bluuebunny/crossref_metadata_2025_split huggingface dataset:
Downregulation of Mitochondrial Porin Inhibits Cell Growth and Alters Respiratory Phenotype in
Trypanosoma brucei
Authors: Singha Ujjal K. , Sharma Shvetank , Chaudhuri Minu 
Published: July 2009

ABSTRACT

Porin is the most abundant outer membrane (OM) protein of mitochondria. It forms the aqueous channel on the mitochondrial OM and mediates major metabolite flux between mitochondria and cytosol. Mitochondrial porin in
Trypanosoma brucei
, a unicellular parasitic protozoan and the causative agent of African trypanosomiasis, possesses a β-barrel structure similar to the bacterial OM porin OmpA.
T. brucei
porin (TbPorin) is present as a monomer as well as an oligomer on the mitochondrial OM, and its expression is developmentally regulated. In spite of its distinct structure, the TbPorin function is similar to those of other eukaryotic porins. TbPorin RNA interference (RNAi) reduced cell growth in both procyclic and bloodstream forms. The depletion of TbPorin decreased ATP production by inhibiting metabolite flux through the OM. Additionally, the level of trypanosome alternative oxidase (TAO) decreased, whereas the levels of cytochrome-dependent respiratory complexes III and IV increased in TbPorin-depleted mitochondria. Furthermore, the depletion of TbPorin reduced cellular respiration via TAO, which is not coupled with oxidative phosphorylation, but increased the capacity for cyanide-sensitive respiration. Together, these data reveal that TbPorin knockdown reduced the mitochondrial ATP level, which in turn increased the capacity of the cytochrome-dependent respiratory pathway (CP), in an attempt to compensate for the mitochondrial energy crisis. However, a simultaneous decrease in the substrate-level phosphorylation due to TbPorin RNAi caused growth inhibition in the procyclic form. We also found that the expressions of TAO and CP proteins are coordinately regulated in
T. brucei
according to mitochondrial energy demand.
Role for Chitin and Chitooligomers in the Capsular Architecture of
Cryptococcus neoformans
Authors: Fonseca Fernanda L. , Nimrichter Leonardo , Cordero Radames J. B. , Frases Susana , Rodrigues Jessica , Goldman David L. , Andruszkiewicz Ryszard , Milewski Sławomir , Travassos Luiz R. , Casadevall Arturo , Rodrigues Marcio L. 
Published: July 2009

ABSTRACT

Molecules composed of β-1,4-linked
N
-acetylglucosamine (GlcNAc) and deacetylated glucosamine units play key roles as surface constituents of the human pathogenic fungus
Cryptococcus neoformans
. GlcNAc is the monomeric unit of chitin and chitooligomers, which participate in the connection of capsular polysaccharides to the cryptococcal cell wall. In the present study, we evaluated the role of GlcNAc-containing structures in the assembly of the cryptococcal capsule. The in vivo expression of chitooligomers in
C. neoformans
varied depending on the infected tissue, as inferred from the differential reactivity of yeast forms to the wheat germ agglutinin (WGA) in infected brain and lungs of rats. Chromatographic and dynamic light-scattering analyses demonstrated that glucuronoxylomannan (GXM), the major cryptococcal capsular component, interacts with chitin and chitooligomers. When added to
C. neoformans
cultures, chitooligomers formed soluble complexes with GXM and interfered in capsular assembly, as manifested by aberrant capsules with defective connections with the cell wall and no reactivity with a monoclonal antibody to GXM. Cultivation of
C. neoformans
in the presence of an inhibitor of glucosamine 6-phosphate synthase resulted in altered expression of cell wall chitin. These cells formed capsules that were loosely connected to the cryptococcal wall and contained fibers with decreased diameters and altered monosaccharide composition. These results contribute to our understanding of the role played by chitin and chitooligosaccharides on the cryptococcal capsular structure, broadening the functional activities attributed to GlcNAc-containing structures in this biological system.
Genetic Analysis of Repair and Damage Tolerance Mechanisms for DNA-Protein Cross-Links in
Escherichia coli
Authors: Salem Amir M. H. , Nakano Toshiaki , Takuwa Minako , Matoba Nagisa , Tsuboi Tomohiro , Terato Hiroaki , Yamamoto Kazuo , Yamada Masami , Nohmi Takehiko , Ide Hiroshi 
Published: July 2009

ABSTRACT

DNA-protein cross-links (DPCs) are unique among DNA lesions in their unusually bulky nature. We have recently shown that nucleotide excision repair (NER) and RecBCD-dependent homologous recombination (HR) collaboratively alleviate the lethal effect of DPCs in
Escherichia coli
. In this study, to gain further insight into the damage-processing mechanism for DPCs, we assessed the sensitivities of a panel of repair-deficient
E. coli
mutants to DPC-inducing agents, including formaldehyde (FA) and 5-azacytidine (azaC). We show here that the damage tolerance mechanism involving HR and subsequent replication restart (RR) provides the most effective means of cell survival against DPCs. Translesion synthesis does not serve as an alternative damage tolerance mechanism for DPCs in cell survival. Elimination of DPCs from the genome relies primarily on NER, which provides a second and moderately effective means of cell survival against DPCs. Interestingly, Cho rather than UvrC seems to be an effective nuclease for the NER of DPCs. Together with the genes responsible for HR, RR, and NER, the mutation of genes involved in several aspects of DNA repair and transactions, such as
recQ
,
xth nfo
,
dksA
, and
topA
, rendered cells slightly but significantly sensitive to FA but not azaC, possibly reflecting the complexity of DPCs or cryptic lesions induced by FA. UvrD may have an additional role outside NER, since the
uvrD
mutation conferred a slight azaC sensitivity on cells. Finally, DNA glycosylases mitigate azaC toxicity, independently of the repair of DPCs, presumably by removing 5-azacytosine or its degradation product from the chromosome.
An Alternative Route for Recycling of
N
-Acetylglucosamine from Peptidoglycan Involves the
N
-Acetylglucosamine Phosphotransferase System in
Escherichia coli
Authors: Plumbridge Jacqueline 
Published: July 2009

ABSTRACT

A set of enzymes dedicated to recycling of the amino sugar components of peptidoglycan has previously been identified in
Escherichia coli
. The complete pathway includes the
nagA
-encoded enzyme,
N
-acetylglucosamine-6-phosphate (GlcNAc6P) deacetylase, of the catabolic pathway for use of
N
-acetylglucosamine (GlcNAc). Mutations in
nagA
result in accumulation of millimolar concentrations of GlcNAc6P, presumably by preventing peptidoglycan recycling. Mutations in the genes encoding the key enzymes upstream of
nagA
in the dedicated recycling pathway (
ampG
,
nagZ
,
nagK
,
murQ
, and
anmK
), which were expected to interrupt the recycling process, reduced but did not eliminate accumulation of GlcNAc6P. A mutation in the
nagE
gene of the GlcNAc phosphotransferase system (PTS) was found to reduce by 50% the amount of GlcNAc6P which accumulated in a
nagA
strain and, together with mutations in the dedicated recycling pathway, eliminated all the GlcNAc6P accumulation. This shows that the
n
agE
-encoded PTS transporter makes an important contribution to the recycling of peptidoglycan. The
manXYZ
-encoded PTS transporter makes a minor contribution to the formation of cytoplasmic GlcNAc6P but appears to have a more important role in secretion of GlcNAc and/or GlcNAc6P from the cytoplasm.
Processive Endoglucanases Mediate Degradation of Cellulose by
Saccharophagus degradans
Authors: Watson Brian J. , Zhang Haitao , Longmire Atkinson G. , Moon Young Hwan , Hutcheson Steven W. 
Published: July 2009

ABSTRACT

Bacteria and fungi are thought to degrade cellulose through the activity of either a complexed or a noncomplexed cellulolytic system composed of endoglucanases and cellobiohydrolases. The marine bacterium
Saccharophagus degradans
2-40 produces a multicomponent cellulolytic system that is unusual in its abundance of GH5-containing endoglucanases. Secreted enzymes of this bacterium release high levels of cellobiose from cellulosic materials. Through cloning and purification, the predicted biochemical activities of the one annotated cellobiohydrolase Cel6A and the GH5-containing endoglucanases were evaluated. Cel6A was shown to be a classic endoglucanase, but Cel5H showed significantly higher activity on several types of cellulose, was the highest expressed, and processively released cellobiose from cellulosic substrates. Cel5G, Cel5H, and Cel5J were found to be members of a separate phylogenetic clade and were all shown to be processive. The processive endoglucanases are functionally equivalent to the endoglucanases and cellobiohydrolases required for other cellulolytic systems, thus providing a cellobiohydrolase-independent mechanism for this bacterium to convert cellulose to glucose.
Genomic Insights into the Convergence and Pathogenicity Factors of
Campylobacter jejuni
and
Campylobacter coli
Species
Authors: Caro-Quintero Alejandro , Rodriguez-Castaño Gina P. , Konstantinidis Konstantinos T. 
Published: July 2009

ABSTRACT

Whether or not bacteria form coherent evolutionary groups via means of genetic exchange and, hence, elicit distinct species boundaries remains an unsettled issue. A recent report implied that not only may the former be true but also, in fact, the clearly distinct
Campylobacter jejuni
and
Campylobacter coli
species may be converging as a consequence of increased interspecies gene flow fostered, presumably, by the recent invasion of an overlapping ecological niche (S. K. Sheppard, N. D. McCarthy, D. Falush, and M. C. Maiden, Science 320:237-239, 2008). We have reanalyzed the
Campylobacter
multilocus sequence typing database used in the previous study and found that the number of interspecies gene transfer events may actually be too infrequent to account, unequivocally, for species convergence. For instance, only 1 to 2% of the 4,507
Campylobacter
isolates examined appeared to have imported gene alleles from another
Campylobacter
species. Furthermore, by analyzing the available
Campylobacter
genomic sequences, we show that although there seems to be a slightly higher number of exchanged genes between
C. jejuni
and
C. coli
relative to other comparable species (∼10% versus 2 to 3% of the total genes in the genome, respectively), the function and spatial distribution in the genome of the exchanged genes are far from random, and hence, inconsistent with the species convergence hypothesis. In fact, the exchanged genes appear to be limited to a few environmentally selected cellular functions. Accordingly, these genes may represent important pathogenic determinants of pathogenic
Campylobacter
, and convergence of (any) two bacterial species remains to be seen.
Crystal Structures of
Streptococcus suis
Mannonate Dehydratase (ManD) and Its Complex with Substrate: Genetic and Biochemical Evidence for a Catalytic Mechanism
Authors: Zhang Qiangmin , Gao Feng , Peng Hao , Cheng Hao , Liu Yiwei , Tang Jiaqi , Thompson John , Wei Guohua , Zhang Jingren , Du Yuguo , Yan Jinghua , Gao George F. 
Published: July 2009

ABSTRACT

Mannonate dehydratase (ManD) is found only in certain bacterial species, where it participates in the dissimilation of glucuronate. ManD catalyzes the dehydration of
d
-mannonate to yield 2-keto-3-deoxygluconate (2-KDG), the carbon and energy source for growth. Selective inactivation of ManD by drug targeting is of therapeutic interest in the treatment of human
Streptococcus suis
infections. Here, we report the overexpression, purification, functional characterization, and crystallographic structure of ManD from
S. suis
. Importantly, by Fourier transform mass spectrometry, we show that 2-KDG is formed when the chemically synthesized substrate (
d
-mannonate) is incubated with ManD. Inductively coupled plasma-mass spectrometry revealed the presence of Mn
2+
in the purified protein, and in the solution state catalytically active ManD exists as a homodimer of two 41-kDa subunits. The crystal structures of
S. suis
ManD in native form and in complex with its substrate and Mn
2+
ion have been solved at a resolution of 2.9 Å. The core structure of
S. suis
ManD is a TIM barrel similar to that of other members of the xylose isomerase-like superfamily. Structural analyses and comparative amino acid sequence alignments provide evidence for the importance of His311 and Tyr325 in ManD activity. The results of site-directed mutagenesis confirmed the functional role(s) of these residues in the dehydration reaction and a plausible mechanism for the ManD-catalyzed reaction is proposed.
Paenibacillus dendritiformis
Bacterial Colony Growth Depends on Surfactant but Not on Bacterial Motion
Authors: Be'er Avraham , Smith Rachel S. , Zhang H. P. , Florin E.-L. , Payne Shelley M. , Swinney Harry L. 
Published: July 2009

ABSTRACT

Most research on growing bacterial colonies on agar plates has concerned the effect of genetic or morphotype variation. Some studies have indicated that there is a correlation between microscopic bacterial motion and macroscopic colonial expansion, especially for swarming strains, but no measurements have been obtained for a single strain to relate the microscopic scale to the macroscopic scale. We examined here a single strain (
Paenibacillus dendritiformis
type
T
; tip splitting) to determine both the macroscopic growth of colonies and the microscopic bacterial motion within the colonies. Our multiscale measurements for a variety of growth conditions revealed that motion on the microscopic scale and colonial growth are largely independent. Instead, the growth of the colony is strongly affected by the availability of a surfactant that reduces surface tension.
Region of Difference 1 in Nontuberculous
Mycobacterium
Species Adds a Phylogenetic and Taxonomical Character
Authors: van Ingen Jakko , de Zwaan Rina , Dekhuijzen Richard , Boeree Martin , van Soolingen Dick 
Published: July 2009

ABSTRACT

The
esat-6
and
cfp-10
genes are essential for virulence in
Mycobacterium tuberculosis
. Among nontuberculous mycobacteria, we found these genes only in
M. kansasii
,
M. szulgai
,
M. marinum
, and
M. riyadhense
, with unique sequences. This adds a phylogenetic and taxonomical characteristic and may represent a virulence factor for nontuberculous mycobacteria.
DNA Binding Proteins of the Filamentous Phages CTXφ and VGJφ of V
ibrio cholerae
Authors: Falero Alina , Caballero Andy , Ferrán Beatriz , Izquierdo Yovanny , Fando Rafael , Campos Javier 
Published: July 2009

ABSTRACT

The native product of open reading frame 112 (
orf112
) and a recombinant variant of the RstB protein, encoded by
Vibrio cholerae
pathogen-specific bacteriophages VGJφ and CTXφ, respectively, were purified to more than 90% homogeneity. Orf112 protein was shown to specifically bind single-stranded genomic DNA of VGJφ; however, RstB protein unexpectedly bound double-stranded DNA in addition to the single-stranded genomic DNA. The DNA binding properties of these proteins may explain their requirement for the rolling circle replication of the respective phages and RstB's requirement for single-stranded-DNA chromosomal integration of CTXφ phage dependent on XerCD recombinases.
Cellular Localization of Predicted Transmembrane and Soluble Chemoreceptors in
Sinorhizobium meliloti
Authors: Meier Veronika M. , Scharf Birgit E. 
Published: July 2009

ABSTRACT

Bacterial chemoreceptors primarily locate in clusters at the cell pole, where they form large sensory complexes which recruit cytoplasmic components of the signaling pathway. The genome of the soil bacterium
Sinorhizobium meliloti
encodes seven transmembrane and two soluble chemoreceptors. We have investigated the localization of all nine chemoreceptors in vivo using genome-encoded fusions to a variant of the enhanced green fluorescent protein and to monomeric red fluorescent protein. Six of the transmembrane (McpT to McpX and McpZ) and both soluble (McpY and IcpA) receptors localize to the cell pole. Only McpS, encoded from the symbiotic plasmid pSymA, is evenly distributed in the cell. While the synthesis of all polar localized receptors is confined to exponential growth correlating with the motility phase of cells, McpS is only weakly expressed throughout cell culture growth. Therefore, motile
S. meliloti
cells form one major chemotaxis cluster that harbors all chemoreceptors except for McpS. Colocalization and deletion analysis demonstrated that formation of polar foci by the majority of receptors is dependent on other chemoreceptors and that receptor clusters are stabilized by the presence of the chemotaxis proteins CheA and CheW. The transmembrane McpV and the soluble IcpA localize to the pole independently of CheA and CheW. However, in mutant strains McpV formed delocalized polar caps that spread throughout the cell membrane while IcpA exhibited increased bipolarity. Immunoblotting of fractionated cells revealed that IcpA, which lacks any hydrophobic domains, nevertheless is associated to the cell membrane.
Identification and Characterization of Growth Suppressors ofEscherichia coliStrains Lacking Phosphorolytic Ribonucleases
Authors: Jain Chaitanya 
Published: July 2009

ABSTRACTRNases are involved in critical aspects of RNA metabolism in all organisms. Two classes of RNases that digest RNA from an end (exo-RNases) are known: RNases that use water as a nucleophile to catalyze RNA degradation (hydrolytic RNases) and RNases that use inorganic phosphate (phosphorolytic RNases). It has been shown previously that the absence of the two knownEscherichia coliphosphorolytic RNases, polynucleotide phosphorylase and RNase PH, leads to marked growth and ribosome assembly defects. To investigate the basis for these defects, a screen for growth suppressors was performed. The majority of suppressor mutations were found to lie withinnsrR, which encodes a nitric oxide (NO)-sensitive transcriptional repressor. Further analysis showed that the suppressors function not by inactivatingnsrRbut by causing overexpression of a downstream gene that encodes a hydrolytic RNase, RNase R. Additional studies revealed that overexpression of another hydrolytic RNase, RNase II, similarly suppressed the growth defects. These results suggest that the requirement for phosphorolytic RNases for robust cellular growth and efficient ribosome assembly can be bypassed by increased expression of hydrolytic RNases.
Effect of taping on the shoulders of Australian football players
Authors: Bradley T , Baldwick C , Fischer D , Murrell G A C 
Published: July 2009

Background:Taping of the shoulder is common in many sports, particularly Australian football, a contact sport that often involves marking (catching) the ball overhead and has a high incidence of shoulder instability.Hypothesis:Taping of the shoulder reduces glenohumeral joint laxity and improves proprioception without impairing function.Study design:Crossover study design.Methods:33 male players aged 18–31 years were recruited from a local Australian football club. The dominant shoulder of each player was tested with and without taping in a randomised fashion by an examiner blinded to the presence or absence of taping. The tests were (1) inferior glenohumeral joint laxity (the Orthopaedic Research Institute laxometer), (2) shoulder joint position sense accuracy using an optical tracking system, and (3) handballing accuracy.Results:The methods for testing laxity and joint position sense had good intraobserver reliability and sensitivity. All subjects tolerated the taping and testing. Glenohumeral joint laxity (p = 0.75), joint position sense (p = 0.56) and handballing accuracy (p = 0.6) were not changed by taping.Conclusions:Taping of the shoulder joint in uninjured and non-symptomatic Australian football players in a pattern that attempted not to restrict their range of overhead movement did not significantly affect the accuracy of joint position sense, inferior laxity or handball accuracy.Clinical relevance:These data suggest that taping of the shoulder is unlikely to decrease the incidence of injury—specifically dislocation—of the shoulder in Australian football players.
The effect of smoke-free policies on revenue in bars in Tasmania, Australia
Authors: Lal A , Siahpush M 
Published: July 2009

Objective:To examine the impact of smoke-free policies on revenue in Tasmanian bars.Method:Monthly sales turnover from January 2002 to March 2007, provided by the Australian Bureau of Statistics was analysed. There were two outcome measures: (1) the ratio of monthly bar sales turnover in Tasmania to monthly bar sales turnover in four other Australian states, and (2) the ratio of monthly bar turnover to monthly retail turnover in Tasmania. Linear regression was used to assess the impact of the smoke-free policy on expenditure.Results:The smoke-free policy had no effect on sales turnover.Conclusion:The smoke-free policy protects hospitality workers and patrons from exposure to secondhand smoke and has had no adverse effect on sales turnover.
The hazards and benefits associated with smoking and smoking cessation in Asia: a meta-analysis of prospective studies
Authors: Nakamura K , Huxley R , Ansary-Moghaddam A , Woodward M 
Published: July 2009

Objective:To provide the most reliable evidence as to the nature of the associations between smoking and cause-specific illness, as well as the expected benefits from quitting smoking, in studies conducted in Asia, where smoking remains popular among men.Data sources:Studies published between January 1966 and October 2008, identified in the Medline search strategy with medical subject headings, in addition to studies from the Asia Pacific Cohort Studies Collaboration.Study selection:Studies were considered to be relevant if they were prospective studies, in an Asian setting that reported on the association between smoking, quitting and cause-specific illness.Data extraction:Two reviewers independently screened all identified articles for possible inclusion and extracted data.Data synthesis:The pooled relative risks (RRs) for incidence or mortality, comparing current to never smokers were always significantly higher than unity; the highest was for lung cancer: 3.54 (95% confidence interval 3.00 to 4.17). The pooled RRs for former smokers (compared to never smokers) were also always significantly higher than unity, and were lower than in current smokers, for coronary heart disease, stroke, lung and upper aero-digestive tract cancer. Only for respiratory disease was the RR for former smokers higher than that for current smokers.Conclusions:This meta-analysis has shown that, despite the relative immaturity of the smoking epidemic in Asia, smoking is unquestionably a major contributor to ill health and death. However, the beneficial effects of quitting are not yet always apparent, most probably because quitting is a consequence of ill health and the relative unpopularity of smoking cessation in many Asian populations.