bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evolutionary Relationships among Actinophages and a Putative Adaptation for Growth in Streptomyces spp
Authors: Smith Margaret C. M. , Hendrix Roger W. , Dedrick Rebekah , Mitchell Kaitlin , Ko Ching-Chung , Russell Daniel , Bell Emma , Gregory Matthew , Bibb Maureen J. , Pethick Florence , Jacobs-Sera Deborah , Herron Paul , Buttner Mark J. , Hatfull Graham F. 
Published: August 2013

ABSTRACT

The genome sequences of eight
Streptomyces
phages are presented, four of which were isolated for this study. Phages R4, TG1, ϕHau3, and SV1 were isolated previously and have been exploited as tools for understanding and genetically manipulating
Streptomyces
spp. We also extracted five apparently intact prophages from recent
Streptomyces
spp. genome projects and, together with six phage genomes in the database, we analyzed all 19
Streptomyces
phage genomes with a view to understanding their relationships to each other and to other actinophages, particularly the mycobacteriophages. Fifteen of the
Streptomyces
phages group into four clusters of related genomes. Although the R4-like phages do not share nucleotide sequence similarity with other phages, they clearly have common ancestry with cluster A mycobacteriophages, sharing many protein homologues, common gene syntenies, and similar repressor-stoperator regulatory systems. The R4-like phage ϕHau3 and the prophage StrepC.1 (from
Streptomyces
sp. strain C) appear to have hijacked a unique adaptation of the streptomycetes, i.e., use of the rare UUA codon, to control translation of the essential phage protein, the terminase. The
Streptomyces venezuelae
generalized transducing phage SV1 was used to predict the presence of other generalized transducing phages for different
Streptomyces
species.
Phosphate Concentration and the Putative Sensor Kinase Protein CckA Modulate Cell Lysis and Release of the Rhodobacter capsulatus Gene Transfer Agent
Authors: Westbye A. B. , Leung M. M. , Florizone S. M. , Taylor T. A. , Johnson J. A. , Fogg P. C. , Beatty J. T. 
Published: August 2013

ABSTRACT

The gene transfer agent of
Rhodobacter capsulatus
(RcGTA) is a bacteriophage-like genetic element with the sole known function of horizontal gene transfer. Homologues of RcGTA genes are present in many members of the alphaproteobacteria and may serve an important role in microbial evolution. Transcription of RcGTA genes is induced as cultures enter the stationary phase; however, little is known about
cis
-active sequences. In this work, we identify the promoter of the first gene in the RcGTA structural gene cluster. Additionally, gene transduction frequency depends on the growth medium, and the reason for this is not known. We report that millimolar concentrations of phosphate posttranslationally inhibit the lysis-dependent release of RcGTA from cells in both a complex medium and a defined medium. Furthermore, we found that cell lysis requires the genes
rcc00555
and
rcc00556
, which were expressed and studied in
Escherichia coli
to determine their predicted functions as an endolysin and holin, respectively. Production of RcGTA is regulated by host systems, including a putative histidine kinase, CckA, and we found that CckA is required for maximal expression of
rcc00555
and for maturation of RcGTA to yield gene transduction-functional particles.
Depletion of Glycolytic Intermediates Plays a Key Role in Glucose-Phosphate Stress in Escherichia coli
Authors: Richards Gregory R. , Patel Maulik V. , Lloyd Chelsea R. , Vanderpool Carin K. 
Published: August 2013

ABSTRACT

In bacteria like
Escherichia coli
, the accumulation of glucose-6-phosphate (G6P) or its analogs such as α-methyl glucoside-6-phosphate (αMG6P) results in stress that appears in the form of growth inhibition. The small RNA SgrS is an essential part of the response that helps
E. coli
combat glucose-phosphate stress; the growth of
sgrS
mutants during stress caused by αMG is significantly impaired. The cause of this stress is not currently known but may be due to either toxicity of accumulated sugar-phosphates or to depletion of metabolic intermediates. Here, we present evidence that glucose-phosphate stress results from depletion of glycolytic intermediates. Addition of glycolytic compounds like G6P and fructose-6-phosphate rescues the αMG growth defect of an
sgrS
mutant. These intermediates also markedly decrease induction of the stress response in both wild-type and
sgrS
strains grown with αMG, implying that cells grown with these intermediates experience less stress. Moreover, αMG transport assays confirm that G6P relieves stress even when αMG is taken up by the cell, strongly suggesting that accumulated αMG6P
per se
does not cause stress. We also report that addition of pyruvate during stress has a novel lethal effect on the
sgrS
mutant, resulting in cell lysis. The phosphoenolpyruvate (PEP) synthetase PpsA, which converts pyruvate to PEP, can confer resistance to pyruvate-induced lysis when
ppsA
is ectopically expressed in the
sgrS
mutant. Taken as a whole, these results provide the strongest evidence thus far that depletion of glycolytic intermediates is at the metabolic root of glucose-phosphate stress.
Cyclic AMP Receptor Protein Regulates Pheromone-Mediated Bioluminescence at Multiple Levels in Vibrio fischeri ES114
Authors: Lyell Noreen L. , Colton Deanna M. , Bose Jeffrey L. , Tumen-Velasquez Melissa P. , Kimbrough John H. , Stabb Eric V. 
Published: August 2013

ABSTRACT

Bioluminescence in
Vibrio fischeri
ES114 is activated by autoinducer pheromones, and this regulation serves as a model for bacterial cell-cell signaling. As in other bacteria, pheromone concentration increases with cell density; however, pheromone synthesis and perception are also modulated in response to environmental stimuli. Previous studies suggested that expression of the pheromone-dependent bioluminescence activator LuxR is regulated in response to glucose by cyclic AMP (cAMP) receptor protein (CRP) (P. V. Dunlap and E. P. Greenberg, J. Bacteriol. 164:45–50, 1985; P. V. Dunlap and E. P. Greenberg, J. Bacteriol. 170:4040–4046, 1988; P. V. Dunlap, J. Bacteriol. 171:1199–1202, 1989; and W. F. Friedrich and E. P. Greenberg, Arch. Microbiol. 134:87–91, 1983). Consistent with this model, we found that bioluminescence in
V. fischeri
ES114 is modulated by glucose and stimulated by cAMP. In addition, a Δ
crp
mutant was ∼100-fold dimmer than ES114 and did not increase luminescence in response to added cAMP, even though cells lacking
crp
were still metabolically capable of producing luminescence. We further discovered that CRP regulates not only
luxR
but also the alternative pheromone synthase gene
ainS
. We found that His-tagged
V. fischeri
CRP could bind sequences upstream of both
luxR
and
ainS
, supporting bioinformatic predictions of direct regulation at both promoters. Luminescence increased in response to cAMP if either the
ainS
or
luxR
system was under native regulation, suggesting cAMP-CRP significantly increases luminescence through both systems. Finally, using transcriptional reporters in transgenic
Escherichia coli
, we elucidated two additional regulatory connections. First, LuxR-independent basal transcription of the
luxI
promoter was enhanced by CRP. Second, the effect of CRP on the
ainS
promoter depended on whether the
V. fischeri
regulatory gene
litR
was also introduced. These results suggest an integral role for CRP in pheromone signaling that goes beyond sensing cell density.
Amino Acid Racemization in Pseudomonas putida KT2440
Authors: Radkov Atanas D. , Moe Luke A. 
Published: August 2013

ABSTRACTd-Amino acids have been shown to play an increasingly diverse role in bacterial physiology, yet much remains to be learned about their synthesis and catabolism. Here we used the model soil- and rhizosphere-dwelling organismPseudomonas putidaKT2440 to elaborate on the genomics and enzymology ofd-amino acid metabolism.P. putidaKT2440 catabolized thed-stereoisomers of lysine, phenylalanine, arginine, alanine, and hydroxyproline as the sole carbon and nitrogen sources. With the exception of phenylalanine, each of these amino acids was racemized byP. putidaKT2440 enzymes. Three amino acid racemases were identified from a genomic screen, and the enzymes were further characterizedin vitro. The putative biosynthetic alanine racemase Alr showed broad substrate specificity, exhibiting measurable racemase activity with 9 of the 19 chiral amino acids. Among these amino acids, activity was the highest with lysine, and thekcat/Kmvalues withl- andd-lysine were 3 orders of magnitude greater than thekcat/Kmvalues withl- andd-alanine. Conversely, the putative catabolic alanine racemase DadX showed narrow substrate specificity, clearly preferring only the alanine stereoisomers as the substrates. However, DadX did show 6- and 9-fold higherkcat/Kmvalues than Alr withl- andd-alanine, respectively. The annotated proline racemase ProR ofP. putidaKT2440 showed negligible activity with either stereoisomer of the 19 chiral amino acids but exhibited strong epimerization activity with hydroxyproline as the substrate. Comparative genomic analysis revealed differences among pseudomonads with respect to alanine racemase genes that may point to different roles for these genes among closely related species.
Residues in Conserved Loops of Intramembrane Metalloprotease SpoIVFB Interact with Residues near the Cleavage Site in Pro-σ
K
Authors: Zhang Yang , Luethy Paul M. , Zhou Ruanbao , Kroos Lee 
Published: August 2013

ABSTRACT

Intramembrane metalloproteases (IMMPs) control critical biological processes by cleaving membrane-associated proteins within a transmembrane segment or at a site near the membrane surface. Phylogenetic analysis divides IMMPs into four groups. SpoIVFB is a group III IMMP that regulates
Bacillus subtilis
endospore formation by cleaving Pro-σ
K
and releasing the active sigma factor from a membrane. To elucidate the enzyme-substrate interaction, single-cysteine versions of catalytically inactive SpoIVFB and C-terminally truncated Pro-σ
K
(1-126) (which can be cleaved by active SpoIVFB) were coexpressed in
Escherichia coli
, and proximity was tested by disulfide cross-linking
in vivo
. As expected, the results provided evidence that catalytic residue Glu-44 of SpoIVFB is near the cleavage site in the substrate. Also near the cleavage site were two residues of SpoIVFB in predicted conserved loops; Pro-135 in a short loop and Val-70 in a longer loop. Pro-135 corresponds to Pro-399 of RseP, a group I IMMP, and Pro-399 was reported previously to interact with substrate near the cleavage site, suggesting a conserved interaction across IMMP subfamilies. Val-70 follows a newly recognized conserved motif, PXGG (X is a large hydrophobic residue), which is in a hydrophobic region predicted to be a membrane reentrant loop. Following the hydrophobic region is a negatively charged region that is conserved in IMMPs of groups I and III. At least two residues with a negatively charged side chain are required in this region for activity of SpoIVFB. The region exhibits other features in IMMPs of groups II and IV. Its possible roles, as well as that of the short loop, are discussed. New insights into IMMP-substrate interaction build toward understanding how IMMPs function and may facilitate manipulation of their activity.
The Genome of Pseudomonas fluorescens Strain R124 Demonstrates Phenotypic Adaptation to the Mineral Environment
Authors: Barton Michael D. , Petronio Michael , Giarrizzo Juan G. , Bowling Bethany V. , Barton Hazel A. 
Published: August 2013

ABSTRACTMicrobial adaptation to environmental conditions is a complex process, including acquisition of positive traits through horizontal gene transfer or the modification of existing genes through duplication and/or mutation. In this study, we examined the adaptation of aPseudomonas fluorescensisolate (R124) from the nutrient-limited mineral environment of a silica cave in comparison withP. fluorescensisolates from surface soil and the rhizosphere. Examination of metal homeostasis gene pathways demonstrated a high degree of conservation, suggesting that such systems remain functionally similar across chemical environments. The examination of genomic islands unique to our strain revealed the presence of genes involved in carbohydrate metabolism, aromatic carbon metabolism, and carbon turnover, confirmed through phenotypic assays, suggesting the acquisition of potentially novel mechanisms for energy metabolism in this strain. We also identified a twitching motility phenotype active at low-nutrient concentrations that may allow alternative exploratory mechanisms for this organism in a geochemical environment. Two sets of candidate twitching motility genes are present within the genome, one on the chromosome and one on a plasmid; however, a plasmid knockout identified the functional gene as being present on the chromosome. This work highlights the plasticity of thePseudomonasgenome, allowing the acquisition of novel nutrient-scavenging pathways across diverse geochemical environments while maintaining a core of functional stress response genes.
Streptomyces coelicolor Encodes a Urate-Responsive Transcriptional Regulator with Homology to PecS from Plant Pathogens
Authors: Huang Hao , Mackel Brian J. , Grove Anne 
Published: August 2013

ABSTRACT

Many transcriptional regulators control gene activity by responding to specific ligands. Members of the multiple-antibiotic resistance regulator (MarR) family of transcriptional regulators feature prominently in this regard, and they frequently function as repressors in the absence of their cognate ligands. Plant pathogens such as
Dickeya dadantii
encode a MarR homolog named PecS that controls expression of a gene encoding the efflux pump PecM in addition to other virulence genes. We report here that the soil bacterium
Streptomyces coelicolor
also encodes a PecS homolog (
SCO2647
) that regulates a
pecM
gene (
SCO2646
).
S. coelicolor
PecS, which exists as a homodimer, binds the intergenic region between
pecS
and
pecM
genes with high affinity. Several potential PecS binding sites were found in this intergenic region. The binding of PecS to its target DNA can be efficiently attenuated by the ligand urate, which also quenches the intrinsic fluorescence of PecS, indicating a direct interaction between urate and PecS.
In vivo
measurement of gene expression showed that activity of
pecS
and
pecM
genes is significantly elevated after exposure of
S. coelicolor
cultures to urate. These results indicate that
S. coelicolor
PecS responds to the ligand urate by attenuated DNA binding
in vitro
and upregulation of gene activity
in vivo
. Since production of urate is associated with generation of reactive oxygen species by xanthine dehydrogenase, we propose that PecS functions under conditions of oxidative stress.
Exploring the Roles of DNA Methylation in the Metal-Reducing Bacterium Shewanella oneidensis MR-1
Authors: Bendall Matthew L. , Luong Khai , Wetmore Kelly M. , Blow Matthew , Korlach Jonas , Deutschbauer Adam , Malmstrom Rex R. 
Published: August 2013

ABSTRACT

We performed whole-genome analyses of DNA methylation in
Shewanella oneidensis
MR-1 to examine its possible role in regulating gene expression and other cellular processes. Single-molecule real-time (SMRT) sequencing revealed extensive methylation of adenine (N6mA) throughout the genome. These methylated bases were located in five sequence motifs, including three novel targets for type I restriction/modification enzymes. The sequence motifs targeted by putative methyltranferases were determined via SMRT sequencing of gene knockout mutants. In addition, we found that
S. oneidensis
MR-1 cultures grown under various culture conditions displayed different DNA methylation patterns. However, the small number of differentially methylated sites could not be directly linked to the much larger number of differentially expressed genes under these conditions, suggesting that DNA methylation is not a major regulator of gene expression in
S. oneidensis
MR-1. The enrichment of methylated GATC motifs in the origin of replication indicates that DNA methylation may regulate genome replication in a manner similar to that seen in
Escherichia coli
. Furthermore, comparative analyses suggest that many
Gammaproteobacteria
, including all members of the
Shewanellaceae
family, may also utilize DNA methylation to regulate genome replication.
EutR Is a Direct Regulator of Genes That Contribute to Metabolism and Virulence in Enterohemorrhagic Escherichia coli O157:H7
Authors: Luzader Deborah H. , Clark David E. , Gonyar Laura A. , Kendall Melissa M. 
Published: August 2013

ABSTRACT

Ethanolamine (EA) metabolism is a trait associated with enteric pathogens, including enterohemorrhagic
Escherichia coli
O157:H7 (EHEC). EHEC causes severe bloody diarrhea and hemolytic uremic syndrome. EHEC encodes the ethanolamine utilization (
eut
) operon that allows EHEC to metabolize EA and gain a competitive advantage when colonizing the gastrointestinal tract. The
eut
operon encodes the transcriptional regulator EutR. Genetic studies indicated that EutR expression is induced by EA and vitamin B
12
and that EutR promotes expression of the
eut
operon; however, biochemical evidence for these interactions has been lacking. We performed EA-binding assays and electrophoretic mobility shift assays (EMSAs) to elucidate a mechanism for EutR gene regulation. These studies confirmed EutR interaction with EA, as well as direct binding to the
eutS
promoter. EutR also contributes to expression of the locus of enterocyte effacement (LEE) in an EA-dependent manner. We performed EMSAs to examine EutR activation of the LEE. The results demonstrated that EutR directly binds the regulatory region of the
ler
promoter. These results present the first mechanistic description of EutR gene regulation and reveal a novel role for EutR in EHEC pathogenesis.
Substance P reduces TNF-α-induced apoptosis in human tenocytes through NK-1 receptor stimulation
Authors: Backman Ludvig J , Eriksson Daniella E , Danielson Patrik 
Published: August 2013

BackgroundIt has been hypothesised that an upregulation of the neuropeptide substance P (SP) and its preferred receptor, the neurokinin-1 receptor (NK-1 R), is a causative factor in inducing tenocyte hypercellularity, a characteristic of tendinosis, through both proliferative and antiapoptotic stimuli. We have demonstrated earlier that SP stimulates proliferation of human tenocytes in culture.AimThe aim of this study was to investigate whether SP can mediate an antiapoptotic effect in tumour necrosis factor-α (TNF-α)-induced apoptosis of human tenocytes in vitro.ResultsA majority (approximately 75%) of tenocytes in culture were immunopositive for TNF Receptor-1 and TNF Receptor-2. Exposure of the cells to TNF-α significantly decreased cell viability, as shown with crystal violet staining. TNF-α furthermore significantly increased the amount of caspase-10 and caspase-3 mRNA, as well as both BID and cleaved-poly ADP ribosome polymerase (c-PARP) protein. Incubation of SP together with TNF-α resulted in a decreased amount of BID and c-PARP, and in a reduced lactate dehydrogenase release, as compared to incubation with TNF-α alone. The SP effect was blocked with a NK-1 R inhibitor.DiscussionThis study shows that SP, through stimulation of the NK-1 R, has the ability to reduce TNF-α-induced apoptosis of human tenocytes. Considering that SP has previously been shown to stimulate tenocyte proliferation, the study confirms SP as a potent regulator of cell-turnover in tendon tissue, capable of stimulating hypercellularity through different mechanisms. This gives further support for the theory that the upregulated amount of SP seen in tendinosis could contribute to hypercellularity.
Sign-out snapshot: cross-sectional evaluation of written sign-outs among specialties
Authors: Schoenfeld Amy R , Salim Al-Damluji Mohammed , Horwitz Leora I 
Published: August 2013

BackgroundSign-out is the process (written, verbal or both) by which one clinical team transmits information about patients to another team. Poor quality sign-outs are associated with adverse events and delayed treatment. How different specialties approach written sign-outs is unknown.ObjectiveTo compare written sign-out practices across specialties and to determine consistency of content, format and timeliness.MethodsThe authors evaluated all non-Intensive Care Unit written sign-outs from five inpatient specialties on 18 January 2012, at Yale-New Haven Hospital, focusing on content elements, format style and whether the sign-outs had been updated within 24 h. In our institution, all specialties used a single standardised sign-out template, which was built into the electronic medical record.ResultsThe final cohort included 457 sign-outs: 313 medicine, 64 general surgery, 36 paediatrics, 30 obstetrics, and 14 gynaecology. Though nearly all sign-outs (96%) had been updated within 24 h, they frequently lacked key information. Hospital course prevalence ranged from 57% (gynaecology) to 100% (paediatrics) (p<0.001). Clinical condition prevalence ranged from 34% (surgery) to 72% (paediatrics) (p=0.005).ConclusionsSpecialties have varied sign-out practices, and thus structured templates alone do not guarantee inclusion of critical content. Sign-outs across specialties often lacked complex clinical information such as clinical condition, anticipatory guidance and overnight tasks.
Integrated bio-behavioural HIV surveillance surveys among female sex workers in Sudan, 2011–2012
Authors: Elhadi Magda , Elbadawi Abdulateef , Abdelrahman Samira , Mohammed Ibtisam , Bozicevic Ivana , Hassan Ehab A , Elmukhtar Mohammed , Ahmed Sally , Abdelraheem Mohammed Sidahmed , Mubarak Nazik , Elsanousi Salwa , Setayesh Hamidreza 
Published: August 2013

ObjectivesTo assess HIV and syphilis prevalence, HIV-related behaviours and testing for HIV in female sex workers (FSW) in Sudan.DesignBio-behavioural surveys using respondent-driven sampling were carried out among FSW in the capital cities of 14 states in Sudan in 2011–2012. HIV and syphilis testing was done by rapid tests.Results4220 FSW aged 15–49 years were recruited. The median age of recruited women varied from 21 to 28 years per site. The highest HIV prevalence was measured at two sites in the eastern zone (5.0% and 7.7%), while in the other zones it ranged from 0% to 1.5%. Syphilis prevalence ranged from 1.5% in the northern zone to 8.9% in the eastern zone. Ever having been tested for HIV was reported by 4.4%–23.9% of FSW across all sites. Condom use at last sex with a client varied from 4.7% to 55.1%, while consistent condom use with clients in the month preceding the surveys was reported by 0.7%–24.5% of FSW. The highest reporting of ever injecting drugs was measured at a site in the western zone (5.0%).ConclusionsThe surveys’ findings indicate that the highest burden of HIV in FSW is in the eastern states of the country. Condom use and HIV testing data demonstrate the need for HIV interventions that should focus on HIV testing and risk reduction strategies that include stronger condom promotion programmes in FSW and their clients.