Journal ArticleDOI
Massive gene decay in the leprosy bacillus
Stewart T. Cole,Karin Eiglmeier,Julian Parkhill,Keith D. James,Nicholas R. Thomson,Paul R. Wheeler,Nadine Honoré,Thierry Garnier,Carol Churcher,David Harris,Karen Mungall,D. Basham,D. Brown,Tracey Chillingworth,R. Connor,Robert L. Davies,K. Devlin,Stephanie Duthoy,Theresa Feltwell,Audrey Fraser,N. Hamlin,S. Holroyd,T. Hornsby,Kay Jagels,Céline Lacroix,J. Maclean,Sharon Moule,Lee Murphy,K. Oliver,Michael A. Quail,Marie-Adèle Rajandream,Kim Rutherford,S. Rutter,K. Seeger,Sylvie Simon,Mark Simmonds,Jason Skelton,Rob Squares,S. Squares,K. Stevens,K. Taylor,Sally Whitehead,J. R. Woodward,Bart Barrell +43 more
TLDR
Comparing the 3.27-megabase genome sequence of an armadillo-derived Indian isolate of the leprosy bacillus with that of Mycobacterium tuberculosis provides clear explanations for these properties and reveals an extreme case of reductive evolution.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.read more
Citations
More filters
Journal ArticleDOI
Complete genome sequence of the model actinomycete Streptomyces coelicolor A3(2)
Stephen D. Bentley,Keith F. Chater,Ana Cerdeño-Tárraga,Gregory L. Challis,Gregory L. Challis,Nicholas R. Thomson,Keith D. James,David Harris,Michael A. Quail,H. M. Kieser,D. Harper,Alex Bateman,Steve D.M. Brown,Govind Chandra,Carton W. Chen,Mark O. Collins,Ann Cronin,Andrew G. Fraser,Arlette Goble,J. Hidalgo,T. Hornsby,S. Howarth,Chih-Hung Huang,Tobias Kieser,L. Larke,Lee Murphy,Karen Oliver,Susan O'Neil,Ester Rabbinowitsch,Marie-Adèle Rajandream,Kim Rutherford,Simon Rutter,Kathy Seeger,David L. Saunders,Sarah Sharp,R. Squares,S. Squares,K. Taylor,T. Warren,Andreas Wietzorrek,John Woodward,Bart Barrell,Julian Parkhill,David A. Hopwood +43 more
TL;DR: The 8,667,507 base pair linear chromosome of Streptomyces coelicolor is reported, containing the largest number of genes so far discovered in a bacterium.
Journal ArticleDOI
Genes required for mycobacterial growth defined by high density mutagenesis
TL;DR: The use of transposon site hybridization (TraSH) is described to comprehensively identify the genes required by the causative agent, Mycobacterium tuberculosis, for optimal growth, suggesting that the minimal gene set required for survival varies greatly between organisms with different evolutionary histories.
Journal ArticleDOI
ACT: the Artemis comparison tool
Tim Carver,Kim Rutherford,Matthew Berriman,Marie-Adèle Rajandream,Barclay G. Barrell,Julian Parkhill +5 more
TL;DR: The Artemis Comparison Tool (ACT) allows an interactive visualisation of comparisons between complete genome sequences and associated annotations and so inherits powerful searching and analysis tools.
Journal ArticleDOI
Extreme genome reduction in symbiotic bacteria
TL;DR: Since 2006, numerous cases of bacterial symbionts with extraordinarily small genomes have been reported, pointing to highly degenerate genomes that retain only the most essential functions, often including a considerable fraction of genes that serve the hosts.
Journal ArticleDOI
Complete genome sequence and comparative analysis of the industrial microorganism Streptomyces avermitilis
Haruo Ikeda,Jun Ishikawa,Akiharu Hanamoto,Mayumi Shinose,Hisashi Kikuchi,Tadayoshi Shiba,Yoshiyuki Sakaki,Masahira Hattori,Satoshi Omura +8 more
TL;DR: The complete nucleotide sequence of the linear chromosome of Streptomyces avermitilis is determined and it is revealed that an internal 6.5-Mb region in the S. avermitILis genome was highly conserved with respect to gene order and content, and contained all known essential genes but showed perfectly asymmetric structure at the oriC center.
References
More filters
Journal ArticleDOI
Deciphering the biology of Mycobacterium tuberculosis from the complete genome sequence
Stewart T. Cole,Roland Brosch,Julian Parkhill,Thierry Garnier,Carol Churcher,David Harris,Stephen V. Gordon,Karin Eiglmeier,S. Gas,Clifton E. Barry,Fredj Tekaia,K. Badcock,D. Basham,D. Brown,Tracey Chillingworth,R. Connor,Robert L. Davies,K. Devlin,Theresa Feltwell,S. Gentles,N. Hamlin,S. Holroyd,T. Hornsby,Kay Jagels,Anders Krogh,J. McLean,Sharon Moule,Lee Murphy,K. Oliver,J. Osborne,Michael A. Quail,Marie-Adèle Rajandream,Jane Rogers,S. Rutter,K. Seeger,Jason Skelton,Rob Squares,S. Squares,John Sulston,K. Taylor,Sally Whitehead,Bart Barrell +41 more
TL;DR: The complete genome sequence of the best-characterized strain of Mycobacterium tuberculosis, H37Rv, has been determined and analysed in order to improve the understanding of the biology of this slow-growing pathogen and to help the conception of new prophylactic and therapeutic interventions.
Journal ArticleDOI
Artemis: sequence visualization and annotation.
Kim Rutherford,Julian Parkhill,James Crook,Terry Horsnell,Peter M. Rice,Marie-Adèle Rajandream,Bart Barrell +6 more
TL;DR: Artemis is a DNA sequence visualization and annotation tool that allows the results of any analysis or sets of analyses to be viewed in the context of the sequence and its six-frame translation.
Journal ArticleDOI
The genome sequence of Rickettsia prowazekii and the origin of mitochondria
Siv G. E. Andersson,Alireza Zomorodipour,Jan Andersson,Thomas Sicheritz-Pontén,U. Cecilia M. Alsmark,Raf M. Podowski,A. Kristina Näslund,Ann-Sofie Eriksson,Herbert H. Winkler,Charles G. Kurland +9 more
TL;DR: The complete genome sequence of the obligate intracellular parasite Rickettsia prowazekii, the causative agent of epidemic typhus, is described, which contains 834 protein-coding genes and is more closely related to mitochondria than is any other microbe studied so far.
Journal ArticleDOI
Persistence of Mycobacterium tuberculosis in macrophages and mice requires the glyoxylate shunt enzyme isocitrate lyase
John D. McKinney,John D. McKinney,John D. McKinney,Kerstin Höner zu Bentrup,Kerstin Höner zu Bentrup,Kerstin Höner zu Bentrup,Ernesto J. Muñoz-Elías,Andras Miczak,Andras Miczak,Bing Chen,Wal Tsing Chan,Dana L. Swenson,Dana L. Swenson,Dana L. Swenson,James C. Sacchettini,William R. Jacobs,David G. Russell,David G. Russell +17 more
TL;DR: It is reported that persistence of M. tuberculosis in mice is facilitated by isocitrate lyase (ICL), an enzyme essential for the metabolism of fatty acids, an observation with important implications for the treatment of chronic tuberculosis.
Journal ArticleDOI
A new DNA sequence assembly program
TL;DR: The Genome Assembly Program (GAP), a new program for DNA sequence assembly, is described, which retains the useful components of the previous work, but includes many novel ideas and methods.
Related Papers (5)
Deciphering the biology of Mycobacterium tuberculosis from the complete genome sequence
Stewart T. Cole,Roland Brosch,Julian Parkhill,Thierry Garnier,Carol Churcher,David Harris,Stephen V. Gordon,Karin Eiglmeier,S. Gas,Clifton E. Barry,Fredj Tekaia,K. Badcock,D. Basham,D. Brown,Tracey Chillingworth,R. Connor,Robert L. Davies,K. Devlin,Theresa Feltwell,S. Gentles,N. Hamlin,S. Holroyd,T. Hornsby,Kay Jagels,Anders Krogh,J. McLean,Sharon Moule,Lee Murphy,K. Oliver,J. Osborne,Michael A. Quail,Marie-Adèle Rajandream,Jane Rogers,S. Rutter,K. Seeger,Jason Skelton,Rob Squares,S. Squares,John Sulston,K. Taylor,Sally Whitehead,Bart Barrell +41 more