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Species | Mark PallenSummaryAffiliation: University of Birmingham Country: UK Publications
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Publications
The ESAT-6/WXG100 superfamily -- and a new Gram-positive secretion system?Mark J Pallen
Division of Immunity and Infection, Birmingham University Medical School, Birmingham, UK B15 2TT
Trends Microbiol 10:209-12. 2002..The way is now open to investigate this hypothesis in organisms that are easier to manipulate than pathogenic mycobacteria...- EntrezAJAX: direct web browser access to the Entrez Programming UtilitiesNicholas J Loman
Centre for Systems Biology, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
Source Code Biol Med 5:6. 2010..For the purposes of speed, reliability and scalability, EntrezAJAX has been deployed on Google App Engine, a freely available cloud service. The EntrezAJAX webpage is located at http://entrezajax.appspot.com/.. - Comparative analysis of two Neisseria gonorrhoeae genome sequences reveals evidence of mobilization of Correia Repeat Enclosed Elements and their role in regulationLori A S Snyder
Systems Biology, University of Birmingham, Edgbaston, Birmingham, UK
BMC Genomics 10:70. 2009..These interruptions perhaps remove the expression of CREE-associated genes from ancestral neisserial regulatory networks... - Simple sequence repeats in Helicobacter canadensis and their role in phase variable expression and C-terminal sequence switchingLori A S Snyder
Centre for Systems Biology, School of Biosciences, University of Birmingham, Edgbaston, Birmingham B152TT, UK
BMC Genomics 11:67. 2010..Helicobacter canadensis is an emerging human pathogen and zoonotic agent. The genome of H. canadensis was sequenced previously and determined to contain 29 annotated coding regions associated with homopolymeric tracts... - Genome sequence of the emerging pathogen Helicobacter canadensisN J Loman
Centre for Systems Biology, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom
J Bacteriol 191:5566-7. 2009..Potential virulence determinants carried by the genome include systems for N-linked glycosylation and capsular export. A protein-based phylogenetic analysis places H. canadensis close to Wolinella succinogenes... - Bacterial flagella and Type III secretion: case studies in the evolution of complexityM J Pallen
University of Birmingham Medical School, Birmingham, United Kingdom
Genome Dyn 3:30-47. 2007..In conclusion, rather than providing evidence of intelligent design, flagellar and non-flagellar Type III secretion systems instead provide excellent case studies in the evolution of complex systems from simpler components... - Are diagnostic and public health bacteriology ready to become branches of genomic medicine?Mark J Pallen
Centre for Systems Biology, School of Biosciences, University of Birmingham, Birmingham, B15 2TT, UK
Genome Med 3:53. 2011..mean we are on the brink of a revolution in diagnostic and public health microbiology, in which high-throughput sequencing usurps the traditional 'M, C & S', or will the discipline's innate conservatism stand firm for decades to come?.. - Bioinformatics analysis of the locus for enterocyte effacement provides novel insights into type-III secretionMark J Pallen
Bacterial Pathogenesis and Genomics Unit, Division of Immunity and Infection, Medical School, University of Birmingham, Birmingham, B15 2TT, UK
BMC Microbiol 5:9. 2005..Many of the genes within this locus have been assigned names and functions through homology with the better characterised Ysc-Yop system from Yersinia spp. However, the functions and homologies of many LEE genes remain obscure... - Bioinformatics, genomics and evolution of non-flagellar type-III secretion systems: a Darwinian perspectiveMark J Pallen
Bacterial Pathogenesis and Genomics Unit, Division of Immunity and Infection, Medical School, University of Birmingham, Birmingham, West Midlands B15 2TT, UK
FEMS Microbiol Rev 29:201-29. 2005..The problem of information overload is likely to be ameliorated by launch of a web site devoted to the comparative biology of type-III secretion ()... - Bacterial flagellar diversity in the post-genomic eraMark J Pallen
Bacterial Pathogenesis and Genomics Unit, Division of Immunity and Infection, Medical School, University of Birmingham, Birmingham, UK B15 2TT
Trends Microbiol 13:143-9. 2005..Also described is a new family of flagellar proteins, the FlhX proteins, which resemble the cytoplasmic domain of FlhB... - Bacterial pathogenomicsMark J Pallen
Centre for Systems Biology, University of Birmingham, Birmingham B15 2TT, UK
Nature 449:835-42. 2007..It has also become evident that even the definitions for 'pathogen' and 'virulence factor' need to be re-evaluated... - From The Origin of Species to the origin of bacterial flagellaMark J Pallen
Division of Immunity and Infection, Medical School, University of Birmingham, Birmingham, B15 2TT UK
Nat Rev Microbiol 4:784-90. 2006..We dismiss the need for any great conceptual leaps in creating a model of flagellar evolution and speculate as to how an experimental programme focused on this topic might look... - Time to recognise that mitochondria are bacteria?Mark J Pallen
Centre for Systems Biology, School of Biosciences, University of Birmingham, Birmingham, B15 2TT, UK
Trends Microbiol 19:58-64. 2011..I also explore the consequences of recognizing mitochondria as bacteria for our understanding of the systemic response to trauma and for the prospects of creating transgenic mitochondria... - Genomic analysis of secretion systemsMark J Pallen
Bacterial Pathogenesis and Genomics Unit, Division of Immunity and Infection, The Medical School, University of Birmingham, Vincent Drive, B15 2TT, Birmingham, UK
Curr Opin Microbiol 6:519-27. 2003.... - Glucoamylase-like domains in the alpha- and beta-subunits of phosphorylase kinaseMark J Pallen
Division of Immunity and Infection, University of Birmingham Medical School, Vincent Drive, Edgbaston, Birmingham B15 2TT, UK
Protein Sci 12:1804-7. 2003..If true, this would have important implications for the understanding, diagnosis, and management of glycogen storage diseases. There is thus a clear need to test this hypothesis through enzymatic assays and structural studies... - Evolutionary links between FliH/YscL-like proteins from bacterial type III secretion systems and second-stalk components of the FoF1 and vacuolar ATPasesMark J Pallen
Division of Immunity and Infection, University of Birmingham Medical School, Edgbaston, Birmingham B15 2TT, United Kingdom
Protein Sci 15:935-41. 2006..In particular, we show that the FliH/YscL-like proteins and the E subunits of vacuolar ATPases represent fusions of domains homologous to second-stalk components of the F(o)F(1) ATPase (the b and delta subunits)... - Tricorn-like proteases in bacteriaM J Pallen
Microbial Genomics and Pathogenesis Unit, Division of Immunity and Infection, The Medical School, University of Birmingham, B15 2TT, Birmingham, UK
Trends Microbiol 9:518-21. 2001..We propose various hypotheses as to the function of these domains that can now be tested in the laboratory... - Bacterial FHA domains: neglected players in the phospho-threonine signalling game?Mark Pallen
Division of Immunity and Infection, Birmingham University Medical School, UK
Trends Microbiol 10:556-63. 2002..The way is now open to identify the targets of each FHA domain, and their roles in cellular physiology, and perhaps even to develop novel FHA-blocking antibacterial agents... - High-throughput sequencing and clinical microbiology: progress, opportunities and challengesMark J Pallen
School of Biosciences, University of Birmingham, Birmingham, B15 2TT, United Kingdom
Curr Opin Microbiol 13:625-31. 2010..We should prepare for the coming 'technological singularity' in sequencing, when this technology becomes so fast and so cheap that it threatens to out-compete existing diagnostic and typing methods in microbiology... - Phylogenetic comparisons reveal multiple acquisitions of the toxin genes by enterotoxigenic Escherichia coli strains of different evolutionary lineagesSue M Turner
Division of Immunity and Infection, The Medical School, The University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom, and St. Luke's Episcopal Hospital, Houston, TX 77083, USA
J Clin Microbiol 44:4528-36. 2006..coli revealed that they were not abundant. These observations have significant implications for disease epidemiology and for the design of effective vaccines... - The Flag-2 locus, an ancestral gene cluster, is potentially associated with a novel flagellar system from Escherichia coliChuan Peng Ren
Bacterial Pathogenesis and Genomics Unit, Division of Immunity and Infection, Medical School, University of Birmingham, Birmingham, England B15 2TT
J Bacteriol 187:1430-40. 2005..The fact that the Flag-2 gene cluster was not discovered in the first 10 Escherichia/Shigella genome sequences studied emphasizes the importance of maintaining an energetic program of genome sequencing for this important taxonomic group... - SepL resembles an aberrant effector in binding to a class 1 type III secretion chaperone and carrying an N-terminal secretion signalRasha Younis
School of Biosciences, University of Birmingham, Edgbaston, Birmingham, United Kingdom
J Bacteriol 192:6093-8. 2010..We also show that short N-terminal fragments (?70 amino acids) from SepL are capable of targeting fusion proteins for secretion and translocation... - coliBASE: an online database for Escherichia coli, Shigella and Salmonella comparative genomicsRoy R Chaudhuri
Bacterial Pathogenesis and Genomics Unit, Division of Immunity and Infection, Medical School, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
Nucleic Acids Res 32:D296-9. 2004..are also available at http://campy.bham.ac.uk and http://clostri. bham.ac.uk, respectively. An example of the power of E.coli comparative analyses such as those available through coliBASE is presented... - Type VI secretion: a beginner's guideLewis Eh Bingle
Centre for Systems Biology, University of Birmingham, Edgbaston, Birmingham, UK
Curr Opin Microbiol 11:3-8. 2008..In accordance with the general rule that the expression of protein secretion systems is tightly regulated, expression of type VI secretion is controlled at both transcriptional and post-transcriptional levels... - Gene doctoring: a method for recombineering in laboratory and pathogenic Escherichia coli strainsDavid J Lee
School of Biosciences, University of Birmingham, Birmingham B15 2TT, UK
BMC Microbiol 9:252. 2009..coli K-12 strains. However, we have had limited success with these lambda-Red based recombination techniques in pathogenic E. coli strains, which has led us to develop an enhanced protocol for recombineering in such strains... - Genomic analysis of the protein secretion systems in Clostridium acetobutylicum ATCC 824Mickael Desvaux
The Institute for Biomedical Research IBR, The University of Birmingham The Medical School, Division of Immunity and Infection, Bacterial Pathogenesis and Genomics Unit, Edgbaston, Birmingham B15 2TT, UK
Biochim Biophys Acta 1745:223-53. 2005..This investigation highlights the potential use of this saprophytic bacterium in biotechnological and biomedical applications as well as a model organism for studying protein secretion in pathogenic Gram-positive bacteria... - Tetratricopeptide-like repeats in type-III-secretion chaperones and regulatorsMark J Pallen
Division of Immunity and Infection, Medical School, University of Birmingham, Birmingham, B15 2TT, UK
FEMS Microbiol Lett 223:53-60. 2003.... - PDZ domains facilitate binding of high temperature requirement protease A (HtrA) and tail-specific protease (Tsp) to heterologous substrates through recognition of the small stable RNA A (ssrA)-encoded peptideAlison Spiers
School of Biochemistry and Genetics, Medical School, University of Newcastle upon Tyne, Framlington Place, Newcastle upon Tyne NE2 4HH, United Kingdom
J Biol Chem 277:39443-9. 2002.... - Comparative cell wall core biosynthesis in the mycolated pathogens, Mycobacterium tuberculosis and Corynebacterium diphtheriaeLynn G Dover
School of Biosciences, The University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
FEMS Microbiol Rev 28:225-50. 2004..In order to facilitate this aim, this review intends to illustrate the broad similarities and highlight the structural differences between the two bacterial envelopes and discuss the genetics of their biosynthesis... - An analysis of type-III secretion gene clusters in Chromobacterium violaceumHelen J Betts
Bacterial Pathogenesis and Genomics Unit, Division of Immunity and Infection, Institute for Biomedical Research, Medical School, University of Birmingham, Birmingham B15 2TT UK
Trends Microbiol 12:476-82. 2004.... - Bacterial flagellar diversity and evolution: seek simplicity and distrust it?Lori A S Snyder
University of Birmingham, Birmingham, B15 2TT, UK
Trends Microbiol 17:1-5. 2009..However, a fresh examination of the phylogenetic distribution of flagellar genes warns against a simplistic model of early flagellar evolution... - The ETT2 gene cluster, encoding a second type III secretion system from Escherichia coli, is present in the majority of strains but has undergone widespread mutational attritionChuan Peng Ren
Bacterial Pathogenesis and Genomics Unit, Division of Immunity and Infection, Medical School, University of Birmingham, Birmingham B15 2TT, United Kingdom
J Bacteriol 186:3547-60. 2004..coli strains. Intact versions of both ETT2-related clusters are apparently present in enteroaggregative E. coli strain O42... - Regulators encoded in the Escherichia coli type III secretion system 2 gene cluster influence expression of genes within the locus for enterocyte effacement in enterohemorrhagic E. coli O157:H7Lihong Zhang
Bacterial Pathogenesis and Genomics Unit, Division of Immunity and Infection, Medical School, University of Birmingham, Birmingham B15 2TT, United Kingdom
Infect Immun 72:7282-93. 2004..quot; It also seems likely that variations in the ETT2 regulator repertoire might account for strain-to-strain variation in secretion of LEE-encoded proteins... - Variation in bacterial flagellins: from sequence to structureScott A Beatson
Division of Immunity and Infection, University of Birmingham Medical School, Vincent Drive, Edgbaston, Birmingham, UK, B15 2TT
Trends Microbiol 14:151-5. 2006..Flagellins provide a striking illustration of the twin evolutionary themes of conservation and variability... - xBASE2: a comprehensive resource for comparative bacterial genomicsRoy R Chaudhuri
Centre for Systems Biology, University of Birmingham, Birmingham B15 2TT, UK
Nucleic Acids Res 36:D543-6. 2008..bham.ac.uk), now provides comprehensive coverage of all bacterial genomes and features an updated modularized backend and an improved user interface, which includes a taxonomy browser and a powerful full-text search facility... - xBASE, a collection of online databases for bacterial comparative genomicsRoy R Chaudhuri
Division of Immunity and Infection, University of Birmingham, Birmingham, UK
Nucleic Acids Res 34:D335-7. 2006..Examples of how the databases have been, and continue to be, used to generate hypotheses for subsequent laboratory investigation are presented. xBASE is available online at http://xbase.bham.ac.uk... - Point mutations in the DNA- and cNMP-binding domains of the homologue of the cAMP receptor protein (CRP) in Mycobacterium bovis BCG: implications for the inactivation of a global regulator and strain attenuationClaire L Spreadbury
Division of Immunity and Infection, The Medical School, University of Birmingham, Birmingham B15 2TT, UK
Microbiology 151:547-56. 2005..bovis BCG strains. This raises the possibility that a contributing factor to the attenuation of BCG strains may be an inability of this global regulator to control the expression of genes required for in vivo survival and persistence... - Bacterial genomes for the masses: relevance to the clinical laboratoryMark J Pallen
Division on Immunity and Infection, Medical School, University of Birmingham, UK
Methods Mol Biol 266:3-15. 2004..quot; Current progress and future prospects for exploitation of genome sequences in clinical bacteriology are reviewed... - Mutations affecting the Rossman fold of isoleucyl-tRNA synthetase are correlated with low-level mupirocin resistance in Staphylococcus aureusMartin Antonio
Microbial Genomics and Pathogenesis Unit, Division of Immunity and Infection, The Medical School, University of Birmingham, Birmingham, BT15 2TT, United Kingdom
Antimicrob Agents Chemother 46:438-42. 2002..The importance of the V588F mutation was confirmed by an allele-specific PCR survey of 32 additional strains. Additional mutations of uncertain significance were found in residues clustered on the surface of the IleS protein... - Analysis of host response to bacterial infection using error model based gene expression microarray experimentsDov J Stekel
School of Biosciences, The University of Birmingham Birmingham B15 2TT, UK
Nucleic Acids Res 33:e53. 2005..We demonstrate the effectiveness of error model based microarray experiments and propose this as a general strategy for a microarray-based screening of large collections of biological samples... - Enterohemorrhagic Escherichia coli exploits EspA filaments for attachment to salad leavesRobert K Shaw
Division of Immunity and Infection, School of Medicine, University of Birmingham, Birmingham, United Kingdom
Appl Environ Microbiol 74:2908-14. 2008..In this study we have shown that EHEC O157 and O26 strains use the fT3SS apparatus for attachment to leaves. Leaf attachment was independent of effector protein translocation... - Genome sequencing shows that European isolates of Francisella tularensis subspecies tularensis are almost identical to US laboratory strain Schu S4Roy R Chaudhuri
Division of Immunity and Infection, University of Birmingham, Edgbaston, United Kindgom
PLoS ONE 2:e352. 2007..However, a handful of isolates from this subspecies was obtained in the 1980s from ticks and mites from Slovakia and Austria. Our aim was to uncover the origins of these enigmatic European isolates... - Laboratory strains of Escherichia coli: model citizens or deceitful delinquents growing old disgracefully?Jon L Hobman
School of Biosciences, The Medical School, The University of Birmingham, Edgbaston, Birmingham, UK
Mol Microbiol 64:881-5. 2007..Fortunately, a flood of information from high-throughput genome sequencing, together with a new 'eco-evo' view of this model organism, promises to help put K-12 better into context... - Sigma(s)-Dependent carbon-starvation induction of pbpG (PBP 7) is required for the starvation-stress response in Salmonella enterica serovar TyphimuriumWilliam J Kenyon
Department of Biomedical Sciences, University of South Alabama, Mobile, AL 36688, USA
Microbiology 153:2148-58. 2007..Lack of PBP 7, however, can be compensated for by further physiological changes developed in 24 h C-starved cells. This supports the dynamic overlapping and distinct nature of resistance pathways within the Salmonella SSR... - Subversion of actin dynamics by EspM effectors of attaching and effacing bacterial pathogensAna Arbeloa
Division of Cell and Molecular Biology, Imperial College London, London SW7 2AZ, UK
Cell Microbiol 10:1429-41. 2008..These results suggest that the EspM effectors modulate actin dynamics by activating the RhoA signalling pathway... - A degenerate type III secretion system from septicemic Escherichia coli contributes to pathogenesisDiana Ideses
Department of Molecular Microbiology and Biotechnology, Faculty of Life Sciences, Tel Aviv University, Israel
J Bacteriol 187:8164-71. 2005..These results are the first demonstration of the importance of ETT2 for pathogenesis... - Tetratricopeptide repeats in the type III secretion chaperone, LcrH: their role in substrate binding and secretionPetra J Edqvist
Department of Molecular Biology, , SE-901 87 Ume, Sweden
Mol Microbiol 59:31-44. 2006.... - Identification of amino acid residues within the N-terminal domain of EspA that play a role in EspA filament biogenesis and functionMona P Singh
Division of Cell and Molecular Biology, Imperial College, London SW7 2AZ, United Kingdom
J Bacteriol 190:2221-6. 2008..In this study, we have shown that the N-terminal region of EspA has a role in EspA's protein stability, interaction with the CesAB chaperone, and filament biogenesis and function... - An extensive repertoire of type III secretion effectors in Escherichia coli O157 and the role of lambdoid phages in their disseminationToru Tobe
Graduate School of Medicine, Osaka University, 2 2 Yamadaoka, Suita, Osaka 565 0871, Japan
Proc Natl Acad Sci U S A 103:14941-6. 2006..Thus, type III secretion in E. coli is linked to a vast phage "metagenome," acting as a crucible for the evolution of pathogenicity... - Sequencing and analysis of the genome of the Whipple's disease bacterium Tropheryma whippleiStephen D Bentley
The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
Lancet 361:637-44. 2003.... - Shifts from glucose to certain secondary carbon-sources result in activation of the extracytoplasmic function sigma factor sigmaE in Salmonella enterica serovar TyphimuriumWilliam J Kenyon
Department of Biomedical Sciences, University of South Alabama, Mobile, AL 36688, USA
Microbiology 151:2373-83. 2005....