The Adaptive Genome of Desulfovibrio vulgaris Hildenborough
April 18, 2018
Minst.org eJournal Highlight:
2017 Glimpses at the Adaptive Genome
Minst.org Watch Team (martine [at] minst [dot] org)
Kuwahara H, 2017 reported the uncultured bacterium Candidatus Desulfovibrio trichonymphae
"lacks genes for mannose permease, which are commonly found in the genomes
of desulfovibrios (Santana M, 2006)".
Poosarla VG, 2017 referenced to
Santana M, 2006 for supporting the statement that sulfate-reducing
bacteria "are major culprits in microbiologically influenced corrosion".
Even though Santana M, 2006 did not discuss corrosion by sulfate-reducing
bacteria, it is interesting to recall the late Professor John R. Postgate's
account that the Hildenborough strain of
Desulfovibrio vulgaris was isolated in 1946 from a specimen of Wealden clay,
which was associated with a corroding water pipe that was being excavated at
Hildenborough (2006 personal
communication to M. Crasnier-Mednansky).
May 2, 2013
Minst.org eJournal Highlight:
A Glimpse at the Adaptive Genome
Minst.org Watch Team (martine [at] minst [dot] org)
Zapata-Peņasco I, 2013 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 (Santana M, 2006)".
May 17, 2006
Minst.org eJournal Highlight: Adaptation and bacterial IQ: Looking at
Bacterial Genomes beyond the Tip of
the Iceberg
M. Crasnier-Mednansky, Ph.D.,
D.Sc. (martine [at] minst [dot] org)
Copyright © 2006 Mednansky Institute, Inc.
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.
Santana M, 2006 manually analyzed 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 (Kundig W, 1964; Postma PW, 1993). As a result the metabolic diversity and adaptive
character of the sulfate reducer Desulfovibrio vulgaris were emphasized.
Bacterial adaptation has been quantified by defining an adaptability index
or 'bacterial IQ' (Galperin MY, 2005). 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 (Table 1 in Galperin MY, 2005). 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, second on the list, Geobacter sulfurreducens, a metal reducer which, like the sulfate reducer Desulfovibrio
vulgaris Hildenborough, belongs to the delta subdivision of Proteobacteria
(Caccavo F Jr, 1994). Interestingly, both organisms are classified
as strict anaerobes, in contrast with findings that G. sulfurreducens
can grow in the presence of oxygen (Lin WC, 2004), and a close relative of
D. vulgaris, is equipped with the necessary components to live aerobically
(Lemos RS, 2001). In addition, D. vulgaris can efficiently protect itself
against oxygen exposure (Voordouw JK, 1998; Fournier M, 2003). Undoubtedly, the ability to cope with oxygen is a distinct
advantage especially for adapting to environments whose oxygen content is fluctuating
(Cypionka H, 2000), a situation likely to occur in the habitats of these two
'intelligent' bacteria.
Professor John R. 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 (D'Souza M, 2007) for genome analysis of prokaryotic signal transduction
proteins |
|
Comprehensive Microbial Resources for bacterial genomes released
by
JCVI |
| JCVI
Comprehensive Microbial Resource for genome annotation and analyses
|
|
Desulfovibrio vulgaris Hildenborough genome page at JCVI |
|
HAMAP: High-quality Automated and Manual Annotation of Microbial
Proteomes at
ExPASy |
|
GOLD for monitoring complete and ongoing genome projects worldwide
|