bluuebunny/crossref_metadata_2025_split huggingface dataset:
Global Gene Expression Analysis of the Heat Shock Response in the Phytopathogen
Xylella fastidiosa
Authors: Koide Tie , Vêncio Ricardo Z. N. , Gomes Suely L. 
Published: August 2006

ABSTRACT

Xylella fastidiosa
is a phytopathogenic bacterium that is responsible for diseases in many economically important crops. Although different strains have been studied, little is known about
X. fastidiosa
stress responses. One of the better characterized stress responses in bacteria is the heat shock response, which induces the expression of specific genes to prevent protein misfolding and aggregation and to promote degradation of the irreversibly denatured polypeptides. To investigate
X. fastidiosa
genes involved in the heat shock response, we performed a whole-genome microarray analysis in a time course experiment. Globally, 261 genes were induced (9.7%) and 222 genes were repressed (8.3%). The expression profiles of the differentially expressed genes were grouped, and their expression patterns were validated by quantitative reverse transcription-PCR experiments. We determined the transcription start sites of six heat shock-inducible genes and analyzed their promoter regions, which allowed us to propose a putative consensus for σ
32
promoters in
Xylella
and to suggest additional genes as putative members of this regulon. Besides the induction of classical heat shock protein genes, we observed the up-regulation of virulence-associated genes such as
vapD
and of genes for hemagglutinins, hemolysin, and xylan-degrading enzymes, which may indicate the importance of heat stress to bacterial pathogenesis. In addition, we observed the repression of genes related to fimbriae, aerobic respiration, and protein biosynthesis and the induction of genes related to the extracytoplasmic stress response and some phage-related genes, revealing the complex network of genes that work together in response to heat shock.
Growth Phase-Dependent Expression of Drug Exporters in
Escherichia coli
and Its Contribution to Drug Tolerance
Authors: Kobayashi Asuka , Hirakawa Hidetada , Hirata Takahiro , Nishino Kunihiko , Yamaguchi Akihito 
Published: August 2006

ABSTRACT

Drug exporters contribute to the intrinsic drug resistance in many organisms. Although there are at least 20 exporter genes in
Escherichia coli
, most of them apparently do not confer drug resistance in complex laboratory media except for the AcrAB, EmrE, and MdfA efflux systems. In this study, we comprehensively investigated the growth phase-dependent expression of drug exporter genes. The expression of
acrAB
,
emrAB
,
emrD
,
emrE
,
emrKY
,
mdfA
, and
ydgFE
is stable at moderate levels during any growth phase, whereas
mdtEF
promoter activity greatly increased with cell growth and reached the maximum level at the late stationary phase. The growth phase-dependent increase in
mdtEF
expression was also observed on quantitative reverse transcription-PCR analysis. As expected from the transporter expression, the stationary-phase cells actually showed MdtEF-dependent tolerance to drugs and toxic dyes. Growth phase-dependent elevation of
mdtEF
expression was found to be mediated by the stationary-phase σ factor
rpoS
and the RpoS-dependent signaling pathway, Hfq, GadY, and GadX. The induction level was decreased by
tnaAB
deletion, suggesting that indole sensing stimulates this process.
Cyclic AMP-Dependent Osmoregulation of
crp
Gene Expression in
Escherichia coli
Authors: Balsalobre Carlos , Johansson Jörgen , Uhlin Bernt Eric 
Published: August 2006

ABSTRACT

We have found that the cyclic AMP (cAMP) receptor protein (CRP)-cAMP regulatory complex in
Escherichia coli
is subject to osmoregulation at the level of
crp
gene expression. This osmoregulation was lost in a
cya
mutant strain but could be restored by external addition of cAMP, suggesting that the intracellular level of cAMP is a key factor in the osmoregulation of CRP. The ability of the cell to maintain optimal CRP activity was essential for the growth and survival of the bacteria under low-osmolarity conditions as shown by studies with different
crp
mutant alleles. A suppressor mutant with a novel amino acid substitution (L124R) in CRP showed restored growth at low osmolarity. CRP(L124R) was not activated by cAMP and was shown to be dominant negative over the wild type. Our findings suggest that the fine-tuning of the CRP activity may be critical for bacterial viability and adaptability to changing osmotic conditions.
Analysis of the Terminus Region of the
Caulobacter crescentus
Chromosome and Identification of the
dif
Site
Authors: Jensen Rasmus B. 
Published: August 2006

ABSTRACT

The terminus region of the
Caulobacter crescentus
chromosome and the
dif
chromosome dimer resolution site were characterized. The
Caulobacter
genome contains skewed sequences that abruptly switch strands at
dif
and may have roles in chromosome maintenance and segregation. Absence of
dif
or the XerCD recombinase results in a chromosome segregation defect. The
Caulobacter
terminus region is unusual, since it contains many essential or highly expressed genes.
The Mycobacterium-Specific Gene Rv2719c Is DNA Damage Inducible Independently of RecA
Authors: Brooks Patricia C. , Dawson Lisa F. , Rand Lucinda , Davis Elaine O. 
Published: August 2006

ABSTRACTThe mycobacterium-specific gene Rv2719c was found to be expressed primarily from a promoter that was clearly DNA damage inducible independently of RecA. Upstream of the transcriptional start site for this promoter, sequence motifs resembling those observed previously at the RecA-independent, DNA damage-induciblerecApromoter were identified, and the −10 motif was demonstrated by mutational analysis in transcriptional fusion constructs to be important for expression of Rv2719c.
Two Transsulfurylation Pathways in
Klebsiella pneumoniae
Authors: Seiflein Thomas A. , Lawrence Jeffrey G. 
Published: August 2006

ABSTRACT

In most bacteria, inorganic sulfur is assimilated into cysteine, which provides sulfur for methionine biosynthesis via transsulfurylation. Here, cysteine is transferred to the terminal carbon of homoserine via its sulfhydryl group to form cystathionine, which is cleaved to yield homocysteine. In the enteric bacteria
Escherichia coli
and
Salmonella enterica
, these reactions are catalyzed by irreversible cystathionine-γ-synthase and cystathionine-β-lyase enzymes. Alternatively, yeast and some bacteria assimilate sulfur into homocysteine, which serves as a sulfhydryl group donor in the synthesis of cysteine by reverse transsulfurylation with a cystathionine-β-synthase and cystathionine-γ-lyase. Herein we report that the related enteric bacterium
Klebsiella pneumoniae
encodes genes for both transsulfurylation pathways; genetic and biochemical analyses show that they are coordinately regulated to prevent futile cycling.
Klebsiella
uses reverse transsulfurylation to recycle methionine to cysteine during periods of sulfate starvation. This
m
ethionine-
t
o-
c
ysteine (
mtc
) transsulfurylation pathway is activated by cysteine starvation via the CysB protein, by adenosyl-phosphosulfate starvation via the Cbl protein, and by methionine excess via the MetJ protein. While
mtc
mutants cannot use methionine as a sulfur source on solid medium, they will utilize methionine in liquid medium via a sulfide intermediate, suggesting that an additional nontranssulfurylation methionine-to-cysteine recycling pathway(s) operates under these conditions.
The GrlR-GrlA Regulatory System Coordinately Controls the Expression of Flagellar and LEE-Encoded Type III Protein Secretion Systems in EnterohemorrhagicEscherichia coli
Authors: Iyoda Sunao , Koizumi Nobuo , Satou Hitomi , Lu Yan , Saitoh Takehito , Ohnishi Makoto , Watanabe Haruo 
Published: August 2006

ABSTRACTThe gene function of the locus of enterocyte effacement (LEE) is essential for full virulence of enterohemorrhagicEscherichia coli(EHEC). Strict control of LEE gene expression is mediated by the coordinated activities of several regulatory elements. We previously reported that the ClpX/ClpP protease positively controls LEE expression by down-regulating intracellular levels of GrlR, a negative regulator of LEE gene expression. We further revealed that the negative effect of GrlR on LEE expression was mediated through GrlA, a positive regulator of LEE expression. In this study, we found that the FliC protein, a major component of flagellar filament, was overproduced inclpXPmutant EHEC, as previously reported forSalmonella. We further found that FliC expression was reduced in aclpXP grlRdouble mutant. To determine the mediators of this phenotype, FliC protein levels in wild-type,grlR,grlA, andgrlR grlAstrains were compared. Steady-state levels of FliC protein were reduced only in thegrlRmutant, suggesting that positive regulation of FliC expression by GrlR is mediated by GrlA. Correspondingly, cell motility was also reduced in thegrlRmutant, but not in thegrlAorgrlR grlAmutant. Because overexpression ofgrlAfrom a multicopy plasmid strongly represses the FliC level, as well as cell motility, we conclude that GrlA acts as a negative regulator of flagellar-gene expression. The fact that an EHEC strain constitutively expressing FlhD/FlhC cannot adhere to HeLa cells leads us to hypothesize that GrlA-dependent repression of the flagellar regulon is important for efficient cell adhesion of EHEC to host cells.
Distinguishing Characteristics of Hyperrecombinogenic RecA Protein from
Pseudomonas aeruginosa
Acting in
Escherichia coli
Authors: Baitin Dmitry M. , Bakhlanova Irina V. , Kil Yury V. , Cox Michael M. , Lanzov Vladislav A. 
Published: August 2006

ABSTRACT

In
Escherichia coli
, a relatively low frequency of recombination exchanges (FRE) is predetermined by the activity of RecA protein, as modulated by a complex regulatory program involving both autoregulation and other factors. The RecA protein of
Pseudomonas aeruginosa
(RecA
Pa
) exhibits a more robust recombinase activity than its
E. coli
counterpart (RecA
Ec
). Low-level expression of RecA
Pa
in
E. coli
cells results in hyperrecombination (an increase of FRE) even in the presence of RecA
Ec
. This genetic effect is supported by the biochemical finding that the RecA
Pa
protein is more efficient in filament formation than RecA K72R, a mutant protein with RecA
Ec
-like DNA-binding ability. Expression of RecA
Pa
also partially suppresses the effects of
recF
,
recO
, and
recR
mutations. In concordance with the latter, RecA
Pa
filaments initiate recombination equally from both the 5′ and 3′ ends. Besides, these filaments exhibit more resistance to disassembly from the 5′ ends that makes the ends potentially appropriate for initiation of strand exchange. These comparative genetic and biochemical characteristics reveal that multiple levels are used by bacteria for a programmed regulation of their recombination activities.
Peptidyl-Prolyl
cis/trans
Isomerase-Independent Functional NifH Mutant of
Azotobacter vinelandii
Authors: Gavini Nara , Tungtur Sudheer , Pulakat Lakshmi 
Published: August 2006

ABSTRACT

Peptidyl-prolyl
cis/trans
isomerases (PPIases) play a pivotal role in catalyzing the correct folding of many prokaryotic and eukaryotic proteins that are implicated in a variety of biological functions, ranging from cell cycle regulation to bacterial infection. The
nif
accessory protein NifM, which is essential for the biogenesis of a functional NifH component of nitrogenase, is a PPIase. To understand the nature of the molecular signature that defines the NifM dependence of NifH, we screened a library of
nifH
mutants in the nitrogen-fixing bacterium
Azotobacter vinelandii
for mutants that acquired NifM independence. Here, we report that NifH can acquire NifM independence when the conserved Pro258 located in the C-terminal region of NifH, which wraps around the other subunit in the NifH dimer, is replaced by serine.
A Novel Branching Enzyme of the GH-57 Family in the Hyperthermophilic Archaeon
Thermococcus kodakaraensis
KOD1
Authors: Murakami Taira , Kanai Tamotsu , Takata Hiroki , Kuriki Takashi , Imanaka Tadayuki 
Published: August 2006

ABSTRACT

Branching enzyme (BE) catalyzes formation of the branch points in glycogen and amylopectin by cleavage of the α-1,4 linkage and its subsequent transfer to the α-1,6 position. We have identified a novel BE encoded by an uncharacterized open reading frame (TK1436) of the hyperthermophilic archaeon
Thermococcus kodakaraensis
KOD1. TK1436 encodes a conserved protein showing similarity to members of glycoside hydrolase family 57 (GH-57 family). At the C terminus of the TK1436 protein, two copies of a helix-hairpin-helix (HhH) motif were found. TK1436 orthologs are distributed in archaea of the order
Thermococcales
, cyanobacteria, some actinobacteria, and a few other bacterial species. When recombinant TK1436 protein was incubated with amylose used as the substrate, a product peak was detected by high-performance anion-exchange chromatography, eluting more slowly than the substrate. Isoamylase treatment of the reaction mixture significantly increased the level of short-chain α-glucans, indicating that the reaction product contained many α-1,6 branching points. The TK1436 protein showed an optimal pH of 7.0, an optimal temperature of 70°C, and thermostability up to 90°C, as determined by the iodine-staining assay. These properties were the same when a protein devoid of HhH motifs (the TK1436ΔH protein) was used. The average molecular weight of branched glucan after reaction with the TK1436ΔH protein was over 100 times larger than that of the starting substrate. These results clearly indicate that TK1436 encodes a structurally novel BE belonging to the GH-57 family. Identification of an overlooked BE species provides new insights into glycogen biosynthesis in microorganisms.
Paired-End Sequence Mapping Detects Extensive Genomic Rearrangement and Translocation during Divergence of
Francisella tularensis
subsp.
tularensis
and
Francisella tularensis
subsp.
holarctica
Populations
Authors: Dempsey Michael P. , Nietfeldt Joseph , Ravel Jacques , Hinrichs Steven , Crawford Robert , Benson Andrew K. 
Published: August 2006

ABSTRACT

Comparative genome hybridization of the
Francisella tularensis
subsp.
tularensis
and
F. tularensis
subsp.
holarctica
populations have shown that genome content is highly conserved, with relatively few genes in the
F. tularensis
subsp.
tularensis
genome being absent in other
F. tularensis
subspecies. To determine if organization of the genome differs between global populations of
F. tularensis
subsp.
tularensis
and
F. tularensis
subsp.
holarctica
, we have used paired-end sequence mapping (PESM) to identify regions of the genome where synteny is broken. The PESM approach compares the physical distances between paired-end sequencing reads of a library of a wild-type reference
F. tularensis
subsp.
holarctica
strain to the predicted lengths between the reads based on map coordinates of two different
F. tularensis
genome sequences. A total of 17 different continuous regions were identified in the
F. tularensis
subsp.
holarctica
genome (CR
holar
c
tica
) which are noncontiguous in the
F. tularensis
subsp.
tularensis
genome. Six of the 17 different CR
holarctica
are positioned as adjacent pairs in the
F. tularensis
subsp.
tularensis
genome sequence but are translocated in
F. tularensis
subsp.
holarctica
, implying that their arrangements are ancestral in
F. tularensis
subsp.
tularensis
and derived in
F. tularensis
subsp.
holarctica
. PCR analysis of the CR
holarctica
in 88 additional
F. tularensis
subsp.
tularensis
and
F. tularensis
subsp.
holarctica
isolates showed that the arrangements of the CR
holarctica
are highly conserved, particularly in
F. tularensis
subsp.
holarctica
, consistent with the hypothesis that global populations of
F. tularensis
subsp.
holarctica
have recently experienced a periodic selection event or they have emerged from a recent clonal expansion. Two unique
F. tularensis
subsp.
tularensis
-like strains were also observed which likely are derived from evolutionary intermediates and may represent a new taxonomic unit.
The Global Regulator Spx Functions in the Control of Organosulfur Metabolism inBacillus subtilis
Authors: Choi Soon-Yong , Reyes Dindo , Leelakriangsak Montira , Zuber Peter 
Published: August 2006

ABSTRACTSpx is a global transcriptional regulator of the oxidative stress response inBacillus subtilis. Its target is RNA polymerase, where it contacts the α subunit C-terminal domain. Recently, evidence was presented that Spx participates in sulfate-dependent control of organosulfur utilization operons, including theytmI,yxeI,ssu, andyrrToperons. TheyrrToperon includes the genes that function in cysteine synthesis fromS-adenosylmethionine through intermediatesS-adenosylhomocysteine, ribosylhomocysteine, homocysteine, and cystathionine. These operons are also negatively controlled by CymR, the repressor of cysteine biosynthesis operons. All of the operons are repressed in media containing cysteine or sulfate but are derepressed in medium containing the alternative sulfur source, methionine. Spx was found to negatively control the expression of these operons in sulfate medium, in part, by stimulating the expression of thecymRgene. In addition, microarray analysis, monitoring ofyrrT-lacZfusion expression, and in vitro transcription studies indicate that Spx directly activatesyrrToperon expression during growth in medium containing methionine as sole sulfur source. These experiments have uncovered additional roles for Spx in the control of gene expression during unperturbed, steady-state growth.
The Nitric Oxide-Responsive Regulator NsrR Controls ResDE-Dependent Gene Expression
Authors: Nakano Michiko M. , Geng Hao , Nakano Shunji , Kobayashi Kazuo 
Published: August 2006

ABSTRACTThe ResD-ResE signal transduction system is essential for aerobic and anaerobic respiration inBacillus subtilis. ResDE-dependent gene expression is induced by oxygen limitation, but full induction under anaerobic conditions requires nitrite or nitric oxide (NO). Here we report that NsrR (formerly YhdE) is responsible for the NO-dependent up-regulation of the ResDE regulon. The null mutation ofnsrRled to aerobic derepression ofhmp(flavohemoglobin gene) partly in a ResDE-independent manner. In addition to its negative role in aerobichmpexpression, NsrR plays an important role under anaerobic conditions for regulation of ResDE-controlled genes, includinghmp. ResDE-dependent gene expression was increased by thensrRmutation in the absence of NO, but the expression was decreased by the mutation when NO was present. Consequently,B. subtiliscells lacking NsrR no longer sense and respond to NO (and nitrite) to up-regulate the ResDE regulon. Exposure to NO did not significantly change the cellular concentration of NsrR, suggesting that NO likely modulates the activity of NsrR. NsrR is similar to the recently described nitrite- or NO-sensitive transcription repressors present in various bacteria. NsrR likely has an Fe-S cluster, and interaction of NO with the Fe-S center is proposed to modulate NsrR activity.
TheBordetellaBfe System: Growth and Transcriptional Response to Siderophores, Catechols, and Neuroendocrine Catecholamines
Authors: Anderson Mark T. , Armstrong Sandra K. 
Published: August 2006

ABSTRACTFerric enterobactin utilization byBordetella bronchisepticaandBordetella pertussisrequires the BfeA outer membrane receptor. Under iron-depleted growth conditions, transcription ofbfeAis activated by the BfeR regulator by a mechanism requiring the siderophore enterobactin. In this study, enterobactin-induciblebfeAtranscription was shown to be TonB independent. To determine whether other siderophores or nonsiderophore catechols could be utilized by the Bfe system, various compounds were tested for the abilities to promote the growth of iron-starvedB. bronchisepticaand inducebfeAtranscription. The BfeA receptor transported ferric salmochelin, corynebactin, and the synthetic siderophores TRENCAM and MECAM. Salmochelin and MECAM inducedbfeAtranscription in iron-starvedBordetellacells, but induction by corynebactin and TRENCAM was minimal. The neuroendocrine catecholamines epinephrine, norepinephrine, and dopamine exhibited a remarkable capacity to induce transcription ofbfeA. Norepinephrine treatment ofB. bronchisepticaresulted in BfeR-dependentbfeAtranscription, elevated BfeA receptor production, and growth stimulation. Pyrocatechol, carbidopa, and isoproterenol were similarly strong inducers ofbfeAtranscription, whereas tyramine and 3,4-dihydroxymandelic acid demonstrated low inducing activity. The results indicate that the inducer structure requires a catechol group for function and that the ability to inducebfeAtranscription does not necessarily correlate with the ability to stimulate bacterial growth. The expanded range of catechol siderophores transported by the BfeA receptor demonstrates the potential versatility of theBordetellaBfe iron retrieval system. The finding that catecholamine neurotransmitters activatebfeAtranscription and promote growth suggests thatBordetellacells can perceive and may benefit from neuroendocrine catecholamines on the respiratory epithelium.
Relationship among Several Key Cell Cycle Events in the Developmental Cyanobacterium
Anabaena
sp. Strain PCC 7120
Authors: Sakr Samer , Thyssen Melilotus , Denis Michel , Zhang Cheng-Cai 
Published: August 2006

ABSTRACT

When grown in the absence of a source of combined nitrogen, the filamentous cyanobacterium
Anabaena
sp. strain PCC 7120 develops, within 24 h, a differentiated cell type called a heterocyst that is specifically involved in the fixation of N
2
. Cell division is required for heterocyst development, suggesting that the cell cycle could control this developmental process. In this study, we investigated several key events of the cell cycle, such as cell growth, DNA synthesis, and cell division, and explored their relationships to heterocyst development. The results of analyses by flow cytometry indicated that the DNA content increased as the cell size expanded during cell growth. The DNA content of heterocysts corresponded to the subpopulation of vegetative cells that had a big cell size, presumably those at the late stages of cell growth. Consistent with these results, most proheterocysts exhibited two nucleoids, which were resolved into a single nucleoid in most mature heterocysts. The ring structure of FtsZ, a protein required for the initiation of bacterial cell division, was present predominantly in big cells and rarely in small cells. When cell division was inhibited and consequently cells became elongated, little change in DNA content was found by measurement using flow cytometry, suggesting that inhibition of cell division may block further synthesis of DNA. The overexpression of
minC
, which encodes an inhibitor of FtsZ polymerization, led to the inhibition of cell division, but cells expanded in spherical form to become giant cells; structures with several cells attached together in the form of a cloverleaf could be seen frequently. These results may indicate that the relative amounts of FtsZ and MinC affect not only cell division but also the placement of the cell division planes and the cell morphology. MinC overexpression blocked heterocyst differentiation, consistent with the requirement of cell division in the control of heterocyst development.