bluuebunny/crossref_metadata_2025_split huggingface dataset:
Colocation of Genes Encoding a tRNA-mRNA Hybrid and a Putative Signaling Peptide on Complementary Strands in the Genome of the Hyperthermophilic BacteriumThermotoga maritima
Authors: Montero Clemente I. , Lewis Derrick L. , Johnson Matthew R. , Conners Shannon B. , Nance Elizabeth A. , Nichols Jason D. , Kelly Robert M. 
Published: September 2006

ABSTRACTIn the genome of the hyperthermophilic bacteriumThermotoga maritima, TM0504 encodes a putative signaling peptide implicated in population density-dependent exopolysaccharide formation. Although not noted in the original genome annotation, TM0504 was found to colocate, on the opposite strand, with the gene encodingssrA, a hybrid of tRNA and mRNA (tmRNA), which is involved in atrans-translation process related to ribosome rescue and is ubiquitous in bacteria. Specific DNA probes were designed and used in real-time PCR assays to follow the separate transcriptional responses of the colocated open reading frames (ORFs) during transition from exponential to stationary phase, chloramphenicol challenge, and syntrophic coculture withMethanococcus jannaschii. TM0504 transcription did not vary under normal growth conditions. Transcription of the tmRNA gene, however, was significantly up-regulated during chloramphenicol challenge and inT. maritimabound in exopolysaccharide aggregates during methanogenic coculture. The significance of the colocation of ORFs encoding a putative signaling peptide and tmRNA inT. maritimais intriguing, since this overlapping arrangement (tmRNA associated with putative small ORFs) was found to be conserved in at least 181 bacterial genomes sequenced to date. Whether peptides related to TM0504 in other bacteria play a role in quorum sensing is not yet known, but their ubiquitous colocalization with respect to tmRNA merits further examination.
Loss of Expression of
cspC
, a Cold Shock Family Gene, Confers a Gain of Fitness in
Escherichia coli
K-12 Strains
Authors: Rath Devashish , Jawali Narendra 
Published: September 2006

ABSTRACT

The CspA family of cold shock genes in
Escherichia coli
K-12 includes nine paralogs,
cspA
to
cspI
. Some of them have been implicated in cold stress adaptation. Screening for mutations among common laboratory
E. coli
strains showed a high degree of genetic diversity in
cspC
but not in
cspA
and
cspE
. This diversity in
cspC
was due to a wide spectrum of variations including insertions of IS elements, deletion, and point mutation. Northern analysis of these mutants showed loss of
cspC
expression in all but one case. Further analysis of the loss-of-function
cspC
mutants showed that they have a fitness advantage in broth culture after 24 h over their isogenic wild-type derivatives. Conversely, introduction of mutated
cspC
alleles conferred a competitive fitness advantage to AB1157, a commonly used laboratory strain. This provides the evidence that loss of
cspC
expression is both necessary and sufficient to confer a gain of fitness as seen in broth culture over 24 h. Together, these results ascribe a novel role in cellular growth at 37°C for CspC, a member of the cold shock domain-containing protein family.
Chromosome Rearrangement and Diversification of
Francisella tularensis
Revealed by the Type B (OSU18) Genome Sequence
Authors: Petrosino Joseph F. , Xiang Qin , Karpathy Sandor E. , Jiang Huaiyang , Yerrapragada Shailaja , Liu Yamei , Gioia Jason , Hemphill Lisa , Gonzalez Arely , Raghavan T. M. , Uzman Akif , Fox George E. , Highlander Sarah , Reichard Mason , Morton Rebecca J. , Clinkenbeard Kenneth D. , Weinstock George M. 
Published: September 2006

ABSTRACT

The γ-proteobacterium
Francisella tularensis
is one of the most infectious human pathogens, and the highly virulent organism
F. tularensis
subsp.
tularensis
(type A) and less virulent organism
F. tularensis
subsp.
holarctica
(type B) are most commonly associated with significant disease in humans and animals. Here we report the complete genome sequence and annotation for a low-passage type B strain (OSU18) isolated from a dead beaver found near Red Rock, Okla., in 1978. A comparison of the
F. tularensis
subsp.
holarctica
sequence with that of
F. tularensis
subsp.
tularensis
strain Schu4 (P. Larsson et al., Nat. Genet.
37:
153-159, 2005) highlighted genetic differences that may underlie different pathogenicity phenotypes and the evolutionary relationship between type A and type B strains. Despite extensive DNA sequence identity, the most significant difference between type A and type B isolates is the striking amount of genomic rearrangement that exists between the strains. All but two rearrangements can be attributed to homologous recombination occurring between two prominent insertion elements, IS
Ftu1
and IS
Ftu2
. Numerous pseudogenes have been found in the genomes and are likely contributors to the difference in virulence between the strains. In contrast, no rearrangements have been observed between the OSU18 genome and the genome of the type B live vaccine strain (LVS), and only 448 polymorphisms have been found within non-transposase-coding sequences whose homologs are intact in OSU18. Nonconservative differences between the two strains likely include the LVS attenuating mutation(s).
The
atlA
Operon of
Streptococcus mutans
: Role in Autolysin Maturation and Cell Surface Biogenesis
Authors: Ahn Sang-Joon , Burne Robert A. 
Published: September 2006

ABSTRACT

The Smu0630 protein (AtlA) was recently shown to be involved in cell separation, biofilm formation, and autolysis. Here, transcriptional studies revealed that
atlA
is part of a multigene operon under the control of at least three promoters. The morphology and biofilm-forming capacity of a nonpolar
altA
mutant could be restored to that of the wild-type strain by adding purified AtlA protein to the medium. A series of truncated derivatives of AtlA revealed that full activity required the C terminus and repeat regions. AtlA was cell associated and readily extractable from with sodium dodecyl sulfate. Of particular interest, the surface protein profile of AtlA-deficient strains was dramatically altered compared to the wild-type strain, as was the nature of the association of the multifunctional adhesin P1 with the cell wall. In addition, AtlA-deficient strains failed to develop competence as effectively as the parental strain. Mutation of
thmA
, which can be cotranscribed with
atlA
and encodes a putative pore-forming protein, resulted in a phenotype very similar to that of the AtlA-deficient strain. ThmA was also shown to be required for efficient processing of AtlA to its mature form, and treatment of the
thmA
mutant strain with full-length AtlA protein did not restore normal cell separation and biofilm formation. The effects of mutating other genes in the operon on cell division, biofilm formation, or AtlA biogenesis were not as profound. This study reveals that AtlA is a surface-associated protein that plays a critical role in the network connecting cell surface biogenesis, biofilm formation, genetic competence, and autolysis.
Role of an RNase III Binding Site in Transcription Termination at λ
nutL
by HK022 Nun Protein
Authors: Washburn Robert S. , Court Donald L. , Gottesman Max E. 
Published: September 2006

ABSTRACT

The phage HK022 Nun protein excludes phage λ by binding nascent λ
p
L
and
p
R
transcripts at
nutL
and
nutR
, respectively, and inducing transcription termination just downstream of these sites. Termination is more efficient at
nutL
than at
nutR
. One difference between
nutL
and
nutR
is the presence of RNase III processing sites (rIII) located immediately promoter distal to λ
nutL
. We found that deletion of rIII dramatically reduced Nun transcription arrest in vitro but had little effect on termination in vivo. However, consistent with the in vitro results, overexpression of a transcript carrying
nutL
and rIII efficiently titrated Nun, allowing λ to grow on a strain that expressed Nun, whereas a transcript carrying only
nutL
or
nutL-
rIII with nucleotides 97 to 141 deleted was ineffective. Rnc70, an RNase III mutant that binds but does not cleave rIII, also prevented Nun-mediated λ exclusion. We propose that rIII enhances the on-rate of Nun at
nutL
, stimulating Nun-mediated arrest in vitro. We have shown that a specific element in rIII, i.e., box C (G
89
GUGUGUG), strongly enhances arrest on rIII

+

templates. Nun-rIII interactions do not stimulate Nun termination in vivo, presumably because formation of the Nun-
nutL
complex is normally not rate-limiting in the cell. In contrast to Nun, N is not occluded by Rnc70 and is not efficiently titrated by a
nutL
-rIII transcript.
Differential Dependence of StpA on H-NS in Autoregulation of
stpA
and in Regulation of
bgl
Authors: Wolf Tinka , Janzen Wiebke , Blum Corinna , Schnetz Karin 
Published: September 2006

ABSTRACT

StpA has functional similarity to its homologue, the nucleoid structuring protein H-NS. It binds to AT-rich, planar, bent DNA and constrains DNA supercoils. In addition, StpA acts as an RNA chaperone. StpA and H-NS also form heterodimers. However, cellular levels of StpA are low due to repression of
stpA
by H-NS and negative autoregulation. Here we show that effective (30-fold) repression of
stpA
transcription requires a downstream regulator element located within the
stpA
coding region. In addition, we show that StpA represses
stpA
threefold in an
hns
null mutant. In contrast, repression of the
bgl
operon, another H-NS-repressed system, is not achieved by StpA alone. It becomes StpA dependent in the presence of a fusion protein encompassing the N-terminal 37 amino acids of H-NS, which comprise the core of the dimerization domain. StpA also effectively complements H-NS-I119T, a mutant defective in specific DNA binding, in repression of the
bgl
operon. Thus, StpA complements H-NS proteins defective in DNA binding to repress
bgl
, while in autoregulation of
stpA
it acts autonomously, indicating a difference in the mechanisms of repression.
Characterization of Adhesion Threads of
Deinococcus geothermalis
as Type IV Pili
Authors: Saarimaa C. , Peltola M. , Raulio M. , Neu T. R. , Salkinoja-Salonen M. S. , Neubauer P. 
Published: September 2006

ABSTRACT

Deinococcus geothermalis
E50051 forms tenuous biofilms on paper machine surfaces. Field emission electron microscopy analysis revealed peritrichous appendages which mediated cell-to-surface and cell-to-cell interactions but were absent in planktonically grown cells. The major protein component of the extracellular extract of
D. geothermalis
had an N-terminal sequence similar to the fimbrial protein pilin annotated in the
D. geothermalis
DSM 11300 draft sequence. It also showed similarity to the type IV pilin sequence of
D. radiodurans
and several gram-negative pathogenic bacteria. Other proteins in the extract had N-terminal sequences identical to
D. geothermalis
proteins with conservative motifs for serine proteases, metallophosphoesterases, and proteins whose function is unknown. Periodic acid-Schiff staining for carbohydrates indicated that these extracellular proteins may be glycosylated. A further confirmation for the presence of glycoconjugates on the cell surface was obtained by confocal laser scanning imaging of living
D. geothermalis
cells stained with
Amaranthus caudatus
lectin, which specifically binds to galactose residues. The results indicate that the thread-like appendages of
D. geothermalis
E50051 are glycosylated type IV pili, bacterial attachment organelles which have thus far not been described for the genus
Deinococcus
.
Characterization of the
Staphylococcus aureus
Heat Shock, Cold Shock, Stringent, and SOS Responses and Their Effects on Log-Phase mRNA Turnover
Authors: Anderson Kelsi L. , Roberts Corbette , Disz Terrence , Vonstein Veronika , Hwang Kaitlyn , Overbeek Ross , Olson Patrick D. , Projan Steven J. , Dunman Paul M. 
Published: September 2006

ABSTRACT

Despite its being a leading cause of nosocomal and community-acquired infections, surprisingly little is known about
Staphylococcus aureus
stress responses. In the current study, Affymetrix
S. aureus
GeneChips were used to define transcriptome changes in response to cold shock, heat shock, stringent, and SOS response-inducing conditions. Additionally, the RNA turnover properties of each response were measured. Each stress response induced distinct biological processes, subsets of virulence factors, and antibiotic determinants. The results were validated by real-time PCR and stress-mediated changes in antimicrobial agent susceptibility. Collectively, many
S. aureus
stress-responsive functions are conserved across bacteria, whereas others are unique to the organism. Sets of small stable RNA molecules with no open reading frames were also components of each response. Induction of the stringent, cold shock, and heat shock responses dramatically stabilized most mRNA species. Correlations between mRNA turnover properties and transcript titers suggest that
S. aureus
stress response-dependent alterations in transcript abundances can, in part, be attributed to alterations in RNA stability. This phenomenon was not observed within SOS-responsive cells.
Identification and Characterization of a Major Zn(II) Resistance Determinant of
Mycobacterium smegmatis
Authors: Grover Amit , Sharma Rakesh 
Published: September 2006

ABSTRACT

A zinc ion-sensitive mutant of
Mycobacterium smegmatis
was isolated. The transposon insertion was located in
zitA
(MSMEG0750), a gene coding for a cation diffusion facilitator family protein. Zinc ions specifically induced expression of
zitA
. In silico analysis revealed that environmental and opportunistic pathogenic species contain higher numbers of cation diffusion facilitator genes than do obligate pathogens.
PurF-Independent Phosphoribosyl Amine Formation inyjgFMutants ofSalmonella entericaUtilizes the Tryptophan Biosynthetic Enzyme Complex Anthranilate Synthase-Phosphoribosyltransferase
Authors: Browne Beth Ann , Ramos A. Itzel , Downs Diana M. 
Published: September 2006

ABSTRACTInSalmonella enterica, the biosynthetic pathways for the generation of purines and the essential cofactor thiamine pyrophosphate branch after sharing five enzymatic steps. Phosphoribosyl amine (PRA) is the first intermediate in the common portion of the pathway and is generated from phosphoribosylpyrophosphate and glutamine by the PurF enzyme (phosphoribosylpyrophosphate amidotransferase). A null mutation inyjgFallows PurF-independent PRA formation by an unknown mechanism. The tryptophan biosynthetic enzyme complex anthranilate synthase-phosphoribosyltransferase, composed of the TrpD and TrpE proteins, was shown to be essential for PRA formation in strains lacking bothyjgFandpurF. The activity generating PRA in ayjgFmutant background has features that distinguish it from the TrpDE-mediated PRA formation shown previously for this enzyme in strains with an active copy ofyjgF. The data presented here are consistent with a model in which the absence of YjgF uncovers a new catalytic activity of TrpDE.
Biochemical and Molecular Characterization of the Biosynthesis of Glutamine and Glutamate, Two Major Compatible Solutes in the Moderately Halophilic Bacterium
Halobacillus halophilus
Authors: Saum Stephan H. , Sydow Jasmin F. , Palm Peter , Pfeiffer Friedhelm , Oesterhelt Dieter , Müller Volker 
Published: September 2006

ABSTRACT

The moderately halophilic, chloride-dependent bacterium
Halobacillus halophilus
produces glutamate and glutamine as main compatible solutes at external salinities of 1.0 to 1.5 M NaCl. The routes for the biosynthesis of these solutes and their regulation were examined. The genome contains two genes potentially encoding glutamate dehydrogenases and two genes for the small subunit of a glutamate synthase, but only one gene for the large subunit. However, the expression of these genes was not salt dependent, nor were the corresponding enzymatic activities detectable in cell extracts of cells grown at different salinities. In contrast, glutamine synthetase activity was readily detectable in
H. halophilus
. Induction of glutamine synthetase activity was strictly salt dependent and reached a maximum at 3.0 M NaCl; chloride stimulated the production of active enzyme by about 300%. Two potential genes encoding a glutamine synthetase,
glnA1
and
glnA2
, were identified. The expression of
glnA2
but not of
glnA1
was increased up to fourfold in cells adapted to high salt, indicating that GlnA2 is the glutamine synthetase involved in the synthesis of the solutes glutamate and glutamine. Furthermore, expression of
glnA2
was stimulated twofold by the presence of chloride ions. Chloride exerted an even more pronounced effect on the enzymatic activity of preformed enzyme: in the absence of chloride in the assay buffer, glutamine synthetase activity was decreased by as much as 90%. These data demonstrate for the first time a regulatory role of a component of common salt, chloride, in the biosynthesis of compatible solutes.
PhoP-Induced Genes withinSalmonellaPathogenicity Island 1
Authors: Aguirre Andrés , Cabeza María Laura , Spinelli Silvana V. , McClelland Michael , García Véscovi Eleonora , Soncini Fernando C. 
Published: September 2006

ABSTRACTThe invasive pathogenSalmonella entericahas evolved a sophisticated device that allows it to enter nonphagocytic host cells. This process requires the expression ofSalmonellapathogenicity island 1 (SPI-1), which encodes a specialized type III protein secretion system (TTSS). This TTSS delivers a set of effectors that produce a marked rearrangement of the host cytoskeleton, generating a profuse membrane ruffling at the site of interaction, driving bacterial entry. It has been shown that the PhoP/PhoQ two-component system represses the expression of the SPI-1 machinery by down-regulating the transcription of its master regulator, HilA. In this work, we reveal the presence of a PhoP-activated operon within SPI-1. This operon is composed of theorgBandorgCgenes, which encode a protein that interacts with the InvC ATPase and a putative effector protein of the TTSS, respectively. Under PhoP-inducing conditions, expression of this operon is directly activated by the phosphorylated form of the response regulator, which recognizes a PhoP box located at the −35 region relative to the transcription start site. Additionally, under invasion-inducing conditions,orgBCexpression is driven both by theprgHpromoter, induced by the SPI-1 master regulator HilA, and by the directly controlled PhoP/PhoQ promoter. Together, these results indicate that in contrast to the rest of the genes encompassed in the SPI-1 locus,orgBCis expressed during and afterSalmonellaentry into its host cell, and they suggest a role for the products of this operon after host cell internalization.
Molecular and Population Analyses of a Recombination Event in the Catabolic Plasmid pJP4
Authors: Larraín-Linton Juanita , De la Iglesia Rodrigo , Melo Francisco , González Bernardo 
Published: September 2006

ABSTRACT

Cupriavidus necator
JMP134(pJP4) harbors a catabolic plasmid, pJP4, which confers the ability to grow on chloroaromatic compounds. Repeated growth on 3-chlorobenzoate (3-CB) results in selection of a recombinant strain, which degrades 3-CB better but no longer grows on 2,4-dichlorophenoxyacetate (2,4-D). We have previously proposed that this phenotype is due to a double homologous recombination event between inverted repeats of the multicopies of this plasmid within the cell. One recombinant form of this plasmid (pJP4-F3) explains this phenotype, since it harbors two copies of the chlorocatechol degradation
tfd
gene clusters, which are essential to grow on 3-CB, but has lost the
tfdA
gene, encoding the first step in degradation of 2,4-D. The other recombinant plasmid (pJP4-FM) should harbor two copies of the
tfdA
gene but no copies of the
tfd
gene clusters. A molecular analysis using a multiplex PCR approach to distinguish the wild-type plasmid pJP4 from its two recombinant forms, was carried out. Expected PCR products confirming this recombination model were found and sequenced. Few recombinant plasmid forms in cultures grown in several carbon sources were detected. Kinetic studies indicated that cells containing the recombinant plasmid pJP4-FM were not selectable by sole carbon source growth pressure, whereas those cells harboring recombinant plasmid pJP4-F3 were selected upon growth on 3-CB. After 12 days of repeated growth on 3-CB, the complete plasmid population in
C. necator
JMP134 apparently corresponds to this form. However, wild-type plasmid forms could be recovered after growing this culture on 2,4-D, indicating that different plasmid forms can be found in
C. necator
JMP134 at the population level.
Characterization of the Genetic Components of
Streptomyces lividans
Linear Plasmid SLP2 for Replication in Circular and Linear Modes
Authors: Xu Mingxuan , Zhu Yingmin , Zhang Ran , Shen Meijuan , Jiang Weihong , Zhao Guoping , Qin Zhongjun 
Published: September 2006

ABSTRACT

The nucleotide sequence of
Streptomyces lividans
linear plasmid SLP2 consists of 50,410 bp (C. H. Huang, C. Y. Chen, H. H. Tsai, C. Chen, Y. S. Lin, and C. W. Chen, Mol. Microbiol.
47:
1563-1576, 2003). Here we report that the basic SLP2 locus for plasmid replication in circular mode resembles that of
Streptomyces
linear plasmids pSLA2 and SCP1 and comprises iterons
SLP2
and the adjacent
rep

SLP2

gene. More efficient replication additionally required the 47-bp sequence between bp 581 and 628 upstream of the iterons. Replacement of either the iterons or the
rep
gene of SLP2 by the corresponding genes of pSLA2 or SCP1 still allows propagation in
Streptomyces
, although the transformation frequencies were 3 orders of magnitude lower than the original plasmids, suggesting that these plasmids share similar replication mechanisms. To replicate SLP2 in linear mode, additional SLP2 loci—either
mtap

SLP2

/
tpg

SLP2

or
mtap

SLP2

/
ilrA

SLP2

—were required. IlrA
SLP2
protein binds specifically to the iterons
SLP2
in vitro. Interactions were detected between these SLP2-borne replication proteins (Mtap
SLP2
, Tpg
SLP2
, and IlrA
SLP2
) and the telomeric replication proteins (TpgL, TapL, and TpgL) of the
S. lividans
chromosome, respectively, but the SLP2 proteins failed to interact. These results suggest that SLP2 recruits chromosomally encoded replication proteins for its telomere replication.
Characterization of ExsC and ExsD Self-Association and Heterocomplex Formation
Authors: Lykken Guinevere L. , Chen GuoZhou , Brutinel Evan D. , Chen Lingling , Yahr Timothy L. 
Published: September 2006

ABSTRACT

Expression of the
Pseudomonas aeruginosa
type III secretion system (T3SS) is induced by calcium depletion and is positively regulated by the ExsA transcriptional activator and negatively regulated by the ExsD antiactivator. Under conditions permissive for expression of the T3SS, the negative regulatory activity of ExsD is antagonized by a direct binding interaction with ExsC. In the present study, the ExsC-ExsD binding interaction was characterized. Individually, both ExsC and ExsD form self-associated complexes, as judged by bacterial monohybrid and gel filtration experiments. A mixture of purified ExsC and ExsD readily formed a complex that elutes from gel filtration medium as a single included peak. The calculated molecular weight of the ExsC-ExsD complex is consistent with a complex containing multiple copies of ExsC and ExsD. Isothermic titration calorimetry experiments found formation of the ExsC-ExsD complex to be thermodynamically favorable, with a

K
d

of ∼18 nM and a likely binding ratio of 1:1. To identify amino acid residues important for the regulatory activities of ExsC and ExsD, self-association, and complex formation, charged-cluster mutagenesis was performed. Two of the resulting ExsD charged-cluster mutants (DM2 and DM3) demonstrated a hyperrepressive phenotype for expression of the T3SS. By two-hybrid and copurification assays, the DM3 mutant was found to be impaired in its interaction with ExsC. This finding demonstrates that the binding of ExsC to ExsD is required for transcriptional induction of the T3SS under calcium-limiting growth conditions.