bluuebunny/crossref_metadata_2025_split huggingface dataset:
Silencing of Six Hydrophobins in
Cladosporium fulvum
: Complexities of Simultaneously Targeting Multiple Genes
Authors: Lacroix Hélène , Spanu Pietro D. 
Published: November 2008

ABSTRACT

In this study, we have constructed and expressed inverted repeat chimeras from the first exons of the six known hydrophobins of the fungus
Cladosporium fulvum
, the causal agent of tomato leaf mold. We used quantitative PCR to measure specifically the expression levels of the hydrophobins. The targeted genes are silenced to different degrees, but we also detected clear changes in the expression levels of nontargeted genes. This work highlights the difficulties that are likely to be encountered when attempting to silence more than one gene in a multigene family.
Lacticin Q, a Lactococcal Bacteriocin, Causes High-Level Membrane Permeability in the Absence of Specific Receptors
Authors: Yoneyama Fuminori , Imura Yuichi , Ichimasa Shiro , Fujita Koji , Zendo Takeshi , Nakayama Jiro , Matsuzaki Katsumi , Sonomoto Kenji 
Published: November 2008

ABSTRACT
To characterize the mode of action of lacticin Q (LnqQ), its membrane-permeabilizing activity was compared with that of nisin A because of the similar antimicrobial features of these compounds. Lipid II, the receptor for nisin A, was not required for LnqQ activity. LnqQ induced high-level membrane permeability in the absence of specific receptors.
Xylella fastidiosa
Afimbrial Adhesins Mediate Cell Transmission to Plants by Leafhopper Vectors
Authors: Killiny Nabil , Almeida Rodrigo P. P. 
Published: November 2008

ABSTRACT

The interactions between the economically important plant-pathogenic bacterium
Xylella fastidiosa
and its leafhopper vectors are poorly characterized. We used different approaches to determine how
X. fastidiosa
cells interact with the cuticular surface of the foreguts of vectors. We demonstrate that
X. fastidiosa
binds to different polysaccharides with various affinities and that these interactions are mediated by cell surface carbohydrate-binding proteins. In addition, competition assays showed that
N
-acetylglucosamine inhibits bacterial adhesion to vector foregut extracts and intact wings, demonstrating that attachment to leafhopper surfaces is affected in the presence of specific polysaccharides. In vitro experiments with several
X. fastidiosa
knockout mutants indicated that hemagglutinin-like proteins are associated with cell adhesion to polysaccharides. These results were confirmed with biological experiments in which hemagglutinin-like protein mutants were transmitted to plants by vectors at lower rates than that of the wild type. Furthermore, although these mutants were defective in adhesion to the cuticle of vectors, their growth rate once attached to leafhoppers was similar to that of the wild type, suggesting that these proteins are important for initial adhesion of
X. fastidiosa
to leafhoppers. We propose that
X. fastidiosa
colonization of leafhopper vectors is a complex, stepwise process similar to the formation of biofilms on surfaces.
Complete Fermentation of Xylose and Methylglucuronoxylose Derived from Methylglucuronoxylan by
Enterobacter asburiae
Strain JDR-1
Authors: Bi Changhao , Rice John D. , Preston James F. 
Published: November 2008

ABSTRACT

Acid pretreatment is commonly used to release pentoses from the hemicellulose fraction of cellulosic biomass for bioconversion. The predominant pentose in the hemicellulose fraction of hardwoods and crop residues is xylose in the polysaccharide methylglucuronoxylan, in which as many as one in six of the β-1,4-linked xylopyranose residues is substituted with α-1,2-linked 4-
O
-methylglucuronopyranose. Resistance of the α-1,2-methylglucuronosyl linkages to acid hydrolysis results in release of the aldobiuronate 4-
O
-methylglucuronoxylose, which is not fermented by bacterial biocatalysts currently used for bioconversion of hemicellulose.
Enterobacter asburiae
strain JDR-1, isolated from colonized hardwood (sweetgum), efficiently ferments both methylglucuronoxylose and xylose, producing predominantly ethanol and acetate.
13
C-nuclear magnetic resonance studies defined the Embden-Meyerhof pathway for metabolism of glucose and the pentose phosphate pathway for xylose metabolism. Rates of substrate utilization, product formation, and molar growth yields indicated methylglucuronoxylose is transported into the cell and hydrolyzed to release methanol, xylose, and hexauronate.
Enterobacter asburiae
strain JDR-1 is the first microorganism described that ferments methylglucuronoxylose generated along with xylose during the acid-mediated saccharification of hemicellulose. Genetic definition of the methylglucuronoxylose utilization pathway may allow metabolic engineering of established gram-negative bacterial biocatalysts for complete bioconversion of acid hydrolysates of methylglucuronoxylan. Alternatively,
Enterobacter asburiae
strain JDR-1 may be engineered for the efficient conversion of acid hydrolysates of hemicellulose to biofuels and chemical feedstocks.
Dual Role for the Tyrosine Decarboxylation Pathway inEnterococcus faeciumE17: Response to an Acid Challenge and Generation of a Proton Motive Force
Authors: Pereira C. I. , Matos D. , San Romão M. V. , Barreto Crespo M. T. 
Published: November 2008

ABSTRACTIn this work we investigated the role of the tyrosine decarboxylation pathway in the response ofEnterococcus faeciumE17 cells to an acid challenge. It was found that 91% of the cells were able to remain viable in the presence of tyrosine when they were incubated for 3 h in a complex medium at pH 2.5. This effect was shown to be related to the tyrosine decarboxylation pathway. Therefore, the role of tyrosine decarboxylation in pH homeostasis was studied. The membrane potential and pH gradient, the parameters that compose the proton motive force (PMF), were measured at different pHs (pH 4.5 to 7). We obtained evidence showing that the tyrosine decarboxylation pathway generates a PMF composed of a pH gradient formed due to proton consumption in the decarboxylation reaction and by a membrane potential which results from electrogenic transport of tyrosine in exchange for the corresponding biogenic amine tyramine. The properties of the tyrosine transporter were also studied in this work by using whole cells and right-side-out vesicles. The results showed that the transporter catalyzes homologous tyrosine/tyrosine antiport, as well as electrogenic heterologous tyrosine-tyramine exchange. The tyrosine transporter had properties of a typical precursor-product exchanger operating in a proton motive decarboxylation pathway. Therefore, the tyrosine decarboxylation pathway contributes to an acid response mechanism inE. faeciumE17. This decarboxylation pathway gives the strain a competitive advantage in nutrient-depleted conditions, as well as in harsh acidic environments, and a better chance of survival, which contributes to higher cell counts in food fermentation products.
Bioinformatic and Expression Analyses of Genes Mediating Zinc Homeostasis inNostoc punctiforme
Authors: Hudek Lee , Rai L. C. , Freestone David , Michalczyk Agnes , Gibson Maria , Song Y. F. , Ackland M. Leigh 
Published: November 2008

ABSTRACTZinc homeostasis was investigated inNostoc punctiforme. Cell tolerance to Zn2+over 14 days showed that ZnCl2levels above 22 μM significantly reduced cell viability. After 3 days in 22 μM ZnCl2, ca. 12% of the Zn2+was in an EDTA-resistant component, suggesting an intracellular localization. Zinquin fluorescence was detected within cells exposed to concentrations up to 37 μM relative to 0 μM treatment. Radiolabeled65Zn showed Zn2+uptake increased over a 3-day period, while efflux occurred more rapidly within a 3-h time period. Four putative genes involved in Zn2+uptake and efflux inN. punctiformewere identified: (i) the predicted Co/Zn/Cd cation transporter, putative CDF; (ii) the predicted divalent heavy-metal cation transporter, putative Zip; (iii) the ATPase component and Fe/Zn uptake regulation protein, putative Fur; and (iv) an ABC-type Mn/Zn transport system, putative zinc ZnuC, ZnuABC system component. Quantitative real-time PCR indicated the responsiveness of all four genes to 22 μM ZnCl2within 3 h, followed by a reduction to below basal levels after 24 h by putative ZIP, ZnuC, and Fur and a reduction to below basal level after 72 h by putative CDF efflux gene. These results demonstrate differential regulation of zinc transporters over time, indicating a role for them in zinc homeostasis inN. punctiforme.
Diversity and Seasonality of Bioluminescent
Vibrio cholerae
Populations in Chesapeake Bay
Authors: Zo Young-Gun , Chokesajjawatee Nipa , Grim Christopher , Arakawa Eiji , Watanabe Haruo , Colwell Rita R. 
Published: November 2008

ABSTRACT

Association of luminescence with phenotypic and genotypic traits and with environmental parameters was determined for 278 strains of
Vibrio cholerae
isolated from the Chesapeake Bay during 1998 to 2000. Three clusters of luminescent strains (A, B, and C) and two nonluminescent clusters (X and Y) were identified among 180 clonal types.
V. cholerae
O1 strains isolated during pandemics and endemic cholera in the Ganges Delta were related to cluster Y. Heat-stable enterotoxin (encoded by
stn
) and the membrane protein associated with bile resistance (encoded by
ompU
) were found to be linked to luminescence in strains of cluster A. Succession from nonluminescent to luminescent populations of
V. cholerae
occurred during spring to midsummer. Occurrence of cluster A strains in water with neutral pH was contrasted with that of cluster Y strains in water with a pH of >8. Cluster A was found to be associated with a specific calanoid population cooccurring with cyclopoids. Cluster B was related to cluster Y, with its maximal prevalence at pH 8. Occurrence of cluster B strains was more frequent with warmer water temperatures and negatively correlated with maturity of the copepod community. It is concluded that each cluster of luminescent
V. cholerae
strains occupies a distinct ecological niche. Since the dynamics of these niche-specific subpopulations are associated with zooplankton community composition, the ecology of luminescent
V. cholerae
is concluded to be related to its interaction with copepods and related crustacean species.
Flavodiiron Protein from
Trichomonas vaginalis
Hydrogenosomes: the Terminal Oxygen Reductase
Authors: Smutná Tamara , Gonçalves Vera L. , Saraiva Lígia M. , Tachezy Jan , Teixeira Miguel , Hrdý Ivan 
Published: November 2008

ABSTRACT

Trichomonas vaginalis
is one of a few eukaryotes that have been found to encode several homologues of flavodiiron proteins (FDPs). Widespread among anaerobic prokaryotes, these proteins are believed to function as oxygen and/or nitric oxide reductases to provide protection against oxidative/nitrosative stresses and host immune responses. One of the
T. vaginalis
FDP homologues is equipped with a hydrogenosomal targeting sequence and is expressed in the hydrogenosomes, oxygen-sensitive organelles that participate in carbohydrate metabolism and assemble iron-sulfur clusters. The bacterial homologues characterized thus far have been dimers or tetramers; the trichomonad protein is a dimer of identical 45-kDa subunits, each noncovalently binding one flavin mononucleotide. The protein reduces dioxygen to water but is unable to utilize nitric oxide as a substrate, similarly to its closest homologue from another human parasite
Giardia intestinalis
and related archaebacterial proteins.
T. vaginalis
FDP is able to accept electrons derived from pyruvate or NADH via ferredoxin and is proposed to play a role in the protection of hydrogenosomes against oxygen.
Trimeric Autotransporters ofHaemophilus parasuis: Generation of an Extensive Passenger Domain Repertoire Specific for Pathogenic Strains
Authors: Pina Sonia , Olvera Alex , Barceló Anna , Bensaid Albert 
Published: November 2008

ABSTRACTHaemophilus parasuisis the agent responsible for causing Glässer's disease, but little is known about the pathogenic determinants of this major pig disease. Here we describe, for the pathogenic strain Nagasaki, the molecular characterization of 13 trimeric autotransporters as assessed by the presence of YadA C-terminal translocator domains which were classified into three groups. All passenger domains possess motifs and repeats characteristic of adhesins, hemagglutinins, and invasins with various centrally located copies of collagen-like repeats. This domain architecture is shared with two trimeric autotransporter proteins ofH. somnus129Pt. Genomic comparison by microarray hybridization demonstrated homologies amongH. parasuisvirulent strains and high divergence with respect to nonvirulent strains. Therefore, these genes were namedvtaA(virulence-associatedtrimericautotransporters). The sequencing of 17 homologousvtaAgenes of different invasive strains highlighted an extensive mosaic structure. Based also on the presence of DNA uptake signal sequences within thevtaAgenes, we propose a mechanism of evolution by which gene duplication and the accumulation of mutations and recombinations, plus the lateral gene transfer of the passenger domain, led to the diversity of this multigene family. This study provides insights to help understand the tissue colonization and invasiveness characteristic ofH. parasuispathogenic strains.
Eicosapentaenoic Acid Plays a Beneficial Role in Membrane Organization and Cell Division of a Cold-Adapted Bacterium,Shewanella livingstonensisAc10
Authors: Kawamoto Jun , Kurihara Tatsuo , Yamamoto Kentaro , Nagayasu Makiko , Tani Yasushi , Mihara Hisaaki , Hosokawa Masashi , Baba Takeshi , Sato Satoshi B. , Esaki Nobuyoshi 
Published: November 2008

ABSTRACTShewanella livingstonensisAc10, a psychrotrophic gram-negative bacterium isolated from Antarctic seawater, produces eicosapentaenoic acid (EPA) as a component of phospholipids at low temperatures. EPA constitutes about 5% of the total fatty acids of cells grown at 4°C. We found that five genes, termedorf2, orf5, orf6, orf7, andorf8, are specifically required for the synthesis of EPA by targeted disruption of the respective genes. The mutants lacking EPA showed significant growth retardation at 4°C but not at 18°C. Supplementation of a synthetic phosphatidylethanolamine that contained EPA at thesn-2 position complemented the growth defect. The EPA-less mutant became filamentous, and multiple nucleoids were observed in a single cell at 4°C, indicating that the mutant has a defect in cell division. Electron microscopy of the cells by high-pressure freezing and freeze-substitution revealed abnormal intracellular membranes in the EPA-less mutant at 4°C. We also found that the amounts of several membrane proteins were affected by the depletion of EPA. While polyunsaturated fatty acids are often considered to increase the fluidity of the hydrophobic membrane core, diffusion of a small hydrophobic molecule, pyrene, in the cell membranes and large unilamellar vesicles prepared from the lipid extracts was very similar between the EPA-less mutant and the parental strain. These results suggest that EPA inS. livingstonensisAc10 is not required for bulk bilayer fluidity but plays a beneficial role in membrane organization and cell division at low temperatures, possibly through specific interaction between EPA and proteins involved in these cellular processes.
Acid-Susceptible Mutants ofMycobacterium tuberculosisShare Hypersusceptibility to Cell Wall and Oxidative Stress and to the Host Environment
Authors: Vandal Omar H. , Roberts Julia A. , Odaira Toshiko , Schnappinger Dirk , Nathan Carl F. , Ehrt Sabine 
Published: November 2008

ABSTRACTMycobacterium tuberculosiscan persist in macrophage phagosomes that acidify to a pH of ∼4.5 after activation of the macrophage with gamma interferon. How the bacterium resists the low pH of the acidified phagosome is incompletely understood. A screen of 10,100M. tuberculosistransposon mutants for mutants hypersensitive to pH 4.5 led to the discovery of 21 genes whose disruption attenuated survival ofM. tuberculosisat a low pH (41). Here, we show that acid-sensitiveM. tuberculosismutants with transposon insertions in Rv2136c, Rv2224c,ponA2, andlysXwere hypersensitive to antibiotics, sodium dodecyl sulfate, heat shock, and reactive oxygen and nitrogen intermediates, indicating that acid resistance can be associated with protection against other forms of stress. The Rv2136c mutant was impaired in intrabacterial pH homeostasis and unable to maintain a neutral intrabacterial pH in activated macrophages. The Rv2136c, Rv2224c, andponA2mutants were attenuated in mice, with the Rv2136c mutant displaying the most severe level of attenuation. Pathways utilized byM. tuberculosisfor acid resistance and intrabacterial pH maintenance are potential targets for chemotherapy.
Hydrogen Peroxide-Mediated Interference Competition by
Streptococcus pneumoniae
Has No Significant Effect on
Staphylococcus aureus
Nasal Colonization of Neonatal Rats
Authors: Margolis Elisa 
Published: November 2008

ABSTRACT

It has been proposed that the relative scarcity of
Staphylococcus aureus
and
Streptococcus pneumoniae
cocolonization in the nasopharynxes of humans can be attributed to hydrogen peroxide-mediated interference competition. Previously it has been shown in vitro that H
2
O
2
produced by
S. pneumoniae
is bactericidal to
S. aureus
. To ascertain whether H
2
O
2
has this inhibitory effect in the nasal passages of neonatal rats, colonization experiments were performed with
S. aureus
and
S. pneumoniae
. The results of these experiments with neonatal rats are inconsistent with the hypothesis that hydrogen peroxide-mediated killing of
S. aureus
by
S. pneumoniae
is responsible for the relative scarcity of cocolonization by these bacteria. In mixed-inoculum colonization experiments and experiments where
S. aureus
invaded the nasopharynxes of rats with established
S. pneumoniae
populations, the density of
S. aureus
did not differ whether the
S. pneumoniae
strain was H
2
O
2
secreting or non-H
2
O
2
secreting (SpxB). Moreover, the advantage of catalase production by
S. aureus
in competition with a non-catalase-producing strain (KatA) during nasal colonization was no greater in the presence of H
2
O
2
-producing
S. pneumoniae
than in the presence of non-H
2
O
2
-producing
S. pneumoniae
.
Transforming DNA Uptake Gene Orthologs Do Not Mediate Spontaneous Plasmid Transformation in
Escherichia coli
Authors: Sun Dongchang , Zhang Xuewu , Wang Lingyu , Prudhomme Marc , Xie Zhixiong , Martin Bernard , Claverys Jean-Pierre 
Published: November 2008

ABSTRACT

Spontaneous plasmid transformation of
Escherichia coli
occurs on nutrient-containing agar plates.
E. coli
has also been reported to use double-stranded DNA (dsDNA) as a carbon source. The mechanism(s) of entry of exogenous dsDNA that allows plasmid establishment or the use of DNA as a nutrient remain(s) unknown. To further characterize plasmid transformation, we first documented the stimulation of transformation by agar and agarose. We provide evidence that stimulation is not due to agar contributing a supplement of Ca
2+
, Fe
2+
, Mg
2+
, Mn
2+
, or Zn
2+
. Second, we undertook to inactivate the
E. coli
orthologues of
Haemophilus influenzae
components of the transformation machine that allows the uptake of single-stranded DNA (ssDNA) from exogenous dsDNA. The putative outer membrane channel protein (HofQ), transformation pseudopilus component (PpdD), and transmembrane pore (YcaI) are not required for plasmid transformation. We conclude that plasmid DNA does not enter
E. coli
cells as ssDNA. The finding that purified plasmid monomers transform
E. coli
with single-hit kinetics supports this conclusion; it establishes that a unique monomer molecule is sufficient to give rise to a transformant, which is not consistent with the reconstitution of an intact replicon through annealing of partially overlapping complementary ssDNA, taken up from two independent monomers. We therefore propose that plasmid transformation involves internalization of intact dsDNA molecules. Our data together, with previous reports that HofQ is required for the use of dsDNA as a carbon source, suggest the existence of two routes for DNA entry, at least across the outer membrane of
E. coli
.
Defects in the Error Prevention Oxidized Guanine System Potentiate Stationary-Phase Mutagenesis in
Bacillus subtilis
Authors: Vidales Luz E. , Cárdenas Lluvia C. , Robleto Eduardo , Yasbin Ronald E. , Pedraza-Reyes Mario 
Published: November 2008

ABSTRACT

Previous studies showed that a
Bacillus subtilis
strain deficient in mismatch repair (MMR; encoded by the
mutSL
operon) promoted the production of stationary-phase-induced mutations. However, overexpression of the
mutSL
operon did not completely suppress this process, suggesting that additional DNA repair mechanisms are involved in the generation of stationary-phase-associated mutants in this bacterium. In agreement with this hypothesis, the results presented in this work revealed that starved
B. subtilis
cells lacking a functional error prevention GO (8-oxo-G) system (composed of YtkD, MutM, and YfhQ) had a dramatic propensity to increase the number of stationary-phase-induced revertants. These results strongly suggest that the occurrence of mutations is exacerbated by reactive oxygen species in nondividing cells of
B. subtilis
having an inactive GO system. Interestingly, overexpression of the MMR system significantly diminished the accumulation of mutations in cells deficient in the GO repair system during stationary phase. These results suggest that the MMR system plays a general role in correcting base mispairing induced by oxidative stress during stationary phase. Thus, the absence or depression of both the MMR and GO systems contributes to the production of stationary-phase mutants in
B. subtilis.
In conclusion, our results support the idea that oxidative stress is a mechanism that generates genetic diversity in starved cells of
B. subtilis
, promoting stationary-phase-induced mutagenesis in this soil microorganism.
Characterization of themyo-Inositol Utilization Island ofSalmonella entericaserovar Typhimurium
Authors: Kröger Carsten , Fuchs Thilo M. 
Published: November 2008

ABSTRACTKnockout mutation of STM4432 resulted in a growth-deficient phenotype ofSalmonella entericaserovar Typhimurium in the presence ofmyo-inositol (MI) as the sole carbon source. STM4432 is part of a 22.6-kb genomic island which spans STM4417 to STM4436 (genomic island 4417/4436) and is responsible for MI degradation. Genome comparison revealed the presence of this island in only sixSalmonellastrains and a high variability of theiolgene organization in gram-negative bacteria. Upon nonpolar deletion of 11 island loci, the genes involved in six enzymatic steps of the MI pathway were identified. The generation time ofS. entericaserovar Typhimurium in minimal medium with MI decreases with higher concentrations of this polyol. Reverse transcriptase PCR showed five separate transcriptional units encompassing the genesiolA-iolB,iolE-iolG1,iolC1-iolC2,iolD1-iolD2-iolG2, andiolI2-iolH. Luciferase reporter assays revealed a strong induction of their promoters in the presence of MI but not glucose. The main regulator, IolR, was identified due to a reduced lag phase of a strain mutated in STM4417 (iolR). Deletion ofiolRresulted in stimulation of theioloperons, indicating its negative effect on theiolgenes ofS. entericaserovar Typhimurium in rich medium at a transcriptional level. Bandshift assays demonstrated the binding of this putative repressor to promoter sequences ofiolA,iolC1, andiolD1. Binding of IolR to its own promoter and inducediolRexpression in an IolR-negative background demonstrate that its transcription is autoregulated. This is the first characterization of MI degradation in a gram-negative bacterium, revealing a complex transcriptional organization and regulation of theS. entericaserovar Typhimuriumiolgenes.