Complete nucleotide sequence and genome organization of tobacco mosaic virus isolated from Viciafaba

Based on reported TMV-U1 sequence, primers were designed and fragments covering the entire genome of TMV broad bean strain (TMV-B) were obtained with RT-PCR. These fragments were cloned and sequenced and the 5' and 3' end sequences of genome were confirmed with RACE. The complete sequence of TMV-B comprises 6 395 nucleotides (nt) and four open reading frames, which correspond to 126 ku (1 116 amino acids), 183 ku (1 616 amino acids), 30 ku (268 amino acids) and 17.5 ku proteins (159 amino acids). The complete nucleotide sequence of TMV-B is 99.4% identical to that of TMV-U1. The two virus isolates share the same sequence of 5', 3' non-coding region and 17.5 K ORF, and 6, 1 and 3 amino acid changes are found in 126 K protein, 54 K protein and 30 K protein, respectively. The possible mechanism on the infection of TMV-B in Vicia faba is discussed.     

伪狂犬病病毒湖北株糖蛋白gD基因的克隆及序列测定

According to the sequence of gD gene of PRV Rice strain, the primers of 22bp were designed.Using PRV genomic DNA of Hubei and Shuangcheng virus strains which infected BHK 21 cell separately as template, the gD gene of PRV was amplified sucessfully by PCR and cloned into pGEM T vector. Restriction enzyme analysis showed that the cloned gD gene at SmaⅠ,SalⅠ,KpnⅠ,PvuⅡ sites was the same as that of PRV Rice strain. The gD gene consisted of 1,263 nucleotides including an open reading frame spanning 1,197 nucleotieds which could encode a protein of 398 amino acids. The ORF didn′t include an amino acid sequence directing N linked glycosylation (NXT or NXS). Comparison of our complete Hubei strain gD gene sequence with the Rice strain gD gene sequence showed that the nucleotide and deduced amino acid homology were about 97% and there was an 12 basepair deletion in 835 846 nucleotide sites that coded Arg Pro Arg Pro. A region of the amino acid sequence and the positions of the cysteine residues of PRV HB gD were homologous to HSV I glycoprotein D. This work laid foundation for PRV gene immunization and studying PRV sub unit vaccine.     

Isolation and Complete Nucleotide Sequence of the Measles Virus IMB-1 Strain in China

The complete nucleotide sequence of the measles virus strain IMB-1,which was isolated in China,was determined.As in other measles viruses,its genome is 15,894 nucleotides in length and encodes six proteins.The full-length nucleotide sequence of the IMB-1 isolate differed from vaccine strains (including wild-type Edmonston strain) by 4%-5% at the nucleotide sequence level.This isolate has amino acid variations over the full genome,including in the hemagglutinin and fusion genes.This report is the first to de...     

Different quasispecies with great mutations hide in the same subgroup J field strain of avian leukosis virus

Blood samples were collected from a local strain of chickens associated with serious tumor cases in Shandong Province.The samples were inoculated into chicken embryo fibroblast and DF-1 cells for virus isolation and identification,respectively.The inoculated cells were screened for three common chicken tumor viruses.Nine strains of avian leukosis virus subgroup J(ALV-J) were identified,and were designated LY1201‐LY1209.The env gene from the LY1201 strain was amplified and cloned.All nine resultant env clones(clones 01-09) were sequenced,and the gp85 and gp37 amino acid regions were subjected to homology analysis.Clones 01 and 03 had 10 amino acid deletions in the gp85 region compared to the other seven clones,suggesting that at least two quasispecies with obvious mutations coexist in the same field strain.Among these nine clones,three had identical gp85 and gp37 sequences,and were recognized as the dominant LY1201 quasispecies.The amino acid sequence homology of gp37 and gp85 among the nine clones was 98.5%-100.0% and 96.6%-100.0% respectively,suggesting that the gp85 region of the env gene can better display the quasispecies diversity of ALV-J than gp37.     

Cloning of fatty acid elongase1 gene and molecular identification of A and C genome in Brassica species

The fatty acid elongase 1 (FAE1) genes of Brassic napus were cloned from two cultivars, i.e. Zhong- shuan No. 9 with low erucic acid content, and Zhongyou 821 with high erucic acid content, using the degenerate PCR primers. The sequence analysis showed that there was no intron within the FAE1 genes. The FAE1 genes from Zhongyou 821 contained a coding sequence of 1521 nucleotides, and those cloned from Zhongshuan No. 9 contained a 1517 bp coding sequence. Alignment of the FAE1 sequences from Brassica rapa, B. oleracea and B. napus detected 31 single nucleotide polymorphic sites (2.03%), which resulted in 7 amino-acid substitutions. Further analysis indicated that 19 SNPs were genome-specific, of which, 95% were synonymous mutations. The nucleotide substitution at po- sition 1217 in the FAE1 genes led to a specific site of restricted cleavage. An AvrII cleavage site was present only in the C genome genes and absent in the A genome FAE1 genes. Digestion profile of the FAE1 sequences from B. rapa, B. oleracea and B. napus produced with AvrII confirmed that the FAE1 genes of B. oleracea origin was recognized and digested, while that of B. rapa origin could not. The results indicated that by AvrII cleavage it was possible to distinguish B. rapa from B. oleracea and be- tween the A and C genome of B. napus. In addition, the FAE1 genes could be used as marker genes to detect the pollen flow of B. napus, thus providing an alternative method for risk assessment of gene flow.     

Isolation and characterization of resistance and defense gene analogs in cotton (Gossypium barbadense L.)

Plant disease resistance gene (R gene) and defense response gene encode some con-served motifs. In the present work,a PCR strategy was used to clone resistance gene analogs (RGAs) and defense gene analogs (DGAs) from Sea-island cotton variety Hai7124 using oligonucleotide primers based on the nucleotide-binding site (NBS) and serine/threonine kinase (STK) in the R-gene and pathogenesis-related proteins of class 2 (PR2) of defense response gene. 79 NBS sequences,21 STK sequences and 11 DGAs were cloned from disease-resistance cotton. Phylogenic analysis of 79 NBS-RGAs and NBS-RGAs nucleotide sequences of cotton already deposited in GenBank identified one new sub-cluster. The deduced amino acid sequences of NBS-RGAs and STK-RGAs were divided into two distinct groups respectively: Toll/Interleukin-1 receptor (TIR) group and non-TIR group,A group and B group. The expression of RGAs and DGAs having consecutive open reading frame (ORF) was also investigated and it was found that 6 NBS-RGAs and 1 STK-RGA were induced,and 1 DGA was up-regulated by infection of Verticillium dahliae strain VD8. 4 TIR-NBS-RGAs and 4 non-TIR-NBS-RGAs were arbitrarily used as probes for Southern-blotting. There existed 2-10 blotted bands. In addition,since three non-TIR-NBS-RGAs have the same hybridization pattern,we conjecture that these three RGAs form a cluster distribution in the genome.     

Cloning and sequence analysis of genome from the Inner Mongolia strain of the endogenous betaretroviruses (enJSRV)

In order to amplify the complete genome of enJSRV from the strain of Inner Mongolia (enJSRV-NM), we used enJSRV-specific and JSRV-specific DNA probes in dot blot hybridization. Seven pairs of primers were designed based on Genbank sequences. Seven fragments were obtained by PCR and were cloned into the PMD19- T vectors. The recombinant plasmids were sequenced and analyzed. The results showed that the genome was 7 942 bp in length and contained four overlapping open reading frames corresponding to the gag, pro, pol and env genes as well as an additional open reading frame (orf-x) that overlaps the 3' end of the pol gene. The nucleotide acid sequences of the enJSRV-NM loci were compared with the sequences of South Africa enJS56A1 strain (Accession No. AF153615) and USA JSRV21 strain (Accession No. AF105220). The nucleotide acid identities were 99.2% and 92.3% respectively. Two zinc fingers were found in the NC region in the predicted amino acid sequence. However, the YXXM motif, which is a reliable molecular marker for the infectious exogenous virus, was not found in the TM region. It was found that the enJSRV-NM region was 90%-98% identical at the amino acid level to its exogenous infectious counterparts in most of the retroviral genome. This is the first nucleotide sequence of enJSRV reported in P.R China. The resource work has provided a wide range of information useful not only for expression genomics and annotation of genomic DNA sequence, but also for further research on the clinical diagnosis of OPA.     

Murine mammary tumor virus pol-related sequences in human DNA: characterization and sequence comparison with the complete murine mammary tumor virus pol gene.

Sequences in the human genome with homology to the murine mammary tumor virus (MMTV) pol gene were isolated from a human phage library. Ten clones with extensive pol homology were shown to define five separate loci. These loci share common sequences immediately adjacent to the pol-like segments and, in addition, contain a related repeat element which bounds this region. This organization is suggestive of a proviral structure. We estimate that the human genome contains 30 to 40 copies of these pol-related sequences. The pol region of one of the cloned segments (HM16) and the complete MMTV pol gene were sequenced and compared. The nucleotide homology between these pol sequences is 52% and is concentrated in the terminal regions. The MMTV pol gene contains a single long open reading frame encoding 899 amino acids and is demarcated from the partially overlapping putative gag gene by termination codons and a shift in translational reading frame. The pol sequence of HM16 is multiply terminated but does contain open reading frames which encode 370, 105, and 112 amino acid residues in separate reading frames. We deduced a composite pol protein sequence for HM16 by aligning it to the MMTV pol gene and then compared these sequences with other retroviral pol protein sequences. Conserved sequences occur in both the amino and carboxyl regions which lie within the polymerase and endonuclease domains of pol, respectively.     

Nucleotide sequence analysis of cDNA encoding the coat protein of cucumber mosaic virus: genome organization and molecular features of the protein

The cDNA sequence coding for the coat protein of cucumber mosaic virus (Japanese Y strain) was cloned, and its nucleotide sequence was determined. The sequence contains an open reading frame that encodes the coat protein composed of 218 amino acids. The nucleotide and deduced amino acid sequences of the coat protein of this strain were compared with those of the Q strain; the homologies of the sequences were 78% and 81%, respectively. Further study of the sequences gave an insight into the genome organization and the molecular features of the coat protein. The coding region can be divided into three characteristic regions. The N-terminal region has conserved features in the positively charged structure, the hydropathy pattern and the predicted secondary structure, although the amino acid sequence is varied mainly due to frameshift mutations. It is noteworthy that the positions of arginine residues in this region are highly conserved. Both the nucleotide and amino acid sequences of the central region are well conserved. The amino acid sequence of the C-terminal region is not conserved, because of frameshift mutations, however, the total number of amino acids is conserved. The nucleotide sequence of the 3'-noncoding region is divergent, but it could form a tRNA-like structure similar to those reported for other viruses. Detailed investigation suggests that the Y and Q strains are evolutionarily distant.     

Identification of a protease gene of human T-cell leukemia virus type I (HTLV-I) and its structural comparison

We determined the nucleotide sequence of a region between the gag and pol genes of a replication-competent proviral clone of a human T-cell leukemia virus type I (HTLV-I) from MT-2 cells. This region overlapping the gag and pol genes contains an open reading frame with a different phase from others. The deduced amino acid sequences show significant homology with the known protease gene of other retroviruses, and harbors highly conserved amino acid sequences that are well conserved in other retroviral protease domains. These results indicate that this open reading frame encodes a HTLV-I protease.     

绵羊肺腺瘤病毒中国NM株部分gag基因的克隆与序列分析

参照GenBank中已发表的绵羊肺腺瘤病毒的基因序列,设计合成一对引物,对绵羊肺腺瘤病毒(Jaagsiekte sheep retrovirus,JSRV)内蒙株的gag基因中主要编码CA蛋白的基因段进行PCR扩增,产物经琼脂糖凝胶电泳分析,呈现一条约897bp的特异条带,将其回收后克隆入pMD—18T载体中,并进行序列测定与分析。结果表明,与南非株(基因序列号NC—001494)的gag基囚序列比较,核苷酸同源性为83％,推导出的氨基酸同源性为84％。与美国株(基因序列号AF105220)的gag基因序列比较,核苷酸同源性为81．5％,氨基酸同源性为83％。这是我国首次报道的绵羊肺腺瘤病毒的gag基因的一段序列,为我国科研工作者进行更深入的研究奠定基础。     

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.     

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…     

Analysis of the nucleotide sequence of a fragment (92-100%) of the CELO avian adenovirus genome]

The nucleotide sequence of 92-100% of the adenovirus CELO (FAV1), strain Phelps, genome has been determined. The computer analysis of the sequences revealed a ClaI site methylated by m*Ecodam. A recognition site for XbaI and two sites for PstI, not found in the corresponding genome of CELO, strain Ote, have been determined. Three extensive (more than 100 amino acid residues) open reading frames exist, coding for the polypeptides with molecular weights of 31.5, 19.3 and 14.5 kD (276, 178 and 128 amino acids, respectively). Some shorter open reading frames have been detected as well within the sequences studied.     

Isolation of cDNAs encoding for two distinct isoforms of the TATA-Box binding proteins from common bean (<Emphasis Type="Italic">Phaseolus vulgaris</Emphasis> L.)

The TATA-box binding protein (TBP) is one of the 4 DNA-binding proteins that has been shown to associate with the proximal promoter region (−295) of the gene for bean seed storage protein phaseolin. The −295 promoter is essential for spatial and temporal control of the phaseolin gene expression. We designed a pair of degenerated primers based on the highly conserved sequence of the carboxyl-terminal domain of yeast TBP and used PCR to amplify the corresponding sequence from the bean cDNA. By using the amplified fragment as a probe, we screened a cDNA library derived from poly A(+) RNA from developing bean seeds and isolated 2 nearly full-length cDNA clones (813 and 826 bp long). The cDNAs encode 2 distinct isoforms of bean TBP, PV1 and PV2, each with an open reading frame of 200 amino acid residues. The 2 cDNA sequences share an 85.8% overall nucleotide sequence identity, with the coding region showing a higher degree of identity (94.4%) than the 5′- and 3′-untranslated regions (69%). The deduced amino acid sequence of the bean TBP isoforms differ in only 3 amino acid residues at positions 5, 9, and 16, all located in the amino-terminal region. The carboxyl-terminal domain of 180 amino acid residues shows a high degree (>82%) of evolutionary sequence conservation with the TBP sequences from other eukaryotic species. This domain possesses the 3 highly conserved structural motifs, namely the 2 direct repeat sequences, a central basic region rich in basic amino acid residues, and a region similar to the sigma factor of prokaryote. On the basis of this and other findings, we suggest that higher plants in general may have at least 2 copies of TBP gene, presumably resulting from the global duplication of the genome. Accession numbers AF015784 and AF015785 at the GenBank.