bluuebunny/crossref_metadata_2025_split huggingface dataset:
Acetate Production from Oil under Sulfate-Reducing Conditions in Bioreactors Injected with Sulfate and Nitrate
Authors: Callbeck Cameron M. , Agrawal Akhil , Voordouw Gerrit 
Published: June 2013

ABSTRACT

Oil production by water injection can cause souring in which sulfate in the injection water is reduced to sulfide by resident sulfate-reducing bacteria (SRB). Sulfate (2 mM) in medium injected at a rate of 1 pore volume per day into upflow bioreactors containing residual heavy oil from the Medicine Hat Glauconitic C field was nearly completely reduced to sulfide, and this was associated with the generation of 3 to 4 mM acetate. Inclusion of 4 mM nitrate inhibited souring for 60 days, after which complete sulfate reduction and associated acetate production were once again observed. Sulfate reduction was permanently inhibited when 100 mM nitrate was injected by the nitrite formed under these conditions. Pulsed injection of 4 or 100 mM nitrate inhibited sulfate reduction temporarily. Sulfate reduction resumed once nitrate injection was stopped and was associated with the production of acetate in all cases. The stoichiometry of acetate formation (3 to 4 mM formed per 2 mM sulfate reduced) is consistent with a mechanism in which oil alkanes and water are metabolized to acetate and hydrogen by fermentative and syntrophic bacteria (K. Zengler et al., Nature 401:266–269, 1999), with the hydrogen being used by SRB to reduce sulfate to sulfide. In support of this model, microbial community analyses by pyrosequencing indicated SRB of the genus
Desulfovibrio
, which use hydrogen but not acetate as an electron donor for sulfate reduction, to be a major community component. The model explains the high concentrations of acetate that are sometimes found in waters produced from water-injected oil fields.
Proteome of the Nematode-Trapping Cells of the Fungus Monacrosporium haptotylum
Authors: Andersson Karl-Magnus , Meerupati Tejashwari , Levander Fredrik , Friman Eva , Ahrén Dag , Tunlid Anders 
Published: June 2013

ABSTRACT

Many nematophagous fungi use morphological structures called traps to capture nematodes by adhesion or mechanically. To better understand the cellular functions of adhesive traps, the trap cell proteome of the fungus
Monacrosporium haptotylum
was characterized. The trap of
M. haptotylum
consists of a unicellular structure called a knob that develops at the apex of a hypha. Proteins extracted from knobs and mycelia were analyzed using SDS-PAGE and liquid chromatography-tandem mass spectrometry (LC–MS-MS). The peptide sequences were matched against predicted gene models from the recently sequenced
M. haptotylum
genome. In total, 336 proteins were identified, with 54 expressed at significantly higher levels in the knobs than in the mycelia. The upregulated knob proteins included peptidases, small secreted proteins with unknown functions, and putative cell surface adhesins containing carbohydrate-binding domains, including the WSC domain. Phylogenetic analysis showed that all upregulated WSC domain proteins belonged to a large, expanded cluster of paralogs in
M. haptotylum
. Several peptidases and homologs of experimentally verified proteins in other pathogenic fungi were also upregulated in the knob proteome. Complementary profiling of gene expression at the transcriptome level showed poor correlation between the upregulation of knob proteins and their corresponding transcripts. We propose that the traps of
M. haptotylum
contain many of the proteins needed in the early stages of infection and that the trap cells can tightly control the translation and degradation of these proteins to minimize the cost of protein synthesis.
Real-Time PCR for Quantitative Analysis of Human Commensal Escherichia coli Populations Reveals a High Frequency of Subdominant Phylogroups
Authors: Smati Mounira , Clermont Olivier , Le Gal Frédéric , Schichmanoff Olivier , Jauréguy Françoise , Eddi Alain , Denamur Erick , Picard Bertrand ,   for the Coliville Group
Published: June 2013

ABSTRACT

Escherichia coli
is divided into four main phylogenetic groups, which each exhibit ecological specialization. To understand the population structure of
E. coli
in its primary habitat, we directly assessed the relative proportions of these phylogroups from the stools of 100 healthy human subjects using a new real-time PCR method, which allows a large number of samples to be studied. The detection threshold for our technique was 0.1% of the
E. coli
population, i.e., 10
5
CFU/g of feces; in other methods based on individual colony analysis, the threshold is 10%. One, two, three, or four phylogenetic groups were simultaneously found in 21%, 48%, 21%, and 8% of the subjects, respectively. Phylogroups present at a threshold of less than 10% of the population were found in 40% of the subjects, revealing high within-individual diversity. Phylogroups A and B2 were detected in 74% and 70% of the subjects, respectively; phylogroups B1 and D were detected in 36% and 32%, respectively. When phylogroup B2 was dominant, it tended not to cooccur with other phylogroups. In contrast, other phylogroups were present when phylogroup A was dominant. These data indicate a complex pattern of interactions between the members of a single species within the human gut and identify a reservoir of clones that are present at a low frequency. The presence of these minor clones could explain the fluctuation in the composition of the
E. coli
microbiota within single individuals that may be seen over time. They could also constitute reservoirs of virulent and/or resistant strains.
Inhibition of Aspergillus niger Phosphate Solubilization by Fluoride Released from Rock Phosphate
Authors: Mendes Gilberto de Oliveira , Vassilev Nikolay Bojkov , Bonduki Victor Hugo Araújo , da Silva Ivo Ribeiro , Ribeiro José Ivo , Costa Maurício Dutra 
Published: June 2013

ABSTRACT

The simultaneous release of various chemical elements with inhibitory potential for phosphate solubilization from rock phosphate (RP) was studied in this work. Al, B, Ba, Ca, F, Fe, Mn, Mo, Na, Ni, Pb, Rb, Si, Sr, V, Zn, and Zr were released concomitantly with P during the solubilization of Araxá RP (Brazil), but only F showed inhibitory effects on the process at the concentrations detected in the growth medium. Besides P solubilization, fluoride decreased fungal growth, citric acid production, and medium acidification by
Aspergillus niger
. At the maximum concentration found during Araxá RP solubilization (22.9 mg F
−
per liter), fluoride decreased P solubilization by 55%. These findings show that fluoride negatively affects RP solubilization by
A. niger
through its inhibitory action on the fungal metabolism. Given that fluoride is a common component of RPs, the data presented here suggest that most of the microbial RP solubilization systems studied so far were probably operated under suboptimal conditions.
Multilocus Genotype Analysis of Escherichia coli O157 Isolates from Australia and the United States Provides Evidence of Geographic Divergence
Authors: Mellor Glen E. , Besser Thomas E. , Davis Margaret A. , Beavis Brittany , Jung WooKyung , Smith Helen V. , Jennison Amy V. , Doyle Christine J. , Chandry P. Scott , Gobius Kari S. , Fegan Narelle 
Published: June 2013

ABSTRACT

Escherichia coli
O157 is a food-borne pathogen whose major reservoir has been identified as cattle. Recent genetic information has indicated that populations of
E. coli
O157 from cattle and humans can differ genetically and that this variation may have an impact on their ability to cause severe human disease. In addition, there is emerging evidence that
E. coli
O157 strains from different geographical regions may also be genetically divergent. To investigate the extent of this variation, we used Shiga toxin bacteriophage insertion sites (SBI), lineage-specific polymorphisms (LSPA-6), multilocus variable-number tandem-repeat analysis (MLVA), and a
tir
255T>A polymorphism to examine 606 isolates representing both Australian and U.S. cattle and human populations. Both uni- and multivariate analyses of these data show a strong association between the country of origin and multilocus genotypes (
P
< 0.0001). In addition, our results identify factors that may play a role in virulence that also differed in isolates from each country, including the carriage of
stx
1
in the
argW
locus uniquely observed in Australian isolates and the much higher frequency of
stx
2
-positive (also referred to as
stx
2a
) strains in the U.S. isolates (4% of Australian isolates versus 72% of U.S. isolates). LSPA-6 lineages differed between the two continents, with the majority of Australian isolates belonging to lineage I/II (LI/II) (LI, 2%; LI/II, 85%; LII, 13%) and the majority of U.S. isolates belonging to LI (LI, 60%; LI/II, 16%; LII, 25%). The results of this study provide strong evidence of phylogeographic structuring of
E. coli
O157 populations, suggesting divergent evolution of enterohemorrhagic
E. coli
O157 in Australia and the United States.
Histidine Phosphotransfer Proteins in Fungal Two-Component Signal Transduction Pathways
Authors: Fassler Jan S. , West Ann H. 
Published: June 2013

ABSTRACT

The histidine phosphotransfer (HPt) protein Ypd1 is an important participant in the
Saccharomyces cerevisiae
multistep two-component signal transduction pathway and, unlike the expanded histidine kinase gene family, is encoded by a single gene in nearly all model and pathogenic fungi. Ypd1 is essential for viability in both
S. cerevisiae
and in
Cryptococcus neoformans
. These and other aspects of Ypd1 biology, combined with the availability of structural and mutational data in
S. cerevisiae
, suggest that the essential interactions between Ypd1 and response regulator domains would be a good target for antifungal drug development. The goal of this minireview is to summarize the wealth of data on
S. cerevisiae
Ypd1 and to consider the potential benefits of conducting related studies in pathogenic fungi.
Candida albicans Forms a Specialized “Sexual” as Well as “Pathogenic” Biofilm
Authors: Park Yang-Nim , Daniels Karla J. , Pujol Claude , Srikantha Thyagarajan , Soll David R. 
Published: June 2013

ABSTRACT

Candida albicans
forms two types of biofilm in RPMI 1640 medium, depending upon the configuration of the mating type locus. In the prevalent
a
/α configuration, cells form a biofilm that is impermeable, impenetrable by leukocytes, and fluconazole resistant. It is regulated by the Ras1/cyclic AMP (cAMP) pathway. In the
a/a
or α/α configuration, white cells form a biofilm that is architecturally similar to an
a
/α biofilm but, in contrast, is permeable, penetrable, and fluconazole susceptible. It is regulated by the mitogen-activated protein (MAP) kinase pathway. The
MTL
-homozygous biofilm has been shown to facilitate chemotropism, a step in the mating process. This has led to the hypothesis that specialized
MTL
-homozygous biofilms facilitate mating. If true, then
MTL
-homozygous biofilms should have an advantage over
MTL
-heterozygous biofilms in supporting mating. We have tested this prediction using a complementation strategy and show that minority opaque
a/a
and α/α cells seeded in
MTL
-homozygous biofilms mate at frequencies 1 to 2 orders of magnitude higher than in
MTL
-heterozygous biofilms. No difference in mating frequencies was observed between seeded patches of
MTL
-heterozygous and
MTL
-homozygous cells grown on agar at 28°C in air or 20% CO
2
and at 37°C. Mating frequencies are negligible in seeded patches of both
a
/α and
a/a
cells, in contrast to seeded biofilms. Together, these results support the hypothesis that
MTL
-homozygous (
a/a
or α/α) white cells form a specialized “sexual biofilm.”
Genetic and Physiological Responses of Bifidobacterium animalis subsp. lactis to Hydrogen Peroxide Stress
Authors: Oberg Taylor S. , Ward Robert E. , Steele James L. , Broadbent Jeff R. 
Published: June 2013

ABSTRACT

Consumer interest in probiotic bifidobacteria is increasing, but industry efforts to secure high cell viability in foods is undermined by these anaerobes' sensitivity to oxidative stress. To address this limitation, we investigated genetic and physiological responses of two fully sequenced
Bifidobacterium animalis
subsp.
lactis
strains, BL-04 and DSM 10140, to hydrogen peroxide (H
2
O
2
) stress. Although the genome sequences for these strains are highly clonal, prior work showed that they differ in both intrinsic and inducible H
2
O
2
resistance. Transcriptome analysis of early-stationary-phase cells exposed to a sublethal H
2
O
2
concentration detected significant (
P
< 0.05) changes in expression of 138 genes in strain BL-04 after 5 min and 27 genes after 20 min. Surprisingly, no significant changes in gene expression were detected in DSM 10140 at either time. Genomic data suggested that differences in H
2
O
2
stress resistance might be due to a mutation in a BL-04 gene encoding long-chain fatty acid coenzyme A (CoA) ligase. To explore this possibility, membrane fatty acids were isolated and analyzed by gas chromatography-mass spectrometry (GC-MS). Results confirmed that the strains had significantly different lipid profiles: the BL-04 membrane contained higher percentages of C
14:0
and C
16:0
and lower percentages of C
18:1n9
. Alteration of the DSM 10140 membrane lipid composition using modified growth medium to more closely mimic that of BL-04 yielded cells that showed increased intrinsic resistance to lethal H
2
O
2
challenge but did not display an inducible H
2
O
2
stress response. The results show that deliberate stress induction or membrane lipid modification can be employed to significantly improve H
2
O
2
resistance in
B. animalis
subsp.
lactis
strains.
Isolation and Characterization of Mutant Sinorhizobium meliloti NodD1 Proteins with Altered Responses to Luteolin
Authors: Peck Melicent C. , Fisher Robert F. , Bliss Robert , Long Sharon R. 
Published: June 2013

ABSTRACT

NodD1, a member of the NodD family of LysR-type transcriptional regulators (LTTRs), mediates nodulation (
nod
) gene expression in the soil bacterium
Sinorhizobium meliloti
in response to the plant-secreted flavonoid luteolin. We used genetic screens and targeted approaches to identify NodD1 residues that show altered responses to luteolin during the activation of
nod
gene transcription. Here we report four types of NodD1 mutants. Type I (NodD1 L69F, S104L, D134N, and M193I mutants) displays reduced or no activation of
nod
gene expression. Type II (NodD1 K205N) is constitutively active but repressed by luteolin. Type III (NodD1 L280F) demonstrates enhanced activity with luteolin compared to that of wild-type NodD1. Type IV (NodD1 D284N) shows moderate constitutive activity yet can still be induced by luteolin. In the absence of luteolin, many mutants display a low binding affinity for
nod
gene promoter DNA
in vitro
. Several mutants also show, as does wild-type NodD1, increased affinity for
nod
gene promoters with added luteolin. All of the NodD1 mutant proteins can homodimerize and heterodimerize with wild-type NodD1. Based on these data and the crystal structures of several LTTRs, we present a structural model of wild-type NodD1, identifying residues important for inducer binding, protein multimerization, and interaction with RNA polymerase at
nod
gene promoters.
Transcription of the Escherichia coli Fatty Acid Synthesis OperonfabHDGIs Directly Activated by FadR and Inhibited by ppGpp
Authors: My Laetitia , Rekoske Brian , Lemke Justin J. , Viala Julie P. , Gourse Richard L. , Bouveret Emmanuelle 
Published: June 2013

ABSTRACTInEscherichia coli, FadR and FabR are transcriptional regulators that control the expression of fatty acid degradation and unsaturated fatty acid synthesis genes, depending on the availability of fatty acids. In this report, we focus on the dual transcriptional regulator FadR. In the absence of fatty acids, FadR represses the transcription offadgenes required for fatty acid degradation. However, FadR is also an activator, stimulating transcription of the products of thefabAandfabBgenes responsible for unsaturated fatty acid synthesis. In this study, we show that FadR directly activates another fatty acid synthesis promoter, PfabH, which transcribes thefabHDGoperon, indicating that FadR is a global regulator of both fatty acid degradation and fatty acid synthesis. We also demonstrate that ppGpp and its cofactor DksA, known primarily for their role in regulation of the synthesis of the translational machinery, directly inhibit transcription from thefabHpromoter. ppGpp also inhibits thefadRpromoter, thereby reducing transcription activation offabHby FadR indirectly. Our study shows that both ppGpp and FadR have direct roles in the control of fatty acid promoters, linking expression in response to both translation activity and fatty acid availability.
Dual Mechanisms of Metabolite Acquisition by the Obligate Intracytosolic Pathogen Rickettsia prowazekii Reveal Novel Aspects of Triose Phosphate Transport
Authors: Frohlich Kyla M. , Audia Jonathon P. 
Published: June 2013

ABSTRACT

Rickettsia prowazekii
is an obligate intracytosolic pathogen and the causative agent of epidemic typhus fever in humans. As an evolutionary model of intracellular pathogenesis, rickettsiae are notorious for their use of transport systems that parasitize eukaryotic host cell biochemical pathways. Rickettsial transport systems for substrates found only in eukaryotic cell cytoplasm are uncommon among free-living microorganisms and often possess distinctive mechanisms. We previously reported that
R. prowazekii
acquires triose phosphates for phospholipid biosynthesis via the coordinated activities of a novel dihydroxyacetone phosphate transport system and an
sn
-glycerol-3-phosphate dehydrogenase (K. M. Frohlich et al., J. Bacteriol. 192:4281–4288, 2010). In the present study, we have determined that
R. prowazekii
utilizes a second, independent triose phosphate acquisition pathway whereby
sn
-glycerol-3-phosphate is directly transported and incorporated into phospholipids. Herein we describe the
sn
-glycerol-3-phosphate and dihydroxyacetone phosphate transport systems in isolated
R. prowazekii
with respect to kinetics, energy coupling, transport mechanisms, and substrate specificity. These data suggest the existence of multiple rickettsial triose phosphate transport systems. Furthermore, the
R. prowazekii
dihydroxyacetone phosphate transport systems displayed unexpected mechanistic properties compared to well-characterized triose phosphate transport systems from plant plastids. Questions regarding possible roles for dual-substrate acquisition pathways as metabolic virulence factors in the context of a pathogen undergoing reductive evolution are discussed.
Role for Skp in LptD Assembly in Escherichia coli
Authors: Schwalm Jaclyn , Mahoney Tara F. , Soltes Garner R. , Silhavy Thomas J. 
Published: June 2013

ABSTRACT

The periplasmic chaperone Skp has long been implicated in the assembly of outer membrane proteins (OMPs) in
Escherichia coli
. It has been shown to interact with unfolded OMPs, and the simultaneous loss of Skp and the main periplasmic chaperone in
E. coli
, SurA, results in synthetic lethality. However, a Δ
skp
mutant displays only minor OMP assembly defects, and no OMPs have been shown to require Skp for their assembly. Here, we report a role for Skp in the assembly of the essential OMP LptD. This role may be compensated for by other OMP assembly proteins; in the absence of both Skp and FkpA or Skp and BamB, LptD assembly is impaired. Overexpression of SurA does not restore LptD levels in a Δ
skp
Δ
fkpA
double mutant, nor does the overexpression of Skp or FkpA restore LptD levels in the Δ
surA
mutant, suggesting that Skp acts in concert with SurA to efficiently assemble LptD in
E. coli
. Other OMPs, including LamB, are less affected in the Δ
skp
Δ
fkpA
and Δ
skp bamB
::
kan
double mutants, suggesting that Skp is specifically necessary for the assembly of certain OMPs. Analysis of an OMP with a domain structure similar to that of LptD, FhuA, suggests that common structural features may determine which OMPs require Skp for their assembly.
Crippling the Essential GTPase Der Causes Dependence on Ribosomal Protein L9
Authors: Naganathan Anusha , Moore Sean D. 
Published: June 2013

ABSTRACT

Ribosomal protein L9 is a component of all eubacterial ribosomes, yet deletion strains display only subtle growth defects. Although L9 has been implicated in helping ribosomes maintain translation reading frame and in regulating translation bypass, no portion of the ribosome-bound protein seems capable of contacting either the peptidyltransferase center or the decoding center, so it is a mystery how L9 can influence these important processes. To reveal the physiological roles of L9 that have maintained it in evolution, we identified mutants of
Escherichia coli
that depend on L9 for fitness. In this report, we describe a class of L9-dependent mutants in the ribosome biogenesis GTPase Der (EngA/YphC). Purified mutant proteins were severely compromised in their GTPase activities, despite the fact that the mutations are not present in GTP hydrolysis sites. Moreover, although L9 and YihI complemented the slow-growth
der
phenotypes, neither factor could rescue the GTPase activities
in vitro
. Complementation studies revealed that the N-terminal domain of L9 is necessary and sufficient to improve the fitness of these Der mutants, suggesting that this domain may help stabilize compromised ribosomes that accumulate when Der is defective. Finally, we employed a targeted degradation system to rapidly deplete L9 from a highly compromised
der
mutant strain and show that the L9-dependent phenotype coincides with a cell division defect.
The
agr
Locus Regulates Virulence and Colonization Genes in Clostridium difficile 027
Authors: Martin Melissa J. , Clare Simon , Goulding David , Faulds-Pain Alexandra , Barquist Lars , Browne Hilary P. , Pettit Laura , Dougan Gordon , Lawley Trevor D. , Wren Brendan W. 
Published: June 2013

ABSTRACT

The transcriptional regulator AgrA, a member of the LytTR family of proteins, plays a key role in controlling gene expression in some Gram-positive pathogens, including
Staphylococcus aureus
and
Enterococcus faecalis
. AgrA is encoded by the
agrACDB
global regulatory locus, and orthologues are found within the genome of most
Clostridium difficile
isolates, including the epidemic lineage 027/BI/NAP1. Comparative RNA sequencing of the wild type and otherwise isogenic
agrA
null mutant derivatives of
C. difficile
R20291 revealed a network of approximately 75 differentially regulated transcripts at late exponential growth phase, including many genes associated with flagellar assembly and function, such as the major structural subunit, FliC. Other differentially regulated genes include several involved in bis-(3′-5′)-cyclic dimeric GMP (c-di-GMP) synthesis and toxin A expression.
C. difficile
027 R20291
agrA
mutant derivatives were poorly flagellated and exhibited reduced levels of colonization and relapses in the murine infection model. Thus, the
agr
locus likely plays a contributory role in the fitness and virulence potential of
C. difficile
strains in the 027/BI/NAP1 lineage.