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      DNA Replication and Strand Asymmetry in Prokaryotic and Mitochondrial Genomes

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          Abstract

          Different patterns of strand asymmetry have been documented in a variety of prokaryotic genomes as well as mitochondrial genomes. Because different replication mechanisms often lead to different patterns of strand asymmetry, much can be learned of replication mechanisms by examining strand asymmetry. Here I summarize the diverse patterns of strand asymmetry among different taxonomic groups to suggest that (1) the single-origin replication may not be universal among bacterial species as the endosymbionts Wigglesworthia glossinidia, Wolbachia species, cyanobacterium Synechocystis 6803 and Mycoplasma pulmonis genomes all exhibit strand asymmetry patterns consistent with the multiple origins of replication, (2) different replication origins in some archaeal genomes leave quite different patterns of strand asymmetry, suggesting that different replication origins in the same genome may be differentially used, (3) mitochondrial genomes from representative vertebrate species share one strand asymmetry pattern consistent with the strand-displacement replication documented in mammalian mtDNA, suggesting that the mtDNA replication mechanism in mammals may be shared among all vertebrate species, and (4) mitochondrial genomes from primitive forms of metazoans such as the sponge and hydra (representing Porifera and Cnidaria, respectively), as well as those from plants, have strand asymmetry patterns similar to single-origin or multi-origin replications observed in prokaryotes and are drastically different from mitochondrial genomes from other metazoans. This may explain why sponge and hydra mitochondrial genomes, as well as plant mitochondrial genomes, evolves much slower than those from other metazoans.

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          Most cited references65

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          Replication of animal mitochondrial DNA.

          D Clayton (1982)
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            Mitochondrial DNA maintenance in vertebrates.

            The discovery that mutations in mitochondrial DNA (mtDNA) can be pathogenic in humans has increased interest in understanding mtDNA maintenance. The functional state of mtDNA requires a great number of factors for gene expression, DNA replication, and DNA repair. These processes are ultimately controlled by the cell nucleus, because the requisite proteins are all encoded by nuclear genes and imported into the mitochondrion. DNA replication and transcription are linked in vertebrate mitochondria because RNA transcripts initiated at the light-strand promoter are the primers for mtDNA replication at the heavy-strand origin. Study of this transcription-primed DNA replication mechanism has led to isolation of key factors involved in mtDNA replication and transcription and to elucidation of unique nucleic acid structures formed at this origin. Because features of a transcription-primed mechanism appear to be conserved in vertebrates, a general model for initiation of vertebrate heavy-strand DNA synthesis is proposed. In many organisms, mtDNA maintenance requires not only faithful mtDNA replication, but also mtDNA repair and recombination. The extent to which these latter two processes are involved in mtDNA maintenance in vertebrates is also appraised.
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              DNA replication initiation: mechanisms and regulation in bacteria.

              In all organisms, multi-subunit replicases are responsible for the accurate duplication of genetic material during cellular division. Initiator proteins control the onset of DNA replication and direct the assembly of replisomal components through a series of precisely timed protein-DNA and protein-protein interactions. Recent structural studies of the bacterial protein DnaA have helped to clarify the molecular mechanisms underlying initiator function, and suggest that key structural features of cellular initiators are universally conserved. Moreover, it appears that bacteria use a diverse range of regulatory strategies dedicated to tightly controlling replication initiation; in many cases, these mechanisms are intricately connected to the activities of DnaA at the origin of replication. This Review presents an overview of both the mechanism and regulation of bacterial DNA replication initiation, with emphasis on the features that are similar in eukaryotic and archaeal systems.
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                Author and article information

                Journal
                Curr Genomics
                CG
                Current Genomics
                Bentham Science Publishers
                1389-2029
                1875-5488
                March 2012
                March 2012
                : 13
                : 1
                : 16-27
                Affiliations
                [1 ]Department of Biology and Center for Advanced Research in Environmental Genomics, University of Ottawa, 30 Marie Curie, P.O. Box 450, Station A, Ottawa, Ontario, Canada
                [2 ]Ottawa Institute of Systems Biology, Ottawa, Canada
                Author notes
                [* ]Address correspondence to this author at the Department of Biology and Center for Advanced Research in Environmental Genomics, University of Ottawa, 30 Marie Curie, P.O. Box 450, Station A, Ottawa, Ontario, K1N 6N5, Canada; Tel: (613) 562-5800 ext. 6886; Fax: (613) 562-5486; E-mail: xxia@ 123456uottawa.ca
                Article
                CG-13-16
                10.2174/138920212799034776
                3269012
                22942672
                39847fa2-dbbf-4bfb-a197-3688472a7422
                ©2012 Bentham Science Publishers

                This is an open access article distributed under the terms of the Creative Commons Attribution License ( http://creativecommons.org/licenses/by/2.5/), which permits unrestrictive use, distribution, and reproduction in any medium, provided the original work is properly cited.

                History
                : 7 July 2011
                : 26 September 2011
                : 2 October 2011
                Categories
                Article

                Genetics
                mutation,origin of replication,archaea,selection.,deamination,dna replication,gc skew,mitochondria
                Genetics
                mutation, origin of replication, archaea, selection., deamination, dna replication, gc skew, mitochondria

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