bluuebunny/crossref_metadata_2025_split huggingface dataset:
Energy Taxis Is the Dominant Behavior in
Azospirillum brasilense
Authors: Alexandre Gladys , Greer Suzanne E. , Zhulin Igor B. 
Published: July 2002

ABSTRACT

Energy taxis encompasses aerotaxis, phototaxis, redox taxis, taxis to alternative electron acceptors, and chemotaxis to oxidizable substrates. The signal for this type of behavior is originated within the electron transport system. Energy taxis was demonstrated, as a part of an overall behavior, in several microbial species, but it did not appear as the dominant determinant in any of them. In this study, we show that most behavioral responses proceed through this mechanism in the alpha-proteobacterium
Azospirillum brasilense
. First, chemotaxis to most chemoeffectors typical of the azospirilla habitat was found to be metabolism dependent and required a functional electron transport system. Second, other energy-related responses, such as aerotaxis, redox taxis, and taxis to alternative electron acceptors, were found in
A. brasilense
. Finally, a mutant lacking a cytochrome
c
oxidase of the
cbb
3
type was affected in chemotaxis, redox taxis, and aerotaxis. Altogether, the results indicate that behavioral responses to most stimuli in
A. brasilense
are triggered by changes in the electron transport system.
An
Escherichia coli
Reference Collection Group B2- and Uropathogen-Associated Polymorphism in the
rpoS-mutS
Region of the
E. coli
Chromosome
Authors: Culham Doreen E. , Wood Janet M. 
Published: July 2002

ABSTRACT

Chromosomal DNAs of enterohemorrhagic, uropathogenic, and laboratory attenuated
Escherichia coli
strains differ in the
rpoS-mutS
region. Many uropathogens lack a deletion and an insertion characteristic of enterohemorrhagic strains. At the same chromosomal position, they harbor a 2.1-kb insertion of unknown origin with a base composition suggestive of horizontal gene transfer. Unlike virulence determinants associated with urinary tract infection and/or neonatal meningitis (
pap
or
prs
,
sfa
,
kps
, and
hly
), the 2.1-kb insertion is shared by all group B2 strains of the
E. coli
Reference Collection.
The Histidine Kinase Domain of UhpB Inhibits UhpA Action at the
Escherichia coli uhpT
Promoter
Authors: Wright Jesse S. , Olekhnovich Igor N. , Touchie Gail , Kadner Robert J. 
Published: July 2002

ABSTRACT

The histidine kinase (HK) component of many two-component regulatory systems exhibits regulated ability to phosphorylate itself and to participate in transfer of phosphate to and from its cognate response regulator. The signaling system that controls expression of the UhpT sugar phosphate transporter in
Escherichia coli
in response to external glucose 6-phosphate includes the HK protein UhpB and the polytopic membrane protein UhpC, a UhpT homolog which is required for responsiveness to an inducer and activation of UhpB. The existence of a UhpBC signaling complex is suggested by the requirement for UhpC for the activity of certain constitutively active variants of UhpB, the dominance and epistasis relationships of
uhp
alleles, and the finding that expression of UhpB in excess of UhpC has a strong dominant-negative effect. Expression of a hybrid protein containing the cytoplasmic C-terminal half of UhpB fused to glutathione
S
-transferase (GST) also interfered with Uhp signaling. This interference phenotype could not result solely from the phosphatase activity of UhpB, because interference affected both overexpressed UhpA and UhpA variants which are active in the absence of phosphorylation. Variant forms of UhpB which were active in the absence of UhpC carried amino acid substitutions near motifs conserved in HK proteins. The GST fusion protein inhibited the ability of UhpA to bind and activate transcription at the
uhpT
promoter. Unlike the wild-type situation, a GST fusion variant carrying one of the UhpB-activating substitutions, R324C, displayed autokinase activity and phosphate transfer to UhpA but retained the ability to sequester UhpA when it was altered in the conserved residues important for phosphate transfer. Thus, the default state of UhpB is kinase off, and activation of its phosphate transfer activity requires either the action of UhpC or the occurrence of certain mutations in UhpB. The interference phenotype shown by UhpB in excess of UhpC appears to include the binding and sequestration of UhpA.
Mutational Analysis of Conserved Residues in the Putative DNA-Binding Domain of the Response Regulator Spo0A of
Bacillus subtilis
Authors: Hatt Janet K. , Youngman Philip 
Published: July 2002

ABSTRACT

The Spo0A protein of
Bacillus subtilis
is a DNA-binding protein that is required for the expression of genes involved in the initiation of sporulation. Spo0A binds directly to and both activates and represses transcription from the promoters of several genes required during the onset of endospore formation. The C-terminal 113 residues are known to contain the DNA-binding activity of Spo0A. Previous studies identified a region of the C-terminal half of Spo0A that is highly conserved among species of endospore-forming
Bacillus
and
Clostridium
and which encodes a putative helix-turn-helix DNA-binding domain. To test the functional significance of this region and determine if this motif is involved in DNA binding, we changed three conserved residues, S210, E213, and R214, to Gly and/or Ala by site-directed mutagenesis. We then isolated and analyzed the five substitution-containing Spo0A proteins for DNA binding and sporulation-specific gene activation. The S210A Spo0A mutant exhibited no change from wild-type binding, although it was defective in
spoIIA
and
spoIIE
promoter activation. In contrast, both the E213G and E213A Spo0A variants showed decreased binding and completely abolished transcriptional activation of
spoIIA
and
spoIIE
, while the R214G and R214A variants completely abolished both DNA binding and transcriptional activation. These data suggest that these conserved residues are important for transcriptional activation and that the E213 residue is involved in DNA binding.
Antigen 43 and Type 1 Fimbriae Determine Colony Morphology of
Escherichia coli
K-12
Authors: Hasman Henrik , Schembri Mark A. , Klemm Per 
Published: July 2002

ABSTRACT

Colony morphology has been used as an important identification and characterization criterion in bacteriology for many decades. However, the molecular mechanisms underlying the appearance of different colony types have been given little attention. The synthesis of O antigen is defunct in
Escherichia coli
K-12, and colonies should accordingly only appear to be rough. However, previous reports have noted the presence of different interchangeable colony morphology types. In this study we have addressed the influence of two phase-variable surface structures, antigen 43 and type 1 fimbriae, on colony morphology. Due to differential expression of these structures, four different colony phenotypes could be distinguished. By creating and studying defined mutants of the respective loci, i.e.,
flu
and
fim
, we conclude that the presence or absence of the corresponding gene products on the cells correlates with the observed colony morphology forms. Interestingly, the habitat specificity of bacteria under static liquid conditions seems to correlate with the colony phenotypes.
Enhanced Nitrogenase Activity in Strains of
Rhodobacter capsulatus
That Overexpress the
rnf
Genes
Authors: Jeong Ho-Sang , Jouanneau Yves 
Published: July 2002

ABSTRACT

In the photosynthetic bacterium
Rhodobacter capsulatus
, a putative membrane-bound complex encoded by the
rnfABCDGEH
operon is thought to be dedicated to electron transport to nitrogenase. In this study, the whole
rnf
operon was cloned under the control of the
nifH
promoter in plasmid pNR117 and expressed in several
rnf
mutants. Complementation analysis demonstrated that transconjugants which integrated plasmid pNR117 directed effective biosynthesis of a functionally competent complex in
R. capsulatus
. Moreover, it was found that strains carrying pNR117 displayed nitrogenase activities 50 to 100% higher than the wild-type level. The results of radioactive labeling experiments indicated that the intracellular content of nitrogenase polypeptides was marginally altered in strains containing pNR117, whereas the levels of the RnfB and RnfC proteins present in the membrane were four- and twofold, respectively, higher than the wild-type level. Hence, the enhancement of in vivo nitrogenase activity was correlated with a commensurate overproduction of the Rnf polypeptides. In vitro nitrogenase assays performed in the presence of an artificial electron donor indicated that the catalytic activity of the enzyme was not increased in strains overproducing the Rnf polypeptides. It is proposed that the supply of reductants through the Rnf complex might be rate limiting for nitrogenase activity in vivo. Immunoprecipitation experiments performed on solubilized membrane proteins revealed that RnfB and RnfC are associated with each other and with additional polypeptides which may be components of the membrane-bound complex.
The RofA Binding Site inStreptococcus pyogenesIs Utilized in Multiple Transcriptional Pathways
Authors: Granok Alexander B. , Parsonage Derek , Ross R. Paul , Caparon Michael G. 
Published: July 2002

ABSTRACTUnderstanding the regulation of adhesins defines a pathogenic bacterium's interaction with the local environment within the host. In certain strains ofStreptococcus pyogenes, transcription ofprtF, the gene which encodes the fibronectin-binding adhesin protein F, is activated by RofA under anaerobic conditions. RofA binds specifically to DNA in its target promoters and autoregulates its own expression. In this study, we have used DNase I protection assays to further investigate the interaction of RofA with its target promoters. In the region betweenrofAand the gene which encodes protein F (prtF), RofA binds to two distinct sites: a smaller site (17 bp) adjacent to therofApromoter, and a larger site (40 bp) adjacent to theprtFpromoter. Analysis of fusions to a novel reporter gene whose product consists of the fusion of the N-terminal secretion domain of protein F with the C-terminal enzymatic domain of the enterococcal alkaline phosphatase (PhoZ) revealed that the small RofA binding site had no direct role in control ofprtFtranscription but contributed to regulation ofrofA. Comparison in several strains representing different patterns ofprtFexpression indicated that the larger site was required for activation ofrofAand ofprtFin all strains by both RofA-dependent and -independent pathways. Thus, it would appear that a common recognition sequence provides separate entries to a final common pathway inS. pyogenesvirulence gene expression. The identification of multiple RofA-like proteins and promoters with RofA binding sites implies the existence of a widespread interacting regulatory network.
EFG1
Null Mutants of
Candida albicans
Switch but Cannot Express the Complete Phenotype of White-Phase Budding Cells
Authors: Srikantha Thyagarajan , Tsai Luong K. , Daniels Karla , Soll David R. 
Published: July 2002

ABSTRACT

The
Candida albicans
gene
EFG1
encodes a putative
trans
-acting factor. In strain WO-1, which undergoes the white-opaque transition,
EFG1
is transcribed as a 3.2-kb mRNA in white-phase cells and a less-abundant 2.2-kb mRNA in opaque-phase cells. cDNA sequencing and 5′ rapid amplification of cDNA ends analysis demonstrate that the major difference in molecular mass of the two transcripts is due to different transcription start sites.
EFG1
null mutants form opaque-phase colonies and express the opaque-phase cell phenotype at 25°C. When shifted from 25 to 42°C, mutant opaque-phase cells undergo phenotypic commitment to the white phase, which includes deactivation of the opaque-phase-specific gene
OP4
and activation of the white-phase-specific gene
WH11
, as do wild-type opaque-phase cells. After the commitment event,
EFG1
null mutant cells form daughter cells which have the smooth (pimpleless) surface of white-phase cells but the elongate morphology of opaque-phase cells. Taken together, these results demonstrate that
EFG1
expression is not essential for the switch event per se, but is essential for a subset of phenotypic characteristics necessary for the full expression of the phenotype of white-phase cells. These results demonstrate that
EFG1
is not the site of the switch event, but is, rather, downstream of the switch event.
Replication of Staphylococcal Multiresistance Plasmids
Authors: Firth Neville , Apisiridej Sumalee , Berg Tracey , O'Rourke Brendon A. , Curnock Steve , Dyke Keith G. H. , Skurray Ronald A. 
Published: July 2002

ABSTRACT

Based on structural and functional properties, three groups of large staphylococcal multiresistance plasmids have been recognized, viz., the pSK1 family, pSK41-like conjugative plasmids, and β-lactamase–heavy-metal resistance plasmids. Here we describe an analysis of the replication functions of a representative of each of these plasmid groups. The replication initiation genes from the
Staphylococcus aureus
plasmids pSK1, pSK41, and pI9789::Tn
552
were found to be related to each other and to the
Staphylococcus xylosus
plasmid pSX267 and are also related to
rep
genes of several plasmids from other gram-positive genera. Nucleotide sequence similarity between pSK1 and pI9789::Tn
552
extended beyond their
rep
genes, encompassing upstream divergently transcribed genes,
orf245
and
orf256
, respectively. Our analyses revealed that genes encoding proteins related to the deduced
orf245
product are variously represented, in several types of organization, on plasmids possessing six seemingly evolutionarily distinct types of replication initiation genes and including both theta-mode and rolling-circle replicons. Construction of minireplicons and subsequent functional analysis demonstrated that
orf245
is required for the segregational stability of the pSK1 replicon. In contrast, no gene equivalent to
orf245
is evident on the conjugative plasmid pSK41, and a minireplicon encoding only the pSK41
rep
gene was found to exhibit a segregational stability approaching that of the parent plasmid. Significantly, the results described establish that many of the large multiresistance plasmids that have been identified in clinical staphylococci, which were formerly presumed to be unrelated, actually utilize an evolutionarily related theta-mode replication system.
Evidence for the Presence of an F-Type ATP Synthase Involved in Sulfate Respiration in
Desulfovibrio vulgaris
Authors: Ozawa Kiyoshi , Meikari Takanori , Motohashi Ken , Yoshida Masasuke , Akutsu Hideo 
Published: July 2002

ABSTRACT

Using a library of genomic DNA from
Desulfovibrio vulgaris
Miyazaki F, a strict anaerobe, and two synthetic deoxyoligonucleotide probes designed for F-type ATPases, the genes for open reading frames (ORFs) 1 to 5 were cloned and sequenced. The predicted protein sequences of the gene products indicate that they are composed of 172, 488, 294, 471, and 134 amino acids, respectively, and that they share considerable identity at the amino acid level with δ, α, γ, β, and ɛ subunits found in other F-type ATPases, respectively. Furthermore, a component carrying ATPase activity was partially purified from the cytoplasmic membrane fraction of the
D. vulgaris
Miyazaki F cells. The N-terminal amino acid sequences of three major polypeptides separated by sodium dodecyl sulfate–12% polyacrylamide gel electrophoresis were identical to those of the products predicted by the sequences of ORF-2, ORF-3, and ORF-4, suggesting that an F-type ATPase is functioning in the
D. vulgaris
Miyazaki F cytoplasmic membrane. The amount of the F-type ATPase produced in the
D. vulgaris
Miyazaki F cells is similar to that in the
Escherichia coli
cells cultured aerobically. It indicates that the enzyme works as an ATP synthase in the
D. vulgaris
Miyazaki F cells in connection with sulfate respiration.
A
Bacillus subtilis
Gene of Previously Unknown Function,
yhaG
, Is Translationally Regulated by Tryptophan-Activated TRAP and Appears To Be Involved in Tryptophan Transport
Authors: Sarsero Joseph P. , Merino Enrique , Yanofsky Charles 
Published: July 2002

ABSTRACT

Computer analysis of the
Bacillus subtilis
genome sequence revealed a gene with no previously attributed function,
yhaG
, specifying a transcript containing a presumptive binding site for the tryptophan-activated regulatory protein, TRAP. The presumptive TRAP binding site overlaps the
yhaG
Shine-Dalgarno sequence and translation initiation region. TRAP was shown to regulate expression of
yhaG
translationally. Production of the
yhaG
transcript in vivo was found to compete for the binding of TRAP to other known TRAP binding sites. YhaG is likely to be a transmembrane protein involved in tryptophan transport.
Heterologous Expression of Bacterial Epoxyalkane:Coenzyme M Transferase and Inducible Coenzyme M Biosynthesis inXanthobacterStrain Py2 andRhodococcus rhodochrousB276
Authors: Krum Jonathan G. , Ensign Scott A. 
Published: July 2002

ABSTRACTCoenzyme M (CoM) (2-mercaptoethanesulfonic acid) biosynthesis is shown to be coordinately regulated with the expression of the enzymes of alkene and epoxide metabolism in the propylene-oxidizing bacteriaXanthobacterstrain Py2 andRhodococcus rhodochrousstrain B276. These results provide the first evidence for the involvement of CoM in propylene metabolism byR. rhodochrousand demonstrate for the first time the inducible nature of eubacterial CoM biosynthesis.
Transcriptional Organization and Dynamic Expression of the
hbpCAD
Genes, Which Encode the First Three Enzymes for 2-Hydroxybiphenyl Degradation in
Pseudomonas azelaica
HBP1
Authors: Jaspers Marco C. M. , Schmid Andreas , Sturme Mark H. J. , Goslings David A. M. , Kohler Hans-Peter E. , Roelof van der Meer Jan 
Published: July 2002

ABSTRACT

Pseudomonas azelaica
HBP1 degrades the toxic substance 2-hydroxybiphenyl (2-HBP) by means of three enzymes that are encoded by structural genes
hbpC
,
hbpA
, and
hbpD
. These three genes form a small noncontiguous cluster. Their expression is activated by the product of regulatory gene
hbpR
, which is located directly upstream of the
hbpCAD
genes. The HbpR protein is a transcription activator and belongs to the so-called XylR/DmpR subclass within the NtrC family of transcriptional activators. Transcriptional fusions between the different
hbp
intergenic regions and the
luxAB
genes of
Vibrio harveyi
in
P. azelaica
and in
Escherichia coli
revealed the existence of two HbpR-regulated promoters; one is located in front of
hbpC
, and the other one is located in front of
hbpD
. Northern analysis confirmed that the
hbpC
and
hbpA
genes are cotranscribed, whereas the
hbpD
gene is transcribed separately. No transcripts comprising the entire
hbpCAD
cluster were detected, indicating that transcription from P

hbpC

is terminated after the
hbpA
gene.
E. coli
mutant strains lacking the structural genes for the RNA polymerase ς
54
subunit or for the integration host factor failed to express bioluminescence from P

hbpC

- and P

hbpD

-luxAB
fusions when a functional
hbpR
gene was provided in
trans
. This pointed to the active role of ς
54
and integration host factor in transcriptional activation from these promoters. Primer extension analysis revealed that both P

hbpC

and P

hbpD

contain the typical motifs at position −24 (GG) and −12 (GC) found in ς
54
-dependent promoters. Analysis of changes in the synthesis of the
hbp
mRNAs, in activities of the 2-HBP pathway enzymes, and in concentrations of 2-HBP intermediates during the first 4 h after induction of continuously grown
P. azelaica
cells with 2-HBP demonstrated that the specific transcriptional organization of the
hbp
genes ensured smooth pathway expression.
Differential Responses of
Escherichia coli
Cells Expressing Cytoplasmic Domain Mutants of Penicillin-Binding Protein 1b after Impairment of Penicillin-Binding Proteins 1a and 3
Authors: Chalut Christian , Charpentier Xavier , Remy Marie-Hélène , Masson Jean-Michel 
Published: July 2002

ABSTRACT

Penicillin-binding protein 1b (PBP1b) is the major high-molecular-weight PBP in
Escherichia coli
. Although it is coded by a single gene, it is usually found as a mixture of three isoforms which vary with regard to the length of their N-terminal cytoplasmic tail. We show here that although the cytoplasmic tail seems to play no role in the dimerization of PBP1b, as was originally suspected, only the full-length protein is able to protect the cells against lysis when both PBP1a and PBP3 are inhibited by antibiotics. This suggests a specific role for the full-length PBP1b in the multienzyme peptidoglycan-synthesizing complex that cannot be fulfilled by either PBP1a or the shorter PBP1b proteins. Moreover, we have shown by alanine-stretch-scanning mutagenesis that (i) residues R
11
to G
13
are major determinants for correct translocation and folding of PBP1b and that (ii) the specific interactions involving the full-length PBP1b can be ascribed to the first six residues at the N-terminal end of the cytoplasmic domain. These results are discussed in terms of the interactions with other components of the murein-synthesizing complex.
YLR209c
Encodes
Saccharomyces cerevisiae
Purine Nucleoside Phosphorylase
Authors: Lecoq K. , Belloc I. , Desgranges C. , Konrad M. , Daignan-Fornier B. 
Published: July 2002

ABSTRACT

The yeast
YLR209c
(
PNP1
) gene encodes a protein highly similar to purine nucleoside phosphorylases. This protein specifically metabolized inosine and guanosine. Disruption of
PNP1
led to inosine and guanosine excretion in the medium, thus showing that
PNP1
plays an important role in the metabolism of these purine nucleosides in vivo.
Transcriptional Regulation of the Two Sterol Esterification Genes in the Yeast
Saccharomyces cerevisiae
Authors: Jensen-Pergakes Kristen , Guo Zhongmin , Giattina Mara , Sturley Stephen L. , Bard Martin 
Published: July 2002

ABSTRACT

Saccharomyces cerevisiae
transcribes two genes,
ARE1
and
ARE2
, that contribute disproportionately to the esterification of sterols. Are2p is the major enzyme isoform in a wild-type cell growing aerobically. This likely results from a combination of differential transcription initiation and transcript stability. By using
ARE1
and
ARE2
promoter fusions to
lacZ
reporters, we demonstrated that transcriptional initiation from the
ARE1
promoter is significantly reduced compared to that from the
ARE2
promoter. Furthermore, the half-life of the
ARE2
mRNA is approximately 12 times as long as that of the
ARE1
transcript. We present evidence that the primary role of the minor sterol esterification isoform encoded by
ARE1
is to esterify sterol intermediates, whereas the role of the
ARE2
enzyme is to esterify ergosterol, the end product of the pathway. Accordingly, the
ARE1
promoter is upregulated in strains that accumulate ergosterol precursors. Furthermore,
ARE1
and
ARE2
are oppositely regulated by heme. Under heme-deficient growth conditions,
ARE1
was upregulated fivefold while
ARE2
was down-regulated.
ARE2
requires the
HAP1
transcription factor for optimal expression, and both
ARE
genes are derepressed in a
rox1
(repressor of oxygen) mutant genetic background. We further report that the
ARE
genes are not subject to end product inhibition; neither
ARE1
nor
ARE2
transcription is altered in an
are
mutant background, nor does overexpression of either
ARE
gene alter the response of the
ARE-lacZ
reporter constructs. Our observations are consistent with an important physiological role for Are1p during anaerobic growth when heme is limiting and sterol precursors may accumulate. Conversely, Are2p is optimally required during aerobiosis when ergosterol is plentiful.