-
1
-
-
0348057949
-
Hymns of the Atharva-veda
-
Translated by Maurice Bloomfield. Edited by Oxford: Clarendon Press; Hymns 1.23, 1.24, 11.31
-
Hymns of the Atharva-veda. Translated by Maurice Bloomfield. In The Sacred Books of the East, vol 42. Edited by Muller FM. Oxford: Clarendon Press; 1897: Hymns 1.23, 1.24, 11.31.
-
(1897)
In the Sacred Books of the East
, vol.42
-
-
Muller, F.M.1
-
2
-
-
85031627891
-
-
TM Entrez Genome division, contains a constantly updated list of ongoing, non-commercial microbial genome sequencing projects. It has links to similar lists maintained at TIGR, University of Illinois, Argonne National Lab, and INFOBIOGEN, to the list of bacterial genomes being sequenced at the Sanger Centre, and to the two major US funding agencies, The Department of Energy (DOE) and National Institute of Allergy and Infectious Diseases (NIAID). Exploring the latter two sites provides useful information on the status of major projects and the motivation behind them
-
TM Entrez Genome division, contains a constantly updated list of ongoing, non-commercial microbial genome sequencing projects. It has links to similar lists maintained at TIGR, University of Illinois, Argonne National Lab, and INFOBIOGEN, to the list of bacterial genomes being sequenced at the Sanger Centre, and to the two major US funding agencies, The Department of Energy (DOE) and National Institute of Allergy and Infectious Diseases (NIAID). Exploring the latter two sites provides useful information on the status of major projects and the motivation behind them.
-
-
-
-
3
-
-
15444350252
-
The complete genome sequence of Escherichia coli K-12
-
Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V., Riley M., Collado-Vides J., Glasner J.D., Rode C.K.et al. The complete genome sequence of Escherichia coli K-12. Science. 277:1997;1453-1474.
-
(1997)
Science
, vol.277
, pp. 1453-1474
-
-
Blattner, F.R.1
Plunkett G. III2
Bloch, C.A.3
Perna, N.T.4
Burland, V.5
Riley, M.6
Collado-Vides, J.7
Glasner, J.D.8
Rode, C.K.9
-
4
-
-
0029653518
-
Whole-genome random sequencing and assembly of Haemophilus influenzae Rd.
-
Fleischmann R.D., Adams M.D., White O., Clayton R.A., Kirkness E.F., Kerlavage A.R., Bult C.J., Tomb J.-F., Dougherty B.A., Merrick J.M.et al. Whole-genome random sequencing and assembly of Haemophilus influenzae Rd. Science. 269:1995;496-512.
-
(1995)
Science
, vol.269
, pp. 496-512
-
-
Fleischmann, R.D.1
Adams, M.D.2
White, O.3
Clayton, R.A.4
Kirkness, E.F.5
Kerlavage, A.R.6
Bult, C.J.7
Tomb, J.-F.8
Dougherty, B.A.9
Merrick, J.M.10
-
5
-
-
0030835739
-
The complete genome sequence of the gastric pathogen Helicobacter pylori
-
Tomb J.-F., White O., Kerlavage A.R., Clayton R.A., Sutton G.G., Fleishmann R.F., Ketchum K.A., Klenk H.P., Gill S., Dougherty B.A.et al. The complete genome sequence of the gastric pathogen Helicobacter pylori. Nature. 388:1997;539-547.
-
(1997)
Nature
, vol.388
, pp. 539-547
-
-
Tomb, J.-F.1
White, O.2
Kerlavage, A.R.3
Clayton, R.A.4
Sutton, G.G.5
Fleishmann, R.F.6
Ketchum, K.A.7
Klenk, H.P.8
Gill, S.9
Dougherty, B.A.10
-
6
-
-
0032512051
-
The genome sequence of Rickettsia prowazekii and the origin of mitochondria
-
+-ATPase are similar to mitochondrial ones, but ATP/ADP translocase is related to that of chlamydia. The close relation of R. prowazekii to mitochondria will pose a challenge to devising effective anti-rickettsial drugs.
-
+-ATPase are similar to mitochondrial ones, but ATP/ADP translocase is related to that of chlamydia. The close relation of R. prowazekii to mitochondria will pose a challenge to devising effective anti-rickettsial drugs.
-
(1998)
Nature
, vol.396
, pp. 133-140
-
-
Andersson, S.G.1
Zomorodipour, A.2
Andersson, J.O.3
Sicheritz-Ponten, T.4
Alsmark, U.C.5
Podowski, R.M.6
Naslund, A.K.7
Eriksson, A.S.8
Winkler, H.H.9
Kurland, C.G.10
-
7
-
-
0030731108
-
The complete genome sequence of the gram-positive bacterium Bacillus subtilis
-
Kunst F., Ogasawara N., Moszer I., Albertini A.M., Alloni G., Azevedo V., Bertero M.G., Bessieres P., Bolotin A., Borchert S.et al. The complete genome sequence of the gram-positive bacterium Bacillus subtilis. Nature. 390:1997;249-256.
-
(1997)
Nature
, vol.390
, pp. 249-256
-
-
Kunst, F.1
Ogasawara, N.2
Moszer, I.3
Albertini, A.M.4
Alloni, G.5
Azevedo, V.6
Bertero, M.G.7
Bessieres, P.8
Bolotin, A.9
Borchert, S.10
-
8
-
-
0028829125
-
The minimal gene complement of Mycoplasma genitalium
-
Fraser C.M., Gocayne J.D., White O., Adams M.D., Clayton R.A., Fleischmann R.D., Bult C.J., Kerlavage A.R., Sutton G., Kelley J.M.et al. The minimal gene complement of Mycoplasma genitalium. Science. 270:1995;397-403.
-
(1995)
Science
, vol.270
, pp. 397-403
-
-
Fraser, C.M.1
Gocayne, J.D.2
White, O.3
Adams, M.D.4
Clayton, R.A.5
Fleischmann, R.D.6
Bult, C.J.7
Kerlavage, A.R.8
Sutton, G.9
Kelley, J.M.10
-
9
-
-
10544255079
-
Complete sequence analysis of the genome of the bacterium Mycoplasma pneumoniae
-
Himmelreich R., Hilbert H., Plagens H., Pirkl E., Li B.C., Herrmann R. Complete sequence analysis of the genome of the bacterium Mycoplasma pneumoniae. Nucleic Acids Res. 24:1996;4420-4449.
-
(1996)
Nucleic Acids Res
, vol.24
, pp. 4420-4449
-
-
Himmelreich, R.1
Hilbert, H.2
Plagens, H.3
Pirkl, E.4
Li, B.C.5
Herrmann, R.6
-
10
-
-
0032508046
-
Deciphering the biology of Mycobacterium tuberculosis from the complete genome sequence
-
Genome sequencing of one of the deadliest human pathogens revealed that it is not a typical parasite, after all [61]. The M. tuberculosis genome is comparable in size to those of free-living B. subtilis and Synechocystis sp. It contains genes for most of the biosynthetic enzymes, which are lacking in most other pathogens, and M. tuberculosis does not seem to depend upon the host as much as other pathogens do. The reason for the extremely slow growth of this organism has not become immediately clear. Significant follow-up research will be needed to come up with effective anti-tuberculine drugs.
-
Cole S.T., Brosch R., Parkhill J., Garnier T., Churcher C., Harris D., Gordon S.V., Eiglmeier K., Gas S., Barry C.E. III et al. Deciphering the biology of Mycobacterium tuberculosis from the complete genome sequence. Nature. 393:1998;537-544. Genome sequencing of one of the deadliest human pathogens revealed that it is not a typical parasite, after all [61]. The M. tuberculosis genome is comparable in size to those of free-living B. subtilis and Synechocystis sp. It contains genes for most of the biosynthetic enzymes, which are lacking in most other pathogens, and M. tuberculosis does not seem to depend upon the host as much as other pathogens do. The reason for the extremely slow growth of this organism has not become immediately clear. Significant follow-up research will be needed to come up with effective anti-tuberculine drugs.
-
(1998)
Nature
, vol.393
, pp. 537-544
-
-
Cole, S.T.1
Brosch, R.2
Parkhill, J.3
Garnier, T.4
Churcher, C.5
Harris, D.6
Gordon, S.V.7
Eiglmeier, K.8
Gas, S.9
Barry C.E. III10
-
11
-
-
0031470826
-
Genomic sequence of a Lyme disease spirochaete, Borrelia burgdorferi
-
Fraser C.M., Casjens S., Huang W.M., Sutton G.G., Clayton R., Lathigra R., White O., Ketchum K.A., Dodson R., Hickey E.K.et al. Genomic sequence of a Lyme disease spirochaete, Borrelia burgdorferi. Nature. 390:1997;580-586.
-
(1997)
Nature
, vol.390
, pp. 580-586
-
-
Fraser, C.M.1
Casjens, S.2
Huang, W.M.3
Sutton, G.G.4
Clayton, R.5
Lathigra, R.6
White, O.7
Ketchum, K.A.8
Dodson, R.9
Hickey, E.K.10
-
12
-
-
0032540874
-
Complete genome sequence of Treponema pallidum, the syphilis spirochete
-
With syphilis remaining one of the most common human diseases, the complete genome of T. pallidum provides much needed information about the metabolic capacities and other cellulor functions of this pathogen. Its similarity to previously sequenced B. burgdorferi genome offers interesting possibilities for comparative genomics of these two spirochetes. Remarkably, the T. pallidus chromosome is circular, leaving B. burgdorferi as the only known bacterium with a linear one.
-
Fraser C.M., Norris S.J., Weinstock G.M., White O., Sutton G.G., Dodson R., Gwinn M., Hickey E.K., Clayton R., Ketchum K.A.et al. Complete genome sequence of Treponema pallidum, the syphilis spirochete. Science. 281:1998;375-388. With syphilis remaining one of the most common human diseases, the complete genome of T. pallidum provides much needed information about the metabolic capacities and other cellulor functions of this pathogen. Its similarity to previously sequenced B. burgdorferi genome offers interesting possibilities for comparative genomics of these two spirochetes. Remarkably, the T. pallidus chromosome is circular, leaving B. burgdorferi as the only known bacterium with a linear one.
-
(1998)
Science
, vol.281
, pp. 375-388
-
-
Fraser, C.M.1
Norris, S.J.2
Weinstock, G.M.3
White, O.4
Sutton, G.G.5
Dodson, R.6
Gwinn, M.7
Hickey, E.K.8
Clayton, R.9
Ketchum, K.A.10
-
13
-
-
0032561496
-
Genome sequence of an obligate intracellular pathogen of humans: Chlamydia trachomatis
-
A comprehensive analysis of the chlamydial genome in an attempt to characterize this organism in as much detail as possible. While some of the motif-based annotations have already been confirmed by direct experimentation (e.g. assignment of fructose-1,6-bisphosphatase activity to CT215 supported by [50]), many of them remain to be verified. The most unexpected result of this genome analysis is probably the observation that certain chlamydial genes may have been recruited from the host eukaryotic cell.
-
Stephens R.S., Kalman S., Lammel C., Fan J., Marathe R., Aravind L., Mitchell W., Olinger L., Tatusov R.L., Zhao Q.et al. Genome sequence of an obligate intracellular pathogen of humans: Chlamydia trachomatis. Science. 282:1998;754-759. A comprehensive analysis of the chlamydial genome in an attempt to characterize this organism in as much detail as possible. While some of the motif-based annotations have already been confirmed by direct experimentation (e.g. assignment of fructose-1,6-bisphosphatase activity to CT215 supported by [50]), many of them remain to be verified. The most unexpected result of this genome analysis is probably the observation that certain chlamydial genes may have been recruited from the host eukaryotic cell.
-
(1998)
Science
, vol.282
, pp. 754-759
-
-
Stephens, R.S.1
Kalman, S.2
Lammel, C.3
Fan, J.4
Marathe, R.5
Aravind, L.6
Mitchell, W.7
Olinger, L.8
Tatusov, R.L.9
Zhao, Q.10
-
14
-
-
0032953228
-
Comparative genomes of Chlamydia pneumoniae and C. trachomatis
-
Comparative analysis of the two chlamydial genomes found 214 additional genes in C. pneumoniae compared to C. trachomatis. The most conspicuous differences are found in outer membrane proteins, the secretion system, and biosynthetic capabilities. C. pneumoniae is a suspect accomplice in a variety of supposedly non-infectious diseases, such as atherosclerosis, heart disease, adult-onset asthma and even lung cancer.
-
Kalman S., Mitchell W., Marathe R., Lammel C., Fan J., Hyman R.W., Olinger L., Grimwood J., Davis R.W., Stephens R.S. Comparative genomes of Chlamydia pneumoniae and C. trachomatis. Nat Genet. 21:1999;385-389. Comparative analysis of the two chlamydial genomes found 214 additional genes in C. pneumoniae compared to C. trachomatis. The most conspicuous differences are found in outer membrane proteins, the secretion system, and biosynthetic capabilities. C. pneumoniae is a suspect accomplice in a variety of supposedly non-infectious diseases, such as atherosclerosis, heart disease, adult-onset asthma and even lung cancer.
-
(1999)
Nat Genet
, vol.21
, pp. 385-389
-
-
Kalman, S.1
Mitchell, W.2
Marathe, R.3
Lammel, C.4
Fan, J.5
Hyman, R.W.6
Olinger, L.7
Grimwood, J.8
Davis, R.W.9
Stephens, R.S.10
-
15
-
-
0032401709
-
Implications of sequencing bacterial genomes for pathogenesis and vaccine development
-
Saunders N.J., Moxon E.R. Implications of sequencing bacterial genomes for pathogenesis and vaccine development. Curr Opin Biotechnol. 9:1998;618-623.
-
(1998)
Curr Opin Biotechnol
, vol.9
, pp. 618-623
-
-
Saunders, N.J.1
Moxon, E.R.2
-
17
-
-
0028275230
-
In vivo expression technology for selection of bacterial genes specifically induced in host tissues
-
Slauch J.M., Mahan M.J., Mekalanos J.J. In vivo expression technology for selection of bacterial genes specifically induced in host tissues. Methods Enzymol. 235:1994;481-492.
-
(1994)
Methods Enzymol
, vol.235
, pp. 481-492
-
-
Slauch, J.M.1
Mahan, M.J.2
Mekalanos, J.J.3
-
18
-
-
0028878965
-
Antibiotic-based selection for bacterial genes that are specifically induced during infection of a host
-
Mahan M.J., Tobias J.W., Slauch J.M., Hanna P.C., Collier R.J., Mekalanos J.J. Antibiotic-based selection for bacterial genes that are specifically induced during infection of a host. Proc Natl Acad Sci USA. 92:1995;669-673.
-
(1995)
Proc Natl Acad Sci USA
, vol.92
, pp. 669-673
-
-
Mahan, M.J.1
Tobias, J.W.2
Slauch, J.M.3
Hanna, P.C.4
Collier, R.J.5
Mekalanos, J.J.6
-
19
-
-
84984934048
-
DNA microarrays in drug discovery and development
-
Debouck C., Goodfellow P.N. DNA microarrays in drug discovery and development. Nat Genet. 21:1999;48-50.
-
(1999)
Nat Genet
, vol.21
, pp. 48-50
-
-
Debouck, C.1
Goodfellow, P.N.2
-
20
-
-
0031823632
-
Molecular evolution of a pathogenicity island from enterohemorrhagic Escherichia coli O157:H7
-
Comparison of pathogenicity islands from distantly related enterohemorrhagic and enteropathogenic strains of E. coli showed that although shared genes of the secretion apparatus were more than 98% identical, the genes coding for host interaction factors were much more divergent. Variability of genes responsible for the colonization of the host appears to be an important mechanism of pathogen evolution.
-
Perna N.T., Mayhew G.F., Posfai G., Elliott S., Donnenberg M.S., Kaper J.B., Blattner F.R. Molecular evolution of a pathogenicity island from enterohemorrhagic Escherichia coli O157:H7. Infect Immun. 66:1998;3810-3817. Comparison of pathogenicity islands from distantly related enterohemorrhagic and enteropathogenic strains of E. coli showed that although shared genes of the secretion apparatus were more than 98% identical, the genes coding for host interaction factors were much more divergent. Variability of genes responsible for the colonization of the host appears to be an important mechanism of pathogen evolution.
-
(1998)
Infect Immun
, vol.66
, pp. 3810-3817
-
-
Perna, N.T.1
Mayhew, G.F.2
Posfai, G.3
Elliott, S.4
Donnenberg, M.S.5
Kaper, J.B.6
Blattner, F.R.7
-
21
-
-
0033046314
-
Sample sequencing of a Salmonella typhimurium LT2 lambda library: Comparison to the Escherichia coli K12 genome
-
Wong R.M., Wong K.K., Benson N.R., McClelland M. Sample sequencing of a Salmonella typhimurium LT2 lambda library: comparison to the Escherichia coli K12 genome. FEMS Microbiol Lett. 173:1999;411-423.
-
(1999)
FEMS Microbiol Lett
, vol.173
, pp. 411-423
-
-
Wong, R.M.1
Wong, K.K.2
Benson, N.R.3
McClelland, M.4
-
22
-
-
0031669416
-
Comparison of sample sequences of the Salmonella typhi genome to the sequence of the complete Escherichia coli K-12 genome
-
McClelland M., Wilson R.K. Comparison of sample sequences of the Salmonella typhi genome to the sequence of the complete Escherichia coli K-12 genome. Infect Immun. 66:1998;4305-4312.
-
(1998)
Infect Immun
, vol.66
, pp. 4305-4312
-
-
McClelland, M.1
Wilson, R.K.2
-
23
-
-
0030901705
-
Pathogenicity islands of virulent bacteria: Structure, function and impact on microbial evolution
-
Hacker J., Blum-Oehler G., Muhldorfer I., Tschape H. Pathogenicity islands of virulent bacteria: structure, function and impact on microbial evolution. Mol Microbiol. 23:1997;1089-1097.
-
(1997)
Mol Microbiol
, vol.23
, pp. 1089-1097
-
-
Hacker, J.1
Blum-Oehler, G.2
Muhldorfer, I.3
Tschape, H.4
-
24
-
-
0033056680
-
Sequence of Shiga toxin 2 phage 933W from Escherichia coli O157:H7: Shiga toxin as a phage late-gene product
-
The evidence suggesting that the Shiga toxin production might be coupled with lytic growth of the lysogenic phage 933W brings up a heretical question: maybe we should target the phage itself and not its unfortunate host?
-
Plunkett G. III, Rose D.J., Durfee T.J., Blattner F.R. Sequence of Shiga toxin 2 phage 933W from Escherichia coli O157:H7: Shiga toxin as a phage late-gene product. J Bacteriol. 181:1999;1767-1778. The evidence suggesting that the Shiga toxin production might be coupled with lytic growth of the lysogenic phage 933W brings up a heretical question: maybe we should target the phage itself and not its unfortunate host?
-
(1999)
J Bacteriol
, vol.181
, pp. 1767-1778
-
-
Plunkett G. III1
Rose, D.J.2
Durfee, T.J.3
Blattner, F.R.4
-
25
-
-
0031796312
-
Complete DNA sequence and detailed analysis of the Yersinia pestis KIM5 plasmid encoding murine toxin and capsular antigen
-
Lindler L.E., Plano G.V., Burland V., Mayhew G.F., Blattner F.R. Complete DNA sequence and detailed analysis of the Yersinia pestis KIM5 plasmid encoding murine toxin and capsular antigen. Infect Immun. 66:1998;5731-5742.
-
(1998)
Infect Immun
, vol.66
, pp. 5731-5742
-
-
Lindler, L.E.1
Plano, G.V.2
Burland, V.3
Mayhew, G.F.4
Blattner, F.R.5
-
27
-
-
0032530804
-
The complete DNA sequence and analysis of the large virulence plasmid of Escherichia coli O157:H7
-
Burland V., Shao Y., Perna N.T., Plunkett G., Sofia H.J., Blattner F.R. The complete DNA sequence and analysis of the large virulence plasmid of Escherichia coli O157:H7. Nucleic Acids Res. 26:1998;4196-4204.
-
(1998)
Nucleic Acids Res
, vol.26
, pp. 4196-4204
-
-
Burland, V.1
Shao, Y.2
Perna, N.T.3
Plunkett, G.4
Sofia, H.J.5
Blattner, F.R.6
-
28
-
-
0032584169
-
'Black holes' and bacterial pathogenicity: A large genomic deletion that enhances the virulence of Shigella spp. and enteroinvasive Escherichia coli
-
A conclusive demonstration that a pathogen is not just a capricious bacterium with a pathogenicity island. Evolution to pathogenicity appears to involve gene loss as well as gene acquisition.
-
Maurelli A.T., Fernández R.E., Bloch C.A., Rode C.K., Fasano A. 'Black holes' and bacterial pathogenicity: a large genomic deletion that enhances the virulence of Shigella spp. and enteroinvasive Escherichia coli. Proc Natl Acad Sci USA. 95:1998;3943-3948. A conclusive demonstration that a pathogen is not just a capricious bacterium with a pathogenicity island. Evolution to pathogenicity appears to involve gene loss as well as gene acquisition.
-
(1998)
Proc Natl Acad Sci USA
, vol.95
, pp. 3943-3948
-
-
Maurelli, A.T.1
Fernández, R.E.2
Bloch, C.A.3
Rode, C.K.4
Fasano, A.5
-
29
-
-
0032573069
-
PCR-based subtractive hybridization and differences in gene content among strains of Helicobacter pylori
-
A long-needed experimental method to identify and amplify DNA fragments that differ in two otherwise closely related organisms. This should be extremely useful in comparing various new isolates against the reference genome sequence.
-
Akopyants N.S., Fradkov A., Diatchenko L., Hill J.E., Siebert P.D., Lukyanov S.A., Sverdlov E.D., Berg D.E. PCR-based subtractive hybridization and differences in gene content among strains of Helicobacter pylori. Proc Natl Acad Sci USA. 95:1998;13108-13113. A long-needed experimental method to identify and amplify DNA fragments that differ in two otherwise closely related organisms. This should be extremely useful in comparing various new isolates against the reference genome sequence.
-
(1998)
Proc Natl Acad Sci USA
, vol.95
, pp. 13108-13113
-
-
Akopyants, N.S.1
Fradkov, A.2
Diatchenko, L.3
Hill, J.E.4
Siebert, P.D.5
Lukyanov, S.A.6
Sverdlov, E.D.7
Berg, D.E.8
-
30
-
-
0030796260
-
Methods for generating precise deletions and insertions in the genome of wild-type Escherichia coli: Application to open reading frame characterization
-
Link A.J., Phillips D., Church G.M. Methods for generating precise deletions and insertions in the genome of wild-type Escherichia coli: application to open reading frame characterization. J Bacteriol. 179:1997;6228-6237.
-
(1997)
J Bacteriol
, vol.179
, pp. 6228-6237
-
-
Link, A.J.1
Phillips, D.2
Church, G.M.3
-
31
-
-
0032555218
-
Systematic identification of essential genes by in vitro mariner mutagenesis
-
A direct method for detecting essential genes in pre-amplified genomic fragments of up to 10 kb in size. As the method identifies transposon insertions that are lethal under given growth conditions, it should be useful for sorting out which genes are essential under each particular condition.
-
Akerley B.J., Rubin E.J., Camilli A., Lampe D.J., Robertson H.M., Mekalanos J.J. Systematic identification of essential genes by in vitro mariner mutagenesis. Proc Natl Acad Sci USA. 95:1998;8927-8932. A direct method for detecting essential genes in pre-amplified genomic fragments of up to 10 kb in size. As the method identifies transposon insertions that are lethal under given growth conditions, it should be useful for sorting out which genes are essential under each particular condition.
-
(1998)
Proc Natl Acad Sci USA
, vol.95
, pp. 8927-8932
-
-
Akerley, B.J.1
Rubin, E.J.2
Camilli, A.3
Lampe, D.J.4
Robertson, H.M.5
Mekalanos, J.J.6
-
32
-
-
0029789824
-
A minimal gene set for cellular life derived by comparison of complete bacterial genomes
-
Mushegian A.R., Koonin E.V. A minimal gene set for cellular life derived by comparison of complete bacterial genomes. Proc Natl Acad Sci USA. 93:1996;10268-10273.
-
(1996)
Proc Natl Acad Sci USA
, vol.93
, pp. 10268-10273
-
-
Mushegian, A.R.1
Koonin, E.V.2
-
33
-
-
0031784044
-
A genome-based approach for the identification of essential bacterial genes
-
This paper from the now defunct Geneva Biomedical Research Institute contains the only comprehensive investigation of the essentiality of conserved genes to date. Of 26 genes that are conserved in E. coli and M. genitalium, but have not been experimentally characterized, five were found to be essential for growth of both E. coli and B. subtilis; one more gene turned out to be essential for E. coli, but not B. subtilis. As genomes of both E. coli and B. subtilis, in contrast to much smaller genomes of pathogens, are highly redundant, these results look extremely encouraging.
-
Arigoni F., Talabot F., Peitsch M., Edgerton M.D., Meldrum E., Allet E., Fish R., Jamotte T., Curchod M.L., Loferer H. A genome-based approach for the identification of essential bacterial genes. Nat Biotechnol. 16:1998;851-856. This paper from the now defunct Geneva Biomedical Research Institute contains the only comprehensive investigation of the essentiality of conserved genes to date. Of 26 genes that are conserved in E. coli and M. genitalium, but have not been experimentally characterized, five were found to be essential for growth of both E. coli and B. subtilis; one more gene turned out to be essential for E. coli, but not B. subtilis. As genomes of both E. coli and B. subtilis, in contrast to much smaller genomes of pathogens, are highly redundant, these results look extremely encouraging.
-
(1998)
Nat Biotechnol
, vol.16
, pp. 851-856
-
-
Arigoni, F.1
Talabot, F.2
Peitsch, M.3
Edgerton, M.D.4
Meldrum, E.5
Allet, E.6
Fish, R.7
Jamotte, T.8
Curchod, M.L.9
Loferer, H.10
-
34
-
-
0345313624
-
Use of genomics to identify bacterial undecaprenyl pyrophosphate synthetase: Cloning, expression, and characterization of the essential uppS gene
-
This paper from a Hoffmann-La Roche group is another example of corporate giants going after uncharacterized conserved genes and getting valuable information of general importance. Even if the uppS gene, characterized in this paper, turned out to be a poor drug target, an important missing link in our understanding of lipid biosynthesis has been closed.
-
Apfel C.M., Takacs B., Fountoulakis M., Stieger M., Keck W. Use of genomics to identify bacterial undecaprenyl pyrophosphate synthetase: cloning, expression, and characterization of the essential uppS gene. J Bacteriol. 181:1999;483-492. This paper from a Hoffmann-La Roche group is another example of corporate giants going after uncharacterized conserved genes and getting valuable information of general importance. Even if the uppS gene, characterized in this paper, turned out to be a poor drug target, an important missing link in our understanding of lipid biosynthesis has been closed.
-
(1999)
J Bacteriol
, vol.181
, pp. 483-492
-
-
Apfel, C.M.1
Takacs, B.2
Fountoulakis, M.3
Stieger, M.4
Keck, W.5
-
36
-
-
0032102671
-
Beyond the complete genomes: From sequences to structure and function
-
This paper and [35] give a general description of the Clusters of Orthologous Groups (COG) database (
-
Koonin E.V., Tatusov R.L., Galperin M.Y. Beyond the complete genomes: from sequences to structure and function. Curr Opin Struct Biol. 8:1998;355-363. This paper and [35] give a general description of the Clusters of Orthologous Groups (COG) database ( http://www.ncbi.nlm.nih.gov/COG/ ) which consists of families of conserved proteins from completely sequenced genomes, identified in all-against-all similarity searches. Because orthologous proteins in different genomes tend to carry out the same or very closely related functions, assignment of proteins to the same COG allows one to deduce its function(s), based on the function(s) of the better studied members of the COG.
-
(1998)
Curr Opin Struct Biol
, vol.8
, pp. 355-363
-
-
Koonin, E.V.1
Tatusov, R.L.2
Galperin, M.Y.3
-
37
-
-
0032944238
-
The PROSITE database, its status in 1999
-
Hofmann K., Bucher P., Falquet L., Bairoch A. The PROSITE database, its status in 1999. Nucleic Acids Res. 27:1999;215-219.
-
(1999)
Nucleic Acids Res
, vol.27
, pp. 215-219
-
-
Hofmann, K.1
Bucher, P.2
Falquet, L.3
Bairoch, A.4
-
39
-
-
0032502899
-
Differential genome analysis applied to the species-specific features of Helicobacter pylori
-
This reference and the previous one describe an interesting approach to the identification of species-specific genes, which are likely to comprise potential drug targets.
-
Huynen M., Dandekar T., Bork P. Differential genome analysis applied to the species-specific features of Helicobacter pylori. FEBS Lett. 426:1998;1-5. This reference and the previous one describe an interesting approach to the identification of species-specific genes, which are likely to comprise potential drug targets.
-
(1998)
FEBS Lett
, vol.426
, pp. 1-5
-
-
Huynen, M.1
Dandekar, T.2
Bork, P.3
-
40
-
-
0033001042
-
Molecular and cellular activities of Helicobacter pylori pathogenic factors
-
Montecucco C., Papini E., de Bernard M., Zoratti M. Molecular and cellular activities of Helicobacter pylori pathogenic factors. FEBS Lett. 452:1999;16-21.
-
(1999)
FEBS Lett
, vol.452
, pp. 16-21
-
-
Montecucco, C.1
Papini, E.2
De Bernard, M.3
Zoratti, M.4
-
41
-
-
0032189860
-
Concordance analysis of microbial genomes
-
Another description of a 'genome subtraction' technique that can potentially be used for comparison of any number of genomes, including incomplete and proprietory ones.
-
Bruccoleri R.E., Dougherty T.J., Davison D.B. Concordance analysis of microbial genomes. Nucleic Acids Res. 26:1998;4482-4486. Another description of a 'genome subtraction' technique that can potentially be used for comparison of any number of genomes, including incomplete and proprietory ones.
-
(1998)
Nucleic Acids Res
, vol.26
, pp. 4482-4486
-
-
Bruccoleri, R.E.1
Dougherty, T.J.2
Davison, D.B.3
-
42
-
-
0030943595
-
Sequence analysis of an exceptionally conserved operon suggests enzymes for a new link between histidine and purine biosynthesis
-
Galperin M.Y., Koonin E.V. Sequence analysis of an exceptionally conserved operon suggests enzymes for a new link between histidine and purine biosynthesis. Mol Microbiol. 24:1997;443-445.
-
(1997)
Mol Microbiol
, vol.24
, pp. 443-445
-
-
Galperin, M.Y.1
Koonin, E.V.2
-
43
-
-
0031795758
-
The highly conserved, coregulated SNO and SNZ gene families in Saccharomyces cerevisiae respond to nutrient limitation
-
Padilla P.A., Fuge E.K., Crawford M.E., Errett A., Werner-Washburne M. The highly conserved, coregulated SNO and SNZ gene families in Saccharomyces cerevisiae respond to nutrient limitation. J Bacteriol. 180:1998;5718-5726.
-
(1998)
J Bacteriol
, vol.180
, pp. 5718-5726
-
-
Padilla, P.A.1
Fuge, E.K.2
Crawford, M.E.3
Errett, A.4
Werner-Washburne, M.5
-
44
-
-
0033551830
-
The extremely conserved pyroA gene of Aspergillus nidulans is required for pyridoxine synthesis and indirectly for resistance to photosensitizers
-
Osmani A.H., May G.S., Osmani S.A. The extremely conserved pyroA gene of Aspergillus nidulans is required for pyridoxine synthesis and indirectly for resistance to photosensitizers. J Biol Chem. 274:1999;23565-23569.
-
(1999)
J Biol Chem
, vol.274
, pp. 23565-23569
-
-
Osmani, A.H.1
May, G.S.2
Osmani, S.A.3
-
46
-
-
0033168258
-
Integrated pathway genome databases and their role in drug discovery
-
in comparison to the two other major pathway databases, KEGG ( http://www.genome.ad.jp/kegg ) and WIT ( http://wit.mcs.anl.gov/WIT2 ). The pathway comparison approach to identification of potential drug targets is discussed in detail
-
•] describe the current state of the EcoCyc database ( http://ecocyc.pangeasystems.com ) in comparison to the two other major pathway databases, KEGG ( http://www.genome.ad.jp/kegg ) and WIT ( http://wit.mcs.anl.gov/WIT2 ). The pathway comparison approach to identification of potential drug targets is discussed in detail.
-
(1999)
Trends Biotechnol
, vol.17
, pp. 275-281
-
-
Karp, P.D.1
Krummenacker, M.2
Paley, S.3
Wagg, J.4
-
48
-
-
0031459310
-
Prokaryotic genomes: The emerging paradigm of genome-based microbiology
-
Koonin E.V., Galperin M.Y. Prokaryotic genomes: the emerging paradigm of genome-based microbiology. Curr Opin Genet Dev. 7:1997;757-763.
-
(1997)
Curr Opin Genet Dev
, vol.7
, pp. 757-763
-
-
Koonin, E.V.1
Galperin, M.Y.2
-
49
-
-
0031666414
-
Analogous enzymes: Independent inventions in enzyme evolution
-
A study of the extreme cases of non-orthologous gene displacement, whereby the enzymes catalyzing the same biochemical reaction have no recognizable sequence similarity. In at least 34 cases out of the total 105 cases identified in this work, the two isoenzymes have or are predicted to have different three-dimensional structures, making them truly analogous (i.e. non-homologous) enzymes. Bacterial enzymes that have no significant sequence similarity to their human (mammalian) counterparts can be considered attractive drug targets.
-
Galperin M.Y., Walker D.R., Koonin E.V. Analogous enzymes: independent inventions in enzyme evolution. Genome Res. 8:1998;779-790. A study of the extreme cases of non-orthologous gene displacement, whereby the enzymes catalyzing the same biochemical reaction have no recognizable sequence similarity. In at least 34 cases out of the total 105 cases identified in this work, the two isoenzymes have or are predicted to have different three-dimensional structures, making them truly analogous (i.e. non-homologous) enzymes. Bacterial enzymes that have no significant sequence similarity to their human (mammalian) counterparts can be considered attractive drug targets.
-
(1998)
Genome Res
, vol.8
, pp. 779-790
-
-
Galperin, M.Y.1
Walker, D.R.2
Koonin, E.V.3
-
50
-
-
0032522706
-
The dhnA gene of Escherichia coli encodes a class I fructose bisphosphate aldolase
-
Thomson G.J., Howlett G.J., Ashcroft A.E., Berry A. The dhnA gene of Escherichia coli encodes a class I fructose bisphosphate aldolase. Biochem J. 331:1998;437-445.
-
(1998)
Biochem J
, vol.331
, pp. 437-445
-
-
Thomson, G.J.1
Howlett, G.J.2
Ashcroft, A.E.3
Berry, A.4
-
51
-
-
0027381599
-
The uraA locus and homologous recombination in Mycobacterium bovis BCG
-
Aldovini A., Husson R.N., Young R.A. The uraA locus and homologous recombination in Mycobacterium bovis BCG. J Bacteriol. 175:1993;7282-7289.
-
(1993)
J Bacteriol
, vol.175
, pp. 7282-7289
-
-
Aldovini, A.1
Husson, R.N.2
Young, R.A.3
-
53
-
-
0001819554
-
Comparing microbial genomes: How the gene set determines the lifestyle
-
R.L. Charlebois. Washington: ASM Press
-
Galperin M.Y., Tatusov R.L., Koonin E.V. Comparing microbial genomes: how the gene set determines the lifestyle. Charlebois R.L. Organization of the Prokaryotic Genome. 1999;91-108 ASM Press, Washington.
-
(1999)
Organization of the Prokaryotic Genome
, pp. 91-108
-
-
Galperin, M.Y.1
Tatusov, R.L.2
Koonin, E.V.3
-
54
-
-
0032902048
-
Eukaryotic transmembrane solute transport systems
-
Saier M.H. Jr. Eukaryotic transmembrane solute transport systems. Int Rev Cytol. 190:1999;61-136.
-
(1999)
Int Rev Cytol
, vol.190
, pp. 61-136
-
-
Saier M.H., Jr.1
-
55
-
-
0032962345
-
Rickettsiae and Chlamydiae: Evidence of horizontal gene transfer and gene exchange
-
Wolf Y.I., Aravind L., Koonin E.V. Rickettsiae and Chlamydiae: evidence of horizontal gene transfer and gene exchange. Trends Genet. 15:1999;173-175.
-
(1999)
Trends Genet
, vol.15
, pp. 173-175
-
-
Wolf, Y.I.1
Aravind, L.2
Koonin, E.V.3
-
56
-
-
0033519668
-
Multidrug resistance: Versatile drug sensors of bacterial cells
-
Lewis K. Multidrug resistance: versatile drug sensors of bacterial cells. Curr Biol. 9:1999;R403-R407.
-
(1999)
Curr Biol
, vol.9
-
-
Lewis, K.1
-
58
-
-
0032779638
-
Reversal of tetracycline resistance mediated by different bacterial tetracycline resistance determinants by an inhibitor of the Tet(B) antiport protein
-
•] show that mutidrug pumps play significant role in determining the level of bacterial sensitivity to commonly used antibiotics. Inhibiting these pumps or disrupting the respective genes may restore antibacterial activity of drugs that otherwise would be exported out the cell before they can induce any damage. This makes multidrug pumps natural targets for future antibacterial drugs.
-
•] show that mutidrug pumps play significant role in determining the level of bacterial sensitivity to commonly used antibiotics. Inhibiting these pumps or disrupting the respective genes may restore antibacterial activity of drugs that otherwise would be exported out the cell before they can induce any damage. This makes multidrug pumps natural targets for future antibacterial drugs.
-
(1999)
Antimicrob Agents Chemother
, vol.43
, pp. 1719-1724
-
-
Nelson, M.L.1
Levy, S.B.2
-
59
-
-
0033039066
-
Learning from the genome sequence of Mycobacterium tuberculosis H37Rv
-
Cole S.T. Learning from the genome sequence of Mycobacterium tuberculosis H37Rv. FEBS Lett. 452:1999;7-10.
-
(1999)
FEBS Lett
, vol.452
, pp. 7-10
-
-
Cole, S.T.1
-
60
-
-
0031447172
-
Archaeal-type lysyl-tRNA synthetase in the Lyme disease spirochete Borrelia burgdorferi
-
Ibba M., Bono J.L., Rosa P.A., Soll D. Archaeal-type lysyl-tRNA synthetase in the Lyme disease spirochete Borrelia burgdorferi. Proc Natl Acad Sci USA. 94:1997;14383-14388.
-
(1997)
Proc Natl Acad Sci USA
, vol.94
, pp. 14383-14388
-
-
Ibba, M.1
Bono, J.L.2
Rosa, P.A.3
Soll, D.4
-
61
-
-
0032461412
-
A superfamily of metalloenzymes unifies phosphopentomutase and cofactor-independent phosphoglycerate mutase with alkaline phosphatases and sulfatases
-
Galperin M.Y., Bairoch A., Koonin E.V. A superfamily of metalloenzymes unifies phosphopentomutase and cofactor-independent phosphoglycerate mutase with alkaline phosphatases and sulfatases. Protein Sci. 7:1998;1829-1835.
-
(1998)
Protein Sci
, vol.7
, pp. 1829-1835
-
-
Galperin, M.Y.1
Bairoch, A.2
Koonin, E.V.3
|