Asymmetric substitution patterns: a review of possible underlying mutational or selective mechanisms

Frank, A. Carolin; Lobry, Jean R.

doi:10.1016/s0378-1119(99)00297-8

Cited by 263 publications

(200 citation statements)

References 95 publications

Supporting

Mentioning

187

Contrasting

Unclassified

Order By: Relevance

“…This finding suggests that there are multiple replication origins that fire asynchronously, as in eukaryotic nuclear chromosomal replication. Leading and lagging strand replication are subjected to different mutational pressures, resulting in an asymmetric genomic composition (Lobry and Sueoka, 2002;Lobry and Louarn, 2003), including GC skew, that has been used to predict the DNA replication origin at the shift point of GC skew (Frank and Lobry, 1999;Arakawa and Tomita, 2007). However, in Synechocystis, the replication origin was not predicted from GC skew, as there are many shift points (Watanabe et al, 2012).…”

Section: Dnaa Is Not Essential For Dna Replication and Cell Growth Inmentioning

confidence: 99%

Diversification of DnaA dependency for DNA replication in cyanobacterial evolution

et al. 2015

View full text Add to dashboard Cite

Regulating DNA replication is essential for all living cells. The DNA replication initiation factor DnaA is highly conserved in prokaryotes and is required for accurate initiation of chromosomal replication at oriC. DnaA-independent free-living bacteria have not been identified. The dnaA gene is absent in plastids and some symbiotic bacteria, although it is not known when or how DnaA-independent mechanisms were acquired. Here, we show that the degree of dependency of DNA replication on DnaA varies among cyanobacterial species. Deletion of the dnaA gene in Synechococcus elongatus PCC 7942 shifted DNA replication from oriC to a different site as a result of the integration of an episomal plasmid. Moreover, viability during the stationary phase was higher in dnaA disruptants than in wild-type cells. Deletion of dnaA did not affect DNA replication or cell growth in Synechocystis sp. PCC 6803 or Anabaena sp. PCC 7120, indicating that functional dependency on DnaA was already lost in some nonsymbiotic cyanobacterial lineages during diversification. Therefore, we proposed that cyanobacteria acquired DnaA-independent replication mechanisms before symbiosis and such an ancestral cyanobacterium was the sole primary endosymbiont to form a plastid precursor.

show abstract

Section: Dnaa Is Not Essential For Dna Replication and Cell Growth Inmentioning

confidence: 99%

Diversification of DnaA dependency for DNA replication in cyanobacterial evolution

et al. 2015

View full text Add to dashboard Cite

show abstract

“…The site type-independent part MS ' I ϩ E is close to the identity matrix because the probability of a letter mutating is very small (Ͻ10Ϫ 6 ) and the selection on efficiency of replication weak (Sis can be normalized to be close to unity). Correspondingly, (MS)Ϫ 1 Ϸ I Ϫ E within an accuracy far greater than that coming from other assumptions and the mutation-selection equilibrium can be rewritten as r si ϵ log͑R si ͒ ϭ log s Ϫ ͑Eu s ͒ i /u si .…”

Section: Dynamicsmentioning

confidence: 99%

“…skew ͉ GC content ͉ codon bias ͉ multistability ͉ coevolution L iving organisms exhibit a variety of statistical patterns of their genome composition (1), including species-specific codon usage bias (2,3), GC content (4,5), and asymmetry of nucleotide composition of leading and lagging strands (skews) (6). Despite many proposals, no single satisfactory explanation of skews and their diversity exists (7).…”

mentioning

confidence: 99%

Genome rhetoric and the emergence of compositional bias

Vetsigian

Goldenfeld

2009

Proc. Natl. Acad. Sci. U.S.A.

View full text Add to dashboard Cite

Genomes exhibit diverse patterns of species-specific GC content, GC and AT skews, codon bias, and mutation bias. Despite intensive investigations and the rapid accumulation of sequence data, the causes of these a priori different genome biases have not been agreed on and seem multifactorial and idiosyncratic. We show that these biases can arise generically from an instability of the coevolutionary dynamics between genome composition and resource allocation for translation, transcription, and replication. Thus, we offer a unifying framework for understanding and analyzing different genome biases. We develop a test of multistability of nucleotide composition of completely sequenced genomes and reveal a bistability for Borrelia burgdorferi, a genome with pronounced replication-related biases. These results indicate that evolution generates rhetoric, it improves the efficiency of the genome's communication with the cell without modifying the message, and this leads to bias.skew ͉ GC content ͉ codon bias ͉ multistability ͉ coevolution

show abstract

“…Substitution rates are asymmetric in transcribed regions of the genome, with A3G transitions occurring at a higher rate than T3C transitions on the coding strand (11), the magnitude of the effect correlating with gene expression level (12,13). While mechanisms for transcriptional mutagenesis have been described in model systems (14,15), the mechanism responsible for this asymmetry is currently unknown.…”

mentioning

confidence: 99%

Mutation patterns in cancer genomes

Rubin

Green

2009

Proc. Natl. Acad. Sci. U.S.A.

View full text Add to dashboard Cite

Recent large-scale cancer sequencing studies have focused primarily on identifying cancer-associated genes, but as an important byproduct provide ''passenger mutation'' data that can potentially illuminate the mutational mechanisms at work in cancer cells. Here, we explore patterns of nucleotide substitution in several cancer types using published data. We first show that selection (negative or positive) has affected only a small fraction of mutations, allowing us to attribute observed trends to underlying mutational processes rather than selection. We then show that the increased CpG mutation frequency observed in some cancers primarily occurs outside of CpG islands and CpG island shores, thus rejecting the hypothesis that the increase is a byproduct of island or shore methylation followed by deamination. We observe an A3 G vs. T3 C mutational asymmetry in some cancers similar to one that has been observed in germline mutations in transcribed regions, suggesting that the mutation process may be influenced by gene expression. We also demonstrate that the relative frequency of mutations at dinucleotide ''hotspots'' can be used as a tool to detect likely technical artifacts in large-scale studies.CpG island ͉ dinucleotide hotspot ͉ mutation and selection ͉ mutational asymmetry ͉

show abstract

Asymmetric substitution patterns: a review of possible underlying mutational or selective mechanisms

Cited by 263 publications

References 95 publications

Diversification of DnaA dependency for DNA replication in cyanobacterial evolution

Diversification of DnaA dependency for DNA replication in cyanobacterial evolution

Genome rhetoric and the emergence of compositional bias

Mutation patterns in cancer genomes

Contact Info

Product

Resources

About