bluuebunny/crossref_metadata_2025_split huggingface dataset:
Characterization of CprK1, a CRP/FNR-Type Transcriptional Regulator of Halorespiration from
Desulfitobacterium hafniense
Authors: Gábor Krisztina , Veríssimo Carla S. , Cyran Barbara C. , ter Horst Paul , Meijer Nienke P. , Smidt Hauke , de Vos Willem M. , van der Oost John 
Published: March 2006

ABSTRACT

The recently identified CprK branch of the CRP (cyclic AMP receptor protein)-FNR (fumarate and nitrate reduction regulator) family of transcriptional regulators includes proteins that activate the transcription of genes encoding proteins involved in reductive dehalogenation of chlorinated aromatic compounds. Here we report the characterization of the CprK1 protein from
Desulfitobacterium hafniense
, an anaerobic low-G+C gram-positive bacterium that is capable of reductive dechlorination of 3-chloro-4-hydroxyphenylacetic acid (Cl-OHPA). The gene encoding CprK1 was cloned and functionally overexpressed in
Escherichia coli
, and the protein was subsequently purified to homogeneity. To investigate the interaction of CprK1 with three of its predicted binding sequences (dehaloboxes), we performed in vitro DNA-binding assays (electrophoretic mobility shift assays) as well as in vivo promoter probe assays. Our results show that CprK1 binds its target dehaloboxes with high affinity (dissociation constant, 90 nM) in the presence of Cl-OHPA and that transcriptional initiation by CprK1 is influenced by deviations in the dehaloboxes from the consensus TTAAT----ATTAA sequence. A mutant CprK1 protein was created by a Val→Glu substitution at a conserved position in the recognition α-helix that gained FNR-type DNA-binding specificity, recognizing the TTGAT----ATCAA sequence (FNR box) instead of the dehaloboxes. CprK1 was subject to oxidative inactivation in vitro, most likely caused by the formation of an intermolecular disulfide bridge between Cys11 and Cys200. The possibility of redox regulation of CprK1 by a thiol-disulfide exchange reaction was investigated by using two Cys→Ser mutants. Our results indicate that a Cys11-Cys200 disulfide bridge does not appear to play a physiological role in the regulation of CprK1.
Transcriptional Analysis of the
cip-cel
Gene Cluster from
Clostridium cellulolyticum
Authors: Maamar Hédia , Abdou Laetitia , Boileau Céline , Valette Odile , Tardif Chantal 
Published: March 2006

ABSTRACT

Twelve genes encoding key components of
Clostridium cellulolyticum
cellulosomes are clustered. Among them, the first, second, and fifth genes encode the assembly factor CipC and the two major cellulases Cel48F and Cel9E, respectively. Cellulolytic clones were selected from the noncellulolytic
cipC
insertional mutant
trans
-complemented with a
cipC
expression vector, in which one homologous recombination event between the 3′ end of the chromosomal
cipC
gene and the plasmidic
cipC
gene has restored the cluster continuity. The absence of the enzymes encoded by the cluster in the
cipC
mutant was thus only due to a strong polar effect, indicating that all genes were transcriptionally linked. Two large transcripts were detected in cellulose-grown cells by Northern hybridization: a 14-kb messenger which carries the
cipC-cel48F-cel8C-cel9G-cel9E
coding sequences and, in a smaller amount, a 12-kb messenger which carries the genes located in the 3′ part of the cluster. Four smaller transcripts were found in large amounts: a
cipC-cel48F
bicistronic one and three monocistronic ones,
cipC
,
cel48F
, and
cel9E
. The
cipC-cel48F
and
cel48F
messengers were shown to be stable. Analysis by reverse transcription-PCR suggested transcriptional linkage of all of the open reading frames. The production of a primary very large transcript covering the entire cluster was hypothesized. Primer extension analysis has identified two putative transcriptional start sites located 638/637 and 194 nucleotides upstream of the
cipC
translational start. The processing of the primary transcript would lead to the production of several secondary messengers displaying different stabilities, contributing to fine tuning of expression of individual genes of the operon.
Three New Regulators of Swarming inVibrio parahaemolyticus
Authors: Jaques Sandford , McCarter Linda L. 
Published: March 2006

ABSTRACTMovement on surfaces, or swarming motility, is effectively mediated by the lateral flagellar (laf) system inVibrio parahaemolyticus. Expression oflafis induced by conditions inhibiting rotation of the polar flagellum, which is used for swimming in liquid. However, not allV. parahaemolyticusisolates swarm proficiently. The organism undergoes phase variation between opaque (OP) and translucent (TR) cell types. The OP cell produces copious capsular polysaccharide and swarms poorly, whereas the TR type produces minimal capsule and swarms readily. OP↔TR switching is often the result of genetic alterations in theopaRlocus. Previously, OpaR, aVibrio harveyiLuxR homolog, was shown to activate expression of thecpsAlocus, encoding capsular polysaccharide biosynthetic genes. Here, we show that OpaR also regulates swarming by repressinglafgene expression. However, in the absence of OpaR, the swarming phenotype remains tightly surface regulated. To further investigate the genetic controls governing swarming, transposon mutagenesis of a TR (ΔopaR1) strain was performed, and SwrT, a TetR-type regulator, was identified. Loss ofswrT, a homolog ofV. harveyi luxT, created a profound defect in swarming. This defect could be rescued upon isolation of suppressor mutations that restored swarming. One class of suppressors mapped inswrZ, encoding a GntR-type transcriptional regulator. Overexpression ofswrZrepressedlafexpression. Using reporter fusions and quantitative reverse transcription-PCR, SwrT was demonstrated to repressswrZtranscription. Thus, we have identified the regulatory link that inhibits swarming of OP strains and have begun to elucidate a regulatory circuit that modulates swarming in TR strains.
Properties of Succinyl-Coenzyme A:
l
-Malate Coenzyme A Transferase and Its Role in the Autotrophic 3-Hydroxypropionate Cycle of
Chloroflexus aurantiacus
Authors: Friedmann Silke , Steindorf Astrid , Alber Birgit E. , Fuchs Georg 
Published: March 2006

ABSTRACT

The 3-hydroxypropionate cycle has been proposed to operate as the autotrophic CO
2
fixation pathway in the phototrophic bacterium
Chloroflexus aurantiacus
. In this pathway, acetyl coenzyme A (acetyl-CoA) and two bicarbonate molecules are converted to malate. Acetyl-CoA is regenerated from malyl-CoA by
l
-malyl-CoA lyase. The enzyme forming malyl-CoA, succinyl-CoA:
l
-malate coenzyme A transferase, was purified. Based on the N-terminal amino acid sequence of its two subunits, the corresponding genes were identified on a gene cluster which also contains the gene for
l
-malyl-CoA lyase, the subsequent enzyme in the pathway. Both enzymes were severalfold up-regulated under autotrophic conditions, which is in line with their proposed function in CO
2
fixation. The two CoA transferase genes were cloned and heterologously expressed in
Escherichia coli
, and the recombinant enzyme was purified and studied. Succinyl-CoA:
l
-malate CoA transferase forms a large (αβ)
n
complex consisting of 46- and 44-kDa subunits and catalyzes the reversible reaction succinyl-CoA +
l
-malate → succinate +
l
-malyl-CoA. It is specific for succinyl-CoA as the CoA donor but accepts
l
-citramalate instead of
l
-malate as the CoA acceptor; the corresponding
d
-stereoisomers are not accepted. The enzyme is a member of the class III of the CoA transferase family. The demonstration of the missing CoA transferase closes the last gap in the proposed 3-hydroxypropionate cycle.
The
Helicobacter pylori
Chemotaxis Receptor TlpB (HP0103) Is Required for pH Taxis and for Colonization of the Gastric Mucosa
Authors: Croxen Matthew A. , Sisson Gary , Melano Roberto , Hoffman Paul S. 
Published: March 2006

ABSTRACT

The location of
Helicobacter pylori
in the gastric mucosa of mammals is defined by natural pH gradients within the gastric mucus, which are more alkaline proximal to the mucosal epithelial cells and more acidic toward the lumen. We have used a microscope slide-based pH gradient assay and video data collection system to document pH-tactic behavior. In response to hydrochloric acid (HCl),
H. pylori
changes its swimming pattern from straight-line random swimming to arcing or circular patterns that move the motile population away from the strong acid. Bacteria in more-alkaline regions did not swim toward the acid, suggesting the pH taxis is a form of negative chemotaxis. To identify the chemoreceptor(s) responsible for the transduction of pH-tactic signals, a vector-free allelic replacement strategy was used to construct mutations in each of the four annotated chemoreceptor genes (
tlpA
,
tlpB
,
tlpC
, and
tlpD
) in
H. pylori
strain SS1 and a motile variant of strain KE26695. All deletion mutants were motile and displayed normal chemotaxis in brucella soft agar, but only
tlpB
mutants were defective for pH taxis.
tlpD
mutants exhibited more tumbling and arcing swimming, while
tlpC
mutants were hypermotile and responsive to acid. While
tlpA
,
tlpC
, and
tlpD
mutants colonized mice to near wild-type levels,
tlpB
mutants were defective for colonization of highly permissive C57BL/6 interleukin-12 (IL-12) (p40
−/−
)-deficient mice. Complementation of the
tlpB
mutant (
tlpB
expressed from the
rdxA
locus) restored pH taxis and infectivity for mice. pH taxis, like motility and urease activity, is essential for colonization and persistence in the gastric mucosa, and thus TlpB function might represent a novel target in the development of therapeutics that blind tactic behavior.
Genes and Enzymes Involved in Caffeic Acid Biosynthesis in the Actinomycete
Saccharothrix espanaensis
Authors: Berner Martin , Krug Daniel , Bihlmaier Corina , Vente Andreas , Müller Rolf , Bechthold Andreas 
Published: March 2006

ABSTRACT

The saccharomicins A and B, produced by the actinomycete
Saccharothrix espanaensis
, are oligosaccharide antibiotics. They consist of 17 monosaccharide units and the unique aglycon
N
-(
m
,
p
-dihydroxycinnamoyl)taurine. To investigate candidate genes responsible for the formation of
trans-m
,
p
-dihydroxycinnamic acid (caffeic acid) as part of the saccharomicin aglycon, gene expression experiments were carried out in
Streptomyces fradiae
XKS. It is shown that the biosynthetic pathway for
trans
-caffeic acid proceeds from
l
-tyrosine via
trans-p
-coumaric acid directly to
trans
-caffeic acid, since heterologous expression of s
am8
, encoding a tyrosine ammonia-lyase, led to the production of
trans-p
-hydroxycinnamic acid (coumaric acid), and coexpression of
sam8
and
sam5
, the latter encoding a 4-coumarate 3-hydroxylase, led to the production of
trans-m
,
p
-dihydroxycinnamic acid. This is not in accordance with the general phenylpropanoid pathway in plants, where
trans-p
-coumaric acid is first activated before the 3-hydroxylation of its ring takes place.
Control of Formation and Cellular Detachment from
Shewanella oneidensis
MR-1 Biofilms by Cyclic di-GMP
Authors: Thormann Kai M. , Duttler Stefanie , Saville Renee M. , Hyodo Mamoru , Shukla Soni , Hayakawa Yoshihiro , Spormann Alfred M. 
Published: March 2006

ABSTRACT

Stability and resilience against environmental perturbations are critical properties of medical and environmental biofilms and pose important targets for their control. Biofilm stability is determined by two mutually exclusive processes: attachment of cells to and detachment from the biofilm matrix. Using
Shewanella oneidensis
MR-1, an environmentally versatile, Fe(III) and Mn(IV) mineral-reducing microorganism, we identified
mxdABCD
as a new set of genes essential for formation of a three-dimensional biofilm. Molecular analysis revealed that
mxdA
encodes a cyclic bis(3′,5′)guanylic acid (cyclic di-GMP)-forming enzyme with an unusual GGDEF motif, i.e., NVDEF, which is essential for its function.
mxdB
encodes a putative membrane-associated glycosyl transferase. Both genes are essential for matrix attachment. The attachment-deficient phenotype of a
ΔmxdA
mutant was rescued by ectopic expression of VCA0956, encoding another diguanylate cyclase. Interestingly, a rapid cellular detachment from the biofilm occurred upon induction of
yhjH
, a gene encoding an enzyme that has been shown to have phosphodiesterase activity. In this way, it was possible to bypass the previously identified sudden depletion of molecular oxygen as an environmental trigger to induce biofilm dissolution. We propose a model for c-di-GMP as a key intracellular regulator for controlling biofilm stability by shifting the state of a biofilm cell between attachment and detachment in a concentration-dependent manner.
The Intestinal Life Cycle of
Bacillus subtilis
and Close Relatives
Authors: Tam Nguyen K. M. , Uyen Nguyen Q. , Hong Huynh A. , Duc Le H. , Hoa Tran T. , Serra Claudia R. , Henriques Adriano O. , Cutting Simon M. 
Published: March 2006

ABSTRACT

Bacillus subtilis
is considered a soil organism for which endospore formation provides a means to ensure long-term survival in the environment. We have addressed here the question of what happens to a spore when ingested. Spores displaying on their surface a heterologous antigen, tetanus toxin fragment C (TTFC), were shown to generate anti-TTFC responses not to the antigen contained in the primary oral inoculum but to those displayed on spores that had germinated and then resporulated. We then used reverse transcription-PCR to determine expression of vegetative genes and sporulation-specific genes in the mouse gut following oral dosing with spores. Significant levels of germination and sporulation were documented. Using natural isolates of
B. subtilis
that could form biofilms, we showed that these strains could persist in the mouse gut for significantly longer than the laboratory strain. Moreover, these isolates could grow and sporulate anaerobically and exhibited a novel phenomenon of being able to form spores in almost half the time required for the laboratory isolate. This suggests that spores are not transient passengers of the gastrointestinal tract but have adapted to carry out their entire life cycle within this environment. This is the first report showing an intestinal life cycle of
B. subtilis
and suggests that other
Bacillus
species could also be members of the gut microflora.
An Intergenic Stem-Loop Mutation in the
Bacillus subtilis ccpA-motPS
Operon Increases
motPS
Transcription and the MotPS Contribution to Motility
Authors: Terahara Naoya , Fujisawa Makoto , Powers Benjamin , Henkin Tina M. , Krulwich Terry A. , Ito Masahiro 
Published: March 2006

ABSTRACT

A stem-loop mutation between
ccpA
and
motP
in the
Bacillus subtilis ccpA-motPS
operon increased
motPS
transcription and membrane-associated MotPS levels, motility, and number of flagella/cell when MotPS is the sole stator and the MotPS contribution to motility at high pH, Na
+
, and viscosity when MotAB is also present.
Analysis of the PixA Inclusion Body Protein of
Xenorhabdus nematophila
Authors: Goetsch M. , Owen H. , Goldman B. , Forst S. 
Published: March 2006

ABSTRACT

The symbiotic pathogenic bacterium
Xenorhabdus nematophila
produces two distinct intracellular inclusion bodies. The
pixA
gene, which encodes the 185-residue methionine-rich PixA inclusion body protein, was analyzed in the present study. The
pixA
gene was optimally expressed under stationary-phase conditions but its expression did not require RpoS. Analysis of a
pixA
mutant strain showed that PixA was not required for virulence towards the insect host or for colonization of or survival within the nematode host, and was not essential for nematode reproduction. The
pixA
gene was not present in the genome of
Xenorhabdus bovienii
, which also produces proteinaceous inclusions, indicating that PixA is specifically produced in
X. nematophila
.
PlyPH, a Bacteriolytic Enzyme with a Broad pH Range of Activity and Lytic Action against
Bacillus anthracis
Authors: Yoong Pauline , Schuch Raymond , Nelson Daniel , Fischetti Vincent A. 
Published: March 2006

ABSTRACT

We have cloned a lytic enzyme, PlyPH, with a specific lytic effect on
Bacillus anthracis
strains. PlyPH remains active between pH 4 and 10.5, and a single dose rescued a significant percentage of mice infected intraperitoneally with an attenuated
B. anthracis
strain. We propose PlyPH as a novel therapeutic agent.
Liberation of Zinc-Containing L31 (RpmE) from Ribosomes by Its Paralogous Gene Product, YtiA, inBacillus subtilis
Authors: Akanuma Genki , Nanamiya Hideaki , Natori Yousuke , Nomura Naofumi , Kawamura Fujio 
Published: March 2006

ABSTRACTWe have found that alternative localization of two types of L31 ribosomal protein, RpmE and YtiA, is controlled by the intracellular concentration of zinc inBacillus subtilis. The detailed mechanisms for the alternation of L31 proteins under zinc-deficient conditions were previously unknown. To obtain further information about this regulatory mechanism, we have studied the stability of RpmE in vivo and the binding affinity of these proteins to ribosomes in vitro, and we have found that liberation of RpmE from ribosomes is triggered by the expression ofytiA, which is induced by the derepression of Zur under zinc-deficient conditions.
Microarray Analysis of the Osmotic Stress Response inPseudomonas aeruginosa
Authors: Aspedon Arden , Palmer Kelli , Whiteley Marvin 
Published: March 2006

ABSTRACTTranscriptional profiling ofPseudomonas aeruginosagrown under steady-state hyperosmotic stress conditions showed an up-regulation of genes associated with osmoprotectant synthesis, putative hydrophilins, and the type III secretion system with associated cytotoxins. A large number of regulatory genes, including several two-component systems not previously known to be influenced by osmolarity, were differentially expressed byP. aeruginosain immediate response to hyperosmotic shock.
β-Lactam Antibiotics Induce the SOS Response and Horizontal Transfer of Virulence Factors inStaphylococcus aureus
Authors: Maiques Elisa , Úbeda Carles , Campoy Susana , Salvador Noelia , Lasa Íñigo , Novick Richard P. , Barbé Jordi , Penadés José R. 
Published: March 2006

ABSTRACTAntibiotics that interfere with DNA replication and cell viability activate the SOS response. InStaphylococcus aureus, the antibiotic-induced SOS response promotes replication and high-frequency horizontal transfer of pathogenicity island-encoded virulence factors. Here we report that β-lactams induce a bona fide SOS response inS. aureus, characterized by the activation of the RecA and LexA proteins, the two master regulators of the SOS response. Moreover, we show that β-lactams are capable of triggering staphylococcal prophage induction inS. aureuslysogens. Consequently, and as previously described for SOS induction by commonly used fluoroquinolone antibiotics, β-lactam-mediated phage induction also resulted in replication and high-frequency transfer of the staphylococcal pathogenicity islands, showing that such antibiotics may have the unintended consequence of promoting the spread of bacterial virulence factors.
P
II
-Regulated Arginine Synthesis Controls Accumulation of Cyanophycin in
Synechocystis
sp. Strain PCC 6803
Authors: Maheswaran Mani , Ziegler Karl , Lockau Wolfgang , Hagemann Martin , Forchhammer Karl 
Published: March 2006

ABSTRACT

Cyanophycin (multi-
l
-arginyl-poly-
l
-aspartic acid) is a nitrogen storage polymer found in most cyanobacteria and some heterotrophic bacteria. The cyanobacterium
Synechocystis
sp. strain PCC 6803 accumulates cyanophycin following a transition from nitrogen-limited to nitrogen-excess conditions. Here we show that the accumulation of cyanophycin depends on the activation of the key enzyme of arginine biosynthesis,
N
-acetyl-
l
-glutamate kinase, by signal transduction protein P
II
.
Altering the Length of the Lipopolysaccharide O Antigen Has an Impact on the Interaction ofSalmonella entericaSerovar Typhimurium with Macrophages and Complement
Authors: Murray Gerald L. , Attridge Stephen R. , Morona Renato 
Published: March 2006

ABSTRACTA panel of isogenicSalmonella entericaserovar Typhimurium strains that vary only in the length of the O antigen was constructed through complementation of awzzdouble mutant (displaying unregulated O-antigen length) with one of two homologous (wzzSTandwzzfepE) or three heterologous (wzzO139ofVibrio choleraeandwzzSFandwzzpHS-2ofShigella flexneri)wzzgenes. Each gene was functional in theS. entericaserovar Typhimurium host and specified production of O-antigen polymers with lengths typical of those synthesized by the donor bacteria (ranging from 2 to >100 O-antigen repeat units). By use of this panel of strains, it was found that O-antigen length influences invasion/uptake by macrophage cells; this is the first time this has been shown withSalmonella. O-antigen length was confirmed to be related to complement resistance, with a minimum protective length of >4 and <15 repeat units. O antigen of 16 to 35 repeat units was found to activate complement more efficiently than other lengths, but this was unrelated to complement resistance. No evidence was found to suggest that modifying the length of the O-antigen polymer affected expression of the O1, O4, or O5 antigenic factors.
ThecobZGene ofMethanosarcina mazeiGö1 Encodes the Nonorthologous Replacement of the α-Ribazole-5′-Phosphate Phosphatase (CobC) Enzyme ofSalmonella enterica
Authors: Zayas Carmen L. , Woodson Jesse D. , Escalante-Semerena Jorge C. 
Published: March 2006

ABSTRACTOpen reading frame (ORF) Mm2058 of the methanogenic archaeonMethanosarcina mazeistrain Gö1 was shown in vivo and in vitro to encode the nonorthologous replacement of the α-ribazole-phosphate phosphatase (CobC; EC 3.1.3.73) enzyme ofSalmonella entericaserovar Typhimurium LT2. Bioinformatics analysis of sequences available in databases tentatively identified ORF Mm2058, which was cloned under the control of an inducible promoter and was used to support growth of anS. entericastrain under conditions that demanded CobC-like activity. The Mm2058 protein was expressed with a decahistidine tag at its N terminus and was purified to homogeneity using nickel affinity chromatography. High-performance liquid chromatography followed by electrospray ionization mass spectrometry showed that the Mm2058 protein had phosphatase activity that converted α-ribazole-5′-phosphate to α-ribazole, as reported for the bacterial CobC enzyme. On the basis of the data reported here, we refer to ORF Mm2058 ascobZ. We tested the prediction by Rodionov et al. (D. A. Rodionov, A. G. Vitreschak, A. A. Mironov, and M. S. Gelfand, J. Biol. Chem.278:41148-41159, 2003) that ORF HSL01294 (also called Vng1577) encoded the nonorthologous replacement of the bacterial CobC enzyme in the extremely halophilic archaeonHalobacteriumsp. strain NRC-1. A strain of the latter carrying an in-frame deletion of ORF Vng1577 was not a cobalamin auxotroph, suggesting that either there is redundancy of this function inHalobacteriumor the gene was misannotated.