacidae), from which two cDNA fragments of the viral genome S5 and S10 were amplified
simultaneously. Two primer pairs, S5-F1 / S5-R2 (5′-ttacaactggagaagcattaacacg-3′ / 5′-atgaggtattgcgtaactgagcc -3′) and S10-oF / S10-oR(5cgcgtcatctcaaactacag -3′ / 5′-tttgtcagcatctaaagcgc -3′), were selectedfrom 40 primer pairs based on SRBSDV genome sequences, and amplified viral S5 ORF1 fragment (819 bp) and cp gene fragment ( 682 bp), respectively. Using total RNA extracts from infected plant leaf tissue or individual planthopper adult as templates, one step RT-PCR reaction in the conditions of annealing temperature of 53℃ with the final concentrations of 240 nmol / L S5-F1 / S5-R2 and 120 nmol / L S10-oF / S10-oR generated a similar yield of two amplicons in argrose electrophoresis analysis. Sequence analysis confirmed the correct
result of the amplification. Additionally, several commercal RNA extraction kits was proven to be fit for the template preparation, and the protocol for total RNA extraction from plant leaf tissue and individual planthopper was simplified by sample grinding direct in eppendorf tube. This method can be used for SRBSDV detection of dried or 70% alcochol soaked planthopper samples stored over one month in room temprature. Key words: Southern rice black-streaked dwarf virus; Sogatella furcifera Horvath     

Characterization and detection of a novel idaeovirus infecting blackcurrant

A novel virus was discovered in a blackcurrant accession (Ribes nigrum L.) at the USDA genebank in Oregon, USA. The genome consists of two positive-sense, single-stranded RNAs with the first encoding a 197 kDa multifunctional protein with methyl transferase, helicase and RNA-dependent RNA polymerase enzymatic motifs. The second molecule encodes two putative proteins; the 39 kDa movement and 30 kDa coat proteins. Both RNAs have conserved sequences and structures at the 5′ and 3′ termini. The genome organization, sequence and phylogenetic analyses indicate that the virus is a putative new member of the genus Idaeovirus, as it consistently groups with privet leaf blotch-associated virus and raspberry bushy dwarf virus. A duplex RT-PCR assay was developed for rapid detection of both genomic RNAs simultaneously. The work presented in this communication will assure the health status of blackcurrant plants in mother blocks, nurseries and production fields alike.     

Sequence Analysis Shows that a Dwarfing Disease on Rice, Wheat and Maize in China is Caused by Rice Black-streaked Dwarf Virus

Isolates of plant reoviruses causing severe stunting and dark leaf symptoms on wheat in Hebei province, on maize in Hubei province and on rice in Zhejiang province, China have been characterized. Four of the ten genome segments corresponding to Rice black-streaked dwarf virus (RBSDV) S7, S8, S9, S10 were amplified by RT-PCR from the Hebei and Zhejiang isolates and sequenced. Sequences of S9 and S10 were also obtained from the Hubei isolate. Sequences of corresponding segments of the Chinese isolates were very similar to each other (94.0–99.0% identical nucleotides and 96.3–100% identical amino acids) and were closer to those of a previously reported Japanese RBSDV isolate (90.0–94.9% identical nucleotides and 91.1–98.6% identical amino acids) than to those of an Italian Maize rough dwarf virus isolate (85.1–88.1% identical nucleotides and 85.5–94.3% identical amino acids). The Chinese isolates should be classified as RBSDV.     

Evidence for a phytoreovirus associated with tobacco exhibiting leaf curl symptoms in South Africa

ABSTRACT Three forms of tobacco leaf curl (termed classes I, II, and III, based on symptomatology) recently have been described in southern Africa. Numerous attempts to isolate virus particles responsible for a nongeminivirus-induced leaf curl disease (class I) of tobacco in South Africa have been unsuccessful. Recently, 12 dsRNA segments were isolated from tobacco exhibiting class I leaf curl symptoms, suggesting a possible reovirus genome. The objective of our study was to confirm whether the dsRNA segments are associated with a reovirus. Isolation of icosahedral particles with an outer core 60 to 65 nm in diameter and an inner core 40 to 45 nm in diameter was achieved. Twelve distinct nonpolyadenylated dsRNAs were isolated from purified virions, and the total molecular masses of the dsRNAs ranged from 17.86 to 18.40 x 10(6) Da in polyacrylamide and agarose gels, respectively. Using hybridization analysis, dsRNAs were identified as non-homologous distinct segments. Comparisons with other known reoviruses revealed a unique banding pattern that was most similar to the wound tumor virus (WTV), the type species of the genus Phytoreovirus. Hybridizations of WTV cloned DNA probes (segments S4 and S6 to S9) and dsRNAs from infected tobacco indicated no significant sequence similarity, whereas indirect enzyme-linked immunosorbent assay with a polyclonal antiserum to WTV showed strong positive cross-reactivity to tobacco virions. Our results indicate a virus with features consistent with those of phytoreoviruses. This is the first report of a plant reovirus in tobacco, the first record in Africa, and the second example of a field-isolated dicot phytoreovirus.     

基于全基因组序列的黄瓜绿斑驳花叶病毒重组和系统发育分析

 通过RT-PCR扩增了黄瓜绿斑驳花叶病毒(Cucumber green mottle mosaic virus,CGMMV)济南分离物(CGMMV-JN)的基因组片段。序列测定结果表明CGMMV-JN基因组全长6 424核苷酸(nt),5′-和3′-UTR分别为60和176 nt,含有4个ORF,分别编码129 kDa和186 kDa复制酶相关蛋白、29 kDa移动蛋白及17.4 kDa外壳蛋白。CGMMV-JN与另外29个CGMMV分离物全基因组核苷酸序列一致率为90.0%~99.7%。重组分析发现韩国KOM(AF417243)、以色列EC(KF155231)、印度(DQ767631)和我国河北的CHB(KJ658958)4个分离物在RdRp编码区存在重组。系统发育分析结果表明,这些分离物可分成3个组。选择压力分析结果表明cp基因处于正选择,其它基因处于负选择。本文研究的结果为黄瓜绿斑驳花叶病毒的监测及防控提供了理论依据。     

南方水稻黑条矮缩病毒安徽分离物S7片段的克隆及其S7-1基因编码蛋白的原核表达

为探讨南方水稻黑条矮缩病毒(Southern rice black-streaked dwarf virus,SRBSDV)的种群变异并获得S7-1原核表达蛋白,采用RT-PCR技术扩增SRBSDV安徽分离物S7片段,并进行克隆、测序及序列分析,再利用特异性引物扩增该分离物S7-1基因并克隆到原核表达载体p ET-GST上,重组质粒p ET-S7-1转化大肠杆菌BL21(DE3),IPTG诱导及Ni~(2+)-NTA亲和柱纯化融合蛋白,再进行Western blot检测。结果显示,SRBSDV安徽分离物S7片段与其它SRBSDV各个分离物S7片段的序列相似性极高,达99.3%~99.9%,而与斐济病毒属Fijivirus其它种之间的序列相似性较低,为35.5%~73.3%。SRBSDV安徽分离物与其它SRBSDV各个分离物聚成1个单独的分支,彼此间亲缘关系较近。试验获得了分子质量约为68 k D的S7-1融合蛋白,且GST单抗能够与S7-1融合蛋白发生特异性反应,表明本研究得到的融合蛋白确为靶标蛋白。     

湖南省南方水稻黑条矮缩病毒分离物组分S10编码的ORF序列克隆与分析

采用RT-PCR方法扩增并克隆了2013年湖南省水稻上发生的南方水稻黑条矮缩病毒(Southern rice blackstreaked dwarf virus,SRBSDV)S10片段的近全长序列,采用生物信息学软件Mega、RDP和DnaSP分析其编码的开放阅读框(open reading fragment,ORF)遗传多样性。结果表明:2013年湖南省15个SRBSDV分离物S10编码的ORF序列同源性在99.5%以上,不同分离物中存在3~30个突变位点,绝大部分的核酸突变为无义突变,没有发现可能的重组。在系统发育树上,15个分离物聚类为2个分支,其中湖南汉寿的10个分离物和永州的2个分离物(HuNyz12和HuNyz29)与我国浙江分离物聚为1个亚组、湖南永州的其他3个分离物与我国南部的云南、海南等及越南的分离物聚为1个亚组。系统发育结果表明,SRBSDV随传毒介体白背飞虱迁飞从我国南部向北部扩散。     

Phylogenetic relationships between rice dwarf phytoreovirus isolates from five countries

Rice dwarf virus isolates were collected from several locations in Japan, the Philippines, China, Nepal and Korea. Genomic dsRNA segment profiles in polyacrylamide gel electrophoresis differed among the isolates. There were less differences in the profiles between isolates from Japan and Korea than in those between these two Countries and others. Nucleic acid hybridization was used to examine the extent of genomic variation. Full-length cDNAs to all genomic segments encoding non-structural proteins (S4, S6, S9, S10, S11 and S12) were synthesized from two Japanese isolates, and were used for dot-blot hybridization. Hybridizations using probes generated from the full-length cDNA clones failed to differentiate isolates from different geographical areas. However, cDNA probes covering a variable region of S12 were able to distinguish Japanese and Korean isolates from those of other countries. Phylogenetic tree analysis based on the amino acid sequence of P12 encoded by S12 grouped Japanese and Korean isolates together. The Chinese isolates from two different locations (Yunnan and Fujian) were closely related to each other, and were the most distantly related to Japanese and Korean isolates.     

水稻黑条矮缩病毒外壳蛋白基因的克隆、原核表达及抗体制备

为探讨水稻黑条矮缩病毒（Rice black-streaked dwarf virus,RBSDV）的种群变异,采用RT-PCR方法从感染RBSDV山东分离物RBSDV-JN1的水稻中克隆该病毒的S10片段,并进行序列分析,进而构建包含RBSDV-JN1的CP基因的原核表达载体,导入大肠杆菌Escherichia coli BL21（DE3）诱导表达;并以表达的融合蛋白为抗原,制备病毒的多克隆抗体。结果显示：S10片段全长为1 801 bp,包含1个1 677 bp编码框,编码558个氨基酸的外壳蛋白（CP）;与GenBank已注册的19个RBSDV的CP基因序列相比较发现,病毒各分离物间核苷酸的序列相似性为90.5%~99.8%,氨基酸的序列相似性为95.9%~100.0%;地理位置较近的分离物间序列相似性较高,RBSDV种群分布呈现区域性差异。原核表达载体pET-RBSDV-CP经IPTG诱导,获得了分子量约为63 kD带有His标签的目的蛋白。用该蛋白制备的多克隆抗体经ELISA、Western blot和Dot-blot ELISA检测显示,效价为1：81 000,且具有良好的特异性。     

水稻黑条矮缩病毒江苏玉米分离物全基因组序列及进化分析

 利用RT-PCR从江苏玉米上克隆水稻黑条矮缩病毒(RBSDV)的全基因组,其基因组10个片段核苷酸数目和蛋白编码情况与已报道的RBSDV分离物基本一致。 基因组的序列一致性分析和系统进化树表明,RBSDV基因组片段间存在频繁的RNA重排现象;江苏玉米分离物(JS)与湖北玉米分离物(HuB)和河北小麦分离物(HeB)的整体亲缘关系较近,而与安徽分离物(AH-MX8)的整体亲缘关系最远。综合本研究及前人对S8 和S10的研究,RBSDV基因组不同片段的进化中RNA重组的作用不同: S1、S2和S4中没有RNA重组;S3、S5、S6、S8和S10中存在低频率重组;S7 和S9存在较高频率重组,其中S7的高频率重组尤为显著。     

玉米粗缩病毒及抗病策略

玉米粗缩病毒属于植物呼肠孤病毒组的斐济病毒属，是一种有双层衣壳的球状病毒。该病毒基因组包含10条线状的双链RNA片段，近年来已经完成了其中4条RNA片段的测序工作。玉米粗缩病毒对我国玉米生产的危害最为严重。该病毒主要由介体昆虫传播，侵染的植株表现严重矮化和叶片浓绿等病症。玉米对该病毒的抗性表现出多基因控制的数量性状遗传的特征。作者描述了玉米粗缩病病原、病症及侵染循环的特点，对玉米粗缩病毒基因组的研究进展进行了评述，并对抗病策略进行了讨论。     

水稻瘤矮病毒S11基因沉默抑制子的原核表达及抗血清制备

以采自广东省水稻瘤矮病的典型病株为材料,通过RT-PCR法扩增和克隆了水稻瘤矮病毒(Rice gall dwarf virus,RGDV)S11组分核苷酸序列全长。序列分析结果表明,RGDV广东分离物S11(登录号EF532326)核苷酸序列全长1168bp,含有一个1068bp的开放阅读框,编码一条355个氨基酸的多肽,推测分子量约40kD,与泰国分离物基因结构基本一致,其核苷酸与氨基酸序列相似性分别为94.3%和98.8%。将广东分离物S11基因克隆至pBV221温敏表达载体上,在大肠杆菌DH5α中实现了高效表达。以诱导蛋白为抗原免疫家兔获得了抗血清。利用ELISA法测定抗血清的效价为1∶4096,Western blot分析结果表明,抗血清能与S11蛋白发生特异血清学反应。这可为进一步研究S11蛋白的结构和功能,揭示其抑制基因沉默的作用机制提供参考。     

Comparison of the ribosomal RNA operon from Texas Phoenix decline and lethal yellowing phytoplasmas

A comparison was made of the two palm yellows phytoplasmas affecting palms to determine if the entire ribosomal RNA operon portion of the phytoplasma genome, or portions thereof, could account for the observed palm host differences. Polymerase chain reaction (PCR) was used to amplify a 5.0?kb DNA fragment consisting of the entire ribosomal RNA operon from a subgroup 16SrIV-D phytoplasma that causes Texas Phoenix palm decline (TPD) in cabbage (Sabal palmetto) palm in west central Florida and from a subgroup 16SrIV-A phytoplasma that causes lethal yellowing (LY) in coconut (Cocos nucifera) palm in Jamaica. Before the PCR reaction, we sequenced by 454 sequencing a draft genome of the coconut LY phytoplasma, strain LYFL, that infects C. nucifera in Florida, and obtained from this draft sequence both copies of the entire ribosomal operon. Sequence analysis of the ribosomal RNA operons from both the LY and TPD phytoplasmas revealed the gene composition and orientation for the operons to be 5′16S rRNA-tRNA^Ile-23S rRNA-5S rRNA3′ and a tRNA^Val3′ downstream of the 5S rRNA gene. Based on molecular comparisons using the sequences of the ribosomal RNA operon, the TPD (16SrIV-D) strain was 98?% similar to the LY (16SrIV-A) strains.     

甜瓜黄斑病毒三亚分离物S RNA的分子特征

 甜瓜黄斑病毒（Melon yellow spot virus, MYSV）首次发生于日本,造成甜瓜和黄瓜的严重损失,Kato等系统地研究了病毒的传播方式、寄主范围、超微结构和基因组特征,认为MYSV应为番茄斑萎病毒属（Tospovirus）的1个新种［1,2］。2006年以来,台湾的西瓜［3］和黄瓜［4］上相继发现MYSV。2009年春季,古勤生在海南三亚的保护地甜瓜上发现一种新发生的病毒病,发病率30%~100%,病株出现系统性黄化坏死斑点,为MYSV侵染的典型症状,结合分子检测结果判定病原为MYSV。     

引起玉米粗缩病的水稻黑条矮缩病毒河南分离物的分子特征

<正>目前已报道的造成玉米粗缩病的病原有3种,分别是玉米粗缩病毒(Maize rough dwarf virus,M RDV),水稻黑条矮缩病毒(Rice black-streaked dwarf virus,RBSDV)和南方水稻黑条矮缩病毒(Southern rice black-streaked dwarf virus,SRBSDV)[1]。我国于1954年在新疆和甘肃发现该病,上世纪60年代曾在中东部夏玉米区流行,至70年代以来各玉米产区已陆续发生[2],近年来在黄淮海夏玉米区特别是套播或晚春播、早夏播玉米田发生危害严重。     

甘薯病毒C中国分离物全基因组序列测定及比较分析

利用RT-PCR结合RACE方法,从采自河南南阳的甘薯样品上获得甘薯病毒C中国分离物(SPVC-Ch1)的全长基因组序列。序列分析结果表明,SPVC-Ch1基因组由1 0846个核苷酸组成,3'末端包含poly(A)尾序。基因组含有1个由10 446个核苷酸构成的开放阅读框,编码一个由3 481个氨基酸残基构成的393 k Da多聚蛋白。将SPVC-Ch1与Gen Bank中登录的其他SPVC分离物序列进行比较分析发现,SPVC不同分离物间全基因组核苷酸序列相似性为92.7%~98.9%,多聚蛋白的氨基酸序列相似性为95.1%~99.2%,SPVC-Ch1与Bungo分离物的相似性最高,与C1分离物的相似性最低。系统进化树分析结果表明,SPVC-Ch1与日本的Bungo、以色列的IL、韩国的CW135和UN202等分离物形成一个分支,亲缘关系较近。这是SPVC中国分离物全基因组序列的首次报道,研究结果丰富了SPVC全基因组序列信息,有助于全面了解SPVC种群的遗传进化关系。     

Turnip mosaic virus VPg does not disrupt the translation initiation complex but interferes with cap binding

Plant potyvirus RNAs have a virus protein covalently attached at their 5′-end: the VPg (virus protein genome-linked). In part because of its position at the 5′end of the virus RNA, the VPg has been speculated to play a role in virus translation and replication. We report that the VPg of Turnip mosaic virus (TuMV) interacts with, and does not disrupt, the translation initiation complex eIF(iso)4E-eIF(iso)4G. The purification of VPgPro or 6K2VPgPro by affinity chromatography from infected plant tissue also led to the recovery of eIF(iso)4G. The cap analogue m⁷GTP competed with the binding of VPg to both eIF(iso)4E and the eIF(iso)4E-eIF(iso)4G complex. This suggested that the viral VPg bound to the translation initiation complex but that interaction did not result in disassociation of the subunits but rather in competition for the binding of the 5′ cap structure. This would result in decreased affinity of the translation initiation machinery for capped cellular mRNAs.     

水稻矮缩病毒基因组及毒粒三维结构的研究进展

水稻矮缩病毒(Rice dwarf virus,RDV)为双层壳、二十面体的双链RNA病毒,是水稻的重要病原物之一.文中比较了RDV中国福建分离物与日本分离物基因组各片段核苷酸序列的相似性,发现RDV两个不同分离物基因组相应片段的相似性均在92%以上,最高可达96%;分析了相应基因组片段编码的结构蛋白P1、P2、P3、P5、P7、P8及以前一直被认为是非结构蛋白的P9和非结构蛋白Pns4、Pns6、Pns10 、Pns11和Pns12在RDV复制、组装过程中的功能;回顾了RDV粒子三维结构的研究概况,对RDV粒子内、外层衣壳的晶体学结构作了较详细的描述;简要介绍了RDV复制与组装的机制,发现核心蛋白与dsRNA间相互作用成为一个单元是病毒RNA的分拣及包装到病毒粒子核心内的可能机制.同时,指出基于PDR的植物抗病毒基因工程在水稻矮缩病毒防治上的可能性.