bluuebunny/crossref_metadata_2025_split huggingface dataset:
Transcriptomic Analysis of
Rhizobium leguminosarum
Biovar viciae in Symbiosis with Host Plants
Pisum sativum
and
Vicia cracca
Authors: Karunakaran R. , Ramachandran V. K. , Seaman J. C. , East A. K. , Mouhsine B. , Mauchline T. H. , Prell J. , Skeffington A. , Poole P. S. 
Published: April 2009

ABSTRACT

Rhizobium leguminosarum
bv. viciae forms nitrogen-fixing nodules on several legumes, including pea (
Pisum sativum
) and vetch (
Vicia cracca
), and has been widely used as a model to study nodule biochemistry. To understand the complex biochemical and developmental changes undergone by
R. leguminosarum
bv. viciae during bacteroid development, microarray experiments were first performed with cultured bacteria grown on a variety of carbon substrates (glucose, pyruvate, succinate, inositol, acetate, and acetoacetate) and then compared to bacteroids. Bacteroid metabolism is essentially that of dicarboxylate-grown cells (i.e., induction of dicarboxylate transport, gluconeogenesis and alanine synthesis, and repression of sugar utilization). The decarboxylating arm of the tricarboxylic acid cycle is highly induced, as is γ-aminobutyrate metabolism, particularly in bacteroids from early (7-day) nodules. To investigate bacteroid development, gene expression in bacteroids was analyzed at 7, 15, and 21 days postinoculation of peas. This revealed that bacterial rRNA isolated from pea, but not vetch, is extensively processed in mature bacteroids. In early development (7 days), there were large changes in the expression of regulators, exported and cell surface molecules, multidrug exporters, and heat and cold shock proteins.
fix
genes were induced early but continued to increase in mature bacteroids, while
nif
genes were induced strongly in older bacteroids. Mutation of 37 genes that were strongly upregulated in mature bacteroids revealed that none were essential for nitrogen fixation. However, screening of 3,072 mini-Tn
5
mutants on peas revealed previously uncharacterized genes essential for nitrogen fixation. These encoded a potential magnesium transporter, an AAA domain protein, and proteins involved in cytochrome synthesis.
ATP-Binding Site Lesions in FtsE Impair Cell Division
Authors: Arends S. J. Ryan , Kustusch Ryan J. , Weiss David S. 
Published: April 2009

ABSTRACTFtsE and FtsX ofEscherichia coliconstitute an apparent ABC transporter that localizes to the septal ring. In the absence of FtsEX, cells divide poorly and several membrane proteins essential for cell division are largely absent from the septal ring, including FtsK, FtsQ, FtsI, and FtsN. These observations, together with the fact thatftsEandftsXare cotranscribed withftsY, which helps to target some proteins for insertion into the cytoplasmic membrane, suggested that FtsEX might contribute to insertion of division proteins into the membrane. Here we show that this hypothesis is probably wrong, because cells depleted of FtsEX had normal amounts of FtsK, FtsQ, FtsI, and FtsN in the membrane fraction. We also show that FtsX localizes to septal rings in cells that lack FtsE, arguing that FtsX targets the FtsEX complex to the ring. Nevertheless, both proteins had to be present to recruit further Fts proteins to the ring. Mutant FtsE proteins with lesions in the ATP-binding site supported septal ring assembly (when produced together with FtsX), but these rings constricted poorly. This finding implies that FtsEX uses ATP to facilitate constriction rather than assembly of the septal ring. Finally, topology analysis revealed that FtsX has only four transmembrane segments, none of which contains a charged amino acid. This structure is not what one would expect of a substrate-specific transmembrane channel, leading us to suggest that FtsEX is not really a transporter even though it probably has to hydrolyze ATP to support cell division.
Microarray Identification of
Clostridium difficile
Core Components and Divergent Regions Associated with Host Origin
Authors: Janvilisri Tavan , Scaria Joy , Thompson Angela D. , Nicholson Ainsley , Limbago Brandi M. , Arroyo Luis G. , Songer J. Glenn , Gröhn Yrjö T. , Chang Yung-Fu 
Published: April 2009

ABSTRACT

Clostridium difficile
is a gram-positive, spore-forming enteric anaerobe which can infect humans and a wide variety of animal species. Recently, the incidence and severity of human
C. difficile
infection has markedly increased. In this study, we evaluated the genomic content of 73
C. difficile
strains isolated from humans, horses, cattle, and pigs by comparative genomic hybridization with microarrays containing coding sequences from
C. difficile
strains 630 and QCD-32g58. The sequenced genome of
C. difficile
strain 630 was used as a reference to define a candidate core genome of
C. difficile
and to explore correlations between host origins and genetic diversity. Approximately 16% of the genes in strain 630 were highly conserved among all strains, representing the core complement of functional genes defining
C. difficile
. Absent or divergent genes in the tested strains were distributed across the entire
C. difficile
630 genome and across all the predicted functional categories. Interestingly, certain genes were conserved among strains from a specific host species, but divergent in isolates with other host origins. This information provides insight into the genomic changes which might contribute to host adaptation. Due to a high degree of divergence among
C. difficile
strains, a core gene list from this study offers the first step toward the construction of diagnostic arrays for
C. difficile
.
In Vivo Analysis of Cobinamide Salvaging inRhodobacter sphaeroidesStrain 2.4.1
Authors: Gray Michael J. , Escalante-Semerena Jorge C. 
Published: April 2009

ABSTRACTThe genome ofRhodobacter sphaeroidesencodes the components of two distinct pathways for salvaging cobinamide (Cbi), a precursor of adenosylcobalamin (AdoCbl, coenzyme B12). One pathway, conserved among bacteria, depends on a bifunctional kinase/guanylyltransferase (CobP) enzyme to convert adenosylcobinamide (AdoCbi) to AdoCbi-phosphate (AdoCbi-P), an intermediate in de novo AdoCbl biosynthesis. The other pathway, of archaeal origin, depends on an AdoCbi amidohydrolase (CbiZ) enzyme to generate adenosylcobyric acid (AdoCby), which is converted to AdoCbi-P by the AdoCbi-P synthetase (CobD) enzyme. Here we report thatR. sphaeroidesstrain 2.4.1 synthesizes AdoCbl de novo and that it salvages Cbi using both of the predicted Cbi salvaging pathways. AdoCbl produced byR. sphaeroideswas identified and quantified by high-performance liquid chromatography and bioassay. The deletion ofcobB(encoding an essential enzyme of the de novo corrin ring biosynthetic pathway) resulted in a strain ofR. sphaeroidesthat would not grow on acetate in the absence of exogenous corrinoids. The results from a nutritional analysis showed that the presence of either CbiZ or CobP was necessary and sufficient for Cbi salvaging, that CbiZ-dependent Cbi salvaging depended on the presence of CobD, and that CobP-dependent Cbi salvaging occurred in acbiZ+strain. Possible reasons whyR. sphaeroidesmaintains two distinct pathways for Cbi salvaging are discussed.
Occurrence, Plasticity, and Evolution of the
vpma
Gene Family, a Genetic System Devoted to High-Frequency Surface Variation in
Mycoplasma agalactiae
Authors: Nouvel Laurent-Xavier , Marenda Marc , Sirand-Pugnet Pascal , Sagné Eveline , Glew Michelle , Mangenot Sophie , Barbe Valérie , Barré Aurélien , Claverol Stéphane , Citti Christine 
Published: April 2009

ABSTRACT

Mycoplasma agalactiae
, an important pathogen of small ruminants, exhibits a very versatile surface architecture by switching multiple, related lipoproteins (Vpmas) on and off. In the type strain, PG2, Vpma phase variation is generated by a cluster of six
vpma
genes that undergo frequent DNA rearrangements via site-specific recombination. To further comprehend the degree of diversity that can be generated at the
M. agalactiae
surface, the
vpma
gene repertoire of a field strain, 5632, was analyzed and shown to contain an extended repertoire of 23
vpma
genes distributed between two loci located 250 kbp apart. Loci I and II include 16 and 7
vpma
genes, respectively, with all
vpma
genes of locus II being duplicated at locus I. Several Vpmas displayed a chimeric structure suggestive of homologous recombination, and a global proteomic analysis further indicated that at least 13 of the 16 Vpmas can be expressed by the 5632 strain. Because a single promoter is present in each
vpma
locus, concomitant Vpma expression can occur in a strain with duplicated loci. Consequently, the number of possible surface combinations is much higher for strain 5632 than for the type strain. Finally, our data suggested that insertion sequences are likely to be involved in 5632
vpma
locus duplication at a remote chromosomal position. The role of such mobile genetic elements in chromosomal shuffling of genes encoding major surface components may have important evolutionary and epidemiological consequences for pathogens, such as mycoplasmas, that have a reduced genome and no cell wall.
A Role for the EAL-Like Protein STM1344 in Regulation of CsgD Expression and Motility inSalmonella entericaSerovar Typhimurium
Authors: Simm Roger , Remminghorst Uwe , Ahmad Irfan , Zakikhany Katherina , Römling Ute 
Published: April 2009

ABSTRACTThe bacterial second messenger cyclic di-GMP (c-di-GMP) regulates the transition between sessility and motility. InSalmonella entericaserovar Typhimurium, the expression of CsgD, the regulator of multicellular rdar morphotype behavior, is a major target of c-di-GMP signaling. CsgD expression is positively regulated by at least two diguanylate cyclases, GGDEF domain proteins, and negatively regulated by at least four phosphodiesterases, EAL domain proteins. Here, we show that in contrast to EAL domain proteins acting as phosphodiesterases, the EAL-like protein STM1344 regulated CsgD expression positively and motility negatively. STM1344, however, did not have a role in c-di-GMP turnover and also did not bind the nucleotide. STM1344 acted upstream of the phosphodiesterases STM1703 and STM3611, previously identified to participate in CsgD downregulation, where it repressed their expression. Consequently, although STM1344 has not retained a direct role in c-di-GMP metabolism, it still participates in the regulation of c-di-GMP turnover and has a role in the transition between sessility and motility.
Endotoxin, Capsule, and Bacterial Attachment Contribute to
Neisseria meningitidis
Resistance to the Human Antimicrobial Peptide LL-37
Authors: Jones Allison , Geörg Miriam , Maudsdotter Lisa , Jonsson Ann-Beth 
Published: April 2009

ABSTRACT

Pathogenic bacteria have evolved numerous mechanisms to evade the human immune system and have developed widespread resistance to traditional antibiotics. We studied the human pathogen
Neisseria meningitidis
and present evidence of novel mechanisms of resistance to the human antimicrobial peptide LL-37. We found that bacteria attached to host epithelial cells are resistant to 10 μM LL-37 whereas bacteria in solution or attached to plastic are killed, indicating that the cell microenvironment protects bacteria. The bacterial endotoxin lipooligosaccharide and the polysaccharide capsule contribute to LL-37 resistance, probably by preventing LL-37 from reaching the bacterial membrane, as more LL-37 reaches the bacterial membrane on both lipooligosaccharide-deficient and capsule-deficient mutants whereas both mutants are also more susceptible to LL-37 killing than the wild-type strain.
N. meningitidis
bacteria respond to sublethal doses of LL-37 and upregulate two of their capsule genes,
siaC
and
siaD
, which further results in upregulation of capsule biosynthesis.
SoxRS-Mediated Lipopolysaccharide Modification Enhances Resistance against Multiple Drugs in
Escherichia coli
Authors: Lee Joon-Hee , Lee Kang-Lok , Yeo Won-Sik , Park Su-Jin , Roe Jung-Hye 
Published: April 2009

ABSTRACT

Lipopolysaccharide (LPS) is a major constituent of the outer membrane of gram-negative bacteria that serves as a barrier against harmful molecules, including antibiotics. The
waaYZ
locus that encodes the LPS core biosynthetic function in
Escherichia coli
was found to be induced strongly by superoxide generators but not by H
2
O
2
, ethanol, or heat shock. This induction was dependent on SoxRS, a superoxide and nitric oxide sensing system, through a soxbox in the
waaY
promoter that binds SoxS. A Δ
waaYZ
mutant became more sensitive to some superoxide generators, and the activation of SoxR by these drugs became more sensitized in the mutant. Through phenotypic microarray analysis, we found that the mutant became sensitive to a wide variety of chemicals not restricted to oxidizing agents. We found that the mutant is under envelope stress and is altered in LPS composition, as monitored by the level of σ
E
activation and changes in the electrophoretic mobility of LPS, respectively.
waaY
expression was also regulated by MarA (multiple-antibiotic resistance regulator), which shares a binding site (soxbox) with SoxS, and was induced by salicylate, a nonoxidative compound. These results demonstrate a novel way of protecting gram-negative bacteria against various compounds by modifying LPS, possibly through phosphorylation. Since either oxidant or nonoxidant compounds elicit resistance toward themselves and other toxic drugs, this mechanism could serve as an efficient way for pathogenic bacteria to enhance survival during antibiotic treatment within an oxidant-rich host immune environment.
Role of the Extracytoplasmic Function Sigma Factor RpoE4 in Oxidative and Osmotic Stress Responses in
Rhizobium etli
Authors: Martínez-Salazar Jaime M. , Salazar Emmanuel , Encarnación Sergio , Ramírez-Romero Miguel A. , Rivera Javier 
Published: April 2009

ABSTRACT

The aims of this study were to functionally characterize and analyze the transcriptional regulation and transcriptome of the
Rhizobium etli rpoE4
gene. An
R. etli rpoE4
mutant was sensitive to oxidative, saline, and osmotic stresses. Using transcriptional fusions, we determined that RpoE4 controls its own transcription and that it is negatively regulated by
rseF
(
r
egulator of
s
igma
rpo
E
4
; CH03274), which is cotranscribed with
rpoE4
.
rpoE4
expression was induced not only after oxidative, saline, and osmotic shocks, but also under microaerobic and stationary-phase growth conditions. The transcriptome analyses of an
rpoE4
mutant and an
rpoE4
-overexpressing strain revealed that the RpoE4 extracytoplasmic function sigma factor regulates about 98 genes; 50 of them have the
rpoE4
promoter motifs in the upstream regulatory regions. Interestingly, 16 of 38 genes upregulated in the
rpoE4
-overexpressing strain encode unknown putative cell envelope proteins. Other genes controlled by RpoE4 include
rpoH2
, CH00462, CH02434, CH03474, and
xthA1
, which encode proteins involved in the stress response (a heat shock sigma factor, a putative Mn-catalase, an alkylation DNA repair protein, pyridoxine phosphate oxidase, and exonuclease III, respectively), as well as several genes, such as CH01253, CH03555, and PF00247, encoding putative proteins involved in cell envelope biogenesis (a putative peptidoglycan binding protein, a cell wall degradation protein, and phospholipase D, respectively). These results suggest that
rpoE4
has a relevant function in cell envelope biogenesis and that it plays a role as a general regulator in the responses to several kinds of stress.
Differential Accumulation of Form I RubisCO in
Rhodopseudomonas palustris
CGA010 under Photoheterotrophic Growth Conditions with Reduced Carbon Sources
Authors: Joshi Gauri S. , Romagnoli Simona , VerBerkmoes Nathan C. , Hettich Robert L. , Pelletier Dale , Tabita F. Robert 
Published: April 2009

ABSTRACT

Rhodopseudomonas palustris
is unique among characterized nonsulfur purple bacteria because of its capacity for anaerobic photoheterotrophic growth using aromatic acids. Like growth with other reduced electron donors, this growth typically requires the presence of bicarbonate/CO
2
or some other added electron acceptor in the growth medium. Proteomic studies indicated that there was specific accumulation of form I ribulose 1, 5-bisphosphate carboxylase/oxygenase (RubisCO) subunit proteins (CbbL and CbbS), as well as the CbbX protein, in cells grown on benzoate without added bicarbonate; such cells used the small amounts of dissolved CO
2
in the medium to support growth. These proteins were not observed in extracts from cells grown in the presence of high levels (10 mM) of added bicarbonate. To confirm the results of the proteomics studies, it was shown that the total RubisCO activity levels were significantly higher (five- to sevenfold higher) in wild-type (CGA010) cells grown on benzoate with a low level (0.5 mM) of added bicarbonate. Immunoblots indicated that the increase in RubisCO activity levels was due to a specific increase in the amount of form I RubisCO (CbbLS) and not in the amount of form II RubisCO (CbbM), which was constitutively expressed. Deletion of the main transcriptional regulator gene,
cbbR
, resulted in impaired growth on benzoate-containing low-bicarbonate media, and it was established that form I RubisCO synthesis was absolutely and specifically dependent on CbbR. To understand the regulatory role of the CbbRRS two-component system, strains with nonpolar deletions of the
cbbRRS
genes were grown on benzoate. Distinct from the results obtained with photoautotrophic growth conditions, the results of studies with various CbbRRS mutant strains indicated that this two-component system did not affect the observed enhanced synthesis of form I RubisCO under benzoate growth conditions. These studies indicate that diverse growth conditions differentially affect the ability of the CbbRRS two-component system to influence
cbb
transcription.
Efficient Strand Transfer by the RadA Recombinase from the Hyperthermophilic Archaeon
Desulfurococcus amylolyticus
Authors: Kil Yuri V. , Baitin Dmitry M. , Masui Ryoji , Bonch-Osmolovskaya Elizaveta A. , Kuramitsu Seiki , Lanzov Vladislav A. 
Published: April 2009

ABSTRACT

The
radA
gene predicted to be responsible for homologous recombination in a hyperthermophilic archaeon,
Desulfurococcus amylolyticus
, was cloned, sequenced, and overexpressed in
Escherichia coli
cells. The deduced amino acid sequence of the gene product, RadA, was more similar to the human Rad51 protein (65% homology) than to the
E. coli
RecA protein (35%). A highly purified RadA protein was shown to exclusively catalyze single-stranded DNA-dependent ATP hydrolysis, which monitored presynaptic recombinational complex formation, at temperatures above 65°C (catalytic rate constant of 1.2 to 2.5 min
−1
at 80 to 95°C). The RadA protein alone efficiently promoted the strand exchange reaction at the range of temperatures from 80 to 90°C, i.e., at temperatures approaching the melting point of DNA. It is noteworthy that both ATP hydrolysis and strand exchange are very efficient at temperatures optimal for host cell growth (90 to 92°C).
Opa Expression Correlates with Elevated Transformation Rates in
Neisseria gonorrhoeae
Authors: Hill Stuart A. 
Published: April 2009

ABSTRACT

Neisseria gonorrhoeae
is naturally competent for DNA transformation. Under most conditions encountered in vivo, gonococci express one or more opacity (Opa) proteins on their surfaces. Recently, it was shown that DNA preferentially binds to the surfaces of Opa-expressing organisms compared to those of isogenic Opa-negative strains, presumably due to the numerous cationic residues in the predicted surface-exposed loops of the Opa protein. This study examined whether Opa-DNA interactions actually influence DNA transformation of the gonococcus. The data show that Opa-expressing gonococci are more efficient recipients of DNA for transformation and are more susceptible to exogenous DNase I treatment at early stages during the DNA transformation process than non-Opa expressors. Furthermore, inhibition of the transformation process was demonstrable for Opa
+
populations when either nonspecific DNA or the polyanion heparin was used. Overall, the data suggest that Opa expression, with its presumptive positive surface charge contribution, promotes DNA transformation by causing a more prolonged sequestration of donor DNA at the cell surface, which translates into more efficient transformation over time.
Monoubiquitination Is Sufficient To Signal Internalization of the Maltose Transporter in
Saccharomyces cerevisiae
Authors: Lucero Pilar , Peñalver Élida , Vela Laura , Lagunas Rosario 
Published: April 2009

ABSTRACT

Monoubiquitination of the 12-transmembrane segment (12-TMS)
Saccharomyces cerevisiae
maltose transporter promoted the maximal internalization rate of this protein. This modification is similar to that of the 7-TMS α-factor receptor but different from that of the 12-TMS uracil and general amino acid permeases. This result shows that binding of ubiquitin-Lys63 chains is not required for maximal internalization of all 12-TMS-containing proteins.
Elongation Factor Tu and DnaK Are Transferred from the Cytoplasm to the Periplasm of
Escherichia coli
during Osmotic Downshock Presumably via the Mechanosensitive Channel MscL
Authors: Berrier Catherine , Garrigues Alexia , Richarme Gilbert , Ghazi Alexandre 
Published: April 2009

ABSTRACT

Upon osmotic downshock, a few cytoplasmic proteins, including thioredoxin, elongation factor Tu (EF-Tu), and DnaK, are released from Tris-EDTA-treated
Escherichia coli
cells by an unknown mechanism. We have shown previously that deletion of
mscL
, the gene coding for the mechanosensitive channel of the plasma membrane with the highest conductance, prevents the release of thioredoxin. We confirm and extend the implication of MscL in this process by showing that the release of EF-Tu and DnaK is severely impaired in MscL-deficient strains. Release of these proteins is not observed in the absence of a Tris-EDTA treatment which disrupts the outer membrane, indicating that, in intact cells, they are transferred to the periplasm upon shock, presumably through the MscL channel.
DNA-Binding Properties of the
Fremyella diplosiphon
RpbA Repressor
Authors: Manna Pradip , Nieder Roxanne P. , Schaefer Michael R. 
Published: April 2009

ABSTRACT

Mutant strain FdBM1 of the cyanobacterium
Fremyella diplosiphon
is characterized by elevated transcription of the
cpcB1A1
gene set due to inactivation of
rpbA
by Tn
5469
. The predicted RpbA protein contains two regions resembling the characterized helix-turn-helix (HTH) motif involved in DNA recognition by many phage and bacterial transcription regulator proteins. It was therefore hypothesized that RpbA functions as a DNA-binding repressor involved in the control of transcription from
cpcB1A1
. A histidine-tagged form of RpbA, designated RpbA-His
6
, was examined for its ability to bind to the defined promoter region for
cpcB1A1
. Gel mobility shift assays showed that RpbA-His
6
specifically binds to a DNA fragment containing the
cpcB1A1
promoter and that significant binding can be achieved with equimolar amounts of RpbA-His
6
and the
cpcB1A1
promoter probe. DNase I footprint analysis localized the RpbA-His
6
binding site to an asymmetric 21-bp region that overlaps the putative −10 promoter sequence. A mutational analysis suggested that binding by RpbA-His
6
to its cognate DNA may involve both putative HTH motif-like regions. We conclude that RpbA functions as a transcriptional repressor for
cpcB1A1
and suggest that binding by RpbA to its cognate DNA may represent an atypical protein-DNA interaction.