RNA3 nucleotide sequence analyses ofpeanut stunt virusMi strain

2005 ◽  
Vol 2 (1) ◽  
pp. 33-38
Author(s):  
Xu Ze-Yong ◽  
Yan Li-Ying ◽  
Chen Kun-Rong ◽  
Marcel Prins
Keyword(s):  
Nucleotide Sequence ◽  
Movement Protein ◽  
Amino Acid Identity ◽  
Open Reading Frames ◽  
Sequence Analyses ◽  
Tomato Aspermy Virus ◽  
Subgroup Ii ◽  
Putative Movement Protein ◽  
Peanut Stunt Virus ◽  
Reading Frames

AbstractNucleotide sequence of full-length cDNA ofpeanut stunt virus(PSV) Mi strain RNA3 was determined and compared with those of PSV-ER and -J (subgroup I) and PSV-W (subgroup II), strains ofcucumber mosaic virus(CMV) andtomato aspermy virus(TAV). PSV-Mi RNA3 consists of 2170 nt and has two open reading frames, encoding a putative movement protein (3a protein) and a coat protein (CP). PSV-Mi RNA3 is 77.7% and 78.5% identical to those of PSV-ER and -J, whereas it shares 76.6% identity with PSV-W. Nucleotide identity of3aandcpgenes between PSV strains Mi and ER, J and W was 78.3–79.3% and 74.4–77.8%, respectively. Amino acid identity of 3a and CP between PSV-Mi and -ER, -J and -W was 73.9–77.4% and 64.8–77.5%, respectively. RNA3 of PSV-Mi (GenBank accession no. AY775057) had a varied intercistronic and 5′-untranslated region compared with those of PSV strains ER, J and W. Results indicate that PSV-Mi represents a new PSV subgroup from China, designated as subgroup III.

scholarly journals Evidence for a Third Taxonomic Subgroup of Peanut Stunt Virus from China

Plant Disease ◽  
1998 ◽  
Vol 82 (9) ◽  
pp. 992-998 ◽  
Author(s):  
Xu Zeyong ◽  
Colleen M. Higgins ◽  
Chen Kunrong ◽  
Ralf G. Dietzgen ◽  
Zhang Zhongyi ◽  
...  
Keyword(s):  
Nucleotide Sequence ◽  
Amino Acid Identity ◽  
Specific Primers ◽  
Chenopodium Amaranticolor ◽  
Acid Identity ◽  
Cp Gene ◽  
Gene Nucleotide Sequence ◽  
Subgroup Ii ◽  
Peanut Stunt Virus ◽  
Type Strains

On the basis of host reactions and serology, six Chinese peanut stunt virus (PSV) strains were found to be distinct from PSV-E and PSV-W, two type strains representing distinct serological subgroups. Chinese PSV strains were characterized by infecting Chenopodium amaranticolor and C. quinoa systemically. All Chinese strains were serologically closely related to each other, but distinct from PSV-E and more distant from PSV-W. Using two PSV-specific primers designed from conserved regions of the PSV RNA3 nucleotide sequence, cDNA transcribed from RNA3 of two Chinese PSV strains, Mi and S, was amplified by PCR and cloned. The sequenced cDNA of the two PSV strains included 654 nt of the coat protein (CP) gene. The identity of the CP gene nucleotide sequence between PSV-Mi and PSV-S was 99.0%, with 99.5% amino acid identity. Identity of the CP gene nucleotide sequence was 75.6 to 77.8% between PSV-Mi and -S (the two Chinese strains) and PSV-ER and -J in PSV subgroup I; and 74.1 to 74.4% between PSV-Mi and -S, and PSV-W in subgroup II. Based on these results, we propose placing PSV Chinese strains into a new PSV subgroup III.

scholarly journals Expression of the Peanut stunt virus Coat Protein Gene Is Essential and Sufficient for Production of Host-Dependent Ribbon-Like Inclusions in Infected Plants

2004 ◽  
Vol 94 (7) ◽  
pp. 722-729 ◽  
Author(s):  
N. S. Bashir ◽  
M. Sanger ◽  
U. Järlfors ◽  
S. A. Ghabrial
Keyword(s):  
Coat Protein ◽  
Leaf Tissue ◽  
Potato Virus X ◽  
Open Reading Frames ◽  
Subgroup Ii ◽  
Enzymelinked Immunosorbent Assay ◽  
Polymerase Chain ◽  
Peanut Stunt Virus ◽  
Virus Coat ◽  
Reading Frames

We previously have reported that infection of tobacco protoplasts or leaf tissue with the cucumovirus Peanut stunt virus (PSV) induced the production of unusual cytoplasmic ribbon-like inclusions. The formation of these novel inclusions is strain-specific, because infection of tobacco with subgroup II PSV strains, but not subgroup I strains, induced the production of inclusions. Furthermore, we have demonstrated that induction of the ribbon-like inclusions maps to PSV subgroup II RNA3, which codes for the coat protein (CP) and movement protein (MP). We have now extended these studies using chimeric constructs containing CP and MP open reading frames (ORFs) from PSV strains ER and W that belong to subgroups I and II, respectively. Additionally, recombinant Potato virus X (PVX) vectors containing translatable and untranslatable PSV CP ORF were constructed. Plants inoculated with infectious chimeric PSV or recombinant PVX transcripts were analyzed for CP expression by enzymelinked immunosorbent assay and reverse transcription-polymerase chain reaction and for inclusion production by electron microscopy. The results of these experiments indicated that translation of the CP ORF alone is essential and sufficient for inclusion production. In immunogold labeling experiments using an antiserum to PSV virions, abundant gold labeling of the inclusions was observed, suggesting that PSV CP is probably a major component of the inclusions. Because inclusion production is host specific, a host factor is likely to be involved. In addition to their diagnostic importance, these novel inclusions may also prove valuable in identifying the host factors that interact with PSV CP.

scholarly journals Pineapple bacilliform CO virus: Diversity, Detection, Distribution, and Transmission

Plant Disease ◽  
2012 ◽  
Vol 96 (12) ◽  
pp. 1798-1804 ◽  
Author(s):  
D. M. Sether ◽  
M. J. Melzer ◽  
W. B. Borth ◽  
J. S. Hu
Keyword(s):  
Reverse Transcriptase ◽  
Movement Protein ◽  
Rnase H ◽  
Open Reading Frames ◽  
Ananas Comosus ◽  
Genomic Variants ◽  
Virus Diversity ◽  
Putative Movement Protein ◽  
Dysmicoccus Neobrevipes ◽  
Reading Frames

Members of the genus Badnavirus (family Caulimovirdae) have been identified in dicots and monocots worldwide. The genome of a pineapple badnavirus, designated Pineapple bacilliform CO virus-HI1 (PBCOV-HI1), and nine genomic variants (A through H) were isolated and sequenced from pineapple, Ananas comosus, in Hawaii. The 7,451-nucleotide genome of PBCOV-HI1 possesses three open reading frames (ORFs) encoding putative proteins of 20 (ORF1), 15 (ORF2), and 211 (ORF3) kDa. ORF3 encodes a polyprotein that includes a putative movement protein and viral aspartyl proteinase, reverse transcriptase, and RNase H regions. Three distinct groups of putative endogenous pineapple pararetroviral sequences and Metaviridae-like retrotransposons encoding long terminal repeat, reverse-transcriptase, RNase H, and integrase regions were also identified from the pineapple genome. Detection assays were developed to distinguish PBCOV-HI1 and genomic variants, putative endogenous pararetrovirus sequences, and Ananas Metaviridae sequences also identified in pineapple. PBCOV-HI1 incidences in two commercially grown pineapple hybrids, PRI 73-114 and PRI 73-50, was 34 to 68%. PBCOV-HI1 was transmitted by gray pineapple mealybugs, Dysmicoccus neobrevipes, to pineapple.

scholarly journals Complete Nucleotide Sequence and Genetic Organization of the 210-Kilobase Linear Plasmid of Rhodococcus erythropolis BD2

2003 ◽  
Vol 185 (17) ◽  
pp. 5269-5274 ◽  
Author(s):  
Christiane Stecker ◽  
Andre Johann ◽  
Christina Herzberg ◽  
Beate Averhoff ◽  
Gerhard Gottschalk
Keyword(s):  
Nucleotide Sequence ◽  
Complete Nucleotide Sequence ◽  
Protein Modification ◽  
Rhodococcus Erythropolis ◽  
Open Reading Frames ◽  
Linear Plasmid ◽  
Sequence Analyses ◽  
Transposition Regulation ◽  
Sequence Similarities ◽  
Reading Frames

ABSTRACT The complete nucleotide sequence of the linear plasmid pBD2 from Rhodococcus erythropolis BD2 comprises 210,205 bp. Sequence analyses of pBD2 revealed 212 putative open reading frames (ORFs), 97 of which had an annotatable function. These ORFs could be assigned to six functional groups: plasmid replication and maintenance, transport and metalloresistance, catabolism, transposition, regulation, and protein modification. Many of the transposon-related sequences were found to flank the isopropylbenzene pathway genes. This finding together with the significant sequence similarities of the ipb genes to genes of the linear plasmid-encoded biphenyl pathway in other rhodococci suggests that the ipb genes were acquired via transposition events and subsequently distributed among the rhodococci via horizontal transfer.

scholarly journals The Nucleotide Sequence of Shiga Toxin (Stx) 2e-Encoding Phage φP27 Is Not Related to Other Stx Phage Genomes, but the Modular Genetic Structure Is Conserved

2002 ◽  
Vol 70 (4) ◽  
pp. 1896-1908 ◽  
Author(s):  
Jürgen Recktenwald ◽  
Herbert Schmidt
Keyword(s):  
Nucleotide Sequence ◽  
Shiga Toxin ◽  
Phage Genome ◽  
Genetic Recombination ◽  
Genome Structure ◽  
Open Reading Frames ◽  
Functional Modules ◽  
Phage Propagation ◽  
Reading Frames ◽  
Lambdoid Phages

ABSTRACT In this study we determined the complete nucleotide sequence of Shiga toxin 2e-encoding bacteriophage φP27, isolated from the Shiga toxin-producing Escherichia coli patient isolate 2771/97. φP27 is integrated as a prophage in the chromosomal yecE gene. This integration generates identity segments of attL and attR sites with lengths of 11 nucleotides. The integrated prophage genome has a size of 42,575 bp. We identified 58 open reading frames (ORFs), each with a length of >150 nucleotides. The deduced proteins of 44 ORFs showed significant homologies to other proteins present in sequence databases, whereas 14 putative proteins did not. For 29 proteins, we could deduce a putative function. Most of these are related to the basic phage propagation cycle. The φP27 genome represents a mosaic composed of genetic elements which are obviously derived from related and unrelated phages. We identified five short linker sequences of 22 to 151 bp in the φP27 sequence which have also been detected in a couple of other lambdoid phages. These linkers are located between functional modules in the phage genome and are thought to play a role in genetic recombination. Although the overall DNA sequence of φP27 is not highly related to other known phages, the data obtained demonstrate a typical lambdoid genome structure.

scholarly journals Nucleotide Sequence and Genetic Structure of a Novel Carbaryl Hydrolase Gene (cehA) from Rhizobium sp. Strain AC100

2002 ◽  
Vol 68 (3) ◽  
pp. 1220-1227 ◽  
Author(s):  
Masayuki Hashimoto ◽  
Mitsuru Fukui ◽  
Kouichi Hayano ◽  
Masahito Hayatsu
Keyword(s):  
Nucleotide Sequence ◽  
Insertion Sequence ◽  
Amino Acid Sequences ◽  
Open Reading Frames ◽  
Homology Search ◽  
Sequencing Analysis ◽  
Terminal Sequence ◽  
Homologous Sequences ◽  
Naphthyl Acetate ◽  
Reading Frames

ABSTRACT Rhizobium sp. strain AC100, which is capable of degrading carbaryl (1-naphthyl-N-methylcarbamate), was isolated from soil treated with carbaryl. This bacterium hydrolyzed carbaryl to 1-naphthol and methylamine. Carbaryl hydrolase from the strain was purified to homogeneity, and its N-terminal sequence, molecular mass (82 kDa), and enzymatic properties were determined. The purified enzyme hydrolyzed 1-naphthyl acetate and 4-nitrophenyl acetate indicating that the enzyme is an esterase. We then cloned the carbaryl hydrolase gene (cehA) from the plasmid DNA of the strain and determined the nucleotide sequence of the 10-kb region containing cehA. No homologous sequences were found by a database homology search using the nucleotide and deduced amino acid sequences of the cehA gene. Six open reading frames including the cehA gene were found in the 10-kb region, and sequencing analysis shows that the cehA gene is flanked by two copies of insertion sequence-like sequence, suggesting that it makes part of a composite transposon.

scholarly journals Complete Nucleotide Sequence and Genome Organization of Hibiscus Chlorotic Ringspot Virus, a New Member of the Genus Carmovirus: Evidence for the Presence and Expression of Two Novel Open Reading Frames

2000 ◽  
Vol 74 (7) ◽  
pp. 3149-3155 ◽  
Author(s):  
Mei Huang ◽  
Dora Chin-Yen Koh ◽  
Li-Juan Weng ◽  
Min-Li Chang ◽  
Yun-Kiam Yap ◽  
...  
Keyword(s):  
Nucleotide Sequence ◽  
Genome Organization ◽  
Complete Nucleotide Sequence ◽  
Full Length ◽  
Open Reading Frames ◽  
Ringspot Virus ◽  
In Vitro Translation ◽  
Cdna Clones ◽  
High Amino Acid ◽  
Reading Frames

ABSTRACT The complete nucleotide sequence of hibiscus chlorotic ringspot virus (HCRSV) was determined. The genomic RNA (gRNA) is 3,911 nucleotides long and has the potential to encode seven viral proteins in the order of 28 (p28), 23 (p23), 81 (p81), 8 (p8), 9 (p9), 38 (p38), and 25 (p25) kDa. Excluding two unique open reading frames (ORFs) encoding p23 and p25, the ORFs encode proteins with high amino acid similarity to those of carmoviruses. In addition to gRNA, two 3′-coterminated subgenomic RNA (sgRNA) species were identified. Full-length cDNA clones derived from gRNA and sgRNA were constructed under the control of a T7 promoter. Both capped and uncapped transcripts derived from the full-length genomic cDNA clone were infectious. In vitro translation and mutagenesis assays confirmed that all the predicted ORFs except the ORF encoding p8 are translatable, and the two novel ORFs (those encoding p23 and p25) may be functionally indispensable for the viral infection cycle. Based on virion morphology and genome organization, we propose that HCRSV be classified as a new member of the genus Carmovirus in familyTombusviridae.

The Nucleotide Sequence of a 39 kb Segment of Yeast Chromosome IV: 12 New Open Reading Frames, Nine Known Genes and One Gene for Gly-tRNA

Yeast ◽  
1997 ◽  
Vol 13 (2) ◽  
pp. 163-169 ◽  
Author(s):  
ANDRÉ BAHR ◽  
SABINE MÖLLER-RIEKER ◽  
THOMAS HANKELN ◽  
CHRISTIANE KRAEMER ◽  
URSULA PROTIN ◽  
...  
Keyword(s):  
Nucleotide Sequence ◽  
Open Reading Frames ◽  
Yeast Chromosome ◽  
Reading Frames

scholarly journals Purification and Molecular Characterization of a Tripeptidase (PepT) from Lactobacillus helveticus

2000 ◽  
Vol 66 (2) ◽  
pp. 794-800 ◽  
Author(s):  
Kirsi Savijoki ◽  
Airi Palva
Keyword(s):  
Maximum Activity ◽  
Lactobacillus Helveticus ◽  
Open Reading Frames ◽  
Transcription Start ◽  
Sequence Analyses ◽  
Repeat Structure ◽  
Flanking Regions ◽  
Dairy Starter ◽  
Reading Frames

ABSTRACT A tripeptidase (PepT) from a thermophilic dairy starter strain ofLactobacillus helveticus was purified by four chromatographic steps. PepT appeared to be a trimeric metallopeptidase with a molecular mass of 150 kDa. PepT exhibited maximum activity against hydrophobic tripeptides, with the highest activity for Met-Gly-Gly (Km , 2.6 mM;V max, 80.2 μmol · min−1 · μg−1). Some of the hydrophobic dipeptides were slowly hydrolyzed, distinguishing theLactobacillus PepT from its counterpart in mesophilicLactococcus lactis. No activity against tetrapeptides or amino acid p-nitroanilide derivatives was observed. ThepepT gene and its flanking regions were isolated by PCR and sequenced by cyclic sequencing. The sequence analyses revealed open reading frames (ORFs) 816 bp (ORF1) and 1,239 bp (ORF2) long. ORF2 encoded a 47-kDa PepT protein which exhibited 53% identity with the PepT from L. lactis. The mRNA analyses indicated thatpepT conforms a novel operon structure with an ORF1 located upstream. Several putative −35/−10 regions preceded the operon, but only one transcription start site located downstream of the first putative −10 region was identified. An inverted repeat structure with ΔG of −64.8 kJ/mol was found downstream of the PepT-encoding region.

scholarly journals Nucleotide Sequence of Plasmid pCNB1 from Comamonas Strain CNB-1 Reveals Novel Genetic Organization and Evolution for 4-Chloronitrobenzene Degradation

2007 ◽  
Vol 73 (14) ◽  
pp. 4477-4483 ◽  
Author(s):  
Ying-Fei Ma ◽  
Jian-Feng Wu ◽  
Sheng-Yue Wang ◽  
Cheng-Ying Jiang ◽  
Yun Zhang ◽  
...  
Keyword(s):  
Nucleotide Sequence ◽  
Resistance Genes ◽  
Gene Deletion ◽  
Degradation Pathway ◽  
Open Reading Frames ◽  
Mercury Resistance ◽  
Dna Molecules ◽  
Chromate Resistance ◽  
Reverse Transcription Pcr ◽  
Reading Frames

ABSTRACT The nucleotide sequence of a new plasmid pCNB1 from Comamonas sp. strain CNB-1 that degrades 4-chloronitrobenzene (4CNB) was determined. pCNB1 belongs to the IncP-1β group and is 91,181 bp in length. A total of 95 open reading frames appear to be involved in (i) the replication, maintenance, and transfer of pCNB1; (ii) resistance to arsenate and chromate; and (iii) the degradation of 4CNB. The 4CNB degradative genes and arsenate resistance genes were located on an extraordinarily large transposon (44.5 kb), proposed as TnCNB1. TnCNB1 was flanked by two IS1071 elements and represents a new member of the composite I transposon family. The 4CNB degradative genes within TnCNB1 were separated by various truncated genes and genetic homologs from other DNA molecules. Genes for chromate resistance were located on another transposon that was similar to the Tn21 transposon of the class II replicative family that is frequently responsible for the mobilization of mercury resistance genes. Resistance to arsenate and chromate were experimentally confirmed, and transcriptions of arsenate and chromate resistance genes were demonstrated by reverse transcription-PCR. These results described a new member of the IncP-1β plasmid family, and the findings suggest that gene deletion and acquisition as well as genetic rearrangement of DNA molecules happened during the evolution of the 4CNB degradation pathway on pCNB1.

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