MIeJResearch Highlights

Highlights for the adaptive genome of Desulfovibrio vulgaris Hildenborough

May 2, 2013
A glimpse at the adaptive genome
Minst.org Watch Team

In an article titled 'Bisulfite reductase and nitrogenase genes retrieved from biocorrosive bacteria in saline produced waters of offshore oil recovery facilities' (Int Biodeterior Biodegradation), I. Zapata-Peñasco et al. further reinforced the contention Desulfovibrio has an adaptive genome by stating "Desulfovibrio is a remarkably versatile taxon in metabolic pathways among the SRB [Sulfate Reducing Bacteria]; for instance, it is capable of bidirectional transmigration and adaptation to both water and terrestrial environments due to its adaptive genome (FEMS Microbiol Lett)."

May 17, 2006
Adaptation and bacterial IQ: Looking at bacterial genomes beyond the tip of the iceberg
Martine Crasnier-Mednansky, Ph.D., D.Sc.
Copyright © 2006 Mednansky Institute, Inc.
Contact: martine [at] minst [dot] org

Portuguese version

Integrating the vast amount of data released by sequencing bacterial genomes and metagenomes is a colossal task.  Currently the avalanche of information is classified and analyzed by automatic means however a need exists for manual search.  The latter allows pieces of the 'genomic puzzle' to be assembled while focusing on specific features of interest.  This type of search avails the possibility of novel avenues for discovery.

The collaborative research published in FEMS Microbiology Letters entitled 'The adaptive genome of Desulfovibrio vulgaris Hildenborough' (FEMS Microbiol Lett) manually analyzes the genome of Desulfovibrio vulgaris subsp. vulgaris strain Hildenborough by assimilating data in relation to the presence of genes encoding proteins belonging to the phosphotransferase system (Proc Natl Acad Sci U S A, Microbiol Mol Biol Rev).  As a result the metabolic diversity and adaptive character of the sulfate reducer Desulfovibrio vulgaris were emphasized.

US-Portuguese collaboration

Bacterial adaptation has been quantified by defining an adaptability index or 'bacterial IQ' (BMC Microbiol).  The IQ was determined by specifically looking for the presence of signal transduction proteins in bacterial and archaeal proteomes derived from 167 genome sequences.  Despite the conscientious perspective by the author, that "better ways to evaluate bacterial IQ are needed", the deductive proposal that Desulfovibrio vulgaris Hildenborough has an adaptive genome is in agreement with his IQ-derived classification.  Indeed, D. vulgaris Hildenborough appears as the fourth most 'intelligent' organisms among the 167 analyzed (BMC Microbiol, Table 1).  In contrast, the model organism Escherichia coli as well as other members of the Enterobacteriaceae family are reported as being 'dumb'.

Among the 'bacterial leaders' was found Geobacter sulfurreducens strain PCA (second on the list, Table 1), a metal reducer which, like the sulfate reducer Desulfovibrio vulgaris Hildenborough, belongs to the delta subdivision of Proteobacteria (Appl Environ Microbiol).  Interestingly both of these organisms are classified as strict anaerobes.  This is in contrast with findings that G. sulfurreducens can grow in the presence of oxygen (Appl Environ Microbiol) and Desulfovibrio gigas, a close relative of D. vulgaris, is equipped with the necessary components to live aerobically (FEBS Lett).  In addition, D. vulgaris can efficiently protect itself against oxygen exposure (Appl Environ Microbiol, J Bacteriol).  Undoubtedly, the ability to cope with oxygen is a distinct advantage especially for adapting to environments whose oxygen content is fluctuating (Annu Rev Microbiol), a situation likely to occur in the habitats of these two 'intelligent' bacteria.

Professor John Postgate, F.R.S., illuminated the remarkable versatility of the sulfate reducer group of bacteria as he wrote "… they have, so to speak, grown from a couple of microbiological eccentrics to a positive menageries of species, comprising a variety of physiologies, but all strict anaerobes".  Could this versatility be accounted for by their adaptive genomes?  Bacterial genomes are dynamic after all, and the existence of unique strain-specific genes within bacterial genomes may reveal their hosts not-too-distant past.

SENTRA (Nucleic Acids Research) for genome analysis of prokaryotic signal transduction proteins

Desulfovibrio vulgaris Hildenborough at SENTRA (no longer maintained) see NCBI

JCVI Comprehensive Microbial Resources for bacterial genomes released by JCVI

Genomic Sequencing Center for infectious diseases at JCVI

JCVI Comprehensive Microbial Resource for genome annotation and analyses

Desulfovibrio vulgaris Hildenborough genome page

HAMAP: High-quality Automated and Manual Annotation of Microbial Proteomes at ExPASy

Desulfovibrio vulgaris Hildenborough proteome

GOLD for monitoring complete and ongoing genome projects worldwide

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