bluuebunny/crossref_metadata_2025_split huggingface dataset:
Conjugative Plasmid Transfer and Adhesion Dynamics in an
Escherichia coli
Biofilm
Authors: Ong Cheryl-Lynn Y. , Beatson Scott A. , McEwan Alastair G. , Schembri Mark A. 
Published: August 2009

ABSTRACT

A conjugative plasmid from the catheter-associated urinary tract infection strain
Escherichia coli
MS2027 was sequenced and annotated. This 42,644-bp plasmid, designated pMAS2027, contains 58 putative genes and is most closely related to plasmids belonging to incompatibility group X (IncX1). Plasmid pMAS2027 encodes two important virulence factors: type 3 fimbriae and a type IV secretion (T4S) system. Type 3 fimbriae, recently found to be functionally expressed in
E. coli
, played an important role in biofilm formation. Biofilm formation by
E. coli
MS2027 was specifically due to expression of type 3 fimbriae and not the T4S system. The T4S system, however, accounted for the conjugative ability of pMAS2027 and enabled a non-biofilm-forming strain to grow as part of a mixed biofilm following acquisition of this plasmid. Thus, the importance of conjugation as a mechanism to spread biofilm determinants was demonstrated. Conjugation may represent an important mechanism by which type 3 fimbria genes are transferred among the
Enterobacteriaceae
that cause device-related infections in nosocomial settings.
Proteogenomic Monitoring of
Geobacter
Physiology during Stimulated Uranium Bioremediation
Authors: Wilkins Michael J. , VerBerkmoes Nathan C. , Williams Kenneth H. , Callister Stephen J. , Mouser Paula J. , Elifantz Hila , N′Guessan A. Lucie , Thomas Brian C. , Nicora Carrie D. , Shah Manesh B. , Abraham Paul , Lipton Mary S. , Lovley Derek R. , Hettich Robert L. , Long Philip E. , Banfield Jillian F. 
Published: August 2009

ABSTRACT

Implementation of uranium bioremediation requires methods for monitoring the membership and activities of the subsurface microbial communities that are responsible for reduction of soluble U(VI) to insoluble U(IV). Here, we report a proteomics-based approach for simultaneously documenting the strain membership and microbial physiology of the dominant
Geobacter
community members during in situ acetate amendment of the U-contaminated Rifle, CO, aquifer. Three planktonic
Geobacter
-dominated samples were obtained from two wells down-gradient of acetate addition. Over 2,500 proteins from each of these samples were identified by matching liquid chromatography-tandem mass spectrometry spectra to peptides predicted from seven isolate
Geobacter
genomes. Genome-specific peptides indicate early proliferation of multiple M21 and
Geobacter bemidjiensis
-like strains and later possible emergence of M21 and
G. bemidjiensis
-like strains more closely related to
Geobacter lovleyi
. Throughout biostimulation, the proteome is dominated by enzymes that convert acetate to acetyl-coenzyme A and pyruvate for central metabolism, while abundant peptides matching tricarboxylic acid cycle proteins and ATP synthase subunits were also detected, indicating the importance of energy generation during the period of rapid growth following the start of biostimulation. Evolving
Geobacter
strain composition may be linked to changes in protein abundance over the course of biostimulation and may reflect changes in metabolic functioning. Thus, metagenomics-independent community proteogenomics can be used to diagnose the status of the subsurface consortia upon which remediation biotechnology relies.
Temperature-Dependent Expression of
phzM
and Its Regulatory Genes
lasI
and
ptsP
in Rhizosphere Isolate
Pseudomonas
sp. Strain M18
Authors: Huang Jiaofang , Xu Yuquan , Zhang Hongyan , Li Yaqian , Huang Xianqing , Ren Bin , Zhang Xuehong 
Published: August 2009

ABSTRACT

Pseudomonas
sp. strain M18, an effective biological control agent isolated from the melon rhizosphere, has a genetic background similar to that of the opportunistic human pathogen
Pseudomonas aeruginosa
PAO1. However, the predominant phenazine produced by strain M18 is phenazine-1-carboxylic acid (PCA) rather than pyocyanin (PYO); the quantitative ratio of PCA to PYO is 105 to 1 at 28°C in strain M18, while the ratio is 1 to 2 at 37°C in strain PAO1. We first provided evidence that the differential production of the two phenazines in strains M18 and PAO1 is related to the temperature-dependent and strain-specific expression patterns of
phzM
, a gene involved in the conversion of PCA to PYO. Transcriptional levels of
phzM
were measured by quantitative real-time PCR, and the activities of both transcriptional and translational
phzM
′-′
lacZ
fusions were determined in strains M18 and PAO1, respectively. Using
lasI
::Gm and
ptsP
::Gm inactivation M18 mutants, we further show that expression of the
phzM
gene is positively regulated by the quorum-sensing protein LasI and negatively regulated by the phosphoenolpyruvate phosphotransferase protein PtsP. Surprisingly, the
lasI
and
ptsP
regulatory genes were also expressed in a temperature-dependent and strain-specific manner. The differential production of the phenazines PCA and PYO by strains M18 and PAO1 may be a consequence of selective pressure imposed on
P. aeruginosa
PAO1 and its relative M18 in the two different niches over a long evolutionary process.
Small-Colony Variant Selection as a Survival Strategy for
Staphylococcus aureus
in the Presence of
Pseudomonas aeruginosa
Authors: Biswas Lalitha , Biswas Raja , Schlag Martin , Bertram Ralph , Götz Friedrich 
Published: August 2009

ABSTRACT

Previously it has been demonstrated that
Staphylococcus aureus
is sensitive toward
Pseudomonas
-secreted exotoxins, which preferentially target the electron transport chain in staphylococci. Here it is shown that a subpopulation of
S. aureus
survives these respiratory toxins of
P
seudomonas aeruginosa
by selection of the small-colony variant (SCV) phenotype. Purified pyocyanin alone causes the same effect. A
hem
B
mutant of
S. aureus
survives cocultivation with
P. aeruginosa
without a decrease in CFU.
Protozoan-Induced Regulation of Cyclic Lipopeptide Biosynthesis Is an Effective Predation Defense Mechanism forPseudomonas fluorescens
Authors: Mazzola Mark , de Bruijn Irene , Cohen Michael F. , Raaijmakers Jos M. 
Published: August 2009

ABSTRACTEnvironmental bacteria are exposed to a myriad of biotic interactions that influence their function and survival. The grazing activity of protozoan predators significantly impacts the dynamics, diversification, and evolution of bacterial communities in soil ecosystems. To evade protozoan predation, bacteria employ various defense strategies. Soil-dwellingPseudomonas fluorescensstrains SS101 and SBW25 produce the cyclic lipopeptide surfactants (CLPs) massetolide and viscosin, respectively, in a quorum-sensing-independent manner. In this study, CLP production was shown to protect these bacteria from protozoan predation as, compared to CLP-deficient mutants, strains SS101 and SBW25 exhibited resistance to grazing byNaegleria americanain vitro and superior persistence in soil in the presence of this bacterial predator. In the wheat rhizosphere, CLP-producing strains had a direct deleterious impact on the survival ofN. americana. In vitro assays further showed thatN. americanawas three times more sensitive to viscosin than to massetolide and that exposure of strain SS101 or SBW25 to this protozoan resulted in upregulation of CLP biosynthesis genes. Enhanced expression of themassABCandviscABCgenes did not require physical contact between the two organisms as gene expression levels were up to threefold higher in bacterial cells harvested 1 cm from feeding protozoans than in cells collected 4 cm from feeding protozoans. These findings document a new natural function of CLPs and highlight that bacterium-protozoan interactions can result in activation of an antipredator response in prey populations.
The Bacterially Produced Metabolite Violacein Is Associated with Survival of Amphibians Infected with a Lethal Fungus
Authors: Becker Matthew H. , Brucker Robert M. , Schwantes Christian R. , Harris Reid N. , Minbiole Kevin P. C. 
Published: August 2009

ABSTRACT

The disease chytridiomycosis, which is caused by the chytrid fungus
Batrachochytrium dendrobatidis
, is associated with recent declines in amphibian populations. Susceptibility to this disease varies among amphibian populations and species, and resistance appears to be attributable in part to the presence of antifungal microbial species associated with the skin of amphibians. The betaproteobacterium
Janthinobacterium lividum
has been isolated from the skins of several amphibian species and produces the antifungal metabolite violacein, which inhibits
B. dendrobatidis
. In this study, we added
J. lividum
to red-backed salamanders (
Plethodon cinereus
) to obtain an increased range of violacein concentrations on the skin. Adding
J. lividum
to the skin of the salamander increased the concentration of violacein on the skin, which was strongly associated with survival after experimental exposure to
B. dendrobatidis
. As expected from previous work, some individuals that did not receive
J. lividum
and were exposed to
B. dendrobatidis
survived. These individuals had concentrations of bacterially produced violacein on their skins that were predicted to kill
B. dendrobatidis
. Our study suggests that a threshold violacein concentration of about 18 μM on a salamander's skin prevents mortality and morbidity caused by
B. dendrobatidis
. In addition, we show that over one-half of individuals in nature support antifungal bacteria that produce violacein, which suggests that there is a mutualism between violacein-producing bacteria and
P. cinereus
and that adding
J. lividum
is effective for protecting individuals that lack violacein-producing skin bacteria.
Novel Features of the Polysaccharide-Digesting Gliding Bacterium
Flavobacterium johnsoniae
as Revealed by Genome Sequence Analysis
Authors: McBride Mark J. , Xie Gary , Martens Eric C. , Lapidus Alla , Henrissat Bernard , Rhodes Ryan G. , Goltsman Eugene , Wang Wei , Xu Jian , Hunnicutt David W. , Staroscik Andrew M. , Hoover Timothy R. , Cheng Yi-Qiang , Stein Jennifer L. 
Published: August 2009

ABSTRACT

The 6.10-Mb genome sequence of the aerobic chitin-digesting gliding bacterium
Flavobacterium johnsoniae
(phylum
Bacteroidetes
) is presented.
F. johnsoniae
is a model organism for studies of bacteroidete gliding motility, gene regulation, and biochemistry. The mechanism of
F. johnsoniae
gliding is novel, and genome analysis confirms that it does not involve well-studied motility organelles, such as flagella or type IV pili. The motility machinery is composed of Gld proteins in the cell envelope that are thought to comprise the “motor” and SprB, which is thought to function as a cell surface adhesin that is propelled by the motor. Analysis of the genome identified genes related to
sprB
that may encode alternative adhesins used for movement over different surfaces. Comparative genome analysis revealed that some of the
gld
and
spr
genes are found in nongliding bacteroidetes and may encode components of a novel protein secretion system.
F. johnsoniae
digests proteins, and 125 predicted peptidases were identified.
F. johnsoniae
also digests numerous polysaccharides, and 138 glycoside hydrolases, 9 polysaccharide lyases, and 17 carbohydrate esterases were predicted. The unexpected ability of
F. johnsoniae
to digest hemicelluloses, such as xylans, mannans, and xyloglucans, was predicted based on the genome analysis and confirmed experimentally. Numerous predicted cell surface proteins related to
Bacteroides thetaiotaomicron
SusC and SusD, which are likely involved in binding of oligosaccharides and transport across the outer membrane, were also identified. Genes required for synthesis of the novel outer membrane flexirubin pigments were identified by a combination of genome analysis and genetic experiments. Genes predicted to encode components of a multienzyme nonribosomal peptide synthetase were identified, as were novel aspects of gene regulation. The availability of techniques for genetic manipulation allows rapid exploration of the features identified for the polysaccharide-digesting gliding bacteroidete
F. johnsoniae
.
Goa1p of
Candida albicans
Localizes to the Mitochondria during Stress and Is Required for Mitochondrial Function and Virulence
Authors: Bambach Adrienne , Fernandes Mariana P. , Ghosh Anup , Kruppa Michael , Alex Deepu , Li Dongmei , Fonzi William A. , Chauhan Neeraj , Sun Nuo , Agrellos Orlando A. , Vercesi Anibal E. , Rolfes Ronda J. , Calderone Richard 
Published: August 2009

ABSTRACT

Using a Tn
7
transposon library of
Candida albicans
, we have identified a mutant that exhibited sensitivity in drop plate assays to oxidants such as menadione and hydrogen peroxide. To verify the role of the mutated gene in stress adaptation, null mutants were constructed and phenotypically characterized. Because of its apparent functions in growth and oxidant adaptation, we have named the gene
GOA1
. Goa1p appears to be unique to the CTG subclade of the
Saccharomycotina
, including
C. albicans
. Mutants of
C. albicans
lacking
goa1
(strain GOA31) were more sensitive to 6 mM H
2
O
2
and 0.125 mM menadione than the wild type (wt) or a gene-reconstituted (GOA32) strain. The sensitivity to oxidants correlated with reduced survival of the GOA31 mutant in human neutrophils and avirulence compared to control strains. Other phenotypes of GOA31 include reduced growth and filamentation in 10% serum, Spider, and SLAD agar media and an inability to form chlamydospores. Since Goa1p has an N-terminal mitochondrion localization site, we also show that green fluorescent protein-tagged Goa1p shows a mitochondrionlike distribution during oxidant or osmotic stress. Further, the inability of GOA31 to grow in medium containing lactate, ethanol, or glycerol as the sole carbon source indicates that the mitochondria are defective in the mutant. To determine how Goa1p contributes to mitochondrial function, we compared the wt, GOA32, and GOA31 strains for mitochondrial electrical membrane potential, respiration, and oxidative phosphorylation. We now show that GOA31, but not the wt or GOA32, had decreased respiration and mitochondrial membrane potential such that mutant cells are unable to drive oxidative phosphorylation. This is the first report in
C. albicans
of a respiratory defect caused by a loss of mitochondrial membrane potential.
Streptococcus mutansCompetence-Stimulating Peptide InhibitsCandida albicansHypha Formation
Authors: Jarosz Lucja M. , Deng Dong Mei , van der Mei Henny C. , Crielaard Wim , Krom Bastiaan P. 
Published: August 2009

ABSTRACTThe oral cavity is colonized by microorganisms growing in biofilms in which interspecies interactions take place.Streptococcus mutansgrows in biofilms on enamel surfaces and is considered one of the main etiological agents of human dental caries.Candida albicansis also commonly found in the human oral cavity, where it interacts withS. mutans. C. albicansis a polymorphic fungus, and the yeast-to-hypha transition is involved in virulence and biofilm formation. The aim of this study was to investigate interkingdom communication betweenC. albicansandS. mutansbased on the production of secreted molecules.S. mutansUA159 inhibitedC. albicansgerm tube (GT) formation in cocultures even when physically separated fromC. albicans. OnlyS. mutansspent medium collected in the early exponential phase (4-h-old cultures) inhibited the GT formation ofC. albicans. During this phase,S. mutansUA159 produces a quorum-sensing molecule, competence-stimulating peptide (CSP). The role of CSP in inhibiting GT formation was confirmed by using synthetic CSP and acomCdeletion strain ofS. mutansUA159, which lacks the ability to produce CSP. OtherS. mutansstrains and otherStreptococcusspp. also inhibited GT formation but to different extents, possibly reflecting differences in CSP amino acid sequences amongStreptococcusspp. or differences in CSP accumulation in the media. In conclusion, CSP, anS. mutansquorum-sensing molecule secreted during the early stages of growth, inhibits theC. albicansmorphological switch.
Replacement of α-Tocopherol by β-Tocopherol Enhances Resistance to Photooxidative Stress in a Xanthophyll-Deficient Strain of
Chlamydomonas reinhardtii
Authors: Sirikhachornkit Anchalee , Shin Jai W. , Baroli Irene , Niyogi Krishna K. 
Published: August 2009

ABSTRACT

Tocopherols (vitamin E) comprise a class of lipid-soluble antioxidants synthesized only in plants, algae, and some cyanobacteria. The majority of tocopherols in photosynthetic cells is in the α form, which has the highest vitamin E activity in humans, whereas the β, γ, and δ forms normally account for a small percentage of total tocopherols. The antioxidant activities of these forms of tocopherol differ depending on the experimental system, and their relative activities in vivo are unclear. In a screen for suppressors of the xanthophyll-deficient
npq1 lor1
double mutant of
Chlamydomonas reinhardtii
, we isolated a
vte3
mutant lacking α-tocopherol but instead accumulating β-tocopherol. The
vte3
mutant contains a mutation in the homolog of a 2-methyl-6-phytyl-1,4-benzoquinone methyltransferase gene found in plants. The
vte3 npq1 lor1
triple mutant with β-tocopherol survived better under photooxidative stress than did the
npq1 lor1
mutant, but the
vte3
mutant on its own did not have an obvious phenotype. Following transfer from low light to high light, the triple mutant showed a higher efficiency of photosystem II, a higher level of cell viability, and a lower level of lipid peroxide, a marker for oxidative stress, than did the
npq1 lor1
mutant. After high-light transfer, the level of the photosystem II reaction center protein, D1, was also higher in the
vte3 npq1 lor1
mutant, but the rate of D1 photodamage was not significantly different from that of the
npq1 lor1
mutant. Taken together, these results suggest that the replacement of α-tocopherol by β-tocopherol in a xanthophyll-deficient strain of
Chlamydomonas reinhardtii
contributes to better survival under conditions of photooxidative stress.
The Monothiol Single-Domain Glutaredoxin Is Conserved in the Highly Reduced Mitochondria of
Giardia intestinalis
Authors: Rada Petr , Šmíd Ondřej , Sutak Robert , Doležal Pavel , Pyrih Jan , Žárský Vojtěch , Montagne Jean-Jacques , Hrdý Ivan , Camadro Jean-Michel , Tachezy Jan 
Published: August 2009

ABSTRACT

The highly reduced mitochondria (mitosomes) of
Giardia intestinalis
are recently discovered organelles for which, it was suggested, iron-sulfur cluster assembly was their only conserved function. However, only an incomplete set of the components required for FeS cluster biogenesis was localized to the mitosomes. Via proteomic analysis of a mitosome-rich cellular fraction together with immunofluorescence microscopy, we identified a novel mitosomal protein homologous to monothiol glutaredoxins containing a CGFS motif at the active site. Sequence analysis revealed the presence of long nonconserved N-terminal extension of 77 amino acids, which was absent in the mature protein. Expression of the complete and N-terminally truncated forms of the glutaredoxin indicated that the extension is involved in glutaredoxin import into mitosomes. However, the mechanism of preprotein processing is unclear, as the mitosomal processing peptidase is unable to cleave this type of extension. The recombinant mature protein was shown to form a homodimeric structure, which binds a labile FeS cluster. The cluster is stabilized by glutathione and dithiothreitol. Phylogenetic analysis showed that giardial glutaredoxin is related to the mitochondrial monothiol glutaredoxins involved in FeS cluster assembly. The identification of a mitochondrial-type monothiol glutaredoxin in the mitosomes of
G. intestinalis
thus completes the mitosomal FeS cluster biosynthetic pathway and provides further evidence for the mitochondrial origin of these organelles.
Our Paths Might Cross: the Role of the Fungal Cell Wall Integrity Pathway in Stress Response and Cross Talk with Other Stress Response Pathways
Authors: Fuchs Beth Burgwyn , Mylonakis Eleftherios 
Published: August 2009

ABSTRACT

Fungi occupy diverse environments and are subjected to many extreme conditions. Among the stressful conditions faced by fungi are pH changes, osmotic changes, thermal changes, oxide radicals, nutrient deprivation, and exposure to chemicals. These adversities can be found either in the environment or in animal and human hosts. The cell wall integrity (CWI) pathway provides a means to fortify and repair damages to the cell wall in order to withstand stressful environments. The CWI pathway in comprised of cell wall stress sensors that lead to activation of a mitogen-activated protein kinase (MAPK) cascade. Signaling through the MAPK cascade leads to expression of transcription factors that facilitate biosynthesis of cell wall components and actin organization. Given the relatively limited number of components of the CWI pathway and the very diverse stimuli, there must be a means of expanding the pathway. To manage the diverse stress conditions, the CWI pathway cross talks with other pathways or proteins, and these cross talk events enhance the signaling capabilities of the CWI pathway. Lateral influences that facilitate maintaining the cell wall under stress conditions are TOR signaling, calcineurin signaling, the high-osmolarity glycerol pathway, the cyclic AMP-protein kinase A pathway, and additional proteins. In this article, we highlight several of the cross talk events that have been described for
Saccharomyces cerevisiae
and several other fungi.
Neurofibromin Homologs Ira1 and Ira2 Affect Glycerophosphoinositol Production and Transport in
Saccharomyces cerevisiae
Authors: Bishop Andrew C. , Surlow Beth A. , Anand Puneet , Hofer Katherine , Henkel Matthew , Patton-Vogt Jana 
Published: August 2009

ABSTRACT

Saccharomyces cerevisiae
produces extracellular glycerophosphoinositol through phospholipase-mediated turnover of phosphatidylinositol and transports glycerophosphoinositol into the cell upon nutrient limitation. A screening identified the RAS GTPase-activating proteins Ira1 and Ira2 as required for utilization of glycerophosphoinositol as the sole phosphate source, but the RAS/cyclic AMP pathway does not appear to be involved in the growth phenotype. Ira1 and Ira2 affect both the production and transport of glycerophosphoinositol.