Genome-level homology and phylogeny of Shewanella (Gammaproteobacteria: lteromonadales: Shewanellaceae)

<p>Abstract</p> <p>Background</p> <p>The explosion in availability of whole genome data provides the opportunity to build phylogenetic hypotheses based on these data as well as the ability to learn more about the genomes themselves. The biological history of genes and genomes can be investigated based on the taxomonic history provided by the phylogeny. A phylogenetic hypothesis based on complete genome data is presented for the genus <it>Shewanella </it>(Gammaproteobacteria: Alteromonadales: Shewanellaceae). Nineteen taxa from <it>Shewanella </it>(16 species and 3 additional strains of one species) as well as three outgroup species representing the genera <it>Aeromonas </it>(Gammaproteobacteria: Aeromonadales: Aeromonadaceae), <it>Alteromonas </it>(Gammaproteobacteria: Alteromonadales: Alteromonadaceae) and <it>Colwellia </it>(Gammaproteobacteria: Alteromonadales: Colwelliaceae) are included for a total of 22 taxa.</p> <p>Results</p> <p>Putatively homologous regions were found across unannotated genomes and tested with a phylogenetic analysis. Two genome-wide data-sets are considered, one including only those genomic regions for which all taxa are represented, which included 3,361,015 aligned nucleotide base-pairs (bp) and a second that additionally includes those regions present in only subsets of taxa, which totaled 12,456,624 aligned bp. Alignment columns in these large data-sets were then randomly sampled to create smaller data-sets. After the phylogenetic hypothesis was generated, genome annotations were projected onto the DNA sequence alignment to compare the historical hypothesis generated by the phylogeny with the functional hypothesis posited by annotation.</p> <p>Conclusions</p> <p>Individual phylogenetic analyses of the 243 locally co-linear genome regions all failed to recover the genome topology, but the smaller data-sets that were random samplings of the large concatenated alignments all produced the genome topology. It is shown that there is not a single orthologous copy of 16S rRNA across the taxon sampling included in this study and that the relationships among the multiple copies are consistent with 16S rRNA undergoing concerted evolution. Unannotated whole genome data can provide excellent raw material for generating hypotheses of historical homology, which can be tested with phylogenetic analysis and compared with hypotheses of gene function.</p

Biochemistry and Genetics of Bacterial Bioluminescence

Bacterial light production involves enzymes-luciferase, fatty acid reductase, and flavin reductase-and substrates-reduced flavin mononucleotide and long-chain fatty aldehyde-that are specific to bioluminescence in bacteria. The bacterial genes coding for these enzymes, luxA and luxB for the subunits of luciferase; luxC, luxD, and luxE for the components of the fatty acid reductase; and luxG for flavin reductase, are found as an operon in light-emitting bacteria, with the gene order, luxCDABEG. Over 30 species of marine and terrestrial bacteria, which cluster phylogenetically in Aliivibrio, Photobacterium, and Vibrio (Vibrionaceae), Shewanella (Shewanellaceae), and Photorhabdus (Enterobacteriaceae), carry lux operon genes. The luminescence operons of some of these bacteria also contain genes involved in the synthesis of riboflavin, ribEBHA, and in some species, regulatory genes luxI and luxR are associated with the lux operon. In well-studied cases, lux genes are coordinately expressed in a population density-responsive, self-inducing manner called quorum sensing. The evolutionary origins and physiological function of bioluminescence in bacteria are not well understood but are thought to relate to utilization of oxygen as a substrate in the luminescence reaction

Characteristics and genetic diversity of bioluminescent Shewanella woodyi strains isolated from the Gulf of Izmir, Turkey

WOS: 000329099800012PubMed ID: 23900860The purpose of this study was to isolate bioluminescent strains and to phenotypically and biochemically identify them based on the 16S rRNA gene sequence. 16S rRNA gene sequence analysis of the 11 isolates revealed that they belonged to Shewanella woodyi. Nevertheless, they were determined to exhibit various growth characteristics, enzymatic activities, assimilation of carbon and nitrogen sources, and different characteristics in antibiotic resistance profiles, and also, it was determined that different growth conditions affect the amount of biofilm. Pulsed-field gel electrophoresis (PFGE) analysis of S. woodyi strains performed with SmaI and NotI restriction enzymes revealed that they exhibited restriction fragment pattern homology ranging from 56 to 89 % and from 82 to 94 %, respectively. As a result, PFGE analysis of the genome S. woodyi (as the first record) revealed that although these strains inhabiting the Gulf of Izmir exhibit common characteristics, they also have high levels of genomic polymorphism.Ege UniversityEge University [2007 FEN 024]The authors thank Izmir Institute of Technology, Biotechnology and Bioengineering Research and Application Center for molecular assays. This work was supported by BAP Project (2007 FEN 024), Ege University