bluuebunny/crossref_metadata_2025_split huggingface dataset:
Characteristics and Dynamics of
Salmonella
Contamination along the Coast of Agadir, Morocco
Authors: Setti Ibtissame , Rodriguez-Castro Alba , Pata Maria P. , Cadarso-Suarez Carmen , Yacoubi Bouchra , Bensmael Laila , Moukrim Abdellatif , Martinez-Urtaza Jaime 
Published: October 2009

ABSTRACT

The occurrence of
Salmonella enterica
in the environment of tropical and desert regions has remained largely uninvestigated in many areas of the world, including Africa. In the present study, we investigated the presence of
Salmonella
spp. along 122 km of the coastline of Agadir (southern Morocco) in relation to environmental parameters. A total of 801 samples of seawater (243), marine sediment (279), and mussels (279) were collected from six sites between July 2004 and May 2008. The overall prevalence of
Salmonella
spp. was 7.1%, with the highest occurrence in mussels (10%), followed by sediment (6.8%) and seawater (4.1%). Only three serotypes were identified among the 57
Salmonella
sp. strains isolated.
S. enterica
serotype Blockley represented 43.8% of all
Salmonella
strains and was identified in mussel and sediment samples.
S. enterica
serotype Kentucky (29.8%) was found almost exclusively in mussels, whereas
S. enterica
serotype Senftenberg (26.3%) was detected in sediment and seawater. Statistical analysis using generalized additive models identified seawater temperature, environmental temperature, rainfall, and solar radiation as significant factors associated with the presence of
Salmonella
. Rainfall was the only variable showing a linear positive effect on the presence of
Salmonella
in the sea, whereas the remaining variables showed more complex nonlinear effects. Twenty-eight (49.1%)
Salmonella
isolates displayed resistance to ampicillin (22 isolates), nalidixic acid (9 isolates), sulfonamide compounds (2 isolates), and tetracycline (1 isolate), with six of these isolates displaying multiple resistance to two of these antimicrobial agents. Pulsed-field gel electrophoresis analysis revealed homogenous restriction patterns within each serotype that were uncorrelated with the resistance pattern profiles.
Evidence for Nitrogen Fixation by “
Dehalococcoides ethenogenes
” Strain 195
Authors: Lee Patrick K. H. , He Jianzhong , Zinder Stephen H. , Alvarez-Cohen Lisa 
Published: October 2009

ABSTRACT

Genome annotation of the chlorinated ethene-respiring “
Dehalococcoides ethenogenes
” strain 195 indicated the presence of a complete nitrogenase operon. Here, results from long-term growth experiments, gene expression, and
15
N
2
-isotope measurements confirm that strain 195 is capable of fixing atmospheric dinitrogen when a defined fixed-nitrogen source such as ammonium is unavailable.
Detection and Quantification ofDehalogenimonasand “Dehalococcoides” Populations via PCR-Based Protocols Targeting 16S rRNA Genes
Authors: Yan Jun , Rash Brian A. , Rainey Fred A. , Moe William M. 
Published: October 2009

ABSTRACTMembers of the haloalkane dechlorinating genusDehalogenimonasare distantly related to “Dehalococcoides” but share high homology in some variable regions of their 16S rRNA gene sequences. In this study, primers and PCR protocols intended to uniquely targetDehalococcoideswere reevaluated, and primers and PCR protocols intended to uniquely targetDehalogenimonaswere developed and tested. Use of the genus-specific primers revealed the presence of both bacterial groups in groundwater at a Louisiana Superfund site.
Structure and Function of Glycosylated Tandem Repeats from Candida albicans Als Adhesins
Authors: Frank Aaron T. , Ramsook Caleen B. , Otoo Henry N. , Tan Cho , Soybelman Gregory , Rauceo Jason M. , Gaur Nand K. , Klotz Stephen A. , Lipke Peter N. 
Published: October 2009

ABSTRACT

Tandem repeat (TR) regions are common in yeast adhesins, but their structures are unknown, and their activities are poorly understood. TR regions in
Candida albicans
Als proteins are conserved glycosylated 36-residue sequences with cell-cell aggregation activity (J. M. Rauceo, R. De Armond, H. Otoo, P. C. Kahn, S. A. Klotz, N. K. Gaur, and P. N. Lipke, Eukaryot. Cell 5:1664–1673, 2006).
Ab initio
modeling with either Rosetta or LINUS generated consistent structures of three-stranded antiparallel β-sheet domains, whereas randomly shuffled sequences with the same composition generated various structures with consistently higher energies. O- and N-glycosylation patterns showed that each TR domain had exposed hydrophobic surfaces surrounded by glycosylation sites. These structures are consistent with domain dimensions and stability measurements by atomic force microscopy (D. Alsteen, V. Dupres, S. A. Klotz, N. K. Gaur, P. N. Lipke, and Y. F. Dufrene, ACS Nano
3:
1677–1682, 2009) and with circular dichroism determination of secondary structure and thermal stability. Functional assays showed that the hydrophobic surfaces of TR domains supported binding to polystyrene surfaces and other TR domains, leading to nonsaturable homophilic binding. The domain structures are like “classic” subunit interaction surfaces and can explain previously observed patterns of promiscuous interactions between TR domains in any Als proteins or between TR domains and surfaces of other proteins. Together, the modeling techniques and the supporting data lead to an approach that relates structure and function in many kinds of repeat domains in fungal adhesins.
Regulatory Diversity ofTUP1inCryptococcus neoformans
Authors: Lee Hyeseung , Chang Yun C. , Varma Ashok , Kwon-Chung Kyung J. 
Published: October 2009

ABSTRACTCryptococcus neoformansserotype A strains, the major cause of cryptococcosis, are distributed worldwide, while serotype D strains are more concentrated in Central Europe. We have previously shown that deletion of the global regulatorTUP1in serotype D isolates results in a novel peptide-mediated, density-dependent growth phenotype that mimics quorum sensing and is not known to exist in other fungi. Unlike fortup1Δ strains of serotype D, the density-dependent growth phenotype was found to be absent intup1Δ strains of serotype A which had been derived from several different genetic clusters. The serotype A H99tup1Δ strain showed less retardation in the growth rate thantup1Δ strains of serotype D, but the mating efficiency was found to be similar in both serotypes. Deletion ofTUP1in the H99 strain resulted in significantly enhanced capsule production and defective melanin formation and also revealed a unique regulatory role of theTUP1gene in maintaining iron/copper homeostasis. Differential expression of various genes involved in capsule formation and iron/copper homeostasis was observed between the wild-type andtup1Δ H99 strains. Furthermore, the H99tup1Δ strain displayed pleiotropic effects which included sensitivity to sodium dodecyl sulfate, susceptibility to fluconazole, and attenuated virulence. These results demonstrate that the global regulatorTUP1has pathobiological significance and plays both conserved and distinct roles in serotype A and D strains ofC. neoformans.
Growth Phase and (p)ppGpp Control of IraD, a Regulator of RpoS Stability, in
Escherichia coli
Authors: Merrikh Houra , Ferrazzoli Alexander E. , Lovett Susan T. 
Published: October 2009

ABSTRACT

The antiadaptor protein IraD inhibits the proteolysis of the alternative sigma factor, RpoS, which promotes the synthesis of >100 genes during the general stress response and during stationary phase. Our previous results showed that IraD determines RpoS steady-state levels during exponential growth and mediates its stabilization after DNA damage. In this study, we show by promoter fusions that
iraD
was upregulated during the transition from exponential growth to stationary phase. The levels of RpoS likewise rose during this transition in a partially IraD-dependent manner. The expression of
iraD
was under the control of ppGpp. The expression of
iraD
required RelA and SpoT (p)ppGpp synthetase activities and was dramatically induced by a “stringent” allele of RNA polymerase, culminating in elevated levels of RpoS. Surprisingly, DksA, normally required for transcriptional effects of the stringent response, repressed
iraD
expression, suggesting that DksA can exert regulatory effects independent of and opposing those of (p)ppGpp. Northern blot analysis and 5′ rapid amplification of cDNA ends revealed two transcripts for
iraD
in wild-type strains; the smaller was regulated positively by RelA during growth; the larger transcript was induced specifically upon transition to stationary phase and was RelA SpoT dependent. A reporter fusion to the distal promoter indicated that it accounts for growth-phase regulation and DNA damage inducibility. DNA damage inducibility occurred in strains unable to synthesize (p)ppGpp, indicating an additional mode of regulation. Our results suggest that the induction of RpoS during transition to stationary phase and by (p)ppGpp occurs at least partially through IraD.
Structural Plasticity and Distinct Drug-Binding Modes of LfrR, a Mycobacterial Efflux Pump Regulator
Authors: Bellinzoni Marco , Buroni Silvia , Schaeffer Francis , Riccardi Giovanna , De Rossi Edda , Alzari Pedro M. 
Published: October 2009

ABSTRACT

The TetR-like transcriptional repressor LfrR controls the expression of the gene encoding the
Mycobacterium smegmatis
efflux pump LfrA, which actively extrudes fluoroquinolones, cationic dyes, and anthracyclines from the cell and promotes intrinsic antibiotic resistance. The crystal structure of the apoprotein form of the repressor reveals a structurally asymmetric homodimer exhibiting local unfolding and a blocked drug-binding site, emphasizing the significant conformational plasticity of the protein necessary for DNA and multidrug recognition. Crystallographic and calorimetric studies of LfrR-drug complexes further confirm the intrinsic flexibility of the homodimer, which provides a dynamic mechanism to broaden multidrug binding specificity and may be a general property of transcriptional repressors regulating microbial efflux pump expression.
Mycobacterium tuberculosis
PhoP Recognizes Two Adjacent Direct-Repeat Sequences To Form Head-to-Head Dimers
Authors: Gupta Sankalp , Pathak Anuj , Sinha Akesh , Sarkar Dibyendu 
Published: October 2009

ABSTRACT

Mycobacterium tuberculosis
PhoP of the PhoP-PhoR two-component signaling system orchestrates a complex transcription program and is essential for the growth and virulence of the tubercle bacillus. PhoP comprises a phosphorylation domain at the amino-terminal half and a DNA-binding domain in the carboxy-terminal half of the protein. We show here that the protein recognizes a 23-bp sequence of the
phoP
upstream region comprising two adjacent direct repeat motifs believed to promote transcription regulation. DNA binding, which involves the recruitment of two monomeric PhoP molecules, was dependent on conserved adenines of the repeat sequences and the orientation of the repeat motifs relative to each other. Although response regulators such as PhoB and FixJ dimerize upon phosphorylation, we demonstrate here that PhoP dimerization can also be stimulated by DNA binding. Using the established asymmetric tandem binding model by members of the OmpR/PhoB protein family as a guide, we set out to examine intermolecular interactions between PhoP dimers by protein cross-linking. Our results are consistent with a model in which two PhoP protomers bind the duplex DNA with a symmetric head-to-head orientation to project their N termini toward one another, arguing against previously proposed head-to-tail tandem dimer formation for members of the OmpR/PhoB protein subfamily.
Deletion of Citrate Synthase Restores Growth of
Sinorhizobium meliloti
1021 Aconitase Mutants
Authors: Koziol Uriel , Hannibal Luciana , Rodríguez María Cecilia , Fabiano Elena , Kahn Michael L. , Noya Francisco 
Published: October 2009

ABSTRACT

The symbiotic nitrogen-fixing bacterium
Sinorhizobium meliloti
1021 encodes only one predicted aconitase (AcnA) in its genome. AcnA has a significant degree of similarity with other bacterial aconitases that behave as dual proteins: enzymes and posttranscriptional regulators of gene expression. Similar to the case with these bacterial aconitases, AcnA activity was reversibly labile and was regained upon reconstitution with reduced iron. The aconitase promoter was active in root nodules.
acnA
mutants grew very poorly, had secondary mutations, and were quickly outgrown by pseudorevertants. The
acnA
gene was stably interrupted in a citrate synthase (
gltA
) null background, indicating that the intracellular accumulation of citrate may be deleterious for survival of strain 1021. No aconitase activity was detected in this mutant, suggesting that the
acnA
gene encodes the only functional aconitase of strain 1021. To uncover a function of AcnA beyond its catalytic role in the tricarboxylic acid cycle pathway, the
gltA acnA
double mutant was compared with the
gltA
single mutant for differences in motility, resistance to oxidative stress, nodulation, and growth on different substrates. However, no differences in any of these characteristics were found.
A Comprehensive Analysis of the Peroxiredoxin Reduction System in the Cyanobacterium
Synechocystis
sp. Strain PCC 6803 Reveals that All Five Peroxiredoxins Are Thioredoxin Dependent
Authors: Pérez-Pérez María Esther , Mata-Cabana Alejandro , Sánchez-Riego Ana María , Lindahl Marika , Florencio Francisco J. 
Published: October 2009

ABSTRACT

Cyanobacteria perform oxygenic photosynthesis, which gives rise to the continuous production of reactive oxygen species, such as superoxide anion radicals and hydrogen peroxide, particularly under unfavorable growth conditions. Peroxiredoxins, which are present in both chloroplasts and cyanobacteria, constitute a class of thiol-dependent peroxidases capable of reducing hydrogen peroxide as well as alkyl hydroperoxides. Chloroplast peroxiredoxins have been studied extensively and have been found to use a variety of endogenous electron donors, such as thioredoxins, glutaredoxins, or cyclophilin, to sustain their activities. To date, however, the endogenous reduction systems for cyanobacterial peroxiredoxins have not been systematically studied. We have expressed and purified all five
Synechocystis
sp. strain PCC 6803 peroxiredoxins, which belong to the classes 1-Cys Prx, 2-Cys Prx, type II Prx (PrxII), and Prx Q, and we have examined their capacities to interact with and receive electrons from the
m
-,
x
-, and
y
-type thioredoxins from the same organism, which are called TrxA, TrxB, and TrxQ, respectively. Assays for peroxidase activity demonstrated that all five enzymes could use thioredoxins as electron donors, whereas glutathione and
Synechocystis
sp. strain PCC 6803 glutaredoxins were inefficient. The highest catalytic efficiency was obtained for the couple consisting of PrxII and TrxQ thioredoxin. Studies of transcript levels for the peroxiredoxins and thioredoxins under different stress conditions highlighted the similarity between the PrxII and TrxQ thioredoxin expression patterns.
FadD from
Pseudomonas putida
CA-3 Is a True Long-Chain Fatty Acyl Coenzyme A Synthetase That Activates Phenylalkanoic and Alkanoic Acids
Authors: Hume Aisling R. , Nikodinovic-Runic Jasmina , O'Connor Kevin E. 
Published: October 2009

ABSTRACT

A fatty acyl coenzyme A synthetase (FadD) from
Pseudomonas putida
CA-3 is capable of activating a wide range of phenylalkanoic and alkanoic acids. It exhibits the highest rates of reaction and catalytic efficiency with long-chain aromatic and aliphatic substrates. FadD exhibits higher
k
cat
and

K
m

values for aromatic substrates than for the aliphatic equivalents (e.g., 15-phenylpentadecanoic acid versus pentadecanoic acid). FadD is inhibited noncompetitively by both acrylic acid and 2-bromooctanoic acid. The deletion of the
fadD
gene from
P. putida
CA-3 resulted in no detectable growth or polyhydroxyalkanoate (PHA) accumulation with 10-phenyldecanoic acid, decanoic acid, and longer-chain substrates. The results suggest that FadD is solely responsible for the activation of long-chain phenylalkanoic and alkanoic acids. While the CA-3Δ
fadD
mutant could grow on medium-chain substrates, a decrease in growth yield and PHA accumulation was observed. The PHA accumulated by CA-3Δ
fadD
contained a greater proportion of short-chain monomers than did wild-type PHA. Growth of CA-3Δ
fadD
was unaffected, but PHA accumulation decreased modestly with shorter-chain substrates. The complemented mutant regained 70% to 90% of the growth and PHA-accumulating ability of the wild-type strain depending on the substrate. The expression of an extra copy of
fadD
in
P. putida
CA-3 resulted in increased levels of PHA accumulation (up to 1.6-fold) and an increase in the incorporation of longer-monomer units into the PHA polymer.
Tn
917
Targets the Region Where DNA Replication Terminates in
Bacillus subtilis
, Highlighting a Difference in Chromosome Processing in the
Firmicutes
Authors: Shi Qiaojuan , Huguet-Tapia Jose C. , Peters Joseph E. 
Published: October 2009

ABSTRACT

The bacterial transposon Tn
917
inserts preferentially in the terminus region of some members of the
Firmicutes
. To determine what molecular process was being targeted by the element, we analyzed Tn
917
target site selection in
Bacillus subtilis
. We find that Tn
917
insertions accumulate around the central terminators,
terI
and
terII
, in wild-type cells with or without the SPβ lysogen. Highly focused targeting around
terI
and
terII
requires the
trans
-acting termination protein RTP, but it is unaffected in strains compromised in dimer resolution or chromosome translocation. This work indicates that Tn
917
is sensitive to differences in DNA replication termination between the
Firmicutes
.
Elucidation of the Mechanism by Which Catecholamine Stress Hormones Liberate Iron from the Innate Immune Defense Proteins Transferrin and Lactoferrin
Authors: Sandrini Sara M. , Shergill Raminder , Woodward Jonathan , Muralikuttan Remya , Haigh Richard D. , Lyte Mark , Freestone Primrose P. 
Published: October 2009

ABSTRACT
The ability of catecholamine stress hormones and inotropes to stimulate the growth of infectious bacteria is now well established. A major element of the growth induction process has been shown to involve the catecholamines binding to the high-affinity ferric-iron-binding proteins transferrin (Tf) and lactoferrin, which then enables bacterial acquisition of normally inaccessible sequestered host iron. The nature of the mechanism(s) by which the stress hormones perturb iron binding of these key innate immune defense proteins has not been fully elucidated. The present study employed electron paramagnetic resonance spectroscopy and chemical iron-binding analyses to demonstrate that catecholamine stress hormones form direct complexes with the ferric iron within transferrin and lactoferrin. Moreover, these complexes were shown to result in the reduction of Fe(III) to Fe(II) and the loss of protein-complexed iron. The use of bacterial ferric iron uptake mutants further showed that both the Fe(II) and Fe(III) released from the Tf could be directly used as bacterial nutrient sources. We also analyzed the transferrin-catecholamine interactions in human serum and found that therapeutically relevant concentrations of stress hormones and inotropes could directly affect the iron binding of serum-transferrin so that the normally highly bacteriostatic tissue fluid became significantly more supportive of the growth of bacteria. The relevance of these catecholamine-transferrin/lactoferrin interactions to the infectious disease process is considered.
Functional and Biochemical Analysis of theChlamydia trachomatisLigase MurE
Authors: Patin Delphine , Bostock Julieanne , Blanot Didier , Mengin-Lecreulx Dominique , Chopra Ian 
Published: October 2009

ABSTRACTChlamydiae are unusual obligately intracellular bacteria that do not synthesize detectable peptidoglycan. However, they possess genes that appear to encode products with peptidoglycan biosynthetic activity. Bioinformatic analysis predicts that chlamydial MurE possesses UDP-MurNAc-l-Ala-d-Glu:meso-diaminopimelic acid (UDP-MurNAc-l-Ala-d-Glu:meso-A2pm) ligase activity. Nevertheless, there are no experimental data to confirm this hypothesis. In this paper we demonstrate that themurEgene fromChlamydia trachomatisis capable of complementing a conditionalEscherichia colimutant impaired in UDP-MurNAc-l-Ala-d-Glu:meso-A2pm ligase activity. Recombinant MurE fromC. trachomatis(MurECt) was overproduced in and purified fromE. coliin order to investigate its kinetic parameters in vitro. By use of UDP-MurNAc-l-Ala-d-Glu as the nucleotide substrate, MurECtdemonstrated ATP-dependentmeso-A2pm ligase activity with pH and magnesium ion optima of 8.6 and 30 mM, respectively. Other amino acids (meso-lanthionine, thellandddisomers of A2pm,d-lysine) were also recognized by MurECt.However, the activities for these amino acid substrates were weaker than that formeso-A2pm. The specificity of MurECtfor three possibleC. trachomatispeptidoglycan nucleotide substrates was also determined in order to deduce which amino acid might be present at the first position of the UDP-MurNAc-pentapeptide. Relativekcat/Kmratios for UDP-MurNAc-l-Ala-d-Glu, UDP-MurNAc-l-Ser-d-Glu, and UDP-MurNAc-Gly-d-Glu were 100, 115, and 27, respectively. Our results are consistent with the synthesis in chlamydiae of a UDP-MurNAc-pentapeptide in which the third amino acid ismeso-A2pm. However, due to the lack of specificity of MurECtfor nucleotide substrates in vitro, it is not obvious which amino acid is present at the first position of the pentapeptide.
Pathway Evolution by Horizontal Transfer and Positive Selection Is Accommodated by Relaxed Negative Selection upon Upstream Pathway Genes in Purple Bacterial Carotenoid Biosynthesis
Authors: Klassen Jonathan L. 
Published: October 2009

ABSTRACT

Horizontal gene transfer and selection are major forces driving microbial evolution. However, interactions between them are rarely studied. Phylogenetic analyses of purple bacterial carotenoid biosynthesis genes suggest two lineages: one producing spheroidenone and the other producing spirilloxanthin. Of the latter lineage,
Rubrivivax gelatinosus
S1 and
Hoeflea phototrophica
DFL-43 also or instead produce spheroidenone. Evolution of the spheroidenone pathway from that producing spirilloxanthin theoretically requires changes in the substrate specificity of upstream pathway enzymes and acquisition of a terminal ketolase (CrtA). In
R. gelatinosus
and likely also in
H. phototrophica
, CrtA was acquired from the
Bacteroidetes
, in which it functions as a hydroxylase. Estimation of nonsynonymous and synonymous mutations using several pairwise methods indicated positive selection upon both genes, consistent with their functional changes from hydroxylases to ketolases. Relaxed negative selection upon all other carotenoid biosynthetic genes in these organisms was also apparent, likely facilitating changes in their substrate specificities. Furthermore, all genes responsible for terminal carotenoid biosynthetic pathway steps were under reduced negative selection compared to those known to govern biosynthetic pathway specificity. Horizontal transfer of
crtA
into
R. gelatinosus
and
H. phototrophica
has therefore likely been promoted by (i) the apparent selective advantage of spheroidenone production relative to spirilloxanthin production, (ii) reduced negative selection upon other carotenoid biosynthetic genes, facilitating changes in their substrate specificities, and (iii) preexisting low enzyme substrate specificities due to relaxed negative selection. These results highlight the importance and complexity of selection acting upon both a horizontally transferred gene and the biochemical network into which it is integrating.