Characterization of the rrn operons in the channel catfish pathogen Edwardsiella ictaluri

Williams, Michele L.; Waldbieser, Geoffrey C.; Dyer, David W.; Gillaspy, Allison F.; Lawrence, Mark L.

doi:10.1111/j.1365-2672.2007.03704.x

Cited by 8 publications

(11 citation statements)

References 29 publications

(46 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The chromosome is predicted to distinctly harbor 8 rRNA operons, 95 tRNA genes, and 8 stable noncoding RNAs, relatively higher than that of other sequenced enterobacteria (Table S1) and in consistent with the rapid growth of the bacterium [12]. The eight rRNA operons, among which one operon contains a duplication in 5S rRNA gene, are scattered in the circular genome except for two locating in tandem as previously reported [13] (Figure 1). In addition to 77 pseudogenes (including 32 phage and 31 transposase genes), 3,486 coding sequences (CDSs) with an average length of 906 bp were encoded in the chromosome, representing 83.9% of the genome.…”

Section: Resultssupporting

confidence: 78%

Genome Sequence of the Versatile Fish Pathogen Edwardsiella tarda Provides Insights into its Adaptation to Broad Host Ranges and Intracellular Niches

et al. 2009

View full text Add to dashboard Cite

Background Edwardsiella tarda is the etiologic agent of edwardsiellosis, a devastating fish disease prevailing in worldwide aquaculture industries. Here we describe the complete genome of E. tarda, EIB202, a highly virulent and multi-drug resistant isolate in China.Methodology/Principal Findings E. tarda EIB202 possesses a single chromosome of 3,760,463 base pairs containing 3,486 predicted protein coding sequences, 8 ribosomal rRNA operons, and 95 tRNA genes, and a 43,703 bp conjugative plasmid harboring multi-drug resistant determinants and encoding type IV A secretion system components. We identified a full spectrum of genetic properties related to its genome plasticity such as repeated sequences, insertion sequences, phage-like proteins, integrases, recombinases and genomic islands. In addition, analysis also indicated that a substantial proportion of the E. tarda genome might be devoted to the growth and survival under diverse conditions including intracellular niches, with a large number of aerobic or anaerobic respiration-associated proteins, signal transduction proteins as well as proteins involved in various stress adaptations. A pool of genes for secretion systems, pili formation, nonfimbrial adhesions, invasions and hemagglutinins, chondroitinases, hemolysins, iron scavenging systems as well as the incomplete flagellar biogenesis might feature its surface structures and pathogenesis in a fish body.Conclusion/SignificanceGenomic analysis of the bacterium offered insights into the phylogeny, metabolism, drug-resistance, stress adaptation, and virulence characteristics of this versatile pathogen, which constitutes an important first step in understanding the pathogenesis of E. tarda to facilitate construction of a practical effective vaccine used for combating fish edwardsiellosis.

show abstract

Section: Resultssupporting

confidence: 78%

Genome Sequence of the Versatile Fish Pathogen Edwardsiella tarda Provides Insights into its Adaptation to Broad Host Ranges and Intracellular Niches

et al. 2009

View full text Add to dashboard Cite

show abstract

“…The 16S rRNA gene copy numbers for the rest of type strains were determined via pulse-field gel electrophoresis (PFGE) as described by Williams [64].…”

Section: Methodsmentioning

confidence: 99%

Evaluation of Methods for the Extraction and Purification of DNA from the Human Microbiome

et al. 2012

View full text Add to dashboard Cite

Background DNA extraction is an essential step in all cultivation-independent approaches to characterize microbial diversity, including that associated with the human body. A fundamental challenge in using these approaches has been to isolate DNA that is representative of the microbial community sampled. Methodology/Principal Findings In this study, we statistically evaluated six commonly used DNA extraction procedures using eleven human-associated bacterial species and a mock community that contained equal numbers of those eleven species. These methods were compared on the basis of DNA yield, DNA shearing, reproducibility, and most importantly representation of microbial diversity. The analysis of 16S rRNA gene sequences from a mock community showed that the observed species abundances were significantly different from the expected species abundances for all six DNA extraction methods used. Conclusions/Significance Protocols that included bead beating and/or mutanolysin produced significantly better bacterial community structure representation than methods without both of them. The reproducibility of all six methods was similar, and results from different experimenters and different times were in good agreement. Based on the evaluations done it appears that DNA extraction procedures for bacterial community analysis of human associated samples should include bead beating and/or mutanolysin to effectively lyse cells.

show abstract

“…The DNA sequence flanking each transposon insertion site was identified by single primer PCR and sequencing as described by Karlyshev et al (2000) and modified by Karsi et al (2009). Sequences were identified by BLAST search against the E. ictaluri genome (GenBank #CP001600) (Williams et al, 2008). Predicted protein sequences from the identified E. ictaluri genes were compared to the closest matching protein sequences from the nonredundant protein database at NCBI using the Cluster-V method.…”

Section: Mutant Identificationsmentioning

confidence: 99%

Use of bioluminescence mutant screening for identification of Edwardsiella ictaluri genes involved in channel catfish (Ictalurus punctatus) skin colonization

Menanteau–Ledouble

Lawrence

2013

Veterinary Microbiology

View full text Add to dashboard Cite

Characterization of the rrn operons in the channel catfish pathogen Edwardsiella ictaluri

Cited by 8 publications

References 29 publications

Genome Sequence of the Versatile Fish Pathogen Edwardsiella tarda Provides Insights into its Adaptation to Broad Host Ranges and Intracellular Niches

Genome Sequence of the Versatile Fish Pathogen Edwardsiella tarda Provides Insights into its Adaptation to Broad Host Ranges and Intracellular Niches

Evaluation of Methods for the Extraction and Purification of DNA from the Human Microbiome

Use of bioluminescence mutant screening for identification of Edwardsiella ictaluri genes involved in channel catfish (Ictalurus punctatus) skin colonization

Contact Info

Product

Resources

About