Author Report for: Holroyd SNo contact information in database for Holroyd S
Holden MT, Scott A, Cherevach I, Chillingworth T, Churcher C, Cronin A, Dowd L, Feltwell T, Hamlin N and Parkhill J <12 more author(s)> Holden MT, Scott A, Cherevach I, Chillingworth T, Churcher C, Cronin A, Dowd L, Feltwell T, Hamlin N, Holroyd S, Jagels K, Moule S, Mungall K, Quail MA, Price C, Rabbinowitsch E, Sharp S, Skelton J, Whitehead S, Barrell BG, Kehoe M, Parkhill J (- 12) Ref: Journal of Bacteriology, 189:1473, 2007 : PubMed ESTHER: Holden_2007_J.Bacteriol_189_1473 PubMedSearch: Holden 2007 J.Bacteriol 189 1473 PubMedID: 17012393 Gene_locus related to this paper: strpy-ESTA, strpy-PEPXP, strpy-SPY1308, strpy-SPYM18.1727 Abstract Comparisons of the 1.84-Mb genome of serotype M5 Streptococcus pyogenes strain Manfredo with previously sequenced genomes emphasized the role of prophages in diversification of S. pyogenes and the close relationship between strain Manfredo and MGAS8232, another acute rheumatic fever-associated strain. Title: The multidrug-resistant human pathogen Clostridium difficile has a highly mobile, mosaic genome Sebaihia M, Wren BW, Mullany P, Fairweather NF, Minton N, Stabler R, Thomson NR, Roberts AP, Cerdeno-Tarraga AM and Parkhill J <29 more author(s)> Sebaihia M, Wren BW, Mullany P, Fairweather NF, Minton N, Stabler R, Thomson NR, Roberts AP, Cerdeno-Tarraga AM, Wang H, Holden MT, Wright A, Churcher C, Quail MA, Baker S, Bason N, Brooks K, Chillingworth T, Cronin A, Davis P, Dowd L, Fraser A, Feltwell T, Hance Z, Holroyd S, Jagels K, Moule S, Mungall K, Price C, Rabbinowitsch E, Sharp S, Simmonds M, Stevens K, Unwin L, Whithead S, Dupuy B, Dougan G, Barrell B, Parkhill J (- 29) Ref: Nat Genet, 38:779, 2006 : PubMed ESTHER: Sebaihia_2006_Nat.Genet_38_779 PubMedSearch: Sebaihia 2006 Nat.Genet 38 779 PubMedID: 16804543 Gene_locus related to this paper: pepdi-t4eki5, clod6-q18a60, clod6-q183v0, clodi-HYDD, clodr-c9ynf2, pepd6-pip, pepdi-g6brr4 Abstract We determined the complete genome sequence of Clostridium difficile strain 630, a virulent and multidrug-resistant strain. Our analysis indicates that a large proportion (11%) of the genome consists of mobile genetic elements, mainly in the form of conjugative transposons. These mobile elements are putatively responsible for the acquisition by C. difficile of an extensive array of genes involved in antimicrobial resistance, virulence, host interaction and the production of surface structures. The metabolic capabilities encoded in the genome show multiple adaptations for survival and growth within the gut environment. The extreme genome variability was confirmed by whole-genome microarray analysis; it may reflect the organism's niche in the gut and should provide information on the evolution of virulence in this organism. Title: Complete genomes of two clinical Staphylococcus aureus strains: evidence for the rapid evolution of virulence and drug resistance Holden MT, Feil EJ, Lindsay JA, Peacock SJ, Day NP, Enright MC, Foster TJ, Moore CE, Hurst L and Parkhill J <35 more author(s)> Holden MT, Feil EJ, Lindsay JA, Peacock SJ, Day NP, Enright MC, Foster TJ, Moore CE, Hurst L, Atkin R, Barron A, Bason N, Bentley SD, Chillingworth C, Chillingworth T, Churcher C, Clark L, Corton C, Cronin A, Doggett J, Dowd L, Feltwell T, Hance Z, Harris B, Hauser H, Holroyd S, Jagels K, James KD, Lennard N, Line A, Mayes R, Moule S, Mungall K, Ormond D, Quail MA, Rabbinowitsch E, Rutherford K, Sanders M, Sharp S, Simmonds M, Stevens K, Whitehead S, Barrell BG, Spratt BG, Parkhill J (- 35) Ref: Proc Natl Acad Sci U S A, 101:9786, 2004 : PubMed ESTHER: Holden_2004_Proc.Natl.Acad.Sci.U.S.A_101_9786 PubMedSearch: Holden 2004 Proc.Natl.Acad.Sci.U.S.A 101 9786 PubMedID: 15213324 Gene_locus related to this paper: staau-d2feb3, staau-d2uin3, staau-LIP, staau-lipas, staau-MW0741, staau-MW2456, staau-q6gfm6, staau-SA0011, staau-SA0569, staau-SA0572, staau-SA0897, staau-SA1143, staau-SA2240, staau-SA2306, staau-SA2367, staau-SA2422, staau-SAV0321, staau-SAV0446, staau-SAV0457, staau-SAV0655, staau-SAV1014, staau-SAV1765, staau-SAV1793, staau-SAV2188, staau-SAV2350, staau-SAV2594 Abstract Staphylococcus aureus is an important nosocomial and community-acquired pathogen. Its genetic plasticity has facilitated the evolution of many virulent and drug-resistant strains, presenting a major and constantly changing clinical challenge. We sequenced the approximately 2.8-Mbp genomes of two disease-causing S. aureus strains isolated from distinct clinical settings: a recent hospital-acquired representative of the epidemic methicillin-resistant S. aureus EMRSA-16 clone (MRSA252), a clinically important and globally prevalent lineage; and a representative of an invasive community-acquired methicillin-susceptible S. aureus clone (MSSA476). A comparative-genomics approach was used to explore the mechanisms of evolution of clinically important S. aureus genomes and to identify regions affecting virulence and drug resistance. The genome sequences of MRSA252 and MSSA476 have a well conserved core region but differ markedly in their accessory genetic elements. MRSA252 is the most genetically diverse S. aureus strain sequenced to date: approximately 6% of the genome is novel compared with other published genomes, and it contains several unique genetic elements. MSSA476 is methicillin-susceptible, but it contains a novel Staphylococcal chromosomal cassette (SCC) mec-like element (designated SCC(476)), which is integrated at the same site on the chromosome as SCCmec elements in MRSA strains but encodes a putative fusidic acid resistance protein. The crucial role that accessory elements play in the rapid evolution of S. aureus is clearly illustrated by comparing the MSSA476 genome with that of an extremely closely related MRSA community-acquired strain; the differential distribution of large mobile elements carrying virulence and drug-resistance determinants may be responsible for the clinically important phenotypic differences in these strains. Title: Genomic plasticity of the causative agent of melioidosis, Burkholderia pseudomallei Holden MT, Titball RW, Peacock SJ, Cerdeno-Tarraga AM, Atkins T, Crossman LC, Pitt T, Churcher C, Mungall K and Parkhill J <38 more author(s)> Holden MT, Titball RW, Peacock SJ, Cerdeno-Tarraga AM, Atkins T, Crossman LC, Pitt T, Churcher C, Mungall K, Bentley SD, Sebaihia M, Thomson NR, Bason N, Beacham IR, Brooks K, Brown KA, Brown NF, Challis GL, Cherevach I, Chillingworth T, Cronin A, Crossett B, Davis P, DeShazer D, Feltwell T, Fraser A, Hance Z, Hauser H, Holroyd S, Jagels K, Keith KE, Maddison M, Moule S, Price C, Quail MA, Rabbinowitsch E, Rutherford K, Sanders M, Simmonds M, Songsivilai S, Stevens K, Tumapa S, Vesaratchavest M, Whitehead S, Yeats C, Barrell BG, Oyston PC, Parkhill J (- 38) Ref: Proc Natl Acad Sci U S A, 101:14240, 2004 : PubMed ESTHER: Holden_2004_Proc.Natl.Acad.Sci.U.S.A_101_14240 PubMedSearch: Holden 2004 Proc.Natl.Acad.Sci.U.S.A 101 14240 PubMedID: 15377794 Gene_locus related to this paper: burma-a5j5w8, burma-a5tj72, burma-a5tq93, burma-metx, burma-q62a61, burma-q62ar2.1, burma-q62ar2.2, burma-q62ax8, burma-q62b60, burma-q62b79, burma-q62bh9, burma-q62bl4, burma-q62bl7, burma-q62c00, burma-q62cg5, burma-q62d41, burma-q62d56, burma-q62d83, burma-q62dg2, burma-q62du7, burma-q62e67, burma-q62eb8, burma-q62ed8, burma-q62f28, burma-q62fx7, burma-q62g26, burma-q62gx9, burma-q62gy2, burma-q62hq2, burma-q62i62, burma-q62ib8, burma-q62ie8, burma-q62j07, burma-q62j15, burma-q62jn5, burma-q62jy7, burma-q62kb7, burma-q62kg0, burma-q62kh9, burma-q62lp7, burma-q62m40, burma-q62mc3, burma-q62mf4, burma-q62mq7, burma-q629m1, burma-q629p4, burma-q629u0, burp1-q3jvq2, burps-a4lm41, burps-q3v7s4, burps-q63hx2, burps-q63i95, burps-q63im5, burps-q63is4, burps-q63ja6, burps-q63ja9, burps-q63jh5, burps-q63l17, burps-q63l41, burps-q63l44, burps-q63lt9, burps-q63me1, burps-q63mj7, burps-q63mj8, burps-q63mn8, burps-q63mr2, burps-q63n52, burps-q63p18, burps-q63p99, burps-q63ug2, burps-q63ug5, burps-q63xf9, burps-q63y36, burps-q63y45, burps-q63y52, burps-q63y59, burta-q2t474, burps-hboh Abstract Burkholderia pseudomallei is a recognized biothreat agent and the causative agent of melioidosis. This Gram-negative bacterium exists as a soil saprophyte in melioidosis-endemic areas of the world and accounts for 20% of community-acquired septicaemias in northeastern Thailand where half of those affected die. Here we report the complete genome of B. pseudomallei, which is composed of two chromosomes of 4.07 megabase pairs and 3.17 megabase pairs, showing significant functional partitioning of genes between them. The large chromosome encodes many of the core functions associated with central metabolism and cell growth, whereas the small chromosome carries more accessory functions associated with adaptation and survival in different niches. Genomic comparisons with closely and more distantly related bacteria revealed a greater level of gene order conservation and a greater number of orthologous genes on the large chromosome, suggesting that the two replicons have distinct evolutionary origins. A striking feature of the genome was the presence of 16 genomic islands (GIs) that together made up 6.1% of the genome. Further analysis revealed these islands to be variably present in a collection of invasive and soil isolates but entirely absent from the clonally related organism B. mallei. We propose that variable horizontal gene acquisition by B. pseudomallei is an important feature of recent genetic evolution and that this has resulted in a genetically diverse pathogenic species. Title: The complete genome sequence and analysis of Corynebacterium diphtheriae NCTC13129 Cerdeno-Tarraga AM, Efstratiou A, Dover LG, Holden MT, Pallen M, Bentley SD, Besra GS, Churcher C, James KD and Parkhill J <16 more author(s)> Cerdeno-Tarraga AM, Efstratiou A, Dover LG, Holden MT, Pallen M, Bentley SD, Besra GS, Churcher C, James KD, De Zoysa A, Chillingworth T, Cronin A, Dowd L, Feltwell T, Hamlin N, Holroyd S, Jagels K, Moule S, Quail MA, Rabbinowitsch E, Rutherford KM, Thomson NR, Unwin L, Whitehead S, Barrell BG, Parkhill J (- 16) Ref: Nucleic Acids Research, 31:6516, 2003 : PubMed ESTHER: Cerdeno-Tarraga_2003_Nucleic.Acids.Res_31_6516 PubMedSearch: Cerdeno-Tarraga 2003 Nucleic.Acids.Res 31 6516 PubMedID: 14602910 Gene_locus related to this paper: cordi-DIP1007, cordi-DIP1729, cordi-q6ned6, cordi-q6nes3, cordi-q6nes4, cordi-q6nes6, cordi-q6nes8, cordi-q6nev5, cordi-q6nex0, cordi-q6nez6, cordi-q6nf79, cordi-q6nfa8, cordi-q6nfg5, cordi-q6nfz1, cordi-q6ng42, cordi-q6ngl8, cordi-q6nhd8, cordi-q6niz3, cordi-q6nj46, cordi-q6njn3, cordi-q6njn4, cordi-q6njt5, cordi-q6nkb6, cordk-h2hkn5 Abstract Corynebacterium diphtheriae is a Gram-positive, non-spore forming, non-motile, pleomorphic rod belonging to the genus Corynebacterium and the actinomycete group of organisms. The organism produces a potent bacteriophage-encoded protein exotoxin, diphtheria toxin (DT), which causes the symptoms of diphtheria. This potentially fatal infectious disease is controlled in many developed countries by an effective immunisation programme. However, the disease has made a dramatic return in recent years, in particular within the Eastern European region. The largest, and still on-going, outbreak since the advent of mass immunisation started within Russia and the newly independent states of the former Soviet Union in the 1990s. We have sequenced the genome of a UK clinical isolate (biotype gravis strain NCTC13129), representative of the clone responsible for this outbreak. The genome consists of a single circular chromosome of 2 488 635 bp, with no plasmids. It provides evidence that recent acquisition of pathogenicity factors goes beyond the toxin itself, and includes iron-uptake systems, adhesins and fimbrial proteins. This is in contrast to Corynebacterium's nearest sequenced pathogenic relative, Mycobacterium tuberculosis, where there is little evidence of recent horizontal DNA acquisition. The genome itself shows an unusually extreme large-scale compositional bias, being noticeably higher in G+C near the origin than at the terminus. Title: Comparative analysis of the genome sequences of Bordetella pertussis, Bordetella parapertussis and Bordetella bronchiseptica Parkhill J, Sebaihia M, Preston A, Murphy LD, Thomson N, Harris DE, Holden MT, Churcher CM, Bentley SD and Maskell DJ <43 more author(s)> Parkhill J, Sebaihia M, Preston A, Murphy LD, Thomson N, Harris DE, Holden MT, Churcher CM, Bentley SD, Mungall KL, Cerdeno-Tarraga AM, Temple L, James K, Harris B, Quail MA, Achtman M, Atkin R, Baker S, Basham D, Bason N, Cherevach I, Chillingworth T, Collins M, Cronin A, Davis P, Doggett J, Feltwell T, Goble A, Hamlin N, Hauser H, Holroyd S, Jagels K, Leather S, Moule S, Norberczak H, O'Neil S, Ormond D, Price C, Rabbinowitsch E, Rutter S, Sanders M, Saunders D, Seeger K, Sharp S, Simmonds M, Skelton J, Squares R, Squares S, Stevens K, Unwin L, Whitehead S, Barrell BG, Maskell DJ (- 43) Ref: Nat Genet, 35:32, 2003 : PubMed ESTHER: Parkhill_2003_Nat.Genet_35_32 PubMedSearch: Parkhill 2003 Nat.Genet 35 32 PubMedID: 12910271 Gene_locus related to this paper: borbr-BB0273, borbr-BB0570, borbr-BB0670, borbr-BB1064, borbr-BB1079, borbr-BB1247, borbr-BB1498, borbr-BB2718, borbr-BB4129, borbr-BB4247, borbr-MHPC, borbr-q7wdw1, borbr-q7wiz8, borbr-q7wk25, borbr-q7wmc2, borbr-q7wpd9, borpa-q7w3f3, borpa-q7w9v8, borpe-BIOH, borpe-BP0300, borpe-BP2114, borpe-BP2146, borpe-BP2511, borpe-BP3096, borpe-BP3623, borpe-BP3691, borpe-CATD2, borpe-METX, borpe-O30449, borpe-PHBC, borpe-q7vsl4, borpe-q7vt07, borpe-q7vtg0, borpe-q7vtv2, borpe-q7vus4, borpe-q7vuv4, borpe-q7vv11, borpe-q7vv48, borpe-q7vvf6, borpe-q7vwu4, borpe-q7vyn0, borpe-q7vyq4, borpe-q7vz26, borpe-q7vzb4, borpe-q7vzj6, borpe-q7w073 Abstract Bordetella pertussis, Bordetella parapertussis and Bordetella bronchiseptica are closely related Gram-negative beta-proteobacteria that colonize the respiratory tracts of mammals. B. pertussis is a strict human pathogen of recent evolutionary origin and is the primary etiologic agent of whooping cough. B. parapertussis can also cause whooping cough, and B. bronchiseptica causes chronic respiratory infections in a wide range of animals. We sequenced the genomes of B. bronchiseptica RB50 (5,338,400 bp; 5,007 predicted genes), B. parapertussis 12822 (4,773,551 bp; 4,404 genes) and B. pertussis Tohama I (4,086,186 bp; 3,816 genes). Our analysis indicates that B. parapertussis and B. pertussis are independent derivatives of B. bronchiseptica-like ancestors. During the evolution of these two host-restricted species there was large-scale gene loss and inactivation; host adaptation seems to be a consequence of loss, not gain, of function, and differences in virulence may be related to loss of regulatory or control functions. Title: Sequence of Plasmodium falciparum chromosomes 1, 3-9 and 13 Hall N, Pain A, Berriman M, Churcher C, Harris B, Harris D, Mungall K, Bowman S, Atkin R and Barrell BG <70 more author(s)> Hall N, Pain A, Berriman M, Churcher C, Harris B, Harris D, Mungall K, Bowman S, Atkin R, Baker S, Barron A, Brooks K, Buckee CO, Burrows C, Cherevach I, Chillingworth C, Chillingworth T, Christodoulou Z, Clark L, Clark R, Corton C, Cronin A, Davies R, Davis P, Dear P, Dearden F, Doggett J, Feltwell T, Goble A, Goodhead I, Gwilliam R, Hamlin N, Hance Z, Harper D, Hauser H, Hornsby T, Holroyd S, Horrocks P, Humphray S, Jagels K, James KD, Johnson D, Kerhornou A, Knights A, Konfortov B, Kyes S, Larke N, Lawson D, Lennard N, Line A, Maddison M, McLean J, Mooney P, Moule S, Murphy L, Oliver K, Ormond D, Price C, Quail MA, Rabbinowitsch E, Rajandream MA, Rutter S, Rutherford KM, Sanders M, Simmonds M, Seeger K, Sharp S, Smith R, Squares R, Squares S, Stevens K, Taylor K, Tivey A, Unwin L, Whitehead S, Woodward J, Sulston JE, Craig A, Newbold C, Barrell BG (- 70) Ref: Nature, 419:527, 2002 : PubMed ESTHER: Hall_2002_Nature_419_527 PubMedSearch: Hall 2002 Nature 419 527 PubMedID: 12368867 Gene_locus related to this paper: plaf7-c0h4q4, plafa-MAL6P1.135, plafa-PFD0185C, plafa-PFI1775W, plafa-PFI1800W Abstract Since the sequencing of the first two chromosomes of the malaria parasite, Plasmodium falciparum, there has been a concerted effort to sequence and assemble the entire genome of this organism. Here we report the sequence of chromosomes 1, 3-9 and 13 of P. falciparum clone 3D7--these chromosomes account for approximately 55% of the total genome. We describe the methods used to map, sequence and annotate these chromosomes. By comparing our assemblies with the optical map, we indicate the completeness of the resulting sequence. During annotation, we assign Gene Ontology terms to the predicted gene products, and observe clustering of some malaria-specific terms to specific chromosomes. We identify a highly conserved sequence element found in the intergenic region of internal var genes that is not associated with their telomeric counterparts. Title: The genome sequence of Schizosaccharomyces pombe Wood V, Gwilliam R, Rajandream MA, Lyne M, Lyne R, Stewart A, Sgouros J, Peat N, Hayles J and Nurse P <124 more author(s)> Wood V, Gwilliam R, Rajandream MA, Lyne M, Lyne R, Stewart A, Sgouros J, Peat N, Hayles J, Baker S, Basham D, Bowman S, Brooks K, Brown D, Brown S, Chillingworth T, Churcher C, Collins M, Connor R, Cronin A, Davis P, Feltwell T, Fraser A, Gentles S, Goble A, Hamlin N, Harris D, Hidalgo J, Hodgson G, Holroyd S, Hornsby T, Howarth S, Huckle EJ, Hunt S, Jagels K, James K, Jones L, Jones M, Leather S, McDonald S, McLean J, Mooney P, Moule S, Mungall K, Murphy L, Niblett D, Odell C, Oliver K, O'Neil S, Pearson D, Quail MA, Rabbinowitsch E, Rutherford K, Rutter S, Saunders D, Seeger K, Sharp S, Skelton J, Simmonds M, Squares R, Squares S, Stevens K, Taylor K, Taylor RG, Tivey A, Walsh S, Warren T, Whitehead S, Woodward J, Volckaert G, Aert R, Robben J, Grymonprez B, Weltjens I, Vanstreels E, Rieger M, Schafer M, Muller-Auer S, Gabel C, Fuchs M, Dusterhoft A, Fritzc C, Holzer E, Moestl D, Hilbert H, Borzym K, Langer I, Beck A, Lehrach H, Reinhardt R, Pohl TM, Eger P, Zimmermann W, Wedler H, Wambutt R, Purnelle B, Goffeau A, Cadieu E, Dreano S, Gloux S, Lelaure V, Mottier S, Galibert F, Aves SJ, Xiang Z, Hunt C, Moore K, Hurst SM, Lucas M, Rochet M, Gaillardin C, Tallada VA, Garzon A, Thode G, Daga RR, Cruzado L, Jimenez J, Sanchez M, del Rey F, Benito J, Dominguez A, Revuelta JL, Moreno S, Armstrong J, Forsburg SL, Cerutti L, Lowe T, McCombie WR, Paulsen I, Potashkin J, Shpakovski GV, Ussery D, Barrell BG, Nurse P (- 124) Ref: Nature, 415:871, 2002 : PubMed ESTHER: Wood_2002_Nature_415_871 PubMedSearch: Wood 2002 Nature 415 871 PubMedID: 11859360 Gene_locus related to this paper: schpo-APTH1, schpo-be46, schpo-BST1, schpo-C2E11.08, schpo-C14C4.15C, schpo-C22H12.03, schpo-C23C4.16C, schpo-C57A10.08C, schpo-dyr, schpo-este1, schpo-KEX1, schpo-PCY1, schpo-pdat, schpo-PLG7, schpo-ppme1, schpo-q9c0y8, schpo-SPAC4A8.06C, schpo-C22A12.06C, schpo-SPAC977.15, schpo-SPAPB1A11.02, schpo-SPBC14C8.15, schpo-SPBC530.12C, schpo-SPBC1711.12, schpo-SPBPB2B2.02, schpo-SPCC5E4.05C, schpo-SPCC417.12, schpo-SPCC1672.09, schpo-yb4e, schpo-yblh, schpo-ydw6, schpo-ye7a, schpo-ye63, schpo-ye88, schpo-yeld, schpo-yk68, schpo-clr3, schpo-ykv6 Abstract We have sequenced and annotated the genome of fission yeast (Schizosaccharomyces pombe), which contains the smallest number of protein-coding genes yet recorded for a eukaryote: 4,824. The centromeres are between 35 and 110 kilobases (kb) and contain related repeats including a highly conserved 1.8-kb element. Regions upstream of genes are longer than in budding yeast (Saccharomyces cerevisiae), possibly reflecting more-extended control regions. Some 43% of the genes contain introns, of which there are 4,730. Fifty genes have significant similarity with human disease genes; half of these are cancer related. We identify highly conserved genes important for eukaryotic cell organization including those required for the cytoskeleton, compartmentation, cell-cycle control, proteolysis, protein phosphorylation and RNA splicing. These genes may have originated with the appearance of eukaryotic life. Few similarly conserved genes that are important for multicellular organization were identified, suggesting that the transition from prokaryotes to eukaryotes required more new genes than did the transition from unicellular to multicellular organization. Title: Massive gene decay in the leprosy bacillus Cole ST, Eiglmeier K, Parkhill J, James KD, Thomson NR, Wheeler PR, Honore N, Garnier T, Churcher C and Barrell BG <34 more author(s)> Cole ST, Eiglmeier K, Parkhill J, James KD, Thomson NR, Wheeler PR, Honore N, Garnier T, Churcher C, Harris D, Mungall K, Basham D, Brown D, Chillingworth T, Connor R, Davies RM, Devlin K, Duthoy S, Feltwell T, Fraser A, Hamlin N, Holroyd S, Hornsby T, Jagels K, Lacroix C, Maclean J, Moule S, Murphy L, Oliver K, Quail MA, Rajandream MA, Rutherford KM, Rutter S, Seeger K, Simon S, Simmonds M, Skelton J, Squares R, Squares S, Stevens K, Taylor K, Whitehead S, Woodward JR, Barrell BG (- 34) Ref: Nature, 409:1007, 2001 : PubMed ESTHER: Cole_2001_Nature_409_1007 PubMedSearch: Cole 2001 Nature 409 1007 PubMedID: 11234002 Gene_locus related to this paper: mycle-a85a, mycle-a85b, mycle-a85c, mycle-lipG, mycle-LPQC, mycle-metx, mycle-ML0314, mycle-ML0370, mycle-ML0376, mycle-ML1339, mycle-ML1444, mycle-ML1632, mycle-ML1633, mycle-ML1921, mycle-ML2269, mycle-ML2297, mycle-ML2359, mycle-ML2603, mycle-mpt5, mycle-PKS13, mycle-PTRB, mycle-q9cc62, mycle-q9cdb3 Abstract Leprosy, a chronic human neurological disease, results from infection with the obligate intracellular pathogen Mycobacterium leprae, a close relative of the tubercle bacillus. Mycobacterium leprae has the longest doubling time of all known bacteria and has thwarted every effort at culture in the laboratory. Comparing the 3.27-megabase (Mb) genome sequence of an armadillo-derived Indian isolate of the leprosy bacillus with that of Mycobacterium tuberculosis (4.41 Mb) provides clear explanations for these properties and reveals an extreme case of reductive evolution. Less than half of the genome contains functional genes but pseudogenes, with intact counterparts in M. tuberculosis, abound. Genome downsizing and the current mosaic arrangement appear to have resulted from extensive recombination events between dispersed repetitive sequences. Gene deletion and decay have eliminated many important metabolic activities including siderophore production, part of the oxidative and most of the microaerophilic and anaerobic respiratory chains, and numerous catabolic systems and their regulatory circuits. Title: Genome sequence of Yersinia pestis, the causative agent of plague. Parkhill J, Wren BW, Thomson NR, Titball RW, Holden MTG, Prentice MB, Sebaihia M, James KD, Churcher C and Barrell BG <25 more author(s)> Parkhill J, Wren BW, Thomson NR, Titball RW, Holden MTG, Prentice MB, Sebaihia M, James KD, Churcher C, Mungall KL, Baker S, Basham D, Bentley SD, Brooks K, Cerdeno-Tarraga AM, Chillingworth T, Cronin A, Davies RM, Davis P, Dougan G, Feltwell T, Hamlin N, Holroyd S, Jagels K, Karlyshev AV, Leather S, Moule S, Oyston PCF, Quail M, Rutherford K, Simmonds M, Skelton J, Stevens K, Whitehead S, Barrell BG (- 25) Ref: Nature, 413:523, 2001 : PubMed ESTHER: Parkhill_2001_Nature_413_523 PubMedSearch: Parkhill 2001 Nature 413 523 PubMedID: 11586360 Gene_locus related to this paper: yerpe-BIOH, yerpe-dlhh, yerpe-IRP1, yerpe-PIP, yerpe-PLDB, yerpe-PTRB, yerpe-q8zey9, yerpe-y1616, yerpe-y3224, yerpe-YBTT, yerpe-YPLA, yerpe-YPO0180, yerpe-YPO0667, yerpe-YPO0773, yerpe-YPO0776, yerpe-YPO0986, yerpe-YPO1501, yerpe-YPO1997, yerpe-YPO2002, yerpe-YPO2336, yerpe-YPO2526, yerpe-YPO2638, yerpe-YPO2814, yerpe-YPO4014 Abstract The Gram-negative bacterium Yersinia pestis is the causative agent of the systemic invasive infectious disease classically referred to as plague, and has been responsible for three human pandemics: the Justinian plague (sixth to eighth centuries), the Black Death (fourteenth to nineteenth centuries) and modern plague (nineteenth century to the present day). The recent identification of strains resistant to multiple drugs and the potential use of Y. pestis as an agent of biological warfare mean that plague still poses a threat to human health. Here we report the complete genome sequence of Y. pestis strain CO92, consisting of a 4.65-megabase (Mb) chromosome and three plasmids of 96.2 kilobases (kb), 70.3 kb and 9.6 kb. The genome is unusually rich in insertion sequences and displays anomalies in GC base-composition bias, indicating frequent intragenomic recombination. Many genes seem to have been acquired from other bacteria and viruses (including adhesins, secretion systems and insecticidal toxins). The genome contains around 150 pseudogenes, many of which are remnants of a redundant enteropathogenic lifestyle. The evidence of ongoing genome fluidity, expansion and decay suggests Y. pestis is a pathogen that has undergone large-scale genetic flux and provides a unique insight into the ways in which new and highly virulent pathogens evolve. Title: Complete genome sequence of a multiple drug resistant Salmonella enterica serovar Typhi CT18 Parkhill J, Dougan G, James KD, Thomson NR, Pickard D, Wain J, Churcher C, Mungall KL, Bentley SD and Barrell BG <31 more author(s)> Parkhill J, Dougan G, James KD, Thomson NR, Pickard D, Wain J, Churcher C, Mungall KL, Bentley SD, Holden MT, Sebaihia M, Baker S, Basham D, Brooks K, Chillingworth T, Connerton P, Cronin A, Davis P, Davies RM, Dowd L, White N, Farrar J, Feltwell T, Hamlin N, Haque A, Hien TT, Holroyd S, Jagels K, Krogh A, Larsen TS, Leather S, Moule S, O'Gaora P, Parry C, Quail M, Rutherford K, Simmonds M, Skelton J, Stevens K, Whitehead S, Barrell BG (- 31) Ref: Nature, 413:848, 2001 : PubMed ESTHER: Parkhill_2001_Nature_413_848 PubMedSearch: Parkhill 2001 Nature 413 848 PubMedID: 11677608 Gene_locus related to this paper: salen-OPDB, salti-q8z717, salty-AES, salty-BIOH, salty-ENTF, salty-FES, salty-IROD, salty-IROE, salty-PLDB, salty-STM2547, salty-STM4506, salty-STY1441, salty-STY2428, salty-STY3846, salty-yafa, salty-YBFF, salty-ycfp, salty-YFBB, salty-YJFP, salty-YQIA Abstract Salmonella enterica serovar Typhi (S. typhi) is the aetiological agent of typhoid fever, a serious invasive bacterial disease of humans with an annual global burden of approximately 16 million cases, leading to 600,000 fatalities. Many S. enterica serovars actively invade the mucosal surface of the intestine but are normally contained in healthy individuals by the local immune defence mechanisms. However, S. typhi has evolved the ability to spread to the deeper tissues of humans, including liver, spleen and bone marrow. Here we have sequenced the 4,809,037-base pair (bp) genome of a S. typhi (CT18) that is resistant to multiple drugs, revealing the presence of hundreds of insertions and deletions compared with the Escherichia coli genome, ranging in size from single genes to large islands. Notably, the genome sequence identifies over two hundred pseudogenes, several corresponding to genes that are known to contribute to virulence in Salmonella typhimurium. This genetic degradation may contribute to the human-restricted host range for S. typhi. CT18 harbours a 218,150-bp multiple-drug-resistance incH1 plasmid (pHCM1), and a 106,516-bp cryptic plasmid (pHCM2), which shows recent common ancestry with a virulence plasmid of Yersinia pestis. Title: Complete DNA sequence of a serogroup A strain of Neisseria meningitidis Z2491 Parkhill J, Achtman M, James KD, Bentley SD, Churcher C, Klee SR, Morelli G, Basham D, Brown D and Barrell BG <18 more author(s)> Parkhill J, Achtman M, James KD, Bentley SD, Churcher C, Klee SR, Morelli G, Basham D, Brown D, Chillingworth T, Davies RM, Davis P, Devlin K, Feltwell T, Hamlin N, Holroyd S, Jagels K, Leather S, Moule S, Mungall K, Quail MA, Rajandream MA, Rutherford KM, Simmonds M, Skelton J, Whitehead S, Spratt BG, Barrell BG (- 18) Ref: Nature, 404:502, 2000 : PubMed ESTHER: Parkhill_2000_Nature_404_502 PubMedSearch: Parkhill 2000 Nature 404 502 PubMedID: 10761919 Gene_locus related to this paper: neima-metx, neimb-q9k0t9, neime-ESD, neime-NMA2216, neime-NMB0276, neime-NMB1877, neimf-a1kta9, neime-r0tza2 Abstract Neisseria meningitidis causes bacterial meningitis and is therefore responsible for considerable morbidity and mortality in both the developed and the developing world. Meningococci are opportunistic pathogens that colonize the nasopharynges and oropharynges of asymptomatic carriers. For reasons that are still mostly unknown, they occasionally gain access to the blood, and subsequently to the cerebrospinal fluid, to cause septicaemia and meningitis. N. meningitidis strains are divided into a number of serogroups on the basis of the immunochemistry of their capsular polysaccharides; serogroup A strains are responsible for major epidemics and pandemics of meningococcal disease, and therefore most of the morbidity and mortality associated with this disease. Here we have determined the complete genome sequence of a serogroup A strain of Neisseria meningitidis, Z2491. The sequence is 2,184,406 base pairs in length, with an overall G+C content of 51.8%, and contains 2,121 predicted coding sequences. The most notable feature of the genome is the presence of many hundreds of repetitive elements, ranging from short repeats, positioned either singly or in large multiple arrays, to insertion sequences and gene duplications of one kilobase or more. Many of these repeats appear to be involved in genome fluidity and antigenic variation in this important human pathogen. Title: The genome sequence of the food-borne pathogen Campylobacter jejuni reveals hypervariable sequences Parkhill J, Wren BW, Mungall K, Ketley JM, Churcher C, Basham D, Chillingworth T, Davies RM, Feltwell T and Barrell BG <11 more author(s)> Parkhill J, Wren BW, Mungall K, Ketley JM, Churcher C, Basham D, Chillingworth T, Davies RM, Feltwell T, Holroyd S, Jagels K, Karlyshev AV, Moule S, Pallen MJ, Penn CW, Quail MA, Rajandream MA, Rutherford KM, van Vliet AH, Whitehead S, Barrell BG (- 11) Ref: Nature, 403:665, 2000 : PubMed ESTHER: Parkhill_2000_Nature_403_665 PubMedSearch: Parkhill 2000 Nature 403 665 PubMedID: 10688204 Gene_locus related to this paper: camco-e0qbj3, camco-q4hhu5, camje-a3zji1, camje-CJ0796C, camjr-q5ht69, camju-a3yll6, camju-Q9ZF63 Abstract Campylobacter jejuni, from the delta-epsilon group of proteobacteria, is a microaerophilic, Gram-negative, flagellate, spiral bacterium-properties it shares with the related gastric pathogen Helicobacter pylori. It is the leading cause of bacterial food-borne diarrhoeal disease throughout the world. In addition, infection with C. jejuni is the most frequent antecedent to a form of neuromuscular paralysis known as Guillain-Barre syndrome. Here we report the genome sequence of C. jejuni NCTC11168. C. jejuni has a circular chromosome of 1,641,481 base pairs (30.6% G+C) which is predicted to encode 1,654 proteins and 54 stable RNA species. The genome is unusual in that there are virtually no insertion sequences or phage-associated sequences and very few repeat sequences. One of the most striking findings in the genome was the presence of hypervariable sequences. These short homopolymeric runs of nucleotides were commonly found in genes encoding the biosynthesis or modification of surface structures, or in closely linked genes of unknown function. The apparently high rate of variation of these homopolymeric tracts may be important in the survival strategy of C. jejuni. Title: The complete nucleotide sequence of chromosome 3 of Plasmodium falciparum Bowman S, Lawson D, Basham D, Brown D, Chillingworth T, Churcher CM, Craig A, Davies RM, Devlin K and Barrell BG <26 more author(s)> Bowman S, Lawson D, Basham D, Brown D, Chillingworth T, Churcher CM, Craig A, Davies RM, Devlin K, Feltwell T, Gentles S, Gwilliam R, Hamlin N, Harris D, Holroyd S, Hornsby T, Horrocks P, Jagels K, Jassal B, Kyes S, McLean J, Moule S, Mungall K, Murphy L, Oliver K, Quail MA, Rajandream MA, Rutter S, Skelton J, Squares R, Squares S, Sulston JE, Whitehead S, Woodward JR, Newbold C, Barrell BG (- 26) Ref: Nature, 400:532, 1999 : PubMed ESTHER: Bowman_1999_Nature_400_532 PubMedSearch: Bowman 1999 Nature 400 532 PubMedID: 10448855 Gene_locus related to this paper: plafa-PFC0950C Abstract Analysis of Plasmodium falciparum chromosome 3, and comparison with chromosome 2, highlights novel features of chromosome organization and gene structure. The sub-telomeric regions of chromosome 3 show a conserved order of features, including repetitive DNA sequences, members of multigene families involved in pathogenesis and antigenic variation, a number of conserved pseudogenes, and several genes of unknown function. A putative centromere has been identified that has a core region of about 2 kilobases with an extremely high (adenine + thymidine) composition and arrays of tandem repeats. We have predicted 215 protein-coding genes and two transfer RNA genes in the 1,060,106-base-pair chromosome sequence. The predicted protein-coding genes can be divided into three main classes: 52.6% are not spliced, 45.1% have a large exon with short additional 5' or 3' exons, and 2.3% have a multiple exon structure more typical of higher eukaryotes. Title: Deciphering the biology of Mycobacterium tuberculosis from the complete genome sequence Cole ST, Brosch R, Parkhill J, Garnier T, Churcher C, Harris D, Gordon SV, Eiglmeier K, Gas S and Barrell BG <32 more author(s)> Cole ST, Brosch R, Parkhill J, Garnier T, Churcher C, Harris D, Gordon SV, Eiglmeier K, Gas S, Barry CE, 3rd, Tekaia F, Badcock K, Basham D, Brown D, Chillingworth T, Connor R, Davies R, Devlin K, Feltwell T, Gentles S, Hamlin N, Holroyd S, Hornsby T, Jagels K, Krogh A, McLean J, Moule S, Murphy L, Oliver K, Osborne J, Quail MA, Rajandream MA, Rogers J, Rutter S, Seeger K, Skelton J, Squares R, Squares S, Sulston JE, Taylor K, Whitehead S, Barrell BG (- 32) Ref: Nature, 393:537, 1998 : PubMed ESTHER: Cole_1998_Nature_393_537 PubMedSearch: Cole 1998 Nature 393 537 PubMedID: 9634230 Gene_locus related to this paper: myctu-a85a, myctu-a85b, myctu-a85c, myctu-bpoC, myctu-cut3, myctu-cutas1, myctu-cutas2, myctu-d5yk66, myctu-ephA, myctu-ephB, myctu-ephc, myctu-ephd, myctu-ephE, myctu-ephF, myctu-hpx, myctu-linb, myctu-lipG, myctu-lipJ, myctu-LIPS, myctu-lipv, myctu-LPQC, myctu-LPQP, myctu-MBTB, myctu-metx, myctu-mpt51, myctu-MT1628, myctu-MT3441, myctu-p71654, myctu-p95011, myctu-PKS6, myctu-PKS13, myctu-ppe42, myctu-ppe63, myctu-Rv1430, myctu-RV0045C, myctu-Rv0077c, myctu-Rv0151c, myctu-Rv0152c, myctu-Rv0159c, myctu-Rv0160c, myctu-rv0183, myctu-Rv0217c, myctu-Rv0220, myctu-Rv0272c, myctu-RV0293C, myctu-RV0421C, myctu-RV0457C, myctu-RV0519C, myctu-RV0774C, myctu-RV0782, myctu-RV0840C, myctu-Rv1069c, myctu-Rv1076, myctu-RV1123C, myctu-Rv1184c, myctu-Rv1190, myctu-Rv1191, myctu-RV1192, myctu-RV1215C, myctu-Rv1399c, myctu-Rv1400c, myctu-Rv1426c, myctu-RV1639C, myctu-RV1683, myctu-RV1758, myctu-Rv1800, myctu-Rv1833c, myctu-RV2054, myctu-RV2296, myctu-Rv2385, myctu-Rv2485c, myctu-RV2627C, myctu-RV2672, myctu-RV2695, myctu-RV2765, myctu-RV2800, myctu-RV2854, myctu-Rv2970c, myctu-Rv3084, myctu-Rv3097c, myctu-rv3177, myctu-Rv3312c, myctu-RV3452, myctu-RV3473C, myctu-Rv3487c, myctu-Rv3569c, myctu-Rv3591c, myctu-RV3724, myctu-Rv3802c, myctu-Rv3822, myctu-y0571, myctu-y963, myctu-Y1834, myctu-y1835, myctu-y2079, myctu-Y2307, myctu-yc88, myctu-ym23, myctu-ym24, myctu-YR15, myctu-yt28 Abstract Countless millions of people have died from tuberculosis, a chronic infectious disease caused by the tubercle bacillus. The complete genome sequence of the best-characterized strain of Mycobacterium tuberculosis, H37Rv, has been determined and analysed in order to improve our understanding of the biology of this slow-growing pathogen and to help the conception of new prophylactic and therapeutic interventions. The genome comprises 4,411,529 base pairs, contains around 4,000 genes, and has a very high guanine + cytosine content that is reflected in the biased amino-acid content of the proteins. M. tuberculosis differs radically from other bacteria in that a very large portion of its coding capacity is devoted to the production of enzymes involved in lipogenesis and lipolysis, and to two new families of glycine-rich proteins with a repetitive structure that may represent a source of antigenic variation. | |||||||
|
