bluuebunny/crossref_metadata_2025_split huggingface dataset:
Sigma Factor Genes
sigC
,
sigE
, and
sigG
Are Upregulated in Heterocysts of the Cyanobacterium
Anabaena
sp. Strain PCC 7120
Authors: Aldea M. Ramona , Mella-Herrera Rodrigo A. , Golden James W. 
Published: September 2007

ABSTRACT

We used
gfp
transcriptional fusions to investigate the regulation of eight sigma factor genes during heterocyst development in the cyanobacterium
Anabaena
sp. strain PCC 7120. Reporter strains containing
gfp
fusions with the upstream regions of
sigB2
,
sigD
,
sigI
, and
sigJ
did not show developmental regulation. Time-lapse microscopy of
sigC
,
sigE
, and
sigG
reporter strains showed increased green fluorescent protein fluorescence in differentiating cells at 4 h, 16 h, and 9 h, respectively, after nitrogen step down.
Distribution, Functional Expression, and Genetic Organization of Cif, a Phage-Encoded Type III-Secreted Effector from Enteropathogenic and EnterohemorrhagicEscherichia coli
Authors: Loukiadis Estelle , Nobe Rika , Herold Sylvia , Tramuta Clara , Ogura Yoshitoshi , Ooka Tadasuke , Morabito Stefano , Kérourédan Monique , Brugère Hubert , Schmidt Herbert , Hayashi Tetsuya , Oswald Eric 
Published: September 2007

ABSTRACTEnteropathogenicEscherichia coli(EPEC) and enterohemorrhagicE. coli(EHEC) inject effector proteins into host cells via a type III secretion system encoded by the locus of enterocyte effacement (LEE). One of these effectors is Cif, encoded outside the LEE by a lambdoid prophage. In this study, we demonstrated that the Cif-encoding prophage of EPEC strain E22 is inducible and produces infectious phage particles. We investigated the distribution and functional expression of Cif in 5,049E. colistrains of human, animal, and environmental origins. A total of 115E. coliisolates from diverse origins and geographic locations carriedcif. The presence ofcifwas tightly associated with the LEE, since all thecif-positive isolates were positive for the LEE. These results suggested that the Cif-encoding prophages have been widely disseminated within the natural population ofE. colibut positively selected within the population of LEE-positive strains. Nonetheless, 66% ofcif-positiveE. colistrains did not induce a typical Cif-related phenotype in eukaryotic cells due to frameshift mutations or insertion of an IS element in thecifgene. The passenger region of the prophages carryingcifwas highly variable and showed various combinations of IS elements and genes coding for other effectors such asnleB,nleC,nleH,nleG,espJ, andnleA/espI(some of which were also truncated). This diversity and the presence of nonfunctional effectors should be taken into account to assess EPEC and EHEC pathogenicity and tropism.
A Functional Two-Partner Secretion System Contributes to Adhesion of
Neisseria meningitidis
to Epithelial Cells
Authors: Schmitt Corinna , Turner David , Boesl Maria , Abele Marion , Frosch Matthias , Kurzai Oliver 
Published: September 2007

ABSTRACT

Neisseria meningitidis
is a frequent commensal of the human nasopharynx causing severe invasive infections in rare cases. A functional two-partner secretion (TPS) system in
N. meningitidis
, composed of the secreted effector protein HrpA and its cognate transporter HrpB, is identified and characterized in this study. Although all meningococcal strains harbor at least one TPS system, the
hrpA
genes display significant C-terminal sequence variation. Meningococcal genes encoding the TPS effector proteins and their transporters are closely associated and transcribed into a single mRNA. HrpA proteins are translocated across the meningococcal outer membrane by their cognate transporters HrpB and mainly released into the environment. During this process, HrpA is proteolytically processed to a mature 180-kDa form. In contrast to other known TPS systems, immature HrpA proteins are stable in the absence of HrpB and accumulate within the bacterial cell. A small percentage of mature HrpA remains associated with the bacteria and contributes to the interaction of meningococci with epithelial cells.
Flagella Facilitate Escape ofSalmonellafrom Oncotic Macrophages
Authors: Sano Gen-ichiro , Takada Yasunari , Goto Shinichi , Maruyama Kenta , Shindo Yutaka , Oka Kotaro , Matsui Hidenori , Matsuo Koichi 
Published: September 2007

ABSTRACTThe intracellular parasiteSalmonella entericaserovar Typhimurium causes a typhoid-like systemic disease in mice. Whereas the survival ofSalmonellain phagocytes is well understood, little has been documented about the exit of intracellularSalmonellafrom host cells. Here we report that in a population of infected macrophagesSalmonellainduces “oncosis,” an irreversible progression to eukaryotic cell death characterized by swelling of the entire cell body. Oncotic macrophages (OnMφs) are terminal deoxynucleotidyltransferase-mediated dUTP-biotin nick end labeling negative and lack actin filaments (F-actin). The plasma membrane of OnMφs filled with bacilli remains impermeable, and intracellularSalmonellabacilli move vigorously using flagella. Eventually, intracellularSalmonellabacilli intermittently exit host cells in a flagellum-dependent manner. These results suggest that induction of macrophage oncosis and intracellular accumulation of flagellated bacilli constitute a strategy wherebySalmonellaescapes from host macrophages.
Biofilm Formation-Gene Expression Relay System inEscherichia coli: Modulation of σS-Dependent Gene Expression by the CsgD Regulatory Protein via σSProtein Stabilization
Authors: Gualdi Luciana , Tagliabue Letizia , Landini Paolo 
Published: September 2007

ABSTRACTBacteria can switch from a single-cell (planktonic) mode to a multicellular community (biofilm) mode via production of cell-cell aggregation and surface adhesion factors. In this report, we present evidence that the CsgD protein, a transcription regulator involved in biofilm formation inEscherichia coli, modulates the expression of therpoS(σS) regulon. Protein pattern analysis ofE. colicells in stationary phase shows that CsgD affects the expression of several proteins encoded by σS-dependent genes. CsgD regulation of σS-dependent genes takes place at gene transcription level, does not bypass the need forrpoS, and is abolished in anrpoS-null mutant. Consistent with these results, we find that CsgD expression leads to an increase in σSintracellular concentration. Increase in σScellular amount is mediated by CsgD-dependent transcription activation ofiraP, encoding a factor involved in σSprotein stabilization. Our results strongly suggest that the CsgD regulatory protein plays a major role as a relay between adhesion factors production and σS-dependent gene expression via σSprotein stabilization. Direct coordination between biofilm formation and expression of therpoSregulon could positively impact important biological processes, such as host colonization or response to environmental stresses.
Iteron-Binding ORF157 and FtsZ-Like ORF156 Proteins Encoded by pBtoxis Play a Role in Its Replication inBacillus thuringiensissubsp.israelensis
Authors: Tang Mujin , Bideshi Dennis K. , Park Hyun-Woo , Federici Brian A. 
Published: September 2007

ABSTRACTWe recently identified a minireplicon of pBtoxis fromBacillus thuringiensissubsp.israelensisthat contained an operon encoding two novel proteins (ORF156 and ORF157), both of which are required for replication. ORF157 contains a helix-turn-helix motif and shares no homology with known plasmid replication proteins (Rep), and ORF156 contains the signature motif present in FtsZ/tubulin proteins, the latter of which are known to function in cell division and chromosome segregation. Here we show that the minimal sequence composed of four 12-bp imperfect direct repeats (iterons) in the pBtoxis minireplicon was sufficient to replicate a reporter plasmid inB. thuringiensissubsp.israelensiswhen ORF156 and ORF157 functions were provided intrans. To further investigate the roles of ORF156 and ORF157 in pBtoxis replication, six-histidine-tagged recombinant rORF156 and rORF157 proteins were purified fromEscherichia coliand used in electrophoretic mobility shift assays. Our results demonstrated that rORF157, but not rORF156, binds specifically to the pBtoxis iterons, suggesting that ORF157 functions as a Rep protein. Although rORF156 did not bind to the iteron sequence, we showed that it bound to rORF157-DNA complexes. In addition, we showed that rORF156 has GTPase activity characteristic of the FtsZ/tubulin superfamily of proteins. Taken together, these results suggest that the iterons compose the minimal replication origin (ori) of pBtoxis and that ORF157 and ORF156 are involved in the initiation of pBtoxis replication and possibly in the segregation and partitioning of this plasmid to daughter cells.
Diminished LcrV Secretion Attenuates
Yersinia pseudotuberculosis
Virulence
Authors: Bröms Jeanette E. , Francis Matthew S. , Forsberg Åke 
Published: September 2007

ABSTRACT
Many gram-negative bacterial pathogenicity factors that function beyond the outer membrane are secreted via a contact-dependent type III secretion system. Two types of substrates are predestined for this mode of secretion, namely, antihost effectors that are translocated directly into target cells and the translocators required for targeting of the effectors across the host cell membrane. N-terminal secretion signals are important for recognition of the protein cargo by the type III secretion machinery. Even though such signals are known for several effectors, a consensus signal sequence is not obvious. One of the translocators, LcrV, has been attributed other functions in addition to its role in translocation. These functions include regulation, presumably via interaction with LcrG inside bacteria, and immunomodulation via interaction with Toll-like receptor 2. Here we wanted to address the significance of the specific targeting of LcrV to the exterior for its function in regulation, effector targeting, and virulence. The results, highlighting key N-terminal amino acids important for LcrV secretion, allowed us to dissect the role of LcrV in regulation from that in effector targeting/virulence. While only low levels of exported LcrV were required for in vitro effector translocation, as deduced by a cell infection assay, fully functional export of LcrV was found to be a prerequisite for its role in virulence in the systemic murine infection model.
Role for the RecBCD Recombination Pathway for
pilE
Gene Variation in Repair-Proficient
Neisseria gonorrhoeae
Authors: Hill Stuart A. , Woodward Tracy , Reger Andrew , Baker Rachel , Dinse Theresa 
Published: September 2007

ABSTRACT

The role of the RecBCD recombination pathway in PilE antigenic variation in
Neisseria gonorrhoeae
is contentious and appears to be strain dependent. In this study,
N. gonorrhoeae
strain MS11
recB
mutants were assessed for recombination/repair. MS11
recB
mutants were found to be highly susceptible to DNA treatments that caused double-chain breaks and were severely impaired for growth;
recB
growth suppressor mutants arose at high frequencies. When the recombination/repair capacity of strain MS11 was compared to that of strains FA1090 and P9, innate differences were observed between the strains, with FA1090 and P9
rec
+
bacteria presenting pronounced recombination/repair defects. Consequently, MS11
recB
mutants present a more robust phenotype than the other strains that were tested. In addition, MS11
recB
mutants are also shown to be defective for
pilE/pilS
recombination. Moreover,
pilE/pilS
recombination is shown to proceed with gonococci that carry inverted
pilE
loci. Consequently, a novel RecBCD-mediated double-chain-break repair model for PilE antigenic variation is proposed.
Dissection of the Caffeate Respiratory Chain in the Acetogen
Acetobacterium woodii
: Identification of an Rnf-Type NADH Dehydrogenase as a Potential Coupling Site
Authors: Imkamp Frank , Biegel Eva , Jayamani Elamparithi , Buckel Wolfgang , Müller Volker 
Published: September 2007

ABSTRACT

The anaerobic acetogenic bacterium
Acetobacterium woodii
couples caffeate reduction with electrons derived from hydrogen to the synthesis of ATP by a chemiosmotic mechanism with sodium ions as coupling ions, a process referred to as caffeate respiration. We addressed the nature of the hitherto unknown enzymatic activities involved in this process and their cellular localization. Cell extract of
A. woodii
catalyzes H
2
-dependent caffeate reduction. This reaction is strictly ATP dependent but can be activated also by acetyl coenzyme A (CoA), indicating that there is formation of caffeyl-CoA prior to reduction. Two-dimensional gel electrophoresis revealed proteins present only in caffeate-grown cells. Two proteins were identified by electrospray ionization-mass spectrometry/mass spectrometry, and the encoding genes were cloned. These proteins are very similar to subunits α (EtfA) and β (EtfB) of electron transfer flavoproteins present in various anaerobic bacteria. Western blot analysis demonstrated that they are induced by caffeate and localized in the cytoplasm. Etf proteins are known electron carriers that shuttle electrons from NADH to different acceptors. Indeed, NADH was used as an electron donor for cytosolic caffeate reduction. Since the hydrogenase was soluble and used ferredoxin as an electron acceptor, the missing link was a ferredoxin:NAD
+
oxidoreductase. This activity could be determined and, interestingly, was membrane bound. A search for genes that could encode this activity revealed DNA fragments encoding subunits C and D of a membrane-bound Rnf-type NADH dehydrogenase that is a potential Na
+
pump. These data suggest the following electron transport chain: H
2
→ ferredoxin → NAD
+
→ Etf → caffeyl-CoA reductase. They also imply that the sodium motive step in the chain is the ferredoxin-dependent NAD
+
reduction catalyzed by Rnf.
Computational Prediction and Experimental Verification of the Gene Encoding the NAD+/NADP+-Dependent Succinate Semialdehyde Dehydrogenase inEscherichia coli
Authors: Fuhrer Tobias , Chen Lifeng , Sauer Uwe , Vitkup Dennis 
Published: September 2007

ABSTRACTAlthough NAD+-dependent succinate semialdehyde dehydrogenase activity was first described inEscherichia colimore than 25 years ago, the responsible gene has remained elusive so far. As an experimental proof of concept for a gap-filling algorithm for metabolic networks developed earlier, we demonstrate here that theE. coligeneyneIis responsible for this activity. Our biochemical results demonstrate that theyneI-encoded succinate semialdehyde dehydrogenase can use either NAD+or NADP+to oxidize succinate semialdehyde to succinate. The gene is induced by succinate semialdehyde, and expression data indicate thatyneIplays a unique physiological role in the general nitrogen metabolism ofE. coli. In particular, we demonstrate using mutant growth experiments that theyneIgene has an important, but not essential, role during growth on arginine and probably has an essential function during growth on putrescine as the nitrogen source. The NADP+-dependent succinate semialdehyde dehydrogenase activity encoded by the functional homologgabDappears to be important for nitrogen metabolism under N limitation conditions. TheyneI-encoded activity, in contrast, functions primarily as a valve to prevent toxic accumulation of succinate semialdehyde. Analysis of available genome sequences demonstrated that orthologs of bothyneIandgabDare broadly distributed across phylogenetic space.
The
Escherichia coli
Yej Transporter Is Required for the Uptake of Translation Inhibitor Microcin C
Authors: Novikova Maria , Metlitskaya Anastasia , Datsenko Kirill , Kazakov Teymur , Kazakov Alexey , Wanner Barry , Severinov Konstantin 
Published: September 2007

ABSTRACT

Microcin C (McC), a peptide-nucleotide antibiotic, targets aspartyl-tRNA synthetase. By analyzing a random transposon library, we identified
Escherichia coli
mutants resistant to McC. Transposon insertions were localized to a single locus,
yejABEF
, which encodes components of a putative inner membrane ABC transporter. Analysis of site-specific mutants established that all four components of the transporter are required for McC sensitivity. Since aspartyl-tRNA synthetase in
yej
mutant extracts was fully sensitive to McC, we conclude that
yej
mutations interfere with McC uptake and that YejABEF is the only inner membrane transporter responsible for McC uptake in
E. coli
. Other substrates of YejABEF remain to be identified.
Identification of a
Vibrio furnissii
Oligopeptide Permease and Characterization of Its In Vitro Hemolytic Activity
Authors: Wu Tung-Kung , Wang Yu-Kuo , Chen Yi-Chin , Feng Jen-Min , Liu Yen-Hsi , Wang Ting-Yi 
Published: September 2007

ABSTRACT

We describe purification and characterization of an oligopeptide permease protein (Hly-OppA) from
Vibrio furnissii
that has multifaceted functions in solute binding, in in vitro hemolysis, in antibiotic resistance, and as a virulence factor in bacterial pathogenesis. The solute-binding function was revealed by N-terminal and internal peptide sequences of the purified protein and was confirmed by discernible effects on oligopeptide binding, by accumulation of fluorescent substrates, and by fluorescent substrate-antibiotic competition assay experiments. The purified protein exhibited host-specific in vitro hemolytic activity against various mammalian erythrocytes and apparent cytotoxicity in CHO-K1 cells. Recombinant Hly-OppA protein and an anti-Hly-OppA monoclonal antibody exhibited and neutralized the in vitro hemolytic activity, respectively, which further confirmed the hemolytic activity of the gene product. In addition, a
V. furnissii hly-oppA
knockout mutant caused less mortality than the wild-type strain when it was inoculated into BALB/c mice, indicating the virulence function of this protein. Finally, the in vitro hemolytic activity was also confirmed with homologous ATP-binding cassette-type transporter proteins from other
Vibrio
species.
In Vivo DNA Binding of Bacteriophage GA-1 Protein p6
Authors: Alcorlo Martín , Salas Margarita , Hermoso José M. 
Published: September 2007

ABSTRACT

Bacteriophage GA-1 infects
Bacillus
sp. strain G1R and has a linear double-stranded DNA genome with a terminal protein covalently linked to its 5′ ends. GA-1 protein p6 is very abundant in infected cells and binds DNA with no sequence specificity. We show here that it binds in vivo to the whole viral genome, as detected by cross-linking, chromatin immunoprecipitation, and real-time PCR analyses, and has the characteristics of a histone-like protein. Binding to DNA of GA-1 protein p6 shows little supercoiling dependency, in contrast to the ortholog protein of the evolutionary related
Bacillus subtilis
phage φ29. This feature is a property of the protein rather than the DNA or the cellular background, since φ29 protein p6 shows supercoiling-dependent binding to GA-1 DNA in
Bacillus
sp. strain G1R. GA-1 DNA replication is impaired in the presence of the gyrase inhibitors novobiocin and nalidixic acid, which indicates that, although noncovalently closed, the viral genome is topologically constrained in vivo. GA-1 protein p6 is also able to bind φ29 DNA in
B. subtilis
cells; however, as expected, the binding is less supercoiling dependent than the one observed with the φ29 protein p6. In addition, the nucleoprotein complex formed is not functional, since it is not able to transcomplement the DNA replication deficiency of a φ29
sus6
mutant. Furthermore, we took advantage of φ29 protein p6 binding to GA-1 DNA to find that the viral DNA ejection mechanism seems to take place, as in the case of φ29, with a right to left polarity in a two-step, push-pull process.
Array-Based Genomic Comparative Hybridization Analysis of Field Strains ofMycoplasma hyopneumoniae
Authors: Madsen Melissa L. , Oneal Michael J. , Gardner Stuart W. , Strait Erin L. , Nettleton Dan , Thacker Eileen L. , Minion F. Chris 
Published: September 2007

ABSTRACTMycoplasma hyopneumoniaeis the causative agent of porcine enzootic pneumonia and a major factor in the porcine respiratory disease complex. A clear understanding of the mechanisms of pathogenesis does not exist, although it is clear thatM. hyopneumoniaeadheres to porcine ciliated epithelium by action of a protein called P97. Previous studies have shown variation in the gene encoding the P97 cilium adhesin in different strains ofM. hyopneumoniae, but the extent of genetic variation among field strains across the genome is not known. SinceM. hyopneumoniaeis a worldwide problem, it is reasonable to expect that a wide range of genetic variability may exist given all of the different breeds and housing conditions. This variation may impact the overall virulence of a single strain. Using microarray technology, this study examined the potential variation of 14 field strains compared to strain 232, on which the array was based. Genomic DNA was obtained, amplified with TempliPhi, and labeled indirectly with Alexa dyes. After genomic hybridization, the arrays were scanned and data were analyzed using a linear statistical model. The results indicated that genetic variation could be detected in all 14 field strains but across different loci, suggesting that variation occurs throughout the genome. Fifty-nine percent of the variable loci were hypothetical genes. Twenty-two percent of the lipoprotein genes showed variation in at least one field strain. A permutation test identified a location in theM. hyopneumoniaegenome where there is spatial clustering of variability between the field strains and strain 232.
Nutritional Cues ControlPseudomonas aeruginosaMulticellular Behavior in Cystic Fibrosis Sputum
Authors: Palmer Kelli L. , Aye Lindsay M. , Whiteley Marvin 
Published: September 2007

ABSTRACTThe sputum (mucus) layer of the cystic fibrosis (CF) lung is a complex substrate that providesPseudomonas aeruginosawith carbon and energy to support high-density growth during chronic colonization. Unfortunately, the CF lung sputum layer has been difficult to mimic in animal models of CF disease, and mechanistic studies ofP. aeruginosaphysiology during growth in CF sputum are hampered by its complexity. In this study, we performed chromatographic and enzymatic analyses of CF sputum to develop a defined,syntheticCFsputummedium (SCFM) that mimics the nutritional composition of CF sputum. Importantly,P. aeruginosadisplays similar phenotypes during growth in CF sputum and in SCFM, including similar growth rates, gene expression profiles, carbon substrate preferences, and cell-cell signaling profiles. Using SCFM, we provide evidence that aromatic amino acids serve as nutritional cues that influence cell-cell signaling and antimicrobial activity ofP. aeruginosaduring growth in CF sputum.