bluuebunny/crossref_metadata_2025_split huggingface dataset:
Functional Analyses of Two Acetyl Coenzyme A Synthetases in the Ascomycete Gibberella zeae
Authors: Lee Seunghoon , Son Hokyoung , Lee Jungkwan , Min Kyunghun , Choi Gyung Ja , Kim Jin-Cheol , Lee Yin-Won 
Published: June 2011

ABSTRACTAcetyl coenzyme A (acetyl-CoA) is a crucial metabolite for energy metabolism and biosynthetic pathways and is produced in various cellular compartments with spatial and temporal precision. Our previous study on ATP citrate lyase (ACL) inGibberella zeaerevealed that ACL-dependent acetyl-CoA production is important for histone acetylation, especially in sexual development, but is not involved in lipid synthesis. In this study, we deleted additional acetyl-CoA synthetic genes, the acetyl-CoA synthetases (ACSgenesACS1andACS2), to identify alternative acetyl-CoA production mechanisms for ACL. TheACS1deletion resulted in a defect in sexual development that was mainly due to a reduction in 1-palmitoyl-2-oleoyl-3-linoleoyl-rac-glycerol production, which is required for perithecium development and maturation. Another ACS coding gene,ACS2, has accessorial functions forACS1and has compensatory functions forACLas a nuclear acetyl-CoA producer. This study showed that acetate is readily generated during the entire life cycle ofG. zeaeand has a pivotal role in fungal metabolism. Because ACSs are components of the pyruvate-acetaldehyde-acetate pathway, this fermentation process might have crucial roles in various physiological processes for filamentous fungi.
Recombination Can either Help Maintain Very Short Telomeres or Generate Longer Telomeres in Yeast Cells with Weak Telomerase Activity
Authors: Basenko Evelina , Topcu Zeki , McEachern Michael J. 
Published: June 2011

ABSTRACT

Yeast mutants lacking telomerase are able to elongate their telomeres through processes involving homologous recombination. In this study, we investigated telomeric recombination in several mutants that normally maintain very short telomeres due to the presence of a partially functional telomerase. The abnormal colony morphology present in some mutants was correlated with especially short average telomere length and with a requirement for
RAD52
for indefinite growth. Better-growing derivatives of some of the mutants were occasionally observed and were found to have substantially elongated telomeres. These telomeres were composed of alternating patterns of mutationally tagged telomeric repeats and wild-type repeats, an outcome consistent with amplification occurring via recombination rather than telomerase. Our results suggest that recombination at telomeres can produce two distinct outcomes in the mutants we studied. In occasional cells, recombination generates substantially longer telomeres, apparently through the roll-and-spread mechanism. However, in most cells, recombination appears limited to helping to maintain very short telomeres. The latter outcome likely represents a simplified form of recombinational telomere maintenance that is independent of the generation and copying of telomeric circles.
The Essential β-Barrel Assembly Machinery Complex Components BamD and BamA Are Required for Autotransporter Biogenesis
Authors: Rossiter Amanda E. , Leyton Denisse L. , Tveen-Jensen Karina , Browning Douglas F. , Sevastsyanovich Yanina , Knowles Timothy J. , Nichols Katie B. , Cunningham Adam F. , Overduin Michael , Schembri Mark A. , Henderson Ian R. 
Published: June 2011

ABSTRACT
Autotransporter biogenesis is dependent upon BamA, a central component of the β-barrel assembly machinery (BAM) complex. In this report, we detail the role of the other BAM components (BamB-E). We identify the importance of BamD in autotransporter biogenesis and show that BamB, BamC, and BamE are not required.
Genome-Wide Identification of
In Vivo
Binding Sites of GlxR, a Cyclic AMP Receptor Protein-Type Regulator in Corynebacterium glutamicum
Authors: Toyoda Koichi , Teramoto Haruhiko , Inui Masayuki , Yukawa Hideaki 
Published: June 2011

ABSTRACT

Corynebacterium glutamicum
GlxR is a cyclic AMP (cAMP) receptor protein-type regulator. Although over 200 GlxR-binding sites in the
C. glutamicum
genome are predicted
in silico
, studies on the physiological function of GlxR have been hindered by the severe growth defects of a
glxR
mutant. This study identified the GlxR regulon by chromatin immunoprecipitation in conjunction with microarray (ChIP-chip) analyses. In total, 209 regions were detected as
in vivo
GlxR-binding sites.
In vitro
binding assays and promoter-reporter assays demonstrated that GlxR directly activates expression of genes for aerobic respiration, ATP synthesis, and glycolysis and that it is required for expression of genes for cell separation and mechanosensitive channels. GlxR also directly represses a citrate uptake gene in the presence of citrate. Moreover, ChIP-chip analyses showed that GlxR was still able to interact with its target sites in a mutant with a deletion of
cyaB
, the sole adenylate cyclase gene in the genome, even though binding affinity was markedly decreased. Thus, GlxR is physiologically functional at the relatively low cAMP levels in the
cyaB
mutant, allowing the
cyaB
mutant to grow much better than the
glxR
mutant.
Importance of a Hydrophobic Pocket for Peptide Binding in Lactococcal OppA
Authors: Berntsson Ronnie P.-A. , Thunnissen Andy-Mark W. H. , Poolman Bert , Slotboom Dirk-Jan 
Published: June 2011

ABSTRACT
Lactococcal oligopeptide-binding protein A (OppA) binds peptides with widely varied lengths and sequences. We previously hypothesized that a hydrophobic pocket in OppA preferentially binds a hydrophobic peptide side chain and thus determines its binding register. Two crystal structures of OppA with different nonapeptides now indeed show binding in different registers.
Crystal Structure of the Pseudomonas aeruginosa Virulence Factor Regulator
Authors: Cordes Timothy J. , Worzalla Gregory A. , Ginster Aaron M. , Forest Katrina T. 
Published: June 2011

ABSTRACT

Virulence factor regulator (Vfr) enhances
Pseudomonas aeruginosa
pathogenicity through its role as a global transcriptional regulator. The crystal structure of Vfr shows that it is a winged-helix DNA-binding protein like its homologue cyclic AMP receptor protein (CRP). In addition to an expected primary cyclic AMP-binding site, a second ligand-binding site is nestled between the N-terminal domain and the C-terminal helix-turn-helix domain. Unlike CRP, Vfr is a symmetric dimer in the absence of DNA. Removal of seven disordered N-terminal residues of Vfr prevents the growth of
P. aeruginosa
.
Mechanism of Citrate Metabolism by an Oxaloacetate Decarboxylase-Deficient Mutant of Lactococcus lactis IL1403
Authors: Pudlik Agata M. , Lolkema Juke S. 
Published: June 2011

ABSTRACT

Citrate metabolism in resting cells of
Lactococcus lactis
IL1403(pFL3) results in the formation of two end products from the intermediate pyruvate, acetoin and acetate (A. M. Pudlik and J. S. Lolkema, J. Bacteriol. 193:706–714, 2011). Pyruvate is formed from citrate following uptake by the transporter CitP through the subsequent actions of citrate lyase and oxaloacetate decarboxylase. The present study describes the metabolic response of
L. lactis
when oxaloacetate accumulates in the cytoplasm. The oxaloacetate decarboxylase-deficient mutant ILCitM(pFL3) showed nearly identical rates of citrate consumption, but the end product profile in the presence of glucose shifted from mainly acetoin to only acetate. In addition, in contrast to the parental strain, the mutant strain did not generate proton motive force. Citrate consumption by the mutant strain was coupled to the excretion of oxaloacetate, with a yield of 80 to 85%. Following citrate consumption, oxaloacetate was slowly taken up by the cells and converted to pyruvate by a cryptic decarboxylase and, subsequently, to acetate. The transport of oxaloacetate is catalyzed by CitP. The parental strain IL1403(pFL3) containing CitP consumed oxaloacetate, while the original strain, IL1403, not containing CitP, did not. Moreover, oxaloacetate consumption was enhanced in the presence of
l
-lactate, indicating exchange between oxaloacetate and
l
-lactate catalyzed by CitP. Hence, when oxaloacetate inadvertently accumulates in the cytoplasm, the physiological response of
L. lactis
is to excrete oxaloacetate in exchange with citrate by an electroneutral mechanism catalyzed by CitP. Subsequently, in a second step, oxaloacetate is taken up by CitP and metabolized to pyruvate and acetate.
RcnB Is a Periplasmic Protein Essential for Maintaining Intracellular Ni and Co Concentrations in Escherichia coli
Authors: Blériot Camille , Effantin Géraldine , Lagarde Florence , Mandrand-Berthelot Marie-Andrée , Rodrigue Agnès 
Published: June 2011

ABSTRACTNickel and cobalt are both essential trace elements that are toxic when present in excess. The main resistance mechanism that bacteria use to overcome this toxicity is the efflux of these cations out of the cytoplasm. RND (resistance-nodulation-cell division)- and MFS (major facilitator superfamily)-type efflux systems are known to export either nickel or cobalt. The RcnA efflux pump, which belongs to a unique family, is responsible for the detoxification of Ni and Co inEscherichia coli. In this work, the role of the geneyohN, which is located downstream ofrcnA, is investigated.yohNis cotranscribed withrcnA, and its expression is induced by Ni and Co. Surprisingly, in contrast to the effect of deletingrcnA, deletion ofyohNconferred enhanced resistance to Ni and Co inE. coli, accompanied by decreased metal accumulation. We show that YohN is localized to the periplasm and does not bind Ni or Co ions directly. Physiological and genetic experiments demonstrate that YohN is not involved in Ni import. YohN is conserved among proteobacteria and belongs to a new family of proteins; consequently,yohNhas been renamedrcnB.We show that the enhanced resistance ofrcnBmutants to Ni and Co and their decreased Ni and Co intracellular accumulation are linked to the greater efflux of these ions in the absence ofrcnB. Taken together, these results suggest that RcnB is required to maintain metal ion homeostasis, in conjunction with the efflux pump RcnA, presumably by modulating RcnA-mediated export of Ni and Co to avoid excess efflux of Ni and Co ions via an unknown novel mechanism.
Amino Acid Precursor Supply in the Biosynthesis of the RNA Polymerase Inhibitor Streptolydigin by Streptomyces lydicus
Authors: Gómez Cristina , Horna Dina H. , Olano Carlos , Palomino-Schätzlein Martina , Pineda-Lucena Antonio , Carbajo Rodrigo J. , Braña Alfredo F. , Méndez Carmen , Salas José A. 
Published: June 2011

ABSTRACT

Biosynthesis of the hybrid polyketide-nonribosomal peptide antibiotic streptolydigin, 3-methylaspartate, is utilized as precursor of the tetramic acid moiety. The three genes from the
Streptomyces lydicus
streptolydigin gene cluster
slgE1-slgE2-slgE3
are involved in 3-methylaspartate supply. SlgE3, a ferredoxin-dependent glutamate synthase, is responsible for the biosynthesis of glutamate from glutamine and 2-oxoglutarate. In addition to
slgE3
, housekeeping NADPH- and ferredoxin-dependent glutamate synthase genes have been identified in
S. lydicus
. The expression of
slgE3
is increased up to 9-fold at the onset of streptolydigin biosynthesis and later decreases to ∼2-fold over the basal level. In contrast, the expression of housekeeping glutamate synthases decreases when streptolydigin begins to be synthesized. SlgE1 and SlgE2 are the two subunits of a glutamate mutase that would convert glutamate into 3-methylaspartate. Deletion of
slgE1-slgE2
led to the production of two compounds containing a lateral side chain derived from glutamate instead of 3-methylaspartate. Expression of this glutamate mutase also reaches a peak increase of up to 5.5-fold coinciding with the onset of antibiotic production. Overexpression of either
slgE3
or
slgE1-slgE2
in
S. lydicus
led to an increase in the yield of streptolydigin.
Role of Ferredoxin and Flavodoxins in Bacillus subtilis Fatty Acid Desaturation
Authors: Chazarreta-Cifre Lorena , Martiarena Leticia , de Mendoza Diego , Altabe Silvia G. 
Published: June 2011

ABSTRACT

The
Bacillus subtilis
acyl lipid desaturase (Δ5-Des) is an iron-dependent integral membrane protein able to selectively introduce double bonds into long-chain fatty acids. In the last decade since its discovery, the molecular mechanism of Δ5-Des expression has been studied extensively. However, the mechanism of desaturation, which must rely on unknown bacterial proteins for electron transfer, has not yet been explored. The
B. subtilis
genome encodes three proteins that can act as potential electron donors of Δ5-Des, ferredoxin (Fer) and two flavodoxins (Flds) (YkuN and YkuP), which are encoded by the
ykuNOP
operon. Here we report that the disruption of either the
fer
gene or the
ykuNOP
operon decreases the desaturation of palmitic acid by ∼30%. Nevertheless, a
fer ykuNOP
mutant abolished the desaturation reaction almost completely. Our results establish Fer and the two Flds as redox partners for Δ5-Des and suggest that the Fer and Fld proteins could function physiologically in the biosynthesis of unsaturated fatty acids in
B. subtilis
. Although Flds have extensively been described as partners in a number of redox processes, this is the first report describing their role as electron donors in the fatty acid desaturation reaction.
Self-Transmissibility of the Integrative and Conjugative Element ICEPm1between Clinical Isolates Requires a Functional Integrase, Relaxase, and Type IV Secretion System
Authors: Flannery Erika L. , Antczak Samantha M. , Mobley Harry L. T. 
Published: June 2011

ABSTRACTIntegrative and conjugative elements (ICEs), which are chromosomal mobile elements, can conjugatively transfer between bacteria. Recently, we identified a genomic island ofProteus mirabilis, a common agent of catheter-associated urinary tract infection (UTI), that possesses all the properties consistent with an ICE. This element, designated ICEPm1, is highly conserved in other causative agents of UTI, suggesting its mobility. We demonstrate that ICEPm1can actively excise from the chromosome in a clonal population of bacteria and that this excision is integrase dependent. Although inP. mirabilisHI4320, ICEPm1is annotated as integrated into the phenylalanine tRNA genepheV, we show that ICEPm1can integrate into eitherpheVorpheU. We determined that ICEPm1transfers at a frequency of 1.35 × 10−5transconjugants/donor to ICEPm1-deficientP. mirabilisusing plate mating assays with clinical isolates. Insertional inactivation of a putative integrase gene on ICEPm1decreased transfer frequencies of ICEPm1to below the limit of detection. Mutation of the relaxase of ICEPm1also eliminates transfer and demonstrates that this element is indeed self-transmissible and not transferred intrans, as are some mobilizable genomic islands. Together, these findings clearly demonstrate that ICEPm1can actively excise from the chromosome in an integrase-dependent manner, dynamically integrate into both phenylalanine tRNA genes, and transfer into clinical strains using its own conjugation machinery.
Coevolution of ABC Transporters and Two-Component Regulatory Systems as Resistance Modules against Antimicrobial Peptides in Firmicutes Bacteria
Authors: Dintner Sebastian , Staroń Anna , Berchtold Evi , Petri Tobias , Mascher Thorsten , Gebhard Susanne 
Published: June 2011

ABSTRACT

In
Firmicutes
bacteria, ATP-binding cassette (ABC) transporters have been recognized as important resistance determinants against antimicrobial peptides. Together with neighboring two-component systems (TCSs), which regulate their expression, they form specific detoxification modules. Both the transport permease and sensor kinase components show unusual domain architecture: the permeases contain a large extracellular domain, while the sensor kinases lack an obvious input domain. One of the best-characterized examples is the bacitracin resistance module BceRS-BceAB of
Bacillus subtilis
. Strikingly, in this system, the ABC transporter and TCS have an absolute mutual requirement for each other in both sensing of and resistance to bacitracin, suggesting a novel mode of signal transduction in which the transporter constitutes the actual sensor. We identified over 250 such BceAB-like ABC transporters in the current databases. They occurred almost exclusively in
Firmicutes
bacteria, and 80% of the transporters were associated with a BceRS-like TCS. Phylogenetic analyses of the permease and sensor kinase components revealed a tight evolutionary correlation. Our findings suggest a direct regulatory interaction between the ABC transporters and TCSs, mediating communication between both components. Based on their observed coclustering and conservation of response regulator binding sites, we could identify putative corresponding two-component systems for transporters lacking a regulatory system in their immediate neighborhood. Taken together, our results show that these types of ABC transporters and TCSs have coevolved to form self-sufficient detoxification modules against antimicrobial peptides, widely distributed among
Firmicutes
bacteria.
A Sulfite Respiration Pathway from Thermus thermophilus and the Key Role of Newly Identified Cytochrome
c
550
Authors: Robin Sylvain , Arese Marzia , Forte Elena , Sarti Paolo , Giuffrè Alessandro , Soulimane Tewfik 
Published: June 2011

ABSTRACT

Sulfite, produced for instance during amino acid metabolism, is a very reactive and toxic compound. Various detoxification mechanisms exist, but sulfite oxidoreductases (SORs) are one of the major actors in sulfite remediation in bacteria and animals. Here we describe the existence of an operon in the extreme thermophilic bacterium
Thermus thermophilus
HB8 encoding both a SOR and a diheme
c
-type cytochrome. The
in vitro
analysis clearly showed that the newly identified cytochrome
c
550
acts as an acceptor of the electrons generated by the SOR enzyme during the oxidation of sulfite. The electrons are then rapidly shuttled via cytochrome
c
552
to the terminal
ba
3
- and
caa
3
-type oxidases, thereby unveiling a novel electron transfer pathway, linking sulfite oxidation to oxygen reduction in
T. thermophilus
: sulfite → SOR
HB8
→ cytochrome
c
550
→ cytochrome
c
552
→
ba
3
oxidase/
caa
3
oxidase → O
2
. The description of the complete pathway reveals that electrons generated during sulfite oxidation by the SOR are funneled into the respiratory chain, participating in the energy production of
T. thermophilus
.
Proteins Involved in Formation of the Outermost Layer of Bacillus subtilis Spores
Authors: Imamura Daisuke , Kuwana Ritsuko , Takamatsu Hiromu , Watabe Kazuhito 
Published: June 2011

ABSTRACT

To investigate the outermost structure of the
Bacillus subtilis
spore, we analyzed the accessibility of antibodies to proteins on spores of
B. subtilis
. Anti-green fluorescent protein (GFP) antibodies efficiently accessed GFP fused to CgeA or CotZ, which were previously assigned to the outermost layer termed the spore crust. However, anti-GFP antibodies did not bind to spores of strains expressing GFP fused to 14 outer coat, inner coat, or cortex proteins. Anti-CgeA antibodies bound to spores of wild-type and CgeA-GFP strains but not
cgeA
mutant spores. These results suggest that the spore crust covers the spore coat and is the externally exposed, outermost layer of the
B. subtilis
spore. We found that CotZ was essential for the spore crust to surround the spore but not for spore coat formation, indicating that CotZ plays a critical role in spore crust formation. In addition, we found that CotY-GFP was exposed on the surface of the spore, suggesting that CotY is an additional component of the spore crust. Moreover, the localization of CotY-GFP around the spore depended on CotZ, and CotY and CotZ depended on each other for spore assembly. Furthermore, a disruption of
cotW
affected the assembly of CotV-GFP, and a disruption of
cotX
affected the assembly of both CotV-GFP and CgeA-GFP. These results suggest that
cgeA
and genes in the
cotVWXYZ
cluster are involved in spore crust formation.
Comparative Analysis of the
lux
Operons in Aliivibrio logei KCh1 (a Kamchatka Isolate) and Aliivibrio salmonicida
Authors: Manukhov Ilya V. , Khrul'nova Svetlana A. , Baranova Ancha , Zavilgelsky Gennadii B. 
Published: June 2011

ABSTRACT

Here we provide a molecular description of a new psychrophilic strain, KCh11, of marine luminescent bacteria classified as
Aliivibrio logei
. We sequenced the entire
lux
operon of
A. logei
KCh1 and showed that it is substantially similar to the
lux
operon of
Aliivibrio salmonicida
. It was demonstrated that the reduced production of bioluminescence in
A. salmonicida
is most likely defined by a specific defect in its
luxD
gene.
Rule-based decision support system in the biopsy diagnosis of glomerular diseases
Authors: Gupta Ruchika , Sharma Alok , Singh Sompal , Dinda Amit K 
Published: June 2011

AimsTo develop a rule-based decision support system (RDSS) to assist in the diagnosis of glomerular diseases on the basis of clinical, histological and immunohistological findings.MethodsThe computer software for the RDSS was written by one of the authors. The prototypical clinical and histomorphological features, including immunofluorescence findings of various glomerular diseases, were selected by three pathologists with experience in renal pathology. For every case included, all the relevant features were fed into the RDSS in the form of one or more vectors. Diagnosis was achieved by the RDSS on the basis of shortest Euclidean distance between the vector of features of a particular ‘test’ case and vectors of the prototypical features. The diagnoses rendered by the RDSS were compared with the final diagnosis signed out by the renal pathologists; the percentage of correct diagnoses was calculated for the RDSS.ResultsA total of 612 cases of glomerular diseases were included in the analysis. The RDSS developed in this study gave the correct diagnosis in 83.2% of the cases included. Of all the cases, membranous glomerulonephritis and lupus nephritis were most frequently diagnosed accurately. However, immunotactoid glomerulonephritis was misdiagnosed due to the lack of ultrastructural findings in the study.ConclusionThe decision support system developed in the present study holds promise, given the high accuracy in diagnosis of glomerular diseases on the basis of clinical, histological and immunofluorescence features. Such a system may prove useful not only for diagnosis but also for postgraduate teaching and self-assessment. Results need to be confirmed in further larger studies.