bluuebunny/crossref_metadata_2025_split huggingface dataset:
Repression of the
pyr
Operon in
Lactobacillus plantarum
Prevents Its Ability To Grow at Low Carbon Dioxide Levels
Authors: Nicoloff Hervé , Elagöz Aram , Arsène-Ploetze Florence , Kammerer Benoît , Martinussen Jan , Bringel Françoise 
Published: March 2005

ABSTRACT

Carbamoyl phosphate is a precursor for both arginine and pyrimidine biosynthesis. In
Lactobacillus plantarum
, carbamoyl phosphate is synthesized from glutamine, ATP, and carbon dioxide by two sets of identified genes encoding carbamoyl phosphate synthase (CPS). The expression of the
carAB
operon (encoding CPS-A) responds to arginine availability, whereas
pyrAaAb
(encoding CPS-P) is part of the
pyrR1BCAaAbDFE
operon coding for the de novo pyrimidine pathway repressed by exogenous uracil. The
pyr
operon is regulated by transcription attenuation mediated by a
trans
-acting repressor that binds to the
pyr
mRNA attenuation site in response to intracellular UMP/phosphoribosyl pyrophosphate pools. Intracellular pyrimidine triphosphate nucleoside pools were lower in mutant FB335 (
carAB
deletion) harboring only CPS-P than in the wild-type strain harboring both CPS-A and CPS-P. Thus, CPS-P activity is the limiting step in pyrimidine synthesis. FB335 is unable to grow in the presence of uracil due to a lack of sufficient carbamoyl phosphate required for arginine biosynthesis. Forty independent spontaneous FB335-derived mutants that have lost regulation of the
pyr
operon were readily obtained by their ability to grow in the presence of uracil and absence of arginine; 26 harbored mutations in the
pyrR1-pyrB
loci. One was a prototroph with a deletion of both
pyrR1
and the transcription attenuation site that resulted in large amounts of excreted pyrimidine nucleotides and increased intracellular UTP and CTP pools compared to wild-type levels. Low pyrimidine-independent expression of the
pyr
operon was obtained by antiterminator site-directed mutagenesis. The resulting AE1023 strain had reduced UTP and CTP pools and had the phenotype of a high-CO
2
-requiring auxotroph, since it was able to synthesize sufficient arginine and pyrimidines only in CO
2
-enriched air. Therefore, growth inhibition without CO
2
enrichment may be due to low carbamoyl phosphate pools from lack of CPS activity.
Regulating Pilin Expression Reveals a Threshold for S Motility inMyxococcus xanthus
Authors: Jelsbak Lotte , Kaiser Dale 
Published: March 2005

ABSTRACTAn isopropyl-β-d-thiogalactopyranoside (IPTG)-inducible promoter was constructed inMyxococcus xanthus. The single-copypilAgene encodes pilin, the monomer unit ofM. xanthustype IV pili. To vary the level ofpilAexpression, we cloned its promoter in front of thelacoperator, and a plasmid containing the construct was inserted into the chromosome of a ΔpilAstrain. Induction of pilin expression increased smoothly as the dose of IPTG added to the culture was increased. IPTG-induced pilin rescued S motility of the ΔpilAstrain to wild-type levels. The rate of S-motile swarming was found to be proportional to the number of pili (shear-sensitive pilin) produced rather than to the level of total pilin. In fact, S motility was not rescued until the total level of pilin was more than 50% of the wild-type level. This observation implies that a threshold concentration of pilin must be exceeded before the shear-sensitive material (pili) is polymerized inM. xanthus.
Comparative Genomic Analysis of the pPT23A Plasmid Family of
Pseudomonas syringae
Authors: Zhao Youfu , Ma Zhonghua , Sundin George W. 
Published: March 2005

ABSTRACT

Members
of the pPT23A plasmid family of
Pseudomonas syringae
play an
important role in the interaction of this bacterial pathogen with host
plants. Complete sequence analysis of several pPT23A family plasmids
(PFPs) has provided a glimpse of the gene content and virulence
function of these plasmids. We constructed a macroarray containing 161
genes to estimate and compare the gene contents of 23 newly analyzed
and eight known PFPs from 12 pathovars of
P. syringae
, which
belong to four genomospecies. Hybridization results revealed that PFPs
could be distinguished by the type IV secretion system (T4SS) encoded
and separated into four groups. Twelve PFPs along with pPSR1 from
P. syringae
pv. syringae, pPh1448B from
P. syringae
pv. phaseolicola, and pPMA4326A from
P. syringae
pv.
maculicola encoded a type IVA T4SS (VirB-VirD4 conjugative system),
whereas 10 PFPs along with pDC3000A and pDC3000B from
P.
syringae
pv. tomato encoded a type IVB T4SS (
tra
system).
Two plasmids encoded both T4SSs, whereas six other plasmids carried
none or only a few genes of either the type IVA or type IVB secretion
system. Most PFPs hybridized to more than one putative type III
secretion system effector gene and to a variety of additional genes
encoding known
P. syringae
virulence factors. The overall gene
contents of individual PFPs were more similar among plasmids within
each of the four groups based on T4SS genes; however, a number of
genes, encoding plasmid-specific functions or hypothetical proteins,
were shared among plasmids from different T4SS groups. The only gene
shared by all PFPs in this study was the
repA
gene, which
encoded sequences with 87 to 99% amino acid identityamong 25 sequences examined. We proposed a model to illustrate the
evolution and gene acquisition of the pPT23A plasmid family. To our
knowledge, this is the first such attempt to conduct a global genetic
analysis of this important plasmid
family.
Simultaneous Force and Fluorescence Measurements of a Protein That Forms a Bond between a Living Bacterium and a Solid Surface
Authors: Lower Brian H. , Yongsunthon Ruchirej , Vellano F. Paul , Lower Steven K. 
Published: March 2005

ABSTRACT

All microbial biofilms are initiated through direct physical contact between a bacterium and a solid surface, a step that is controlled by inter- and intramolecular forces. Atomic force microscopy and confocal laser scanning microscopy were used simultaneously to observe the formation of a bond between a fluorescent chimeric protein on the surface of a living
Escherichia coli
bacterium and a solid substrate in situ. The chimera was composed of a portion of outer membrane protein A (OmpA) fused to the cyan-fluorescent protein AmCyan. Sucrose gradient centrifugation and fluorescent confocal slices through bacteria demonstrated that the chimeric protein was targeted and anchored to the external cell surface. The wormlike chain theory predicted that this protein should exhibit a nonlinear force-extension “signature” consistent with the sequential unraveling of the AmCyan and OmpA domains. Experimentally measured force-extension curves revealed a unique pair of “sawtooth” features that were present when a bond formed between a silicon nitride surface (atomic force microscopy tip) and
E. coli
cells expressing the OmpA-AmCyan protein. The observed sawtooth pair closely matched the wormlike chain model prediction for the mechanical unfolding of the AmCyan and OmpA substructures in series. These sawteeth disappeared from the measured force-extension curves when cells were treated with proteinase K. Furthermore, these unique sawteeth were absent for a mutant stain of
E. coli
incapable of expressing the AmCyan protein on its outer surface. Together, these data show that specific proteins exhibit unique force signatures characteristic of the bond that is formed between a living bacterium and another surface.
Evidence for Diversifying Selection at the Pyoverdine Locus of
Pseudomonas aeruginosa
Authors: Smith Eric E. , Sims Elizabeth H. , Spencer David H. , Kaul Rajinder , Olson Maynard V. 
Published: March 2005

ABSTRACT

Pyoverdine is the primary siderophore of the gram-negative bacterium
Pseudomonas aeruginosa
. The pyoverdine region was recently identified as the most divergent locus alignable between strains in the
P. aeruginosa
genome. Here we report the nucleotide sequence and analysis of more than 50 kb in the pyoverdine region from nine strains of
P. aeruginosa
. There are three divergent sequence types in the pyoverdine region, which correspond to the three structural types of pyoverdine. The pyoverdine outer membrane receptor
fpvA
may be driving diversity at the locus: it is the most divergent alignable gene in the region, is the only gene that showed substantial intratype variation that did not appear to be generated by recombination, and shows evidence of positive selection. The hypothetical membrane protein PA2403 also shows evidence of positive selection; residues on one side of the membrane after protein folding are under positive selection. R′, previously identified as a type IV strain, is clearly derived from a type III strain via a 3.4-kb deletion which removes one amino acid from the pyoverdine side chain peptide. This deletion represents a natural modification of the product of a nonribosomal peptide synthetase enzyme, whose consequences are predictive from the DNA sequence. There is also linkage disequilibrium between the pyoverdine region and
pvdY
, a pyoverdine gene separated by 30 kb from the pyoverdine region. The pyoverdine region shows evidence of horizontal transfer; we propose that some alleles in the region were introduced from other soil bacteria and have been subsequently maintained by diversifying selection.
Transcriptome Analysis of the
Rhodobacter sphaeroides
PpsR Regulon: PpsR as a Master Regulator of Photosystem Development
Authors: Moskvin Oleg V. , Gomelsky Larissa , Gomelsky Mark 
Published: March 2005

ABSTRACT

PpsR from the anoxygenic phototrophic bacterium
Rhodobacter sphaeroides
has been known as an oxygen- and light-dependent repressor of bacteriochlorophyll and carotenoid biosynthesis genes and
puc
operons involved in photosystem development. However, the putative PpsR-binding sites, TGTN
12
ACA, are also located upstream of numerous nonphotosystem genes, thus raising the possibility that the role of PpsR is broader. To characterize the PpsR regulon, transcriptome profiling was performed on the wild-type strain grown at high and low oxygen tensions, on the strain overproducing PpsR, and on the
ppsR
mutant. Transcriptome analysis showed that PpsR primarily regulates photosystem genes; the consensus PpsR binding sequence is TGTcN
10
gACA (lowercase letters indicate lesser conservation); the presence of two binding sites is required for repression in vivo. These findings explain why numerous single TGTN
12
ACA sequences are nonfunctional. In addition to photosystem genes, the
hemC
and
hemE
genes involved in the early steps of tetrapyrrole biosynthesis were identified as new direct targets of PpsR repression. Unexpectedly, PpsR was found to indirectly repress the
puf
and
puhA
operons encoding photosystem core proteins. The upstream regions of these operons contain no PpsR binding sites. Involvement in regulation of these operons suggests that PpsR functions as a master regulator of photosystem development. Upregulation of the
puf
and
puhA
operons that resulted from
ppsR
inactivation was sufficient to restore the ability to grow phototrophically to the
prrA
mutant. PrrA, the global redox-dependent activator, was previously considered indispensable for phototrophic growth. It is revealed that the PrrBA and AppA-PpsR systems, believed to work independently, in fact interact and coordinately regulate photosystem development.
Role of the PhoP-PhoQ System in the Virulence of
Erwinia chrysanthemi
Strain 3937: Involvement in Sensitivity to Plant Antimicrobial Peptides, Survival at Acid pH, and Regulation of Pectolytic Enzymes
Authors: Llama-Palacios Arancha , López-Solanilla Emilia , Rodríguez-Palenzuela Pablo 
Published: March 2005

ABSTRACT

Erwinia chrysanthemi
is a phytopathogenic bacterium that causes soft-rot diseases in a broad number of crops. The PhoP-PhoQ system is a key factor in pathogenicity of several bacteria and is involved in the bacterial resistance to different factors, including acid stress. Since
E. chrysanthemi
is confronted by acid pH during pathogenesis, we have studied the role of this system in the virulence of this bacterium. In this work, we have isolated and characterized the
phoP
and
phoQ
mutants of
E. chrysanthemi
strain 3937. It was found that: (i) they were not altered in their growth at acid pH; (ii) the
phoQ
mutant showed diminished ability to survive at acid pH; (iii) susceptibility to the antimicrobial peptide thionin was increased; (iv) the virulence of the
phoQ
mutant was diminished at low and high magnesium concentrations, whereas the virulence of the
phoP
was diminished only at low magnesium concentrations; (v) in planta Pel activity of both mutant strains was drastically reduced; and (vi) both mutants lagged behind the wild type in their capacity to change the apoplastic pH. These results suggest that the PhoP-PhoQ system plays a role in the virulence of this bacterium in plant tissues, although it does not contribute to bacterial growth at acid pH.
Phosphatidylethanolamine Domains and Localization of Phospholipid Synthases in
Bacillus subtilis
Membranes
Authors: Nishibori Ayako , Kusaka Jin , Hara Hiroshi , Umeda Masato , Matsumoto Kouji 
Published: March 2005

ABSTRACT

Application of the cardiolipin (CL)-specific fluorescent dye 10-
N
-nonyl-acridine orange has recently revealed CL-rich domains in the septal regions and at the poles of the
Bacillus subtilis
membrane (F. Kawai, M. Shoda, R. Harashima, Y. Sadaie, H. Hara, and K. Matsumoto, J. Bacteriol.
186:
1475-1483, 2004). This finding prompted us to examine the localization of another phospholipid, phosphatidylethanolamine (PE), with the cyclic peptide probe, Ro09-0198 (Ro), that binds specifically to PE. Treatment with biotinylated Ro followed by tetramethyl rhodamine-conjugated streptavidin revealed that PE is localized in the septal membranes of vegetative cells and in the membranes of the polar septum and the engulfment membranes of sporulating cells. When the mutant cells of the strains SDB01 (
psd1
::
neo
) and SDB02 (
pssA10
::
spc
), which both lack PE, were examined under the same conditions, no fluorescence was observed. The localization of the fluorescence thus evidently reflected the localization of PE-rich domains in the septal membranes. Similar PE-rich domains were observed in the septal regions of the cells of many
Bacillus
species. In
Escherichia coli
cells, however, no PE-rich domains were found. Green fluorescent protein fusions to the enzymes that catalyze the committed steps in PE synthesis, phosphatidylserine synthase, and in CL synthesis, CL synthase and phosphatidylglycerophosphate synthase, were localized mainly in the septal membranes in
B. subtilis
cells. The majority of the lipid synthases were also localized in the septal membranes; this includes 1-acyl-glycerol-3-phosphate acyltransferase, CDP-diacylglycerol synthase, phosphatidylserine decarboxylase, diacylglycerol kinase, glucolipid synthase, and lysylphosphatidylglycerol synthase. These results suggest that phospholipids are produced mostly in the septal membranes and that CL and PE are kept from diffusing out to lateral ones.
Crystal Structure of Low-Molecular-Weight Protein Tyrosine Phosphatase from
Mycobacterium tuberculosis
at 1.9-Å Resolution
Authors: Madhurantakam Chaithanya , Rajakumara Eerappa , Mazumdar Pooja Anjali , Saha Baisakhee , Mitra Devrani , Wiker Harald G. , Sankaranarayanan Rajan , Das Amit Kumar 
Published: March 2005

ABSTRACT

The low-molecular-weight protein tyrosine phosphatase (LMWPTPase) belongs to a distinctive class of phosphotyrosine phosphatases widely distributed among prokaryotes and eukaryotes. We report here the crystal structure of LMWPTPase of microbial origin, the first of its kind from
Mycobacterium tuberculosis
. The structure was determined to be two crystal forms at 1.9- and 2.5-Å resolutions. These structural forms are compared with those of the LMWPTPases of eukaryotes. Though the overall structure resembles that of the eukaryotic LMWPTPases, there are significant changes around the active site and the protein tyrosine phosphatase (PTP) loop. The variable loop forming the wall of the crevice leading to the active site is conformationally unchanged from that of mammalian LMWPTPase; however, differences are observed in the residues involved, suggesting that they have a role in influencing different substrate specificities. The single amino acid substitution (Leu12Thr [underlined below]) in the consensus sequence of the PTP loop, C

T

GNICRS, has a major role in the stabilization of the PTP loop, unlike what occurs in mammalian LMWPTPases. A chloride ion and a glycerol molecule were modeled in the active site where the chloride ion interacts in a manner similar to that of phosphate with the main chain nitrogens of the PTP loop. This structural study, in addition to identifying specific mycobacterial features, may also form the basis for exploring the mechanism of the substrate specificities of bacterial LMWPTPases.
Environmental pH Sensing: Resolving the VirA/VirG Two-Component System Inputs for
Agrobacterium
Pathogenesis
Authors: Gao Rong , Lynn David G. 
Published: March 2005

ABSTRACT

Agrobacterium tumefaciens
stands as one of biotechnology's greatest successes, with all plant genetic engineering building on the strategies of this pathogen. By integrating responses to external pHs, phenols, and monosaccharides, this organism mobilizes oncogenic elements to efficiently transform most dicotyledonous plants. We now show that the complex signaling network used to regulate lateral gene transfer can be resolved as individual signaling modules. While pH and sugar perception are coupled through a common pathway, requiring both low pH and sugar for maximal virulence gene expression, various VirA and ChvE alleles can decouple pH and monosaccharide perception. This VirA and ChvE system may represent a common mechanism that underpins external pH perception in prokaryotes, and the use of these simple genetic elements may now be extended to research on specific responses to changes in environmental pH.
Global Analysis of Circadian Expression in the CyanobacteriumSynechocystissp. Strain PCC 6803
Authors: Kucho Ken-ichi , Okamoto Kazuhisa , Tsuchiya Yuka , Nomura Satoshi , Nango Mamoru , Kanehisa Minoru , Ishiura Masahiro 
Published: March 2005

ABSTRACTCyanobacteria are the only bacterial species found to have a circadian clock. We used DNA microarrays to examine circadian expression patterns in the cyanobacteriumSynechocystissp. strain PCC 6803. Our analysis identified 54 (2%) and 237 (9%) genes that exhibited circadian rhythms under stringent and relaxed filtering conditions, respectively. The expression of most cycling genes peaked around the time of transition from subjective day to night, suggesting that the main role of the circadian clock inSynechocystisis to adjust the physiological state of the cell to the upcoming night environment. There were several chromosomal regions where neighboring genes were expressed with similar circadian patterns. The physiological functions of the cycling genes were diverse and included a wide variety of metabolic pathways, membrane transport, and signal transduction. Genes involved in respiration and poly(3-hydroxyalkanoate) synthesis showed coordinated circadian expression, suggesting that the regulation is important for the supply of energy and carbon source in the night. Genes involved in transcription and translation also followed circadian cycling patterns. These genes may be important for output of the rhythmic information generated by the circadian clock. Our findings provided critical insights into the importance of the circadian clock on cellular physiology and the mechanism of clock-controlled gene regulation.
A Mutation in the Decoding Center of
Thermus thermophilus
16S rRNA Suggests a Novel Mechanism of Streptomycin Resistance
Authors: Gregory Steven T. , Carr Jennifer F. , Dahlberg Albert E. 
Published: March 2005

ABSTRACT

A spontaneous kanamycin resistance and capreomycin resistance mutation, A1408G, in the decoding center of 16S rRNA, was identified in the extreme thermophile
Thermus thermophilus
. Unexpectedly, this mutation also confers resistance to streptomycin. We propose a novel mechanism of streptomycin resistance by which A1408G influences conformational changes in 16S rRNA during tRNA selection.
Lateral Gene Transfer of Dissimilatory (Bi)Sulfite Reductase Revisited
Authors: Zverlov Vladimir , Klein Michael , Lücker Sebastian , Friedrich Michael W. , Kellermann Josef , Stahl David A. , Loy Alexander , Wagner Michael 
Published: March 2005

ABSTRACT

In contrast to previous findings, we demonstrate that the dissimilatory (bi)sulfite reductase genes (
dsrAB
) of
Desulfobacula toluolica
were vertically inherited. Furthermore,
Desulfobacterium anilini
and strain mXyS1 were identified, by
dsrAB
sequencing of 17 reference strains, as members of the donor lineage for those gram-positive
Desulfotomaculum
species which laterally acquired
dsrAB
.
Plasmid- and Chromosome-Encoded Redundant and Specific Functions Are Involved in Biosynthesis of the Siderophore Anguibactin in
Vibrio anguillarum
775: a Case of Chance and Necessity?
Authors: Alice Alejandro F. , López Claudia S. , Crosa Jorge H. 
Published: March 2005

ABSTRACT

We report the identification of a novel chromosome cluster of genes in
Vibrio anguillarum
775 that includes redundant functional homologues of the pJM1 plasmid-harbored genes
angE
and
angC
that are involved in anguibactin biosynthesis. We also identified in this cluster a chromosomal
angA
gene that is essential in anguibactin biosynthesis.
Kinetic Characterization of the Glycosyltransferase Module of
Staphylococcus aureus
PBP2
Authors: Barrett Dianah , Leimkuhler Catherine , Chen Lan , Walker Deborah , Kahne Daniel , Walker Suzanne 
Published: March 2005

ABSTRACT

We report the heterologous overexpression and purification of
Staphylococcus aureus
PBP2 and demonstrate efficient glycan polymerization from lipid II in vitro.
S. aureus
PBP2 is the first purified gram-positive class A penicillin-binding protein to show good transglycosylase activity. This enables further studies on this important class of enzymes.
Influence of Amino Acid Substitutions in the Leader Peptide on Maturation and Secretion of Mesentericin Y105 by
Leuconostoc mesenteroides
Authors: Aucher Willy , Lacombe Christian , Héquet Arnaud , Frère Jacques , Berjeaud Jean-Marc 
Published: March 2005

ABSTRACT
By site-specific mutagenesis, the hydrophobic conserved amino acids and the C-terminal GG doublet of the leader peptide of pre-mesentericin Y105 were demonstrated to be critical for optimal secretion of mesentericin Y105, as well as for the maturation of the pre-bacteriocin by the protease portion of the ABC transporter MesD.