bluuebunny/crossref_metadata_2025_split huggingface dataset:
Staphylococcus aureusNrdH Redoxin Is a Reductant of the Class Ib Ribonucleotide Reductase
Authors: Rabinovitch Inbal , Yanku Michaela , Yeheskel Adva , Cohen Gerald , Borovok Ilya , Aharonowitz Yair 
Published: July 2010

ABSTRACTStaphylococci contain a class Ib NrdEF ribonucleotide reductase (RNR) that is responsible, under aerobic conditions, for the synthesis of deoxyribonucleotide precursors for DNA synthesis and repair. The genes encoding that RNR are contained in an operon consisting of three genes,nrdIEF, whereas many other class Ib RNR operons contain a fourth gene,nrdH, that determines a thiol redoxin protein, NrdH. We identified a 77-amino-acid open reading frame inStaphylococcus aureusthat resembles NrdH proteins. However,S. aureusNrdH differs significantly from the canonical NrdH both in its redox-active site, C-P-P-C instead of C-M/V-Q-C, and in the absence of the C-terminal [WF]SGFRP[DE] structural motif. We show thatS. aureusNrdH is a thiol redox protein. It is not essential for aerobic or anaerobic growth and appears to have a marginal role in protection against oxidative stress.In vitro,S. aureusNrdH was found to be an efficient reductant of disulfide bonds in low-molecular-weight substrates and proteins using dithiothreitol as the source of reducing power and an effective reductant for the homologous class Ib RNR employing thioredoxin reductase and NADPH as the source of the reducing power. Its ability to reduce NrdEF is comparable to that of thioredoxin-thioredoxin reductase. Hence,S. aureuscontains two alternative thiol redox proteins, NrdH and thioredoxin, with both proteins being able to functionin vitrowith thioredoxin reductase as the immediate hydrogen donors for the class Ib RNR. It remains to be clarified under whichin vivophysiological conditions the two systems are used.
The E2 Domain of OdhA of
Corynebacterium glutamicum
Has Succinyltransferase Activity Dependent on Lipoyl Residues of the Acetyltransferase AceF
Authors: Hoffelder Melanie , Raasch Katharina , van Ooyen Jan , Eggeling Lothar 
Published: July 2010

ABSTRACT

Oxoglutarate dehydrogenase (ODH) and pyruvate dehydrogenase (PDH) complexes catalyze key reactions in central metabolism, and in
Corynebacterium glutamicum
there is indication of an unusual supercomplex consisting of AceE (E1), AceF (E2), and Lpd (E3) together with OdhA. OdhA is a fusion protein of additional E1 and E2 domains, and
odhA
orthologs are present in all
Corynebacterineae
, including, for instance,
Mycobacterium tuberculosis
. Here we show that deletion of any of the individual domains of OdhA in
C. glutamicum
resulted in loss of ODH activity, whereas PDH was still functional. On the other hand, deletion of AceF disabled both PDH activity and ODH activity as well, although isolated AceF protein had solely transacetylase activity and no transsuccinylase activity. Surprisingly, the isolated OdhA protein was inactive with 2-oxoglutarate as the substrate, but it gained transsuccinylase activity upon addition of dihydrolipoamide. Further enzymatic analysis of mutant proteins and mutant cells revealed that OdhA specifically catalyzes the E1 and E2 reaction to convert 2-oxoglutarate to succinyl-coenzyme A (CoA) but fully relies on the lipoyl residues provided by AceF involved in the reactions to convert pyruvate to acetyl-CoA. It therefore appears that in the putative supercomplex in
C. glutamicum
, in addition to dihydrolipoyl dehydrogenase E3, lipoyl domains are also shared, thus confirming the unique evolutionary position of bacteria such as
C. glutamicum
and
M. tuberculosis
.
Catabolic Function of Compartmentalized Alanine Dehydrogenase in the Heterocyst-Forming Cyanobacterium
Anabaena
sp. Strain PCC 7120
Authors: Pernil Rafael , Herrero Antonia , Flores Enrique 
Published: July 2010

ABSTRACT

In the diazotrophic filaments of heterocyst-forming cyanobacteria, an exchange of metabolites takes place between vegetative cells and heterocysts that results in a net transfer of reduced carbon to the heterocysts and of fixed nitrogen to the vegetative cells. Open reading frame
alr2355
of the genome of
Anabaena
sp. strain PCC 7120 is the
ald
gene encoding alanine dehydrogenase. A strain carrying a green fluorescent protein (GFP) fusion to the N terminus of Ald (Ald-N-GFP) showed that the
ald
gene is expressed in differentiating and mature heterocysts. Inactivation of
ald
resulted in a lack of alanine dehydrogenase activity, a substantially decreased nitrogenase activity, and a 50% reduction in the rate of diazotrophic growth. Whereas production of alanine was not affected in the
ald
mutant,
in vivo
labeling with [
14
C]alanine (in whole filaments and isolated heterocysts) or [
14
C]pyruvate (in whole filaments) showed that alanine catabolism was hampered. Thus, alanine catabolism in the heterocysts is needed for normal diazotrophic growth. Our results extend the significance of a previous work that suggested that alanine is transported from vegetative cells into heterocysts in the diazotrophic
Anabaena
filament.
Inclusion Membrane Proteins ofProtochlamydia amoebophilaUWE25 Reveal a Conserved Mechanism for Host Cell Interaction among theChlamydiae
Authors: Heinz Eva , Rockey Daniel D. , Montanaro Jacqueline , Aistleitner Karin , Wagner Michael , Horn Matthias 
Published: July 2010

ABSTRACTChlamydiaeare a group of obligate intracellular bacteria comprising several important human pathogens. Inside the eukaryotic cell, chlamydiae remain within a host-derived vesicular compartment, termed the inclusion. They modify the inclusion membrane through insertion of unique proteins, which are involved in interaction with and manipulation of the host cell. Among chlamydiae, inclusion membrane proteins have been exclusively found in members of the familyChlamydiaceae, which predominantly infect mammalian and avian hosts. Here, the presence of inclusion membrane proteins inProtochlamydia amoebophilaUWE25, a chlamydial endosymbiont of free-living amoebae, is reported. A genome-wide screening for secondary structure motifs resulted in the identification of 23 putative inclusion membrane proteins for this organism. Immunofluorescence analysis demonstrated that five of these proteins were expressed, and four of them could be localized to a halo surrounding the intracellular bacteria. Colocalization studies showed an almost complete overlap of the signals obtained for the four putative inclusion membrane proteins, and immuno-transmission electron microscopy unambiguously demonstrated their location in the inclusion membrane. The presence of inclusion membrane proteins (designated IncA, IncQ, IncR, and IncS) inP. amoebophilashows that this strategy for host cell interaction is conserved among the chlamydiae and is used by chlamydial symbionts and pathogens alike.
ICEEc2, a New Integrative and Conjugative Element Belonging to the pKLC102/PAGI-2 Family, Identified inEscherichia coliStrain BEN374
Authors: Roche David , Fléchard Maud , Lallier Nathalie , Répérant Maryline , Brée Annie , Pascal Géraldine , Schouler Catherine , Germon Pierre 
Published: July 2010

ABSTRACTThe diversity of theEscherichia colispecies is in part due to the large number of mobile genetic elements that are exchanged between strains. We report here the identification of a new integrative and conjugative element (ICE) of the pKLC102/PAGI-2 family located downstream of the tRNA genepheUin theE. colistrain BEN374. Indeed, this new region, which we called ICEEc2, can be transferred by conjugation from strain BEN374 to theE. colistrain C600. We were also able to transfer this region into aSalmonella entericaserovar Typhimurium strain and into aYersinia pseudotuberculosisstrain. This transfer was then followed by the integration of ICEEc2into the host chromosome downstream of aphetRNA gene. Our data indicated that this transfer involved a set of three genes encoding DNA mobility enzymes and a type IV pilus encoded by genes present on ICEEc2. Given the wide distribution of members of this family, these mobile genetic elements are likely to play an important role in the diversification of bacteria.
Inhibiting the Initiation ofClostridium difficileSpore Germination using Analogs of Chenodeoxycholic Acid, a Bile Acid
Authors: Sorg Joseph A. , Sonenshein Abraham L. 
Published: July 2010

ABSTRACTTo cause disease,Clostridium difficilespores must germinate in the host gastrointestinal tract. Germination is initiated upon exposure to glycine and certain bile acids, e.g., taurocholate. Chenodeoxycholate, another bile acid, inhibits taurocholate-mediated germination. By applying Michaelis-Menten kinetic analysis toC. difficilespore germination, we found that chenodeoxycholate is a competitive inhibitor of taurocholate-mediated germination and appears to interact with the spores with greater apparent affinity than does taurocholate. We also report that several analogs of chenodeoxycholate are even more effective inhibitors. Some of these compounds resist 7α-dehydroxylation byClostridium scindens, a core member of the normal human colonic microbiota, suggesting that they are more stable than chenodeoxycholate in the colonic environment.
A Group IIC-Type Intron Interrupts the rRNA Methylase Gene of
Geobacillus stearothermophilus
Strain 10
Authors: Moretz Samuel E. , Lampson Bert C. 
Published: July 2010

ABSTRACT

Group IIC introns insert next to the stem-loop structure of rho-independent transcription terminators, thus avoiding intact genes. The insertion sites of 17 copies of the G.st.I1 intron from
Geobacillus stearothermophilus
were compared. One copy of the intron was found to interrupt an open reading frame (ORF) encoding an rRNA methylase.
Mycobacterial Biofilms Facilitate Horizontal DNA Transfer between Strains ofMycobacterium smegmatis
Authors: Nguyen Kiet T. , Piastro Kristina , Gray Todd A. , Derbyshire Keith M. 
Published: July 2010

ABSTRACTConjugal transfer of chromosomal DNA between strains ofMycobacterium smegmatisoccurs by a novel mechanism. In a transposon mutagenesis screen, three transfer-defective insertions were mapped to thelsr2gene of the donor strain mc2155. Becauselsr2encodes a nonspecific DNA-binding protein, mutations oflsr2give rise to a variety of phenotypes, including an inability to form biofilms. In this study, we show that efficient DNA transfer between strains ofM. smegmatisoccurs in a mixed biofilm and that the process requires expression oflsr2in the donor but not in the recipient strain. Testing cells from different strata of standing cultures showed that transfer occurred predominantly at the biofilm air-liquid interface, as other strata containing higher cell densities produced very few transconjugants. These data suggest that the biofilm plays a role beyond mere facilitation of cell-cell contact. Surprisingly, we found that under standard assay conditions the recipient strain does not form a biofilm. Taking these results together, we conclude that for transfer to occur, the recipient strain is actively recruited into the biofilm. In support of this idea, we show that donor and recipient cells are present in almost equal numbers in biofilms that produce transconjugants. Our demonstration of genetic exchange between mycobacteria in a mixed biofilm suggests that conjugation occurs in the environment. Since biofilms are considered to be the predominant natural microhabitat for bacteria, our finding emphasizes the importance of studying biological and physical processes that occur between cells in mixed biofilms.
The Delta Subunit of RNA Polymerase, RpoE, Is a Global Modulator ofStreptococcus mutansEnvironmental Adaptation
Authors: Xue Xiaoli , Tomasch Jürgen , Sztajer Helena , Wagner-Döbler Irene 
Published: July 2010

ABSTRACTThe delta subunit of RNA polymerase, RpoE, is widespread in low-G+C Gram-positive bacteria and is thought to play a role in enhancing transcriptional specificity by blocking RNA polymerase binding at weak promoter sites and stimulating RNA synthesis by accelerating core enzyme recycling. Despite the well-studied biochemical properties of RpoE, a role for this proteinin vivohas not been defined in depth. In this study, we show that inactivation ofrpoEin the human dental caries pathogenStreptococcus mutanscauses impaired growth and loss of important virulence traits, including biofilm formation, resistance to antibiotics, and tolerance to environmental stresses. Complementation of the mutant withrpoEexpressed intransrestored its phenotype to wild type. The luciferase fusion reporter showed thatrpoEwas highly transcribed throughout growth and that acid and hydrogen peroxide stresses repressedrpoEexpression. Transcriptome profiling of wild-type and ΔrpoEcells in the exponential and early stationary phase of growth, under acid and hydrogen peroxide stress and under both stresses combined, revealed that genes involved in histidine synthesis, malolactic fermentation, biofilm formation, and antibiotic resistance were downregulated in the ΔrpoEmutant under all conditions. Moreover, the loss of RpoE resulted in dramatic changes in transport and metabolism of carbohydrates and amino acids. Interestingly, differential expression, mostly upregulation, of 330 noncoding regions was found. In conclusion, this study demonstrates that RpoE is an important global modulator of gene expression inS. mutanswhich is required for optimal growth and environmental adaptation.
Repair of DNA Double-Strand Breaks following UV Damage in ThreeSulfolobussolfataricusStrains
Authors: Rolfsmeier Michael L. , Laughery Marian F. , Haseltine Cynthia A. 
Published: July 2010

ABSTRACTDNA damage repair mechanisms have been most thoroughly explored in the eubacterial and eukaryotic branches of life. The methods by which members of the archaeal branch repair DNA are significantly less well understood but have been gaining increasing attention. In particular, the approaches employed by hyperthermophilic archaea have been a general source of interest, since these organisms thrive under conditions that likely lead to constant chromosomal damage. In this work we have characterized the responses of threeSulfolobus solfataricusstrains to UV-C irradiation, which often results in double-strand break formation. We examinedS. solfataricusstrain P2 obtained from two different sources andS. solfataricusstrain 98/2, a popular strain for site-directed mutation by homologous recombination. Cellular recovery, as determined by survival curves and the ability to return to growth after irradiation, was found to be strain specific and differed depending on the dose applied. Chromosomal damage was directly visualized using pulsed-field gel electrophoresis and demonstrated repair rate variations among the strains following UV-C irradiation-induced double-strand breaks. Several genes involved in double-strand break repair were found to be significantly upregulated after UV-C irradiation. Transcript abundance levels and temporal expression patterns for double-strand break repair genes were also distinct for each strain, indicating that theseSulfolobus solfataricusstrains have differential responses to UV-C-induced DNA double-strand break damage.
Regulation of a Novel Gene Cluster Involved in Secondary Metabolite Production in
Streptomyces coelicolor
Authors: Hindra  , Pak Patricia , Elliot Marie A. 
Published: July 2010

ABSTRACT

Antibiotic biosynthesis in the streptomycetes is a complex and highly regulated process. Here, we provide evidence for the contribution of a novel genetic locus to antibiotic production in
Streptomyces coelicolor
. The overexpression of a gene cluster comprising four protein-encoding genes (
abeABCD
) and an antisense RNA-encoding gene (α-
abeA
) stimulated the production of the blue-pigmented metabolite actinorhodin on solid medium. Actinorhodin production also was enhanced by the overexpression of an adjacent gene (
abeR
) encoding a predicted
Streptomyces
antibiotic regulatory protein (SARP), while the deletion of this gene impaired actinorhodin production. We found the
abe
genes to be differentially regulated and controlled at multiple levels. Upstream of
abeA
was a promoter that directed the transcription of
abeABCD
at a low but constitutive level. The expression of
abeBCD
was, however, significantly upregulated at a time that coincided with the initiation of aerial development and the onset of secondary metabolism; this expression was activated by the binding of AbeR to four heptameric repeats upstream of a promoter within
abeA
. Expressed divergently to the
abeBCD
promoter was α-
abeA
, whose expression mirrored that of
abeBCD
but did not require activation by AbeR. Instead, α-
abeA
transcript levels were subject to negative control by the double-strand-specific RNase, RNase III.
Complete Genome Sequence of
Lactobacillus salivarius
CECT 5713, a Probiotic Strain Isolated from Human Milk and Infant Feces
Authors: Jiménez Esther , Martín Rocío , Maldonado Antonio , Martín Virginia , Gómez de Segura Aranzazu , Fernández Leonides , Rodríguez Juan M. 
Published: July 2010

ABSTRACT

Lactobacillus salivarius
is a homofermentative lactic acid bacterium and is frequently isolated from mucosal surfaces of healthy humans.
L. salivarius
CECT 5713, a strain isolated simultaneously from breast milk and infant feces of a healthy mother-infant pair, has immunomodulatory, anti-inflammatory, and anti-infectious properties, as revealed by several
in vitro
and
in vivo
assays. Here, we report its complete and annotated genome sequence.
StyA1 and StyA2B from
Rhodococcus opacus
1CP: a Multifunctional Styrene Monooxygenase System
Authors: Tischler Dirk , Kermer René , Gröning Janosch A. D. , Kaschabek Stefan R. , van Berkel Willem J. H. , Schlömann Michael 
Published: July 2010

ABSTRACT

Two-component flavoprotein monooxygenases are emerging biocatalysts that generally consist of a monooxygenase and a reductase component. Here we show that
Rhodococcus opacus
1CP encodes a multifunctional enantioselective flavoprotein monooxygenase system composed of a single styrene monooxygenase (SMO) (StyA1) and another styrene monooxygenase fused to an NADH-flavin oxidoreductase (StyA2B). StyA1 and StyA2B convert styrene and chemical analogues to the corresponding epoxides at the expense of FADH
2
provided from StyA2B. The StyA1/StyA2B system presents the highest monooxygenase activity in an equimolar ratio of StyA1 and StyA2B, indicating (transient) protein complex formation. StyA1 is also active when FADH
2
is supplied by StyB from
Pseudomonas
sp. VLB120 or PheA2 from
Rhodococcus opacus
1CP. However, in both cases the reductase produces an excess of FADH
2
, resulting in a high waste of NADH. The epoxidation rate of StyA1 heavily depends on the type of reductase. This supports that the FADH
2
-induced activation of StyA1 requires interprotein communication. We conclude that the StyA1/StyA2B system represents a novel type of multifunctional flavoprotein monooxygenase. Its unique mechanism of cofactor utilization provides new opportunities for biotechnological applications and is highly relevant from a structural and evolutionary point of view.
The PpaA/AerR Regulators of Photosynthesis Gene Expression from Anoxygenic Phototrophic Proteobacteria Contain Heme-Binding SCHIC Domains
Authors: Moskvin Oleg V. , Gilles-Gonzalez Marie-Alda , Gomelsky Mark 
Published: July 2010

ABSTRACT

The SCHIC domain of the B
12
-binding domain family present in the
Rhodobacter sphaeroides
AppA protein binds heme and senses oxygen. Here we show that the predicted SCHIC domain PpaA/AerR regulators also bind heme and respond to oxygen
in vitro
, despite their low sequence identity with AppA.
Draft Genome Sequences of Two
Neisseria meningitidis
Serogroup C Clinical Isolates
Authors: Lavezzo Enrico , Toppo Stefano , Barzon Luisa , Cobelli Claudio , Di Camillo Barbara , Finotello Francesca , Franchin Elisa , Peruzzo Denis , Toffolo Gianna Maria , Trevisan Marta , Palù Giorgio 
Published: July 2010

ABSTRACT

Neisseria meningitidis
is a human-specific pathogen known for its capability to cause sepsis and meningitis. Here we report the availability of 2 draft genome sequences obtained from patients infected during the same epidemic outbreak. Both bacterial isolates belong to serogroup C, but their genome sequences show local and remarkable differences compared with each other or with the reference genome of strain FAM18.
Complete Genome Sequence of
Lactobacillus casei
Zhang, a New Probiotic Strain Isolated from Traditional Homemade Koumiss in Inner Mongolia, China
Authors: Zhang Wenyi , Yu Dongliang , Sun Zhihong , Wu Rina , Chen Xia , Chen Wei , Meng He , Hu Songnian , Zhang Heping 
Published: July 2010

ABSTRACT

Lactobacillus casei
Zhang is a new probiotic bacterium isolated from koumiss collected in Inner Mongolia, China. Here, we report the main genome features of
L. casei
Zhang and the identification of several predicted proteins implicated in interactions with the host.
The Protection of Minorities and Indigenous Peoples in International Law: A Comparative Temporal Analysis
Authors: Castellino Joshua 
Published: July 2010

AbstractIt is easy to detect a sense of achievement with the extent to which the human rights regime has progressed 60 years after the Universal Declaration of Human Rights. The relative international successes suggest a bright outlook for the future of the human rights regime. However, an important lacuna remains in the attention that ought to be paid to minorities, indigenous peoples and others in vulnerable situations, including in some instances, women. This paper argues that despite the creation of sophisticated systems of international human rights law, the regimes for the protection of minority rights were stronger before the United Nations (UN) era. In support of this argument it seeks to assess regimes that existed at three different times, attempting to extrapolate and analyse the snapshots presented by these through the lens of evolving human rights law.
Minorities and Hatred: Protections and Implications
Authors: Ghanea Nazila 
Published: July 2010

AbstractThe international concern with minorities has benefitted from a range of rationales and gone through a number of permutations over recent decades. Within these are included a wide spectrum of objectives from concern with their very obliteration covered under genocide instruments to soft law instruments concerned with their positive flourishing. This article will address just one aspect of those concerns – those protecting minorities from hate speech.
Dominant Regimes of the Ross Ice Shelf Surface Wind Field during Austral Autumn 2005
Authors: Seefeldt Mark W. , Cassano John J. , Parish Thomas R. 
Published: July 2010

Abstract
An analysis of the surface wind field across the Ross Ice Shelf, Antarctica, is conducted for austral autumn 2005. The airflow is divided into dominant wind regimes identifying similar wind patterns and the associated typical atmospheric forcing. The results of previous research and a seasonal analysis of the recently expanded network of automatic weather stations in the Ross Ice Shelf region are used to define the dominant wind regimes. Events composing each wind regime are identified by matching wind speed and wind direction observations at several automatic weather station sites for durations of at least 10 h. The four different dominant wind regimes are barrier wind, strong katabatic, weak katabatic, and light wind. Each wind regime is studied through the use of wind rose plots and sea level pressure fields from the Antarctic Mesoscale Prediction System. The sea level pressure fields are used to characterize the forcing of the surface wind field by synoptic pressure gradients. The four dominant wind regimes result in classifying less than 50% of the total hours for austral autumn 2005. The results indicate that previous studies of the Ross Ice Shelf surface wind field, focusing on katabatic winds and barrier winds, represent less than one-half of the observed winds. This study provides a better understanding of the composition of the surface wind field in Antarctica and more insight into the characteristics of the Ross Ice Shelf airstream.