Based on three distinct traits of genomic islands, a novel approach was developed to search for and determine genomic islands in special strains. Two genomic islands in Pseudomonas aeruginosa PAO1 and 7 genomic island...Based on three distinct traits of genomic islands, a novel approach was developed to search for and determine genomic islands in special strains. Two genomic islands in Pseudomonas aeruginosa PAO1 and 7 genomic islands in Pseudomonas aeruginosa PA14 were defined with this method. Among the 9 genomic islands, 4 islands had been characterized before, while the other 5 islands were initially determined. The insert sites of 6 genomic islands are tRNA sequences, direct repeats of PA14GI-3 are relative to tRNALeu, and direct repeats of PA14GI-2 are at the 3′ end of bifunctional GMP synthase/ glutamine amidotransferase. Only direct repeats of PA14GI-4 are not clear. Among the 5 newly-found genomic islands, it was supposed that PA14GI-2 is a genomic island related to Hg2+ uptake, PA14GI-3 is a secretory activity genomic island, PA14GI-6 is a pathogenicity island, and functions of PA14GI-1 and PA14GI-5 are not clear. Finally, the tyrosine type integrases in PAO1GI-1, PA14GI-5 and PA14GI-7 were analyzed, and their binding and restriction sites were predicted.展开更多
This article addresses how the functionalities of the cellular machinery of a bacterium might have constrained the genomic arrangement of its genes during evolution and how we can study such problems using computation...This article addresses how the functionalities of the cellular machinery of a bacterium might have constrained the genomic arrangement of its genes during evolution and how we can study such problems using computational approaches, taking full advantage of the rapidly increasing pool of the sequenced bacterial genomes, potentially leading to a much improved understanding of why a bacterial genome is organized in the way it is. This article discusses a number of challenging computational problems in elucidating the genomic structures at multiple levels and the information that is encoded through these genomic structures, gearing towards the ultimate understanding of the governing rules of bacterial genome organization.展开更多
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 oper...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 ar-chaebacteria is remarkable; (ii) some operons only belong to eubacteria or archaebacte-ria; (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.展开更多
基金Supported by the National Natural Science Foundation of China (Grant Nos. 30821005 and 30870075)National Key Basic Research and Development Program of China (Grant No. 2009CB118906)Shanghai Leading Academic Discipline Project (Grant No. B203)
文摘Based on three distinct traits of genomic islands, a novel approach was developed to search for and determine genomic islands in special strains. Two genomic islands in Pseudomonas aeruginosa PAO1 and 7 genomic islands in Pseudomonas aeruginosa PA14 were defined with this method. Among the 9 genomic islands, 4 islands had been characterized before, while the other 5 islands were initially determined. The insert sites of 6 genomic islands are tRNA sequences, direct repeats of PA14GI-3 are relative to tRNALeu, and direct repeats of PA14GI-2 are at the 3′ end of bifunctional GMP synthase/ glutamine amidotransferase. Only direct repeats of PA14GI-4 are not clear. Among the 5 newly-found genomic islands, it was supposed that PA14GI-2 is a genomic island related to Hg2+ uptake, PA14GI-3 is a secretory activity genomic island, PA14GI-6 is a pathogenicity island, and functions of PA14GI-1 and PA14GI-5 are not clear. Finally, the tyrosine type integrases in PAO1GI-1, PA14GI-5 and PA14GI-7 were analyzed, and their binding and restriction sites were predicted.
基金supported in part by the NSF of USA (Grant Nos. DBI-0354771, ITR-IIS-0407204, DBI-0542119, CCF0621700)NIHof USA (Grant Nos. 1R01GM075331 and 1R01GM081682)the grant for the BioEnergy Science Center
文摘This article addresses how the functionalities of the cellular machinery of a bacterium might have constrained the genomic arrangement of its genes during evolution and how we can study such problems using computational approaches, taking full advantage of the rapidly increasing pool of the sequenced bacterial genomes, potentially leading to a much improved understanding of why a bacterial genome is organized in the way it is. This article discusses a number of challenging computational problems in elucidating the genomic structures at multiple levels and the information that is encoded through these genomic structures, gearing towards the ultimate understanding of the governing rules of bacterial genome organization.
文摘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 ar-chaebacteria is remarkable; (ii) some operons only belong to eubacteria or archaebacte-ria; (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.
