XI. Yeast sequencing reports. The complete sequence of an 18,002 bp segment ofSaccharomyces cerevisiae chromosome XI contains theHBS1,MRP-L20 andPRP16 genes, and six new open reading frames

Yeast ◽  
1994 ◽  
Vol 10 (2) ◽  
pp. 231-245 ◽  
Author(s):  
Jesús García-Cantalejo ◽  
Victoriano Baladrón ◽  
Pedro F. Esteban ◽  
M. Angeles Santos ◽  
Germán Bou ◽  
...  
Keyword(s):  
Complete Sequence ◽  
Open Reading Frames ◽  
Reading Frames

An Umbra-related Virus Found in Vasconcellea X Heilbornii (Caricaceae)

2021 ◽  
Author(s):  
Juan F Cornejo-Franco ◽  
Francisco Flores ◽  
Dimitre Mollov ◽  
diego fernando quito-avila
Keyword(s):  
Phylogenetic Analysis ◽  
New Genus ◽  
Complete Sequence ◽  
Open Reading Frames ◽  
Rna Dependent Rna Polymerase ◽  
Sequence Comparisons ◽  
Genomic Features ◽  
Overlapping Open Reading Frames ◽  
Reading Frames

Abstract The complete sequence of a new viral RNA from babaco (Vasconcellea x heilbornii) was determined. The genome consisted of 4,584 nucleotides organized in two non-overlapping open reading frames (ORFs 1 and 2), a 9-nt-long noncoding region (NCR) at the 5’ terminus and a 1,843 -nt-long NCR at the 3’ terminus. Sequence comparisons of ORF 2 revealed homology to the RNA-dependent-RNA-polymerase (RdRp) of several umbra- and umbra-related viruses. Phylogenetic analysis of the RdRp placed the new virus in a well-supported and cohesive clade that includes umbra-like viruses reported from papaya, citrus, opuntia, maize and sugarcane hosts. This clade shares a most recent ancestor with the umbraviruses but has different genomic features. The creation of a new genus, within the Tombusviridae, is proposed for the classification of these novel viruses.

scholarly journals Sequence of the Genome of the Temperate, Serotype-Converting,Pseudomonas aeruginosa Bacteriophage D3

2000 ◽  
Vol 182 (21) ◽  
pp. 6066-6074 ◽  
Author(s):  
Andrew M. Kropinski
Keyword(s):  
Pseudomonas Aeruginosa ◽  
Sequence Similarity ◽  
Complete Sequence ◽  
Open Reading Frames ◽  
Gene Encoding ◽  
Virus Family ◽  
Double Stranded Dna ◽  
High Degree ◽  
Phage Proteins ◽  
Reading Frames

ABSTRACT Temperate bacteriophage D3, a member of the virus familySiphoviridae, is responsible for serotype conversion in its host, Pseudomonas aeruginosa. The complete sequence of the double-stranded DNA genome has been determined. The 56,426 bp contains 90 putative open reading frames (ORFs) and four genes specifying tRNAs. The latter are specific for methionine (AUG), glycine (GGA), asparagine (AAC), and threonine (ACA). The tRNAs may function in the translation of certain highly expressed proteins from this relatively AT-rich genome. D3 proteins which exhibited a high degree of sequence similarity to previously characterized phage proteins included the portal, major head, tail, and tail tape measure proteins, endolysin, integrase, helicase, and NinG. The layout of genes was reminiscent of lambdoid phages, with the exception of the placement of the endolysin gene, which parenthetically also lacked a cognate holin. The greatest sequence similarity was found in the morphogenesis genes to coliphages HK022 and HK97. Among the ORFs was discovered the gene encoding the fucosamine O-acetylase, which is in part responsible for the serotype conversion events.

scholarly journals Molecular and Evolutionary Characterization of the cp32/18 Family of Supercoiled Plasmids in Borrelia burgdorferi297

2000 ◽  
Vol 68 (3) ◽  
pp. 1574-1586 ◽  
Author(s):  
Melissa J. Caimano ◽  
Xiaofeng Yang ◽  
Taissia G. Popova ◽  
Michael L. Clawson ◽  
Darrin R. Akins ◽  
...  
Keyword(s):  
Sequence Analysis ◽  
Genomic Sequence ◽  
Complete Sequence ◽  
Open Reading Frames ◽  
Exogenous Dna ◽  
Variable Regions ◽  
Different Types ◽  
Sequence Relatedness ◽  
Reading Frames

ABSTRACT In this study, we characterized seven members of the cp32/18 family of supercoiled plasmids in Borrelia burgdorferi297. Complete sequence analysis of a 21-kb plasmid (cp18-2) confirmed that the strain 297 plasmids are similar in overall content and organization to their B31 counterparts. Of the 31 open reading frames (ORFs) in cp18-2, only three showed sequence relatedness to proteins with known functions, and only one, a ParA/SopA ortholog, was related to nonborrelial polypeptides. Besides the lipoproteins, none of the ORFs appeared likely to encode a surface-exposed protein. Comparison with the B31 genomic sequence indicated that paralogs for most of the ORFs in cp18-2 can be identified on other genetic elements. cp18-2 was found to lack a 9- to 10-kb fragment present in the 32-kb homologs which, by extrapolation from the B31 cp32 sequences, contains at least 15 genes presumed to be unnecessary for plasmid maintenance. Sequence analysis of the lipoprotein-encoding variable loci provided evidence that recombinatorial processes within these regions may result in the acquisition of exogenous DNA. Pairwise analysis with random shuffling revealed that the multiple lipoproteins (Mlp; formerly designated 2.9 LPs) fall into two distinct homology groups which appear to have arisen by gene fusion events similar to those recently proposed to have generated the three OspE, OspF, and Elp lipoprotein families (D. R. Akins, M. J. Caimano, X. Yang, F. Cerna, M. V. Norgard, and J. D. Radolf, Infect. Immun. 67:1526–1532, 1999). Comparative analysis of the variable regions also indicated that recombination within the loci of each plasmid may occur independently. Last, comparison of variable loci revealed that the cp32/18 plasmid complements of the B31 and 297 isolates differ substantially, indicating that the two strains have been subject to divergent adaptive pressures. In addition to providing evidence for two different types of recombinatorial events involving cp32/18 plasmids, these findings underscore the need for genetic analysis of diverse borrelial isolates in order to elucidate the Lyme disease spirochete's complex parasitic strategies.

scholarly journals Structural analysis of TRAS1, a novel family of telomeric repeat-associated retrotransposons in the silkworm, Bombyx mori.

1995 ◽  
Vol 15 (8) ◽  
pp. 4545-4552 ◽  
Author(s):  
S Okazaki ◽  
H Ishikawa ◽  
H Fujiwara
Keyword(s):  
Bombyx Mori ◽  
Repetitive Sequence ◽  
Repetitive Sequences ◽  
Complete Sequence ◽  
Open Reading Frames ◽  
Ltr Retrotransposons ◽  
Reading Frames ◽  
28S Ribosomal Dna ◽  
Silkworm Bombyx Mori

We characterized TRAS1, a retrotransposable element which was inserted into the telomeric repetitive sequence (CCTAA)n of the silkworm, Bombyx mori. The complete sequence of TRAS1, a stretch of 7.8 kb with a poly(A) tract at the 3' end, was determined. No long terminal repeat (LTR) was found at the termini of the element. TRAS1 contains gag- and pol-like open reading frames (ORFs) which are similar to those of non-LTR retrotransposons. The two ORFs overlap but are one nucleotide out of frame (+1 frameshift). Most of the approximately 250 copies of TRAS1 elements in the genome were highly conserved in the structure. Chromosomal in situ hybridization showed that TRAS1 elements are clustered at the telomeres of Bombyx chromosomes. A phylogenetic analysis using the amino acid sequence of the reverse transcriptase domain within the pol-like ORF revealed that TRAS1 falls into one lineage with R1, which is a family of non-LTR retrotransposons inserted into the same site within the 28S ribosomal DNA unit in most insects. TRAS1 may have been derived from R1 and changed the target specificity so that TRAS1 inserts into the telomeric repetitive sequence (CCTAA)n. Southern hybridization and Bal 31 exonuclease analyses showed that TRAS1 elements are clustered proximal to the terminal long tract of (CCTAA)n. TRAS1 is a novel family of non-LTR retrotransposons which are inserted into the telomeric repetitive sequences as target sites.

scholarly journals New Small, Acid-Soluble Proteins Unique to Spores ofBacillus subtilis: Identification of the Coding Genes and Regulation and Function of Two of These Genes

1998 ◽  
Vol 180 (24) ◽  
pp. 6704-6712 ◽  
Author(s):  
Irina Bagyan ◽  
Barbara Setlow ◽  
Peter Setlow
Keyword(s):  
Rna Polymerase ◽  
Mother Cell ◽  
Genomic Sequence ◽  
Complete Sequence ◽  
Soluble Proteins ◽  
Open Reading Frames ◽  
Coding Regions ◽  
Spore Outgrowth ◽  
And Function ◽  
Reading Frames

ABSTRACT Eleven small, acid-soluble proteins (SASP) which are present in spores but not in growing cells of Bacillus subtilis were identified by sequence analysis of proteins separated by acrylamide gel electrophoresis of acid extracts from spores which lack the three major SASP (α, β, and γ). Six of these proteins are encoded by open reading frames identified previously or by analysis of the complete sequence of the B. subtilis genome, including two minor α/β-type SASP (SspC and SspD) and a putative spore coat protein (CotK). Five proteins are encoded by short open reading frames that were not identified as coding regions in the analysis of the completeB. subtilis genomic sequence. Studies of the regulation of two of the latter genes, termed sspG and sspJ, showed that both are expressed only in sporulation. ThesspG gene is transcribed in the mother cell compartment by RNA polymerase with the mother cell-specific sigma factor for RNA polymerase, ςK, and is cotranscribed with a downstream gene, yurS; sspG transcription also requires the DNA binding protein GerE. In contrast, sspJ is transcribed in the forespore compartment by RNA polymerase with the forespore-specific ςG and appears to give a monocistronic transcript. A mutation eliminating SspG had no effect on sporulation or spore properties, while loss of SspJ caused a slight decrease in the rate of spore outgrowth in an otherwise wild-type background.

III. Yeast sequencing reports. The complete sequence of a 11,953 bp fragment from C1G on chromosome III encompasses four new open reading frames

Yeast ◽  
1991 ◽  
Vol 7 (5) ◽  
pp. 533-538 ◽  
Author(s):  
Massoud Ramezani Rad ◽  
Katja Lützenkirchen ◽  
Gang Xu ◽  
Ulrich Kleinhans ◽  
Cornelis P. Hollenberg
Keyword(s):  
Complete Sequence ◽  
Open Reading Frames ◽  
Chromosome Iii ◽  
Reading Frames

scholarly journals Detection of novel divergent arenaviruses in boid snakes with inclusion body disease in The Netherlands

2013 ◽  
Vol 94 (6) ◽  
pp. 1206-1210 ◽  
Author(s):  
R. Bodewes ◽  
M. J. L. Kik ◽  
V. Stalin Raj ◽  
C. M. E. Schapendonk ◽  
B. L. Haagmans ◽  
...  
Keyword(s):  
The Netherlands ◽  
Inclusion Body ◽  
The United States ◽  
Complete Sequence ◽  
Open Reading Frames ◽  
Golden Gate ◽  
Inclusion Body Disease ◽  
A New Species ◽  
Generation Sequencing ◽  
Reading Frames

Arenaviruses are bi-segmented negative-stranded RNA viruses, which were until recently only detected in rodents and humans. Now highly divergent arenaviruses have been identified in boid snakes with inclusion body disease (IBD). Here, we describe the identification of a new species and variants of the highly divergent arenaviruses, which were detected in tissues of captive boid snakes with IBD in The Netherlands by next-generation sequencing. Phylogenetic analysis of the complete sequence of the open reading frames of the four predicted proteins of one of the detected viruses revealed that this virus was most closely related to the recently identified Golden Gate virus, while considerable sequence differences were observed between the highly divergent arenaviruses detected in this study. These findings add to the recent identification of the highly divergent arenaviruses in boid snakes with IBD in the United States and indicate that these viruses also circulate among boid snakes in Europe.

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