Replication Orientation Affects the Rate and Direction of Bacterial Gene Evolution

Tillier, Elisabeth R. M.; Collins, Richard A.

doi:10.1007/s002390010108

Cited by 45 publications

(35 citation statements)

References 19 publications

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“…Genes that switch off replicating strands following chromosomal rearrangements evolve faster to adapt to the composition of the new replicating strand. As a result they show lower mean sequence similarity (Tillier & Collins, 2000b). The ratio of synonymous/non-synonymous rates of switched genes is similar to that of the average orthologues, in agreement with a mutational driving force for this process (Rocha & Danchin, 2001).…”

Section: Compositional Strand Biassupporting

confidence: 60%

“…5, compositional strand bias varies significantly from genome to genome. This may be related to the different stability of the genomes, as chromosome shuffling will tend to level off the bias (Achaz et al, 2003;Mackiewicz et al, 2001b;Rocha et al, 1999b;Tillier & Collins, 2000b). The different length of the Okazaki fragments may also contribute to modulating the bias, since a smaller exposure in the ssDNA state would lead to less cytosine deamination (Mrázek & Karlin, 1998).…”

Section: Compositional Strand Biasmentioning

confidence: 99%

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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: Compositional Strand Biassupporting

confidence: 60%

Section: Compositional Strand Biasmentioning

confidence: 99%

The replication-related organization of bacterial genomes

2004

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“…It has been shown that genes evolve faster after shifting from one replicating strand to the other due to mutational biases (Tillier and Collins 2000b;Rocha and Danchin 2001). We have examined the translocated genes that shifted strand, but no significant difference in DNA distance was found between genes that shifted strand and those that did not shift strand (see Figure S5).…”

Section: Discussionmentioning

confidence: 99%

Does Gene Translocation Accelerate the Evolution of Laterally Transferred Genes?

Hao

Golding

2009

Genetics

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Lateral gene transfer (LGT) and gene rearrangement are essential for shaping bacterial genomes during evolution. Separate attention has been focused on understanding the process of lateral gene transfer and the process of gene translocation. However, little is known about how gene translocation affects laterally transferred genes. Here we have examined gene translocations and lateral gene transfers in closely related genome pairs. The results reveal that translocated genes undergo elevated rates of evolution and gene translocation tends to take place preferentially in recently acquired genes. Translocated genes have a high probability to be truncated, suggesting that translocation followed by truncation/deletion might play an important role in the fast turnover of laterally transferred genes. Furthermore, more recently acquired genes have a higher proportion of genes on the leading strand, suggesting a strong strand bias of lateral gene transfer.

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“…Relationship between the number of killed genes and N for different F values for three sets of genes after 1000 MCS of simulation is also higher. That means that the observed divergence of genes which recently changed their positions on chromosome should be higher, which was actually observed in numerous genomic analyses ( [6] - [8]). In Fig.…”

Section: Resultsmentioning

confidence: 83%

Differential Gene Survival under Asymmetric Directional Mutational Pressure

Dudkiewicz

Kowalczuk

Mackiewicz

et al. 2004

Computational Science - ICCS 2004

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Abstract. We have simulated, using Monte Carlo methods, the survival of prokaryotic genes under directional mutational pressure. We have found that the whole pool of genes located on the leading DNA strand differs from that located on the lagging DNA strand and from the subclass of genes coding for ribosomal proteins. The best strategy for most of the non-ribosomal genes is to change the direction of the mutational pressure from time to time or to stay at their recent position. Genes coding for ribosomal proteins do not profit to such an extent from switching the directional pressure which seems to explain their extremely conserved positions on the prokaryotic chromosomes.

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Replication Orientation Affects the Rate and Direction of Bacterial Gene Evolution

Cited by 45 publications

References 19 publications

The replication-related organization of bacterial genomes

The replication-related organization of bacterial genomes

Does Gene Translocation Accelerate the Evolution of Laterally Transferred Genes?

Differential Gene Survival under Asymmetric Directional Mutational Pressure

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