Document Detail

Possible multiple origins of replication in primate mitochondria: Alternative role of tRNA sequences.
MedLine Citation:
PMID:  16430924     Owner:  NLM     Status:  MEDLINE    
DNA replication in vertebrate mitochondria is usually directional, leaving different portions of the genome single-stranded for different periods of time. During this time, mutations resulting from deaminations of cytosines to thymines and adenines to guanines accumulate on the heavy strand. Therefore, T/C and G/A ratios increase along mitochondrial genomes, proportionally to the time spent single-stranded during replication. Such trends exist at third codon positions for base ratios averaged across genes in individual genomes as well as for gene-specific and site-specific substitution frequencies estimated using phylogenetic methods. We use multiple regressions to test for the potential functioning of all 12 tRNA clusters in 19 primate mitochondrial genomes as alternative origins of light strand replication (OL). We provide a general algorithm for calculating time spent single stranded by a given site for any possible locations of the site and OL. For codon positions 1, 2, and 3, respectively, 23%, 9% and 35% of tRNA gene clusters have significant (p < 0.05) deamination gradients originating from them. The strength of the deamination gradient originating from tRNA gene clusters varies among species, and for five clusters, correlates with the tendency of tRNA genes in each of these clusters to form secondary structures that resemble the OL's structure. This is notably true for all codon positions for tRNA-Lys, which in absence of nuclear regulation, forms secondary structures resembling the hairpin structure of OL. For two tRNA gene clusters, correlations were statistically significant, but opposite to the direction expected by the known unidirectional replication, putatively compatible with bi-directional replication. Few substitutions in tRNA sequences can be neutral at the level of cloverleaf structure and function, yet significantly alter capacities to form OL-like structures, causing sudden evolution of genome-wide nucleotide contents.
Hervé Seligmann; Neeraja M Krishnan; Basuthkar J Rao
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Publication Detail:
Type:  Journal Article     Date:  2006-01-23
Journal Detail:
Title:  Journal of theoretical biology     Volume:  241     ISSN:  0022-5193     ISO Abbreviation:  J. Theor. Biol.     Publication Date:  2006 Jul 
Date Detail:
Created Date:  2006-07-10     Completed Date:  2007-06-18     Revised Date:  -    
Medline Journal Info:
Nlm Unique ID:  0376342     Medline TA:  J Theor Biol     Country:  Netherlands    
Other Details:
Languages:  eng     Pagination:  321-32     Citation Subset:  IM    
Department of Evolution, Systematics and Ecology, The Hebrew University of Jerusalem, 91904, Israel.
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MeSH Terms
Computational Biology
DNA Replication / genetics*
DNA, Mitochondrial / genetics*
Evolution, Molecular
Mitochondria / genetics*
Models, Genetic
Multigene Family / genetics
Primates / genetics*
RNA, Transfer / genetics*
Species Specificity
Reg. No./Substance:
0/DNA, Mitochondrial; 9014-25-9/RNA, Transfer

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