bluuebunny/crossref_metadata_2025_split huggingface dataset:
Transcriptional Response of Nitrifying Communities to Wetting of Dry Soil
Authors: Placella Sarah A. , Firestone Mary K. 
Published: March 2013

ABSTRACT

The first rainfall following a severe dry period provides an abrupt water potential change that is both an acute physiological stress and a defined stimulus for the reawakening of soil microbial communities. We followed the responses of indigenous communities of ammonia-oxidizing bacteria, ammonia-oxidizing archaea, and nitrite-oxidizing bacteria to the addition of water to laboratory incubations of soils taken from two California annual grasslands following a typically dry Mediterranean summer. By quantifying transcripts for a subunit of bacterial and archaeal ammonia monooxygenases (
amoA
) and a bacterial nitrite oxidoreductase (
nxrA
) in soil from 15 min to 72 h after water addition, we identified transcriptional response patterns for each of these three groups of nitrifiers. An increase in quantity of bacterial
amoA
transcripts was detectable within 1 h of wet-up and continued until the size of the ammonium pool began to decrease, reflecting a possible role of transcription in upregulation of nitrification after drought-induced stasis. In one soil, the pulse of
amoA
transcription lasted for less than 24 h, demonstrating the transience of transcriptional pools and the tight coupling of transcription to the local soil environment. Analysis of 16S rRNA using a high-density microarray suggested that nitrite-oxidizing
Nitrobacter
spp. respond in tandem with ammonia-oxidizing bacteria while nitrite-oxidizing
Nitrospina
spp. and
Nitrospira
bacteria may not. Archaeal ammonia oxidizers may respond slightly later than bacterial ammonia oxidizers but may maintain elevated transcription longer. Despite months of desiccation-induced inactivation, we found rapid transcriptional response by all three groups of soil nitrifiers.
Microbial Reduction of Fe(III) under Alkaline Conditions Relevant to Geological Disposal
Authors: Williamson Adam J. , Morris Katherine , Shaw Sam , Byrne James M. , Boothman Christopher , Lloyd Jonathan R. 
Published: March 2013

ABSTRACT
To determine whether biologically mediated Fe(III) reduction is possible under alkaline conditions in systems of relevance to geological disposal of radioactive wastes, a series of microcosm experiments was set up using hyperalkaline sediments (pH ∼11.8) surrounding a legacy lime working site in Buxton, United Kingdom. The microcosms were incubated for 28 days and held at pH 10. There was clear evidence for anoxic microbial activity, with consumption of lactate (added as an electron donor) concomitant with the reduction of Fe(III) as ferrihydrite (added as the electron acceptor). The products of microbial Fe(III) reduction were black and magnetic, and a range of analyses, including X-ray diffraction, transmission electron microscopy, X-ray absorption spectroscopy, and X-ray magnetic circular dichroism confirmed the extensive formation of biomagnetite in this system. The addition of soluble exogenous and endogenous electron shuttles such as the humic analogue anthraquinone-2,6-disulfonate and riboflavin increased both the initial rate and the final extent of Fe(III) reduction in comparison to the nonamended experiments. In addition, a soluble humic acid (Aldrich) also increased both the rate and the extent of Fe(III) reduction. These results show that microbial Fe(III) reduction can occur in conditions relevant to a geological disposal facility containing cement-based wasteforms that has evolved into a high pH environment over prolonged periods of time (>100,000 years). The potential impact of such processes on the biogeochemistry of a geological disposal facility is discussed, including possible coupling to the redox conditions and solubility of key radionuclides.
Distribution of Pathogenicity Islands OI-122, OI-43/48, and OI-57 and a High-Pathogenicity Island in Shiga Toxin-Producing Escherichia coli
Authors: Ju Wenting , Shen Jinling , Toro Magaly , Zhao Shaohua , Meng Jianghong 
Published: March 2013

ABSTRACT

Pathogenicity islands (PAIs) play an important role in Shiga toxin-producing
Escherichia coli
(STEC) pathogenicity. The distribution of PAIs OI-122, OI-43/48, and OI-57 and a high-pathogenicity island (HPI) were determined among 98 STEC strains assigned to seropathotypes (SPTs) A to E. PCR and PCR-restriction fragment length polymorphism assays were used to identify 14 virulence genes that belonged to the four PAIs and to subtype
eae
and
stx
genes, respectively. Phylogenetic trees were constructed based on the sequences of
pagC
among 34 STEC strains and
iha
among 67 diverse pathogenic
E. coli
, respectively. Statistical analysis demonstrated that the prevalences of OI-122 (55.82%) and OI-57 (82.35%) were significantly greater in SPTs (i.e., SPTs A, B, and C) that are frequently associated with severe disease than in other SPTs.
terC
(62.5%) and
ureC
(62.5%) in OI-43/48 were also significantly more prevalent in SPTs A, B, and C than in SPTs D and E. In addition, OI-122, OI-57, and OI-43/48 and their associated virulence genes (except
iha
) were found to be primarily associated with
eae
-positive STEC, whereas HPI occurred independently of the
eae
presence. The strong association of OI-122, OI-43/48, and OI-57 with
eae
-positive STEC suggests in part that different pathogenic mechanisms exist between
eae
-positive and
eae
-negative STEC strains. Virulence genes in PAIs that are associated with severe diseases can be used as potential markers to aid in identifying highly virulent STEC.
Detection of Galectin-3 Interaction with Commensal Bacteria
Authors: Kavanaugh Devon , Kane Marian , Joshi Lokesh , Hickey Rita M. 
Published: March 2013

ABSTRACTA panel of commensal bacteria was screened for the ability to interact with galectin-3. Two strains ofBifidobacterium longumsubsp.infantisinteracted to a greater extent than did the pathogenic positive control,Escherichia coliNCTC 12900. Further validation of the interaction was achieved by using agglutination and solid-phase binding assays.
Function-Based Classification of Carbohydrate-Active Enzymes by Recognition of Short, Conserved Peptide Motifs
Authors: Busk Peter Kamp , Lange Lene 
Published: March 2013

ABSTRACT
Functional prediction of carbohydrate-active enzymes is difficult due to low sequence identity. However, similar enzymes often share a few short motifs, e.g., around the active site, even when the overall sequences are very different. To exploit this notion for functional prediction of carbohydrate-active enzymes, we developed a simple algorithm, peptide pattern recognition (PPR), that can divide proteins into groups of sequences that share a set of short conserved sequences. When this method was used on 118 glycoside hydrolase 5 proteins with 9% average pairwise identity and representing four characterized enzymatic functions, 97% of the proteins were sorted into groups correlating with their enzymatic activity. Furthermore, we analyzed 8,138 glycoside hydrolase 13 proteins including 204 experimentally characterized enzymes with 28 different functions. There was a 91% correlation between group and enzyme activity. These results indicate that the function of carbohydrate-active enzymes can be predicted with high precision by finding short, conserved motifs in their sequences. The glycoside hydrolase 61 family is important for fungal biomass conversion, but only a few proteins of this family have been functionally characterized. Interestingly, PPR divided 743 glycoside hydrolase 61 proteins into 16 subfamilies useful for targeted investigation of the function of these proteins and pinpointed three conserved motifs with putative importance for enzyme activity. Furthermore, the conserved sequences were useful for cloning of new, subfamily-specific glycoside hydrolase 61 proteins from 14 fungi. In conclusion, identification of conserved sequence motifs is a new approach to sequence analysis that can predict carbohydrate-active enzyme functions with high precision.
A Pathway Closely Related to the
d
-Tagatose Pathway of Gram-Negative Enterobacteria Identified in the Gram-Positive Bacterium Bacillus licheniformis
Authors: Van der Heiden Edwige , Delmarcelle Michaël , Lebrun Sarah , Freichels Régine , Brans Alain , Vastenavond Christian M. , Galleni Moreno , Joris Bernard 
Published: March 2013

ABSTRACT

We report the first identification of a gene cluster involved in
d
-tagatose catabolism in
Bacillus licheniformis
. The pathway is closely related to the
d
-tagatose pathway of the Gram-negative bacterium
Klebsiella oxytoca
, in contrast to the
d
-tagatose 6-phosphate pathway described in the Gram-positive bacterium
Staphylococcus aureus
.
Camphor Pathway Redux: Functional Recombinant Expression of 2,5- and 3,6-Diketocamphane Monooxygenases of Pseudomonas putida ATCC 17453 with Their Cognate Flavin Reductase Catalyzing Baeyer-Villiger Reactions
Authors: Iwaki Hiroaki , Grosse Stephan , Bergeron Hélène , Leisch Hannes , Morley Krista , Hasegawa Yoshie , Lau Peter C. K. 
Published: March 2013

ABSTRACT

Whereas the biochemical properties of the monooxygenase components that catalyze the oxidation of 2,5-diketocamphane and 3,6-diketocamphane (2,5-DKCMO and 3,6-DKCMO, respectively) in the initial catabolic steps of (+) and (−) isomeric forms of camphor (CAM) metabolism in
Pseudomonas putida
ATCC 17453 are relatively well characterized, the actual identity of the flavin reductase (Fred) component that provides the reduced flavin to the oxygenases has hitherto been ill defined. In this study, a 37-kDa Fred was purified from a camphor-induced culture of
P. putida
ATCC 17453 and this facilitated cloning and characterization of the requisite protein. The active Fred is a homodimer with a subunit molecular weight of 18,000 that uses NADH as an electron donor (
K

m

= 32 μM), and it catalyzes the reduction of flavin mononucleotide (FMN) (
K

m

= 3.6 μM;
k
cat
= 283 s
−1
) in preference to flavin adenine dinucleotide (FAD) (
K

m

= 19 μM;
k
cat
= 128 s
−1
). Sequence determination of ∼40 kb of the CAM degradation plasmid revealed the locations of two isofunctional 2,5-DKCMO genes (
camE
25–1
for 2,5-DKCMO-1 and
camE
25–2
for 2,5-DKCMO-2) as well as that of a 3,6-DKCMO-encoding gene (
camE
36
). In addition, by pulsed-field gel electrophoresis, the CAM plasmid was established to be linear and ∼533 kb in length. To enable functional assessment of the two-component monooxygenase system in Baeyer-Villiger oxidations, recombinant plasmids expressing Fred in tandem with the respective 2,5-DKCMO- and 3,6-DKCMO-encoding genes in
Escherichia coli
were constructed. Comparative substrate profiling of the isofunctional 2,5-DCKMOs did not yield obvious differences in Baeyer-Villiger biooxidations, but they are distinct from 3,6-DKCMO in the stereoselective oxygenations with various mono- and bicyclic ketone substrates.
Molecular and Genetic Evidence for a Tetrapolar Mating System in the Basidiomycetous Yeast Kwoniella mangrovensis and Two Novel Sibling Species
Authors: Guerreiro Marco A. , Springer Deborah J. , Rodrigues Joana A. , Rusche Laura N. , Findley Keisha , Heitman Joseph , Fonseca Álvaro 
Published: March 2013

ABSTRACT

Kwoniella mangrovensis
has been described as a sexual species with a bipolar mating system. Phylogenetic analysis of multiple genes places this species together with
Kwoniella heveanensis
in the
Kwoniella
clade, a sister clade to that containing two pathogenic species of global importance,
Cryptococcus neoformans
and
Cryptococcus gattii
, within the Tremellales. Recent studies defining the mating type loci (
MAT
) of species in these clades showed that, with the exception of
C. neoformans
and
C. gattii
, which are bipolar with a single biallelic multigene
MAT
locus, several other species feature a tetrapolar mating system with two unlinked loci (homeodomain [HD] and pheromone/receptor [P/R] loci). We characterized several strains from the original study describing
K. mangrovensis
; two
MAT
regions were amplified and sequenced: the
STE20
gene (P/R locus) and the divergently transcribed
SXI1
and
SXI2
genes (HD locus). We identified five different mating types with different
STE20
/
SXI
allele combinations that together with results of mating experiments demonstrate that
K. mangrovensis
is not bipolar but instead has a tetrapolar mating system. Sequence and gene analysis for a 43-kb segment of the
K. mangrovensis
type strain
MAT
locus revealed remarkable synteny with the homologous
K. heveanensis
MAT
P/R region, providing new insights into slower evolution of
MAT
loci in the
Kwoniella
compared to the
Cryptococcus
clade of the Tremellales. The study of additional isolates from plant substrates in Europe and Botswana using a combination of multilocus sequencing with
MAT
gene analysis revealed two novel sibling species that we name
Kwoniella europaea
and
Kwoniella botswanensis
and which appear to also have tetrapolar mating systems.
The Transcriptional Response of Cryptococcus neoformans to Ingestion by Acanthamoeba castellanii and Macrophages Provides Insights into the Evolutionary Adaptation to the Mammalian Host
Authors: Derengowski Lorena da S. , Paes Hugo Costa , Albuquerque Patrícia , Tavares Aldo Henrique F. P. , Fernandes Larissa , Silva-Pereira Ildinete , Casadevall Arturo 
Published: March 2013

ABSTRACTVirulence ofCryptococcus neoformansfor mammals, and in particular its intracellular style, was proposed to emerge from evolutionary pressures on its natural environment by protozoan predation, which promoted the selection of strategies that allow intracellular survival in macrophages. In fact,Acanthamoeba castellaniiingests yeast cells, which then can replicate intracellularly. In addition, most fungal factors needed to establish infection in the mammalian host are also important for survival within the amoeba. To better understand the origin ofC. neoformansvirulence, we compared the transcriptional profile of yeast cells internalized by amoebae and murine macrophages after 6 h of infection. Our results showed 656 and 293 genes whose expression changed at least 2-fold in response to the intracellular environments of amoebae and macrophages, respectively. Among the genes that were found in both groups, we focused on open reading frame (ORF) CNAG_05662, which was potentially related to sugar transport but had no determined biological function. To characterize its function, we constructed a mutant strain and evaluated its ability to grow on various carbon sources. The results showed that this gene, namedPTP1(polyol transporter protein 1), is involved in the transport of 5- and 6-carbon polyols such as mannitol and sorbitol, but its presence or absence had no effect on cryptococcal virulence for mice or moth larvae. Overall, these results are consistent with the hypothesis that the capacity for mammalian virulence originated from fungus-protozoan interactions in the environment and provide a better understanding of howC. neoformansadapts to the mammalian host.
Glycine Betaine Catabolism Contributes to Pseudomonas syringae Tolerance to Hyperosmotic Stress by Relieving Betaine-Mediated Suppression of Compatible Solute Synthesis
Authors: Li Shanshan , Yu Xilan , Beattie Gwyn A. 
Published: March 2013

ABSTRACTMany bacteria can accumulate glycine betaine for osmoprotection and catabolize it as a growth substrate, but how they regulate these opposing roles is poorly understood. InPseudomonas syringaeB728a, expression of the betaine catabolism genes was reduced by an osmotic upshift to an intermediate stress level, consistent with betaine accumulation, but was increased by an upshift to a high stress level, as confirmed by an accompanying increase in degradation of radiolabeled betaine. Deletion of thegbcABbetaine catabolism genes reduced osmotolerance at a high osmolarity, and this reduction was due to the relief of betaine-mediated suppression of compatible solute synthesis. This conclusion was supported by the findings that, at high osmolarity, the ΔgbcABmutant accumulated high betaine levels and low endogenous solutes and exhibited reduced expression of the solute synthesis genes. Moreover, the ΔgbcABmutant and a mutant deficient in the synthesis of the compatible solutes NAGGN and trehalose exhibited similar reductions in osmotolerance and also in fitness on bean leaves. Activation of betaine catabolism at high osmotic stress resulted, in part, from induction ofgbdR, which encodes the transcriptional activator GbdR. Betaine catabolism was subject to partial repression by succinate under hyperosmotic stress conditions, in contrast to strong repression in the absence of stress, suggesting that betaine functions both in nutrition and as an intracellular signal modulating solute synthesis under hyperosmotic stress conditions. Collectively, these results begin to provide a detailed mechanistic understanding of howP. syringaetransitions from reliance on exogenously derived betaine to the use of endogenous solutes during adaptation to hyperosmotic conditions.
EscE and EscG Are Cochaperones for the Type III Needle Protein EscF of Enteropathogenic Escherichia coli
Authors: Sal-Man Neta , Setiaputra Dheva , Scholz Roland , Deng Wanyin , Yu Angel C. Y. , Strynadka Natalie C. J. , Finlay B. Brett 
Published: March 2013

ABSTRACT

Type III secretion systems (T3SSs) are central virulence mechanisms used by a variety of Gram-negative bacteria to inject effector proteins into host cells. The needle polymer is an essential part of the T3SS that provides the effector proteins a continuous channel into the host cytoplasm. It has been shown for a few T3SSs that two chaperones stabilize the needle protein within the bacterial cytosol to prevent its premature polymerization. In this study, we characterized the chaperones of the enteropathogenic
Escherichia coli
(EPEC) needle protein EscF. We found that Orf2 and Orf29, two poorly characterized proteins encoded within the EPEC locus of enterocyte effacement (LEE), function as the needle protein cochaperones. Our finding demonstrated that both Orf2 and Orf29 are essential for type III secretion (T3S). In addition, we found that Orf2 and Orf29 associate with the bacterial membrane and form a complex with EscF. Orf2 and Orf29 were also shown to disrupt the polymerization of EscF
in vitro
. Prediction of the tertiary structures of Orf2 and Orf29 showed high structural homology to chaperones of other T3SS needle proteins. Overall, our data suggest that Orf2 and Orf29 function as the chaperones of the needle protein, and therefore, they have been renamed EscE and EscG.
The General Stress Response Factor EcfG Regulates Expression of the C-2 Hopanoid Methylase HpnP in Rhodopseudomonas palustris TIE-1
Authors: Kulkarni Gargi , Wu Chia-Hung , Newman Dianne K. 
Published: March 2013

ABSTRACT

Lipid molecules preserved in sedimentary rocks facilitate the reconstruction of events that have shaped the evolution of the Earth's biosphere. A key limitation for the interpretation of many of these molecular fossils is that their biological roles are still poorly understood. Here, we use
Rhodopseudomonas palustris
TIE-1 to identify factors that induce biosynthesis of 2-methyl hopanoids (2-MeBHPs), progenitors of 2-methyl hopanes, one of the most abundant biomarkers in the rock record. This is the first dissection of the regulation of
hpnP
, the gene encoding the C-2 hopanoid methylase, at the molecular level. We demonstrate that EcfG, the general stress response factor of alphaproteobacteria, regulates expression of
hpnP
under a variety of challenges, including high temperature, pH stress, and presence of nonionic osmolytes. Although higher
hpnP
transcription levels did not always result in higher amounts of total methylated hopanoids, the fraction of a particular kind of hopanoid, 2-methyl bacteriohopanetetrol, was consistently higher in the presence of most stressors in the wild type, but not in the Δ
ecfG
mutant, supporting a beneficial role for 2-MeBHPs in stress tolerance. The Δ
hpnP
mutant, however, did not exhibit a growth defect under the stress conditions tested except in acidic medium. This indicates that the inability to make 2-MeBHPs under most of these conditions can readily be compensated. Although stress is necessary to regulate 2-MeBHP production, the specific conditions under which 2-MeBHP biosynthesis is essential remain to be determined.
A Plasmid-Encoded Phosphatase Regulates Bacillus subtilis Biofilm Architecture, Sporulation, and Genetic Competence
Authors: Parashar Vijay , Konkol Melissa A. , Kearns Daniel B. , Neiditch Matthew B. 
Published: March 2013

ABSTRACT

Bacillus subtilis
biofilm formation is tightly regulated by elaborate signaling pathways. In contrast to domesticated lab strains of
B. subtilis
which form smooth, essentially featureless colonies, undomesticated strains such as NCIB 3610 form architecturally complex biofilms. NCIB 3610 also contains an 80-kb plasmid absent from laboratory strains, and mutations in a plasmid-encoded homolog of a Rap protein, RapP, caused a hyperrugose biofilm phenotype. Here we explored the role of
rapP phrP
in biofilm formation. We found that RapP is a phosphatase that dephosphorylates the intermediate response regulator Spo0F. RapP appears to employ a catalytic glutamate to dephosphorylate the Spo0F aspartyl phosphate, and the implications of the RapP catalytic glutamate are discussed. In addition to regulating
B. subtilis
biofilm formation, we found that RapP regulates sporulation and genetic competence as a result of its ability to dephosphorylate Spo0F. Interestingly, while
rap phr
gene cassettes routinely form regulatory pairs; i.e., the mature
phr
gene product inhibits the activity of the
rap
gene product, the
phrP
gene product did not inhibit RapP activity in our assays. RapP activity was, however, inhibited by PhrH
in vivo
but not
in vitro
. Additional genetic analysis suggests that RapP is directly inhibited by peptide binding. We speculate that PhrH could be subject to posttranslational modification
in vivo
and directly inhibit RapP activity or, more likely, PhrH upregulates the expression of a peptide that, in turn, directly binds to RapP and inhibits its Spo0F phosphatase activity.
Vibrio cholerae VttR
A
and VttR
B
Regulatory Influences Extend beyond the Type 3 Secretion System Genomic Island
Authors: Chaand Mudit , Dziejman Michelle 
Published: March 2013

ABSTRACT

A subset of non-O1/non-O139 serogroup strains of
Vibrio cholerae
cause disease using type 3 secretion system (T3SS)-mediated mechanisms. An ∼50-kb genomic island carries genes encoding the T3SS structural apparatus, effector proteins, and two transmembrane transcriptional regulators, VttR
A
and VttR
B
, which are ToxR homologues. Previous experiments demonstrated that VttR
A
and VttR
B
are necessary for colonization
in vivo
and promote bile-dependent T3SS gene expression
in vitro
. To better understand the scope of genes that are potential targets of VttR
A
and VttR
B
regulation, we performed deep RNA sequencing using O39 serogroup strain AM-19226 and derivatives carrying deletions in
vttR
A
and
vttR
B
grown in bile. Comparison of the transcript profiles from Δ
vttR
A
and Δ
vttR
B
mutant strains to the isogenic parent strain confirmed that VttR
A
and VttR
B
regulate expression of some T3SS island genes and provided additional information about relative expression levels and operon organization. Interestingly, the data also suggested that additional genes, located outside the T3SS island and encoding functions involved in motility, chemotaxis, type 6 secretion, transcriptional regulation, and stress responses, may also by regulated by VttR
A
and VttR
B
. We verified transcript levels for selected genes by quantitative reverse transcription (RT)-PCR and then focused additional studies on motility and biofilm formation. The results suggest that VttR
A
and VttR
B
act as part of a complex transcriptional network that coordinates virulence gene expression with multiple cellular phenotypes. VttR
A
and VttR
B
therefore represent horizontally acquired transcriptional regulators with the ability to influence global gene expression in addition to modulating gene expression within the T3SS genomic island.