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M Sebaihia,
A M Bocsanczy,
B S Biehl,
M A Quail,
N T Perna,
J D Glasner,
G A Declerck,
S Cartinhour,
D J Schneider, S D Bentley,
J Parkhill,
S V Beer
[show abstract]
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ABSTRACT: Erwinia amylovora causes the economically important disease fire blight that affects rosaceous plants,
especially pear and apple. Here we report the complete genome sequence and annotation of strain ATCC 49946. The analysis of the sequence and its comparison with sequenced genomes of closely related enterobacteria revealed signs of pathoadaptation to rosaceous hosts.
Journal of bacteriology 05/2010; 192(7):2020-2021. · 3.94 Impact Factor
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M Sebaihia,
A M Bocsanczy,
B S Biehl,
M A Quail,
N T Perna,
J D Glasner,
G A DeClerck,
S Cartinhour,
D J Schneider, S D Bentley,
J Parkhill,
S V Beer
[show abstract]
[hide abstract]
ABSTRACT: Erwinia amylovora causes the economically important disease fire blight that affects rosaceous plants, especially pear and apple. Here we report the complete genome sequence and annotation of strain ATCC 49946. The analysis of the sequence and its comparison with sequenced genomes of closely related enterobacteria revealed signs of pathoadaptation to rosaceous hosts.
Journal of bacteriology 04/2010; 192(7):2020-1. · 3.94 Impact Factor
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Silby,
Mark W.,
A. M. Cerdeno-Tarraga,
G. Vernikos,
Giddens,
Stephen R.,
R. Jackson,
G.M. Preston,
X.-X. Zhang,
C.D. Moon, [......],
M. A. Quail,
E. Saunders,
K. Mavromatis,
T.S. Brettin, S.D. Bentley,
C. M. Thomas,
J. Parkhill,
S. B. Levy,
P. B. Rainey,
N. R. Thomson
Genome Biology. 01/2009; 10:R51.
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Phytopathology. 01/2007; 97(7):S11-S12.
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K S Bell,
M Sebaihia,
L Pritchard,
M T G Holden,
L J Hyman,
M C Holeva,
N R Thomson, S D Bentley,
L J C Churcher,
K Mungall, [......],
D Ormond,
C Price,
M A Quail,
M Sanders,
D Walker,
S Whitehead,
G P C Salmond,
P R J Birch,
J Parkhill,
I K Toth
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[hide abstract]
ABSTRACT: The bacterial family Enterobacteriaceae is notable for its well studied human pathogens, including Salmonella, Yersinia, Shigella, and Escherichia spp. However, it also contains several plant pathogens. We report the genome sequence of a plant pathogenic enterobacterium, Erwinia carotovora subsp. atroseptica (Eca) strain SCRI1043, the causative agent of soft rot and blackleg potato diseases. Approximately 33% of Eca genes are not shared with sequenced enterobacterial human pathogens, including some predicted to facilitate unexpected metabolic traits, such as nitrogen fixation and opine catabolism. This proportion of genes also contains an overrepresentation of pathogenicity determinants, including possible horizontally acquired gene clusters for putative type IV secretion and polyketide phytotoxin synthesis. To investigate whether these gene clusters play a role in the disease process, an arrayed set of insertional mutants was generated, and mutations were identified. Plant bioassays showed that these mutants were significantly reduced in virulence, demonstrating both the presence of novel pathogenicity determinants in Eca, and the impact of functional genomics in expanding our understanding of phytopathogenicity in the Enterobacteriaceae.
Proceedings of the National Academy of Sciences 08/2004; 101(30):11105-10. · 9.68 Impact Factor
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S D Bentley,
S Brown,
L D Murphy,
D E Harris,
M A Quail,
J Parkhill,
B G Barrell,
J R McCormick,
R I Santamaria,
R Losick,
M Yamasaki,
H Kinashi,
C W Chen,
G Chandra,
D Jakimowicz,
H M Kieser,
T Kieser,
K F Chater
[show abstract]
[hide abstract]
ABSTRACT: The sequencing of the entire genetic complement of Streptomyces coelicolor A3(2) has been completed with the determination of the 365,023 bp sequence of the linear plasmid SCP1. Remarkably, the functional distribution of SCP1 genes somewhat resembles that of the chromosome: predicted gene products/functions include ECF sigma factors, antibiotic biosynthesis, a gamma-butyrolactone signalling system, members of the actinomycete-specific Wbl class of regulatory proteins and 14 secreted proteins. Some of these genes are among the 18 that contain a TTA codon, making them targets for the developmentally important tRNA encoded by the bldA gene. RNA analysis and gene fusions showed that one of the TTA-containing genes is part of a large bldA-dependent operon, the gene products of which include three proteins isolated from the spore surface by detergent washing (SapC, D and E), and several probable metabolic enzymes. SCP1 shows much evidence of recombinational interactions with other replicons and transposable elements during its history. For example, it has two sets of partitioning genes (which may explain why an integrated copy of SCP1 partially suppressed the defective partitioning of a parAB-deleted chromosome during sporulation). SCP1 carries a cluster of probable transfer determinants and genes encoding likely DNA polymerase III subunits, but it lacks an obvious candidate gene for the terminal protein associated with its ends. This may be related to atypical features of its end sequences.
Molecular Microbiology 04/2004; 51(6):1615-28. · 5.01 Impact Factor
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S. D. Bentley,
S. Brown,
L. D. Murphy,
D. E. Harris,
M. A. Quail,
J. Parkhill,
B. G. Barrell,
J. R. McCormick,
R. I. Santamaria,
R. Losick,
M. Yamasaki,
H. Kinashi,
C. W. Chen,
G. Chandra,
D. Jakimowicz,
H. M. Kieser,
T. Kieser,
K. F. Chater
[show abstract]
[hide abstract]
ABSTRACT: The sequencing of the entire genetic complement of Streptomyces coelicolor A3(2) has been completed with the determination of the 365 023 bp sequence of the linear plasmid SCP1. Remarkably, the functional distribution of SCP1 genes somewhat resembles that of the chromosome: predicted gene products/functions include ECF sigma factors, antibiotic biosynthesis, a gamma-butyrolactone signalling system, members of the actinomycete-specific Wbl class of regulatory proteins and 14 secreted proteins. Some of these genes are among the 18 that contain a TTA codon, making them targets for the developmentally important tRNA encoded by the bldA gene. RNA analysis and gene fusions showed that one of the TTA-containing genes is part of a large bldA-dependent operon, the gene products of which include three proteins isolated from the spore surface by detergent washing (SapC, D and E), and several probable metabolic enzymes. SCP1 shows much evidence of recombinational interactions with other replicons and transposable elements during its history. For example, it has two sets of partitioning genes (which may explain why an integrated copy of SCP1 partially suppressed the defective partitioning of a parAB-deleted chromosome during sporulation). SCP1 carries a cluster of probable transfer determinants and genes encoding likely DNA polymerase III subunits, but it lacks an obvious candidate gene for the terminal protein associated with its ends. This may be related to atypical features of its end sequences.
Molecular Microbiology 02/2004; 51(6):1615 - 1628. · 5.01 Impact Factor
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A M Cerdeño-Tárraga,
A Efstratiou,
L G Dover,
M T G Holden,
M Pallen, S D Bentley,
G S Besra,
C Churcher,
K D James,
A De Zoysa, [......],
K Jagels,
S Moule,
M A Quail,
E Rabbinowitsch,
K M Rutherford,
N R Thomson,
L Unwin,
S Whitehead,
B G Barrell,
J Parkhill
[show abstract]
[hide abstract]
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.
Nucleic Acids Research 12/2003; 31(22):6516-23. · 8.03 Impact Factor
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S D Bentley,
K F Chater,
A-M Cerdeño-Tárraga,
G L Challis,
N R Thomson,
K D James,
D E Harris,
M A Quail,
H Kieser,
D Harper, [......],
S Sharp,
R Squares,
S Squares,
K Taylor,
T Warren,
A Wietzorrek,
J Woodward,
B G Barrell,
J Parkhill,
D A Hopwood
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ABSTRACT: Streptomyces coelicolor is a representative of the group of soil-dwelling, filamentous bacteria responsible for producing most natural antibiotics used in human and veterinary medicine. Here we report the 8,667,507 base pair linear chromosome of this organism, containing the largest number of genes so far discovered in a bacterium. The 7,825 predicted genes include more than 20 clusters coding for known or predicted secondary metabolites. The genome contains an unprecedented proportion of regulatory genes, predominantly those likely to be involved in responses to external stimuli and stresses, and many duplicated gene sets that may represent 'tissue-specific' isoforms operating in different phases of colonial development, a unique situation for a bacterium. An ancient synteny was revealed between the central 'core' of the chromosome and the whole chromosome of pathogens Mycobacterium tuberculosis and Corynebacterium diphtheriae. The genome sequence will greatly increase our understanding of microbial life in the soil as well as aiding the generation of new drug candidates by genetic engineering.
Nature 06/2002; 417(6885):141-7. · 36.28 Impact Factor
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J Parkhill,
G Dougan,
K D James,
N R Thomson,
D Pickard,
J Wain,
C Churcher,
K L Mungall, S D Bentley,
M T Holden, [......],
S Moule,
P O'Gaora,
C Parry,
M Quail,
K Rutherford,
M Simmonds,
J Skelton,
K Stevens,
S Whitehead,
B G Barrell
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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.
Nature 11/2001; 413(6858):848-52. · 36.28 Impact Factor
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J Parkhill,
B W Wren,
N R Thomson,
R W Titball,
M T Holden,
M B Prentice,
M Sebaihia,
K D James,
C Churcher,
K L Mungall, [......],
S Leather,
S Moule,
P C Oyston,
M Quail,
K Rutherford,
M Simmonds,
J Skelton,
K Stevens,
S Whitehead,
B G Barrell
[show abstract]
[hide abstract]
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.
Nature 11/2001; 413(6855):523-7. · 36.28 Impact Factor
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J Parkhill,
M Achtman,
K D James, S D Bentley,
C Churcher,
S R Klee,
G Morelli,
D Basham,
D Brown,
T Chillingworth, [......],
S Moule,
K Mungall,
M A Quail,
M A Rajandream,
K M Rutherford,
M Simmonds,
J Skelton,
S Whitehead,
B G Spratt,
B G Barrell
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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.
Nature 04/2000; 404(6777):502-6. · 36.28 Impact Factor
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[show abstract]
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ABSTRACT: Spontaneous bacteriophage-resistant mutants of the phytopathogen Erwinia carotovora subsp. atroseptica (Eca) SCRI1043 were isolated and, out of 40, two were found to exhibit reduced virulence in planta. One of these mutants, A5/22, showed multiple cell surface defects including alterations in synthesis of outer membrane proteins, lipopolysaccharide (LPS), enterobacterial common antigen (ECA), and flagella. Mutant A5/22 also showed reduced synthesis of the exoenzymes pectate lyase (Pel) and cellulase (Cel), major virulence factors for this pathogen. Genetic analysis revealed the pronounced pleiotropic mutant phenotype to be due to a defect in a single gene (rffG) that, in Escherichia coli, is involved in the production of ECA. We also show that while other enteric bacteria possess duplicate homologues of this gene dedicated separately to synthesis of LPS and ECA, Eca has a single gene.
Molecular Plant-Microbe Interactions 07/1999; 12(6):499-507. · 4.43 Impact Factor
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[show abstract]
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ABSTRACT: We have identified a gene important for the regulation of exoenzyme virulence factor synthesis in the plant pathogen Erwinia carotovora ssp. carotovora (Ecc) and virulence and motility in Erwinia carotovora ssp. atroseptica (Eca). This gene, hexA (hyperproduction of exoenzymes), is a close relative of the Erwinia chrysanthemi (Echr) gene pecT and encodes a member of the LysR family of transcriptional regulators. hexA mutants in both Ecc and Eca produce abnormally high levels of the exoenzyme virulence factors pectate lyase, cellulase and protease. In addition, Eca hexA mutants show increased expression of the fliA and fliC genes and hypermotility. Consistent with a role as a global regulator, expression of hexA from even a low-copy plasmid can suppress exoenzyme production in Ecc and Eca and motility in Eca. Production of the quorum-sensing pheromone OHHL in Ecc hexA is higher throughout the growth curve compared with the wild-type strain. Overexpression of Ecc hexA also caused widespread effects in several strains of the opportunistic human pathogen, Serratia. Low-copy hexA expression resulted in repression of exoenzyme, pigment and antibiotic production and repression of the spreading phenotype. Finally, mutations in hexA were shown to increase Ecc or Eca virulence in planta.
Molecular Microbiology 06/1998; 28(4):705-17. · 5.01 Impact Factor
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N.J. Croucher,
D Walker,
P. Romero,
N. Lennard,
G.K. Paterson,
N.C. Bason,
A.M. Mitchell,
M A Quail,
P W Andrew,
J Parkhill, S D Bentley,
T J Mitchell
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ABSTRACT: Streptococcus pneumoniae is a human commensal and pathogen able to cause a variety of diseases that annually result in over a million deaths worldwide. The S. pneumoniae<sup>Spain23F</sup> sequence type 81 lineage was among the first recognized pandemic clones and was responsible for almost 40% of penicillin-resistant pneumococcal infections in the United States in the late 1990s. Analysis of the chromosome sequence of a representative strain, and comparison with other available genomes, indicates roles for integrative and conjugative elements in the evolution of pneumococci and, more particularly, the emergence of the multidrug-resistant <sup>Spain23F</sup>ST81 lineage. A number of recently acquired loci within the chromosome appear to encode proteins involved in the production of, or immunity to, antimicrobial compounds, which may contribute to the proficiency of this strain at nasopharyngeal colonization. However, further sequencing of other pandemic clones will be required to establish whether there are any general attributes shared by these strains that are responsible for their international success
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ABSTRACT: Streptococcus pneumoniae is an important human pathogen that often carries temperate bacteriophages. As part of a program to characterize the genetic makeup of prophages associated with clinical-strains and to assess the potential roles that they play in the biology and pathogenesis of their host we performed comparative genomic of ten temperate pneumococcal phage. All of the genomes are organized into five major gene clusters: lysogeny, replication, packaging, morphogenesis and lysis; and all of the phage particles observed showed a Siphoviridae morphology. The only genes that are well conserved in all the genomes studied are those involved in the integration and the lysis of the host in addition to two genes, of unknown function, within the replication module. We observed that a high percentage of the open reading frames contained no similarities to any sequences catalogued in public databases, however, genes were also identified that were homologous to known phage virulence genes including the pblB gene of Streptococcus mitis and the vapE gene in Dichelobacter nodosus. Interestingly, bioinformatic tools showed the presence of a toxin-antitoxin system in the phage phiSpn_6 which is the first time that an addition system has been identified in a pneumophage. Collectively the temperate pneumophages contain a diverse set of genes with varying levels of similarity among them
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[show abstract]
[hide abstract]
ABSTRACT: Streptococcus pneumoniae is an important human pathogen that often carries temperate bacteriophages. As part of a program to characterize the genetic makeup of prophages associated with clinical strains and to assess the potential roles that they play in the biology and pathogenesis in their host, we performed comparative genomic analysis of 10 temperate pneumococcal phages. All of the genomes are organized into five major gene clusters: lysogeny, replication, packaging, morphogenesis, and lysis clusters. All of the phage particles observed showed a Siphoviridae morphology. The only genes that are well conserved in all the genomes studied are those involved in the integration and the lysis of the host in addition to two genes, of unknown function, within the replication module. We observed that a high percentage of the open reading frames contained no similarities to any sequences catalogued in public databases; however, genes that were homologous to known phage virulence genes, including the pblB gene of Streptococcus mitis and the vapE gene of Dichelobacter nodosus , were also identified. Interestingly, bioinformatic tools showed the presence of a toxin-antitoxin system in the phage ΦSpn_6, and this represents the first time that an addition system in a pneumophage has been identified. Collectively, the temperate pneumophages contain a diverse set of genes with various levels of similarity among them
