bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identification of AlgR-Regulated Genes in
Pseudomonas aeruginosa
by Use of Microarray Analysis
Authors: Lizewski Stephen E. , Schurr Jill R. , Jackson Debra W. , Frisk Anders , Carterson Alexander J. , Schurr Michael J. 
Published: August 2004

ABSTRACT

The
Pseudomonas aeruginosa
transcriptional regulator AlgR controls a variety of different processes, including alginate production, type IV pilus function, and virulence, indicating that AlgR plays a pivotal role in the regulation of gene expression. In order to characterize the AlgR regulon,
Pseudomonas
Affymetrix GeneChips were used to generate the transcriptional profiles of (i)
P. aeruginosa
PAO1 versus its
algR
mutant in mid-logarithmic phase, (ii)
P. aeruginosa
PAO1 versus its
algR
mutant in stationary growth phase, and (iii) PAO1 versus PAO1 harboring an
algR
overexpression plasmid. Expression analysis revealed that, during mid-logarithmic growth, AlgR activated the expression of 58 genes while it repressed the expression of 37 others, while during stationary phase, it activated expression of 45 genes and repression of 14 genes. Confirmatory experiments were performed on two genes found to be AlgR repressed (
hcnA
and
PA1557
) and one AlgR-activated operon (
fimU
-
pilVWXY1Y2
). An S1 nuclease protection assay demonstrated that AlgR repressed both known
hcnA
promoters in PAO1. Additionally, direct measurement of hydrogen cyanide (HCN) production showed that
P. aeruginosa
PAO1 produced threefold-less HCN than did its
algR
deletion strain. AlgR also repressed transcription of two promoters of the uncharacterized open reading frame
PA1557
. Further, the twitching motility defect of an
algR
mutant was complemented by the
fimTU-pilVWXY1Y2E
operon, thus identifying the AlgR-controlled genes responsible for this defect in an
algR
mutant. This study identified four new roles for AlgR: (i) AlgR can repress gene transcription, (ii) AlgR activates the
fimTU-pilVWXY1Y2E
operon, (iii) AlgR regulates HCN production, and (iv) AlgR controls transcription of the putative
cbb
3
-type cytochrome PA1557.
CO
2
-Responsive Expression and Gene Organization of Three Ribulose-1,5-Bisphosphate Carboxylase/Oxygenase Enzymes and Carboxysomes in
Hydrogenovibrio marinus
Strain MH-110
Authors: Yoshizawa Yoichi , Toyoda Koichi , Arai Hiroyuki , Ishii Masaharu , Igarashi Yasuo 
Published: August 2004

ABSTRACT

Hydrogenovibrio marinus
strain MH-110, an obligately lithoautotrophic hydrogen-oxidizing bacterium, fixes CO
2
by the Calvin-Benson-Bassham cycle. Strain MH-110 possesses three different sets of genes for ribulose-1,5-bisphosphate carboxylase/oxygenase (RubisCO): CbbLS-1 and CbbLS-2, which belong to form I (L
8
S
8
), and CbbM, which belongs to form II (L
x
). In this paper, we report that the genes for CbbLS-1 (
cbbLS-1
) and CbbM (
cbbM
) are both followed by the
cbbQO
genes and preceded by the
cbbR
genes encoding LysR-type regulators. In contrast, the gene for CbbLS-2 (
cbbLS-2
) is followed by genes encoding carboxysome shell peptides. We also characterized the three RubisCOs in vivo by examining their expression profiles in environments with different CO
2
availabilities. Immunoblot analyses revealed that when strain MH-110 was cultivated in 15% CO
2
, only the form II RubisCO, CbbM, was expressed. When strain MH-110 was cultivated in 2% CO
2
, CbbLS-1 was expressed in addition to CbbM. In the 0.15% CO
2
culture, the expression of CbbM decreased and that of CbbLS-1 disappeared, and CbbLS-2 was expressed. In the atmospheric CO
2
concentration of approximately 0.03%, all three RubisCOs were expressed. Transcriptional analyses of mRNA by reverse transcription-PCR showed that the regulation was at the transcriptional level. Electron microscopic observation of MH-110 cells revealed the formation of carboxysomes in the 0.15% CO
2
concentration. The results obtained here indicate that strain MH-110 adapts well to various CO
2
concentrations by using different types of RubisCO enzymes.
Identification ofLactobacillus plantarumGenes That Are Induced in the Gastrointestinal Tract of Mice
Authors: Bron Peter A. , Grangette Corinne , Mercenier Annick , de Vos Willem M. , Kleerebezem Michiel 
Published: August 2004

ABSTRACTLactobacillus plantarumis a flexible and versatile microorganism that inhabits a variety of environmental niches, including the human gastrointestinal (GI) tract. Moreover, this lactic acid bacterium can survive passage through the human or mouse stomach in an active form. To investigate the genetic background of this persistence, resolvase-based in vivo expression technology (R-IVET) was performed inL. plantarumWCFS1 by using the mouse GI tract as a model system. This approach identified 72L. plantarumgenes whose expression was induced during passage through the GI tract as compared to laboratory media. Nine of these genes encode sugar-related functions, including ribose, cellobiose, sucrose, and sorbitol transporter genes. Another nine genes encode functions involved in acquisition and synthesis of amino acids, nucleotides, cofactors, and vitamins, indicating their limited availability in the GI tract. Four genes involved in stress-related functions were identified, reflecting the harsh conditions thatL. plantarumencounters in the GI tract. The four extracellular protein encoding genes identified could potentially be involved in interaction with host specific factors. The rest of the genes are part of several functionally unrelated pathways or encode (conserved) hypothetical proteins. Remarkably, a large number of the functions or pathways identified here have previously been identified in pathogens as being important in vivo during infection, strongly suggesting that survival rather than virulence is the explanation for the importance of these genes during host residence.
Identification of Functional
mob
Regions in
Rhizobium etli
: Evidence for Self-Transmissibility of the Symbiotic Plasmid pRetCFN42d
Authors: Pérez-Mendoza Daniel , Domínguez-Ferreras Ana , Muñoz Socorro , Soto María José , Olivares José , Brom Susana , Girard Lourdes , Herrera-Cervera José A. , Sanjuán Juan 
Published: August 2004

ABSTRACT

An approach originally designed to identify functional origins of conjugative transfer (
oriT
or
mob
) in a bacterial genome (J. A. Herrera-Cervera, J. M. Sanjuán-Pinilla, J. Olivares, and J. Sanjuán, J. Bacteriol. 180:4583-4590, 1998) was modified to improve its reliability and prevent selection of undesired false
mob
clones. By following this modified approach, we were able to identify two functional
mob
regions in the genome of
Rhizobium etli
CFN42. One corresponds to the recently characterized transfer region of the nonsymbiotic, self-transmissible plasmid pRetCFN42a (C. Tun-Garrido, P. Bustos, V. González, and S. Brom, J. Bacteriol. 185:1681-1692, 2003), whereas the second
mob
region belongs to the symbiotic plasmid pRetCFN42d. The new transfer region identified contains a putative
oriT
and a typical conjugative (
tra
) gene cluster organization. Although pRetCFN42d had not previously been shown to be self-transmissible, mobilization of cosmids containing this
tra
region required the presence of a wild-type pRetCFN42d in the donor cell; the presence of multiple copies of this
mob
region in CFN42 also promoted conjugal transfer of the Sym plasmid pRetCFN42d. The overexpression of a small open reading frame, named
yp028
, located downstream of the putative relaxase gene
traA
, appeared to be responsible for promoting the conjugal transfer of the
R. etli
pSym under laboratory conditions. This
yp028
-dependent conjugal transfer required a wild-type pRetCFN42d
traA
gene. Our results suggest for the first time that the
R. etli
symbiotic plasmid is self-transmissible and that its transfer is subject to regulation. In wild-type CFN42, pRetCFN42d
tra
gene expression appears to be insufficient to promote plasmid transfer under standard laboratory conditions; gene
yp028
may play some role in the activation of conjugal transfer in response to as-yet-unknown environmental conditions.
ThebzdGene Cluster, Coding for Anaerobic Benzoate Catabolism, inAzoarcussp. Strain CIB
Authors: Barragán María J. López , Carmona Manuel , Zamarro María T. , Thiele Bärbel , Boll Matthias , Fuchs Georg , García José L. , Díaz Eduardo 
Published: August 2004

ABSTRACTWe report here that thebzdgenes for anaerobic benzoate degradation inAzoarcussp. strain CIB are organized as two transcriptional units, i.e., a benzoate-inducible catabolic operon,bzdNOPQMSTUVWXYZA, and a gene,bzdR, encoding a putative transcriptional regulator. The last gene of the catabolic operon,bzdA, has been expressed inEscherichia coliand encodes the benzoate-coenzyme A (CoA) ligase that catalyzes the first step in the benzoate degradation pathway. The BzdA enzyme is able to activate a wider range of aromatic compounds than that reported for other previously characterized benzoate-CoA ligases. The reduction of benzoyl-CoA to a nonaromatic cyclic intermediate is carried out by a benzoyl-CoA reductase (bzdNOPQgene products) detected inAzoarcussp. strain CIB extracts. ThebzdW,bzdX, andbzdYgene products show significant similarity to the hydratase, dehydrogenase, and ring-cleavage hydrolase that act sequentially on the product of the benzoyl-CoA reductase in the benzoate catabolic pathway ofThauera aromatica. Benzoate-CoA ligase assays and transcriptional analyses based onlacZ-reporter fusions revealed that benzoate degradation inAzoarcussp. strain CIB is subject to carbon catabolite repression by some organic acids, indicating the existence of a physiological control that connects the expression of thebzdgenes to the metabolic status of the cell.
Mycoplasma hyopneumoniae
p65 Surface Lipoprotein Is a Lipolytic Enzyme with a Preference for Shorter-Chain Fatty Acids
Authors: Schmidt Jono A. , Browning Glenn F. , Markham Philip F. 
Published: August 2004

ABSTRACT

Mycoplasma hyopneumoniae
is the most significant bacterial pathogen of the respiratory tract of swine. p65 is an immunodominant surface lipoprotein of
M. hyopneumoniae
that is specifically recognized during disease. Analysis of the translated amino acid sequence of the gene encoding p65 revealed similarity to the GDSL family of lipolytic enzymes. To examine the lipolytic activity of p65, the gene was cloned and expressed in
Escherichia coli
after truncation of the prokaryotic lipoprotein signal sequence and mutagenesis of the mycoplasma TGA tryptophan codons. After treatment with thrombin, the recombinant glutathione
S
-transferase (GST)-p65 protein yielded a 66-kDa fusion protein cleavage product corresponding in size to the mature p65 protein. The esterase activity of recombinant GST-p65 was indicated by the formation of a cleared zone on tributyrin agar plates and the hydrolysis of
p
-nitrophenyl esters of caproate (pNPC) and
p
-nitrophenyl esters of palmitate (pNPP). Lipase activity was indicated by the hydrolysis of the artificial triglyceride 1,2-
O
-dilauryl-
rac
-glycero-3-glutaric acid resorufin ester. Using pNPC and pNPP as substrates, recombinant GST-p65 had optimal activity between pHs 9.2 and 10.2 and at a temperature higher than 39°C. Calcium ions did not increase the activity of recombinant GST-p65. Rabbit anti-p65 antibodies inhibited the activity of recombinant GST-p65 and also inhibited the growth of
M. hyopneumoniae
in vitro. Examination of the kinetic parameters of recombinant GST-p65 for the hydrolysis of pNPC and pNPP indicated a preference for the shorter fatty acid chain of pNPC. The physiological and/or pathogenic role of mycoplasma lipolytic enzymes has not been determined, but they are likely to play an important role in mycoplasmas' nutritional requirements for long-chain fatty acids and may reduce the function of lung surfactants in mycoplasma-induced respiratory diseases. This is the first report of the lipolytic activity of a lipid-modified surface immunogen of a mycoplasma.
Worldwide Genetic Relationships among
Francisella tularensis
Isolates Determined by Multiple-Locus Variable-Number Tandem Repeat Analysis
Authors: Johansson Anders , Farlow Jason , Larsson Pär , Dukerich Meghan , Chambers Elias , Byström Mona , Fox James , Chu May , Forsman Mats , Sjöstedt Anders , Keim Paul 
Published: August 2004

ABSTRACT

The intracellular bacterium
Francisella tularensis
is the causative agent of tularemia and poses a serious threat as an agent of bioterrorism. We have developed a highly effective molecular subtyping system from 25 variable-number tandem repeat (VNTR) loci. In our study, multiple-locus VNTR analysis (MLVA) was used to analyze genetic relationships and potential population structure within a global collection of 192
F. tularensis
isolates, including representatives from each of the four subspecies. The VNTR loci displayed between 2 and 31 alleles with Nei's diversity values between 0.05 and 0.95. Neighbor-joining cluster analysis of VNTR data revealed 120 genotypes among the 192
F. tularensis
isolates, including accurate subspecies identification.
F. tularensis
subsp.
tularensis
(type A) isolates showed great diversity at VNTR loci, while
F. tularensis
subsp.
holarctica
(type B) isolates showed much lower levels despite a much broader geographical prevalence. The resolution of two distinct clades within
F. tularensis
subsp.
tularensis
(designated A.I and A.II) revealed a previously unrecognized genetic division within this highly virulent subspecies.
F. tularensis
subsp.
holarctica
appears to have recently spread globally across continents from a single origin, while
F. tularensis
subsp.
tularensis
has a long and complex evolutionary history almost exclusively in North America. The sole non-North American type A isolates (Slovakian) were closely related to the SCHU S4 strain. Significant linkage disequilibrium was detected among VNTR loci of
F. tularensis
consistent with a clonal population structure. Overall, this work greatly augments the study of tularemia ecology and epidemiology, while providing a framework for future forensic analysis of
F. tularensis
isolates.
Hypercyst Mutants in
Rhodospirillum centenum
Identify Regulatory Loci Involved in Cyst Cell Differentiation
Authors: Berleman James E. , Hasselbring Benjamin M. , Bauer Carl E. 
Published: August 2004

ABSTRACT

Rhodospirillum centenum
is a purple photosynthetic bacterium that forms resting cyst cells when starved for nutrients. In this study, we demonstrate that chalcone synthase gene (
chsA
) expression is developmentally regulated, with expression of
chsA
increasing up to 86-fold upon induction of the cyst developmental cycle. Screening for mini-Tn
5
-induced mutants that exhibit elevated
chsA
::
lacZ
expression has led to the isolation of a set of
R. centenum
mutants that display increased
chsA
gene expression concomitant with constitutive induction of the cyst developmental cycle. These “hypercyst” mutants have lost the ability to regulate cyst cell formation in response to nutrient availability. Sequence analysis indicates that the mini-Tn
5
-disrupted genes code for a variety of factors, including metabolic enzymes and a large set of potential regulatory factors, including four gene products with homology to histidine sensor kinases and three with homology to response regulators. Several of the disrupted genes also have sequence similarity to
che
-like signal transduction components.
Complete Genome Sequence ofRickettsia typhiand Comparison with Sequences of Other Rickettsiae
Authors: McLeod Michael P. , Qin Xiang , Karpathy Sandor E. , Gioia Jason , Highlander Sarah K. , Fox George E. , McNeill Thomas Z. , Jiang Huaiyang , Muzny Donna , Jacob Leni S. , Hawes Alicia C. , Sodergren Erica , Gill Rachel , Hume Jennifer , Morgan Maggie , Fan Guangwei , Amin Anita G. , Gibbs Richard A. , Hong Chao , Yu Xue-jie , Walker David H. , Weinstock George M. 
Published: August 2004

ABSTRACTRickettsia typhi, the causative agent of murine typhus, is an obligate intracellular bacterium with a life cycle involving both vertebrate and invertebrate hosts. Here we present the complete genome sequence ofR. typhi(1,111,496 bp) and compare it to the two published rickettsial genome sequences:R. prowazekiiandR. conorii. We identified 877 genes inR. typhiencoding 3 rRNAs, 33 tRNAs, 3 noncoding RNAs, and 838 proteins, 3 of which are frameshifts. In addition, we discovered more than 40 pseudogenes, including the entire cytochromecoxidase system. The three rickettsial genomes share 775 genes: 23 are found only inR. prowazekiiandR. typhi, 15 are found only inR. conoriiandR. typhi, and 24 are unique toR. typhi. Although most of the genes are colinear, there is a 35-kb inversion in gene order, which is close to the replication terminus, inR. typhi, compared toR. prowazekiiandR. conorii. In addition, we found a 124-kbR. typhi-specific inversion, starting 19 kb from the origin of replication, compared toR. prowazekiiandR. conorii. Inversions in this region are also seen in the unpublished genome sequences ofR. sibiricaandR. rickettsii, indicating that this region is a hot spot for rearrangements. Genome comparisons also revealed a 12-kb insertion in theR. prowazekiigenome, relative toR. typhiandR. conorii, which appears to have occurred after the typhus (R. prowazekiiandR. typhi) and spotted fever (R. conorii) groups diverged. The three-way comparison allowed further in silico analysis of the SpoT split genes, leading us to propose that the stringent response system is still functional in these rickettsiae.
The ClpP Peptidase Is the Major Determinant of Bulk Protein Turnover in
Bacillus subtilis
Authors: Kock Holger , Gerth Ulf , Hecker Michael 
Published: August 2004

ABSTRACT

Measurements of overall protein degradation rates in wild-type and
clpP
mutant
Bacillus subtilis
cells revealed that stress- or starvation-induced bulk protein turnover depends virtually exclusively on the ClpP peptidase. ClpP is also essential for intracellular protein quality control, and in its absence newly synthesized proteins were highly prone to aggregation even at 37°C. Proteomic comparisons between the wild type and a Δ
clpP
mutant showed that the absence of ClpP leads to severe perturbations of “normal” physiology, complicating the detection of ClpP substrates. A pulse-chase two-dimensional gel approach was therefore used to compare wild-type and
clpP
mutant cultures that had been radiolabeled in mid-exponential phase, by quantifying changes in relative spot intensities with time. The results showed that overall proteolysis is biased toward proteins with vegetative functions which are no longer required (or are required at lower levels) in the nongrowing state. The identified substrate candidates for ClpP-dependent degradation include metabolic enzymes and aminoacyl-tRNA synthetases. Some substrate candidates catalyze the first committed step of certain biosynthetic pathways. Our data suggest that ClpP-dependent proteolysis spans a broad physiological spectrum, with regulatory processing of key metabolic components and regulatory proteins on the one side and general bulk protein breakdown at the transition from growing to nongrowing phases on the other.
The
htx
and
ptx
Operons of
Pseudomonas stutzeri
WM88 Are New Members of the Pho Regulon
Authors: White Andrea K. , Metcalf William W. 
Published: August 2004

ABSTRACT

The
htx
and
ptx
operons of
Pseudomonas stutzeri
WM88 allow for the use of the inorganic reduced phosphorus (P) compounds hypophosphite (P valence, +1) and phosphite (P valence, +3) as sole P sources. To support the proposed in vivo role for the
htx
and
ptx
operons, namely the use of phosphite and hypophosphite as alternative P sources, we used reporter gene fusions to examine their expression levels with respect to various P conditions. Expression of the
htx
and
ptx
operons was induced up to 17- and 22-fold, respectively, in cultures grown under phosphate starvation conditions relative to expression in medium with excess phosphate (P
i
). However, the presence of the reduced P substrate hypophosphite, phosphite, or methylphosphonate, in addition to excess P
i
, did not result in an increase in the expression of either operon. To provide further support for a role of the
htx
and
ptx
operons in P
i
acquisition, we identified
P. stutzeri phoBR
homologs and constructed deletion mutants. Induction of the
htx
and
ptx
reporter gene fusions in response to growth on limiting P
i
was abolished in Δ
phoB
, Δ
phoR
, and Δ
phoBR
mutants, demonstrating that
htx
and
ptx
expression is
phoBR
dependent. The putative LysR-type regulator encoded by
ptxE
has no apparent role in the expression of the
htx
and
ptx
operons, as no effect was observed on the level of induction of either operon in a Δ
ptxE
mutant.
The
Escherichia coli argU10
(Ts) Phenotype Is Caused by a Reduction in the Cellular Level of the
argU
tRNA for the Rare Codons AGA and AGG
Authors: Sakamoto Kensaku , Ishimaru Satoshi , Kobayashi Takatsugu , Walker James R. , Yokoyama Shigeyuki 
Published: August 2004

ABSTRACT

The
Escherichia coli argU10
(Ts) mutation in the
argU
gene, encoding the minor tRNA
Arg
species for the rare codons AGA and AGG, causes pleiotropic defects, including growth inhibition at high temperatures, as well as the Pin phenotype at 30°C. In the present study, we first showed that the codon selectivity and the arginine-accepting activity of the
argU
tRNA are both essential for complementing the temperature-sensitive growth, indicating that this defect is caused at the level of translation. An in vitro analysis of the effects of the
argU10
(Ts) mutation on tRNA functions revealed that the affinity with elongation factor Tu-GTP of the
argU10
(Ts) mutant tRNA is impaired at 30 and 43°C, and this defect is more serious at the higher temperature. The arginine acceptance is also impaired significantly but to similar extents at the two temperatures. An in vivo analysis of aminoacylation levels showed that 30% of the
argU10
(Ts) tRNA molecules in the mutant cells are actually deacylated at 30°C, while most of the
argU
tRNA molecules in the wild-type cells are aminoacylated. Furthermore, the cellular level of this mutant tRNA is one-tenth that of the wild-type
argU
tRNA. At 43°C, the cellular level of the
argU10
(Ts) tRNA is further reduced to a trace amount, while neither the cellular abundance nor the aminoacylation level of the wild-type
argU
tRNA changes. We concluded that the phenotypic properties of the
argU10
(Ts) mutant result from these reduced intracellular levels of the tRNA, which are probably caused by the defective interactions with elongation factor Tu and arginyl-tRNA synthetase.
Regulation of Ribosomal Protein Synthesis in
Vibrio cholerae
Authors: Allen Todd D. , Watkins Tonya , Lindahl Lasse , Zengel Janice M. 
Published: August 2004

ABSTRACT

We have investigated the regulation of the S10 and
spc
ribosomal protein (r-protein) operons in
Vibrio cholerae
. Both operons are under autogenous control; they are mediated by r-proteins L4 and S8, respectively. Our results suggest that
Escherichia coli
-like strategies for regulating r-protein synthesis extend beyond the enteric members of the gamma subdivision of proteobacteria.
Characterization of the Upper Pathway Genes for Fluorene Metabolism in
Terrabacter
sp. Strain DBF63
Authors: Habe Hiroshi , Chung Jin-Sung , Kato Hiroyuki , Ayabe Yuko , Kasuga Kano , Yoshida Takako , Nojiri Hideaki , Yamane Hisakazu , Omori Toshio 
Published: August 2004

ABSTRACT

Genes involved in the degradation of fluorene to phthalate were characterized in the fluorene degrader
Terrabacter
sp. strain DBF63. The initial attack on both fluorene and 9-fluorenone was catalyzed by DbfA to yield 9-fluorenol and 1,1a-dihydroxy-1-hydro-9-fluorenone, respectively. The FlnB protein exhibited activities against both 9-fluorenol and 1,1a-dihydroxy-1-hydro-9-fluorenone to produce 9-fluorenone and 2′-carboxy-2,3-dihydroxybiphenyl, respectively. FlnD is a heteromeric protein encoded by
flnD1
and ORF16, being a member of the class III two-subunit extradiol dioxygenase. FlnE was identified as a serine hydrolase for the
meta
-cleavage products that yield phthalate.