A Genome-Wide Analysis Reveals Significant Overlap of Transcription and DNA Repair in Stationary Phase Yeast

The association between transcription and DNA repair is acknowledged as a player in the generation of mutations in a non-random fashion in prokaryotes and eukaryotes. Previous studies demonstrated that the transcription complex is capable of directing DNA repair to sites of transcription. This process is especially important to growth-arrested cells, in which many DNA repair capacities are diminished; it may also lead to mutations preferentially in transcribed genes. Using microarray analysis of growth-arrested yeast cultures, we demonstrated on a genomic scale, the co-localization of a DNA-turnover marker, indicative of DNA-repair-associated DNA synthesis, with genes persistently transcribed during stationary phase. This may serve as a clue regarding the non-random manner in which non-dividing cells may potentially mutate in the absence of replication, solely as a result of their inherent, transcriptional stress response

Draft Genome Sequence of Environmental Bacterium Vibrio vulnificus CladeA-yb158

We report the genome sequence of the environmental Vibrio vulnificus biotype 1_cladeA. This draft genome of the CladeA-yb158 strain, isolated in Israel, represents this newly emerged clonal group that contains both clinical and environmental strains

APPLIED GENETICS AND MOLECULAR BIOTECHNOLOGY Improvement of natural isolates of Saccharomyces cerevisiae strains for synthesis of a chiral building block using classic genetics

Abstract The asymmetric bio-reduction of 4-chloro-acetoacetic-acid-ethyl-ester to the pharmaceutical building block (S)-4-chloro-3-hydroxybutanoate-ethyl-ester requires the utilization of an enantioselective robust biocatalyst. Some of the natural Saccharomyces cerevisiae strains, isolated from Mount Carmel National Park in Israel, were characterized as resistant to environmental stress. Nevertheless, these strains showed relatively low enantiomeric-excess (ee), while a laboratory strain, Y103, exhibited a selectivity of 98% ee. The enantioselective lab strain was crossed with the multi-stress resistant environmental isolate (93% ee) followed by backcross with Y103, to subsequently obtain a haploid offspring of backcross-1, exhibiting both high multistress resistance and high enantioselectivity (98% ee). Introducing osmotic (1 M NaCl), oxidative (0.6 mM H 2 O 2 ) and thermal stress (44°C) to growing cultures of the enantioselective parent, resulted in a decrease of 24-32% in specific activity, while the enantioselectivity of the stress-resistant parent decreased by 4-12% ee. Unlike its original parental strains, the new strain maintained constant specific activity and enantioselectivity when introduced to the various stress factors. This work shows that the classic introgression method, can serve as a viable approach for creating a robust enantioselective biocatalyst, designed for industrial production of chiral compounds

Epidemiologic Study of Vibrio vulnificus Infections by Using Variable Number Tandem Repeats

A 3-year environmental and clinical Vibrio vulnificus survey using simple-sequence repeats typing shows that V. vulnificus biotype 3 constitutes ≈21% of the bacterium population in tested aquaculture ponds as opposed to ≈86% of clinical cases. Simple-sequence repeats proved to be a useful epidemiologic tool, providing information on the environmental source of the pathogen

Genome-Wide SNP-genotyping array to study the evolution of the human pathogen Vibrio vulnificus Biotype 3

Vibrio vulnificus is an aquatic bacterium and an important human pathogen. Strains Of V. vulnificus are classified into three different biotypes. The newly emerged biotype 3 has been found to be clonal and restricted to Israel. In the family Vibrionaceae , horizontal gene transfer is the main mechanism responsible for the emergence of new pathogen groups. To better understand the evolution of the bacterium, and in particular to trace the evolution of biotype 3, we performed genome-wide SNP genotyping of 254 clinical and environmental V. vulnificus isolates with worldwide distribution recovered over a 30-year period, representing all phylogeny groups. A custom single-nucleotide polymorphism (SNP) array implemented on the Illumina GoldenGate platform was developed based on 570 SNPs randomly distributed throughout the genome. In general, the genotyping results divided the V. vulnificus species into three main phylogenetic lineages and an additional subgroup, clade B, consisting of environmental and clinical isolates from Israel. Data analysis suggested that 69% of biotype 3 SNPs are similar to SNPs from clade B, indicating that biotype 3 and clade B have a common ancestor. The rest of the biotype 3 SNPs were scattered along the biotype 3 genome, probably representing multiple chromosomal segments that may have been horizontally inserted into the clade B recipient core genome from other phylogroups or bacterial species sharing the same ecological niche. Results emphasize the continuous evolution of V. vulnificus and support the emergence of new pathogenic groups within this species as a recurrent phenomenon. Our findings contribute to a broader understanding of the evolution of this human pathogen

Simple sequence repeats as advantageous mutators in evolution

Simple sequence repeats (SSRs) often serve to modify genes with which they are associated. The influence of SSRs on gene regulation, transcription and protein function typically depends on the number of repeats, while mutations that add or subtract repeat units are both frequent and reversible. SSRs thus provide a prolific source of quantitative and qualitative variation. Over the past decade, researchers have found that this spontaneous variation has been tapped by natural and artificial selection to adjust almost every aspect of gene function. These studies support the hypothesis that SSRs, by virtue of their special mutational and functional qualities, have a major role in generating the genetic variation underlying adaptive evolution