bluuebunny/crossref_metadata_2025_split huggingface dataset:
Functional Characterization and Localization of
Pneumocystis carinii
Lanosterol Synthase
Authors: Joffrion Tiffany M. , Collins Margaret S. , Sesterhenn Thomas , Cushion Melanie T. 
Published: November 2009

ABSTRACT

Organisms in the genus
Pneumocystis
are ubiquitous, opportunistic pathogenic fungi capable of causing a lethal pneumonia in immunocompromised mammalian hosts.
Pneumocystis
spp. are unique members of the fungal kingdom due to the absence of ergosterol in their cellular membranes. Although these organisms were thought to obtain cholesterol by scavenging, transcriptional analyses indicate that
Pneumocystis carinii
encodes gene homologs involved in sterol biosynthesis. To better understand the sterol pathway in these uncultivable fungi, yeast deletion strains were used to interrogate the function and localization of
P. carinii
lanosterol synthase (
ERG7
). The expression of PcErg7p in an
ERG7
-null mutant of the yeast
Saccharomyces cerevisiae
did not alter its growth rate and produced a functional lanosterol synthase, as evidenced by the presence of lanosterol detected by gas chromatographic analysis in levels comparable to that produced by the yeast enzyme. Western blotting and fluorescence microscopy revealed that, like the
S. cerevisiae
Erg7p, the PcErg7p localized to lipid particles in yeast. Using fluorescence microscopy, we show for the first time the presence of apparent lipid particles in
P. carinii
and the localization of PcErg7p to lipid particles in
P. carinii
. The detection of lipid particles in
P. carinii
and their association with PcErg7p therein provide strong evidence that the enzyme serves a similar function in
P. carinii
. Moreover, the yeast heterologous system should be a useful tool for further analysis of the
P. carinii
sterol pathway.
Differential Roles of the Glycogen-Binding Domains of β Subunits in Regulation of the Snf1 Kinase Complex
Authors: Mangat Simmanjeet , Chandrashekarappa Dakshayini , McCartney Rhonda R. , Elbing Karin , Schmidt Martin C. 
Published: November 2009

ABSTRACT

Members of the AMP-activated protein kinase family, including the Snf1 kinase of
Saccharomyces cerevisiae
, are activated under conditions of nutrient stress. AMP-activated protein kinases are heterotrimeric complexes composed of a catalytic α subunit and regulatory β and γ subunits. In this study, the role of the β subunits in the regulation of Snf1 activity was examined. Yeasts express three isoforms of the AMP-activated protein kinase consisting of Snf1 (α), Snf4 (γ), and one of three alternative β subunits, either Sip1, Sip2, or Gal83. The Gal83 isoform of the Snf1 complex is the most abundant and was analyzed in the greatest detail. All three β subunits contain a conserved domain referred to as the glycogen-binding domain. The deletion of this domain from Gal83 results in a deregulation of the Snf1 kinase, as judged by a constitutive activity independent of glucose availability. In contrast, the deletion of this homologous domain from the Sip1 and Sip2 subunits had little effect on Snf1 kinase regulation. Therefore, the different Snf1 kinase isoforms are regulated through distinct mechanisms, which may contribute to their specialized roles in different stress response pathways. In addition, the β subunits are subjected to phosphorylation. The responsible kinases were identified as being Snf1 and casein kinase II. The significance of the phosphorylation is unclear since the deletion of the region containing the phosphorylation sites in Gal83 had little effect on the regulation of Snf1 in response to glucose limitation.
Identification and Characterization of EctR1, a New Transcriptional Regulator of the Ectoine Biosynthesis Genes in the Halotolerant Methanotroph
Methylomicrobium alcaliphilum
20Z
Authors: Mustakhimov Ildar I. , Reshetnikov Alexander S. , Glukhov Anatoly S. , Khmelenina Valentina N. , Kalyuzhnaya Marina G. , Trotsenko Yuri A. 
Published: November 2009

ABSTRACT

Genes encoding key enzymes of the ectoine biosynthesis pathway in the halotolerant obligate methanotroph
Methylomicrobium alcaliphilum
20Z have been shown to be organized into an
ectABC
-
ask
operon. Transcription of the
ect
operon is initiated from two promoters,
ectAp
1
and
ectAp
2
(
ectAp
1
p
2
), similar to the σ
70
-dependent promoters of
Escherichia coli
. Upstream of the gene cluster, an open reading frame (
ectR1
) encoding a MarR-like transcriptional regulator was identified. Investigation of the influence of EctR1 on the activity of the
ectAp
1
p
2
promoters in wild-type
M. alcaliphilum
20Z and
ectR1
mutant strains suggested that EctR1 is a negative regulator of the
ectABC
-
ask
operon. Purified recombinant EctR1-His
6
specifically binds as a homodimer to the putative −10 motif of the
ectAp
1
promoter. The EctR1 binding site contains a pseudopalindromic sequence (TATTTAGT-GT-ACTATATA) composed of 8-bp half-sites separated by 2 bp. Transcription of the
ectR1
gene is initiated from a single σ
70
-like promoter. The location of the EctR1 binding site between the transcriptional and translational start sites of the
ectR1
gene suggests that EctR1 may regulate its own expression. The data presented suggest that in
Methylomicrobium alcaliphilum
20Z, EctR1-mediated control of the transcription of the
ect
genes is not the single mechanism for the regulation of ectoine biosynthesis.
The Mtr Respiratory Pathway Is Essential for Reducing Flavins and Electrodes inShewanella oneidensis
Authors: Coursolle Dan , Baron Daniel B. , Bond Daniel R. , Gralnick Jeffrey A. 
Published: November 2009

ABSTRACTThe Mtr respiratory pathway ofShewanella oneidensisstrain MR-1 is required to effectively respire both soluble and insoluble forms of oxidized iron. Flavins (riboflavin and flavin mononucleotide) recently have been shown to be excreted by MR-1 and facilitate the reduction of insoluble substrates. OtherShewanellaspecies tested accumulated flavins in supernatants to an extent similar to that of MR-1, suggesting that flavin secretion is a general trait of the species. External flavins have been proposed to act as both a soluble electron shuttle and a metal chelator; however, at biologically relevant concentrations, our results suggest that external flavins primarily act as electron shuttles for MR-1. Using deletion mutants lacking various Mtr-associated proteins, we demonstrate that the Mtr extracellular respiratory pathway is essential for the reduction of flavins and that decaheme cytochromes found on the outer surface of the cell (MtrC and OmcA) are required for the majority of this activity. Given the involvement of external flavins in the reduction of electrodes, we monitored current production by Mtr respiratory pathway mutants in three-electrode bioreactors under controlled flavin concentrations. While mutants lacking MtrC were able to reduce flavins at 50% of the rate of the wild type in cell suspension assays, these strains were unable to grow into productive electrode-reducing biofilms. The analysis of mutants lacking OmcA suggests a role for this protein in both electron transfer to electrodes and attachment to surfaces. The parallel phenotypes of Mtr mutants in flavin and electrode reduction blur the distinction between direct contact and the redox shuttling strategies of insoluble substrate reduction by MR-1.
Biochemical and Domain Analyses of FSUAxe6B, a Modular Acetyl Xylan Esterase, Identify a Unique Carbohydrate Binding Module in
Fibrobacter succinogenes
S85
Authors: Yoshida Shosuke , Mackie Roderick I. , Cann Isaac K. O. 
Published: November 2009

ABSTRACT

Acetyl xylan esterase (EC 3.1.1.72) is a member of a set of enzymes required to depolymerize hemicellulose, especially xylan that is composed of a main chain of β-1,4-linked xylopyranoside residues decorated with acetyl side groups.
Fibrobacter succinogenes
S85 Axe6B (FSUAxe6B) is an acetyl xylan esterase encoded in the genome of this rumen bacterium. The enzyme is a modular protein comprised of an esterase domain, a carbohydrate-binding module, and a region of unknown function. Sequences that are homologous to the region of unknown function are paralogously distributed, thus far, only in
F. succinogenes
. Therefore, the sequences were designated
Fibrobacter succinogenes
-specific paralogous module 1 (FPm-1). The FPm-1s are associated with at least 24 polypeptides in the genome of
F. succinogenes
S85. A bioinformatics search showed that most of the FPm-1-appended polypeptides are putative carbohydrate-active enzymes, suggesting a potential role in carbohydrate metabolism. Truncational analysis of FSUAxe6B, together with catalytic and substrate binding studies, has allowed us to delineate the functional modules in the polypeptide. The N-terminal half of FSUAxe6B harbors the activity that cleaves side chain acetyl groups from xylan-like substrates, and the binding of insoluble xylan was determined to originate from FPm-1. Site-directed mutagenesis studies of highly conserved active-site residues in the esterase domain suggested that the esterase activity is derived from a tetrad composed of Ser
44
, His
273
, Glu
194
, and Asp
270
, with both Glu
194
and Asp
270
functioning as helper acids, instead of a single carboxylate residue proposed to initiate catalysis.
Identification of Enhancer Binding Proteins Important for
Myxococcus xanthus
Development
Authors: Giglio Krista M. , Eisenstatt Jessica , Garza Anthony G. 
Published: November 2009

ABSTRACT

Enhancer binding proteins (EBPs) control the temporal expression of fruiting body development-associated genes in
Myxococcus xanthus
. Eleven previously uncharacterized EBP genes were inactivated. Six EBP gene mutations produced minor but reproducible defects in fruiting body development. One EBP gene mutation that affected A-motility produced strong developmental defects.
Identification and Characterization of a Novel Member of the Radical AdoMet Enzyme Superfamily and Implications for the Biosynthesis of the Hmd Hydrogenase Active Site Cofactor
Authors: McGlynn Shawn E. , Boyd Eric S. , Shepard Eric M. , Lange Rachel K. , Gerlach Robin , Broderick Joan B. , Peters John W. 
Published: November 2009

ABSTRACT

The genetic context, phylogeny, and biochemistry of a gene flanking the H
2
-forming methylene-H
4
-methanopterin dehydrogenase gene (
hmdA
), here designated
hmdB
, indicate that it is a new member of the radical
S
-adenosylmethionine enzyme superfamily. In contrast to the characteristic CX
3
CX
2
C or CX
2
CX
4
C motif defining this family, HmdB contains a unique CX
5
CX
2
C motif.
The
Citrobacter rodentium
Genome Sequence Reveals Convergent Evolution with Human Pathogenic
Escherichia coli
Authors: Petty Nicola K. , Bulgin Richard , Crepin Valerie F. , Cerdeño-Tárraga Ana M. , Schroeder Gunnar N. , Quail Michael A. , Lennard Nicola , Corton Craig , Barron Andrew , Clark Louise , Toribio Ana L. , Parkhill Julian , Dougan Gordon , Frankel Gad , Thomson Nicholas R. 
Published: November 2009

ABSTRACT

Citrobacter rodentium
(formally
C
itrobacter
freundii
biotype 4280) is a highly infectious pathogen that causes colitis and transmissible colonic hyperplasia in mice. In common with enteropathogenic and enterohemorrhagic
Escherichia coli
(EPEC and EHEC, respectively),
C. rodentium
exploits a type III secretion system (T3SS) to induce attaching and effacing (A/E) lesions that are essential for virulence. Here, we report the fully annotated genome sequence of the 5.3-Mb chromosome and four plasmids harbored by
C. rodentium
strain ICC168. The genome sequence revealed key information about the phylogeny of
C. rodentium
and identified 1,585
C. rodentium
-specific (without orthologues in EPEC or EHEC) coding sequences, 10 prophage-like regions, and 17 genomic islands, including the locus for enterocyte effacement (LEE) region, which encodes a T3SS and effector proteins. Among the 29 T3SS effectors found in
C. rodentium
are all 22 of the core effectors of EPEC strain E2348/69. In addition, we identified a novel
C. rodentium
effector, named EspS.
C. rodentium
harbors two type VI secretion systems (T6SS) (CTS1 and CTS2), while EHEC contains only one T6SS (EHS). Our analysis suggests that
C. rodentium
and EPEC/EHEC have converged on a common host infection strategy through access to a common pool of mobile DNA and that
C. rodentium
has lost gene functions associated with a previous pathogenic niche.
rRNA Mutations That Inhibit Transfer-Messenger RNA Activity on Stalled Ribosomes
Authors: Crandall Jacob , Rodriguez-Lopez Milagros , Pfeiffer Michael , Mortensen Bailey , Buskirk Allen 
Published: November 2009

ABSTRACTIn eubacteria, stalled ribosomes are rescued by a conserved quality-control mechanism involving transfer-messenger RNA (tmRNA) and its protein partner, SmpB. Mimicking a tRNA, tmRNA enters stalled ribosomes, adds Ala to the nascent polypeptide, and serves as a template to encode a short peptide that tags the nascent protein for destruction. To further characterize the tagging process, we developed two genetic selections that link tmRNA activity to cell death. These negative selections can be used to identify inhibitors of tagging or to identify mutations in key residues essential for ribosome rescue. Little is known about which ribosomal elements are specifically required for tmRNA activity. Using these selections, we isolated rRNA mutations that block the rescue of ribosomes stalled at rare Arg codons or at the inefficient termination signal Pro-opal. We found that deletion of A1150 in the 16S rRNA blocked tagging regardless of the stalling sequence, suggesting that it inhibits tmRNA activity directly. The C889U mutation in 23S rRNA, however, lowered tagging levels at Pro-opal and rare Arg codons, but not at the 3′ end of an mRNA lacking a stop codon. We concluded that the C889U mutation does not inhibit tmRNA activityper sebut interferes with an upstream step intermediate between stalling and tagging. C889 is found in the A-site finger, where it interacts with the S13 protein in the small subunit (forming intersubunit bridge B1a).
Short-Term Signatures of Evolutionary Change in the
Salmonella enterica
Serovar Typhimurium 14028 Genome
Authors: Jarvik Tyler , Smillie Chris , Groisman Eduardo A. , Ochman Howard 
Published: November 2009

ABSTRACT

Salmonella enterica
serovar Typhimurium is a Gram-negative pathogen that causes gastroenteritis in humans and a typhoid-like disease in mice and is often used as a model for the disease promoted by the human-adapted
S. enterica
serovar Typhi. Despite its health importance, the only
S.
Typhimurium strain for which the complete genomic sequence has been determined is the avirulent LT2 strain, which is extensively used in genetic and physiologic studies. Here, we report the complete genomic sequence of the
S.
Typhimurium strain 14028s, as well as those of its progenitor and two additional derivatives. Comparison of these
S.
Typhimurium genomes revealed differences in the patterns of sequence evolution and the complete inventory of genetic alterations incurred in virulent and avirulent strains, as well as the sequence changes accumulated during laboratory passage of pathogenic organisms.
The N-Terminal Transmembrane Domain of λ S Is Required for Holin but Not Antiholin Function
Authors: White Rebecca , Tran Tram Anh T. , Dankenbring Chelsey A. , Deaton John , Young Ry 
Published: November 2009

ABSTRACT

The λ
S
gene encodes a holin, S105, and an antiholin, S107, which differs by its Met-Lys N-terminal extension. The model for the lysis-defective character of S107 stipulates that the additional N-terminal basic residue keeps S107 from assuming the topology of S105, which is N-out, C-in, with three transmembrane domains (TMDs). Here we show that the N terminus of S105 retains its fMet residue but that the N terminus of S107 is fully deformylated. This supports the model that in S105, TMD1 inserts into the membrane very rapidly but that in S107, it is retained in the cytoplasm. Further, it reveals that, compared to S105, S107 has two extra positively charged moieties, Lys2 and the free N-terminal amino group, to hinder its penetration into an energized membrane. Moreover, an allele,

S105
ΔTMD1

, with TMD1 deleted, was found to be defective in lysis, insensitive to membrane depolarization, and dominant to the wild-type allele, indicating that the lysis-defective, antiholin character of S107 is due to the absence of TMD1 from the bilayer rather than to its ectopic localization at the inner face of the cytoplasmic membrane. Finally, the antiholin function of the deletion protein was compromised by the substitution of early-lysis missense mutations in either the deletion protein or parental S105 but restored when both S105
ΔTMD1
and holin carried the substitution.
Bistable Expression of CsgD in Biofilm Development ofSalmonella entericaSerovar Typhimurium
Authors: Grantcharova Nina , Peters Verena , Monteiro Claudia , Zakikhany Katherina , Römling Ute 
Published: November 2009

ABSTRACTBacterial persistence in the environment and in the infected host is often aided by the formation of exopolymer-enclosed communities known as biofilms. Heterogeneous gene expression takes place in microcompartments formed within the complex biofilm structure. This study describes cell differentiation within an isogenic bacterial cell population based on the example of biofilm formation bySalmonella entericaserovar Typhimurium. We analyzed the expression of the major biofilm regulator CsgD at the single-cell level with a chromosomal CsgD-green fluorescent protein (GFP) translational fusion. In individual cells, CsgD-GFP expression is mostly found in the cytoplasm. Quantitative expression analysis and results from three different models ofS.Typhimurium biofilms demonstrated that CsgD is expressed in a bistable manner during biofilm development. CsgD expression is, however, monomodal when CsgD is expressed in larger amounts due to a promoter mutation or elevated levels of the secondary signaling molecule c-di-GMP. High levels of CsgD-GFP are associated with cellular aggregation in all three biofilm models. Furthermore, the subpopulation of cells expressing large amounts of CsgD is engaged in cellulose production during red, dry, and rough (rdar) morphotype development and in microcolony formation under conditions of continuous flow. Consequently, bistability at the level of CsgD expression leads to a corresponding pattern of task distribution inS.Typhimurium biofilms.
Asbestos fibre dimensions and lung cancer mortality among workers exposed to chrysotile
Authors: Loomis Dana , Dement John , Richardson David , Wolf Susanne 
Published: November 2009

ObjectivesTo estimate exposures to asbestos fibres of specific sizes among asbestos textile manufacturing workers exposed to chrysotile using data from transmission electron microscopy (TEM) and to evaluate the extent to which the risk of lung cancer varies with fibre length and diameter.Methods3803 workers employed for at least 1 day between 1 January 1950 and 31 December 1973 in any of three plants in North Carolina, USA that produced asbestos textile products and followed for vital status through 31 December 2003 were included. Historical exposures to asbestos fibres were estimated from work histories and 3578 industrial hygiene measurements taken in 1935–1986. Exposure–response relationships for lung cancer were examined within the cohort using Poisson regression.ResultsIndicators of fibre length and diameter obtained by TEM were positively and significantly associated with increasing risk of lung cancer. Exposures to longer and thinner fibres tended to be most strongly associated with lung cancer, and models for these fibres fit the data best. Simultaneously modelling indicators of cumulative mean fibre length and diameter yielded a positive coefficient for fibre length and a negative coefficient for fibre diameter.ConclusionsThe results support the hypothesis that the risk of lung cancer among workers exposed to chrysotile asbestos increases with exposure to longer fibres. More research is needed to improve the characterisation of exposures by fibre size and number and to analyse the associated risks in a variety of industries and populations.
Bibliography
Authors: Barman R.K. , Tandon J.C. , Singh Dalip 
Published: November 2009

NOTE : This bibliography on Indo-Pakistani relations consists of two parts. Part I, prepared by Miss R. K. Barman, lists the various books and pamphlets in the English language dealing with the subject, as also such general works on the foreign policies and relations of the two states as have some portions devoted to it. In most cases the relevant pages have been indicated. Part II, prepared by Mr J. C. Tandon and Mr Dalip Singh, presents selected periodical articles published in India and Pakistan, as well as in other countries, in a classified arrangement. The compilers have tried to make this bibliographical survey as comprehensive as possible. In addition to the scholarly journals, journals of opinion representing various shades of political opinion, especially in this country, ranging from the Jana Sangh on the one hand to the Communist Party of India on the other have been surveyed. Several foreign weeklies like the New Statesman and The Economist have also been covered extensively for comments, rather than any scholarly exposition of the issues under dispute between the two States. The major topics covered include defence and security, border incidents, India-Pakistan conflict of I965, minorities, economic relations and the river-waters disputes. The foreign relations in general and the Kashmir question have been covered in much detail; the two issues have been further highlighted by placing the world, Indian, and Pakistani opinions in juxtaposition.
Respondents' and Nonrespondents' Views on Stimulating Response to Mail Surveys in Travel Research
Authors: Goodrich Jonathan N. 
Published: November 2009

Numerous studies have evaluated techniques for increasing the response to mail questionnaire surveys, e.g., self-addressed, postage-paid return envelopes and monetary/nonmonetary incentives. These studies have traditionally made judgments on the relative efficacy of various response-stimulating methods through comparisons of the response rates of these methods, using the same questionnaire and the same or similar population. Surprisingly, none of these studies has solicited the views of the respondents and nonrespondents on how to increase participation in these surveys or cautions for researchers who use mail surveys. This article reports the results of such a study in travel research. Respondents and nonrespondents in a mail questionnaire study of tourism and travel behavior were telephoned and asked questions pertaining to factors that enhanced and also tended to discourage their response to the tourism and travel questionnaire. Their views on what reserachers who use mail surveys can do to stimulate response to mail surveys were also solicited. Implications of the study's findings for travel researchers and other users of mail questionnaires are discussed.