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The term 'universal' emphasises the fact that, when there exists a bias between the lagging and leading strand, it has always the same form in terms of nucleotides, codons and amino acids. When present, this demonstrates a remarkable stability in a genome: if genes were to shuffle too frequently, this would have smoothed out the bias
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Rocha EPC, Danchin A, Viari A Universal replication biases in bacteria. Mol Microbiol. 32:1999;11-16. The term 'universal' emphasises the fact that, when there exists a bias between the lagging and leading strand, it has always the same form in terms of nucleotides, codons and amino acids. When present, this demonstrates a remarkable stability in a genome: if genes were to shuffle too frequently, this would have smoothed out the bias.
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Is the control of replication termination transferred by lateral gene exchange? The nine 30 bp terminator sequences of B. subtilis 168 are located within the terminus region, outside of protein coding sequences and adjacent to an AT-rich region. The sequence is conserved in several related Bacillus species, but cannot be detected by Southern hybridisation in B. licheniformis. The homolog of the replication terminator protein has not been discovered either in this organism. The authors speculate that this might be the sign of a recent lateral gene transfer event
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Griffiths AA, Andersen PA, Wake RG Replication terminator protein-based replication fork-arrest systems in various Bacillus species. J Bacteriol. 180:1998;3360-3367. Is the control of replication termination transferred by lateral gene exchange? The nine 30 bp terminator sequences of B. subtilis 168 are located within the terminus region, outside of protein coding sequences and adjacent to an AT-rich region. The sequence is conserved in several related Bacillus species, but cannot be detected by Southern hybridisation in B. licheniformis. The homolog of the replication terminator protein has not been discovered either in this organism. The authors speculate that this might be the sign of a recent lateral gene transfer event.
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This paper, along with [14], tries to delineate general approaches for the study of gene exchange, and exposes the consequences of horizontal gene transfer for genome organisation. These issues will have an increasingly important impact on our ideas about the origin of the first cells
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Lawrence JG, Ochman H Molecular archaeology of the Escherichia coli genome. Proc Natl Acad Sci USA. 95:1998;9413-9417. This paper, along with [14], tries to delineate general approaches for the study of gene exchange, and exposes the consequences of horizontal gene transfer for genome organisation. These issues will have an increasingly important impact on our ideas about the origin of the first cells.
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Synonymous nucleotide divergence and saturation: Effects of site-specific variations in codon bias and mutation rates
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Analysis of synonymous codon divergence in E. coli and S. typhimurium: a similar comparison is much awaited for B. subtilis!
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The maximum rate of gene expression is dependent on the downstream context of unfavourable codons
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Poole ES, Major LL, Mannering SA, Tate WP Translational termination in Escherichia coli: three bases following the stop codon crosslink to release factor 2 and affect the decoding efficiency of UGA-containing signals. Nucleic Acids Res. 26:1998;954-960.
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The influence of the 5′ codon context on translation termination in Bacillus subtilis and Escherichia coli is similar but different from Salmonella typhimurium
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Codon context seems to be important for translation termination. At the present time we still do not possess laws explaining observed regularities. It seems necessary to reinterpret data using a partition of genes into various classes, in particular treating in a separate way genes that have been horizontally transferred
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Frequency and istribution of DNA uptake signal sequences in the Haemophilus influenzae Rd genome
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Ribosomal-1 frameshifting during decoding of Bacillus subtilis cdd occurs at the sequence CGA AAG
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These authors demonstrate that programmed frameshifting exists in B. subtilis
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Mejlhede N, Atkins JF, Neuhard J Ribosomal-1 frameshifting during decoding of Bacillus subtilis cdd occurs at the sequence CGA AAG. J Bacteriol. 181:1999;2930-2937. These authors demonstrate that programmed frameshifting exists in B. subtilis.
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Mapping the bacterial cell architecture in the chromosome
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in press, A general model of the organisation of the bacterial cytoplasm is discussed, with reference to the position of the genes in the genome
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Danchin A, Guerdoux-Jamet P, Moszer I, Nitschké P Mapping the bacterial cell architecture in the chromosome. Philos Trans R Soc Lond B Biol Sci. 1999;. in press, A general model of the organisation of the bacterial cytoplasm is discussed, with reference to the position of the genes in the genome.
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The SubtiList World-Wide Web Server on URL:
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The SubtiList World-Wide Web Server on URL: http://bioweb.pasteur.fr/GenoList/SubtiList/.
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