Author Report for: Cerdeno-Tarraga AMNo contact information in database for Cerdeno-Tarraga AM
Crossman LC, Chen H, Cerdeno-Tarraga AM, Brooks K, Quail MA, Pineiro SA, Hobley L, Sockett RE, Bentley SD and Stine OC <2 more author(s)> Crossman LC, Chen H, Cerdeno-Tarraga AM, Brooks K, Quail MA, Pineiro SA, Hobley L, Sockett RE, Bentley SD, Parkhill J, Williams HN, Stine OC (- 2) Ref: Isme J, 7:148, 2013 : PubMed ESTHER: Crossman_2013_ISME.J_7_148 PubMedSearch: Crossman 2013 ISME.J 7 148 PubMedID: 22955231 Gene_locus related to this paper: bacms-e1x4r0, bacms-e1wxp3 Abstract Bacteriovorax marinus SJ is a predatory delta-proteobacterium isolated from a marine environment. The genome sequence of this strain provides an interesting contrast to that of the terrestrial predatory bacterium Bdellovibrio bacteriovorus HD100. Based on their predatory lifestyle, Bacteriovorax were originally designated as members of the genus Bdellovibrio but subsequently were re-assigned to a new genus and family based on genetic and phenotypic differences. B. marinus attaches to gram-negative bacteria, penetrates through the cell wall to form a bdelloplast, in which it replicates, as shown using microscopy. Bacteriovorax is distinct, as it shares only 30% of its gene products with its closest sequenced relatives. Remarkably, 34% of predicted genes over 500 nt in length were completely unique with no significant matches in the databases. As expected, Bacteriovorax shares several characteristic loci with the other delta-proteobacteria. A geneset shared between Bacteriovorax and Bdellovibrio that is not conserved among other delta-proteobacteria such as Myxobacteria (which destroy prey bacteria externally via lysis), or the non-predatory Desulfo-bacteria and Geobacter species was identified. These 291 gene orthologues common to both Bacteriovorax and Bdellovibrio may be the key indicators of host-interaction predatory-specific processes required for prey entry. The locus from Bdellovibrio bacteriovorus is implicated in the switch from predatory to prey/host-independent growth. Although the locus is conserved in B. marinus, the sequence has only limited similarity. The results of this study advance understanding of both the similarities and differences between Bdellovibrio and Bacteriovorax and confirm the distant relationship between the two and their separation into different families. Title: The Citrobacter rodentium genome sequence reveals convergent evolution with human pathogenic Escherichia coli Petty NK, Bulgin R, Crepin VF, Cerdeno-Tarraga AM, Schroeder GN, Quail MA, Lennard N, Corton C, Barron A and Thomson NR <5 more author(s)> Petty NK, Bulgin R, Crepin VF, Cerdeno-Tarraga AM, Schroeder GN, Quail MA, Lennard N, Corton C, Barron A, Clark L, Toribio AL, Parkhill J, Dougan G, Frankel G, Thomson NR (- 5) Ref: Journal of Bacteriology, 192:525, 2010 : PubMed ESTHER: Petty_2010_J.Bacteriol_192_525 PubMedSearch: Petty 2010 J.Bacteriol 192 525 PubMedID: 19897651 Gene_locus related to this paper: citk8-bioh, citk8-y1948, citri-d2th08, citri-d2tjf8, citri-d2tjy8, citri-d2tk80, citri-d2tmm5, citri-d2tmq5, citri-d2tri3, citri-d2trm8 Abstract Citrobacter rodentium (formally Citrobacter freundii biotype 4280) is a highly infectious pathogen that causes colitis and transmissible colonic hyperplasia in mice. In common with enteropathogenic and enterohemorrhagic Escherichia coli (EPEC and EHEC, respectively), C. rodentium exploits a type III secretion system (T3SS) to induce attaching and effacing (A/E) lesions that are essential for virulence. Here, we report the fully annotated genome sequence of the 5.3-Mb chromosome and four plasmids harbored by C. rodentium strain ICC168. The genome sequence revealed key information about the phylogeny of C. rodentium and identified 1,585 C. rodentium-specific (without orthologues in EPEC or EHEC) coding sequences, 10 prophage-like regions, and 17 genomic islands, including the locus for enterocyte effacement (LEE) region, which encodes a T3SS and effector proteins. Among the 29 T3SS effectors found in C. rodentium are all 22 of the core effectors of EPEC strain E2348/69. In addition, we identified a novel C. rodentium effector, named EspS. C. rodentium harbors two type VI secretion systems (T6SS) (CTS1 and CTS2), while EHEC contains only one T6SS (EHS). Our analysis suggests that C. rodentium and EPEC/EHEC have converged on a common host infection strategy through access to a common pool of mobile DNA and that C. rodentium has lost gene functions associated with a previous pathogenic niche. Title: The genome of Burkholderia cenocepacia J2315, an epidemic pathogen of cystic fibrosis patients Holden MT, Seth-Smith HM, Crossman LC, Sebaihia M, Bentley SD, Cerdeno-Tarraga AM, Thomson NR, Bason N, Quail MA and Parkhill J <22 more author(s)> Holden MT, Seth-Smith HM, Crossman LC, Sebaihia M, Bentley SD, Cerdeno-Tarraga AM, Thomson NR, Bason N, Quail MA, Sharp S, Cherevach I, Churcher C, Goodhead I, Hauser H, Holroyd N, Mungall K, Scott P, Walker D, White B, Rose H, Iversen P, Mil-Homens D, Rocha EP, Fialho AM, Baldwin A, Dowson C, Barrell BG, Govan JR, Vandamme P, Hart CA, Mahenthiralingam E, Parkhill J (- 22) Ref: Journal of Bacteriology, 191:261, 2009 : PubMed ESTHER: Holden_2009_J.Bacteriol_191_261 PubMedSearch: Holden 2009 J.Bacteriol 191 261 PubMedID: 18931103 Gene_locus related to this paper: burcj-b4e794, 9burk-a0u8m3, burcj-b4ek59, burcj-b4ehl7, burca-q1bk56, burce-a0a088tsj6, burcj-b4ecv6 Abstract Bacterial infections of the lungs of cystic fibrosis (CF) patients cause major complications in the treatment of this common genetic disease. Burkholderia cenocepacia infection is particularly problematic since this organism has high levels of antibiotic resistance, making it difficult to eradicate; the resulting chronic infections are associated with severe declines in lung function and increased mortality rates. B. cenocepacia strain J2315 was isolated from a CF patient and is a member of the epidemic ET12 lineage that originated in Canada or the United Kingdom and spread to Europe. The 8.06-Mb genome of this highly transmissible pathogen comprises three circular chromosomes and a plasmid and encodes a broad array of functions typical of this metabolically versatile genus, as well as numerous virulence and drug resistance functions. Although B. cenocepacia strains can be isolated from soil and can be pathogenic to both plants and man, J2315 is representative of a lineage of B. cenocepacia rarely isolated from the environment and which spreads between CF patients. Comparative analysis revealed that ca. 21% of the genome is unique in comparison to other strains of B. cenocepacia, highlighting the genomic plasticity of this species. Pseudogenes in virulence determinants suggest that the pathogenic response of J2315 may have been recently selected to promote persistence in the CF lung. The J2315 genome contains evidence that its unique and highly adapted genetic content has played a significant role in its success as an epidemic CF pathogen. Title: Genomic and genetic analyses of diversity and plant interactions of Pseudomonas fluorescens Silby MW, Cerdeno-Tarraga AM, Vernikos GS, Giddens SR, Jackson RW, Preston GM, Zhang XX, Moon CD, Gehrig SM and Thomson NR <24 more author(s)> Silby MW, Cerdeno-Tarraga AM, Vernikos GS, Giddens SR, Jackson RW, Preston GM, Zhang XX, Moon CD, Gehrig SM, Godfrey SA, Knight CG, Malone JG, Robinson Z, Spiers AJ, Harris S, Challis GL, Yaxley AM, Harris D, Seeger K, Murphy L, Rutter S, Squares R, Quail MA, Saunders E, Mavromatis K, Brettin TS, Bentley SD, Hothersall J, Stephens E, Thomas CM, Parkhill J, Levy SB, Rainey PB, Thomson NR (- 24) Ref: Genome Biol, 10:R51, 2009 : PubMed ESTHER: Silby_2009_Genome.Biol_10_R51 PubMedSearch: Silby 2009 Genome.Biol 10 R51 PubMedID: 19432983 Gene_locus related to this paper: psef5-metx, psefl-este, psefs-c3jz63, psefs-c3jzq8, psefs-c3k1v7, psefs-c3k3d6, psefs-c3k3m8, psefs-c3k3s9, psefs-c3k5q5, psefs-c3k6c6, psefs-c3k7v4, psefs-c3k8m7, psefs-c3k8y7, psefs-c3k9z2, psefs-c3k032, psefs-c3k320, psefs-c3k362, psefs-c3k632, psefs-c3k927, psefs-c3kan9, psefs-c3kbe5, psefs-c3kdh9, psefs-c3ke34, psefs-laaa, psepf-q3k5t9, psepf-q3k6f3, psepf-q3k524, psepf-q3kcu9, psepf-q3kd07, psepf-q3kf33, psepf-q3kh87, psefs-c3jxp6, psepf-q3kf85, psefs-c3k813, psefs-c3keb8, psefl-e2xkc8, psefs-c3k9x6 Abstract BACKGROUND: Pseudomonas fluorescens are common soil bacteria that can improve plant health through nutrient cycling, pathogen antagonism and induction of plant defenses. The genome sequences of strains SBW25 and Pf0-1 were determined and compared to each other and with P. fluorescens Pf-5. A functional genomic in vivo expression technology (IVET) screen provided insight into genes used by P. fluorescens in its natural environment and an improved understanding of the ecological significance of diversity within this species. RESULTS: Comparisons of three P. fluorescens genomes (SBW25, Pf0-1, Pf-5) revealed considerable divergence: 61% of genes are shared, the majority located near the replication origin. Phylogenetic and average amino acid identity analyses showed a low overall relationship. A functional screen of SBW25 defined 125 plant-induced genes including a range of functions specific to the plant environment. Orthologues of 83 of these exist in Pf0-1 and Pf-5, with 73 shared by both strains. The P. fluorescens genomes carry numerous complex repetitive DNA sequences, some resembling Miniature Inverted-repeat Transposable Elements (MITEs). In SBW25, repeat density and distribution revealed 'repeat deserts' lacking repeats, covering approximately 40% of the genome. CONCLUSIONS: P. fluorescens genomes are highly diverse. Strain-specific regions around the replication terminus suggest genome compartmentalization. The genomic heterogeneity among the three strains is reminiscent of a species complex rather than a single species. That 42% of plant-inducible genes were not shared by all strains reinforces this conclusion and shows that ecological success requires specialized and core functions. The diversity also indicates the significant size of genetic information within the Pseudomonas pan genome. Title: Genome sequence of a proteolytic (Group I) Clostridium botulinum strain Hall A and comparative analysis of the clostridial genomes Sebaihia M, Peck MW, Minton NP, Thomson NR, Holden MT, Mitchell WJ, Carter AT, Bentley SD, Mason DR and Parkhill J <24 more author(s)> Sebaihia M, Peck MW, Minton NP, Thomson NR, Holden MT, Mitchell WJ, Carter AT, Bentley SD, Mason DR, Crossman L, Paul CJ, Ivens A, Wells-Bennik MH, Davis IJ, Cerdeno-Tarraga AM, Churcher C, Quail MA, Chillingworth T, Feltwell T, Fraser A, Goodhead I, Hance Z, Jagels K, Larke N, Maddison M, Moule S, Mungall K, Norbertczak H, Rabbinowitsch E, Sanders M, Simmonds M, White B, Whithead S, Parkhill J (- 24) Ref: Genome Res, 17:1082, 2007 : PubMed ESTHER: Sebaihia_2007_Genome.Res_17_1082 PubMedSearch: Sebaihia 2007 Genome.Res 17 1082 PubMedID: 17519437 Gene_locus related to this paper: clobh-A5I3I2, clobh-A51055, clob1-a7fqm2, clob1-a7fv94, clobl-a7gbn0, clobh-pip, clobh-a5i3m0 Abstract Clostridium botulinum is a heterogeneous Gram-positive species that comprises four genetically and physiologically distinct groups of bacteria that share the ability to produce botulinum neurotoxin, the most poisonous toxin known to man, and the causative agent of botulism, a severe disease of humans and animals. We report here the complete genome sequence of a representative of Group I (proteolytic) C. botulinum (strain Hall A, ATCC 3502). The genome consists of a chromosome (3,886,916 bp) and a plasmid (16,344 bp), which carry 3650 and 19 predicted genes, respectively. Consistent with the proteolytic phenotype of this strain, the genome harbors a large number of genes encoding secreted proteases and enzymes involved in uptake and metabolism of amino acids. The genome also reveals a hitherto unknown ability of C. botulinum to degrade chitin. There is a significant lack of recently acquired DNA, indicating a stable genomic content, in strong contrast to the fluid genome of Clostridium difficile, which can form longer-term relationships with its host. Overall, the genome indicates that C. botulinum is adapted to a saprophytic lifestyle both in soil and aquatic environments. This pathogen relies on its toxin to rapidly kill a wide range of prey species, and to gain access to nutrient sources, it releases a large number of extracellular enzymes to soften and destroy rotting or decayed tissues. Title: Multireplicon genome architecture of Lactobacillus salivarius Claesson MJ, Li Y, Leahy S, Canchaya C, van Pijkeren JP, Cerdeno-Tarraga AM, Parkhill J, Flynn S, O'Sullivan GC and O'Toole PW <5 more author(s)> Claesson MJ, Li Y, Leahy S, Canchaya C, van Pijkeren JP, Cerdeno-Tarraga AM, Parkhill J, Flynn S, O'Sullivan GC, Collins JK, Higgins D, Shanahan F, Fitzgerald GF, van Sinderen D, O'Toole PW (- 5) Ref: Proc Natl Acad Sci U S A, 103:6718, 2006 : PubMed ESTHER: Claesson_2006_Proc.Natl.Acad.Sci.U.S.A_103_6718 PubMedSearch: Claesson 2006 Proc.Natl.Acad.Sci.U.S.A 103 6718 PubMedID: 16617113 Gene_locus related to this paper: lacs1-PEPX, lacs1-q1wrt6, lacs1-q1ws61, lacs1-q1wtn9, lacs1-q1wv71 Abstract Lactobacillus salivarius subsp. salivarius strain UCC118 is a bacteriocin-producing strain with probiotic characteristics. The 2.13-Mb genome was shown by sequencing to comprise a 1.83 Mb chromosome, a 242-kb megaplasmid (pMP118), and two smaller plasmids. Megaplasmids previously have not been characterized in lactic acid bacteria or intestinal lactobacilli. Annotation of the genome sequence indicated an intermediate level of auxotrophy compared with other sequenced lactobacilli. No single-copy essential genes were located on the megaplasmid. However, contingency amino acid metabolism genes and carbohydrate utilization genes, including two genes for completion of the pentose phosphate pathway, were megaplasmid encoded. The megaplasmid also harbored genes for the Abp118 bacteriocin, a bile salt hydrolase, a presumptive conjugation locus, and other genes potentially relevant for probiotic properties. Two subspecies of L. salivarius are recognized, salivarius and salicinius, and we detected megaplasmids in both subspecies by pulsed-field gel electrophoresis of sizes ranging from 100 kb to 380 kb. The discovery of megaplasmids of widely varying size in L. salivarius suggests a possible mechanism for genome expansion or contraction to adapt to different environments. 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: Extensive DNA inversions in the B. fragilis genome control variable gene expression Cerdeno-Tarraga AM, Patrick S, Crossman LC, Blakely G, Abratt V, Lennard N, Poxton I, Duerden B, Harris B and Parkhill J <15 more author(s)> Cerdeno-Tarraga AM, Patrick S, Crossman LC, Blakely G, Abratt V, Lennard N, Poxton I, Duerden B, Harris B, Quail MA, Barron A, Clark L, Corton C, Doggett J, Holden MT, Larke N, Line A, Lord A, Norbertczak H, Ormond D, Price C, Rabbinowitsch E, Woodward J, Barrell B, Parkhill J (- 15) Ref: Science, 307:1463, 2005 : PubMed ESTHER: Cerdeno-Tarraga_2005_Science_307_1463 PubMedSearch: Cerdeno-Tarraga 2005 Science 307 1463 PubMedID: 15746427 Gene_locus related to this paper: bacfn-q5l8p8, bacfn-q5lef1, bacfn-q5lh43, bacfn-q5lhv2, bacfr-q64mh3, bacfr-q64n33, bacfr-q64qs3, bacfr-q64t24, bacfr-q64uj8, bacfr-q64vx6, bacfr-q64wh2, bacfr-q64xp9, bacfr-q650j0 Abstract The obligately anaerobic bacterium Bacteroides fragilis, an opportunistic pathogen and inhabitant of the normal human colonic microbiota, exhibits considerable within-strain phase and antigenic variation of surface components. The complete genome sequence has revealed an unusual breadth (in number and in effect) of DNA inversion events that potentially control expression of many different components, including surface and secreted components, regulatory molecules, and restriction-modification proteins. Invertible promoters of two different types (12 group 1 and 11 group 2) were identified. One group has inversion crossover (fix) sites similar to the hix sites of Salmonella typhimurium. There are also four independent intergenic shufflons that potentially alter the expression and function of varied genes. The composition of the 10 different polysaccharide biosynthesis gene clusters identified (7 with associated invertible promoters) suggests a mechanism of synthesis similar to the O-antigen capsules of Escherichia coli. Title: The Chlamydophila abortus genome sequence reveals an array of variable proteins that contribute to interspecies variation Thomson NR, Yeats C, Bell K, Holden MT, Bentley SD, Livingstone M, Cerdeno-Tarraga AM, Harris B, Doggett J and Longbottom D <10 more author(s)> Thomson NR, Yeats C, Bell K, Holden MT, Bentley SD, Livingstone M, Cerdeno-Tarraga AM, Harris B, Doggett J, Ormond D, Mungall K, Clarke K, Feltwell T, Hance Z, Sanders M, Quail MA, Price C, Barrell BG, Parkhill J, Longbottom D (- 10) Ref: Genome Res, 15:629, 2005 : PubMed ESTHER: Thomson_2005_Genome.Res_15_629 PubMedSearch: Thomson 2005 Genome.Res 15 629 PubMedID: 15837807 Gene_locus related to this paper: chlab-q5l5y2, chlab-q5l6t6 Abstract The obligate intracellular bacterial pathogen Chlamydophila abortus strain S26/3 (formerly the abortion subtype of Chlamydia psittaci) is an important cause of late gestation abortions in ruminants and pigs. Furthermore, although relatively rare, zoonotic infection can result in acute illness and miscarriage in pregnant women. The complete genome sequence was determined and shows a high level of conservation in both sequence and overall gene content in comparison to other Chlamydiaceae. The 1,144,377-bp genome contains 961 predicted coding sequences, 842 of which are conserved with those of Chlamydophila caviae and Chlamydophila pneumoniae. Within this conserved Cp. abortus core genome we have identified the major regions of variation and have focused our analysis on these loci, several of which were found to encode highly variable protein families, such as TMH/Inc and Pmp families, which are strong candidates for the source of diversity in host tropism and disease causation in this group of organisms. Significantly, Cp. abortus lacks any toxin genes, and also lacks genes involved in tryptophan metabolism and nucleotide salvaging (guaB is present as a pseudogene), suggesting that the genetic basis of niche adaptation of this species is distinct from those previously proposed for other chlamydial species. 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: Complete genome sequence of the model actinomycete Streptomyces coelicolor A3(2) Bentley SD, Chater KF, Cerdeno-Tarraga AM, Challis GL, Thomson NR, James KD, Harris DE, Quail MA, Kieser H and Hopwood DA <33 more author(s)> Bentley SD, Chater KF, Cerdeno-Tarraga AM, Challis GL, Thomson NR, James KD, Harris DE, Quail MA, Kieser H, Harper D, Bateman A, Brown S, Chandra G, Chen CW, Collins M, Cronin A, Fraser A, Goble A, Hidalgo J, Hornsby T, Howarth S, Huang CH, Kieser T, Larke L, Murphy L, Oliver K, O'Neil S, Rabbinowitsch E, Rajandream MA, Rutherford K, Rutter S, Seeger K, Saunders D, Sharp S, Squares R, Squares S, Taylor K, Warren T, Wietzorrek A, Woodward J, Barrell BG, Parkhill J, Hopwood DA (- 33) Ref: Nature, 417:141, 2002 : PubMed ESTHER: Bentley_2002_Nature_417_141 PubMedSearch: Bentley 2002 Nature 417 141 PubMedID: 12000953 Gene_locus related to this paper: strco-cxest, strco-cxest2, strco-ester, strco-estli, strco-MMYT, strco-ORF3, strco-q9f2m1, strco-q9rdq9, strco-q9x8r0, strco-SC1A6.21, strco-SC3F7.14, strco-SC4C2.18, strco-SC10F4.23, strco-SCBAC20F6.10, strco-SCD95A, strco-SCE8.12C, strco-SCE63.01, strco-SCF43.16C, strco-SCJ9A.33C, strco-SCO0047, strco-SCO0135, strco-SCO0490, strco-SCO0503, strco-SCO0556.1, strco-SCO0556.2, strco-SCO1265, strco-SCO2123, strco-SCO2516, strco-SCO2723, strco-SCO2761, strco-SCO3396, strco-SCO3772, strco-SCO4160, strco-SCO4900, strco-SCO5215, strco-SCO5489, strco-SCO5986, strco-SCO6351, strco-SCO6488, strco-SCO7057, strco-SCO7121, strco-SCO7396, strco-SCO7609, strco-SCOT, strco-SLPD, strco-TAP 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. 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. | |||||||
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