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Regulation of Transcription of Compatible Solute Transporters by the General Stress Sigma Factor,  B,
in Listeria monocytogenes.Mehmet Sevket Cetin, 2004.Listeria monocytogenes is well known for its durable physiological characteristics, which allow the organism to grow at low temperature and pH and high osmolarity . Growth under high osmolarity depends on the accumulation of compatible solutes, among which glycine betaine and carnitine are the preferred solutes for this organism . Three different transport systems, Gbu, BetL, and OpuC, have been identified in L . monocytogenes which serve to scavenge the preferred compatible solutes . The general stress response regulator B
has been shown to play an important role in osmotic adaptation in
L . monocytogenes, presumably by directing transcription from one
or more of the solute transport genes . In the studies presented here,
we have used primer extension analyses to identify the promoter
elements responsible for transcription of the opuC, gbuA,
and betL genes . All three genes are osmotically inducible to
some degree . betL is transcribed from a
B-independent
promoter, while gbuA is transcribed from dual promoters, one
of which is
B
dependent . opuC is transcribed exclusively from a
B-dependent
promoter . The betL promoter is similar in sequence to the
B-independent
gbuAP1 promoter . Kinetic analysis of transcript accumulation
after osmotic upshift demonstrated that
B-dependent
transcripts from gbuAP2 and sigB accumulate for an
extended period after upshift, suggesting that
B
activity may provide a mechanism for sustained high-level expression
during osmotic challenge . In contrast to osmotic upshift, expression
from the
B-dependent
opuC and gbuAP2 promoters after temperature upshift and
ethanol stress was minimal, suggesting that additional mechanisms may
also participate in regulating transcription from these
B-dependent
promoters .
Discordant Phylogenies within the rrn Loci of Rhizobia. Peter van Berkum, 2003.It is evident from complete genome sequencing results that lateral gene transfer and recombination are essential components in the evolutionary process of bacterial genomes . Since this has important implications for bacterial systematics, the primary objective of this study was to compare estimated evolutionary relationships among a representative set of  -Proteobacteria
by sequencing analysis of three loci within their rrn operons .
Tree topologies generated with 16S rRNA gene sequences were
significantly different from corresponding trees assembled with 23S
rRNA gene and internally transcribed space region sequences . Besides
the incongruence in tree topologies, evidence that distinct segments
along the 16S rRNA gene sequences of bacteria currently classified
within the genera Bradyrhizobium, Mesorhizobium and
Sinorhizobium have a reticulate evolutionary history was also
obtained . Our data have important implications for bacterial
taxonomy, because currently most taxonomic decisions are based on
comparative 16S rRNA gene sequence analysis . Since phylogenetic
placement based on 16S rRNA gene sequence divergence perhaps is
questionable, we suggest that the proposals of bacterial nomenclature
or changes in their taxonomy that have been made may not necessarily
be warranted . Accordingly, a more conservative approach should be
taken in the future, in which taxonomic decisions are based on the
analysis of a wider variety of loci and comparative analytical
methods are used to estimate phylogenetic relationships among the
genomes under consideration .
Two Morphological Types of Cell Appendages on a Strongly Adhesive Bacterium, Acinetobacter sp . Strain Tol 5. Shun'ichi Ishii, 2004. Tools for Characterization of Escherichia coli Genes of Unknown Function. Christophe Merlin, 2002.Despite the power of sequencing and of emerging high-throughput technologies to collect data rapidly, the definitive functional characterization of unknown genes still requires biochemical and genetic analysis in case-by-case studies . This often involves the deletion of target genes and phenotypic characterization of the deletants . We describe here modifications of an existing deletion method which facilitates the deletion process and enables convenient analysis of the expression properties of the target gene by replacing it with an FRT-lacZ-aph-Plac-FRT cassette . The lacZ gene specifically reports the activity of the deleted gene and therefore allows the determination of the conditions under which it is actively expressed . The aph gene, encoding resistance to kanamycin, provides a selectable means of transducing a deleted locus between strains so that the deletion can be combined with other relevant mutations . The lac promoter helps to overcome possible polar effects on downstream genes within an operon . Because the cassette is flanked by two directly repeated FRT sites, the cassette can be excised by the Flp recombinase provided in trans . Removing the cassette leaves an in-frame deletion with a short scar which should not interfere with downstream expression . Replacements of yacF, yacG, yacH, yacK (cueO), yacL, ruvA, ruvB, yabB, and yabC made with the cassette were used to verify its properties .
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