bluuebunny/crossref_metadata_2025_split huggingface dataset:
The
Escherichia coli
O111 and
Salmonella enterica
O35 Gene Clusters: Gene Clusters Encoding the Same Colitose-Containing O Antigen Are Highly Conserved
Authors: Wang Lei , Reeves Peter R. 
Published: July 2002

ABSTRACT

O antigen is part of the lipopolysaccharide present in the outer membrane of gram-negative bacteria.
Escherichia coli
and
Salmonella enterica
each have many forms of O antigen, but only three are common to the two species. It has been found that, in general, O-antigen genes are of low GC content. This deviation in GC content from that of typical
S. enterica
or
E. coli
genes (51%) is thought to indicate that the O-antigen DNA originated in species other than
S. enterica
or
E. coli
and was captured by lateral transfer. The O-antigen structure of
Salmonella enterica
O35 is identical to that of
E. coli
O111, commonly found in enteropathogenic
E. coli
strains. This O antigen, which has been shown to be a virulence factor in
E. coli
, contains colitose, a 3,6-dideoxyhexose found only rarely in the
Enterobacteriaceae
. Sequencing of the O35-antigen gene cluster of
S. enterica
serovar Adelaide revealed the same gene order and flanking genes as in
E. coli
O111. The divergence between corresponding genes of these two gene clusters at the nucleotide level ranges from 21.8 to 11.7%, within the normal range of divergence between
S. enterica
and
E. coli
. We conclude that the ancestor of
E. coli
and
S. enterica
had an O antigen identical to the O111 and O35 antigens, respectively, of these species and that the gene cluster encoding it has survived in both species.
An Operon for a Putative ATP-Binding Cassette Transport System Involved in Acetoin Utilization of
Bacillus subtilis
Authors: Yoshida Ken-Ichi , Fujita Yasutaro , Ehrlich S. Dusko 
Published: July 2002

ABSTRACT

The
ytrABCDEF
operon of
Bacillus subtilis
was deduced to encode a putative ATP-binding cassette (ABC) transport system. YtrB and YtrE could be the ABC subunits, and YtrC and YtrD are highly hydrophobic and could form a channel through the cell membrane, while YtrF could be a periplasmic lipoprotein for substrate binding. Expression of the operon was examined in cells grown in a minimal medium. The results indicate that the expression was induced only early in the stationary phase. The six
ytr
genes form a single operon, transcribed from a putative ς
A
-dependent promoter present upstream of
ytrA
. YtrA, which possesses a helix-turn-helix motif of the GntR family, acts probably as a repressor and regulates its own transcription. Inactivation of the operon led to a decrease in maximum cell yield and less-efficient sporulation, suggesting its involvement in the growth in stationary phase and sporulation. It is known that
B. subtilis
produces acetoin as an external carbon storage compound and then reuses it later during stationary phase and sporulation. When either the entire
ytr
operon or its last gene,
ytrF
, was inactivated, the production of acetoin was not affected, but the reuse of acetoin became less efficient. We suggest that the Ytr transport system plays a role in acetoin utilization during stationary phase and sporulation.
Analysis of the Essential Cell Division GeneftsLofBacillus subtilisby Mutagenesis and Heterologous Complementation
Authors: Sievers Jörg , Errington Jeff 
Published: July 2002

ABSTRACTTheftsLgene is required for the initiation of cell division in a broad range of bacteria.Bacillus subtilis ftsLencodes a 13-kDa protein with a membrane-spanning domain near its N terminus. The external C-terminal domain has features of an α-helical leucine zipper, which is likely to be involved in the heterodimerization with another division protein, DivIC. To determine what residues are important for FtsL function, we used both random and site-directed mutagenesis. Unexpectedly, all chemically induced mutations fell into two clear classes, those either weakening the ribosome-binding site or producing a stop codon. It appears that the random mutagenesis was efficient, so many missense mutations must have been generated but with no phenotypic effect. Substitutions affecting hydrophobic residues in the putative coiled-coil domain, introduced by site-directed mutagenesis, also gave no observable phenotype except for insertion of a helix-breaking proline residue, which destroyed FtsL function.ftsLhomologues cloned from three diverseBacillusspecies,Bacillus licheniformis,Bacillus badius, andBacillus circulans, could complement anftsLnull mutation inB. subtilis, even though up to 66% of the amino acid residues of the predicted proteins were different fromB. subtilisFtsL. However, theftsLgene fromStaphylococcus aureus(whose product has 73% of its amino acids different from those of theB. subtilis ftsLproduct) was not functional. We conclude that FtsL is a highly malleable protein that can accommodate a large number of sequence changes without loss of function.
Mutation of the Lipopolysaccharide Core Glycosyltransferase Encoded by
waaG
Destabilizes the Outer Membrane of
Escherichia coli
by Interfering with Core Phosphorylation
Authors: Yethon Jeremy A. , Vinogradov Evgeny , Perry Malcolm B. , Whitfield Chris 
Published: July 2002

ABSTRACT

In
Escherichia coli
, phosphoryl substituents in the lipopolysaccharide core region are essential for outer membrane stability. Mutation of the core glucosyltransferase encoded by
waaG
(formerly
rfaG
) resulted in lipopolysaccharide truncated immediately after the inner core heptose residues, which serve as the sites for phosphorylation. Surprisingly, mutation of
waaG
also destabilized the outer membrane. Structural analyses of
waaG
mutant lipopolysaccharide showed that the cause for this phenotype was a decrease in core phosphorylation, an unexpected side effect of the
waaG
mutation.
Differential Processing of Propeptide Inhibitors of Rap Phosphatases in
Bacillus subtilis
Authors: Jiang Min , Grau Roberto , Perego Marta 
Published: July 2002

ABSTRACT

In the phosphorelay signal transduction system for sporulation initiation in
Bacillus subtilis
, the opposing activities of histidine kinases and aspartyl phosphate phosphatases determine the cell's decision whether to continue with vegetative growth or to initiate the differentiation process. Regulated dephosphorylation of the Spo0A and Spo0F response regulators allows a variety of negative signals from physiological processes that are antithetical to sporulation to impact on the activation level of the phosphorelay. Spo0F∼P is the known target of two related phosphatases, RapA and RapB. In addition to RapA and RapB, a third member of the Rap family of phosphatases, RapE, specifically dephosphorylated the Spo0F∼P intermediate in response to competence development. RapE phosphatase activity was found to be controlled by a pentapeptide (SRNVT) generated from within the carboxy-terminal domain of the
phrE
gene product. A synthetic PhrE pentapeptide could (i) complement the sporulation deficiency caused by deregulated RapE activity of a
phrE
mutant and (ii) inhibit RapE-dependent dephosphorylation of Spo0F∼P in in vitro experiments. The PhrE pentapeptide did not inhibit the phosphatase activity of RapA and RapB. These results confirm previous conclusions that the specificity for recognition of the target phosphatase is contained within the amino acid sequence of the pentapeptide inhibitor.
Dimerization between the Holin and Holin Inhibitor of Phage λ
Authors: Gründling Angelika , Smith David L. , Bläsi Udo , Young Ry 
Published: July 2002

ABSTRACT

Holins are integral membrane proteins that control the access of phage-encoded muralytic enzymes, or endolysins, to the cell wall by the sudden formation of an uncharacterized homo-oligomeric lesion, or hole, in the membrane, at a precisely defined time. The timing of λ-infected cell lysis depends solely on the 107 codon
S
gene, which encodes two proteins, S105 and S107, which are the holin and holin inhibitor, respectively. Here we report the results of biochemical and genetic studies on the interaction between the holin and the holin inhibitor. A unique cysteine at position 51, in the middle of the second transmembrane domain, is shown to cause the formation of disulfide-linked dimers during detergent membrane extraction. Forced oxidation of membranes containing S molecules also results in the formation of covalently linked dimers. This technique is used to demonstrate efficient dimeric interactions between S105 and S107. These results, coupled with the previous finding that the timing of lysis depends on the excess of the amount of S105 over S107, suggest a model in which the inhibitor functions by titrating out the effector in a stoichiometric fashion. This provides a basis for understanding two evolutionary advantages provided by the inhibitor system, in which the production of the inhibitor not only causes a delay in the timing of lysis, allowing the assembly of more virions, but also increases effective hole formation after triggering.
Characterization of the ς
B
Regulon in
Staphylococcus aureus
Authors: Gertz Silke , Engelmann Susanne , Schmid Roland , Ziebandt Anne-Kathrin , Tischer Karsten , Scharf Christian , Hacker Jörg , Hecker Michael 
Published: July 2002

ABSTRACT

The ς
B
-dependent stress regulon in gram-positive bacteria might fulfill a physiological role in stress response and virulence similar to that of the ς
S
regulon in
Escherichia coli
and other gram-negative bacteria. In order to obtain evidence for the function of the ς
B
regulon of
Staphylococcus aureus
, especially in virulence control, ς
B
-dependent stress genes were identified. The two-dimensional protein pattern of wild-type cells of
S. aureus
COL was compared with that of an isogenic
sigB
mutant. By this approach, we found that the synthesis of about 27 cytoplasmic proteins seemed to be under the positive control of ς
B
. N-terminal sequencing of 18 proteins allowed the identification of their genes on the almost finished genome sequence of
S. aureus
COL and the analysis of the promoter structure. Transcriptional analyses of 11 of these genes confirmed their ς
B
dependency, and moreover, about 7 additional ς
B
-dependent genes were found which are cotranscribed with the newly detected genes, forming operons. Altogether, we identified 23 ς
B
-dependent genes and their corresponding proteins. Among them are proteins probably involved in the generation of NADH or in membrane transport mechanisms. Furthermore, at least one
clpC
-homologous gene was localized on the
S. aureus
sequence solely transcribed by ς
B
. In contrast, a second
clpC
-homologous gene in
S. aureus
forming an operon with
ctsR
,
yacH
, and
yacI
was ς
B
independently expressed.
TheAgrobacteriumT-DNA Transport Pore Proteins VirB8, VirB9, and VirB10 Interact with One Another
Authors: Das Anath , Xie Yong-Hong 
Published: July 2002

ABSTRACTThe VirB proteins ofAgrobacterium tumefaciensform a transport pore to transfer DNA from bacteria to plants. The assembly of the transport pore will require interaction among the constituent proteins. The identification of proteins that interact with one another can provide clues to the assembly of the transport pore. We studied interaction among four putative transport pore proteins, VirB7, VirB8, VirB9 and VirB10. Using the yeast two-hybrid assay, we observed that VirB8, VirB9, and VirB10 interact with one another. In vitro studies using protein fusions demonstrated that VirB10 interacts with VirB9 and itself. These results suggest that the outer membrane VirB7-VirB9 complex interacts with the inner membrane proteins VirB8 and VirB10 for the assembly of the transport pore. Fusions that contain small, defined segments of the proteins were used to define the interaction domains of VirB8 and VirB9. All interaction domains of both proteins mapped to the N-terminal half of the proteins. Two separate domains at the N- and C-terminal ends of VirB9 are involved in its homotypic interaction, suggesting that VirB9 forms a higher oligomer. We observed that the alteration of serine at position 87 of VirB8 to leucine abolished its DNA transfer function. Studies on the interaction of the mutant protein with the other VirB proteins showed that the VirB8S87L mutant is defective in interaction with VirB9. The mutant, however, interacted efficiently with VirB8 and VirB10, suggesting that the VirB8-VirB9 interaction is essential for DNA transfer.
Extracellular Glycanases of
Rhizobium leguminosarum
Are Activated on the Cell Surface by an Exopolysaccharide-Related Component
Authors: Zorreguieta Angeles , Finnie Christine , Downie J. Allan 
Published: July 2002

ABSTRACT

Rhizobium leguminosarum
secretes two extracellular glycanases, PlyA and PlyB, that can degrade exopolysaccharide (EPS) and carboxymethyl cellulose (CMC), which is used as a model substrate of plant cell wall cellulose polymers. When grown on agar medium, CMC degradation occurred only directly below colonies of
R. leguminosarum
, suggesting that the enzymes remain attached to the bacteria. Unexpectedly, when a PlyA-PlyB-secreting colony was grown in close proximity to mutants unable to produce or secrete PlyA and PlyB, CMC degradation occurred below that part of the mutant colonies closest to the wild type. There was no CMC degradation in the region between the colonies. By growing PlyB-secreting colonies on a lawn of CMC-nondegrading mutants, we could observe a halo of CMC degradation around the colony. Using various mutant strains, we demonstrate that PlyB diffuses beyond the edge of the colony but does not degrade CMC unless it is in contact with the appropriate colony surface. PlyA appears to remain attached to the cells since no such diffusion of PlyA activity was observed. EPS defective mutants could secrete both PlyA and PlyB, but these enzymes were inactive unless they came into contact with an EPS
+
strain, indicating that EPS is required for activation of PlyA and PlyB. However, we were unable to activate CMC degradation with a crude EPS fraction, indicating that activation of CMC degradation may require an intermediate in EPS biosynthesis. Transfer of PlyB to
Agrobacterium tumefaciens
enabled it to degrade CMC, but this was only observed if it was grown on a lawn of
R. leguminosarum
. This indicates that the surface of
A. tumefaciens
is inappropriate to activate CMC degradation by PlyB. Analysis of CMC degradation by other rhizobia suggests that activation of secreted glycanases by surface components may occur in other species.
AcrD of
Escherichia coli
Is an Aminoglycoside Efflux Pump
Authors: Rosenberg Emiko Y. , Ma Dzwokai , Nikaido Hiroshi 
Published: July 2002

ABSTRACT

AcrD, a transporter belonging to the resistance-nodulation-division family, was shown to participate in the efflux of aminoglycosides. Deletion of the
acrD
gene decreased the MICs of amikacin, gentamicin, neomycin, kanamycin, and tobramycin by a factor of two to eight, and
ΔacrD
cells accumulated higher levels of [
3
H]dihydrostreptomycin and [
3
H]gentamicin than did the parent strain.
Dephosphorylation of the
Escherichia coli
Transcriptional Antiterminator BglG by the Sugar Sensor BglF Is the Reversal of Its Phosphorylation
Authors: Chen Qing , Postma Pieter W. , Amster-Choder Orna 
Published: July 2002

ABSTRACT

The
Escherichia coli
BglF protein catalyzes transport and phosphorylation of β-glucosides. In addition, BglF is a membrane sensor which reversibly phosphorylates the transcriptional regulator BglG, depending on β-glucoside availability. Therefore, BglF has three enzymatic activities: β-glucoside phosphotransferase, BglG phosphorylase, and phospho-BglG (BglG-P) dephosphorylase. Cys-24 of BglF is the active site which delivers the phosphoryl group either to the sugar or to BglG. To characterize the dephosphorylase activity, we asked whether BglG-P can give the phosphoryl group back to Cys-24 of BglF. Here we provide evidence which is consistent with the interpretation that Cys-24–P is an intermediate in the BglG-P dephosphorylation reaction. Hence, the dephosphorylation reaction catalyzed by BglF proceeds via reversal of the phosphorylation reaction.
Genome Plasticity among Related
Lactococcus
Strains: Identification of Genetic Events Associated with Macrorestriction Polymorphisms
Authors: Le Bourgeois Pascal , Daveran-Mingot Marie-Line , Ritzenthaler Paul 
Published: July 2002

ABSTRACT

The genomic diversity of nine strains of the
Lactococcus lactis
subsp.
cremoris
(NCDO712, NCDO505, NCDO2031, NCDO763, MMS36, C2, LM0230, LM2301, and MG1363) was studied by macrorestriction enzyme analysis using pulsed-field gel electrophoresis. These strains were considered adequate for the investigation of genomic plasticity because they have been described as belonging to the same genetic lineage. Comparison of
Apa
I and
Sma
I genome fingerprints of each strain revealed the presence of several macrorestriction fragment length polymorphisms (RFLPs), despite a high degree of similarity of the generated restriction patterns. The physical map of the MG1363 chromosome was used to establish a genome map of the other strains and allocate the RFLPs to five regions. Southern hybridization analysis correlated the polymorphic regions with genetic events such as chromosomal inversion, integration of prophage DNA, and location of the transposon-like structures carrying conjugative factor or oligopeptide transport system.
Characterization of a Three-Component Vanillate
O
-Demethylase from
Moorella thermoacetica
Authors: Naidu Devendra , Ragsdale Stephen W. 
Published: July 2002

ABSTRACT

The
Moorella thermoacetica
aromatic
O
-demethylase was characterized as an inducible three-component system with similarity to the methanogenic methanol, methylamine, and methanethiol methyltransferases and to the
O
-demethylase system from
Acetobacterium dehalogenans
. MtvB catalyzes methyl transfer from a phenylmethylether to the cobalt center of MtvC, a corrinoid protein. MtvA catalyzes transmethylation from MtvC to tetrahydrofolate, forming methyltetrahydrofolate. Cobalamin can substitute for MtvC.
Characterization of the Role of the ToxR-Modulated Outer Membrane Porins OmpU and OmpT in
Vibrio cholerae
Virulence
Authors: Provenzano Daniele , Lauriano Crystal M. , Klose Karl E. 
Published: July 2002

ABSTRACT

ToxR, the transmembrane regulatory protein required for expression of virulence factors in the human diarrheal pathogen
Vibrio cholerae
, directly activates and represses the transcription of two outer membrane porins, OmpU and OmpT, respectively. In an attempt to dissect the role of the OmpU and OmpT porins in viability and virulence factor expression, in-frame chromosomal deletions were constructed in the coding sequences of
ompU
and
ompT
of
V. cholerae
. Two separate deletions were introduced into
ompU
; the first (small) deletion, Δ
ompU1
, removed the coding sequence for 84 internal amino acids (aa), while the second (large) deletion, Δ
ompU2
, removed the coding sequence for the entire amino-terminal 274 aa. The Δ
ompU1
strain had a growth defect that could not be complemented by episomal expression of full-length
ompU
. In contrast, a strain with Δ
ompU2
displayed wild-type growth kinetics in rich media, suggesting that this is the true phenotype of a strain lacking OmpU and that the truncated OmpU protein, rather than the absence of OmpU, may be the cause for the Δ
ompU1
phenotype. A large deletion removing the coding sequence for the entire N-terminal 273 aa of OmpT (Δ
ompT
) was also constructed in wild-type as well as Δ
toxR
and Δ
ompU2
strains, and these strains displayed wild-type growth kinetics in rich media. However, the Δ
ompU2
strain was deficient for growth in deoxycholate compared to wild-type, Δ
ompT
, and Δ
ompU2
Δ
ompT
strains, reinforcing a positive role for the OmpU porin and a negative role for the OmpT porin in
V. cholerae
resistance to anionic detergents. The Δ
ompU2
, Δ
ompT
, and Δ
ompU2
Δ
ompT
strains exhibited wild-type levels of in vitro virulence factor expression and resistance to polymyxin B and serum and in vivo colonization levels similar to a wild-type strain in the infant mouse intestine. Our results demonstrate that (i) OmpU and OmpT are not essential proteins, as was previously thought; (ii) these porins contribute to
V. cholerae
resistance to anionic detergents; and (iii) OmpU and OmpT are not essential for virulence factor expression in vitro or intestinal colonization in vivo.
Complex Regulation of the Organic Hydroperoxide Resistance Gene (
ohr
) from
Xanthomonas
Involves OhrR, a Novel Organic Peroxide-Inducible Negative Regulator, and Posttranscriptional Modifications
Authors: Sukchawalit Rojana , Loprasert Suvit , Atichartpongkul Sopapan , Mongkolsuk Skorn 
Published: July 2002

ABSTRACT

Analysis of the sequence immediate upstream of
ohr
revealed an open reading frame, designated
ohrR,
with the potential to encode a 17-kDa peptide with moderate amino acid sequence homology to the MarR family of negative regulators of gene expression.
ohrR
was transcribed as bicistronic mRNA with
ohr,
while
ohr
mRNA was found to be 95% monocistronic and 5% bicistronic with
ohrR
. Expression of both genes was induced by
tert
-butyl hydroperoxide (tBOOH) treatment. High-level expression of
ohrR
negatively regulated
ohr
expression. This repression could be overcome by tBOOH treatment. In vivo promoter analysis showed that the
ohrR
promoter (P1) has organic peroxide-inducible, strong activity, while the
ohr
promoter (P2) has constitutive, weak activity. Only P1 is autoregulated by OhrR.
ohr
primer extension results revealed three major primer extension products corresponding to the 5′ ends of
ohr
mRNA, and their levels were strongly induced by tBOOH treatment. Sequence analysis of regions upstream of these sites showed no typical
Xanthomonas
promoter. Instead, the regions can form a stem-loop secondary structure with the 5′ ends of
ohr
mRNA located in the loop section. The secondary structure resembles the structure recognized and processed by RNase III enzyme. These findings suggest that the P1 promoter is responsible for tBOOH-induced expression of the
ohrR-ohr
operon. The bicistronic mRNA is then processed by RNase III-like enzymes to give high levels of
ohr
mRNA, while
ohrR
mRNA is rapidly degraded.
The
licC
Gene of
Streptococcus pneumoniae
Encodes a CTP:Phosphocholine Cytidylyltransferase
Authors: Rock Charles O. , Heath Richard J. , Park Hee-Won , Jackowski Suzanne 
Published: July 2002

ABSTRACT

The
licC
gene product of
Streptococcus pneumoniae
was expressed and characterized. LicC is a nucleoside triphosphate transferase family member and possesses CTP:phosphocholine cytidylyltransferase activity. Phosphoethanolamine is a poor substrate. The LicC protein plays a role in the biosynthesis of the phosphocholine-derivatized cell wall constituents that are critical for cell separation and pathogenesis.