bluuebunny/crossref_metadata_2025_split huggingface dataset:
Bioenergetics of the Moderately Halophilic Bacterium Halobacillus halophilus: Composition and Regulation of the Respiratory Chain
Authors: Pade Nadin , Kï¿½cher Saskia , Roeï¿½ler Markus , Hï¿½nelt Inga , Mï¿½ller Volker 
Published: April 2013

ABSTRACT

In their natural environments, moderately halophilic bacteria are confronted not only with high salinities but also with low oxygen tensions due to the high salinities. The growth of
H. halophilus
is strictly aerobic. To analyze the dependence of respiration on the NaCl concentration and oxygen availability of the medium, resting cell experiments were performed. The respiration rates were dependent on the NaCl concentration of the growth medium, as well as on the NaCl concentration of the assay buffer, indicating regulation on the transcriptional and the activity level. Respiration was accompanied by the generation of an electrochemical proton potential (Δμ̃

H
+

) across the cytoplasmic membrane whose magnitude was dependent on the external pH. Genes encoding proteins involved in respiration and Δμ̃

H
+

generation, such as a noncoupled NADH dehydrogenase (NDH-2), complex II, and complex III, were identified in the genome. In addition, genes encoding five different terminal oxidases are present. Inhibitor profiling revealed the presence of NDH-2 and complex III, but the nature of the oxidases could not be resolved using this approach. Expression analysis demonstrated that all the different terminal oxidases were indeed expressed, but by far the most prominent was
cta
, encoding cytochrome
caa
3
oxidase. The expression of all of the different oxidase genes increased at high NaCl concentrations, and the transcript levels of
cta
and
qox
(encoding cytochrome
aa
3
oxidase) also increased at low oxygen concentrations. These data culminate in a model of the composition and variation of the respiratory chain of
H. halophilus
.
ω-Transaminase from Ochrobactrum anthropi Is Devoid of Substrate and Product Inhibitions
Authors: Park Eul-Soo , Shin Jong-Shik 
Published: April 2013

ABSTRACT

ω-Transaminases display complicated inhibitions by ketone products and both enantiomers of amine substrates. Here, we report the first example of ω-transaminase devoid of such inhibitions. Owing to the lack of enzyme inhibitions, the ω-transaminase from
Ochrobactrum anthropi
enabled efficient kinetic resolution of α-methylbenzylamine (500 mM) even without product removal.
Leucoagaricus gongylophorus Produces Diverse Enzymes for the Degradation of Recalcitrant Plant Polymers in Leaf-Cutter Ant Fungus Gardens
Authors: Aylward Frank O. , Burnum-Johnson Kristin E. , Tringe Susannah G. , Teiling Clotilde , Tremmel Daniel M. , Moeller Joseph A. , Scott Jarrod J. , Barry Kerrie W. , Piehowski Paul D. , Nicora Carrie D. , Malfatti Stephanie A. , Monroe Matthew E. , Purvine Samuel O. , Goodwin Lynne A. , Smith Richard D. , Weinstock George M. , Gerardo Nicole M. , Suen Garret , Lipton Mary S. , Currie Cameron R. 
Published: April 2013

ABSTRACT

Plants represent a large reservoir of organic carbon comprised primarily of recalcitrant polymers that most metazoans are unable to deconstruct. Many herbivores gain access to nutrients in this material indirectly by associating with microbial symbionts, and leaf-cutter ants are a paradigmatic example. These ants use fresh foliar biomass as manure to cultivate gardens composed primarily of
Leucoagaricus gongylophorus
, a basidiomycetous fungus that produces specialized hyphal swellings that serve as a food source for the host ant colony. Although leaf-cutter ants are conspicuous herbivores that contribute substantially to carbon turnover in Neotropical ecosystems, the process through which plant biomass is degraded in their fungus gardens is not well understood. Here we present the first draft genome of
L. gongylophorus
, and, using genomic and metaproteomic tools, we investigate its role in lignocellulose degradation in the gardens of both
Atta cephalotes
and
Acromyrmex echinatior
leaf-cutter ants. We show that
L. gongylophorus
produces a diversity of lignocellulases in ant gardens and is likely the primary driver of plant biomass degradation in these ecosystems. We also show that this fungus produces distinct sets of lignocellulases throughout the different stages of biomass degradation, including numerous cellulases and laccases that likely play an important role in lignocellulose degradation. Our study provides a detailed analysis of plant biomass degradation in leaf-cutter ant fungus gardens and insight into the enzymes underlying the symbiosis between these dominant herbivores and their obligate fungal cultivar.
Molecular Detection of Campylobacter spp. and Fecal Indicator Bacteria during the Northern Migration of Sandhill Cranes (Grus canadensis) at the Central Platte River
Authors: Lu Jingrang , Ryu Hodon , Vogel Jason , Santo Domingo Jorge , Ashbolt Nicholas J. 
Published: April 2013

ABSTRACT

The risk to human health of the annual sandhill crane (
Grus canadensis
) migration through Nebraska, which is thought to be a major source of fecal pollution of the central Platte River, is unknown. To better understand potential risks, the presence of
Campylobacter
species and three fecal indicator bacterial groups (
Enterococcus
spp.,
Escherichia coli
, and
Bacteroidetes
) was assayed by PCR from crane excreta and water samples collected during their stopover at the Platte River, Nebraska, in 2010. Genus-specific PCR assays and sequence analyses identified
Campylobacter jejuni
as the predominant
Campylobacter
species in sandhill crane excreta.
Campylobacter
spp. were detected in 48% of crane excreta, 24% of water samples, and 11% of sediment samples. The estimated densities of
Enterococcus
spp. were highest in excreta samples (mean, 4.6 ï¿½ 10
8
cell equivalents [CE]/g), while water samples contained higher levels of
Bacteroidetes
(mean, 5.1 ï¿½ 10
5
CE/100 ml).
Enterococcus
spp.,
E. coli
, and
Campylobacter
spp. were significantly increased in river water and sediments during the crane migration period, with
Enterococcus
sp. densities (∼3.3 ï¿½ 10
5
CE/g) 2 to 4 orders of magnitude higher than those of
Bacteroidetes
(4.9 ï¿½ 10
3
CE/g),
E. coli
(2.2 ï¿½ 10
3
CE/g), and
Campylobacter
spp. (37 CE/g). Sequencing data for the 16S rRNA gene and
Campylobacter
species-specific PCR assays indicated that
C. jejuni
was the major
Campylobacter
species present in water, sediments, and crane excreta. Overall, migration appeared to result in a significant, but temporary, change in water quality in spring, when there may be a
C. jejuni
health hazard associated with water and crops visited by the migrating birds.
Cytochrome
b
5
Coexpression Increases Tetrahymena thermophila Δ6 Fatty Acid Desaturase Activity in Saccharomyces cerevisiae
Authors: Dahmen Jeremy L. , Olsen Rebecca , Fahy Deirdre , Wallis James G. , Browse John 
Published: April 2013

ABSTRACT

Very-long-chain polyunsaturated fatty acids such as arachidonic, eicosapentaenoic, and docosahexaenoic acids, are important to the physiology of many microorganisms and metazoans and are vital to human development and health. The production of these and related fatty acids depends on Δ6 desaturases, the final components of an electron transfer chain that introduces double bonds into 18-carbon fatty acid chains. When a Δ6 desaturase identified from the ciliated protist
Tetrahymena thermophila
was expressed in
Saccharomyces cerevisiae
cultures supplemented with the 18:2
Δ9,12
substrate, only 4% of the incorporated substrate was desaturated. Cytochrome
b
5
protein sequences identified from the genome of
T. thermophila
included one sequence with two conserved cytochrome
b
5
domains. Desaturation by the Δ6 enzyme increased as much as 10-fold when
T. thermophila
cytochrome
b
5
s were coexpressed with the desaturase. Coexpression of a cytochrome
b
5
from
Arabidopsis thaliana
with the Δ6 enzyme also increased desaturation. A split ubiquitin growth assay indicated that the strength of interaction between cytochrome
b
5
proteins and the desaturase plays a vital role in fatty acid desaturase activity, illustrating the importance of protein-protein interactions in this enzyme activity.
Crystal Structure and Mode of Helicase Binding of the C-Terminal Domain of Primase from Helicobacter pylori
Authors: Abdul Rehman Syed Arif , Verma Vijay , Mazumder Mohit , Dhar Suman K. , Gourinath S. 
Published: April 2013

ABSTRACTTo better understand the poor conservation of the helicase binding domain of primases (DnaGs) among the eubacteria, we determined the crystal structure of theHelicobacter pyloriDnaG C-terminal domain (HpDnaG-CTD) at 1.78 Å. The structure has a globular subdomain connected to a helical hairpin. Structural comparison has revealed that globular subdomains, despite the variation in number of helices, have broadly similar arrangements across the species, whereas helical hairpins show different orientations. Further, to study the helicase-primase interaction inH. pylori, a complex was modeled using theHpDnaG-CTD andHpDnaB-NTD (helicase) crystal structures using theBacillus stearothermophilusBstDnaB-BstDnaG-CTD (helicase-primase) complex structure as a template. By using this model, a nonconserved critical residue Phe534 on helicase binding interface of DnaG-CTD was identified. Mutation guided by molecular dynamics, biophysical, and biochemical studies validated our model. We further concluded that species-specific helicase-primase interactions are influenced by electrostatic surface potentials apart from the critical hydrophobic surface residues.
Structural Requirement in Clostridium perfringens Collagenase mRNA 5′ Leader Sequence for Translational Induction through Small RNA-mRNA Base Pairing
Authors: Obana Nozomu , Nomura Nobuhiko , Nakamura Kouji 
Published: April 2013

ABSTRACT

The Gram-positive anaerobic bacterium
Clostridium perfringens
is pathogenic to humans and animals, and the production of its toxins is strictly regulated during the exponential phase. We recently found that the 5′ leader sequence of the
colA
transcript encoding collagenase, which is a major toxin of this organism, is processed and stabilized in the presence of the small RNA VR-RNA. The primary
colA
5′-untranslated region (5′UTR) forms a long stem-loop structure containing an internal bulge and masks its own ribosomal binding site. Here we found that VR-RNA directly regulates
colA
expression through base pairing with
colA
mRNA
in vivo
. However, when the internal bulge structure was closed by point mutations in
colA
mRNA, translation ceased despite the presence of VR-RNA. In addition, a mutation disrupting the
colA
stem-loop structure induced mRNA processing and ColA-FLAG translational activation in the absence of VR-RNA, indicating that the stem-loop and internal bulge structure of the
colA
5′ leader sequence is important for regulation by VR-RNA. On the other hand, processing was required for maximal ColA expression but was not essential for VR-RNA-dependent
colA
regulation. Finally,
colA
processing and translational activation were induced at a high temperature without VR-RNA. These results suggest that inhibition of the
colA
5′ leader structure through base pairing is the primary role of VR-RNA in
colA
regulation and that the
colA
5′ leader structure is a possible thermosensor.
Analysis of Novel Iron-Regulated, Surface-Anchored Hemin-Binding Proteins in Corynebacterium diphtheriae
Authors: Allen Courtni E. , Burgos Jonathan M. , Schmitt Michael P. 
Published: April 2013

ABSTRACT

Corynebacterium diphtheriae
utilizes hemin and hemoglobin (Hb) as iron sources during growth in iron-depleted environments, and recent studies have shown that the surface-exposed HtaA protein binds both hemin and Hb and also contributes to the utilization of hemin iron. Conserved (CR) domains within HtaA and in the associated hemin-binding protein, HtaB, are required for the ability to bind hemin and Hb. In this study, we identified and characterized two novel genetic loci in
C. diphtheriae
that encode factors that bind hemin and Hb. Both genetic systems contain two-gene operons that are transcriptionally regulated by DtxR and iron. The gene products of these operons are ChtA-ChtB and ChtC-CirA (previously DIP0522-DIP0523). The
chtA
and
chtB
genes are carried on a putative composite transposon associated with
C. diphtheriae
isolates that dominated the diphtheria outbreak in the former Soviet Union in the 1990s. ChtA and ChtC each contain a single N-terminal CR domain and exhibit significant sequence similarity to each other but only limited similarity with HtaA. The
chtB
and
htaB
gene products exhibited a high level of sequence similarity throughout their sequences, and both proteins contain a single CR domain. Whole-cell binding studies as well as protease analysis indicated that all four of the proteins encoded by these two operons are surface exposed, which is consistent with the presence of a transmembrane segment in their C-terminal regions. ChtA, ChtB, and ChtC are able to bind hemin and Hb, with ChtA showing the highest affinity. Site-directed mutagenesis showed that specific tyrosine residues within the ChtA CR domain were critical for hemin and Hb binding. Hemin iron utilization assays using various
C. diphtheriae
mutants indicate that deletion of the
chtA-chtB
region and the
chtC
gene has no affect on the ability of
C. diphtheriae
to use hemin or Hb as iron sources; however, a
chtB htaB
double mutant exhibits a significant decrease in hemin iron use, indicating a role in hemin transport for HtaB and ChtB.
Unique Regulatory Mechanism of Sporulation and Enterotoxin Production in Clostridium perfringens
Authors: Ohtani Kaori , Hirakawa Hideki , Paredes-Sabja Daniel , Tashiro Kosuke , Kuhara Satoru , Sarker Mahfuzur R. , Shimizu Tohru 
Published: April 2013

ABSTRACT

Clostridium perfringens
causes gas gangrene and gastrointestinal (GI) diseases in humans. The most common cause of
C. perfringens
-associated food poisoning is the consumption of
C. perfringens
vegetative cells followed by sporulation and production of enterotoxin in the gut. Despite the importance of spore formation in
C. perfringens
pathogenesis, the details of the regulation of sporulation have not yet been defined fully. In this study, microarray and bioinformatic analyses identified a candidate gene (the RNA regulator
virX
) for the repression of genes encoding positive regulators (Spo0A and sigma factors) of
C. perfringens
sporulation. A
virX
mutant constructed in the food poisoning strain SM101 had a much higher sporulation efficiency than that of the wild type. The transcription of
sigE
,
sigF
, and
sigK
was strongly induced at 2.5 h of culture of the
virX
mutant. Moreover, the transcription of the enterotoxin gene was also strongly induced in the
virX
mutant. Western blotting confirmed that the levels of enterotoxin production were higher in the
virX
mutant than in the wild type. These observations indicated that the higher levels of sporulation and enterotoxin production in the
virX
mutant were specifically due to inactivation of the
virX
gene. Since
virX
homologues were not found in any
Bacillus
species but were present in other clostridial species, our findings identify further differences in the regulation of sporulation between
Bacillus
and certain
Clostridium
species. The
virX
RNA regulator plays a key role in the drastic shift in lifestyle of the anaerobic flesh eater
C. perfringens
between the vegetative state (for gas gangrene) and the sporulating state (for food poisoning).
Evidence that a Metabolic Microcompartment Contains and Recycles Private Cofactor Pools
Authors: Huseby Douglas L. , Roth John R. 
Published: April 2013

ABSTRACT

Microcompartments are loose protein cages that encapsulate enzymes for particular bacterial metabolic pathways. These structures are thought to retain and perhaps concentrate pools of small, uncharged intermediates that would otherwise diffuse from the cell. In
Salmonella enterica
, a microcompartment encloses enzymes for ethanolamine catabolism. The cage has been thought to retain the volatile intermediate acetaldehyde but allow diffusion of the much larger cofactors NAD and coenzyme A (CoA). Genetic tests support an alternative idea that the microcompartment contains and recycles private pools of the large cofactors NAD and CoA. Two central enzymes convert ethanolamine to acetaldehyde (EutBC) and then to acetyl-CoA (EutE). Two seemingly peripheral redundant enzymes encoded by the
eut
operon proved to be essential for ethanolamine utilization, when subjected to sufficiently stringent tests. These are EutD (acetyl-CoA to acetyl phosphate) and EutG (acetaldehyde to ethanol). Obligatory recycling of cofactors couples the three reactions and drives acetaldehyde consumption. Loss and toxic effects of acetaldehyde are minimized by accelerating its consumption. In a
eutD
mutant, acetyl-CoA cannot escape the compartment but is released by mutations that disrupt the structure. The model predicts that EutBC (ethanolamine-ammonia lyase) lies outside the compartment, using external coenzyme B
12
and injecting its product, acetaldehyde, into the lumen, where it is degraded by the EutE, EutD, and EutG enzymes using private pools of CoA and NAD. The compartment appears to allow free diffusion of the intermediates ethanol and acetyl-PO
4
but (to our great surprise) restricts diffusion of acetaldehyde.
Defining the Escherichia coli SecA Dimer Interface Residues through
In Vivo
Site-Specific Photo-Cross-Linking
Authors: Yu Dongmei , Wowor Andy J. , Cole James L. , Kendall Debra A. 
Published: April 2013

ABSTRACT

The motor protein SecA is a core component of the bacterial general secretory (Sec) pathway and is essential for cell viability. Despite evidence showing that SecA exists in a dynamic monomer-dimer equilibrium favoring the dimeric form in solution and in the cytoplasm, there is considerable debate as to the quaternary structural organization of the SecA dimer. Here, a site-directed photo-cross-linking technique was utilized to identify residues on the
Escherichia coli
SecA (
ec
SecA) dimer interface in the cytosol of intact cells. The feasibility of this method was demonstrated with residue Leu6, which is essential for
ec
SecA dimerization based on our analytical ultracentrifugation studies of SecA L6A and shown to form the cross-linked SecA dimer
in vivo
with
p
-benzoyl-phenylalanine (
p
Bpa) substituted at position 6. Subsequently, the amino terminus (residues 2 to 11) in the nucleotide binding domain (NBD), Phe263 in the preprotein binding domain (PBD), and Tyr794 and Arg805 in the intramolecular regulator of the ATPase 1 domain (IRA1) were identified to be involved in
ec
SecA dimerization. Furthermore, the incorporation of
p
Bpa at position 805 did not form a cross-linked dimer in the SecA Δ2-11 context, indicating the possibility that the amino terminus may directly contact Arg805 or that the deletion of residues 2 to 11 alters the topology of the naturally occurring
ec
SecA dimer.
Evolution of Pan-Genomes of Escherichia coli, Shigella spp., and Salmonella enterica
Authors: Gordienko Evgeny N. , Kazanov Marat D. , Gelfand Mikhail S. 
Published: April 2013

ABSTRACTMultiple sequencing of genomes belonging to a bacterial species allows one to analyze and compare statistics and dynamics of the gene complements of species, their pan-genomes. Here, we analyzed multiple genomes ofEscherichia coli,Shigellaspp., andSalmonella enterica. We demonstrate that the distribution of the number of genomes harboring a gene is well approximated by a sum of two power functions, describing frequent genes (present in many strains) and rare genes (present in few strains). The virtual absence ofShigella-specific genes not present inE. coligenomes confirms previous observations thatShigellais not an independent genus. While the pan-genome size is increasing with each new strain, the number of genes present in a fixed fraction of strains stabilizes quickly. For instance, slightly fewer than 4,000 genes are present in at least half of any group ofE. coligenomes. Comparison ofS. entericaandE. colipan-genomes revealed the existence of a common periphery, that is, genes present in some but not all strains of both species. Analysis of phylogenetic trees demonstrates that rare genes from the periphery likely evolve under horizontal transfer, whereas frequent periphery genes may have been inherited from the periphery genome of the common ancestor.
Prevention and management of chronic disease in Aboriginal and Islander Community Controlled Health Services in Queensland: a quality improvement study assessing change in selected clinical performance indicators over time in a cohort of services
Authors: Panaretto K S , Gardner K L , Button S , Carson A , Schibasaki R , Wason G , Baker D , Mein J , Dellit A , Lewis D , Wenitong M , Ring I 
Published: April 2013

ObjectiveTo evaluate clinical healthcare performance in Aboriginal Medical Services in Queensland and to consider future directions in supporting improvement through measurement, target setting and standards development.DesignLongitudinal study assessing baseline performance and improvements in service delivery, clinical care and selected outcomes against key performance indicators 2009–2010.Setting27 Aboriginal and Islander Community Controlled Health Services (AICCHSs) in Queensland, who are members of the Queensland Aboriginal and Islander Health Council (QAIHC).Participants22 AICCHS with medical clinics.InterventionImplementation and use of an electronic clinical information system that integrates with electronic health records supported by the QAIHC quality improvement programme—the Close the Gap Collaborative.Main outcome measuresProportion of patients with current recording of key healthcare activities and the prevalence of risk factors and chronic disease.ResultsAggregated performance was high on a number of key risk factors and healthcare activities including assessment of tobacco use and management of hypertension but low for others. Performance between services showed greatest variation for care planning and health check activity.ConclusionsData collected by the QAIHC health information system highlight the risk factor workload facing the AICCHS in Queensland, demonstrating the need for ongoing support and workforce planning. Development of targets and weighting models is necessary to enable robust between-service comparisons of performance, which has implications for health reform initiatives in Australia. The limited information available suggests that although performance on key activities in the AICCHS sector has potential for improvement in some areas, it is nonetheless at a higher level than for mainstream providers.ImplicationsThe work demonstrates the role that the Community Controlled sector can play in closing the gap in Aboriginal and Torres Strait Islander health outcomes by leading the use of clinical data to record and assess the quality of services and health outcome.