bluuebunny/crossref_metadata_2025_split huggingface dataset:
Formate-Dependent H
2
Production by the Mesophilic Methanogen
Methanococcus maripaludis
Authors: Lupa Boguslaw , Hendrickson Erik L. , Leigh John A. , Whitman William B. 
Published: September 2008

ABSTRACT

Methanococcus maripaludis
, an H
2
- and formate-utilizing methanogen, produced H
2
at high rates from formate. The rates and kinetics of H
2
production depended upon the growth conditions, and H
2
availability during growth was a major factor. Specific activities of resting cells grown with formate or H
2
were 0.4 to 1.4 U·mg
−1
(dry weight). H
2
production in formate-grown cells followed Michaelis-Menten kinetics, and the concentration of formate required for half-maximal activity (

K
f

) was 3.6 mM. In contrast, in H
2
-grown cells this process followed sigmoidal kinetics, and the

K
f

was 9 mM. A key enzyme for formate-dependent H
2
production was formate dehydrogenase, Fdh. H
2
production and growth were severely reduced in a mutant containing a deletion of the gene encoding the Fdh1 isozyme, indicating that it was the primary Fdh. In contrast, a mutant containing a deletion of the gene encoding the Fdh2 isozyme possessed near-wild-type activities, indicating that this isozyme did not play a major role. H
2
production by a mutant containing a deletion of the coenzyme F
420
-reducing hydrogenase Fru was also severely reduced, suggesting that the major pathway of H
2
production comprised Fdh1 and Fru. Because a Δ
fru
-Δ
frc
mutant retained 10% of the wild-type activity, an additional pathway is present. Mutants possessing deletions of the gene encoding the F
420
-dependent methylene-H
4
MTP dehydrogenase (Mtd) or the H
2
-forming methylene-H
4
MTP dehydrogenase (Hmd) also possessed reduced activity, which suggested that this second pathway was comprised of Fdh1-Mtd-Hmd. In contrast to H
2
production, the cellular rates of methanogenesis were unaffected in these mutants, which suggested that the observed H
2
production was not a direct intermediate of methanogenesis. In conclusion, high rates of formate-dependent H
2
production demonstrated the potential of
M. maripaludis
for the microbial production of H
2
from formate.
Construction and Expression of Sugar Kinase Transcriptional Gene Fusions by Using the
Sinorhizobium meliloti
ORFeome
Authors: Humann Jodi L. , Schroeder Brenda K. , Mortimer Michael W. , House Brent L. , Yurgel Svetlana N. , Maloney Scott C. , Ward Kristel L. , Fallquist Heather M. , Ziemkiewicz Hope T. , Kahn Michael L. 
Published: September 2008

ABSTRACT

The
Sinorhizobium meliloti
ORFeome project cloned 6,314 open reading frames (ORFs) into a modified Gateway entry vector system from which the ORFs could be transferred to destination vectors in vivo via bacterial conjugation. In this work, a reporter gene destination vector, pMK2030, was constructed and used to generate ORF-specific transcriptional fusions to β-glucuronidase (
gusA
) and green fluorescent protein (
gfp
) reporter genes. A total of 6,290 ORFs were successfully transferred from the entry vector library into pMK2030. To demonstrate the utility of this system, reporter plasmids corresponding to 30 annotated sugar kinase genes were integrated into the
S. meliloti
SM1021 and/or SM8530 genome. Expression of these genes was measured using a high-throughput β-glucuronidase assay to track expression on nine different carbon sources. Six ORFs integrated into SM1021 and SM8530 had different basal levels of expression in the two strains. The annotated activities of three other sugar kinases were also confirmed.
Hydrogen Peroxide Induces Hyphal Differentiation in
Candida albicans
Authors: Nasution Olviyani , Srinivasa Kavitha , Kim Minsun , Kim Yeo-Jung , Kim Wankee , Jeong Woojin , Choi Wonja 
Published: September 2008

ABSTRACT

In this study, we demonstrate that hyphal differentiation is induced by the subtoxic concentration of exogenous H
2
O
2
in
Candida albicans.
This finding is confirmed by the changing intracellular concentration of H
2
O
2
. In order to induce the same level of differentiation, low concentrations of exogenous H
2
O
2
are required for the null mutants of the thiol-specific antioxidant and catalase, while higher concentrations are needed for cells treated with ascorbic acid, an antioxidant chemical.
African Trypanosomes Contain 5-Methylcytosine in Nuclear DNA
Authors: Militello Kevin T. , Wang Ping , Jayakar Sangeeta K. , Pietrasik Rebecca L. , Dupont Christopher D. , Dodd Kristi , King Anthony M. , Valenti Paul R. 
Published: September 2008

ABSTRACT

It is currently unclear if there are modified DNA bases in
Trypanosoma brucei
other than J-base. We identify herein a cytosine-5 DNA methyltransferase gene and report the presence and location of 5-methylcytosine in genomic DNA. Our data demonstrate that African trypanosomes contain a functional cytosine DNA methylation pathway.
Role of the Histone-Like Nucleoid Structuring Protein in the Regulation of
rpoS
and RpoS-Dependent Genes in
Vibrio cholerae
Authors: Silva Anisia J. , Sultan Syed Zafar , Liang Weili , Benitez Jorge A. 
Published: September 2008

ABSTRACT

Production of the Zn-metalloprotease hemagglutinin (HA)/protease by
Vibrio cholerae
has been reported to enhance enterotoxicity in rabbit ileal loops and the reactogenicity of live cholera vaccine candidates. Expression of HA/protease requires the alternate sigma factor σ
S
(RpoS), encoded by
rpoS
. The histone-like nucleoid structuring protein (H-NS) has been shown to repress
rpoS
expression in
Escherichia coli
. In
V. cholerae
strains of the classical biotype, H-NS has been reported to silence virulence gene expression. In this study we examined the role of H-NS in the expression of HA/protease and motility in an El Tor biotype strain by constructing a Δ
hns
mutant. The Δ
hns
mutant exhibited multiple phenotypes, such as production of cholera toxin in nonpermissive LB medium, reduced resistance to high osmolarity, enhanced resistance to low pH and hydrogen peroxide, and reduced motility. Depletion of H-NS by overexpression of a dominant-negative allele or by deletion of
hns
resulted in diminished expression of HA/protease. Epistasis analysis of HA/protease expression in Δ
hns
, Δ
rpoS
, and Δ
hns
Δ
rpoS
mutants, analysis of RpoS reporter fusions, quantitative reverse transcription-PCR measurements, and ectopic expression of RpoS in Δ
rpoS
and Δ
rpoS
Δ
hns
mutants showed that H-NS posttranscriptionally enhances RpoS expression. The Δ
hns
mutant exhibited a lower degree of motility and lower levels of expression of
flaA
,
flaC
,
cheR
-
2
, and
motX
mRNAs than the wild type. Comparison of the mRNA abundances of these genes in wild-type, Δ
hns
, Δ
rpoS
, and Δ
hns
Δ
rpoS
strains revealed that deletion of
rpoS
had a more severe negative effect on their expression. Interestingly, deletion of
hns
in the
rpoS
background resulted in higher expression levels of
flaA
,
flaC
, and
motX
, suggesting that H-NS represses the expression of these genes in the absence of σ
S
. Finally, we show that the cyclic AMP receptor protein and H-NS act along the same pathway to positively affect RpoS expression.
A Possible Extended Family of Regulators of Sigma Factor Activity inStreptomyces coelicolor
Authors: Kim Eun Sook , Song Ju Yeon , Kim Dae Wi , Chater Keith F. , Lee Kye Joon 
Published: September 2008

ABSTRACTSCO4677 is one of a large number of similar genes inStreptomyces coelicolorthat encode proteins with an HATPase_c domain resembling that of anti-sigma factors such as SpoIIAB ofBacillus subtilis. However, SCO4677 is not located close to genes likely to encode a cognate sigma or anti-anti-sigma factor. SCO4677 was found to regulate antibiotic production and morphological differentiation, both of which were significantly enhanced by the deletion of SCO4677. Through protein-protein interaction screening of candidate sigma factor partners using the yeast two-hybrid system, SCO4677 protein was found to interact with the developmentally specific σF, suggesting that it is an antagonistic regulator of σF. Two other proteins, encoded by SCO0781 and SCO0869, were found to interact with the SCO4677 anti-σFduring a subsequent global yeast two-hybrid screen, and the SCO0869-SCO4677 protein-protein interaction was confirmed by coimmunoprecipitation. The SCO0781 and SCO0869 proteins resemble well-known anti-anti-sigma factors such as SpoIIAA ofB. subtilis. It appears that streptomycetes may possess an extraordinary abundance of anti-sigma factors, some of which may influence diverse processes through interactions with multiple partners: a novel feature for such regulatory proteins.
The ABC-Type Multidrug Resistance Transporter LmrCD Is Responsible for an Extrusion-Based Mechanism of Bile Acid Resistance in
Lactococcus lactis
Authors: Zaidi Arsalan Haseeb , Bakkes Patrick J. , Lubelski Jacek , Agustiandari Herfita , Kuipers Oscar P. , Driessen Arnold J. M. 
Published: September 2008

ABSTRACT

Upon prolonged exposure to cholate and other toxic compounds,
Lactococcus lactis
develops a multidrug resistance phenotype that has been attributed to an elevated expression of the heterodimeric ABC-type multidrug transporter LmrCD. To investigate the molecular basis of bile acid resistance in
L. lactis
and to evaluate the contribution of efflux-based mechanisms in this process, the drug-sensitive
L. lactis
NZ9000 Δ
lmrCD
strain was challenged with cholate. A resistant strain was obtained that, compared to the parental strain, showed (i) significantly improved resistance toward several bile acids but not to drugs, (ii) morphological changes, and (iii) an altered susceptibility to antimicrobial peptides. Transcriptome and transport analyses suggest that the acquired resistance is unrelated to elevated transport activity but, instead, results from a multitude of stress responses, changes to the cell envelope, and metabolic changes. In contrast, wild-type cells induce the expression of
lmrCD
upon exposure to cholate, whereupon the cholate is actively extruded from the cells. Together, these data suggest a central role for an efflux-based mechanism in bile acid resistance and implicate LmrCD as the main system responsible in
L. lactis
.
Identification and Characterization of Cyclic Diguanylate Signaling Systems Controlling Rugosity in
Vibrio cholerae
Authors: Beyhan Sinem , Odell Lindsay S. , Yildiz Fitnat H. 
Published: September 2008

ABSTRACT

Vibrio cholerae
, the causative agent of the disease cholera, can generate rugose variants that have an increased capacity to form biofilms. Rugosity and biofilm formation are critical for the environmental survival and transmission of the pathogen, and these processes are controlled by cyclic diguanylate (c-di-GMP) signaling systems. c-di-GMP is produced by diguanylate cyclases (DGCs) and degraded by phosphodiesterases (PDEs). Proteins that contain GGDEF domains act as DGCs, whereas proteins that contain EAL or HD-GYP domains act as PDEs. In the
V. cholerae
genome there are 62 genes that are predicted to encode proteins capable of modulating the cellular c-di-GMP concentration. We previously identified two DGCs, VpvC and CdgA, that can control the switch between smooth and rugose. To identify other c-di-GMP signaling proteins involved in rugosity, we generated in-frame deletion mutants of all genes predicted to encode proteins with GGDEF and EAL domains and then searched for mutants with altered rugosity. In this study, we identified two new genes,
cdgG
and
cdgH
, involved in rugosity control. We determined that CdgH acts as a DGC and positively regulates rugosity, whereas CdgG does not have DGC activity and negatively regulates rugosity. In addition, epistasis analysis with CdgG, CdgH, and other DGCs and PDEs controlling rugosity revealed that CdgG and CdgH act in parallel with previously identified c-di-GMP signaling proteins to control rugosity in
V. cholerae
. We also determined that PilZ domain-containing c-di-GMP binding proteins contribute minimally to rugosity, indicating that there are additional c-di-GMP binding proteins controlling rugosity in
V. cholerae
.
Lipoteichoic Acid Is a Major Component of the
Bacillus subtilis
Periplasm
Authors: Matias Valério R. F. , Beveridge Terry J. 
Published: September 2008

ABSTRACT

Cryo-electron microscopy (cryo-EM) of frozen-hydrated specimens allows high-resolution observation of structures in optimally preserved samples. In gram-positive bacteria, this method reveals the presence of a periplasmic space between the plasma membrane and an often differentiated cell wall matrix. Since virtually nothing is known about the composition of its constituent matter (i.e., the periplasm), it is still unclear what structures (or mechanism) sustain a gram-positive periplasmic space. Here we have used cryo-EM of frozen-hydrated sections in combination with various labels to probe the model gram-positive organism
Bacillus subtilis
for major periplasmic components. Incubation of cells with positively charged gold nanoparticles showed almost similar levels of gold binding to the periplasm and the cell wall. On cells whose cell walls were enzymatically hydrolyzed (i.e., on protoplasts), a surface diffuse layer extending ∼30 nm from the membrane was revealed. The thickness and density of this layer were not significantly altered after treatment with a nonspecific protease, whereas it was labeled with anti-lipoteichoic acid (LTA) antibodies conjugated to nanogold. Further, the LTA layer spans most of the thickness of the periplasmic space, which strongly suggests that LTA is a major component of the
B. subtilis
periplasm.
Outer and Inner Membrane Proteins Compose an Arginine-Agmatine Exchange System inChlamydophila pneumoniae
Authors: Smith Conor B. , Graham David E. 
Published: September 2008

ABSTRACTMost chlamydial strains have a pyruvoyl-dependent decarboxylase protein that convertsl-arginine to agmatine. However, chlamydiae do not produce arginine, so they must import it from their host.Chlamydophila pneumoniaehas a gene cluster encoding a putative outer membrane porin (CPn1033 oraaxA), an arginine decarboxylase (CPn1032 oraaxB), and a putative cytoplasmic membrane transporter (CPn1031 oraaxC). TheaaxCgene was expressed inEscherichia coliproducing an integral cytoplasmic membrane protein that catalyzed the exchange ofl-arginine for agmatine. Expression of theaaxAgene produced an outer membrane protein that enhanced the arginine uptake and decarboxylation activity of cells coexpressingaaxBandaaxC. This chlamydial arginine/agmatine exchange system complemented anE. colimutant missing the native arginine-dependent acid resistance system. These cells survived extreme acid shock in the presence ofl-arginine. Biochemical and evolutionary analysis showed theaaxABCgenes evolved convergently with the enteric arginine degradation system, and they could have a different physiological role in chlamydial cells. The chlamydial system uniquely includes an outer membrane porin, and it is most active at a higher pH from 3 to 5. The chlamydial AaxC transporter was resistant to cadaverine,l-lysine andl-ornithine, which inhibit theE. coliAdiC antiporter.
Hypernegative Supercoiling Inhibits Growth by Causing RNA Degradation
Authors: Baaklini Imad , Usongo Valentine , Nolent Flora , Sanscartier Patrick , Hraiky Chadi , Drlica Karl , Drolet Marc 
Published: September 2008

ABSTRACTTranscription-induced hypernegative supercoiling is a hallmark ofEscherichia colitopoisomerase I (topA) mutants. However, its physiological significance has remained unclear. Temperature downshift of a mutant yielded transient growth arrest and a parallel increase in hypernegative supercoiling that was more severe with lower temperature. Both properties were alleviated by overexpression of RNase HI. While ribosomes in extracts showed normal activity when obtained during growth arrest, mRNA on ribosomes was reduced forfisand shorter forcrp, polysomes were much less abundant relative to monosomes, and protein synthesis rate dropped, as did the ratio of large to small proteins. Altered processing and degradation oflacAandfismRNA was also observed. These data are consistent with truncation of mRNA during growth arrest. These effects were not affected by a mutation in the gene encoding RNase E, indicating that this endonuclease is not involved in the abnormal mRNA processing. They were also unaffected by spectinomycin, an inhibitor of protein synthesis, which argued against induction of RNase activity. In vitro transcription revealed that R-loop formation is more extensive on hypernegatively supercoiled templates. These results allow us, for the first time, to present a model by which hypernegative supercoiling inhibits growth. In this model, the introduction of hypernegative supercoiling by gyrase facilitates degradation of nascent RNA; overproduction of RNase HI limits the accumulation of hypernegative supercoiling, thereby preventing extensive RNA degradation.
The Complete Genome Sequence of
Thermococcus onnurineus
NA1 Reveals a Mixed Heterotrophic and Carboxydotrophic Metabolism
Authors: Lee Hyun Sook , Kang Sung Gyun , Bae Seung Seob , Lim Jae Kyu , Cho Yona , Kim Yun Jae , Jeon Jeong Ho , Cha Sun-Shin , Kwon Kae Kyoung , Kim Hyung-Tae , Park Cheol-Joo , Lee Hee-Wook , Kim Seung Il , Chun Jongsik , Colwell Rita R. , Kim Sang-Jin , Lee Jung-Hyun 
Published: September 2008

ABSTRACT

Members of the genus
Thermococcus
, sulfur-reducing hyperthermophilic archaea, are ubiquitously present in various deep-sea hydrothermal vent systems and are considered to play a significant role in the microbial consortia. We present the complete genome sequence and feature analysis of
Thermococcus onnurineus
NA1 isolated from a deep-sea hydrothermal vent area, which reveal clues to its physiology. Based on results of genomic analysis,
T. onnurineus
NA1 possesses the metabolic pathways for organotrophic growth on peptides, amino acids, or sugars. More interesting was the discovery that the genome encoded unique proteins that are involved in carboxydotrophy to generate energy by oxidation of CO to CO
2
, thereby providing a mechanistic basis for growth with CO as a substrate. This lithotrophic feature in combination with carbon fixation via RuBisCO (ribulose 1,5-bisphosphate carboxylase/oxygenase) introduces a new strategy with a complementing energy supply for
T. onnurineus
NA1 potentially allowing it to cope with nutrient stress in the surrounding of hydrothermal vents, providing the first genomic evidence for the carboxydotrophy in
Thermococcus
.
RstA-Promoted Expression of the Ferrous Iron Transporter FeoB under Iron-Replete Conditions Enhances Fur Activity in
Salmonella enterica
Authors: Jeon Jihye , Kim Hyunkeun , Yun Jiae , Ryu Sangryeol , Groisman Eduardo A. , Shin Dongwoo 
Published: September 2008

ABSTRACT

The Fur protein is a primary regulator that monitors and controls cytoplasmic iron levels. We now report the identification of a regulatory pathway mediated by the
Salmonella
response regulator RstA that promotes Fur activity. Genome-wide expression experiments revealed that under iron-replete conditions, expression of the RstA protein from a plasmid lowered transcription levels of various genes involved in iron acquisition. The RstA protein controlled iron-responsive genes through the Fur-Fe(II) protein because deletion of the
fur
gene or iron depletion abrogated RstA-mediated repression of these genes. The RstA protein maintained wild-type levels of the Fur protein but exceptionally activated transcription of the
feoAB
operon encoding the ferrous iron transporter FeoB by binding directly to the
feoA
promoter. This FeoB induction resulted in increased ferrous iron uptake, which associates with the Fur protein because lack of RstA-dependent transcriptional activation of the
feoA
promoter and
feoB
-deletion abolished repression of the Fur target genes by the RstA protein. Under iron-replete conditions, RstA expression retarded
Salmonella
growth but enabled the Fur protein to repress the target genes beyond the levels which were simply accomplished by iron.
DNA Microarray Comparisons of Plant Factor- and Nitrogen Deprivation-Induced Hormogonia Reveal Decision-Making Transcriptional Regulation Patterns in
Nostoc punctiforme
Authors: Campbell Elsie L. , Christman Harry , Meeks John C. 
Published: September 2008

ABSTRACT

Hormogonia are nongrowing filaments, motile by means of a gliding mechanism, that are produced by certain cyanobacteria. Their differentiation is induced by positive and negative factors for growth, such as deprivation of combined nitrogen (nitrogen stress induction [NSI]). In
Nostoc punctiforme
, they are also induced by the exudate (hormogonium-inducing factor [HIF]) of a symbiotic plant partner. Time course (0.5 to 24 h) transcription profiles were determined by DNA microarray assays for hormogonia of
N. punctiforme
following induction by HIF and NSI. Clustering analysis revealed both common and distinct transcriptional patterns for the two methods of induction. By 24 h, a common set of 1,328 genes was identified. This 24-h common set of genes arose by the transition of 474 genes from an 819-member common set of genes at 1 h after induction; 405 and 51 genes unique to the HIF and NSI groups at 1 h, respectively; and 398 genes differentially transcribed at later time points. The NSI hormogonia showed a transcriptional checkpoint at 12 h following induction in which up- and downregulated genes were transiently down- or upregulated, respectively. The transient changes in these 1,043 genes appeared to reflect a switch back to a vegetative growth state. Such a checkpoint was not seen in HIF hormogonia. Genes uniquely upregulated in HIF hormogonia included those encoding proteins hypothesized to synthesize a metabolite repressor of hormogonium differentiation. Approximately 34 to 42% of the 6,893 printed genes were differentially transcribed during hormogonium differentiation; about half of those genes were upregulated, and 1,034 genes responded within 0.5 h after induction. These collective results indicate extensive and rapid global changes in the transcription of specific genes during the differentiation of these specialized filaments.
Divergence among Genes Encoding the Elongation Factor Tu of
Yersinia
Species
Authors: Isabel Sandra , Leblanc Éric , Boissinot Maurice , Boudreau Dominique K. , Grondin Myrian , Picard François J. , Martel Eric A. , Parham Nicholas J. , Chain Patrick S. G. , Bader Douglas E. , Mulvey Michael R. , Bryden Louis , Roy Paul H. , Ouellette Marc , Bergeron Michel G. 
Published: September 2008

ABSTRACT

Elongation factor Tu (EF-Tu), encoded by
tuf
genes, carries aminoacyl-tRNA to the ribosome during protein synthesis. Duplicated
tuf
genes (
tufA
and
tufB
), which are commonly found in enterobacterial species, usually coevolve via gene conversion and are very similar to one another. However, sequence analysis of
tuf
genes in our laboratory has revealed highly divergent copies in 72 strains spanning the genus
Yersinia
(representing 12
Yersinia
species). The levels of intragenomic divergence between
tufA
and
tufB
sequences ranged from 8.3 to 16.2% for the genus
Yersinia
, which is significantly greater than the 0.0 to 3.6% divergence observed for other enterobacterial genera. We further explored
tuf
gene evolution in
Yersinia
and other
Enterobacteriaceae
by performing directed sequencing and phylogenetic analyses. Phylogenetic trees constructed using concatenated
tufA
and
tufB
sequences revealed a monophyletic genus
Yersinia
in the family
Enterobacteriaceae
. Moreover,
Yersinia
strains form clades within the genus that mostly correlate with their phenotypic and genetic classifications. These genetic analyses revealed an unusual divergence between
Yersinia tufA
and
tufB
sequences, a feature unique among sequenced
Enterobacteriaceae
and indicative of a genus-wide loss of gene conversion. Furthermore, they provided valuable phylogenetic information for possible reclassification and identification of
Yersinia
species.