bluuebunny/crossref_metadata_2025_split huggingface dataset:
Agrobacterium tumefaciens
C58 Uses ActR and FnrN To Control
nirK
and
nor
Expression
Authors: Baek Seung-Hun , Hartsock Angela , Shapleigh James P. 
Published: November 2007

ABSTRACT

Agrobacterium tumefaciens
can grow anaerobically via denitrification. To learn more about how cells regulate production of nitrite and nitric oxide, experiments were carried out to identify proteins involved in regulating expression and activity of nitrite and nitric oxide reductase. Transcription of NnrR, required for expression of these two reductases, was found to be under control of FnrN. Insertional inactivation of the response regulator
actR
significantly reduced
nirK
expression and Nir activity but not
nnrR
expression. Purified ActR bound to the
nirK
promoter but not the
nor
or
nnrR
promoter. A putative ActR binding site was identified in the
nirK
promoter region using mutational analysis and an in vitro binding assay. A
nirK
promoter containing mutations preventing the binding of ActR showed delayed expression but eventually reached about 65% of the activity of an equivalent wild-type promoter
lacZ
fusion. Truncation of the
nirK
promoter revealed that truncation up to and within the ActR binding site reduced expression, but fragments lacking the ActR binding site and retaining the NnrR binding site showed expression as high as or higher than the full-length fragment. Additional experiments revealed that expression of
paz
, encoding the copper protein pseudoazurin, was highly reduced in the
actR
or
fnrN
mutants and that ActR binds to the
paz
promoter. Inactivation of
paz
reduced Nir activity by 55%. These results help explain why Nir activity is very low in the
actR
mutant even though a
nirK
promoter with mutations in the ActR binding site showed significant expression.
Characterization of the Saframycin A Gene Cluster fromStreptomyces lavendulaeNRRL 11002 Revealing a Nonribosomal Peptide Synthetase System for Assembling the Unusual Tetrapeptidyl Skeleton in an Iterative Manner
Authors: Li Lei , Deng Wei , Song Jie , Ding Wei , Zhao Qun-Fei , Peng Chao , Song Wei-Wen , Tang Gong-Li , Liu Wen 
Published: November 2007

ABSTRACTSaframycin A (SFM-A), produced byStreptomyces lavendulaeNRRL 11002, belongs to the tetrahydroisoquinoline family of antibiotics, and its core is structurally similar to the core of ecteinascidin 743, which is a highly potent antitumor drug isolated from a marine tunicate. In this study, the biosynthetic gene cluster for SFM-A was cloned and localized to a 62-kb contiguous DNA region. Sequence analysis revealed 30 genes that constitute the SFM-A gene cluster, encoding an unusual nonribosomal peptide synthetase (NRPS) system and tailoring enzymes and regulatory and resistance proteins. The results of substrate prediction and in vitro characterization of the adenylation specificities of this NRPS system support the hypothesis that the last module acts in an iterative manner to form a tetrapeptidyl intermediate and that the colinearity rule does not apply. Although this mechanism is different from those proposed for the SFM-A analogs SFM-Mx1 and safracin B (SAC-B), based on the high similarity of these systems, it is likely they share a common mechanism of biosynthesis as we describe here. Construction of the biosynthetic pathway of SFM-Y3, an aminated SFM-A, was achieved in the SAC-B producer (Pseudomonas fluorescens). These findings not only shed new insight on tetrahydroisoquinoline biosynthesis but also demonstrate the feasibility of engineering microorganisms to generate structurally more complex and biologically more active analogs by combinatorial biosynthesis.
Autoinducer-2-Regulated Genes inStreptococcus mutansUA159 and Global Metabolic Effect of theluxSMutation
Authors: Sztajer Helena , Lemme André , Vilchez Ramiro , Schulz Stefan , Geffers Robert , Yip Cindy Ying Yin , Levesque Celine M. , Cvitkovitch Dennis G. , Wagner-Döbler Irene 
Published: November 2007

ABSTRACTAutoinducer 2 (AI-2) is the only species-nonspecific autoinducer known in bacteria and is produced by both gram-negative and gram-positive organisms. Consequently, it is proposed to function as a universal quorum-sensing signal for interaction between bacterial species. AI-2 is produced as the by-product of a metabolic transformation carried out by the LuxS enzyme. To separate the metabolic function of the LuxS enzyme from the signaling role of AI-2, we carried out a global transcriptome analysis of aluxSnull mutant culture ofStreptococcus mutansUA159, an important cariogenic bacterium and a crucial component of the dental plaque biofilm community, in comparison to aluxSnull mutant culture supplemented with chemically pure 4,5-dihydroxy-2,3-pentanedione, the precursor of AI-2. The data revealed fundamental changes in gene expression affecting 585 genes (30% of the genome) which could not be restored by the signal molecule AI-2 and are therefore not caused by quorum sensing but by lack of the transformation carried out by the LuxS enzyme in the activated methyl cycle. All functional classes of enzymes were affected, including genes known to be important for biofilm formation, bacteriocin synthesis, competence, and acid tolerance. At the same time, 59 genes were identified whose transcription clearly responded to the addition of AI-2. Some of them were related to protein synthesis, stress, and cell division. Three membrane transport proteins were upregulated which are not related to any of the known AI-2 transporters. Three transcription factors were identified whose transcription was stimulated repeatedly by AI-2 addition during growth. Finally, a global regulatory protein, the δ subunit of the RNA polymerase (rpoE), was induced 147-fold by AI-2, representing the largest differential gene expression observed. The data show that many phenotypes related to theluxSmutation cannot be ascribed to quorum sensing and have identified for the first time regulatory proteins potentially mediating AI-2-based signaling in gram-positive bacteria.
Protein-Protein Interactions within Type III Secretion System-Dependent Pili of
Rhizobium
sp. Strain NGR234
Authors: Saad Maged M. , Staehelin Christian , Broughton William J. , Deakin William J. 
Published: November 2007

ABSTRACT

Pili synthesized by the type III secretion system of
Rhizobium
species strain NGR234 are essential for protein secretion and thus for efficient symbiosis with many legumes. Isolation and partial purification of these pili showed that they are composed of at least three proteins, NopA, NopB, and NopX. Using biochemical assays, we show here that these proteins interact directly with one another.
Nisin-Triggered Activity of Lys44, the Secreted Endolysin from
Oenococcus oeni
Phage fOg44
Authors: Nascimento João Gil , Guerreiro-Pereira Maria Carolina , Costa Sérgio Fernandes , São-José Carlos , Santos Mário Almeida 
Published: November 2007

ABSTRACT

The intrinsic resistance of
Oenococcus oeni
cells to the secreted endolysin from oenophage fOg44 (Lys44) was investigated. Experiments with several antimicrobials support the hypothesis that the full activity of Lys44 requires sudden ion-nonspecific dissipation of the proton motive force, an event undertaken by the fOg44 holin in the phage infection context.
Clp-Dependent Proteolysis Down-Regulates Central Metabolic Pathways in Glucose-StarvedBacillus subtilis
Authors: Gerth Ulf , Kock Holger , Kusters Ilja , Michalik Stephan , Switzer Robert L. , Hecker Michael 
Published: November 2007

ABSTRACTEntry into stationary phase inBacillus subtilisis linked not only to a redirection of the gene expression program but also to posttranslational events such as protein degradation. Using35S-labeled methionine pulse-chase labeling and two-dimensional polyacrylamide gel electrophoresis we monitored the intracellular proteolysis pattern during glucose starvation. Approximately 200 protein spots diminished in the wild-type cells during an 8-h time course. The degradation rate of at least 80 proteins was significantly reduced inclpP,clpC, andclpXmutant strains. Enzymes of amino acid and nucleotide metabolism were overrepresented among these Clp substrate candidates. Notably, several first-committed-step enzymes for biosynthesis of aromatic and branched-chain amino acids, cell wall precursors, purines, and pyrimidines appeared as putative Clp substrates. Radioimmunoprecipitation demonstrated GlmS, IlvB, PurF, and PyrB to be novel ClpCP targets. Our data imply that Clp proteases down-regulate central metabolic pathways upon entry into a nongrowing state and thus contribute to the adaptation to nutrient starvation. Proteins that are obviously nonfunctional, unprotected, or even “unemployed” seem to be recognized and proteolyzed by Clp proteases when the resources for growth become limited.
Growth of
Streptococcus pneumoniae
on Human Glycoconjugates Is Dependent upon the Sequential Activity of Bacterial Exoglycosidases
Authors: Burnaugh Amanda M. , Frantz Laura J. , King Samantha J. 
Published: November 2007

ABSTRACT

In the human host,
Streptococcus pneumoniae
encounters a variety of glycoconjugates, including mucin, host defense molecules, and glycans associated with the epithelial surface.
S. pneumoniae
is known to encode a number of glycosidases that may modify these glycoconjugates in vivo. Three exoglycosidases, a neuraminidase (NanA), β-galactosidase (BgaA), and
N
-acetylglucosaminidase (StrH), have been previously demonstrated to sequentially deglycosylate N-linked glycans on host defense molecules, which coat the pneumococcal surface in vivo. This cleavage is proposed to alter the clearance function of these molecules, allowing pneumococci to persist in the airway. However, we propose that the exoglycosidase-dependent liberation of monosaccharides from these glycoconjugates in close proximity to the pneumococcal surface provides
S. pneumoniae
with a convenient source of fermentable carbohydrate in vivo. In this study, we demonstrate that
S. pneumoniae
is able to utilize complex N-linked human glycoconjugates as a sole source of carbon to sustain growth and that efficient growth is dependent upon the sequential deglycosylation of the glycoconjugate substrate by pneumococcal exoglycosidases. In addition to demonstrating a role for NanA, BgaA, and StrH, we have identified a function for the second pneumococcal neuraminidase, NanB, in the deglycosylation of host glycoconjugates and have demonstrated that NanB activity can partially compensate for the loss or dysfunction of NanA. To date, all known functions of pneumococcal neuraminidase have been attributed to NanA. Thus, this study describes the first proposed role for NanB by which it may contribute to
S. pneumoniae
colonization and pathogenesis.
Cell Wall Carbohydrate Compositions of Strains from the
Bacillus cereus
Group of Species Correlate with Phylogenetic Relatedness
Authors: Leoff Christine , Saile Elke , Sue David , Wilkins Patricia , Quinn Conrad P. , Carlson Russell W. , Kannenberg Elmar L. 
Published: November 2007

ABSTRACT

Members of the
Bacillus cereus
group contain cell wall carbohydrates that vary in their glycosyl compositions. Recent multilocus sequence typing (MLST) refined the relatedness of
B. cereus
group members by separating them into clades and lineages. Based on MLST, we selected several
B. anthracis
,
B. cereus
, and
B. thuringiensis
strains and compared their cell wall carbohydrates. The cell walls of different
B. anthracis
strains (clade 1/Anthracis) were composed of glucose (Glc), galactose (Gal),
N
-acetyl mannosamine (ManNAc), and
N
-acetylglucosamine (GlcNAc). In contrast, the cell walls from clade 2 strains (
B. cereus
type strain ATCC 14579 and
B. thuringiensis
strains) lacked Gal and contained
N
-acetylgalactosamine (GalNAc). The
B. cereus
clade 1 strains had cell walls that were similar in composition to
B. anthracis
in that they all contained Gal. However, the cell walls from some clade 1 strains also contained GalNAc, which was not present in
B. anthracis
cell walls. Three recently identified clade 1 strains of
B. cereus
that caused severe pneumonia, i.e., strains 03BB102, 03BB87, and G9241, had cell wall compositions that closely resembled those of the
B. anthracis
strains. It was also observed that
B. anthracis
strains cell wall glycosyl compositions differed from one another in a plasmid-dependent manner. When plasmid pXO2 was absent, the ManNAc/Gal ratio decreased, while the Glc/Gal ratio increased. Also, deletion of
atxA
, a global regulatory gene, from a pXO2
−
strain resulted in cell walls with an even greater level of Glc.
The NtrC Family Regulator AlgB, Which Controls Alginate Biosynthesis in MucoidPseudomonas aeruginosa, Binds Directly to thealgDPromoter
Authors: Leech Andrew J. , Sprinkle April , Wood Lynn , Wozniak Daniel J. , Ohman Dennis E. 
Published: November 2007

ABSTRACTAlginate production in mucoid (MucA-defective)Pseudomonas aeruginosais dependent upon several transcriptional regulators, including AlgB, a two-component response regulator belonging to the NtrC family. This role of AlgB was apparently independent of its sensor kinase, KinB, and even the N-terminal phosphorylation domain of AlgB was dispensable for alginate biosynthetic gene (i.e.,algDoperon) activation. However, it remained unclear whether AlgB stimulatedalgDtranscription directly or indirectly. In this study, microarray analyses were used to examine a set of potential AlgB-dependent, KinB-independent genes in a PAO1mucAbackground that overlapped with genes induced byd-cycloserine, which is known to activatealgDexpression. This set contained only thealgDoperon plus one other gene that was shown to be uninvolved in alginate production. This suggested that AlgB promotes alginate production by directly binding to thealgDpromoter (PalgD). Chromosome immunoprecipitation revealed that AlgB bound in vivo to PalgDbut did not bind when AlgB had an R442E substitution that disrupted the DNA binding domain. AlgB also showed binding to PalgDfragments in an electrophoretic mobility shift assay at pH 4.5 but not at pH 8.0. A direct systematic evolution of ligands by exponential enrichment approach showed AlgB binding to a 50-bp fragment located at bp −224 to −274 relative to the start of PalgDtranscription. Thus, AlgB belongs to a subclass of NtrC family proteins that can activate promoters which utilize a sigma factor other than σ54, in this case to stimulate transcription from the σ22-dependent PalgDpromoter.
A Mycobacterial
smc
Null Mutant Is Proficient in DNA Repair and Long-Term Survival
Authors: Güthlein Carolin , Wanner Roger M. , Sander Peter , Böttger Erik C. , Springer Burkhard 
Published: November 2007

ABSTRACT

SMC (structural maintenance of chromosomes) proteins play fundamental roles in various aspects of chromosome organization and dynamics, including repair of DNA damage. Mutant strains of
Mycobacterium smegmatis
and
Mycobacterium tuberculosis
defective in SMC were constructed. Surprisingly, inactivation of
smc
did not result in recognizable phenotypes in hallmark assays characteristic for the function of these genes. This is in contrast to data for
smc
null mutants in other species.
Enterobacterial Common Antigen Integrity Is a Checkpoint for Flagellar Biogenesis inSerratia marcescens
Authors: Castelli María E. , Fedrigo Griselda V. , Clementín Ana L. , Ielmini M. Verónica , Feldman Mario F. , Véscovi Eleonora García 
Published: November 2007

ABSTRACTSerratia marcescensstrains are ubiquitous bacteria isolated from environmental niches, such as soil, water, and air, and also constitute emergent nosocomial opportunistic pathogens. Among the numerous extracellular factors thatS. marcescensis able to produce, the PhlA phospholipase is the only described exoprotein secreted by the flagellar apparatus while simultaneously being a member of the flagellar regulon. To gain insight into the regulatory mechanism that couples PhlA and flagellar expression, we conducted a generalized insertional mutagenesis and screened for PhlA-deficient strains. We found that three independent mutations in theweccluster, which impaired the assembly of enterobacterial common antigen (ECA), provoked the inhibition of PhlA expression. Swimming and swarming assays showed that in these strains, motility was severely affected. Microscopic examination and flagellin immunodetection demonstrated that a strong defect in flagellum expression was responsible for the reduced motility in thewecmutant strains. Furthermore, we determined that in the ECA-defective strains, the transcriptional cascade that controls flagellar assembly was turned off due to the down-regulation offlhDCexpression. These findings provide a new perspective on the physiological role of the ECA, providing evidence that inS. marcescens, its biosynthesis conditions the expression of the flagellar regulon.
Dam Methyltransferase Is Required for Stable Lysogeny of the Shiga Toxin (Stx2)-Encoding Bacteriophage 933W of Enterohemorrhagic
Escherichia coli
O157:H7
Authors: Murphy Kenan C. , Ritchie Jennifer M. , Waldor Matthew K. , Løbner-Olesen Anders , Marinus M. G. 
Published: November 2007

ABSTRACT

Shiga toxin 2 (Stx2), one of the principal virulence factors of enterohemorrhagic
Escherichia coli
, is encoded by 933W, a lambda-like prophage. 933W prophage induction contributes to Stx2 production, and here, we provide evidence that Dam methyltransferase is essential for maintenance of 933W lysogeny. Our findings are consistent with the idea that the 933W prophage has a relatively low threshold for induction, which may promote Stx2 production during infection.
A Novel Caffeine Dehydrogenase in
Pseudomonas
sp. Strain CBB1 Oxidizes Caffeine to Trimethyluric Acid
Authors: Yu Chi Li , Kale Yogesh , Gopishetty Sridhar , Louie Tai Man , Subramanian Mani 
Published: November 2007

ABSTRACT

A unique heterotrimeric caffeine dehydrogenase was purified from
Pseudomonas
sp. strain CBB1. This enzyme oxidized caffeine to trimethyluric acid stoichiometrically and hydrolytically, without producing hydrogen peroxide. The enzyme was not NAD(P)
+
dependent; coenzyme Q
0
was the preferred electron acceptor. The enzyme was specific for caffeine and theobromine and showed no activity with xanthine.
The Amino Acid Valine Is Secreted in Continuous-Flow Bacterial Biofilms
Authors: Valle Jaione , Da Re Sandra , Schmid Solveig , Skurnik David , D'Ari Richard , Ghigo Jean-Marc 
Published: November 2007

ABSTRACTBiofilms are structured communities characterized by distinctive gene expression patterns and profound physiological changes compared to those of planktonic cultures. Here, we show that many gram-negative bacterial biofilms secrete high levels of a small-molecular-weight compound, which inhibits the growth of onlyEscherichia coliK-12 and a rare few other natural isolates. We demonstrate both genetically and biochemically that this molecule is the amino acid valine, and we provide evidence that valine production within biofilms results from metabolic changes occurring within high-density biofilm communities when carbon sources are not limiting. This finding identifies a natural environment in which bacteria can encounter high amounts of valine, and we propose that in-biofilm valine secretion may be the long-sought reason for widespread but unexplained valine resistance found in most enterobacteria. Our results experimentally validate the postulated production of metabolites that is characteristic of the conditions associated with some biofilm environments. The identification of such molecules may lead to new approaches for biofilm monitoring and control.
Carbon Catabolite Repression of Type IV Pilus-Dependent Gliding Motility in the Anaerobic Pathogen
Clostridium perfringens
Authors: Mendez Marcelo , Huang I-Hsiu , Ohtani Kaori , Grau Roberto , Shimizu Tohru , Sarker Mahfuzur R. 
Published: November 2007

ABSTRACT

Clostridium perfringens
is an anaerobic, gram-positive, spore-forming bacterium responsible for the production of severe histotoxic and gastrointestinal diseases in humans and animals. In silico analysis of the three available genome-sequenced
C. perfringens
strains (13, SM101, and ATCC13124) revealed that genes that encode flagellar proteins and genes involved in chemotaxis are absent. However, those strains exhibit type IV pilus (TFP)-dependent gliding motility. Since carbon catabolite regulation has been implicated in the control of different bacterial behaviors, we investigated the effects of glucose and other readily metabolized carbohydrates on
C. perfringens
gliding motility. Our results demonstrate that carbon catabolite regulation constitutes an important physiological regulatory mechanism that reduces the proficiencies of the gliding motilities of a large number of unrelated human- and animal-derived pathogenic
C. perfringens
strains. Glucose produces a strong dose-dependent inhibition of gliding development without affecting vegetative growth. Maximum gliding inhibition was observed at a glucose concentration (1%) previously reported to also inhibit other important behaviors in
C. perfringens
, such as spore development. The inhibition of gliding development in the presence of glucose was due, at least in part, to the repression of the genes
pilT
and
pilD
, whose products are essential for TFP-dependent gliding proficiency. The inhibitory effects of glucose on
pilT
and
pilD
expression were under the control of the key regulatory protein CcpA (
c
atabolite
c
ontrol
p
rotein A). The deficiency in CcpA activity of a
ccpA
knockout
C. perfringens
mutant strain restored the expressions of
pilT
and
pilD
and gliding proficiency in the presence of 1% glucose. The carbon catabolite repression of the gliding motility of the
ccpA
mutant strain was restored after the introduction of a complementing plasmid harboring a wild-type copy of
ccpA
. These results point to a central role for CcpA in orchestrating the negative effect of carbon catabolite regulation on
C. perfringens
gliding motility. Furthermore, we discovered a novel positive role for CcpA in
pilT
and
pilD
expression and gliding proficiency in the absence of catabolite regulation. Carbon catabolite repression of gliding motility and the dual role of CcpA, either as repressor or as activator of gliding, are analyzed in the context of the different social behaviors and diseases produced by
C. perfringens
.
A Novel Role for Enzyme I of the
Vibrio cholerae
Phosphoenolpyruvate Phosphotransferase System in Regulation of Growth in a Biofilm
Authors: Houot Laetitia , Watnick Paula I. 
Published: November 2007

ABSTRACT

Glucose is a universal energy source and a potent inducer of surface colonization for many microbial species. Highly efficient sugar assimilation pathways ensure successful competition for this preferred carbon source. One such pathway is the phosphoenolpyruvate phosphotransferase system (PTS), a multicomponent sugar transport system that phosphorylates the sugar as it enters the cell. Components required for transport of glucose through the PTS include enzyme I, histidine protein, enzyme IIA
Glc
, and enzyme IIBC
Glc
. In
Escherichia coli
, components of the PTS fulfill many regulatory roles, including regulation of nutrient scavenging and catabolism, chemotaxis, glycogen utilization, catabolite repression, and inducer exclusion. We previously observed that genes encoding the components of the
Vibrio cholerae
PTS were coregulated with the
vps
genes, which are required for synthesis of the biofilm matrix exopolysaccharide. In this work, we identify the PTS components required for transport of glucose and investigate the role of each of these components in regulation of biofilm formation. Our results establish a novel role for the phosphorylated form of enzyme I in specific regulation of biofilm-associated growth. As the PTS is highly conserved among bacteria, the enzyme I regulatory pathway may be relevant to a number of biofilm-based infections.