bluuebunny/crossref_metadata_2025_split huggingface dataset:
Phototrophic Fe(II) Oxidation Promotes Organic Carbon Acquisition by
Rhodobacter capsulatus
SB1003
Authors: Caiazza Nicky C. , Lies Douglas P. , Newman Dianne K. 
Published: August 2007

ABSTRACT

Anoxygenic phototrophic Fe(II) oxidation is usually considered to be a lithoautotrophic metabolism that contributes to primary production in Fe-based ecosystems. In this study, we employed
Rhodobacter capsulatus
SB1003 as a model organism to test the hypothesis that phototrophic Fe(II) oxidation can be coupled to organic carbon acquisition.
R. capsulatus
SB1003 oxidized Fe(II) under anoxic conditions in a light-dependent manner, but it failed to grow lithoautotrophically on soluble Fe(II). When the strain was provided with Fe(II)-citrate, however, growth was observed that was dependent upon microbially catalyzed Fe(II) oxidation, resulting in the formation of Fe(III)-citrate. Subsequent photochemical breakdown of Fe(III)-citrate yielded acetoacetic acid that supported growth in the light but not the dark. The deletion of genes (RRC00247 and RRC00248) that encode homologs of
atoA
and
atoD
, required for acetoacetic acid utilization, severely impaired the ability of
R. capsulatus
SB1003 to grow on Fe(II)-citrate. The growth yield achieved by
R. capsulatus
SB1003 in the presence of citrate cannot be explained by lithoautotrophic growth on Fe(II) enabled by indirect effects of the ligand [such as altering the thermodynamics of Fe(II) oxidation or preventing cell encrustation]. Together, these results demonstrate that
R. capsulatus
SB1003 grows photoheterotrophically on Fe(II)-citrate. Nitrilotriacetic acid also supported light-dependent growth on Fe(II), suggesting that Fe(II) oxidation may be a general mechanism whereby some Fe(II)-oxidizing bacteria mine otherwise inaccessible organic carbon sources.
Internal and Surface-Localized Major Surface Proteases ofLeishmaniaspp. and Their Differential Release from Promastigotes
Authors: Yao Chaoqun , Donelson John E. , Wilson Mary E. 
Published: August 2007

ABSTRACTMajor surface protease (MSP), also called GP63, is a virulence factor ofLeishmaniaspp. protozoa. There are three pools of MSP, located either internally within the parasite, anchored to the surface membrane, or released into the extracellular environment. The regulation and biological functions of these MSP pools are unknown. We investigated here the trafficking and extrusion of surface versus internal MSPs. VirulentLeishmania chagasiundergo a growth-associated lengthening in thet1/2of surface-localized MSP, but this did not occur in the attenuated L5 strain. The release of surface-localized MSP was enhanced in a dose-dependent manner by MβCD, which chelates membrane cholesterol-ergosterol. Furthermore, incubation of promastigotes at 37°C with Matrigel matrix, a soluble basement membrane extract of Engelbreth-Holm-Swarm tumor cells, stimulated the release of internal MSP but not of surface-located MSP. Taken together, these data indicate that MSP subpopulations in distinct cellular locations are released from the parasite under different environmental conditions. We hypothesize that the internal MSP with its lengthyt1/2does not serve as a pool for promastigote surface MSP in the sand fly vector but that it instead functions as an MSP pool ready for quick release upon inoculation of metacyclic promastigotes into mammals. We present a model in which these different MSP pools are released under distinct life cycle-specific conditions.
Ku Heterodimer-Independent End Joining inTrypanosoma bruceiCell Extracts Relies upon Sequence Microhomology
Authors: Burton Peter , McBride David J. , Wilkes Jonathan M. , Barry J. David , McCulloch Richard 
Published: August 2007

ABSTRACTDNA double-strand breaks (DSBs) are repaired primarily by two distinct pathways: homologous recombination and nonhomologous end joining (NHEJ). NHEJ has been found in all eukaryotes examined to date and has been described recently for some bacterial species, illustrating its ancestry.Trypanosoma bruceiis a divergent eukaryotic protist that evades host immunity by antigenic variation, a process in which homologous recombination plays a crucial function. While homologous recombination has been examined in some detail inT. brucei, little work has been done to examine what other DSB repair pathways the parasite utilizes. Here we show thatT. bruceicell extracts support the end joining of linear DNA molecules. These reactions are independent of the Ku heterodimer, indicating that they are distinct from NHEJ, and are guided by sequence microhomology. We also demonstrate bioinformatically thatT. brucei, in common with other kinetoplastids, does not encode recognizable homologues of DNA ligase IV or XRCC4, suggesting that NHEJ is either absent or mechanistically diverged in these pathogens.
Site-Directed Mutagenesis Studies of Tn
5
Transposase Residues Involved in Synaptic Complex Formation
Authors: Vaezeslami Soheila , Sterling Rachel , Reznikoff William S. 
Published: August 2007

ABSTRACT

Transposition (the movement of discrete segments of DNA, resulting in rearrangement of genomic DNA) initiates when transposase forms a dimeric DNA-protein synaptic complex with transposon DNA end sequences. The synaptic complex is a prerequisite for catalytic reactions that occur during the transposition process. The transposase-DNA interactions involved in the synaptic complex have been of great interest. Here we undertook a study to verify the protein-DNA interactions that lead to synapsis in the Tn
5
system. Specifically, we studied (i) Arg342, Glu344, and Asn348 and (ii) Ser438, Lys439, and Ser445, which, based on the previously published cocrystal structure of Tn
5
transposase bound to a precleaved transposon end sequence, make
cis
and
trans
contacts with transposon end sequence DNA, respectively. By using genetic and biochemical assays, we showed that in all cases except one, each of these residues plays an important role in synaptic complex formation, as predicted by the cocrystal structure.
Sequence Analysis of the
Staphylococcus aureus srrAB
Loci Reveals that Truncation of
srrA
Affects Growth and Virulence Factor Expression
Authors: Pragman Alexa A. , Herron-Olson Lisa , Case Laura C. , Vetter Sara M. , Henke Evan E. , Kapur Vivek , Schlievert Patrick M. 
Published: August 2007

ABSTRACT

The SrrAB system regulates metabolism and virulence factors in
Staphylococcus aureus
. We sequenced the
srrAB
loci of 21 isolates and performed a phylogenetic analysis. Vaginal and bovine isolates clustered together, while skin isolates were genetically diverse. Few nucleotide polymorphisms were observed, and most were synonymous. Two strains (N2 and N19) with N-terminal truncations in SrrA displayed defects in growth and abnormally upregulated virulence factor expression under low-oxygen conditions.
Characterization of Riboflavin (Vitamin B2) Transport Proteins fromBacillus subtilisandCorynebacterium glutamicum
Authors: Vogl Christian , Grill Simon , Schilling Oliver , Stülke Jörg , Mack Matthias , Stolz Jürgen 
Published: August 2007

ABSTRACTRiboflavin (vitamin B2) is the direct precursor of the flavin cofactors flavin mononucleotide and flavin adenine dinucleotide, essential components of cellular biochemistry. In this work we investigated the unrelated proteins YpaA fromBacillus subtilisand PnuX fromCorynebacterium glutamicumfor a role in riboflavin uptake. Based on the regulation of the corresponding genes by a riboswitch mechanism, both proteins have been predicted to be involved in flavin metabolism. Moreover, their primary structures suggested that these proteins integrate into the cytoplasmic membrane. We provide experimental evidence that YpaA is a plasma membrane protein with five transmembrane domains and a cytoplasmic C terminus. InB. subtilis, riboflavin uptake was increased whenypaAwas overexpressed and abolished whenypaAwas deleted. Riboflavin uptake activity and the abundance of the YpaA protein were also increased when riboflavin auxotrophic mutants were grown in limiting amounts of riboflavin. YpaA-mediated riboflavin uptake was sensitive to protonophors and reduced in the absence of glucose, demonstrating that the protein requires metabolic energy for substrate translocation. In addition, we demonstrate that PnuX fromC. glutamicumalso is a riboflavin transporter. Transport by PnuX was not energy dependent and had high apparent affinity for riboflavin (Km11 μM). Roseoflavin, a toxic riboflavin analog, appears to be a substrate of PnuX and YpaA. We propose to designate the gene namesribUforypaAandribMforpnuXto reflect that the encoded proteins function in riboflavin uptake and that the genes have different phylogenetic origins.
Biochemical and Genetic Investigation of Initial Reactions in Aerobic Degradation of the Bile Acid Cholate in
Pseudomonas
sp. Strain Chol1
Authors: Birkenmaier Antoinette , Holert Johannes , Erdbrink Henrike , Moeller Heiko M. , Friemel Anke , Schoenenberger René , Suter Marc J.-F. , Klebensberger Janosch , Philipp Bodo 
Published: August 2007

ABSTRACT

Bile acids are surface-active steroid compounds with toxic effects for bacteria. Recently, the isolation and characterization of a bacterium,
Pseudomonas
sp. strain Chol1, growing with bile acids as the carbon and energy source was reported. In this study, initial reactions of the aerobic degradation pathway for the bile acid cholate were investigated on the biochemical and genetic level in strain Chol1. These reactions comprised A-ring oxidation, activation with coenzyme A (CoA), and β-oxidation of the acyl side chain with the C
19
-steroid dihydroxyandrostadienedione as the end product. A-ring oxidizing enzyme activities leading to Δ
1,4
-3-ketocholyl-CoA were detected in cell extracts and confirmed by liquid chromatography-tandem mass spectrometry (LC-MS/MS). Cholate activation with CoA was demonstrated in cell extracts and confirmed with a chemically synthesized standard by LC-MS/MS. A transposon mutant with a block in oxidation of the acyl side chain accumulated a steroid compound in culture supernatants which was identified as 7α,12α-dihydroxy-3-oxopregna-1,4-diene-20-carboxylate (DHOPDC) by nuclear magnetic resonance spectroscopy. The interrupted gene was identified as encoding a putative acyl-CoA-dehydrogenase (ACAD). DHOPDC activation with CoA in cell extracts of strain Chol1 was detected by LC-MS/MS. The growth defect of the transposon mutant could be complemented by the wild-type ACAD gene located on the plasmid pBBR1MCS-5. Based on these results, the initiating reactions of the cholate degradation pathway leading from cholate to dihydroxyandrostadienedione could be reconstructed. In addition, the first bacterial gene encoding an enzyme for a specific reaction step in side chain degradation of steroid compounds was identified, and it showed a high degree of similarity to genes in other steroid-degrading bacteria.
Characterization of an Acid-Dependent Arginine Decarboxylase Enzyme from
Chlamydophila pneumoniae
Authors: Giles Teresa N. , Graham David E. 
Published: August 2007

ABSTRACT

Genome sequences from members of the
Chlamydiales
encode diverged homologs of a pyruvoyl-dependent arginine decarboxylase enzyme that nonpathogenic euryarchaea use in polyamine biosynthesis. The
Chlamydiales
lack subsequent genes required for polyamine biosynthesis and probably obtain polyamines from their host cells. To identify the function of this protein, the CPn1032 homolog from the respiratory pathogen
Chlamydophila pneumoniae
was heterologously expressed and purified. This protein self-cleaved to form a reactive pyruvoyl group, and the subunits assembled into a thermostable (αβ)
3
complex. The mature enzyme specifically catalyzed the decarboxylation of
l
-arginine, with an unusually low pH optimum of 3.4. The CPn1032 gene complemented a mutation in the
Escherichia coli adiA
gene, which encodes a pyridoxal 5′-phosphate-dependent arginine decarboxylase, restoring arginine-dependent acid resistance. Acting together with a putative arginine-agmatine antiporter, the CPn1032 homologs may have evolved convergently to form an arginine-dependent acid resistance system. These genes are the first evidence that obligately intracellular chlamydiae may encounter acidic conditions. Alternatively, this system could reduce the host cell arginine concentration and produce inhibitors of nitric oxide synthase.
The Alcohol Dehydrogenase Gene
adhA
in
Corynebacterium glutamicum
Is Subject to Carbon Catabolite Repression
Authors: Arndt Annette , Eikmanns Bernhard J. 
Published: August 2007

ABSTRACT

Corynebacterium glutamicum
has recently been shown to grow on ethanol as a carbon and energy source and to possess high alcohol dehydrogenase (ADH) activity when growing on this substrate and low ADH activity when growing on ethanol plus glucose or glucose alone. Here we identify the
C. glutamicum
ADH gene (
adhA
), analyze its transcriptional organization, and investigate the relevance of the transcriptional regulators of acetate metabolism RamA and RamB for
adhA
expression. Sequence analysis of
adhA
predicts a polypeptide of 345 amino acids showing up to 57% identity with zinc-dependent ADH enzymes of group I. Inactivation of the chromosomal
adhA
gene led to the inability to grow on ethanol and to the absence of ADH activity, indicating that only a single ethanol-oxidizing ADH enzyme is present in
C. glutamicum
. Transcriptional analysis revealed that the
C. glutamicum adhA
gene is monocistronic and that its expression is repressed in the presence of glucose and of acetate in the growth medium, i.e., that
adhA
expression is subject to catabolite repression. Further analyses revealed that RamA and RamB directly bind to the
adhA
promoter region, that RamA is essential for the expression of
adhA
, and that RamB exerts a negative control on
adhA
expression in the presence of glucose or acetate in the growth medium. However, since the glucose- and acetate-dependent down-regulation of
adhA
expression was only partially released in a RamB-deficient mutant, there might be an additional regulator involved in the catabolite repression of
adhA
.
Recombining Population Structure of
Plesiomonas shigelloides
(
Enterobacteriaceae
) Revealed by Multilocus Sequence Typing
Authors: Salerno Anna , Delétoile Alexis , Lefevre Martine , Ciznar Ivan , Krovacek Karel , Grimont Patrick , Brisse Sylvain 
Published: August 2007

ABSTRACT

Plesiomonas shigelloides
is an emerging pathogen that is widespread in the aquatic environment and is responsible for intestinal diseases and extraintestinal infections in humans and other animals. Virtually nothing is known about its genetic diversity, population structure, and evolution, which severely limits epidemiological control. We addressed these questions by developing a multilocus sequence typing (MLST) system based on five genes (
fusA
,
leuS
,
pyrG
,
recG
, and
rpoB
) and analyzing 77 epidemiologically unrelated strains from several countries and several ecological sources. The phylogenetic position of
P. shigelloides
within family
Enterobacteriaceae
was precisely defined by phylogenetic analysis of the same gene portions in other family members. Within
P. shigelloides
, high levels of nucleotide diversity (average percentage of nucleotide differences between strains, 1.49%) and genotypic diversity (64 distinct sequence types; Simpson's index, 99.7%) were found, with no salient internal phylogenetic structure. We estimated that homologous recombination in housekeeping genes affects
P. shigelloides
alleles and nucleotides 7 and 77 times more frequently than mutation, respectively. These ratios are similar to those observed in the naturally transformable species
Streptococcus pneumoniae
with a high rate of recombination. In contrast, recombination within
Salmonella enterica
,
Escherichia coli
, and
Yersinia enterocolitica
was much less frequent.
P. shigelloides
thus stands out among members of the
Enterobacteriaceae
. Its high rate of recombination results in a lack of association between genomic background and O and H antigenic factors, as observed for the 51 serotypes found in our sample. Given its robustness and discriminatory power, we recommend MLST as a reference method for population biology studies and epidemiological tracking of
P. shigelloides
strains.
Genome Analysis of Phage JS98 Defines a Fourth Major Subgroup of T4-Like Phages in
Escherichia coli
Authors: Zuber Sophie , Ngom-Bru Catherine , Barretto Caroline , Bruttin Anne , Brüssow Harald , Denou Emmanuel 
Published: August 2007

ABSTRACT

Numerous T4-like
Escherichia coli
phages were isolated from human stool and environmental wastewater samples in Bangladesh and Switzerland. The sequences of the major head gene (
g23
) revealed that these coliphages could be placed into four subgroups, represented by the phages T4, RB69, RB49, and JS98. Thus, JS98 defines a new major subgroup of
E. coli
T4-like phages. We conducted an analysis of the 169-kb JS98 genome sequence. Overall, 198 of the 266 JS98 open reading frames (ORFs) shared amino acid sequence identity with the reference T4 phage, 41 shared identity with other T4-like phages, and 27 ORFs lacked any database matches. Genes on the plus strand encoded virion proteins, which showed moderate to high sequence identity with T4 proteins. The right genome half of JS98 showed a higher degree of sequence conservation with T4 and RB69, even for the nonstructural genes, than did the left genome half, containing exclusively nonstructural genes. Most of the JS98-specific genes were found in the left genome half. Two came as a hypervariability cluster, but most represented isolated genes, suggesting that they were acquired separately in multiple acquisition events. No evidence for DNA exchange between JS98 phage and the
E. coli
host genome or coliphages other than T4 was observed. No undesired genes which could compromise its medical use were detected in the JS98 genome sequence.
Synergistic Interaction of
Clostridium cellulovorans
Cellulosomal Cellulases and HbpA
Authors: Matsuoka Satoshi , Yukawa Hideaki , Inui Masayuki , Doi Roy H. 
Published: August 2007

ABSTRACT

Clostridium cellulovorans
, an anaerobic bacterium, produces a small nonenzymatic protein called HbpA, which has a surface layer homology domain and a type I cohesin domain similar to those found in the cellulosomal scaffolding protein CbpA. In this study, we demonstrated that HbpA could bind to cell wall fragments from
C. cellulovorans
and insoluble polysaccharides and form a complex with cellulosomal cellulases endoglucanase B (EngB) and endoglucanase L (EngL). Synergistic degradative action of the cellulosomal cellulase and HbpA complexes was demonstrated on acid-swollen cellulose, Avicel, and corn fiber. We propose that HbpA functions to bind dockerin-containing cellulosomal enzymes to the cell surface and complements the activity of cellulosomes.
Identification of the Origin of Transfer (
oriT
) and DNA Relaxase Required for Conjugation of the Integrative and Conjugative Element ICE
Bs1
of
Bacillus subtilis
Authors: Lee Catherine A. , Grossman Alan D. 
Published: August 2007

ABSTRACT

Integrative and conjugative elements (ICEs), also known as conjugative transposons, are mobile genetic elements that can transfer from one bacterial cell to another by conjugation. ICE
Bs1
is integrated into the
trnS-leu2
gene of
Bacillus subtilis
and is regulated by the SOS response and the RapI-PhrI cell-cell peptide signaling system. When
B. subtilis
senses DNA damage or high concentrations of potential mating partners that lack the element, ICE
Bs1
excises from the chromosome and can transfer to recipients. Bacterial conjugation usually requires a DNA relaxase that nicks an origin of transfer (
oriT
) on the conjugative element and initiates the 5′-to-3′ transfer of one strand of the element into recipient cells. The ICE
Bs1 ydcR
(
nicK
) gene product is homologous to the pT181 family of plasmid DNA relaxases. We found that transfer of ICE
Bs1
requires
nicK
and identified a
cis
-acting
oriT
that is also required for transfer. Expression of
nicK
leads to nicking of ICE
Bs1
between a GC-rich inverted repeat in
oriT
, and NicK was the only ICE
Bs1
gene product needed for nicking. NicK likely mediates conjugation of ICE
Bs1
by nicking at
oriT
and facilitating the translocation of a single strand of ICE
Bs1
DNA through a transmembrane conjugation pore.
Cell Surface Filaments of the Gliding Bacterium
Flavobacterium johnsoniae
Revealed by Cryo-Electron Tomography
Authors: Liu Jun , McBride Mark J. , Subramaniam Sriram 
Published: August 2007

ABSTRACT

Flavobacterium johnsoniae
cells glide rapidly over surfaces by an as-yet-unknown mechanism. Using cryo-electron tomography, we show that wild-type cells display tufts of ∼5-nm-wide cell surface filaments that appear to be anchored to the inner surface of the outer membrane. These filaments are absent in cells of a nonmotile
gldF
mutant but are restored upon expression of plasmid-encoded GldF, a component of a putative ATP-binding cassette transporter.
Quorum-Sensing Regulation of the Production of Blp Bacteriocins in
Streptococcus thermophilus
Authors: Fontaine Laetitia , Boutry Céline , Guédon Eric , Guillot Alain , Ibrahim Mariam , Grossiord Benoît , Hols Pascal 
Published: August 2007

ABSTRACT

The
blp
gene cluster identified in the genome sequences of
Streptococcus thermophilus
(
blp
St
) LMG18311, CNRZ1066, and LMD-9 displays all the characteristics of a class II bacteriocin locus. In the present study, we showed that the
blp
St
locus is only fully functional in strain LMD-9 and regulates the production of antimicrobial peptides that inhibit strains LMG18311 and CNRZ1066. The
blp
St
cluster of LMD-9 contains 23 genes that are transcriptionally organized in six operons:
blpABC
St
(peptide transporter genes and pheromone gene);
blpRH
St
(two-component regulatory system genes);
blpD
St
-
orf1, blpU
St
-
orf3
, and
blpE-F
St
(bacteriocin precursors and immunity genes); and
blpG-X
St
(unknown function). All the operons, except the regulatory unit
blpRH
St
, were shown to be coregulated at the transcriptional level by a quorum-sensing mechanism involving the mature
S. thermophilus
pheromone BlpC* (BlpC*
St
), which was extracellularly detected as two active forms (30 and 19 amino acids). These operons are differentially transcribed depending on growth phase and pheromone concentration. They all contain a motif with two imperfect direct repeats in their mapped promoter regions that could serve as binding sites of the response regulator BlpR
St
. Through the construction of deletion mutants, the
blp
St
locus of strain LMD-9 was shown to encode all the essential functions associated with bacteriocin production, quorum-sensing regulation, and immunity.
Complex Formation by the
mrpABCDEFG
Gene Products, Which Constitute a Principal Na
+
/H
+
Antiporter in
Bacillus subtilis
Authors: Kajiyama Yusuke , Otagiri Masato , Sekiguchi Junichi , Kosono Saori , Kudo Toshiaki 
Published: August 2007

ABSTRACT

The
Bacillus subtilis
Mrp (also referred to as Sha) is a particularly unusual Na
+
/H
+
antiporter encoded by
mrpABCDEFG
. Using His tagging of Mrp proteins, we showed complex formation by the
mrpABCDEFG
gene products by pull-down and blue native polyacrylamide gel electrophoresis analyses. This is the first molecular evidence that the Mrp is a multicomponent antiporter in the cation-proton antiporter 3 family.