Conservation of ribosomal protein gene ordering in 16 complete genomes
Tóm tắt
The organization of ribosomal proteins in 16 prokaryotic genomes was studied as an example of comparative genome analyses of gene systems. Hypothetical ribosomal protein-containing operons were constructed. These operons also contained putative genes and other non-ribosomal genes. The correspondences among these genes across different organisms were clarified by sequence homology computations. In this way a cross tabulation of 70 ribosomal proteins genes was constructed. On average, these were organized into 9–14 operons in each genome. There were also 25 non-ribosomal or putative genes in these mainly ribosomal protein operons. Hence the table contains 95 genes in total. It was found that: (i) the conservation of the block of about 20 r-proteins in the L3 and L4 operons across almost the entire eubacteria and archaebacteria is remarkable; (ii) some operons only belong to eubacteria or archaebacteria; (iii) although the ribosomal protein operons are highly conserved within domain, there are fine variations in some operons across different organisms within each domain, and these variations are informative on the evolutionary relations among the organisms. This method provides a new potential for studying the origin and evolution of old species.
Từ khóa
Tài liệu tham khảo
Koonin, E. V., Big time for small genomes, Genome Research, 1997, 7: 418.
Deckert, G., Warren, P. V., Gaasterland, T. et al., The complete genome of the hyperthermophilic bacteriumAquifex aeolicus, Nature, 1998, 392: 353.
Fraser, C. M., Casjens, S., Huang, W. M. et al., Genomic sequence of a Lyme disease spirochete,Borrelia burgdorferi, Nature, 1997, 390: 580.
Fraser, C. M., Norris, S. J., Weinstock, G. M. et al., Complete genome sequence ofTreponema pallidum, the syphilis spirochete, Science, 1998, 281: 375.
Blattner, F. R., Plunkett III G., Bloch C. A. et al., The complete genome sequence ofEscherichia coli K-12, Science, 1997, 277: 1453.
Fleischmann, R. D., Adams M. D., White, O. et al., Whole-genome random sequencing and assembly ofHaemophilus influenzae Rd, Science, 1995, 269: 496.
Tomb, J. F., White, O., Kerlavage, A. R. et al., The complete genome sequence of the gastric pathogenHelicobacter pylori, Nature, 1997, 388: 539.
Fraser, C. M., Gocayne, J. D., White, O. et al., The minimal gene complement ofMycoplasma genitalium, Science, 1995, 270: 397.
Himmelreich, R., Hilbert, H., Plagens, H. et al., Complete sequence analysis of the genome of the bacteriumMycoplasma pneumoniae, Nucleic. Acids Res., 1996, 24: 4420.
Kunst, F., Ogasawara, N., Moszer, I. et al., The complete genome sequence of the Gram-positive bacteriumBacillus subtilis, Nature, 1997, 390: 249.
Cole, S.T., Brosch, R., Parkhill, J. et al., Deciphering the biology ofMycobacterium tuberculosis from the complete genome sequence, Nature, 1998, 393: 537.
Kaneko, T., Sato, S., Kotani, H. et al., Sequence analysis of the genome of the unicellular cyanobacteriumSynechocystis sp. strain PCC6803. II. Sequence determination of the entire genome and assignment of potential-coding regions, DNA Res., 1996, 3: 109.
Bult, C. J., White, O., Olsen, G. J. et al., Complete genome sequence of the methanogenic archaeon,Methanococcus jannaschii, Science, 1996, 273: 1058.
Smith, D. R., Doucette-Stamm, L. A., Deloughery, C. et al., Complete genome sequence of methanobacterium thermoautotrophicum delta H: functional analysis and comparative genomics, J. Bacteriol., 1997, 179: 7135.
Klenk, H. P., Clayton, R. A., Tomb, J. et al., The complete genome sequence of the hyperthermophilic, sulphate-reducing archaeonArchaeoglobus fulgidus, Nature, 1997, 390: 364.
Kawarabayasi, Y., Sawada, M., Horikawa, H. et al., Complete sequence and gene organization of the genome of a hyperthermophilic archaebacterium,Pyrococcus horikoshii OT3, J. DNARes., 1998, 5: 147.
Pearon, W. R., Rapid and sensitive sequence comparison with FASTP and FASTA, Methods Enzymol., 1990, 183: 63.
Sander, C., Schneider R., Database of homology-derived protein structures and the structural meaning of sequence alignment, Proteins, 1991, 9: 56.
Woese, C. R.,Archaebacteria, Sci. Amer., 1981, 244: 98.
Nomura, M., Gourse, R., Bauthman, G., Regulation of the synthesis of ribosomes and ribosomal components, Ann. Rev. Biochem., 1984, 53: 75.