棉铃虫多核型多角体病毒v-cath同源基因的克隆及序列分析

为获得棉铃虫多核衣壳型多角体病毒(Helicoverpa armigera multiple nucleocapsid nucleopolyhedrovirus)基因组序列,采用随机克隆方法,建立HearMNPV的质粒基因文库,并通过对插入片段进行克隆鉴定和序列分析,获得编码组织蛋白酶基因v-cath。该基因阅读框为1026bp,共编码341个氨基酸。核苷酸和氨基酸同源性比较结果表明:HearMNPV的v-cath基因与蓓带夜蛾核型多角体病毒B(Mamestra configurata NPV-B)的同源性最高,而与苹果皮小卷蛾颗粒体病毒(Cydiapomonella GV CpGV)同源性最低,由此认为,杆状病毒科的v-cath基因在进化上存在2种进化方式:一类以点突变为主,基因长度变化不明显;另一类突变以小片段的碱基增减为特征。     

中国棉铃虫单粒包埋核多角体病毒（HaSNPV）HindⅢ-Ⅰ片段的序列分析与基因排列研究

对中国棉铃虫单粒包埋核多角体病毒（HaSNPV)基因组中的HindⅢ-Ⅰ片段的序列进行分析,该片段全长7501nt,包括10个开放阅读框：AcMNPV ORF111的同源基因（Ac 111),晚期表达因子2（lef-2）基因,病毒核壳结构蛋白p24基因、gp16基因、多角体包膜蛋白（polyhedron envelope protein,pep)基因、AcMNPV ORF63的同源基因（Ac63),38.7kD基因,晚期表达因子1（lef-1) 基因,及两个特有基因HaSNPV orf591和HasSNPV orf435。基因组的排列比较分析发现与AcMNPV有较大区别。     

Genetic variation and virulence of nucleopolyhedroviruses isolated worldwide from the heliothine pests Helicoverpa armigera, Helicoverpa zea, and Heliothis virescens

To assess the diversity and relationships of baculoviruses found in insects of the heliothine pest complex, a PCR-based method was used to classify 90 samples of nucleopolyhedrovirus (NPV; Baculoviridae: Alphabaculovirus) obtained worldwide from larvae of Heliothis virescens, Helicoverpa zea, and Helicoverpa armigera. Partial nucleotide sequencing and phylogenetic analysis of three highly conserved genes (lef-8, lef-9, and polh) indicated that 67 of these samples contained isolates of the H. zea-H. armigera single nucleopolyhedrovirus (Hz/HaSNPV) species group. Eighteen of the samples contained isolates of a multiple NPV from H. armigera, HearMNPV, and five of the samples contained isolates of Autographa californica MNPV (AcMNPV). Sequencing and analysis of an additional seven loci (orf5/orf5b, hr3-orf62, orf26, orf79, orf124/orf117a, orf42, and a part of the region between hr2 and hr3) in the Hz/HearSNPV isolates further classified these viruses into two groups of HearSNPV variants mostly from India and China and a third group of HzSNPV variants. Some of the samples contained isolates of more than one virus. In bioassays of a selection of isolates against H. zea, the commercially available Gemstar® isolate of HzSNPV killed larvae faster than most other Hz/HaSNPV and HearMNPV isolates. Gemstar® and two HearMNPV isolates exhibited significantly higher LC₅₀s than the Hz/HearSNPV isolates tested. This study expands significantly on what we know about the variation of heliothine NPV populations, provides novel information on the distinct groups in which these NPVs occur, and contributes to the knowledge required for improvement of heliothine baculoviruses as biological control agents.     

一种棉铃虫多角体病毒的纯化与鉴定

对一株纯化的棉铃虫多角体病毒进行电镜观察,形态呈不规则型,直径约2 μm,命名为棉铃虫多角体-B(Helicoverpa armigera nucleocapsid nucleopolyhedrovirus-B,HaNPV-B),它对东方粘虫有较好的感染性,与棉铃虫单核型多角体病毒(Helicoverpa armigera single nucleocapsid NPV,HaSNPV)有不同的宿主域.通过半补齐法建立HaNPV-B基因组文库,拼接了一个6 035 bp的核苷酸片段,推测包含6个ORF,其包含基因内容及基因结构与HaSNPV不同,分析表明两者是不同种病毒,这为杆状病毒与宿主的相互作用及共同进化提供了信息.     

油桐尺蠖单粒包埋核型多角体病毒（BusuNPV）BamHI—H片段的序列分析

对油桐尺蠖单粒包埋核型多用体病毒（Buzurasuppressariasingle－nucleocapsidnucleopolyhedrovirus,BusuNPV）基因组中BamHI－H片段的序列进行分析,该片段全长2422bp,包括三个开放阅读框：p47基因（AcMNPVORF40的同源区）的5′端,完整的组织蛋白酶基因（cathepsin）（AcMNPVORF127的同源区）和p74基因（AcMNPVORF138的同源区）的3′端。序列比较分析表明,BusuNPV的这三个基因与其它杆状病毒的同源基因具有相同的结构保守区。BusuNPV基因组BamHI－H片段上这三个基因的排列顺序完全不同于AcMNPV相应基因的排列顺序。     

棉铃虫多核型多角体病毒38k基因的克隆、序列分析及其蛋白高级结构的预测

采用半补齐方法建立棉铃虫多核衣壳型多角体病毒基因组文库,通过对插入片段进行克隆鉴定和序列分析,获得了38k基因.该基因上游具有晚期调控保守序列TTAAG,是一个晚期表达基因,基因阅读框为903 bp,共编码300个氨基酸,氨基酸序列同源性分析结果表明其与α类杆状病毒的同源性较高,有较近的亲缘关系.氨基酸高级结构的分析表明其与与磷酸酶结构相似性达到95%,与病毒核衣壳的组装有关.     

棉铃虫剂量补偿相关基因Hamsl1的鉴定与功能分析

【目的】棉铃虫Helicoverpa armigera的剂量补偿(dosage compensation, DC)分子机制尚不清楚。本研究旨在通过克隆棉铃虫雄性特异性致死(male specific lethal, msl) 基因Hamsl1,利用RNA干扰技术明确其是否参与调控棉铃虫剂量补偿。【方法】利用RT-PCR同源克隆棉铃虫Hamsl1基因全长cDNA; 利用qPCR技术研究Hamsl1基因在棉铃虫不同发育时期的表达谱;通过显微注射Hamsl1 siRNA到棉铃虫3龄幼虫中对Hamsl1基因进行RNA干扰后,利用qPCR技术检测15个Z染色体基因的表达情况,分析Hamsl1是否调控Z染色体基因剂量。【结果】成功克隆了棉铃虫Hamsl1基因的cDNA序列,鉴定出Hamsl1基因mRNA存在2种剪接体,分别命名为Hamsl1a(GenBank登录号: MK564008)和Hamsl1b(GenBank登录号: MK564009)。功能域分析发现HaMSL1含有典型的PEHE和coiled-coil功能域,具有MSL1蛋白的特征。qPCR分析表明,Hamsl1基因位于棉铃虫Z染色体上;棉铃虫Hamsl1a与Hamsl1b基因表达均具有发育时期特异性,在成虫期表达量最高,且雌雄化蛹后基因表达量差异显著,具有性别特异性。通过同源比对和qPCR分析,在DNA水平鉴定了15个Z染色体候选基因。显微注射Hamsl1 siRNA于3龄幼虫体内72 h,干扰效率为36.01%~64.27%,并未发生雄性致死现象;与对照组相比,Hamsl1 RNAi处理组中棉铃虫15个Z染色体基因在雄性个体中整体呈现表达量上调趋势,而在雌性个体中平均表达水平差异不显著。【结论】本研究初步探明Hamsl1基因位于棉铃虫Z染色体上,且该基因可能通过抑制雄性棉铃虫Z染色体基因表达,调控棉铃虫Z染色体剂量补偿。本研究为深入研究棉铃虫剂量补偿分子机制和绿色防控棉铃虫提供了理论基础。     

Isochores and replication time zones: a perfect match

The mammalian genome is not a random sequence but shows a specific, evolutionarily conserved structure that becomes manifest in its isochore pattern. Isochores, i.e. stretches of DNA with a distinct sequence composition and thus a specific GC content, cause the chromosomal banding pattern. This fundamental level of genome organization is related to several functional features like the replication timing of a DNA sequence. GC richness of genomic regions generally corresponds to an early replication time during S phase. Recently, we demonstrated this interdependency on a molecular level for an abrupt transition from a GC-poor isochore to a GC-rich one in the NF1 gene region; this isochore boundary also separates late from early replicating chromatin. Now, we analyzed another genomic region containing four isochores separated by three sharp isochore transitions. Again, the GC-rich isochores were found to be replicating early, the GC-poor isochores late in S phase; one of the replication time zones was discovered to consist of one single replicon. At the boundaries between isochores, that all show no special sequence elements, the replication machinery stopped for several hours. Thus, our results emphasize the importance of isochores as functional genomic units, and of isochore transitions as genomic landmarks with a key function for chromosome organization and basic biological properties.     

Organization of the ambisense genome of the Helicoverpa armigera Densovirus

A natural densovirus (DNV) of a serious phytophagous pest, Helicoverpa armigera, was isolated. The genome of HaDNV contained 6,039 nucleotides (nt) and included inverted terminal repeats (ITRs) of 545 nt with terminal Y-shaped hairpins of 126 nt. Its DNA sequence and ambisense organization with four typical open reading frames (ORFs) demonstrated that it belonged to the genus Densovirus in the subfamily Densovirinae of the family Parvoviridae.     

Helicoverpa armigera granulovirus interference with progression of H. zea nucleopolyhedrovirus disease in H. zea larvae

Capsular proteins from Helicoverpa armigera granulovirus (HaGV) have previously been shown to enhance H. armigera nucleopolyhedrovirus (HaSNPV) infection in H. armigera larvae. Yet, HaGV and HaS-NPV, as viable viruses, interfered with one another. In our study, we have examined the effects of co-infection of the slow-killing virus HaGV with the fast-killing virus Helicoverpa zea NPV (HzSNPV) on H. zea larvae. The mortality parameter measured was survival time. Virus stocks had 50% lethal concentrations of 3.2x10(-9) g HaGV-infected cadavers (GVC) (HaGV) and 32 occlusion bodies (HzSNPV) per cup. Average survival times were 16.8 and 5.5 days for larvae treated with HaGV and HzSNPV, respectively; death of HzSNPV-treated larvae was as early as 72 h posttreatment. In co-infection experiments in which larvae were treated concurrently with both viruses, the viruses competed in typical fashion for host resources. However, interference with disease progression in HzSNPV-fed larvae occurred even when HaGV was fed to larvae up to 36 h after the NPV, a time at which NPV infection should have been well established in host larvae. At death, co-infected larvae were observed microscopically to be filled with HaGV granules rather than HzSNPV polyhedra. The time study results imply that HaGV might be outcompeting HzSNPV by inhibiting its replication. We also observed that H. zea larvae treated with high dosages of HaGV (> or =3x10(-5) g GVC) were initially stunted but had survival times similar to those of larvae treated with lower dosages.     

A genomic basis for the evolution of vertebrate transcription factors containing amino Acid runs

We have previously shown that polyAla (A) tract-containing proteins frequently present runs of glycine (G), proline (P), and histidine (H) and that, in their ORFs, GC content at all codon positions is higher than that in the rest of the genome. In this study, we present new analyses of these human proteins/ORFs. We detected striking differences in codon usage for A, G, and P in and out of runs. After dividing the ORFs, we found that 5' halves were richer in runs than 3' halves. Afterward, when removing the runs, we observed that the run-rich halves (grouped irrespectively of their 5' or 3' position) had a marked statistical tendency to have more homo- and hetero-dicodons for A, G, P, and H than the run-poor halves. This suggests that, in addition to the necessary GC-rich genomic background, a specific codon organization is probably required to generate these coding repeats. Homo-dicodons may indeed provide primers for run formation through polymerase slippage. The compositional analysis of human HOX genes, the most polyAla-rich family, and their comparison with their zebrafish homologs, support these hypotheses and suggest possible effects of genomic environment on ORF evolution and organismal diversification.     

灰斑古毒蛾核型多角体病毒三个晚期表达因子基因

将灰斑古毒蛾(Orgyiaericae)单粒包埋型核型多角体病毒(OrerSNPV)基因组DNA的各EcoRI酶切片段进行克隆和测序。序列分析结果表明EcoRI-M(3．0kb)与EcoRI-P片段(2．2kb)相连处含有编码晚期表达因子(LEF-2)的开放阅读框(ORF)。同时在EcoRI-E(约10kb)片段两端分别含有ref-3和lef-11基因的部分序列。lef-2基因编码区由648bp组成,可编码216个氨基酸残基的多肽,预计蛋白质分子量为23．7kDa。将OrerSNPVLEF-2氨基酸序列与其它已知的27种杆状病毒的LEF．2序列比较,发现OrerSNPV与其它鳞翅目NPVLEF．2氨基酸有35％-49％同源性,其中与BusuSNPV,MaMNPV-A,HezeSNPV、Hear3NPV和LdMNPV同源性最高,和GV有26％-31％同源性,与膜翅目松柏锯角叶蜂NPV的同源性为32％,与库蚊杆状病毒的同源性只有23％。根据氨基酸序列绘制的分子进化树表明28种杆状病毒lef-2基因可以分为鳞翅目NPV、GV、膜翅目NeseNPV与双翅目Culex nigripalpus Baculovirus四个分支。oret SNPV lef-2与BUSUsnpv在进化树上关系最为接近,而orerSNPV lef-3和LdMNPV的最接近,OrerSNPV lef-11则和SeMNPV的关系最接近。     

Replication fork density increases during DNA synthesis in X. laevis egg extracts

Duplication of the eukaryotic genome depends on the temporal and spatial organization of DNA replication during the cell cycle. To investigate the genomic organization of DNA replication in a higher eukaryote, multiple origins of replication must be simultaneously analyzed over large regions of the genome as DNA synthesis progresses through S phase of the cell cycle. We have employed a novel technique that allows for the quantitative analysis of DNA replication on a genome wide basis. The technique involves stretching and aligning individual DNA molecules on a glass surface. As a model system, Xenopus laevis egg extract was used to differentially label sperm chromatin at successive time points after the start of DNA synthesis. The differentially labeled DNA allows earlier and later replicating sequences to be distinguished, and hence the sites of DNA synthesis at any given time can be directly visualized. Genomic DNA was extracted, and measurements made on the linearized molecules provided a comprehensive analysis of the spatial and temporal organization of DNA replication in the X. laevis in vitro replication system. It was found that: (i) DNA synthesis initiates asynchronously at irregular intervals but continuously as DNA replication advances; and (ii) that the frequency of initiation (the number of activated origins per kilobase) increases as DNA synthesis nears completion. The implications of these findings for the regulation of DNA replication in early embryos is discussed.     

The complete nucleotide sequence and its organization of the genome of Barley yellow dwarf virus-GAV

The Barley yellow dwarf disease (BYD) was firstly recognized as an aphid transmitted virus disease by Oswald and Houston[1] in 1951. Now, Barley yel-low dwarf viruses (BYDVs) belong to members of the plant virus family Luteoviridae. They are phloem- limited and obligately transmitted in the circula-tive/persistent manner by several species of cereal aphids and can cause significant economic losses worldwide because of damage to barley, wheat, and oats. In China, BYDVs cause mainly yello…     

T4-Like genome organization of the Escherichia coli O157:H7 lytic phage AR1

We report the genome organization and analysis of the first completely sequenced T4-like phage, AR1, of Escherichia coli O157:H7. Unlike most of the other sequenced phages of O157:H7, which belong to the temperate Podoviridae and Siphoviridae families, AR1 is a T4-like phage known to efficiently infect this pathogenic bacterial strain. The 167,435-bp AR1 genome is currently the largest among all the sequenced E. coli O157:H7 phages. It carries a total of 281 potential open reading frames (ORFs) and 10 putative tRNA genes. Of these, 126 predicted proteins could be classified into six viral orthologous group categories, with at least 18 proteins of the structural protein category having been detected by tandem mass spectrometry. Comparative genomic analysis of AR1 and four other completely sequenced T4-like genomes (RB32, RB69, T4, and JS98) indicated that they share a well-organized and highly conserved core genome, particularly in the regions encoding DNA replication and virion structural proteins. The major diverse features between these phages include the modules of distal tail fibers and the types and numbers of internal proteins, tRNA genes, and mobile elements. Codon usage analysis suggested that the presence of AR1-encoded tRNAs may be relevant to the codon usage of structural proteins. Furthermore, protein sequence analysis of AR1 gp37, a potential receptor binding protein, indicated that eight residues in the C terminus are unique to O157:H7 T4-like phages AR1 and PP01. These residues are known to be located in the T4 receptor recognition domain, and they may contribute to specificity for adsorption to the O157:H7 strain.     

棉铃虫核型多角体病毒ORF33基因的原核表达和在宿主细胞中亚细胞定位

对棉铃虫Helicoverpa ar migera核型多角体病毒HearSNPV的ORF33基因(ha33)进行克隆和原核表达,hass在E.coli中表达不完全,表达产物的大小为17kDa,小于预测的分子量28.4kDa。用纯化的原核表达产物免疫家兔,制备了多克隆抗体,应用多克隆抗体检测了HearSNPV感染的宿主细胞(HzAMI)中ORF33基因的表达,表达产物的分子量为31kDa。并通过共聚焦荧光显微镜方法,用多克隆抗体检测编码的蛋白在宿主细胞(HzAM1)中的亚细胞定位,发现ha33编码的蛋白存在于宿主细胞的细胞质中,并持续到感染后期。     

Complete genome sequence of an aerobic thermoacidophilic crenarchaeon, Sulfolobus tokodaii strain7.

The complete genomic sequence of an aerobic thermoacidophilic crenarchaeon, Sulfolobus tokodaii strain7 which optimally grows at 80 degrees C, at low pH, and under aerobic conditions, has been determined by the whole genome shotgun method with slight modifications. The genomic size was 2,694,756 bp long and the G + C content was 32.8%. The following RNA-coding genes were identified: a single 16S-23S rRNA cluster, one 5S rRNA gene and 46 tRNA genes (including 24 intron-containing tRNA genes). The repetitive sequences identified were SR-type repetitive sequences, long dispersed-type repetitive sequences and Tn-like repetitive elements. The genome contained 2826 potential protein-coding regions (open reading frames, ORFs). By similarity search against public databases, 911 (32.2%) ORFs were related to functional assigned genes, 921 (32.6%) were related to conserved ORFs of unknown function, 145 (5.1%) contained some motifs, and remaining 849 (30.0%) did not show any significant similarity to the registered sequences. The ORFs with functional assignments included the candidate genes involved in sulfide metabolism, the TCA cycle and the respiratory chain. Sequence comparison provided evidence suggesting the integration of plasmid, rearrangement of genomic structure, and duplication of genomic regions that may be responsible for the larger genomic size of the S. tokodaii strain7 genome. The genome contained eukaryote-type genes which were not identified in other archaea and lacked the CCA sequence in the tRNA genes. The result suggests that this strain is closer to eukaryotes among the archaea strains so far sequenced. The data presented in this paper are also available on the internet homepage (http://www.bio.nite.go.jp/E-home/genome_list-e.html/).     

The complete nucleotide sequence and its organization of the genome of Barley yellow dwarf virus-GAV

The complete nucleotide sequence of genomic RNA of BYDV-GAV was determined. It comprised 5685 nucleotides and contained six open reading frames and four un-translated regions. The size and organization of BYDV-GAV genome were similar to those of BYDV PAV-aus. The nucleotide and deduced amino acid sequences of the six ORFs were aligned and compared with those of other luteoviruses. The results showed that there was a high degree of identity between BYDV-GAV and MAV-PS1 in all ORFs except ORF5 and ORF6, which had only 87.4% and 70.2% identities respectively. The reported genomic nucleotide sequence of MAV was shorter than that of BYDV-GAV, but the comparison of the genomic nucleotide sequences for MAV-PS1 and GAV showed 90.4% sequence identity for the same region of the genome. According to the level of sequence similarities, BYDV-GAV should be closely related to BYDV-MAV.     

Laboratory and field studies on the integrated pest management of Helicoverpa armigera (Hübner) in cotton, based on pheromone trap catch threshold level

Abstract: With a view to using parasitoids and predators in integrated pest management of the target pest Helicoverpa armigera in cotton fields, basic studies on the egg parasitism, toxicity of insecticides to parasitoids and predators and compatibility of nuclear polyhedrosis virus (NPV) of H. armigera with other insecticides were conducted in the laboratory. Results revealed that egg parasitism in the laboratory by Trichogramma chilonis was 75.6%. Among the insecticides tested against T. chilonis and the predator Chrysoperla carnea , nimbecidine (neem product) and dipel resulted in zero mortality, with only a low level of mortality by dimethoate, cypermethrin, fenvalerate, alphamethrin and monocrotophos. Combinations of nimbecidine 2% + NPV at 250 larval equivalents (LE)/ha and dipel 8 l + NPV @250 LE/ha were the most effective treatments against H. armigera . The integrated pest management components ( T . chilonis , C . carnea , NPV, nimbecidine, dipel and synthetic chemicals) were imposed at different intervals on the basis of pheromone trap threshold level (7 moths/trap per night) on a consolidated block of 40 ha cotton (MCU-1) fields at two locations, Shankarabanda and Korlagundi. The results demonstrated a significant superiority of the IPM strategy in terms of both cost versus benefit and environmental safety over that used in the farmer's fields where only conventional control methods were followed.