bluuebunny/crossref_metadata_2025_split huggingface dataset:
Characterization of the NifA-RpoN Regulon in
Rhizobium etli
in Free Life and in Symbiosis with
Phaseolus vulgaris
Authors: Salazar Emmanuel , Díaz-Mejía J. Javier , Moreno-Hagelsieb Gabriel , Martínez-Batallar Gabriel , Mora Yolanda , Mora Jaime , Encarnación Sergio 
Published: May 2010

ABSTRACT

The NifA-RpoN complex is a master regulator of the nitrogen fixation genes in alphaproteobacteria. Based on the complete
Rhizobium etli
genome sequence, we constructed an
R. etli
CFN42 oligonucleotide (70-mer) microarray and utilized this tool, reverse transcription (RT)-PCR analysis (transcriptomics), proteomics, and bioinformatics to decipher the NifA-RpoN regulon under microaerobic conditions (free life) and in symbiosis with bean plants. The
R. etli
NifA-RpoN regulon was determined to contain 78 genes, including the genes involved in nitrogen fixation, and the analyses revealed 42 new NifA-RpoN-dependent genes. More importantly, this study demonstrated that the NifA-RpoN regulon is composed of genes and proteins that have very diverse functions, that play fundamental and previously less appreciated roles in regulating the normal physiology of the cell, and that have important functions in providing adequate conditions for efficient nitrogen fixation in symbiosis. The
R. etli
NifA-RpoN regulon defined here has some components in common with other NifA-RpoN regulons described previously, but the vast majority of the components have been found only in the
R. etli
regulon, suggesting that they have a specific role in this bacterium and particular requirements during nitrogen fixation compared with other symbiotic bacterial models.
Enhancement of Survival and Electricity Production in an Engineered Bacterium by Light-Driven Proton Pumping
Authors: Johnson Ethan T. , Baron Daniel B. , Naranjo Belén , Bond Daniel R. , Schmidt-Dannert Claudia , Gralnick Jeffrey A. 
Published: May 2010

ABSTRACTMicroorganisms can use complex photosystems or light-dependent proton pumps to generate membrane potential and/or reduce electron carriers to support growth. The discovery that proteorhodopsin is a light-dependent proton pump that can be expressed readily in recombinant bacteria enables development of new strategies to probe microbial physiology and to engineer microbes with new light-driven properties. Here, we describe functional expression of proteorhodopsin and light-induced changes in membrane potential in the bacteriumShewanella oneidensisstrain MR-1. We report that there were significant increases in electrical current generation during illumination of electrochemical chambers containingS. oneidensisexpressing proteorhodopsin. We present evidence that an engineered strain is able to consume lactate at an increased rate when it is illuminated, which is consistent with the hypothesis that proteorhodopsin activity enhances lactate uptake by increasing the proton motive force. Our results demonstrate that there is coupling of a light-driven process to electricity generation in a nonphotosynthetic engineered bacterium. Expression of proteorhodopsin also preserved the viability of the bacterium under nutrient-limited conditions, providing evidence that fulfillment of basic energy needs of organisms may explain the widespread distribution of proteorhodopsin in marine environments.
Enhanced Surface Colonization by
Escherichia coli
O157:H7 in Biofilms Formed by an
Acinetobacter calcoaceticus
Isolate from Meat-Processing Environments
Authors: Habimana Olivier , Heir Even , Langsrud Solveig , Åsli Anette Wold , Møretrø Trond 
Published: May 2010

ABSTRACT

A meat factory commensal bacterium,
Acinetobacter calcoaceticus
, affected the spatial distribution of
Escherichia coli
O157:H7 surface colonization. The biovolume of
E. coli
O157:H7 was 400-fold higher (1.2 × 10
6
μm
3
) in a dynamic cocultured biofilm than in a monoculture (3.0 × 10
3
μm
3
), and
E. coli
O157:H7 colonized spaces between
A. calcoaceticus
cell clusters.
Domains III and I-2α, at the Entrance of the Binding Cleft, Play an Important Role in Cold Adaptation of the Periplasmic Dipeptide-Binding Protein (DppA) from the Deep-Sea Psychrophilic Bacterium
Pseudoalteromonas
sp. Strain SM9913
Authors: Zhang Wei-Xin , Xie Bin-Bin , Chen Xiu-Lan , Dong Sheng , Zhang Xi-Ying , Zhou Bai-Cheng , Zhang Yu-Zhong 
Published: May 2010

ABSTRACT

The peptide transporter from a cold-adapted bacterium has never been reported. In the present study, the
dpp
operon from the psychrophilic bacterium
Pseudoalteromonas
sp. strain SM9913 was cloned and analyzed. The dipeptide binding protein DppA of SM9913 was overexpressed in
Escherichia coli
, and its cold adaptation characteristics were studied. The recombinant DppA of SM9913 (
Ps
DppA) displayed the highest ligand-binding affinity at 15°C, whereas the recombinant DppA of
E. coli
(
Ec
DppA) displayed the highest ligand-binding affinity at 35°C. Thermal and guanidium hydrochloride unfolding analyses indicated that
Ps
DppA has more structural instability than
Ec
DppA. Six domain-exchanged mutants of
Ps
DppA were expressed and purified. Analyses of these mutants indicated that domains III, I-2, and I-3 of
Ps
DppA were less stable than those from
Ec
DppA and that domains III and I-2 made a significant contribution to the high binding affinity of
Ps
DppA at low temperatures. Structural and sequence analyses suggested that the state transition-involved regions in domain III and the α part of domain I-2 are the hot spots of optimization during cold adaptation and that decreasing the side-chain size in these regions is an important strategy for the cold adaptation of
Ps
DppA.
Regulation of Neurotoxin Production and Sporulation by a Putative
agrBD
Signaling System in Proteolytic
Clostridium botulinum
Authors: Cooksley Clare M. , Davis Ian J. , Winzer Klaus , Chan Weng C. , Peck Michael W. , Minton Nigel P. 
Published: May 2010

ABSTRACT

A significant number of genome sequences of
Clostridium botulinum
and related species have now been determined.
In silico
analysis of these data revealed the presence of two distinct
agr
loci (
agr
-
1
and
agr
-
2
) in all group I strains, each encoding putative proteins with similarity to AgrB and AgrD of the well-studied
Staphylococcus aureus agr
quorum sensing system. In
S. aureus
, a small diffusible autoinducing peptide is generated from AgrD in a membrane-located processing event that requires AgrB. Here the characterization of both
agr
loci in the group I strain
C. botulinum
ATCC 3502 and of their homologues in a close relative,
Clostridium sporogenes
NCIMB 10696, is reported. In
C. sporogenes
NCIMB 10696,
agr
-
1
and
agr
-
2
appear to form transcriptional units that consist of
agrB
,
agrD
, and flanking genes of unknown function. Several of these flanking genes are conserved in
Clostridium perfringens
. In agreement with their proposed role in quorum sensing, both loci were maximally expressed during late-exponential-phase growth. Modulation of
agrB
expression in
C. sporogenes
was achieved using antisense RNA, whereas in
C. botulinum
, insertional
agrD
mutants were generated using ClosTron technology. In comparison to the wild-type strains, these strains exhibited drastically reduced sporulation and, for
C. botulinum
, also reduced production of neurotoxin, suggesting that both phenotypes are controlled by quorum sensing. Interestingly, while
agr
-
1
appeared to control sporulation,
agr
-
2
appeared to regulate neurotoxin formation.
Application of Whole-Cell Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry for Rapid Identification and Clustering Analysis ofPantoeaSpecies
Authors: Rezzonico Fabio , Vogel Guido , Duffy Brion , Tonolla Mauro 
Published: May 2010

ABSTRACTPantoea agglomeransis an ecologically diverse taxon that includes commercially important plant-beneficial strains and opportunistic clinical isolates. Standard biochemical identification methods in diagnostic laboratories were repeatedly shown to run into false-positive identifications ofP. agglomerans, a fact which is also reflected by the high number of 16S rRNA gene sequences in public databases that are incorrectly assigned to this species. More reliable methods for rapid identification are required to ascertain the prevalence of this species in clinical samples and to evaluate the biosafety of beneficial isolates. Whole-cell matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) methods and reference spectra (SuperSpectrum) were developed for accurate identification ofP. agglomeransand related bacteria and used to detect differences in the protein profile within variants of the same strain, including a ribosomal point mutation conferring streptomycin resistance. MALDI-TOF MS-based clustering was shown to generally agree with classification based ongyrBsequencing, allowing rapid and reliable identification at the species level.
Chromatin-Mediated Epigenetic Regulation in the Malaria Parasite Plasmodium falciparum
Authors: Cui Liwang , Miao Jun 
Published: May 2010

ABSTRACTMalaria is a major public health problem in many developing countries, with the malignant tertian parasitePlasmodium falciparumcausing the most malaria-associated mortality. Extensive research, especially with the advancement of genomics and transfection tools, has highlighted the fundamental importance of chromatin-mediated gene regulation in the developmental program of this early-branching eukaryote. ThePlasmodiumparasite genomes reveal the existence of both canonical and variant histones that make up the nucleosomes, as well as a full collection of conserved enzymes for chromatin remodeling and histone posttranslational modifications (PTMs). Recent studies have identified a wide array of both conserved and novel histone PTMs inP. falciparum, indicating the presence of a complex and divergent “histone code.” Genome-wide analysis has begun to decipher the nucleosome landscape and histone modifications associated with the dynamic organization of chromatin structures during the parasite's life cycle. Focused studies on malaria-specific phenomena such as antigenic variation and red cell invasion pathways shed further light on the involvement of epigenetic mechanisms in these processes. Here we review our current understanding of chromatin-mediated gene regulation in malaria parasites, with specific reference to exemplar studies on antigenic variation and host cell invasion.
Oligomeric Sensor Kinase DcuS in the Membrane of
Escherichia coli
and in Proteoliposomes: Chemical Cross-linking and FRET Spectroscopy
Authors: Scheu Patrick D. , Liao Yun-Feng , Bauer Julia , Kneuper Holger , Basché Thomas , Unden Gottfried , Erker Wolfgang 
Published: May 2010

ABSTRACT

DcuS is the membrane-integral sensor histidine kinase of the DcuSR two-component system in
Escherichia coli
that responds to extracellular C
4
-dicarboxylates. The oligomeric state of full-length DcuS was investigated
in vitro
and in living cells by chemical cross-linking and by

f

luorescence

r

esonance

e

nergy

t

ransfer (FRET) spectroscopy. The FRET results were quantified by an improved method using background-free spectra of living cells for determining FRET efficiency (
E
) and donor fraction {

f
D

= (donor)/[(donor) + (acceptor)]}. Functional fusions of cyan fluorescent protein (CFP) and yellow fluorescent protein (YFP) variants of green fluorescent protein to DcuS were used for
in vivo
FRET measurements. Based on noninteracting membrane proteins and perfectly interacting proteins (a CFP-YFP fusion), the results of FRET of cells coexpressing DcuS-CFP and DcuS-YFP were quantitatively evaluated. In living cells and after reconstitution of purified recombinant DcuS in proteoliposomes, DcuS was found as a dimer or higher oligomer, independent of the presence of an effector. Chemical cross-linking with disuccinimidyl suberate showed tetrameric, in addition to dimeric, DcuS in proteoliposomes and in membranes of bacteria, whereas purified DcuS in nondenaturing detergent was mainly monomeric. The presence and amount of tetrameric DcuS
in vivo
and in proteoliposomes was not dependent on the concentration of DcuS. Only membrane-embedded DcuS (present in the oligomeric state) is active in (auto)phosphorylation. Overall, the FRET and cross-linking data demonstrate the presence in living cells, in bacterial membranes, and in proteoliposomes of full-length DcuS protein in an oligomeric state, including a tetramer.
Evidence that Regulatory Protein MarA of
Escherichia coli
Represses
rob
by Steric Hindrance
Authors: McMurry Laura M. , Levy Stuart B. 
Published: May 2010

ABSTRACT

The MarA protein of
Escherichia coli
can both activate and repress the initiation of transcription, depending on the position and orientation of its degenerate 20-bp binding site (“marbox”) at the promoter. For all three known repressed genes, the marbox overlaps the promoter. It has been reported that MarA represses the
rob
promoter via an RNA polymerase (RNAP)-DNA-MarA ternary complex. Under similar conditions, we found a ternary complex for the repressed
purA
promoter also. These findings, together with the backwards orientation of repressed marboxes, suggested a unique interaction of MarA with RNAP in repression. However, no repression-specific residues of MarA could be found among 38 single-alanine replacement mutations previously shown to retain activation function or among mutants from random mutagenesis. Mutations Thr12Ala, Arg36Ala, Thr95Ile, and Pro106Ala were more damaging for activation than for repression, some up to 10-fold, so these residues may play a specific role in activation. We found that nonspecific binding of RNAP to promoterless regions of DNA was presumably responsible for the ternary complexes seen previously. When RNAP binding was promoter specific, MarA reduced RNAP access to the
rob
promoter; there was little or no ternary complex. These findings strongly implicate steric hindrance as the mechanism of repression of
rob
by MarA.
The Hyperthermophilic Euryarchaeon
Archaeoglobus fulgidus
Repairs Uracil by Single-Nucleotide Replacement
Authors: Knævelsrud Ingeborg , Moen Marivi N. , Grøsvik Kristin , Haugland Gyri T. , Birkeland Nils-Kåre , Klungland Arne , Leiros Ingar , Bjelland Svein 
Published: May 2010

ABSTRACT

Hydrolytic deamination of cytosine to uracil in cellular DNA is a major source of C-to-T transition mutations if uracil is not repaired by the DNA base excision repair (BER) pathway. Since deamination increases rapidly with temperature, hyperthermophiles, in particular, are expected to succumb to such damage. There has been only one report of crenarchaeotic BER showing strong similarities to that in most eukaryotes and bacteria for hyperthermophilic
Archaea
. Here we report a different type of BER performed by extract prepared from cells of the euryarchaeon
Archaeoglobus fulgidus
. Although immunodepletion showed that the monofunctional family 4 type of uracil-DNA glycosylase (UDG) is the principal and probably only UDG in this organism, a β-elimination mechanism rather than a hydrolytic mechanism is employed for incision of the abasic site following uracil removal. The resulting 3′ remnant is removed by efficient 3′-phosphodiesterase activity followed by single-nucleotide insertion and ligation. The finding that repair product formation is stimulated similarly by ATP and ADP
in vitro
raises the question of whether ADP is more important
in vivo
because of its higher heat stability.
Identification of a Novel Arsenite Oxidase Gene,
arxA
, in the Haloalkaliphilic, Arsenite-Oxidizing Bacterium
Alkalilimnicola ehrlichii
Strain MLHE-1
Authors: Zargar Kamrun , Hoeft Shelley , Oremland Ronald , Saltikov Chad W. 
Published: May 2010

ABSTRACT

Although arsenic is highly toxic to most organisms, certain prokaryotes are known to grow on and respire toxic metalloids of arsenic (i.e., arsenate and arsenite). Two enzymes are known to be required for this arsenic-based metabolism: (i) the arsenate respiratory reductase (ArrA) and (ii) arsenite oxidase (AoxB). Both catalytic enzymes contain molybdopterin cofactors and form distinct phylogenetic clades (ArrA and AoxB) within the dimethyl sulfoxide (DMSO) reductase family of enzymes. Here we report on the genetic identification of a “new” type of arsenite oxidase that fills a phylogenetic gap between the ArrA and AoxB clades of arsenic metabolic enzymes. This “new” arsenite oxidase is referred to as ArxA and was identified in the genome sequence of the Mono Lake isolate
Alkalilimnicola ehrlichii
MLHE-1, a chemolithoautotroph that can couple arsenite oxidation to nitrate reduction. A genetic system was developed for MLHE-1 and used to show that
arxA
(gene locus ID
mlg
_
0216
) was required for chemoautotrophic arsenite oxidation. Transcription analysis also showed that
mlg
_
0216
was only expressed under anaerobic conditions in the presence of arsenite. The
mlg
_
0216
gene is referred to as
arxA
because of its greater homology to
arrA
relative to
aoxB
and previous reports that implicated Mlg_0216 (ArxA) of MLHE-1 in reversible arsenite oxidation and arsenate reduction
in vitro
. Our results and past observations support the position that ArxA is a distinct clade within the DMSO reductase family of proteins. These results raise further questions about the evolutionary relationships between arsenite oxidases (AoxB) and arsenate respiratory reductases (ArrA).
Regulation of an Auxiliary, Antibiotic-Resistant Tryptophanyl-tRNA Synthetase Gene via Ribosome-Mediated Transcriptional Attenuation
Authors: Vecchione James J. , Sello Jason K. 
Published: May 2010

ABSTRACT

cis
-Acting RNA elements in the leaders of bacterial mRNA often regulate gene transcription, especially in the context of amino acid metabolism. We determined that the transcription of the auxiliary, antibiotic-resistant tryptophanyl-tRNA synthetase gene (
trpRS1
) in
Streptomyces coelicolor
is regulated by a ribosome-mediated attenuator in the 5′ leader of its mRNA region. This regulatory element controls gene transcription in response to the physiological effects of indolmycin and chuangxinmycin, two antibiotics that inhibit bacterial tryptophanyl-tRNA synthetases. By mining streptomycete genome sequences, we found several orthologs of
trpRS1
that share this regulatory element; we predict that they are regulated in a similar fashion. The validity of this prediction was established through the analysis of a
trpRS1
ortholog (SAV4725) in
Streptomyces avermitilis
. We conclude that the
trpRS1
locus is a widely distributed and self-regulating antibiotic resistance cassette. This study provides insights into how auxiliary aminoacyl-tRNA synthetase genes are regulated in bacteria.
Complete Genome Sequences of
Yersinia pestis
from Natural Foci in China
Authors: Shen Xiaona , Wang Qi , Xia Lianxu , Zhu Xiaoyu , Zhang Zhikai , Liang Ying , Cai Hong , Zhang Enmin , Wei Jianchun , Chen Chen , Song Zhizhong , Zhang Hongtao , Yu Dongzheng , Hai Rong 
Published: May 2010

ABSTRACT

Yersinia pestis
, the causative agent of plague, is a deadly bacterium that affects humans. Strain D106004 was isolated from a new plague focus in Yulong County, China, in 2006. To gain insights into the epidemic origin, we have sequenced the genomes of D106004 and strains Z176003 and D182038, isolated from neighboring regions.
Mutagenesis and Chemical Cross-Linking Suggest that Wzz Dimer Stability and Oligomerization Affect Lipopolysaccharide O-Antigen Modal Chain Length Control
Authors: Papadopoulos Magdalene , Morona Renato 
Published: May 2010

ABSTRACT

In
Shigella flexneri
, the polysaccharide copolymerase (PCP) protein Wzz
SF
confers a modal length of 10 to 17 repeat units (RUs) to the O-antigen (Oag) component of lipopolysaccharide (LPS). PCPs form oligomeric structures believed to be related to their function. To identify functionally important regions within Wzz
SF
, random in-frame linker mutagenesis was used to create mutants with 5-amino-acid insertions (termed Wzz
i
proteins), and DNA sequencing was used to locate the insertions. Analysis of the resulting LPS conferred by Wzz
i
proteins identified five mutant classes. The class I mutants were inactive, resulting in nonregulated LPS Oag chains, while classes II and III conferred shorter LPS Oag chains of 2 to 10 and 8 to 14 RUs, respectively. Class IV mutants retained near-wild-type function, and class V mutants increased the LPS Oag chain length to 16 to 25 RUs
. In vivo
formaldehyde cross-linking indicated class V mutants readily formed high-molecular-mass oligomers; however, class II and III Wzz
i
mutants were not effectively cross-linked. Wzz dimer stability was also investigated by heating cross-linked oligomers at 100°C in the presence of SDS. Unlike the Wzz
SF
wild type and class IV and V Wzz
i
mutants, the class II and III mutant dimers were not detectable. The location of each insertion was mapped onto available PCP three-dimensional (3D) structures, revealing that class V mutations were most likely located within the inner cavity of the PCP oligomer. These data suggest that the ability to produce stable dimers may be important in determining Oag modal chain length.
Preindustrial reconstruction of a perhumid midboreal landscape, Anticosti Island, Quebec
Authors: Barrette Martin , Bélanger Louis , De Grandpré Louis 
Published: May 2010

The knowledge of natural disturbance dynamics and preindustrial landscapes is essential to implement sustainable forest management. Recent findings identify the lack of a forest dynamics model, different from the standard cyclic model of Baskerville (1975. For. Chron. 51: 138–140), for balsam fir ( Abies balsamea (L.) Mill.) ecosystems of maritime eastern Canada. With the use of historical forest maps and dendrochronology, we reconstructed the range of variability of the preindustrial landscape (6798 km2) and inferred on the natural disturbance dynamics of the balsam fir forest of Anticosti Island. The preindustrial landscape was characterized by a forest matrix of overmature softwood stands with inclusions of younger softwood stands ranging from 0.1 to 7837 ha in size. Widespread stand-initiating events were apparently rare in the preindustrial landscape over the last 160 years. Since our results were not well represented by the cyclic model, which predicts the occurrence of a mosaic of stands in different age classes, we proposed an alternative forest dynamics model for eastern balsam fir ecosystems near the Gulf of St. Lawrence. Forest management inspired by this alternative model may be more appropriate to maintain or restore ecological characteristics of balsam fir forests of this region within their range of natural variability.
Crystal tuff in the Stoer Group, Torridonian Supergroup, NW Scotland
Authors: Batchelor Richard A. , Prave Anthony R. 
Published: May 2010

Synopsis
One thin bed in sandstones belonging to the Stoer Group (Torridonian Supergroup) contains feldspar and quartz grains showing deep concave embayments which are interpreted as corrosion features, and are all embedded in a fine-grained illitic or sericitic matrix. Its bulk chemical composition is similar to that of Phanerozoic metabentonites but it differs from the overlying Stac Fada Member which is believed to represent either a volcanogenic deposit or an impact ejecta blanket. Field relationships, petrographic and chemical characteristics point to this bed having a volcanic origin. This thin bed represents a crystal tuff and is the earliest example of a volcanogenic deposit in the Torridonian Supergroup in Scotland.