bluuebunny/crossref_metadata_2025_split huggingface dataset:
Deficiency of aSinorhizobium meliloti bacAMutant in Alfalfa Symbiosis Correlates with Alteration of the Cell Envelope
Authors: Ferguson Gail P. , Roop R. Martin , Walker Graham C. 
Published: September 2002

ABSTRACTThe BacA protein is essential for the long-term survival ofSinorhizobium melilotiandBrucella abortuswithin acidic compartments in plant and animal cells, respectively. Since both theS. melilotiandB. abortus bacAmutants have an increased resistance to bleomycin, it was hypothesized that BacA was a transporter of bleomycin and bleomycin-like compounds into the bacterial cell. However, our finding that theS. meliloti bacAmutant also has an increased sensitivity to detergents, a hydrophobic dye, ethanol, and acid pH supported a model in which BacA function affects the bacterial cell envelope. In addition, anS. meliloti lpsBmutant that is defective at a stage in infection of the host similar to that found for abacAmutant is also sensitive to the same agents, and the carbohydrate content of its lipopolysaccharide (LPS) is altered. However, analysis of crude preparations of thebacAmutant LPS suggested that, unlike that for LpsB, BacA function did not affect the carbohydrate composition of the LPS. Rather, we found that at least one function of BacA is to affect the distribution of LPS fatty acids, including a very-long-chain fatty acid thought to be unique to the α-proteobacteria, includingB. abortus.
Divergent Structure and Regulatory Mechanism of Proline Catabolic Systems: Characterization of the
putAP
Proline Catabolic Operon of
Pseudomonas aeruginosa
PAO1 and Its Regulation by PruR, an AraC/XylS Family Protein
Authors: Nakada Yuji , Nishijyo Takayuki , Itoh Yoshifumi 
Published: September 2002

ABSTRACT

Pseudomonas aeruginosa
PAO1 utilizes proline as the sole source of carbon and nitrogen via a bifunctional enzyme (the
putA
gene product) that has both proline dehydrogenase (EC 1.5.99.8) and pyrroline 5-carboxylate dehydrogenase (EC 1.5.1.12) activities. We characterized the
pruR-putAP
loci encoding the proline catabolic system of this strain. In contrast to the
putA
and
putP
(encoding proline permease) genes of other gram- negative bacteria, which are located at divergent or separate loci, Northern blotting demonstrated that the two genes form an operon in strain PAO1. While the phylogenetic lineage of the PutP protein of strain PAO1 was related to that of the origin (80% identity to the
P. putida
counterpart), PutA of PAO1 (PutA
PAO
) was rather distantly related (47% identity) to the
P. putida
counterpart. Moreover, unlike the PutA proteins of
P. putida
and enteric bacteria, PutA
PAO
appeared to lack a regulatory function. Upstream of the
putAP
operon, the divergent PA0781 gene specified a hypothetical outer membrane protein with a molecular weight of 74,202. This gene appeared to be dispensable for proline utilization as indicated by the normal growth of a knockout mutant of PA0781 on medium containing proline. The
pruR
(proline utilization regulator) gene immediately upstream of PA0781 encoded a transcriptional activator of the AraC/XylS protein family and mediated the proline-responsive expression of
putAP.
Primer extension studies identified a PruR-dependent promoter responsive to proline in the 5′-flanking region of
putA.
Thus, the proline utilization system of
P. aeruginosa
differs from that of
P. putida
with respect to
putA
structure, the organization of the
putAP
genes, and the regulatory mechanism of
putA
expression.
Adaptive, or Stationary-Phase, Mutagenesis, a Component of Bacterial Differentiation in
Bacillus subtilis
Authors: Sung Huang-Mo , Yasbin Ronald E. 
Published: September 2002

ABSTRACT

Adaptive (stationary-phase) mutagenesis occurs in the gram-positive bacterium
Bacillus subtilis
. Furthermore, taking advantage of
B. subtilis
as a paradigm for the study of prokaryotic differentiation and development, we have shown that this type of mutagenesis is subject to regulation involving at least two of the genes that are involved in the regulation of post-exponential phase prokaryotic differentiation, i.e.,
comA
and
comK
. On the other hand, a functional RecA protein was not required for this type of mutagenesis. The results seem to suggest that a small subpopulation(s) of the culture is involved in adaptive mutagenesis and that this subpopulation(s) is hypermutable. The existence of such a hypermutable subpopulation(s) raises important considerations with respect to evolution, the development of specific mutations, the nature of bacterial populations, and the level of communication among bacteria in an ecological niche.
A CheW Homologue Is Required for
Myxococcus xanthus
Fruiting Body Development, Social Gliding Motility, and Fibril Biogenesis
Authors: Bellenger Kristen , Ma Xiaoyuan , Shi Wenyuan , Yang Zhaomin 
Published: September 2002

ABSTRACT

In bacteria with multiple sets of chemotaxis genes, the deletion of homologous genes or even different genes in the same operon can result in disparate phenotypes.
Myxococcus xanthus
is a bacterium with multiple sets of chemotaxis genes and/or homologues. It was shown previously that
difA
and
difE
, encoding homologues of the methyl-accepting chemoreceptor protein (MCP) and the CheA kinase, respectively, are required for
M. xanthus
social gliding (S) motility and development. Both
difA
and
difE
mutants were also defective in the biogenesis of the cell surface appendages known as extracellular matrix fibrils. In this study, we investigated the roles of the CheW homologue encoded by
difC
, a gene at the same locus as
difA
and
difE
. We showed that
difC
mutations resulted in defects in
M. xanthus
developmental aggregation, sporulation, and S motility. We demonstrated that
difC
is indispensable for wild-type cellular cohesion and fibril biogenesis but not for pilus production. We further illustrated the ectopic complementation of a
difC
in-frame deletion by a wild-type
difC
. The identical phenotypes of
difA
,
difC
, and
difE
mutants are consistent and supportive of the hypothesis that the Dif chemotaxis homologues constitute a chemotaxis-like signal transduction pathway that regulates
M. xanthus
fibril biogenesis and S motility.
A Novel Class of Heat and Secretion Stress-Responsive Genes Is Controlled by the Autoregulated CssRS Two-Component System ofBacillus subtilis
Authors: Darmon Elise , Noone David , Masson Anne , Bron Sierd , Kuipers Oscar P. , Devine Kevin M. , Dijl Jan Maarten van 
Published: September 2002

ABSTRACTBacteria need dedicated systems that allow appropriate adaptation to the perpetual changes in their environments. InBacillus subtilis, two HtrA-like proteases, HtrA and HtrB, play critical roles in the cellular response to secretion and heat stresses. Transcription of these genes is induced by the high-level production of a secreted protein or by a temperature upshift. The CssR-CssS two-component regulatory system plays an essential role in this transcriptional activation. Transcription of thecssRSoperon is autoregulated and can be induced by secretion stress, by the absence of either HtrA or HtrB, and by heat stress in a HtrA null mutant strain. Two start sites are used forcssRStranscription, only one of which is responsive to heat and secretion stress. The divergently transcribedhtrBandcssRSgenes share a regulatory region through which their secretion and heat stress-induced expression is linked. This study shows that CssRS-regulated genes represent a novel class of heat-inducible genes, which is referred to as class V and currently includes two genes:htrAandhtrB.
Expression of the
Azotobacter vinelandii
Poly-β-Hydroxybutyrate Biosynthetic
phbBAC
Operon Is Driven by Two Overlapping Promoters and Is Dependent on the Transcriptional Activator PhbR
Authors: Peralta-Gil Martín , Segura Daniel , Guzmán Josefina , Servín-González Luis , Espín Guadalupe 
Published: September 2002

ABSTRACT

The
Azotobacter vinelandii phbBAC
genes encode the enzymes for poly-β-hydroxybutyrate (PHB) synthesis. The
phbR
gene, which is located upstream of and in the opposite direction of
phbBAC
, encodes PhbR, a transcriptional activator which is a member of the AraC family of activators. Here we report that a mutation in
phbR
reduced PHB accumulation and transcription of a
phbB
-
lacZ
fusion. We also report that
phbB
is transcribed from two overlapping promoters, p
B
1 and p
B
2. The region corresponding to the −35 region of p
B
1 overlaps the p
B
2 −10 region. In the
phbR
mutant, expression of
phbB
from the p
B
1 promoter is significantly reduced, whereas expression from the p
B
2 promoter is slightly increased. Two
phbR
promoters, p
R
1 and p
R
2, were also identified. Transcription from p
R
2 was shown to be dependent on σ
S
. Six conserved 18-bp sites, designated R1 to R6, are present within the
phbR-phbB
intergenic region and are proposed to be putative binding targets for PhbR. R1 overlaps the −35 region of the p
B
1 promoter. A model for the regulation of
phbB
transcription by PhbR is proposed.
Biofilm Formation and Acyl Homoserine Lactone Production in the
Burkholderia cepacia
Complex
Authors: Conway Barbara-Ann D. , Venu Vicnays , Speert David P. 
Published: September 2002

ABSTRACT

Acyl homoserine lactone (acyl-HSL)-mediated gene regulation has been shown to influence biofilm formation in one
Burkholderia cepacia
cystic fibrosis isolate, but it is not known whether this relationship is a consistent feature of the several genomic species that make up the
B. cepacia
complex (BCC). We screened strains belonging to genomovars I to V of the BCC for biofilm formation on an abiotic surface and for acyl-HSL synthesis. We determined that organisms from each of these genomovars were capable of biofilm formation. Similarly, acyl-HSL was synthesized by organisms from each of genomovars I to V, with most isolates producing octanoyl-HSL in greatest abundance. When biofilms were grown in Luria broth, acyl-HSL synthesis and biofilm formation appeared to be associated, but these phenotypes were independent when the biofilms were grown in basal salts containing citrate. Genomovar V strains synthesized the greatest quantities of acyl-HSL, and genomovar II and III-A strains elaborated the most abundant biofilms. Quorum sensing may play a role in BCC pathogenesis, but it may not regulate biofilm formation under all growth conditions.
Characterization of theSinorhizobium meliloti sinR/sinILocus and the Production of NovelN-Acyl Homoserine Lactones
Authors: Marketon Melanie M. , Gronquist Matthew R. , Eberhard Anatol , González Juan E. 
Published: September 2002

ABSTRACTSinorhizobium melilotiis a soil bacterium which can establish a nitrogen-fixing symbiosis with the legumeMedicago sativa. Recent work has identified a pair of genes,sinRandsinI, which represent a potential quorum-sensing system and are responsible for the production ofN-acyl homoserine lactones (AHLs) in twoS. melilotistrains, Rm1021 and Rm41. In this work, we characterize thesinRIlocus and show that these genes are responsible for the synthesis of several long-chain AHLs ranging from 12 to 18 carbons in length. Four of these, 3-oxotetradecanoyl HL, 3-oxohexadecenoyl HL, hexadecenoyl HL, and octadecanoyl HL, have novel structures. This is the first report of AHLs having acyl chains longer than 14 carbons. We show that a disruption insinIeliminates these AHLs and that asinRdisruption results in only basal levels of the AHLs. Moreover, the samesinIandsinRmutations also lead to a decrease in the number of pink nodules during nodulation assays, as well as a slight delay in the appearance of pink nodules, indicating a role for quorum sensing in symbiosis. We also show thatsinIandsinRmutants are still capable of producing several short-chain AHLs, one of which was identified as octanoyl HL. We believe that these short-chain AHLs are evidence of a second quorum-sensing system in Rm1021, which we refer to here as themelsystem, for “S. meliloti.”
YfcX Enables Medium-Chain-Length Poly(3-Hydroxyalkanoate) Formation from Fatty Acids in Recombinant
Escherichia coli fadB
Strains
Authors: Snell Kristi D. , Feng Feng , Zhong Luhua , Martin David , Madison Lara L. 
Published: September 2002

ABSTRACT

Expression of
Escherichia coli
open reading frame
yfcX
is shown to be required for medium-chain-length polyhydroxyalkanoate (PHA
MCL
) formation from fatty acids in an
E. coli fadB
mutant. The open reading frame encodes a protein, YfcX, with significant similarity to the large subunit of multifunctional β-oxidation enzymes.
E. coli fadB
strains modified to contain an inactivated copy of
yfcX
and to express a medium-chain-length synthase are unable to form PHA
MCL
s when grown in the presence of fatty acids. Plasmid-based expression of
yfcX
in the FadB
−
YfcX
−
PhaC
+
strain restores polymer formation. YfcX is shown to be a multifunctional enzyme that minimally encodes hydratase and dehydrogenase activities. The gene encoding YfcX is located downstream from
yfcY
, a gene encoding thiolase activity. Results of insertional inactivation studies and enzyme activity analyses suggest a role for
yfcX
in PHA monomer unit formation in recombinant
E. coli fadB
mutant strains. Further studies are required to determine the natural role of YfcX in the metabolism of
E. coli
.
Genes Encoding Specific Nickel Transport Systems Flank the Chromosomal Urease Locus of Pathogenic Yersiniae
Authors: Sebbane Florent , Mandrand-Berthelot Marie-Andrée , Simonet Michel 
Published: September 2002

ABSTRACT

The transition metal nickel is an essential cofactor for a number of bacterial enzymes, one of which is urease. Prior to its incorporation into metalloenzyme active sites, nickel must be imported into the cell. Here, we report identification of two loci corresponding to nickel-specific transport systems in the gram-negative, ureolytic bacterium
Yersinia pseudotuberculosis
. The loci are located on each side of the chromosomal urease gene cluster
ureABCEFGD
and have the same orientation as the latter. The
yntABCDE
locus upstream of the
ure
genes encodes five predicted products with sequence homology to ATP-binding cassette nickel permeases present in several gram-negative bacteria. The
ureH
gene, located downstream of
ure
, encodes a single-component carrier which displays homology to polypeptides of the nickel-cobalt transporter family. Transporters with homology to these two classes are also present (again in proximity to the urease locus) in the other two pathogenic yersiniae,
Y. pestis
and
Y. enterocolitica
. An
Escherichia coli nikA
insertion mutant recovered nickel uptake ability following heterologous complementation with either the
ynt
or the
ureH
plasmid-borne gene of
Y. pseudotuberculosis
, demonstrating that each carrier is necessary and sufficient for nickel transport. Deletion of
ynt
in
Y. pseudotuberculosis
almost completely abolished bacterial urease activity, whereas deletion of
ureH
had no effect. Nevertheless, rates of nickel transport were significantly altered in both
ynt
and
ureH
mutants. Furthermore, the
ynt ureH
double mutant was totally devoid of nickel uptake ability, thus indicating that Ynt and UreH constitute the only routes for nickel entry. Both Ynt and UreH show selectivity for Ni
2+
ions. This is the first reported identification of genes coding for both kinds of nickel-specific permeases situated adjacent to the urease gene cluster in the genome of a microorganism.
Differential Expression of Two Catechol 1,2-Dioxygenases in
Burkholderia
sp. Strain TH2
Authors: Suzuki Katsuhisa , Ichimura Atsushi , Ogawa Naoto , Hasebe Akira , Miyashita Kiyotaka 
Published: September 2002

ABSTRACT

Burkholderia
sp. strain TH2, a 2-chlorobenzoate (2CB)-degrading bacterium, metabolizes benzoate (BA) and 2CB via catechol. Two different gene clusters for the catechol
ortho
-cleavage pathway (
cat1
and
cat2
) were cloned from TH2 and analyzed. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis and Western blot analysis showed that while both catechol dioxygenases (CatA1 and CatA2) were produced in BA-grown cells, CatA1 was undetectable when strain TH2 was grown on 2CB or
cis
,
cis
-muconate (CCM), an intermediate of catechol degradation. However, production of CatA1 during growth on 2CB or CCM was observed when
cat
2 genes were disrupted. The difference in the production of CatA1 and CatA2 was apparently due to a difference in inducer recognition by the regulators of the gene clusters. The inducer of CatA1 was found to be BA, not 2CB, by using a 2-halobenzoate dioxygenase gene (
cbd
) disruptant, which is incapable of transforming (chloro)benzoate. It was also found that CCM or its metabolite acts as an inducer for CatA2. When
cat2
genes were disrupted, the growth rate in 2CB culture was reduced while that in BA culture was not. These results suggest that although
cat2
genes are not indispensable for growth of TH2 on 2CB, they are advantageous.
Construction and Characterization of Transposon Insertion Mutations inCorynebacterium diphtheriaeThat Affect Expression of the Diphtheria Toxin Repressor (DtxR)
Authors: Oram Diana Marra , Avdalovic Ana , Holmes Randall K. 
Published: September 2002

ABSTRACTTranscription of the bacteriophage-borne diphtheria toxin genetoxis negatively regulated, in response to intracellular Fe2+concentration, by the chromosomally encoded diphtheria toxin repressor (DtxR). Due to a scarcity of tools, genetic analysis ofCorynebacterium diphtheriaehas primarily relied on analysis of chemically induced and spontaneously occurring mutants and on the results of experiments withC. diphtheriaegenes cloned inEscherichia colior analyzed in vitro. We modified a Tn5-based mutagenesis technique for use withC. diphtheriae, and we used it to construct the first transposon insertion libraries in the chromosome of this gram-positive pathogen. We isolated two insertions that affected expression of DtxR, one 121 bp upstream ofdtxRand the other within an essential region of thedtxRcoding sequence, indicating for the first time thatdtxRis a dispensable gene inC. diphtheriae. Both mutant strains secrete diphtheria toxin when grown in medium containing sufficient iron to repress secretion of diphtheria toxin by wild-typeC. diphtheriae. The upstream insertion mutant still produces DtxR in decreased amounts and regulates siderophore secretion in response to iron in a manner similar to its wild-type parent. The mutant containing the transposon insertion withindtxRdoes not produce DtxR and overproduces siderophore in the presence of iron. Differences in the ability of the two mutant strains to survive oxidative stress also indicated that the upstream insertion retained slight DtxR activity, whereas the insertion withindtxRabolished DtxR activity. This is the first evidence that DtxR plays a role in protecting the cell from oxidative stress.
Correlations between Shine-Dalgarno Sequences and Gene Features Such as Predicted Expression Levels and Operon Structures
Authors: Ma Jiong , Campbell Allan , Karlin Samuel 
Published: September 2002

ABSTRACTThis work assesses relationships for 30 complete prokaryotic genomes between the presence of the Shine-Dalgarno (SD) sequence and other gene features, including expression levels, type of start codon, and distance between successive genes. A significant positive correlation of the presence of an SD sequence and the predicted expression level of a gene based on codon usage biases was ascertained, such that predicted highly expressed genes are more likely to possess a strong SD sequence than average genes. Genes with AUG start codons are more likely than genes with other start codons, GUG or UUG, to possess an SD sequence. Genes in close proximity to upstream genes on the same coding strand in most genomes are significantly higher in SD presence. In light of these results, we discuss the role of the SD sequence in translation initiation and its relationship with predicted gene expression levels and with operon structure in both bacterial and archaeal genomes.
The
Streptomyces
Genome Contains Multiple Pseudo-
attB
Sites for the φC31-Encoded Site-Specific Recombination System
Authors: Combes Patricia , Till Rob , Bee Sally , Smith Margaret C. M. 
Published: September 2002

ABSTRACT

The integrase from the
Streptomyces
phage φC31 is a member of the serine recombinase family of site-specific recombinases and is fundamentally different from that of λ or its relatives. Moreover, φC31
int
/
attP
is used widely as an essential component of integration vectors (such as pSET152) employed in the genetic analysis of
Streptomyces
species. φC31 or integrating plasmids containing
int
/
attP
have been shown previously to integrate at a locus,
attB
, in the chromosome. The DNA sequences of the
attB
sites of various
Streptomyces
species revealed nonconserved positions. In particular, the crossover site was narrowed to the sequence 5′TT present in both
attP
and
attB
. Strains of
Streptomyces coelicolor
and
S. lividans
were constructed with a deletion of the
attB
site (Δ
attB
), and pSET152 was introduced into these strains by conjugation. Thus, secondary or pseudo-
attB
sites were identified by Southern blotting and after rescue of plasmids containing DNA flanking the insertion sites from the chromosome. The sequences of the integration sites had similarity to those of
attB
. Analysis of the insertions of pSET152 into both

attB
+

and Δ
attB
strains indicated that this plasmid can integrate at several loci via independent recombination events within a transconjugant.
Molecular Characterization of DSR-E, an α-1,2 Linkage-Synthesizing Dextransucrase with Two Catalytic Domains
Authors: Bozonnet Sophie , Dols-Laffargue Marguerite , Fabre Emeline , Pizzut Sandra , Remaud-Simeon Magali , Monsan Pierre , Willemot René-Marc 
Published: September 2002

ABSTRACTA novelLeuconostoc mesenteroidesNRRL B-1299 dextransucrase gene,dsrE, was isolated, sequenced, and cloned inEscherichia coli, and the recombinant enzyme was shown to be an original glucansucrase which catalyses the synthesis of α-1,6 and α-1,2 linkages. The nucleotide sequence of thedsrEgene consists of an open reading frame of 8,508 bp coding for a 2,835-amino-acid protein with a molecular mass of 313,267 Da. This is twice the average mass of the glucosyltransferases (GTFs) known so far, which is consistent with the presence of an additional catalytic domain located at the carboxy terminus of the protein and of a central glucan-binding domain, which is also significantly longer than in other glucansucrases. From sequence comparison with family 70 and α-amylase enzymes, crucial amino acids involved in the catalytic mechanism were identified, and several original sequences located at some highly conserved regions in GTFs were observed in the second catalytic domain.
Escherichia coli
DegP Protease Cleaves between Paired Hydrophobic Residues in a Natural Substrate: the PapA Pilin
Authors: Jones C. Hal , Dexter Paul , Evans Amy K. , Liu Christopher , Hultgren Scott J. , Hruby Dennis E. 
Published: September 2002

ABSTRACT

The DegP protein, a multifunctional chaperone and protease, is essential for clearance of denatured or aggregated proteins from the inner-membrane and periplasmic space in
Escherichia coli.
To date, four natural targets for DegP have been described: colicin A lysis protein, pilin subunits and MalS from
E. coli
, and high-molecular-weight adherence proteins from
Haemophilus influenzae.
In vitro, DegP has shown weak protease activity with casein and several other nonnative substrates. We report here the identification of the major pilin subunit of the Pap pilus, PapA, as a natural DegP substrate and demonstrate binding and proteolysis of this substrate in vitro. Using overlapping peptide arrays, we identified three regions in PapA that are preferentially cleaved by DegP. A 7-mer peptide was found to be a suitable substrate for cleavage by DegP in vitro. In vitro proteolysis of model peptide substrates revealed that cleavage is dependent upon the presence of paired hydrophobic amino acids; moreover, cleavage was found to occur between the hydrophobic residues. Finally, we demonstrate that the conserved carboxyl-terminal sequence in pilin subunits, although not a cleavage substrate for DegP, activates the protease and we propose that the activating peptide is recognized by DegP's PDZ domains.