bluuebunny/crossref_metadata_2025_split huggingface dataset:
Defining the Functional Potential and Active Community Members of a Sediment Microbial Community in a High-Arctic Hypersaline Subzero Spring
Authors: Lay Chih-Ying , Mykytczuk Nadia C. S. , Yergeau ï¿½tienne , Lamarche-Gagnon Guillaume , Greer Charles W. , Whyte Lyle G. 
Published: April 2013

ABSTRACTThe Lost Hammer (LH) Spring is the coldest and saltiest terrestrial spring discovered to date and is characterized by perennial discharges at subzero temperatures (−5ï¿½C), hypersalinity (salinity, 24%), and reducing (≈−165 mV), microoxic, and oligotrophic conditions. It is rich in sulfates (10.0%, wt/wt), dissolved H2S/sulfides (up to 25 ppm), ammonia (≈381 μM), and methane (11.1 g day−1). To determine its total functional and genetic potential and to identify its active microbial components, we performed metagenomic analyses of the LH Spring outlet microbial community and pyrosequencing analyses of the cDNA of its 16S rRNA genes. Reads related toCyanobacteria(19.7%),Bacteroidetes(13.3%), andProteobacteria(6.6%) represented the dominant phyla identified among the classified sequences. Reconstruction of the enzyme pathways responsible for bacterial nitrification/denitrification/ammonification and sulfate reduction appeared nearly complete in the metagenomic data set. In the cDNA profile of the LH Spring active community, ammonia oxidizers (Thaumarchaeota), denitrifiers (Pseudomonasspp.), sulfate reducers (Desulfobulbusspp.), and other sulfur oxidizers (Thermoprotei) were present, highlighting their involvement in nitrogen and sulfur cycling. Stress response genes for adapting to cold, osmotic stress, and oxidative stress were also abundant in the metagenome. Comparison of the composition of the functional community of the LH Spring to metagenomes from other saline/subzero environments revealed a close association between the LH Spring and another Canadian high-Arctic permafrost environment, particularly in genes related to sulfur metabolism and dormancy. Overall, this study provides insights into the metabolic potential and the active microbial populations that exist in this hypersaline cryoenvironment and contributes to our understanding of microbial ecology in extreme environments.
CmPEX6
, a Gene Involved in Peroxisome Biogenesis, Is Essential for Parasitism and Conidiation by the Sclerotial Parasite Coniothyrium minitans
Authors: Wei Wei , Zhu Wenjun , Cheng Jiasen , Xie Jiatao , Li Bo , Jiang Daohong , Li Guoqing , Yi Xianhong , Fu Yanping 
Published: April 2013

ABSTRACT

Coniothyrium minitans
is a sclerotial parasite of the plant-pathogenic fungus
Sclerotinia sclerotiorum
, and conidial production and parasitism are two important aspects for commercialization of this biological control agent. To understand the mechanism of conidiation and parasitism at the molecular level, we constructed a transfer DNA (tDNA) insertional library with the wild-type strain ZS-1. A conidiation-deficient mutant, ZS-1TN22803, was uncovered through screening of this library. This mutant could produce pycnidia on potato dextrose agar (PDA), but most were immature and did not bear conidia. Moreover, this mutant lost the ability to parasitize or rot the sclerotia of
S. sclerotiorum
. Analysis of the tDNA flanking sequences revealed that a peroxisome biogenesis factor 6 (
PEX6
) homolog of
Saccharomyces cerevisiae
, named
CmPEX6
, was disrupted by the tDNA insertion in this mutant. Targeted gene replacement and gene complementation tests confirmed that a null mutation of
CmPEX6
was responsible for the phenotype of ZS-1TN22803. Further analysis showed that both ZS-1TN22803 and the targeted replacement mutants could not grow on PDA medium containing oleic acid, and they produced much less nitric oxide (NO) and hydrogen peroxide (H
2
O
2
) than wild-type strain ZS-1. The conidiation of ZS-1TN22803 was partially restored by adding acetyl-CoA or glyoxylic acid to the growth media. Our results suggest that fatty acid β-oxidation, reactive oxygen and nitrogen species, and possibly other unknown pathways in peroxisomes are involved in conidiation and parasitism by
C. minitans
.
Rational Design of a Novel Propeptide for Improving Active Production of Streptomyces griseus Trypsin in Pichia pastoris
Authors: Ling Zhenmin , Liu Yi , Teng Shaolei , Kang Zhen , Zhang Jingjing , Chen Jian , Du Guocheng 
Published: April 2013

ABSTRACT

Applying
in silico
simulations and
in vitro
experiments, the amino acid proline was proved to have a profound influence on
Streptomyces griseus
trypsinogen, and the hydrogen bond between H
57
and D
102
was found to be crucial for trypsin activity. By introducing an artificial propeptide, IVEF, the titer of trypsin was increased 6.71-fold.
Potentiation of Mycovirus Transmission by Zinc Compounds via Attenuation of Heterogenic Incompatibility in Rosellinia necatrix
Authors: Ikeda Kenichi , Inoue Kanako , Kida Chiaki , Uwamori Takahiro , Sasaki Atsuko , Kanematsu Satoko , Park Pyoyun 
Published: April 2013

ABSTRACT

Heterogenic incompatibility is considered a defense mechanism against deleterious intruders such as mycovirus.
Rosellinia necatrix
shows strong heterogenic incompatibility. In the heterogenic incompatibility reaction, the approaching hyphae hardly anastomosed, a distinctive barrage line formed, and green fluorescent protein (GFP)-labeled hyphae quickly lost their fluorescence when encountering incompatible hyphae. In this study, transmission of a hypovirulence-conferring mycovirus to strains with different genetic backgrounds was attempted. Various chemical reagents considered to affect the programmed cell death pathway or cell wall modification were examined. Treatment with zinc compounds was shown to aid in transmission of mycoviruses to strains with different genetic backgrounds. In incompatible pairings, treatment with zinc compounds accelerated hyphal anastomosis; moreover, cytosolic GFP was transmitted to the newly joined hyphae. These results suggest that zinc compounds not only increase hyphal anastomosis but also attenuate heterogenic incompatibility.
Roles of Alkyl Hydroperoxide Reductase Subunit C (AhpC) in Viable but Nonculturable Vibrio parahaemolyticus
Authors: Wang Hen-Wei , Chung Chun-Hui , Ma Tsung-Yong , Wong Hin-chung 
Published: April 2013

ABSTRACT

Alkyl hydroperoxide reductase subunit C (AhpC) is the catalytic subunit responsible for the detoxification of reactive oxygen species that form in bacterial cells or are derived from the host; thus, AhpC facilitates the survival of pathogenic bacteria under environmental stresses or during infection. This study investigates the role of AhpC in the induction and maintenance of a viable but nonculturable (VBNC) state in
Vibrio parahaemolyticus
. In this investigation,
ahpC1
(VPA1683) and
ahpC2
(VP0580) were identified in chromosomes II and I of this pathogen, respectively. Mutants with deletions of these two
ahpC
genes and their complementary strains were constructed from the parent strain KX-V231. The growth of these strains was monitored on tryptic soy agar–3% NaCl in the presence of the extrinsic peroxides H
2
O
2
and
tert
-butyl hydroperoxide (
t
-BOOH) at different incubation temperatures. The results revealed that both
ahpC
genes were protective against
t
-BOOH, while
ahpC1
was protective against H
2
O
2
. The protective function of
ahpC2
at 4ï¿½C was higher than that of
ahpC1
. The times required to induce the VBNC state (4.7 weeks) at 4ï¿½C in a modified Morita mineral salt solution with 0.5% NaCl and then to maintain the VBNC state (4.7 weeks) in an
ahpC2
mutant and an
ahpC1 ahpC2
double mutant were significantly shorter than those for the parent strain (for induction, 6.2 weeks; for maintenance, 7.8 weeks) and the
ahpC1
mutant (for induction, 6.0 weeks; for maintenance, 8.0 weeks) (
P
< 0.03). Complementation with an
ahpC2
gene reversed the effects of the
ahpC2
mutation in shortening the times for induction and maintenance of the VBNC state. This investigation identified the different functions of the two
ahpC
genes and confirmed the particular role of
ahpC2
in the VBNC state of
V. parahaemolyticus
.
Imidazoacridinone Derivatives as Efficient Sensitizers in Photoantimicrobial Chemotherapy
Authors: Taraszkiewicz Aleksandra , Grinholc Mariusz , Bielawski Krzysztof P. , Kawiak Anna , Nakonieczna Joanna 
Published: April 2013

ABSTRACT

The objective of this study was to investigate a new potential photosensitizer (PS) in the photodynamic inactivation (PDI) of microorganisms
in vitro
(11 reference strains and 13 clinical isolates, representing common Gram-positive and Gram-negative human pathogens), with special emphasis on
Candida albicans
. We studied the light-induced cytotoxicity of the imidazoacridinone derivative C1330 toward fungal cells grown in planktonic form. We examined the influence of various parameters (time of incubation, PDI quencher effect, and C1330 accumulation in
C. albicans
cells) on the efficacy of light-dependent cytotoxicity. Additionally, we checked for the potential cyto- and phototoxic activity of C1330 against human dermal keratinocytes. In our research, we used a broadband incoherent blue light source (380 to 470 nm) with an output power of 100 mW/cm
2
.
In vitro
studies showed that the C1330 action against
C. albicans
was a light-dependent process. C1330 was an efficient photosensitizer in the photodynamic inactivation of
C. albicans
, which reduced the growth of planktonic cells by 6.1 log
10
units. Efficient accumulation of PS in the nucleus and vacuoles was observed after 30 min of incubation, which correlated with the highest photokilling efficacy. Significant changes in intracellular structure were observed upon illumination of C1330-incubated
C. albicans
cells. In the case of the human HaCaT cell line, approximately 40% of cells survived the treatment, which indicates the potential benefit of further study of the application of C1330 in photoantimicrobial chemotherapy. These data suggest that PDI may be a viable approach for the treatment of localized
C. albicans
infections.
Iron and Copper Act Synergistically To Delay Anaerobic Growth of Bacteria
Authors: Bird Lina J. , Coleman Maureen L. , Newman Dianne K. 
Published: April 2013

ABSTRACT

Transition metals are known to cause toxic effects through their interaction with oxygen, but toxicity under anoxic conditions is poorly understood. Here we investigated the effects of iron (Fe) and copper (Cu) on the anaerobic growth and gene expression of the purple phototrophic bacterium
Rhodopseudomonas palustris
TIE-1. We found that Fe(II) and Cu(II) act synergistically to delay anaerobic growth at environmentally relevant metal concentrations. Cu(I) and Cu(II) had similar effects both alone and in the presence of ascorbate, a Cu(II) reductant, indicating that reduction of Cu(II) to Cu(I) by Fe(II) is not sufficient to explain the growth inhibition. Addition of Cu(II) increased the toxicity of Co(II) and Ni(II); in contrast, Ni(II) toxicity was diminished in the presence of Fe(II). The synergistic anaerobic toxicity of Fe(II) and Cu(II) was also observed for
Escherichia coli
MG1655,
Shewanella oneidensis
MR-1, and
Rhodobacter capsulatus
SB1003. Gene expression analyses for
R. palustris
identified three regulatory genes that respond to Cu(II) and not to Fe(II): homologs of
cueR
and
cusR
, two known proteobacterial copper homeostasis regulators, and
csoR
, a copper regulator recently identified in
Mycobacterium tuberculosis
. Two P-type ATPase efflux pumps, along with an F
o
F
1
ATP synthase, were also upregulated by Cu(II) but not by Fe(II). An
Escherichia coli
mutant deficient in
copA
,
cus
, and
cueO
showed a smaller synergistic effect, indicating that iron might interfere with one or more of the copper homeostasis systems. Our results suggest that interactive effects of transition metals on microbial physiology may be widespread under anoxic conditions, although the molecular mechanisms remain to be more fully elucidated.
Identification of Genes Upregulated by the Transcription Factor Bcr1 That Are Involved in Impermeability, Impenetrability, and Drug Resistance of Candida albicans
a/
α Biofilms
Authors: Srikantha Thyagarajan , Daniels Karla J. , Pujol Claude , Kim Elena , Soll David R. 
Published: April 2013

ABSTRACT

Candida albicans
forms two types of biofilm, depending upon the configuration of the mating type locus. Although architecturally similar,
a/
α biofilms are impermeable, impenetrable, and drug resistant, whereas
a/a
and α/α biofilms lack these traits. The difference appears to be the result of an alternative matrix. Overexpression in
a/a
cells of
BCR1
, a master regulator of the
a/
α matrix, conferred impermeability, impenetrability, and drug resistance to
a/a
biofilms. Deletion of
BCR1
in
a/
α cells resulted in the loss of these
a/
α-specific biofilm traits. Using
BCR1
overexpression in
a/a
cells, we screened 107 genes of interest and identified 8 that were upregulated by Bcr1. When each was overexpressed in
a/a
biofilms, the three
a/
α traits were partially conferred, and when each was deleted in
a/
α cells, the traits were partially lost. Five of the eight genes have been implicated in iron homeostasis, and six encode proteins that are either in the wall or plasma membrane or secreted. All six possess sites for O-linked and N-linked glycosylation that, like glycosylphosphatidylinositol (GPI) anchors, can cross-link to the wall and matrix, suggesting that they may exert a structural role in conferring impermeability, impenetrability, and drug resistance, in addition to their physiological functions. The fact that in a screen of 107 genes, all 8 of the Bcr1-upregulated genes identified play a role in impermeability, impenetrability, and drug resistance suggests that the formation of the
a/
α matrix is highly complex and involves a larger number of genes than the initial ones identified here.
Pathway of Glycine Betaine Biosynthesis in Aspergillus fumigatus
Authors: Lambou Karine , Pennati Andrea , Valsecchi Isabel , Tada Rui , Sherman Stephen , Sato Hajime , Beau Remi , Gadda Giovanni , Latgé Jean-Paul 
Published: April 2013

ABSTRACTThe choline oxidase (CHOA) and betaine aldehyde dehydrogenase (BADH) genes identified inAspergillus fumigatusare present as a cluster specific for fungal genomes. Biochemical and molecular analyses of this cluster showed that it has very specific biochemical and functional features that make it unique and different from its plant and bacterial homologs.A. fumigatusChoAp catalyzed the oxidation of choline to glycine betaine with betaine aldehyde as an intermediate and reduced molecular oxygen to hydrogen peroxide using FAD as a cofactor.A. fumigatusBadhp oxidized betaine aldehyde to glycine betaine with reduction of NAD+to NADH. Analysis of theAfchoAΔ::HPHandAfbadAΔ::HPHsingle mutants and theAfchoAΔAfbadAΔ::HPHdouble mutant showed thatAfChoAp is essential for the use of choline as the sole nitrogen, carbon, or carbon and nitrogen source during the germination process.AfChoAp andAfBadAp were localized in the cytosol of germinating conidia and mycelia but were absent from resting conidia. Characterization of the mutant phenotypes showed that glycine betaine inA. fumigatusfunctions exclusively as a metabolic intermediate in the catabolism of choline and not as a stress protectant. This study inA. fumigatusis the first molecular, cellular, and biochemical characterization of the glycine betaine biosynthetic pathway in the fungal kingdom.
A Combination of Glycerol and Manganese Promotes Biofilm Formation in Bacillus subtilis via Histidine Kinase KinD Signaling
Authors: Shemesh Moshe , Chai Yunrong 
Published: April 2013

ABSTRACT

The spore-forming bacterium
Bacillus subtilis
forms matrix-enclosed biofilms in response to environmental cues that to date remain poorly defined. Biofilm formation depends on the synthesis of an extracellular matrix, which is indirectly regulated by the transcriptional regulator Spo0A. The activity of Spo0A depends on its phosphorylation state. The level of phosphorylated Spo0A (Spo0A∼P) is controlled by a network of kinases and phosphatases, which respond to environmental and physiological signals. In spite of significant progress in understanding biofilm development, the fundamental question of how cells sense the environmental cues that trigger biofilm formation has largely remained unaddressed. Here, we report that biofilm formation of
B. subtilis
in LB medium is triggered by a combination of glycerol and manganese (GM). Moreover, LB medium with GM significantly stimulates biofilm-associated sporulation and production of an undefined brown pigment. We further show that transcription of the major operons responsible for matrix production and biofilm formation is dramatically enhanced in response to GM. We also establish that KinD is a principal histidine kinase responsible for sensing the presence of GM exclusively by its extracellular CACHE domain. Finally, we show that GM has a similar biofilm-promoting effect in two related
Bacillus
species,
B. licheniformis
and
B. cereus
, indicating that the biofilm-promoting effect of GM is conserved in
Bacillus
species.
The Escherichia coli Cpx Envelope Stress Response Regulates Genes of Diverse Function That Impact Antibiotic Resistance and Membrane Integrity
Authors: Raivio Tracy L. , Leblanc Shannon K. D. , Price Nancy L. 
Published: April 2013

ABSTRACT

The Cpx envelope stress response mediates adaptation to stresses that cause envelope protein misfolding. Adaptation is partly conferred through increased expression of protein folding and degradation factors. The Cpx response also plays a conserved role in the regulation of virulence determinant expression and impacts antibiotic resistance. We sought to identify adaptive mechanisms that may be involved in these important functions by characterizing changes in the transcriptome of two different
Escherichia coli
strains when the Cpx response is induced. We show that, while there is considerable strain- and condition-specific variability in the Cpx response, the regulon is enriched for proteins and functions that are inner membrane associated under all conditions. Genes that were changed by Cpx pathway induction under all conditions were involved in a number of cellular functions and included several intergenic regions, suggesting that posttranscriptional regulation is important during Cpx-mediated adaptation. Some Cpx-regulated genes are centrally involved in energetics and play a role in antibiotic resistance. We show that a number of small, uncharacterized envelope proteins are Cpx regulated and at least two of these affect phenotypes associated with membrane integrity. Altogether, our work suggests new mechanisms of Cpx-mediated envelope stress adaptation and antibiotic resistance.
Identification of a Hotdog Fold Thioesterase Involved in the Biosynthesis of Menaquinone in Escherichia coli
Authors: Chen Minjiao , Ma Xinyu , Chen Xiaolei , Jiang Ming , Song Haigang , Guo Zhihong 
Published: April 2013

ABSTRACT

Escherichia coli
is used as a model organism for elucidation of menaquinone biosynthesis, for which a hydrolytic step from 1,4-dihydroxy-2-naphthoyl-coenzyme A (DHNA-CoA) to 1,4-dihydroxy-2-naphthoate is still unaccounted for. Recently, a hotdog fold thioesterase has been shown to catalyze this conversion in phylloquinone biosynthesis, suggesting that its closest homolog, YbgC in
Escherichia coli
, may be the DHNA-CoA thioesterase in menaquinone biosynthesis. However, this possibility is excluded by the involvement of YbgC in the Tol-Pal system and its complete lack of hydrolytic activity toward DHNA-CoA. To identify the hydrolytic enzyme, we have performed an activity-based screen of all nine
Escherichia coli
hotdog fold thioesterases and found that YdiI possesses a high level of hydrolytic activity toward DHNA-CoA, with high substrate specificity, and that another thioesterase, EntH, from siderophore biosynthesis exhibits a moderate, much lower DHNA-CoA thioesterase activity. Deletion of the
ydiI
gene from the bacterial genome results in a significant decrease in menaquinone production, which is little affected in Δ
ybgC
and Δ
entH
mutants. These results support the notion that YdiI is the DHNA-CoA thioesterase involved in the biosynthesis of menaquinone in the model bacterium.
Crystal Structure and Site-Directed Mutagenesis Analyses of Haloalkane Dehalogenase LinB from Sphingobium sp. Strain MI1205
Authors: Okai Masahiko , Ohtsuka Jun , Imai Lica Fabiana , Mase Tomoko , Moriuchi Ryota , Tsuda Masataka , Nagata Koji , Nagata Yuji , Tanokura Masaru 
Published: April 2013

ABSTRACT

The enzymes LinB
UT
and LinB
MI
(LinB from
Sphingobium japonicum
UT26 and
Sphingobium
sp. MI1205, respectively) catalyze the hydrolytic dechlorination of β-hexachlorocyclohexane (β-HCH) and yield different products, 2,3,4,5,6-pentachlorocyclohexanol (PCHL) and 2,3,5,6-tetrachlorocyclohexane-1,4-diol (TCDL), respectively, despite their 98% identity in amino acid sequence. To reveal the structural basis of their different enzymatic properties, we performed site-directed mutagenesis and X-ray crystallographic studies of LinB
MI
and its seven point mutants. The mutation analysis revealed that the seven amino acid residues uniquely found in LinB
MI
were categorized into three groups based on the efficiency of the first-step (from β-HCH to PCHL) and second-step (from PCHL to TCDL) conversions. Crystal structure analyses of wild-type LinB
MI
and its seven point mutants indicated how each mutated residue contributed to the first- and second-step conversions by LinB
MI
. The dynamics simulation analyses of wild-type LinB
MI
and LinB
UT
revealed that the entrance of the substrate access tunnel of LinB
UT
was more flexible than that of LinB
MI
, which could lead to the different efficiencies of dehalogenation activity between these dehalogenases.
Subdomains N2N3 of Fibronectin Binding Protein A Mediate Staphylococcus aureus Biofilm Formation and Adherence to Fibrinogen Using Distinct Mechanisms
Authors: Geoghegan Joan A. , Monk Ian R. , O'Gara James P. , Foster Timothy J. 
Published: April 2013

ABSTRACT

Health care-associated methicillin-resistant
Staphylococcus aureus
(HA-MRSA) forms biofilm
in vitro
that is dependent on the surface-located fibronectin binding proteins A and B (FnBPA, FnBPB). Here we provide new insights into the requirements for FnBP-dependent biofilm formation by MRSA. We show that expression of FnBPs is sustained at high levels throughout the growth cycle in the HA-MRSA strain BH1CC in contrast to laboratory strain SH1000, where expression could be detected only in exponential phase. We found that FnBP-mediated biofilm accumulation required Zn
2+
, while the removal of Zn
2+
had no effect on the ability of FnBPA to mediate bacterial adherence to fibrinogen. We also investigated the role of FnBPA expressed on the surface of
S. aureus
in promoting biofilm formation and bacterial adhesion to fibrinogen. The minimum part of FnBPA required for ligand binding has so far been defined only with recombinant proteins. Here we found that the N1 subdomain was not required for biofilm formation or for FnBPA to promote bacterial adherence to fibrinogen. Residues at the C terminus of subdomain N3 required for FnBPA to bind to ligands using the “dock, lock, and latch” mechanism were necessary for FnBPA to promote bacterial adherence to fibrinogen. However, these residues were not necessary to form biofilm, allowing us to localize the region of FnBPA required for biofilm accumulation to residues 166 to 498. Thus, FnBPA mediates biofilm formation and bacterial adhesion to fibrinogen using two distinct mechanisms. Finally, we identified a hitherto-unrecognized thrombin cleavage site close to the boundary between subdomains N1 and N2 of FnBPA.