Sequencing of chromosome I from Saccharomyces cerevisiae: analysis of a 32 kb region between the LTE1 and SPO7 genes

Genome ◽  
1993 ◽  
Vol 36 (1) ◽  
pp. 32-42 ◽  
Author(s):  
B. F. Francis Ouellette ◽  
Michael W. Clark ◽  
Teresa Keng ◽  
Reg K. Storms ◽  
Wuwei Zhong ◽  
...  
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Functional Analysis ◽  
Genome Analysis ◽  
Open Reading Frames ◽  
Average Spacing ◽  
Coding Regions ◽  
Significant Homology ◽  
Yeast Chromosome ◽  
Chromosome I ◽  
Reading Frames

The DNA sequencing and preliminary functional analysis of a 32 kb section of yeast chromosome I has been completed. This region lies on the left arm of the chromosome between the LTE1 and SPO7 genes and contains 14 open reading frames (ORFs) positioned closely together, with an average spacing of approximately 350 nucleotides between coding regions. Three of these ORFs correspond to previously identified genes, a further three show significant homology with other proteins, while the remaining eight ORFs share no significant homology to genes in the databases.Key words: chromosome I, genome analysis, Saccharomyces cerevisiae, yeast.

Sequencing and functional analysis of a 32 560 bp segment on the left arm of yeast chromosome II. Identification of 26 open reading frames, including theKIP1 andSEC17 genes

Yeast ◽  
1993 ◽  
Vol 9 (12) ◽  
pp. 1355-1371 ◽  
Author(s):  
Bart Scherens ◽  
Mohamed El Bakkoury ◽  
Fabienne Vierendeels ◽  
Evelyne Dubois ◽  
Francine Messenguy
Keyword(s):  
Functional Analysis ◽  
Open Reading Frames ◽  
Yeast Chromosome ◽  
Chromosome Ii ◽  
Reading Frames

Functional analysis of three adjacent open reading frames from the right arm of yeast chromosome XVI

Yeast ◽  
1998 ◽  
Vol 14 (11) ◽  
pp. 1027-1039 ◽  
Author(s):  
Beata Waśkiewicz-Staniorowska ◽  
Jacek Skała ◽  
Michał Jasiński ◽  
Marcelle Grenson ◽  
André Goffeau ◽  
...  
Keyword(s):  
Functional Analysis ◽  
Open Reading Frames ◽  
Yeast Chromosome ◽  
The Right ◽  
Reading Frames

scholarly journals Induction and Genome Analysis of HY01, a Newly Reported Prophage from an Emerging Shrimp Pathogen Vibrio campbellii

2021 ◽  
Vol 9 (2) ◽  
pp. 400
Author(s):  
Taiyeebah Nuidate ◽  
Aphiwat Kuaphiriyakul ◽  
Komwit Surachat ◽  
Pimonsri Mittraparp-arthorn
Keyword(s):  
Genome Analysis ◽  
Gene Organization ◽  
Open Reading Frames ◽  
Full Genome Sequence ◽  
Protein Coding ◽  
Coding Regions ◽  
Vibrio Phage ◽  
Vibrio Campbellii ◽  
Vibrio Spp ◽  
Reading Frames

Vibrio campbellii is an emerging aquaculture pathogen that causes luminous vibriosis in farmed shrimp. Although prophages in various aquaculture pathogens have been widely reported, there is still limited knowledge regarding prophages in the genome of pathogenic V. campbellii. Here, we describe the full-genome sequence of a prophage named HY01, induced from the emerging shrimp pathogen V. campbellii HY01. The phage HY01 was induced by mitomycin C and was morphologically characterized as long tailed phage. V. campbellii phage HY01 is composed of 41,772 bp of dsDNA with a G+C content of 47.45%. A total of 60 open reading frames (ORFs) were identified, of which 31 could be predicted for their biological functions. Twenty seven out of 31 predicted protein coding regions were matched with several encoded proteins of various Enterobacteriaceae, Pseudomonadaceae, Vibrionaceae, and other phages of Gram-negative bacteria. Interestingly, the comparative genome analysis revealed that the phage HY01 was only distantly related to Vibrio phage Va_PF430-3_p42 of fish pathogen V. anguillarum but differed in genomic size and gene organization. The phylogenetic tree placed the phage together with Siphoviridae family. Additionally, a survey of Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) spacers revealed two matching sequences between phage HY01 genome and viral spacer sequence of Vibrio spp. The spacer results combined with the synteny results suggest that the evolution of V. campbellii phage HY01 is driven by the horizontal genetic exchange between bacterial families belonging to the class of Gammaproteobacteria.

scholarly journals Extrachromosomal elements cause a reduced division potential in nib 1 strains of Saccharomyces cerevisiae.

Genetics ◽  
1989 ◽  
Vol 122 (4) ◽  
pp. 749-757
Author(s):  
R Sweeney ◽  
V A Zakian
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Open Reading Frames ◽  
Simultaneous Presence ◽  
Extrachromosomal Elements ◽  
Severe Reduction ◽  
Extrachromosomal Element ◽  
Generalized Sensitivity ◽  
Reading Frames

Abstract The nib 1 allele of yeast confers a sensitivity to an endogenous plasmid, 2 mu DNA, in that nib 1 strains bearing 2 mu DNA (cir+) exhibit a reduction in division potential. In the present study, the reduction in division potential characteristic of nib 1 cir+ strains is shown to be dependent on the simultaneous presence of both the A and the D open reading frames of 2 mu DNA as well as on the presence of an unidentified extrachromosomal element other than 2 mu DNA. Furthermore, in nib 1 strains, an uncharacterized extrachromosomal element can cause a less severe reduction of division potential in the absence of intact 2 mu DNA. Thus, the nib 1 allele may confer a generalized sensitivity to extrachromosomal elements.

scholarly journals Improved ribosome-footprint and mRNA measurements provide insights into dynamics and regulation of yeast translation

2015 ◽  
Author(s):  
David E Weinberg ◽  
Premal Shah ◽  
Stephen W Eichhorn ◽  
Jeffrey A Hussmann ◽  
Joshua B Plotkin ◽  
...  
Keyword(s):  
Translational Control ◽  
Nucleotide Composition ◽  
Ribosome Profiling ◽  
Open Reading Frames ◽  
Untranslated Regions ◽  
Coding Regions ◽  
Genome Wide ◽  
Upstream Open Reading Frames ◽  
Improved Methods ◽  
Reading Frames

Ribosome-footprint profiling provides genome-wide snapshots of translation, but technical challenges can confound its analysis. Here, we use improved methods to obtain ribosome-footprint profiles and mRNA abundances that more faithfully reflect gene expression in Saccharomyces cerevisiae. Our results support proposals that both the beginning of coding regions and codons matching rare tRNAs are more slowly translated. They also indicate that emergent polypeptides with as few as three basic residues within a 10-residue window tend to slow translation. With the improved mRNA measurements, the variation attributable to translational control in exponentially growing yeast was less than previously reported, and most of this variation could be predicted with a simple model that considered mRNA abundance, upstream open reading frames, cap-proximal structure and nucleotide composition, and lengths of the coding and 5′- untranslated regions. Collectively, our results reveal key features of translational control in yeast and provide a framework for executing and interpreting ribosome- profiling studies.

scholarly journals Complete Genome Sequence of theBacillus pumilusPhage Leo2

2018 ◽  
Vol 6 (7) ◽  
Author(s):  
Sondos Badran ◽  
Nathanael Morales ◽  
Phillip Schick ◽  
Brandon Jacoby ◽  
William Villella ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
Bacillus Pumilus ◽  
Open Reading Frames ◽  
Gram Positive ◽  
Coding Regions ◽  
Symbiotic Interactions ◽  
Associated Functions ◽  
Reading Frames

ABSTRACTBacillusspp. are ubiquitous Gram-positive microbes with many ecological and symbiotic interactions and can be pathogens. Phage Leo2 was found to infect aBacillus pumilusstrain isolated from soil. The sequence of phage Leo2 revealed 74 genes; 31% of the genes have associated functions, and 67% of coding regions are unidentified open reading frames.

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

XV. Yeast sequencing reports. DNA sequence analysis of a 13 kbp fragment of the left arm of yeast chromosome XV containing seven new open reading frames

Yeast ◽  
1995 ◽  
Vol 11 (13) ◽  
pp. 1281-1288 ◽  
Author(s):  
Antonio Casamayor ◽  
Martí Aldea ◽  
Celia Casas ◽  
Enrique Herrero ◽  
Francisco-Javier Gamo ◽  
...  
Keyword(s):  
Sequence Analysis ◽  
Dna Sequence ◽  
Dna Sequence Analysis ◽  
Open Reading Frames ◽  
Yeast Chromosome ◽  
Reading Frames
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