Gene conversion and concerted evolution in bacterial genomes

Santoyo, Gustavo; Romero, David

doi:10.1016/j.femsre.2004.10.004

Cited by 120 publications

(100 citation statements)

References 116 publications

(183 reference statements)

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“…These are the only two studies that concentrated on intermolecular gene conversion in prokaryotes, and one additional study verified the existence of intermolecular gene conversion in chloroplasts (Khakhlova and Bock, 2006). Many more studies are available that concentrate on intramolecular gene conversion, which results in the concerted evolution of gene families and is a mechanism of antigenic variation or phase variation (Santoyo and Romero, 2005; Palmer and Brayton, 2007). Even if intergenic gene conversion in polyploid prokaryotes is a neglected field of research, it can be predicted to occur in more bacterial and archaeal species than in H. volcanii and Methanococcus maripaludis and result in evolutionary advantages of polyploidy.…”

Section: Intermolecular Gene Conversion In the Absence Of Selectionmentioning

confidence: 99%

Polyploidy in haloarchaea: advantages for growth and survival

Zerulla

Soppa

2014

Front. Microbiol.

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The investigated haloarchaeal species, Halobacterium salinarum, Haloferax mediterranei, and H. volcanii, have all been shown to be polyploid. They contain several replicons that have independent copy number regulation, and most have a higher copy number during exponential growth phase than in stationary phase. The possible evolutionary advantages of polyploidy for haloarchaea, most of which have experimental support for at least one species, are discussed. These advantages include a low mutation rate and high resistance toward X-ray irradiation and desiccation, which depend on homologous recombination. For H. volcanii, it has been shown that gene conversion operates in the absence of selection, which leads to the equalization of genome copies. On the other hand, selective forces might lead to heterozygous cells, which have been verified in the laboratory. Additional advantages of polyploidy are survival over geological times in halite deposits as well as at extreme conditions on earth and at simulated Mars conditions. Recently, it was found that H. volcanii uses genomic DNA as genetic material and as a storage polymer for phosphate. In the absence of phosphate, H. volcanii dramatically decreases its genome copy number, thereby enabling cell multiplication, but diminishing the genetic advantages of polyploidy. Stable storage of phosphate is proposed as an alternative driving force for the emergence of DNA in early evolution. Several additional potential advantages of polyploidy are discussed that have not been addressed experimentally for haloarchaea. An outlook summarizes selected current trends and possible future developments.

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Section: Intermolecular Gene Conversion In the Absence Of Selectionmentioning

confidence: 99%

Polyploidy in haloarchaea: advantages for growth and survival

Zerulla

Soppa

2014

Front. Microbiol.

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“…7). Finally, homozigotization of repeats (when genetic differences between the two repeats are erased in favor of one of the repeats) can also happen and is referred to as “gene conversion” (280) (Fig. 7).…”

Section: Specific Recombination Systemsmentioning

confidence: 99%

Homologous Recombination—Experimental Systems, Analysis, and Significance

Kuzminov

2011

EcoSal Plus

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Homologous recombination is the most complex of all recombination events that shape genomes and produce material for evolution. Homologous recombination events are exchanges between DNA molecules in the lengthy regions of shared identity, catalyzed by a group of dedicated enzymes. There is a variety of experimental systems in E. coli and Salmonella to detect homologous recombination events of several different kinds. Genetic analysis of homologous recombination reveals three separate phases of this process: pre-synapsis (the early phase), synapsis (homologous strand exchange) and post-synapsis (the late phase). In E. coli, there are at least two independent pathway of the early phase and at least two independent pathways of the late phase. All this complexity is incongruent with the originally ascribed role of homologous recombination as accelerator of genome evolution: there is simply not enough duplication and repetition in enterobacterial genomes for homologous recombination to have a detectable evolutionary role, and therefore not enough selection to maintain such a complexity. At the same time, the mechanisms of homologous recombination are uniquely suited for repair of complex DNA lesions called chromosomal lesions. In fact, the two major classes of chromosomal lesions are recognized and processed by the two individual pathways at the early phase of homologous recombination. It follows, therefore, that homologous recombination events are occasional reflections of the continual recombinational repair, made possible in cases of natural or artificial genome redundancy.

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“…Consequently, the region-specific recombinations identified in this study may have occurred mainly through homologous recombination between local homologous regions of viral minichromosomes with the help of host recombination machinery. One homologous recombination mechanism, gene conversion, has been suggested to be responsible for the concerted evolution of ribosomal DNA and other genes [53, 61, 62]. …”

Section: Discussionmentioning

confidence: 99%

Genomic fossils reveal adaptation of non-autonomous pararetroviruses driven by concerted evolution of noncoding regulatory sequences

2017

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The interplay of different virus species in a host cell after infection can affect the adaptation of each virus. Endogenous viral elements, such as endogenous pararetroviruses (PRVs), have arisen from vertical inheritance of viral sequences integrated into host germline genomes. As viral genomic fossils, these sequences can thus serve as valuable paleogenomic data to study the long-term evolutionary dynamics of virus–virus interactions, but they have rarely been applied for this purpose. All extant PRVs have been considered autonomous species in their parasitic life cycle in host cells. Here, we provide evidence for multiple non-autonomous PRV species with structural defects in viral activity that have frequently infected ancient grass hosts and adapted through interplay between viruses. Our paleogenomic analyses using endogenous PRVs in grass genomes revealed that these non-autonomous PRV species have participated in interplay with autonomous PRVs in a possible commensal partnership, or, alternatively, with one another in a possible mutualistic partnership. These partnerships, which have been established by the sharing of noncoding regulatory sequences (NRSs) in intergenic regions between two partner viruses, have been further maintained and altered by the sequence homogenization of NRSs between partners. Strikingly, we found that frequent region-specific recombination, rather than mutation selection, is the main causative mechanism of NRS homogenization. Our results, obtained from ancient DNA records of viruses, suggest that adaptation of PRVs has occurred by concerted evolution of NRSs between different virus species in the same host. Our findings further imply that evaluation of within-host NRS interactions within and between populations of viral pathogens may be important.

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Gene conversion and concerted evolution in bacterial genomes

Cited by 120 publications

References 116 publications

Polyploidy in haloarchaea: advantages for growth and survival

Polyploidy in haloarchaea: advantages for growth and survival

Homologous Recombination—Experimental Systems, Analysis, and Significance

Genomic fossils reveal adaptation of non-autonomous pararetroviruses driven by concerted evolution of noncoding regulatory sequences

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