bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genomic studies in ageing research: the need to integrate genetic and gene expression approaches
Authors: Passtoors W. M. , Beekman M. , Gunn D. , Boer J. M. , Heijmans B. T. , Westendorp R. G. J. , Zwaan B. J. , Slagboom P. E. 
Published: August 2010

Abstract.Genome‐wide and hypothesis‐based approaches to the study of ageing and longevity have been dominated by genetic investigations. To identify essential mechanisms of a complex trait such as ageing in higher species, a holistic understanding of interacting pathways is required. More information on such interactions is expected to be obtained from global gene expression analysis if combined with genetic studies. Genetic sequence variation often provides a functional gene marker for the trait, whereas a gene expression profile may provide a quantitative biomarker representing complex cellular pathway interactions contributing to the trait. Thus far, gene expression studies have associated multiple pathways to ageing including mitochondrial electron transport and the oxidative stress response. However, most of the studies are underpowered to detect small age‐changes. A systematic survey of gene expression changes as a function of age in human individuals and animal models is lacking. Well designed gene expression studies, especially at the level of biological processes, will provide hypotheses on gene–environmental interactions determining biological ageing rate. Cross‐sectional studies monitoring the profile as a chronological marker of ageing must be integrated with prospective studies indicating which profiles represent biomarkers preceding and predicting physiological decline and mortality. New study designs such as the Leiden Longevity Study, including two generations of subjects from longevity families, aim to achieve these combined approaches.
The lactose operon‐controlling elements: a complex paradigm
Authors: Reznikoff William S. 
Published: August 2010

SummaryThe lactose‐controlling elements have been considered to be the simple paradigm of a cis‐acting genetic regulatory system, containing a promoter whose activity is modulated by an operator and a catabolite gene activator protein (CAP)‐binding site. The reality is considerably more complex. We now know that transcription is negatively regulated as a result of the repressor binding to three binding sites: the operator, a secondary repressor‐binding site within the lacZ gene and a tertiary repressor‐binding site upstream near lacl. In addition to the promoter, the lac‐controlling elements contain five promoter‐like elements. The physiological role, if any, of these promoter‐like elements is not clear, although three of them can be activated by single base pair changes to give high levels of in vivo expression. Finally, the positive activator protein CAP has been found to bind to a secondary site which is coincident with the operator. No role has been identified for this secondary CAP‐DNA complex.
Genetics of resistance to third‐generation cephalosporins in clinical isolates of Streptococcus pneumoniae
Authors: Muñoz Rosario , Dowson Christopher G. , Daniels Maggie , Coffey Tracey J. , Martin Christiane , Hakenbeck Regine , Spratt Brian G. 
Published: August 2010

SummaryResistance to third‐generation cephalosporins in a clinical isolate of Streptococcus pneumoniae was shown to be due to the production of altered forms of penicillin‐binding proteins (PBPs) 2X and 1A. The cloned PBP2X gene from the resistant strain was able to transform a susceptible strain to an intermediate level of resistance. The resulting transformant could be transformed to the full level of resistance of the clinical isolate using the cloned PBP1A gene from the latter strain. Chromosomal DNA from the resistant strain (and from other resistant strains) could readily transform a susceptible strain to the full level of resistance to third‐generation cephalosporins (>250‐fold for cefotaxime; >100‐fold for ceftriaxone) in a single step (transformation frequency of about 10‐5). The resistant transformants obtained with chromosomal DNA were shown by gene fingerprinting to have gained both the PBP1A and PBP2X genes from the DNA donor.
Fur regulation in Yersinia species
Authors: Staggs Teanna M. , Perry Robert D. 
Published: August 2010

SummaryThe effects of iron have been linked with several phenomena including regulation of membrane proteins; however, the mechanism of iron regulation is not well characterized in Yersinia pestis. It is well known that in Escherichia coli, the fur gene product mediates negative transcriptional regulation of several genes in response to iron. We have cloned a Y. pestis fur gene which is highly homologous to the E coli fur regulatory gene. The sequence of the Y. pestis fur gene exhibits 75% homology to the E. coli gene at the nucleotide level, and 84% homology at the predicted amino acid level. The Y. pestis fur gene is transcribed as a single gene message of approximately 0.5 kb which encodes an approximately 16 kDa protein when expressed in E coli minicells. A Yersinia enterocolitica fur mutant exhibits hypersensitivity to the Y. pestis bacteriocin, pesticin; the cloned Y. pestis fur gene restores wild‐type levels of pesticin sensitivity. Furthermore, iron regulation of at least five surface proteins in this Y. enterocolitica fur mutant is restored by transcomplementation with the Y. pestis fur gene. These data indicate that Y. pestis and Y. enterocolitica possess homologous Fur systems which regulate expression of proteins in response to iron availability.
RecA protein of Escherichia coli and chromosome partitioning
Authors: Zyskind Judith W. , Svitil Amy L. , Stine W. Blaine , Biery Matthew C. , Smith Douglas W. 
Published: August 2010

Summary Escherichia coli cells deficient in RecA protein frequently contain an abnormal number of chromosomes after completion of ongoing rounds of DNA replication. This suggests that RecA protein may be required for correct timing of initiation of DNA replication; however, we show here that initiation of DNA replication is properly timed in recA mutants. We also find that more than 10% of recA mutant cells contain no DNA. These anucleate cells appear to arise from partitioning of all the DNA into one daughter cell and no DNA into the other daughter cell. Based on these and previously published results, we propose that RecA protein is required for equal partitioning of chromosomes into the two daughter cells.
Light‐induced carotenogenesis in Myxococcus xanthus: light‐dependent membrane sequestration of ECF sigma factor CarQ by anti‐sigma factor CarR
Authors: Gorham Hazel C. , McGowan Simon J. , Robson Paul R. H. , Hodgson David A. 
Published: August 2010

SummaryLight‐induced carotenogenesis in Myxococcus xanthus is under the control of the carQRS operon. CarQ, a proposed extracytoplasmic (ECF) RNA polymerase sigma factor, is required for expression of the operon and the carC gene that encodes phytoene dehydrogenase. CarR, an inner membrane protein in Escherichia coli, is essential for carQRS promoter inactivation in the dark. CarS is required for the light‐dependent expression of the promoter of the carB gene cluster that encodes the rest of the structural genes for carotenogenesis. Regulation of carQRS is dependent on the stoichiometry of CarQ and CarR. Increasing the copy number of carQ over carR led to constitutive carotenogenesis, as did loss of translational coupling between carQ and carR. The severity of the constitutive phenotype depended on the distance between the uncoupled genes. When expressed in M. xanthus, a CarR:β‐galactosidase fusion protein disappeared in the light. We propose that anti‐sigma factor CarR sequesters CarQ to the membrane in the dark, but, in the light, loss of CarR leads to release of the sigma factor.
Novel mitochondrion‐related organelles in the anaerobic amoeba Mastigamoeba balamuthi
Authors: Gill Erin E. , Diaz‐Triviño Sara , Barberà Maria José , Silberman Jeffrey D. , Stechmann Alexandra , Gaston Daniel , Tamas Ivica , Roger Andrew J. 
Published: August 2010

SummaryUnicellular eukaryotes that lack mitochondria typically contain related organelles such as hydrogenosomes or mitosomes. To characterize the evolutionary diversity of these organelles, we conducted an expressed sequence tag (EST) survey on the free‐living amoeba Mastigamoeba balamuthi, a relative of the human parasite Entamoeba histolytica. From 19 182 ESTs, we identified 21 putative mitochondrial proteins implicated in protein import, amino acid interconversion and carbohydrate metabolism, two components of the iron–sulphur cluster (Fe‐S) assembly apparatus as well as two enzymes characteristic of hydrogenosomes. By immunofluorescence microscopy and subcellular fractionation, we show that mitochondrial chaperonin 60 is targeted to small abundant organelles within Mastigamoeba. In transmission electron micrographs, we identified double‐membraned compartments that likely correspond to these mitochondrion‐derived organelles, The predicted organellar proteome of the Mastigamoeba organelle indicates a unique spectrum of functions that collectively have never been observed in mitochondrion‐related organelles. However, like Entamoeba, the Fe‐S cluster assembly proteins in Mastigamoeba were acquired by lateral gene transfer from ε‐proteobacteria and do not possess obvious organellar targeting peptides. These data indicate that the loss of classical aerobic mitochondrial functions and acquisition of anaerobic enzymes and Fe‐S cluster assembly proteins occurred in a free‐living member of the eukaryote super‐kingdom Amoebozoa.
The crystal structure of staphylococcal superantigen‐like protein 11 in complex with sialyl Lewis X reveals the mechanism for cell binding and immune inhibition
Authors: Chung Matthew C. , Wines Bruce D. , Baker Heather , Langley Ries J. , Baker Edward N. , Fraser John D. 
Published: August 2010

Summary Staphylococcus aureus is a major pathogen that produces a family of 14 staphylococcal superantigen‐like (SSL) proteins, which are structurally similar to superantigens but do not stimulate T cells. SSL11 is one member of the family that is found in all staphylococcal strains. Recombinant SSL11 bound to granulocytes and monocytes through a sialic acid‐dependent mechanism and was rapidly internalized. SSL11 also bound to sialic acid‐containing glycoproteins, such as the Fc receptor for IgA (FcαRI) and P‐selectin glycoprotein ligand‐1 (PSGL‐1), and inhibited neutrophil attachment to a P‐selectin‐coated surface. Biosensor analysis of two SSL11 alleles binding to sialyl Lewis X [sLex– Neu5Acα2‐3Galβ1‐4(Fuc1‐3)GlcNAc] coupled to bovine serum albumin gave dissociation constants of 0.7 and 7 μm respectively. Binding of SSL11 to a glycan array revealed specificity for glycans containing the trisaccharide sialyllactosamine (sLacNac – Neu5Acα2‐3Galβ1‐4GlcNAc). A 1.6 Å resolution crystal structure of SSL11 complexed with sLex revealed a discrete binding site in the C‐terminal β‐grasp domain, with predominant interactions with the sialic acid and galactose residues. A single amino acid mutation in the carbohydrate binding site abolished all SSL11 binding. Thus, SSL11 is a staphylococcal protein that targets myeloid cells by binding sialyllactosamine‐containing glycoproteins.
A gene cluster that regulates both heterocyst differentiation and pattern formation in Anabaena sp. strain PCC 7120
Authors: Zhang Wei , Du Ye , Khudyakov Ivan , Fan Qing , Gao Hong , Ning Degang , Wolk C. Peter , Xu Xudong 
Published: August 2010

SummaryWild‐type Anabaena sp. strain PCC 7120, a filamentous nitrogen‐fixing cyanobacterium, produces single heterocysts at semi‐regular intervals. asr0100 (patU5) and alr0101 (patU3) are homologous to the 5′ and 3′ portions of patU of Nostoc punctiforme. alr0099 (hetZ) overlaps the 5′ end of patU5. hetZ, patU5 and patU3 were all upregulated, or expressed specifically, in proheterocysts and heterocysts. Mutants of hetZ showed delayed or no heterocyst differentiation. In contrast, a patU3 mutation produced a multiple contiguous heterocyst (Mch) phenotype and restored the formation of otherwise lost intercalary heterocysts in a patA background. Decreasing the expression of patU3 greatly increased the frequency of heterocysts in a mini‐patS strain. Two promoter regions and two principal, corresponding transcripts were detected in the hetZ‐patU5‐patU3 region. Transcription of hetZ was upregulated in a hetZ mutant and downregulated in a patU3 mutant. When mutants hetZ::C.K2 and hetZ::Tn5‐1087b were nitrogen‐deprived, PhetC‐gfp was very weakly expressed, and in hetZ::Tn5‐1087b, PhetR‐gfp was relatively strongly expressed in cells that had neither a regular pattern nor altered morphology. We conclude that the hetZ‐patU5‐patU3 cluster plays an important role in co‐ordination of heterocyst differentiation and pattern formation. The presence of homologous clusters in filamentous genera without heterocysts is suggestive of a more general role.
Beta toxin is essential for the intestinal virulence of Clostridium perfringens type C disease isolate CN3685 in a rabbit ileal loop model
Authors: Sayeed Sameera , Uzal Francisco A. , Fisher Derek J. , Saputo Juliann , Vidal Jorge E. , Chen Yue , Gupta Phalguni , Rood Julian I. , McClane Bruce A. 
Published: August 2010

Summary Clostridium perfringens type C isolates, which cause enteritis necroticans in humans and enteritis and enterotoxaemias of domestic animals, typically produce (at minimum) beta toxin (CPB), alpha toxin (CPA) and perfringolysin O (PFO) during log‐phase growth. To assist development of improved vaccines and therapeutics, we evaluated the contribution of these three toxins to the intestinal virulence of type C disease isolate CN3685. Similar to natural type C infection, log‐phase vegetative cultures of wild‐type CN3685 caused haemorrhagic necrotizing enteritis in rabbit ileal loops. When isogenic toxin null mutants were prepared using TargeTron® technology, even a double cpa/pfoA null mutant of CN3685 remained virulent in ileal loops. However, two independent cpb null mutants were completely attenuated for virulence in this animal model. Complementation of a cpb mutant restored its CPB production and intestinal virulence. Additionally, pre‐incubation of wild‐type CN3685 with a CPB‐neutralizing monoclonal antibody rendered the strain avirulent for causing intestinal pathology. Finally, highly purified CPB reproduced the intestinal damage of wild‐type CN3685 and that damage was prevented by pre‐incubating purified CPB with a CPB monoclonal antibody. These results indicate that CPB is both required and sufficient for CN3685‐induced enteric pathology, supporting a key role for this toxin in type C intestinal pathogenesis.
Identification and functional analysis of novel (p)ppGpp synthetase genes in Bacillus subtilis
Authors: Nanamiya Hideaki , Kasai Koji , Nozawa Akira , Yun Choong‐Soo , Narisawa Takakuni , Murakami Kana , Natori Yousuke , Kawamura Fujio , Tozawa Yuzuru 
Published: August 2010

SummaryBacterial alarmone (p)ppGpp, is a global regulator responsible for the stringent control. Two homologous (p)ppGpp synthetases, RelA and SpoT, have been identified and characterized in Escherichia coli, whereas Gram‐positive bacteria such as Bacillus subtilis have been thought to possess only a single RelA‐SpoT enzyme. We have now identified two genes, yjbM and ywaC, in B. subtilis that encode a novel type of alarmone synthetase. The predicted products of these genes are relatively small proteins (∼25 kDa) that correspond to the (p)ppGpp synthetase domain of RelA‐SpoT family members. A database survey revealed that genes homologous to yjbM and ywaC are conserved in certain bacteria belonging to Firmicutes or Actinobacteria phyla but not in other phyla such as Proteobacteria. We designated the proteins as small alarmone synthetases (SASs) to distinguish them from RelA‐SpoT proteins. The (p)ppGpp synthetase function of YjbM and YwaC was confirmed by genetic complementation analysis and by in vitro assay of enzyme activity. Molecular genetic analysis also revealed that ywaC is induced by alkaline shock, resulting in the transient accumulation of ppGpp. The SAS proteins thus likely function in the biosynthesis of alarmone with a mode of action distinct from that of RelA‐SpoT homologues.
Mapping a common interaction site used by Plasmodium falciparum Duffy binding‐like domains to bind diverse host receptors
Authors: Howell Dasein P.‐G. , Levin Emily A. , Springer Amy L. , Kraemer Susan M. , Phippard David J. , Schief William R. , Smith Joseph D. 
Published: August 2010

SummaryThe Duffy binding‐like (DBL) domain is a key adhesive module in Plasmodium falciparum, present in both erythrocyte invasion ligands (EBLs) and the large and diverse P. falciparum erythrocyte membrane protein 1 (PfEMP1) family of cytoadherence receptors. DBL domains bind a variety of different host receptors, including intercellular adhesion molecule 1 (ICAM‐1), a receptor interaction that may have a role in infected erythrocyte binding to cerebral blood vessels and cerebral malaria. In this study, we expressed the nearly full complement of DBLβ‐C2 domains from the IT4/25/5 (IT4) parasite isolate and showed that ICAM‐1‐binding domains (DBLβ‐C2ICAM‐1) were confined to group B and group C PfEMP1 proteins and were not present in group A, suggesting that ICAM‐1 selection pressure differs between PfEMP1 groups. To further dissect the molecular determinants of binding, we modelled a DBLβ‐C2ICAM‐1 domain on a solved DBL structure and created alanine substitution mutants in two DBLβ‐C2ICAM‐1 domains. This analysis indicates that the DBLβ‐C2::ICAM‐1 interaction maps to the equivalent glycan binding region of EBLs, and suggests a general model for how DBL domains evolve under dual selection for host receptor binding and immune evasion.
The Bacteroides fragilis transcriptome response to oxygen and H2O2: the role of OxyR and its effect on survival and virulence
Authors: Sund Christian J. , Rocha Edson R. , Tzinabos Arthur O. , Wells W. Greg , Gee Jason M. , Reott Michael A. , O'Rourke Dorcas P. , Smith C. Jeffrey 
Published: August 2010

SummaryThe intestinal anaerobic symbiont, Bacteroides fragilis, is highly aerotolerant and resistant to H2O2. Analysis of the transcriptome showed that expression of 45% of the genome was significantly affected by oxidative stress. The gene expression patterns suggested that exposure to oxidative stress induced an acute response to rapidly minimize the immediate effects of reactive oxygen species, then upon extended exposure a broad metabolic response was induced. This metabolic response induced genes encoding enzymes that can supply reducing power for detoxification and restore energy‐generating capacity. An integral aspect of the metabolic response was downregulation of genes related to translation and biosynthesis which correlated with decreased growth and entry into a stationary phase‐like growth state. Examination of oxyR mutants showed that they were impaired for the acute response and they induced the expanded metabolic response with only minimal exposure to stress. The oxyR mutants were more sensitive to oxidants in vitro and in vivo they were attenuated in an intra‐abdominal abscess infection model. Aerotolerance and resistance to oxidative stress are physiological adaptations of B. fragilis to its environment that enhance survival in extra‐intestinal sites and promote opportunistic infections.
Bistability and biofilm formation in Bacillus subtilis
Authors: Chai Yunrong , Chu Frances , Kolter Roberto , Losick Richard 
Published: August 2010

SummaryBiofilms of Bacillus subtilis consist of long chains of cells that are held together in bundles by an extracellular matrix of exopolysaccharide and the protein TasA. The exopolysaccharide is produced by enzymes encoded by the epsA‐O operon and the gene encoding TasA is located in the yqxM‐sipW‐tasA operon. Both operons are under the control of the repressor SinR. Derepression is mediated by the antirepressor SinI, which binds to SinR with a 1:1 stoichiometry. Paradoxically, in medium promoting derepression of the matrix operons, the overall concentration of SinR in the culture greatly exceeded that of SinI. We show that under biofilm‐promoting conditions sinI, which is under the control of the response regulator Spo0A, was expressed only in a small subpopulation of cells, whereas sinR was expressed in almost all cells. Activation of Spo0A is known to be subject to a bistable switch, and we infer that SinI reaches levels sufficient to trigger matrix production only in the subpopulation of cells in which Spo0A is active. Additionally, evidence suggests that sinI is expressed at intermediate, but not low or high, levels of Spo0A activity, which may explain why certain nutritional conditions are more effective in promoting biofilm formation than others.
Acquisition of a bacterial RumA‐type tRNA(uracil‐54, C5)‐methyltransferase by Archaea through an ancient horizontal gene transfer
Authors: Urbonavičius Jaunius , Auxilien Sylvie , Walbott Hélène , Trachana Kalliopi , Golinelli‐Pimpaneau Béatrice , Brochier‐Armanet Céline , Grosjean Henri 
Published: August 2010

SummaryThe Pyrococcus abyssi genome displays two genes possibly coding for S‐adenosyl‐l‐methionine‐dependent RNA(uracil, C5)‐methyltransferases (PAB0719 and PAB0760). Their amino acid sequences are more closely related to Escherichia coli RumA catalysing the formation of 5‐methyluridine (m5U)‐1939 in 23S rRNA than to E. coli TrmA (tRNA methyltransferase
A) methylating uridine‐54 in tRNA. Comparative genomic and phylogenetic analyses show that homologues of PAB0719 and PAB0760 occur only in a few Archaea, these genes having been acquired via a single horizontal gene transfer from a bacterial donor to the common ancestor of Thermococcales and Nanoarchaea. This transfer event was followed by a duplication event in Thermococcales leading to two closely related genes. None of the gene products of the two P. abyssi paralogues catalyses in vitro the formation of m5U in a P. abyssi rRNA fragment homologous to the bacterial RumA substrate. Instead, PAB0719 enzyme (renamed PabTrmU54) displays an identical specificity to TrmA, as it catalyses the in vitro formation of m5U‐54 in tRNA. Thus, during evolution, at least one of the two P. abyssi RumA‐type enzymes has changed of target specificity. This functional shift probably occurred in an ancestor of all Thermococcales. This study also provides new evidence in favour of a close relationship between Thermococcales and Nanoarchaea.
Binding of Dr adhesins of Escherichia coli to carcinoembryonic antigen triggers receptor dissociation
Authors: Korotkova Natalia , Yang Yi , Le Trong Isolde , Cota Ernesto , Demeler Borries , Marchant Jan , Thomas Wendy E. , Stenkamp Ronald E. , Moseley Steve L. , Matthews Steve 
Published: August 2010

SummaryCarcinoembryonic antigen (CEA)‐related cell adhesion molecules (CEACAMs) are host receptors for the Dr family of adhesins of Escherichia coli. To define the mechanism for binding of Dr adhesins to CEACAM receptors, we carried out structural studies on the N‐terminal domain of CEA and its complex with the Dr adhesin. The crystal structure of CEA reveals a dimer similar to other dimers formed by receptors with IgV‐like domains. The structure of the CEA/Dr adhesin complex is proposed based on NMR spectroscopy and mutagenesis data in combination with biochemical characterization. The Dr adhesin/CEA interface overlaps appreciably with the region responsible for CEA dimerization. Binding kinetics, mutational analysis and spectroscopic examination of CEA dimers suggest that Dr adhesins can dissociate CEA dimers prior to the binding of monomeric forms. Our conclusions include a plausible mechanism for how E. coli, and perhaps other bacterial and viral pathogens, exploit CEACAMs. The present structure of the complex provides a powerful tool for the design of novel inhibitory strategies to treat E. coli infections.