Complete Nucleotide Sequence of a Cryptic Plasmid from the Marine Bacterium Vibrio splendidus and Identification of Open Reading Frames

Plasmid ◽  
2000 ◽  
Vol 44 (3) ◽  
pp. 292
Author(s):  
Leigh G. Powers ◽  
John T. Mallonee ◽  
Patricia A. Sobecky
Keyword(s):  
Nucleotide Sequence ◽  
Complete Nucleotide Sequence ◽  
Marine Bacterium ◽  
Open Reading Frames ◽  
Cryptic Plasmid ◽  
Vibrio Splendidus ◽  
Reading Frames

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.

scholarly journals Complete Nucleotide Sequence of Plasmid Rts1: Implications for Evolution of Large Plasmid Genomes

2002 ◽  
Vol 184 (12) ◽  
pp. 3194-3202 ◽  
Author(s):  
Takahiro Murata ◽  
Makoto Ohnishi ◽  
Takeshi Ara ◽  
Jun Kaneko ◽  
Chang-Gyun Han ◽  
...  
Keyword(s):  
Nucleotide Sequence ◽  
Complete Nucleotide Sequence ◽  
Sequence Similarity ◽  
Open Reading Frames ◽  
Conjugative Plasmid ◽  
Proteus Vulgaris ◽  
Significant Sequence Similarity ◽  
Modular Evolution ◽  
Broad Array ◽  
Reading Frames

ABSTRACT Rts1, a large conjugative plasmid originally isolated from Proteus vulgaris, is a prototype for the IncT plasmids and exhibits pleiotropic thermosensitive phenotypes. Here we report the complete nucleotide sequence of Rts1. The genome is 217,182 bp in length and contains 300 potential open reading frames (ORFs). Among these, the products of 141 ORFs, including 9 previously identified genes, displayed significant sequence similarity to known proteins. The set of genes responsible for the conjugation function of Rts1 has been identified. A broad array of genes related to diverse processes of DNA metabolism were also identified. Of particular interest was the presence of tus-like genes that could be involved in replication termination. Inspection of the overall genome organization revealed that the Rts1 genome is composed of four large modules, providing an example of modular evolution of plasmid genomes.

scholarly journals Complete Nucleotide Sequence of the 27-Kilobase Virulence Related Locus (vrl) of Dichelobacter nodosus: Evidence for Extrachromosomal Origin

1999 ◽  
Vol 67 (3) ◽  
pp. 1277-1286 ◽  
Author(s):  
Stephen J. Billington ◽  
Andrea S. Huggins ◽  
Priscilla A. Johanesen ◽  
Paul K. Crellin ◽  
Jackie K. Cheung ◽  
...  
Keyword(s):  
Nucleotide Sequence ◽  
Complete Nucleotide Sequence ◽  
Expression Vector ◽  
Sequence Similarity ◽  
Open Reading Frames ◽  
Bacteriophage Resistance ◽  
Dichelobacter Nodosus ◽  
Resistance System ◽  
Reading Frames

ABSTRACT The vrl locus is preferentially associated with virulent isolates of the ovine footrot pathogen, Dichelobacter nodosus. The complete nucleotide sequence of this 27.1-kb region has now been determined. The data reveal that the locus has a G+C content much higher than the rest of the D. nodosuschromosome and contains 22 open reading frames (ORFs) encoding products including a putative adenine-specific methylase, two potential DEAH ATP-dependent helicases, and two products with sequence similarity to a bacteriophage resistance system. These ORFs are all in the same orientation, and most are either overlapping or separated by only a few nucleotides, suggesting that they comprise an operon and are translationally coupled. Expression vector studies have led to the identification of proteins that correspond to many of these ORFs. These data, in combination with evidence of insertion of vrl into the 3′ end of an ssrA gene, are consistent with the hypothesis that the vrl locus was derived from the insertion of a bacteriophage or plasmid into the D. nodosusgenome.

scholarly journals Complete nucleotide sequence and genome organization of Grapevine leafroll-associated virus 3, type member of the genus Ampelovirus

2004 ◽  
Vol 85 (7) ◽  
pp. 2099-2102 ◽  
Author(s):  
Kai-Shu Ling ◽  
Hai-Ying Zhu ◽  
Dennis Gonsalves
Keyword(s):  
Phylogenetic Analysis ◽  
Nucleotide Sequence ◽  
Fusion Protein ◽  
Complete Genome Sequence ◽  
Genome Organization ◽  
Complete Nucleotide Sequence ◽  
Open Reading Frames ◽  
The Family ◽  
Mealy Bug ◽  
Reading Frames

This study reports on the complete genome sequence of Grapevine leafroll-associated virus 3, the type member of the genus Ampelovirus. The genome is 17 919 nt in size and contains 13 open reading frames (ORFs). Previously, the sequence of 13 154 nt of the 3′-terminal of the genome was reported. The newly sequenced portion contains a 158 nt 5′ UTR, a single papain-like protease and a methyltransferase-like (MT) domain. ORF1a encodes a large polypeptide with a molecular mass of 245 kDa. With a predicted +1 frameshift, the large fusion protein generated from ORF1a/1b would produce a 306 kDa polypeptide. Phylogenetic analysis using MT domains further supports the creation of the genus Ampelovirus for mealy-bug-transmitted viruses in the family Closteroviridae.

scholarly journals Complete nucleotide sequence of a mouse VL30 retro-element.

1988 ◽  
Vol 8 (8) ◽  
pp. 2989-2998 ◽  
Author(s):  
S E Adams ◽  
P D Rathjen ◽  
C A Stanway ◽  
S M Fulton ◽  
M H Malim ◽  
...  
Keyword(s):  
Nucleotide Sequence ◽  
Complete Nucleotide Sequence ◽  
Leukemia Virus ◽  
Open Reading Frames ◽  
Long Terminal Repeats ◽  
Base Pairs ◽  
Viral Packaging ◽  
Protein Functions ◽  
Active Promoter ◽  
Reading Frames

The complete nucleotide sequence of a mouse retro-element is presented. The cloned element is composed of 4,834 base pairs (bp) with long terminal repeats of 568 bp separated by an internal region of 3,698 bp. The element did not appear to have any open reading frames that would be capable of encoding the functional proteins that are normally produced by retro-elements. However, some regions of the genome showed some homology to retroviral gag and pol open reading frames. There was no region in VL30 corresponding to a retroviral env gene. This implies that VL30 is related to retrotransposons rather than to retroviruses. The sequence also contained regions that were homologous to known reverse transcriptase priming sites and viral packaging sites. These observations, combined with the known transcriptional capacity of the VL30 promoter, suggest that VL30 relies on protein functions of other retro-elements, such as murine leukemia virus, while maintaining highly conserved cis-active promoter, packaging, and priming sites necessary for its replication and cell-to-cell transmission.

scholarly journals Characterization of the Type 8 Capsular Gene Cluster of Streptococcus pneumoniae

1999 ◽  
Vol 181 (19) ◽  
pp. 6214-6219 ◽  
Author(s):  
Rosario Muñoz ◽  
Marta Mollerach ◽  
Rubens López ◽  
Ernesto García
Keyword(s):  
Streptococcus Pneumoniae ◽  
Nucleotide Sequence ◽  
Gene Cluster ◽  
Complete Nucleotide Sequence ◽  
Capsular Polysaccharide ◽  
Open Reading Frames ◽  
Dna Fragment ◽  
Type 3 ◽  
Reading Frames

ABSTRACT The complete nucleotide sequence of the capsular gene cluster (cap8) responsible for the biosynthesis of the capsular polysaccharide of Streptococcus pneumoniae type 8 has been determined. The cap8 gene cluster, located between the genes dexB and aliA, is composed of 12 open reading frames. A 14.7-kb DNA fragment embracing the cap8genes was sufficient to transform an unencapsulated type 3 S. pneumoniae strain to a strain with the type 8 capsule. A possible scenario for the evolution of pneumococcal types 2 and 8 is outlined.

scholarly journals Complete nucleotide sequence and genome organization of a single-stranded RNA virus infecting the marine fungoid protist Schizochytrium sp.

2006 ◽  
Vol 87 (3) ◽  
pp. 723-733 ◽  
Author(s):  
Yoshitake Takao ◽  
Kazuyuki Mise ◽  
Keizo Nagasaki ◽  
Tetsuro Okuno ◽  
Daiske Honda
Keyword(s):  
Amino Acid ◽  
Nucleotide Sequence ◽  
Complete Nucleotide Sequence ◽  
Rna Virus ◽  
Amino Acid Sequences ◽  
Open Reading Frames ◽  
Genome Database ◽  
Virus Family ◽  
Translation Mechanism ◽  
Reading Frames

The complete nucleotide sequence of the genomic RNA of a marine fungoid protist-infecting virus (Schizochytrium single-stranded RNA virus; SssRNAV) has been determined. The viral RNA is single-stranded with a positive sense and is 9018 nt in length [excluding the 3′ poly(A) tail]. It contains two long open reading frames (ORFs), which are separated by an intergenic region of 92 nt. The 5′ ORF (ORF1) is preceded by an untranslated leader sequence of 554 nt. The 3′ large ORF (ORF2) and an additional ORF (ORF3) overlap ORF2 by 431 nt and are followed by an untranslated region of 70 nt [excluding the 3′ poly(A) tail]. The deduced amino acid sequences of ORF1 and ORF2 products show similarity to non-structural and structural proteins of dicistroviruses, respectively. However, Northern blot analysis suggests that SssRNAV synthesizes subgenomic RNAs to translate ORF2 and ORF3, showing that the translation mechanism of downstream ORFs is distinct from that of dicistroviruses. Furthermore, although considerable similarities were detected by using a blast genome database search, phylogenetic analysis based on both the nucleotide and amino acid sequences of the putative RNA-dependent RNA polymerase (RdRp) and the RNA helicase suggests that SssRNAV is phylogenetically distinct from other virus families. Therefore, it is concluded that SssRNAV is not a member of any currently defined virus family and belongs to a novel, unrecognized virus group.

Complete nucleotide sequence of a mouse VL30 retro-element

1988 ◽  
Vol 8 (8) ◽  
pp. 2989-2998
Author(s):  
S E Adams ◽  
P D Rathjen ◽  
C A Stanway ◽  
S M Fulton ◽  
M H Malim ◽  
...  
Keyword(s):  
Nucleotide Sequence ◽  
Complete Nucleotide Sequence ◽  
Leukemia Virus ◽  
Open Reading Frames ◽  
Long Terminal Repeats ◽  
Base Pairs ◽  
Viral Packaging ◽  
Protein Functions ◽  
Active Promoter ◽  
Reading Frames

The complete nucleotide sequence of a mouse retro-element is presented. The cloned element is composed of 4,834 base pairs (bp) with long terminal repeats of 568 bp separated by an internal region of 3,698 bp. The element did not appear to have any open reading frames that would be capable of encoding the functional proteins that are normally produced by retro-elements. However, some regions of the genome showed some homology to retroviral gag and pol open reading frames. There was no region in VL30 corresponding to a retroviral env gene. This implies that VL30 is related to retrotransposons rather than to retroviruses. The sequence also contained regions that were homologous to known reverse transcriptase priming sites and viral packaging sites. These observations, combined with the known transcriptional capacity of the VL30 promoter, suggest that VL30 relies on protein functions of other retro-elements, such as murine leukemia virus, while maintaining highly conserved cis-active promoter, packaging, and priming sites necessary for its replication and cell-to-cell transmission.

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