bluuebunny/crossref_metadata_2025_split huggingface dataset:
Conjugative Transfer between
Escherichia coli
and
Leptospira
spp. as a New Genetic Tool
Authors: Picardeau Mathieu 
Published: November 2007

ABSTRACT

Our understanding of leptospiral pathogenesis, which remains poorly understood, depends on reliable genetic tools for functional analysis of genes in pathogenic strains. In this study, we report the first demonstration of conjugation between
Escherichia coli
and
Leptospira
spp. by using RP4 derivative conjugative plasmids. The DNA transfer described here was due to authentic conjugation, as shown by the requirement for cell-to-cell contact and the resistance of DNA transfers to the addition of DNase I. Transposition via conjugation of a plasmid delivering
Himar1
yielded frequencies ranging from 1 × 10
−6
to 8.5 × 10
−8
transconjugants/recipient cell in the saprophyte
L. biflexa
and the pathogen
L. interrogans
, respectively. Analysis of mutants indicated that transposition occurs randomly, and at single sites in the genome of these strains, allowing the utilization of this system to generate libraries of transposon mutants.
Survival of and In Situ Gene Expression by
Vibrio vulnificus
at Varying Salinities in Estuarine Environments
Authors: Jones Melissa K. , Warner Elizabeth , Oliver James D. 
Published: November 2007

ABSTRACT

The opportunistic human pathogen
Vibrio vulnificus
survives in a wide range of ecological environments, which demonstrates its ability to adapt to highly variable conditions. Survival and gene expression under various conditions have been extensively studied in vitro; however, little work has been done to evaluate this bacterium in its natural habitat. Therefore, this study monitored the long-term survival of
V. vulnificus
in situ and simultaneously evaluated the expression of stress (
rpoS
,
relA
,
hfq
, and
groEL
) and putative virulence (
vvpE
,
smcR
,
viuB
, and
trkA
) genes at estuarine sites of varying salinity. Additionally, the survival and gene expression of an
rpoS
and an
oxyR
mutant were examined under the same conditions. Differences between the sampling sites in the long-term survival of any strain were not seen. However, differences were seen in the expression of
viuB
,
trkA
, and
relA
but our findings differed from what has been previously shown in vitro. These results also routinely demonstrated that genes required for survival under in vitro stress or host conditions are not necessarily required for survival in the water column. Overall, this study highlights the need for further in situ evaluation of this bacterium in order to gain a true understanding of its ecology and how it relates to its natural habitat.
Basic-Zipper-Type Transcription Factor FlbB Controls Asexual Development in
Aspergillus nidulans
Authors: Etxebeste Oier , Ni Min , Garzia Aitor , Kwon Nak-Jung , Fischer Reinhard , Yu Jae-Hyuk , Espeso Eduardo A. , Ugalde Unai 
Published: November 2007

ABSTRACT

The fungal colony is a complex multicellular unit consisting of various cell types and functions. Asexual spore formation (conidiation) is integrated through sensory and regulatory elements into the general morphogenetic plan, in which the activation of the transcription factor BrlA is the first determining step. A number of early regulatory elements acting upstream of BrlA (
fluG
and
flbA-E
) have been identified, but their functional relations remain to be further investigated. In this report we describe FlbB as a putative basic-zipper-type transcription factor restricted to filamentous fungi. FlbB accumulates at the hyphal apex during early vegetative growth but is later found in apical nuclei, suggesting that an activating modification triggers nuclear import. Moreover, proper temporal and quantitative expression of FlbB is a prerequisite for
brlA
transcription, and misscheduled overexpression inhibits conidiation. We also present evidence that FlbB activation results in the production of a second diffusible signal, acting downstream from the FluG factor, to induce conidiation.
Responses of Pathogenic and Nonpathogenic Yeast Species to Steroids Reveal the Functioning and Evolution of Multidrug Resistance Transcriptional Networks
Authors: Banerjee Dibyendu , Lelandais Gaelle , Shukla Sudhanshu , Mukhopadhyay Gauranga , Jacq Claude , Devaux Frederic , Prasad Rajendra 
Published: November 2007

ABSTRACT

Steroids are known to induce pleiotropic drug resistance states in hemiascomycetes, with tremendous potential consequences for human fungal infections. Our analysis of gene expression in
Saccharomyces cerevisiae
and
Candida albicans
cells subjected to three different concentrations of progesterone revealed that their pleiotropic drug resistance (PDR) networks were strikingly sensitive to steroids. In
S. cerevisiae
, 20 of the Pdr1p/Pdr3p target genes, including
PDR3
itself, were rapidly induced by progesterone, which mimics the effects of
PDR1
gain-of-function alleles. This unique property allowed us to decipher the respective roles of Pdr1p and Pdr3p in PDR induction and to define functional modules among their target genes. Although the expression profiles of the major PDR transporters encoding genes Sc
PDR5
and Ca
CDR1
were similar, the
S. cerevisiae
global PDR response to progesterone was only partly conserved in
C. albicans
. In particular, the role of Tac1p, the main
C. albicans
PDR regulator, in the progesterone response was apparently restricted to five genes. These results suggest that the
C. albicans
and
S. cerevisiae
PDR networks, although sharing a conserved core regarding the regulation of membrane properties, have different structures and properties. Additionally, our data indicate that other as yet undiscovered regulators may second Tac1p in the
C. albicans
drug response.
Exit from Host Cells by the Pathogenic Parasite
Toxoplasma gondii
Does Not Require Motility
Authors: Lavine Mark D. , Arrizabalaga Gustavo 
Published: November 2007

ABSTRACT

The process by which the intracellular parasite
Toxoplasma gondii
exits its host cell is central to its propagation and pathogenesis. Experimental induction of motility in intracellular parasites results in parasite egress, leading to the hypothesis that egress depends on the parasite's actin-dependent motility. Using a novel assay to monitor egress without experimental induction, we have established that inhibiting parasite motility does not block this process, although treatment with actin-disrupting drugs does delay egress. However, using an irreversible actin inhibitor, we show that this delay is due to the disruption of host cell actin alone, apparently resulting from the consequent loss of membrane tension. Accordingly, by manipulating osmotic pressure, we show that parasite egress is delayed by releasing membrane tension and promoted by increasing it. Therefore, without artificial induction, egress does not depend on parasite motility and can proceed by mechanical rupture of the host membrane.
Functional Characterization of
Pneumocystis carinii brl1
by Transspecies Complementation Analysis
Authors: Lo Presti Libera , Cockell Moira , Cerutti Lorenzo , Simanis Viesturs , Hauser Philippe M. 
Published: November 2007

ABSTRACT

Pneumocystis jirovecii
is a fungus which causes severe opportunistic infections in immunocompromised humans. The
brl1
gene of
P. carinii
infecting rats was identified and characterized by using bioinformatics in conjunction with functional complementation in
Saccharomyces cerevisiae
and
Schizosaccharomyces pombe
. The ectopic expression of this gene rescues null alleles of essential nuclear membrane proteins of the Brr6/Brl1 family in both yeasts.
ChsVb, a Class VII Chitin Synthase Involved in Septation, Is Critical for Pathogenicity in
Fusarium oxysporum
Authors: Martín-Urdíroz Magdalena , Roncero M. Isabel G. , González-Reyes José Antonio , Ruiz-Roldán Carmen 
Published: November 2007

ABSTRACT

A new myosin motor-like chitin synthase gene,
chsVb
, has been identified in the vascular wilt fungus
Fusarium oxysporum
f. sp.
lycopersici
. Phylogenetic analysis of the deduced amino acid sequence of the
chsVb
chitin synthase 2 domain (CS2) revealed that ChsVb belongs to class VII chitin synthases. The ChsVb myosin motor-like domain (MMD) is shorter than the MMD of class V chitin synthases and does not contain typical ATP-binding motifs. Targeted disrupted single (Δ
chsVb
) and double (Δ
chsV
Δ
chsVb
) mutants were unable to infect and colonize tomato plants or grow invasively on tomato fruit tissue. These strains were hypersensitive to compounds that interfere with fungal cell wall assembly, produced lemon-like shaped conidia, and showed swollen balloon-like structures in hyphal subapical regions, thickened walls, aberrant septa, and intrahyphal hyphae. Our results suggest that the
chsVb
gene is likely to function in polarized growth and confirm the critical importance of cell wall integrity in the complex infection process of this fungus.
Three Pathogenicity Islands of
Vibrio cholerae
Can Excise from the Chromosome and Form Circular Intermediates
Authors: Murphy Ronan A. , Boyd E. Fidelma 
Published: November 2007

ABSTRACT

Vibrio
pathogenicity island-2 (VPI-2) is a 57-kb region integrated at a transfer RNA (tRNA)-serine locus that encompasses VC1758 to VC1809 on the
V. cholerae
N16961 genome and is present in pandemic isolates. VPI-2 encodes a P4-like integrase, a restriction modification system, a Mu phage-like region, and a sialic acid metabolism region, as well as neuraminidase (VC1784), which is a glycosylhydrolase known to release sialic acid from sialoglycoconjugates to unmask GM1 gangliosides, the receptor for cholera toxin. We examined the tRNA-serine locus among the sequenced
V. cholerae
genomes and identified five variant VPI-2 regions, four of which retained the sialometabolism region. Three variant VPI-2 regions contained a type three secretion system. By using an inverse nested PCR approach, we found that the VPI-2 region can form an extrachromosomal circular intermediate (CI) molecule after precise excision from its tRNA-serine attachment site. We constructed a knockout mutant of VC1758 (
int
) with
V. cholerae
strain N16961 and found that no excision PCR product was produced, indicating that a functional cognate, VPI-2 integrase, is required for excision. The
Vibrio
seventh pandemic island-I (VSP-I) and VSP-II regions are present in
V. cholerae
O1 El Tor and O139 serogroup isolates. Novel regions are present at the VSP-I insertion site in strain MZO-3 and at the VSP-II insertion site in strain 623-39. VSP-II is a 27-kb region that integrates at a tRNA-methionine locus, is flanked by direct repeats, and encodes a P4-like integrase. We show that VSP-II can excise and form a CI and that the cognate VSP-II integrase is required for excision. Interestingly, VSP-I is not inserted at a tRNA locus and does encode a XerDC-like recombinase, but similar to VPI-2 and VSP-II, VSP-I does excise from the genome to form a CI. These results show that all three pathogenicity islands can excise from the chromosome, which is likely a first step in their horizontal transfer.
Global Genomic Analysis of
Pseudomonas savastanoi
pv. savastanoi Plasmids
Authors: Pérez-Martínez Isabel , Zhao Youfu , Murillo Jesús , Sundin George W. , Ramos Cayo 
Published: November 2007

ABSTRACT

Pseudomonas savastanoi
pv. savastanoi strains harbor native plasmids belonging to the pPT23A plasmid family (PFPs) which are detected in all pathovars of the related species
Pseudomonas syringae
examined and contribute to the ecological and pathogenic fitness of their host. However, there is a general lack of information about the gene content of
P. savastanoi
pv. savastanoi plasmids and their role in the interaction of this pathogen with olive plants. We designed a DNA macroarray containing 135 plasmid-borne
P. syringae
genes to conduct a global genetic analysis of 32 plasmids obtained from 10
P. savastanoi
pv. savastanoi strains. Hybridization results revealed that the number of PFPs per strain varied from one to four. Additionally, most strains contained at least one plasmid (designated non-PFP) that did not hybridize to the
repA
gene of pPT23A. Only three PFPs contained genes involved in the biosynthesis of the virulence factor indole-3-acetic acid (
iaaM
,
iaaH
, and
iaaL
). In contrast,
ptz
, a gene involved in the biosynthesis of cytokinins, was found in five PFPs and one non-PFP. Genes encoding a type IV secretion system (T4SS), type IVA, were found in both PFPs and non-PFPs; however, type IVB genes were found only on PFPs. Nine plasmids encoded both T4SSs, whereas seven other plasmids carried none of these genes. Most PFPs and non-PFPs hybridized to at least one putative type III secretion system effector gene and to a variety of additional genes encoding known
P. syringae
virulence factors and one or more insertion sequence transposase genes. These results indicate that non-PFPs may contribute to the virulence and fitness of the
P. savastanoi
pv. savastanoi host. The overall gene content of
P. savastanoi
pv. savastanoi plasmids, with their repeated information, mosaic arrangement, and insertion sequences, suggests a possible role in adaptation to a changing environment.
Interaction ofBacillus subtilisCodY with GTP
Authors: Handke Luke D. , Shivers Robert P. , Sonenshein Abraham L. 
Published: November 2007

ABSTRACTMany of the adaptive mechanisms that allowBacillus subtilisto adjust to changes in nutrient availability are controlled by CodY. Binding of CodY to its target genes is stimulated by interaction with its effectors, GTP and the branched-chain amino acids (BCAAs). Upon nutrient limitation, intracellular pools of these effectors are depleted and CodY can no longer repress genes required for adaptation. In vitro studies reported here explored in more detail the interaction of CodY with GTP. DNase I footprinting experiments indicated that CodY has an affinity for GTP in the millimolar range. Further, CodY was shown to interact specifically with GTP and dGTP; no other naturally occurring nucleotides that were tested, including ppGpp and pppGpp, resulted in DNA protection. Two nonhydrolyzable analogs of GTP were fully able to activate CodY binding to target DNA, demonstrating that GTP hydrolysis is not necessary for CodY-dependent regulation. GTP and the BCAAs were shown to act additively to increase the affinity of CodY for DNA; increased protection was observed in DNase I footprinting experiments when both effectors were present, compared to either effector alone, and in in vitro transcription reactions, transcriptional repression by CodY was stronger in the presence of both GTP and BCAAs than of BCAAs alone. Thus, interaction of CodY with GTP is specific and results in increased affinity for its target genes. This increase in affinity is independent of GTP hydrolysis and is augmented in the presence of BCAAs.
LmrR Is a Transcriptional Repressor of Expression of the Multidrug ABC Transporter LmrCD in
Lactococcus lactis
Authors: Agustiandari Herfita , Lubelski Jacek , van den Berg van Saparoea H. Bart , Kuipers Oscar P. , Driessen Arnold J. M. 
Published: November 2007

ABSTRACT

LmrCD is an ABC-type multidrug transporter in
Lactococcus lactis
. LmrR encodes a putative transcriptional regulator. In a Δ
lmrR
strain,
lmrCD
is up-regulated. LmrR binds the promoter region of
lmrCD
and interacts with drugs that cause
lmrCD
up-regulation. This suggests that LmrR is a drug-dependent transcriptional regulator of
lmrCD
expression.
Crystal Structure of PhnH: an Essential Component of Carbon-Phosphorus Lyase in
Escherichia coli
Authors: Adams Melanie A. , Luo Yan , Hove-Jensen Bjarne , He Shu-Mei , van Staalduinen Laura M. , Zechel David L. , Jia Zongchao 
Published: November 2007

ABSTRACT

Organophosphonates are reduced forms of phosphorous that are characterized by the presence of a stable carbon-phosphorus (C-P) bond, which resists chemical hydrolysis, thermal decomposition, and photolysis. The chemically inert nature of the C-P bond has raised environmental concerns as toxic phosphonates accumulate in a number of ecosystems. Carbon-phosphorous lyase (CP lyase) is a multienzyme pathway encoded by the
phn
operon in gram-negative bacteria. In
Escherichia coli
14 cistrons comprise the operon (
phnCDEFGHIJKLMNOP
) and collectively allow the internalization and degradation of phosphonates. Here we report the X-ray crystal structure of the PhnH component at 1.77 Å resolution. The protein exhibits a novel fold, although local similarities with the pyridoxal 5′-phosphate-dependent transferase family of proteins are apparent. PhnH forms a dimer in solution and in the crystal structure, the interface of which is implicated in creating a potential ligand binding pocket. Our studies further suggest that PhnH may be capable of binding negatively charged cyclic compounds through interaction with strictly conserved residues. Finally, we show that PhnH is essential for C-P bond cleavage in the CP lyase pathway.
Genome Sequence of
Lactobacillus helveticus
, an Organism Distinguished by Selective Gene Loss and Insertion Sequence Element Expansion
Authors: Callanan Michael , Kaleta Pawel , O'Callaghan John , O'Sullivan Orla , Jordan Kieran , McAuliffe Olivia , Sangrador-Vegas Amaia , Slattery Lydia , Fitzgerald Gerald F. , Beresford Tom , Ross R. Paul 
Published: November 2007

ABSTRACT

Mobile genetic elements are major contributing factors to the generation of genetic diversity in prokaryotic organisms. For example, insertion sequence (IS) elements have been shown to specifically contribute to niche adaptation by promoting a variety of genetic rearrangements. The complete genome sequence of the cheese culture
Lactobacillus helveticus
DPC 4571 was determined and revealed significant conservation compared to three nondairy gut lactobacilli. Despite originating from significantly different environments, 65 to 75% of the genes were conserved between the commensal and dairy lactobacilli, which allowed key niche-specific gene sets to be described. However, the primary distinguishing feature was 213 IS elements in the DPC 4571 genome, 10 times more than for the other lactobacilli. Moreover, genome alignments revealed an unprecedented level of genome stability between these four
Lactobacillus
species, considering the number of IS elements in the
L. helveticus
genome. Comparative analysis also indicated that the IS elements were not the primary agents of niche adaptation for the
L. helveticus
genome. A clear bias toward the loss of genes reported to be important for gut colonization was observed for the cheese culture, but there was no clear evidence of IS-associated gene deletion and decay for the majority of genes lost. Furthermore, an extraordinary level of sequence diversity exists between copies of certain IS elements in the DPC 4571 genome, indicating they may represent an ancient component of the
L. helveticus
genome. These data suggest a special unobtrusive relationship between the DPC 4571 genome and its mobile DNA complement.
Novel Protein Antigen (JHP940) from the Genomic Plasticity Region ofHelicobacter pyloriInduces Tumor Necrosis Factor Alpha and Interleukin-8 Secretion by Human Macrophages
Authors: Rizwan Mohammed , Alvi Ayesha , Ahmed Niyaz 
Published: November 2007

ABSTRACTThe plasticity region of theHelicobacter pylorigenome comprises strain-specific gene loci. We performed genotyping and functional biology analysis of one such locus (jhp940) that was previously found to be functionally unknown but present in gastric cancer-associated strains from many different countries. We found its geographic prevalence to be independent ofcagApresence and disease status. Cloning, expression, and purification of JHP940 revealed a novel, ∼36-kDa protein in a biologically active form which elicited strong and significant levels of tumor necrosis factor alpha and interleukin-8 in human macrophages. Also, JHP940 was able to induce enhanced translocation of the transcription factor NF-κB complex in cultured macrophages. The induction of the proinflammatory cytokines by JHP940, therefore, points to its putative role in chronic gastric inflammation and, possibly, the various other outcomes ofH. pyloriinfection, including gastric cancer.
Conditional Lethality, Division Defects, Membrane Involution, and Endocytosis inmreandmrdShape Mutants ofEscherichia coli
Authors: Bendezú Felipe O. , de Boer Piet A. J. 
Published: November 2007

ABSTRACTMaintenance of rod shape inEscherichia colirequires the shape proteins MreB, MreC, MreD, MrdA (PBP2), and MrdB (RodA). How loss of the Mre proteins affectsE. coliviability has been unclear. We generated Mre and Mrd depletion strains under conditions that minimize selective pressure for undefined suppressors and found their phenotypes to be very similar. Cells lacking one or more of the five proteins were fully viable and propagated as small spheres under conditions of slow mass increase but formed large nondividing spheroids with noncanonical FtsZ assembly patterns at higher mass doubling rates. Extra FtsZ was sufficient to suppress lethality in each case, allowing cells to propagate as small spheres under any condition. The failure of each unsuppressed mutant to divide under nonpermissive conditions correlated with the presence of elaborate intracytoplasmic membrane-bound compartments, including vesicles/vacuoles and more-complex systems. Many, if not all, of these compartments formed by FtsZ-independent involution of the cytoplasmic membrane (CM) rather than de novo. Remarkably, while some of the compartments were still continuous with the CM and the periplasm, many were topologically separate, indicating they had been released into the cytoplasm by an endocytic-like membrane fission event. Notably, cells failed to adjust the rate of phospholipid synthesis to their new surface requirements upon depletion of MreBCD, providing a rationale for the “excess” membrane in the resulting spheroids. Both FtsZ and MinD readily assembled on intracytoplasmic membrane surfaces, and we propose that this contributes significantly to the lethal division block seen in all shape mutants under nonpermissive conditions.
DNA Polymerase I Is Not Required for Replication of Linear Chromosomes in
Streptomyces
Authors: Huang Tzu-Wen , Chen Carton W. 
Published: November 2007

ABSTRACT

Both
polA
(encoding DNA polymerase I; Pol I) and a paralog were deleted from
Streptomyces
strains. Despite the UV sensitivity and slow growth caused by the Δ
polA
mutation, the double mutant was viable. Thus, in contrast to a previous postulate, Pol I and its paralog are not essential for replication of
Streptomyces
chromosomes.
Transcriptome Analysis of a Phenol-Producing
Pseudomonas putida
S12 Construct: Genetic and Physiological Basis for Improved Production
Authors: Wierckx Nick J. P. , Ballerstedt Hendrik , de Bont Jan A. M. , de Winde Johannes H. , Ruijssenaars Harald J. , Wery Jan 
Published: November 2007

ABSTRACT

The unknown genetic basis for improved phenol production by a recombinant
Pseudomonas putida
S12 derivative bearing the
tpl
(tyrosine-phenol lyase) gene was investigated via comparative transcriptomics, nucleotide sequence analysis, and targeted gene disruption. We show upregulation of tyrosine biosynthetic genes and possibly decreased biosynthesis of tryptophan caused by a mutation in the
trpE
gene as the genetic basis for the enhanced phenol production. In addition, several genes in degradation routes connected to the tyrosine biosynthetic pathway were upregulated. This either may be a side effect that negatively affects phenol production or may point to intracellular accumulation of tyrosine or its intermediates. A number of genes identified by the transcriptome analysis were selected for targeted disruption in
P. putida
S12TPL3. Physiological and biochemical examination of
P. putida
S12TPL3 and these mutants led to the conclusion that the metabolic flux toward tyrosine in
P. putida
S12TPL3 was improved to such an extent that the heterologous tyrosine-phenol lyase enzyme had become the rate-limiting step in phenol biosynthesis.