Correlation of Chi orientation with transcription indicates a fundamental relationship between recombination and transcription

Bell, S.J.; Chow, Yuh-Lit; Ho, Josephine; Forsdyke, Donald R.

doi:10.1016/s0378-1119(98)00333-3

Cited by 25 publications

(23 citation statements)

References 27 publications

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“…However, these sequences are GT-rich and include triplets corresponding to frequent codons. Thus doubts remain as to the biological significance of this overrepresentation in E. coli (Bell et al, 1998;Biaudet et al, 1998;Uno et al, 2000). Furthermore, very different chi sequences have been found in Haemophilus influenzae and B. subtilis, where the leading strand bias is much less pronounced (El Karoui et al, 1999).…”

Section: Oligonucleotide Biasmentioning

confidence: 99%

The replication-related organization of bacterial genomes

2004

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The replication of the chromosome is among the most essential functions of the bacterial cell and influences many other cellular mechanisms, from gene expression to cell division. Yet the way it impacts on the bacterial chromosome was not fully acknowledged until the availability of complete genomes allowed one to look upon genomes as more than bags of genes. Chromosomal replication includes a set of asymmetric mechanisms, among which are a division in a lagging and a leading strand and a gradient between early and late replicating regions. These differences are the causes of many of the organizational features observed in bacterial genomes, in terms of both gene distribution and sequence composition along the chromosome. When asymmetries or gradients increase in some genomes, e.g. due to a different composition of the DNA polymerase or to a higher growth rate, so do the corresponding biases. As some of the features of the chromosome structure seem to be under strong selection, understanding such biases is important for the understanding of chromosome organization and adaptation. Inversely, understanding chromosome organization may shed further light on questions relating to replication and cell division. Ultimately, the understanding of the interplay between these different elements will allow a better understanding of bacterial genetics and evolution.

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Section: Oligonucleotide Biasmentioning

confidence: 99%

The replication-related organization of bacterial genomes

2004

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“…1) are typical of the whole genome, the two Chargaff differences (for the W and S bases) were plotted against each other to generate quadrant plots (Bell et al 1998) for leftward-transcribed ORFs (Fig. 2a) and for rightward-transcribed ORFs (Fig.…”

Section: Quadrant Analysis Of M Jannaschiimentioning

confidence: 99%

“…In previous studies the optimum window (1 kb) for examining Chargaff differences was determined in a range of organisms by comparing natural with the corresponding shuffled sequences (Bell et al 1998;Dang et al 1998;Bell and Forsdyke 1999a). A similar study of the three thermophile genomes considered above indicated that a 1-kb window would also be optimum in these organisms.…”

Section: Same Optimum Window For Thermophiles and Nonthermophilesmentioning

confidence: 99%

“…When transcription is to the left of the promoter, the top, mRNA-template strand tends to be pyrimidine-rich (Szybalski et al 1966;Smithies et al 1981). It follows that mRNAs, whatever the direction of their transcription, tend to be purinerich (Bell et al 1998;Dang et al 1998). Usually one of the two purine bases is most heavily involved in purine-loading, and the other may appear indifferent.…”

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confidence: 99%

“…In previous studies of nonthermophilic organisms, such plots had to be carefully examined to see whether the S or the W bases were the best predictors of transcription direction in accordance with Szybalski's transcription direction rule. Chargaff differences were seldom >20% (especially Chargaff differences for the S bases), and simply plotting the ratio of purines to pyrimidines (R/Y) was not particularly informative (Bell et al 1998;Dang et al 1998;Bell and Forsdyke 1999a,b). In contrast, for M. jannaschii it is observed that (1) both purines follow Szybalski's transcription direction rule, (2) the magnitude of the Chargaff differences is often >20% (especially Chargaff differences for the S bases), and (3) the R/Y ratio strongly correlates with transcription direction.…”

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confidence: 99%

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Thermophilic Bacteria Strictly Obey Szybalski's Transcription Direction Rule and Politely Purine-Load RNAs with Both Adenine and Guanine

Lao¹,

Forsdyke²

2000

Genome Res.

102

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When transcription is to the right of the promoter, the "top," mRNA-synonymous strand of DNA tends to be purine-rich. When transcription is to the left of the promoter, the top, mRNA-template strand tends to be pyrimidine-rich. This transcription-direction rule suggests that there has been an evolutionary selection pressure for the purine-loading of RNAs. The politeness hypothesis states that purine-loading prevents distracting RNA-RNA interactions and excessive formation of double-stranded RNA, which might trigger various intracellular alarms. Because RNA-RNA interactions have a distinct entropy-driven component, the pressure for the evolution of purine-loading might be greater in organisms living at high temperatures. In support of this, we find that Chargaff differences (a measure of purine-loading) are greater in thermophiles than in nonthermophiles and extend to both purine bases. In thermophiles the pressure to purine-load affects codon choice, indicating that some features of their amino acid composition (e.g., high levels of glutamic acid) might reflect purine-loading pressure (i.e., constraints on mRNA) rather than direct constraints on protein structure and function.

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Two Levels of Information in DNA: Relationship of Romanes' “Intrinsic” Variability of the Reproductive System, and Bateson's “Residue” to the Species-Dependent Component of the Base Composition, (C+G)%

Correlation of Chi orientation with transcription indicates a fundamental relationship between recombination and transcription

Cited by 25 publications

References 27 publications

The replication-related organization of bacterial genomes

The replication-related organization of bacterial genomes

Thermophilic Bacteria Strictly Obey Szybalski's Transcription Direction Rule and Politely Purine-Load RNAs with Both Adenine and Guanine

Two Levels of Information in DNA: Relationship of Romanes' “Intrinsic” Variability of the Reproductive System, and Bateson's “Residue” to the Species-Dependent Component of the Base Composition, (C+G)%

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