Comparative genomics of the mycobacteria.

The genus mycobacteria includes two important human pathogens Mycobacterium tuberculosis and Mycobacterium lepra. The former is reputed to have the highest annual global mortality of all pathogens. Their slow growth, virulence for humans and particular physiology makes these organisms extremely difficult to work with. However the rapid development of mycobacterial genomics following the completion of the Mycobacterium tuberculosis genome sequence provides the basis for a powerful new approach for the understanding of these organisms. Five further genome sequencing projects of closely related mycobacterial species with differing host range, virulence for humans and physiology are underway. A comparative genomic analysis of these species has the potential to define the genetic basis of these phenotypes which will be invaluable for the development of urgently needed new vaccines and drugs. This minireview summarises the different techniques that have been employed to compare these genomes and gives an overview of the wealth of data that has already been generated by mycobacterial comparative genomics.

[1]  M. Daffé,et al.  The envelope layers of mycobacteria with reference to their pathogenicity. , 1998, Advances in microbial physiology.

[2]  M. Vasil,et al.  Biochemical and molecular analysis of phospholipase C and phospholipase D activity in mycobacteria , 1996, Infection and immunity.

[3]  C. Ratledge,et al.  Control and location of acyl-hydrolysing phospholipase activity in pathogenic mycobacteria. , 1992, Journal of general microbiology.

[4]  D. Schwartz,et al.  Separation of yeast chromosome-sized DNAs by pulsed field gradient gel electrophoresis , 1984, Cell.

[5]  B. Bloom,et al.  Tuberculosis Pathogenesis, Protection, and Control , 1994 .

[6]  J Hacker,et al.  Pathogenicity islands of virulent bacteria: structure, function and impact on microbial evolution , 1997, Molecular microbiology.

[7]  L. Bliss,et al.  Efficacy of BCG vaccine against leprosy and tuberculosis in northern Malawi , 1992, The Lancet.

[8]  B. Birren,et al.  Construction and characterization of a human bacterial artificial chromosome library. , 1996, Genomics.

[9]  S. Cole,et al.  Physical mapping of Mycobacterium bovis BCG pasteur reveals differences from the genome map of Mycobacterium tuberculosis H37Rv and from M. bovis. , 1996, Microbiology.

[10]  W. Jacobs,et al.  Conditionally replicating mycobacteriophages: a system for transposon delivery to Mycobacterium tuberculosis. , 1997, Proceedings of the National Academy of Sciences of the United States of America.

[11]  P. L. Strickland,et al.  Phenotypic and Genotypic Characterization ofMycobacterium africanum Isolates from West Africa , 1999, Journal of Clinical Microbiology.

[12]  R. Titball.  Bacterial phospholipases C , 1993, Microbiological reviews.

[13]  R. Good,et al.  Current Laboratory Methods for the Diagnosis of Tuberculosis , 1994 .

[14]  G. Mahairas,et al.  Molecular analysis of genetic differences between Mycobacterium bovis BCG and virulent M. bovis , 1996, Journal of bacteriology.

[15]  W. Jacobs,et al.  Efficient allelic exchange and transposon mutagenesis in Mycobacterium tuberculosis. , 1997, Proceedings of the National Academy of Sciences of the United States of America.

[16]  W. Jacobs,et al.  An integrated map of the genome of the tubercle bacillus, Mycobacterium tuberculosis H37Rv, and comparison with Mycobacterium leprae. , 1996, Proceedings of the National Academy of Sciences of the United States of America.

[17]  K. Hasløv,et al.  Development of the Mycobacterium bovis BCG vaccine: review of the historical and biochemical evidence for a genealogical tree. , 1999, Tubercle and lung disease : the official journal of the International Union against Tuberculosis and Lung Disease.

[18]  S T Cole,et al.  Analysis of the proteome of Mycobacterium tuberculosis in silico. , 1999, Tubercle and lung disease : the official journal of the International Union against Tuberculosis and Lung Disease.

[19]  Stewart T. Cole,et al.  Bacterial Genomes—All Shapes and Sizes , 1999 .

[20]  M. Behr,et al.  A historical and molecular phylogeny of BCG strains. , 1999, Vaccine.

[21]  F. Oesch,et al.  Sequence similarity of mammalian epoxide hydrolases to the bacterial haloalkane dehalogenase and other related proteins , 1994, FEBS letters.

[22]  B. Gicquel,et al.  Identification of a virulence gene cluster of Mycobacterium tuberculosis by signature‐tagged transposon mutagenesis , 1999, Molecular microbiology.

[23]  B. Birren,et al.  Cloning and stable maintenance of 300-kilobase-pair fragments of human DNA in Escherichia coli using an F-factor-based vector. , 1992, Proceedings of the National Academy of Sciences of the United States of America.

[24]  G. Schoolnik,et al.  Comparative genomics of BCG vaccines by whole-genome DNA microarray. , 1999, Science.

[25]  S. Cole,et al.  Identification of variable regions in the genomes of tubercle bacilli using bacterial artificial chromosome arrays , 1999, Molecular microbiology.

[26]  T. Whittam,et al.  Restricted structural gene polymorphism in the Mycobacterium tuberculosis complex indicates evolutionarily recent global dissemination. , 1997, Proceedings of the National Academy of Sciences of the United States of America.

[27]  B. Barrell,et al.  Use of a Mycobacterium tuberculosisH37Rv Bacterial Artificial Chromosome Library for Genome Mapping, Sequencing, and Comparative Genomics , 1998, Infection and Immunity.

[28]  D. van Soolingen,et al.  Diagnosis of Mycobacterium microtiInfections among Humans by Using Novel Genetic Markers , 1998, Journal of Clinical Microbiology.

[29]  P. D. Hart,et al.  BCG and vole bacillus vaccines in the prevention of tuberculosis in adolescence and early adult life. , 1977, British medical journal.

[30]  P. Andersen,et al.  Delayed-Type Hypersensitivity Responses to ESAT-6 and MPT64 from Mycobacterium tuberculosis in the Guinea Pig , 1998, Infection and Immunity.

[31]  L. Šula,et al.  Protective effects of M. microti vaccine against tuberculosis. , 1976, Journal of hygiene, epidemiology, microbiology, and immunology.

[32]  P. Fine,et al.  The BCG Experience: Implications for Future Vaccines against Tuberculosis , 1994 .

[33]  M. Horwitz,et al.  Protective immunity against tuberculosis induced by vaccination with major extracellular proteins of Mycobacterium tuberculosis. , 1995, Proceedings of the National Academy of Sciences of the United States of America.

[34]  H. Salamon,et al.  Use of Pulsed-Field Gel Electrophoresis for Molecular Epidemiologic and Population Genetic Studies ofMycobacterium tuberculosis , 1999, Journal of Clinical Microbiology.

[35]  B. Barrell,et al.  Deciphering the biology of Mycobacterium tuberculosis from the complete genome sequence , 1998, Nature.

[36]  W. Haas,et al.  Comparison of DNA fingerprint patterns of isolates of Mycobacterium africanum from east and west Africa , 1997, Journal of clinical microbiology.

[37]  F. Neidhardt,et al.  Escherichia Coli and Salmonella: Typhimurium Cellular and Molecular Biology , 1987 .

[38]  R. Wallace,,et al.  Genetic differences between BCG substrains. , 1995, Tubercle and lung disease : the official journal of the International Union against Tuberculosis and Lung Disease.

[39]  P. E. M. Fine,et al.  Variation in protection by BCG: implications of and for heterologous immunity , 1995, The Lancet.

[40]  R. L. Charlebois.  Organization of the Prokaryotic Genome , 1999 .

[41]  S T Cole,et al.  Use of an ordered cosmid library to deduce the genomic organization of Mycobacterium leprae , 1993, Molecular microbiology.

[42]  M. Theisen,et al.  Identification and Characterization of a 29-Kilodalton Protein from Mycobacterium tuberculosis Culture Filtrate Recognized by Mouse Memory Effector Cells , 1998, Infection and Immunity.

[43]  R. Knights,et al.  Cloning of an M. tuberculosis DNA fragment associated with entry and survival inside cells. , 1993, Science.

[44]  S. Petroff,et al.  BIOLOGICAL STUDIES OF THE TUBERCLE BACILLUS : III. DISSOCIATION AND PATHOGENICITY OF THE R AND S VARIANTS OF THE HUMAN TUBERCLE BACILLUS (H37) , 1934 .

[45]  S. Cole,et al.  Genomic Analysis Reveals Variation between Mycobacterium tuberculosis H37Rv and the AttenuatedM. tuberculosis H37Ra Strain , 1999, Infection and Immunity.