Evidence for variable selective pressures at a large secondary structure of the human mitochondrial DNA control region

Molecular Biology and Evolution

Volumn 25, Issue 12, 2008, Pages 2759-2770

  Pereira, Filipe ^a   Soares, Pedro ^b   Carneiro, João ^a   Pereira, Luísa ^a,c   Richards, Martin B ^b   Samuels, David C ^d   Amorim, António ^a  

^a UNIVERSITY OF PORTO   (Portugal)

^b UNIVERSITY OF LEEDS   (United Kingdom)

^c University of Porto   (Portugal)

^d VIRGINIA BIOINFORMATICS INSTITUTE   (United States)

Author keywords

mtDNA control region; mtDNA deletions; Mutational heterogeneity; Secondary structures

Indexed keywords

MITOCHONDRIAL DNA;

ARTICLE; DNA REPLICATION; DNA SEQUENCE; DNA STRUCTURE; DNA TRANSCRIPTION; GENETIC ANALYSIS; HUMAN; PHYLOGENY; STRUCTURE ANALYSIS;

ANIMALS; BASE COMPOSITION; DNA, MITOCHONDRIAL; GENE DELETION; HUMANS; LOCUS CONTROL REGION; MITOCHONDRIA; NUCLEIC ACID CONFORMATION; PRIMATES; SELECTION (GENETICS);

PRIMATES;

EID: 56449124495     PISSN: 07374038     EISSN: 15371719     Source Type: Journal    
DOI: 10.1093/molbev/msn225     Document Type: Article

References (48)

1. Altschul SF, Erickson BW. 1985. Significance of nucleotide sequence alignments: a method for random sequence permutation that preserves dinucleotide and codon usage. Mol Biol Evol. 2:526-538.
2. Anderson S, Bankier AT, Barrell BG, et al. (14 co-authors). 1981. Sequence and organization of the human mitochondrial genome. Nature. 290:457-465.
3. Andrews RM, Kubacka I, Chinnery PF, Lightowlers R, Turnbull D, Howell N. 1999. Reanalysis and revision of the Cambridge reference sequence for human mitochondrial DNA. Nat Genet. 23:147.
4. Bandelt HJ, Forster P, Sykes BC, Richards MB. 1995. Mitochondrial portraits of human populations using median networks. Genetics. 141:743-753.
5. Bandelt HJ, Kong QP, Richards M, Macaulay V. 2006. Estimation of mutation rates and coalescence times: some caveats. In: Bandelt HJ, Macaulay V, Richards M, editors. Human mitochondrial DNA and the evolution of Homo sapiens, Series: Nucleic Acids and Molecular Biology vol. 18. Berlin: Springer-Verlag. p. 47-92.
6. Brockington M, Sweeney MG, Hammans SR, Morgan-Hughes JA, Harding AE. 1993. A tandem duplication in the D-loop of human mitochondrial DNA is associated with deletions in mitochondrial myopathies. Nat Genet. 4:67-71.
7. Brown GG, Gadaleta G, Pepe G, Saccone C, Sbisa E. 1986. Structural conservation and variation in the D-loop-containing region of vertebrate mitochondrial DNA. J Mol Biol. 192:503-511.
8. Chang DD, Clayton DA. 1985. Priming of human mitochondrial DNA replication occurs at the light-strand promoter. Proc Natl Acad Sci USA. 82:351-355.
9. Cheung AK. 2004. Palindrome regeneration by template strand-switching mechanism at the origin of DNA replication of porcine circovirus via the rolling-circle melting-pot replication model. J Virol. 78:9016-9029.
10. Chinnery PF, Johnson MA, Wardell TM, Singh-Kler R, Hayes C, Brown DT, Taylor RW, Bindoff LA, Turnbull DM. 2000. The epidemiology of pathogenic mitochondrial DNA mutations. Ann Neurol. 48:188-193.
11. Clote P, Ferre F, Kranakis E, Krizanc D. 2005. Structural RNA has lower folding energy than random RNA of the same dinucleotide frequency. RNA. 11:578-591.
12. Doda JN, Wright CT, Clayton DA. 1981. Elongation of displacement-loop strands in human and mouse mitochondrial DNA is arrested near specific template sequences. Proc Natl Acad Sci USA. 78:6116-6120.
13. Excoffier L, Yang Z. 1999. Substitution rate variation among sites in mitochondrial hypervariable region I of humans and chimpanzees. Mol Biol Evol. 16:1357-1368.
14. Forsdyke DR. 1995. A stem-loop "kissing" model for the initiation of recombination and the origin of introns. Mol Biol Evol. 12:949-958.
15. Galtier N, Lobry JR. 1997. Relationships between genomic G+C content, RNA secondary structures, and optimal growth temperature in prokaryotes. J Mol Evol. 44:632-636.
16. Hasegawa M, Kishino H, Yano T. 1985. Dating of the human-ape split by a molecular clock of mitochondrial DNA. J Mol Evol. 22:160-174.
17. Hixson JE, Clayton DA. 1985. Initiation of transcription from each of the two human mitochondrial promoters requires unique nucleotides at the transcriptional start sites. Proc Natl Acad Sci USA. 82:2660-2664.
18. Hoede C, Denamur E, Tenaillon O. 2006. Selection acts on DNA secondary structures to decrease transcriptional mutagenesis. PLoS Genet. 2:e176.
19. Katz L, Burge CB. 2003. Widespread selection for local RNA secondary structure in coding regions of bacterial genes. Genome Res. 13:2042-2051.
20. Kimura M. 1983. The neutral theory of molecular evolution. Cambridge: Cambridge University Press.
21. Markham NR, Zuker M. 2005. DINAMelt web server for nucleic acid melting prediction. Nucleic Acids Res. 33:W577-W581.
22. Meyer S, Weiss G, von Haeseler A. 1999. Pattern of nucleotide substitution and rate heterogeneity in the hypervariable regions I and II of human mtDNA. Genetics. 152:1103-1110.
23. Mishmar D, Ruiz-Pesini E, Golik P, et al. (13 co-authors). 2003. Natural selection shaped regional mtDNA variation in humans. Proc Natl Acad Sci USA. 100:171-176.
24. Mita S, Rizzuto R, Moraes CT, Shanske S, Arnaudo E, Fabrizi GM, Koga Y, DiMauro S, Schon EA. 1990. Recombination via flanking direct repeats is a major cause of large-scale deletions of human mitochondrial DNA. Nucleic Acids Res. 18:561-567.
25. Montoya J, Christianson T, Levens D, Rabinowitz M, Attardi G. 1982. Identification of initiation sites for heavy-strand and light-strand transcription in human mitochondrial DNA. Proc Natl Acad Sci USA. 79:7195-7199.
26. Ojala D, Merkel C, Gelfand R, Attardi G. 1980. The tRNA genes punctuate the reading of genetic information in human mitochondrial DNA. Cell. 22:393-403.
27. Pesole G, Saccone C. 2001. A novel method for estimating substitution rate variation among sites in a large dataset of homologous DNA sequences. Genetics. 157:859-865.
28. Rambaut A, Grassly NC. 1997. Seq-Gen: an application for the Monte Carlo simulation of DNA sequence evolution along phylogenetic trees. Comput Appl Biosci. 13:235-238.
29. Rozas J, Sanchez-DelBarrio JC, Messeguer X, Rozas R. 2003. DnaSP, DNA polymorphism analyses by the coalescent and other methods. Bioinformatics. 19:2496-2497.
30. Samuels DC, Schon EA, Chinnery PF. 2004. Two direct repeats causemost human mtDNA deletions. Trends Genet. 20:393-398.
31. SantaLucia J Jr. 1998. A unified view of polymer, dumbbell, and oligonucleotide DNA nearest-neighbor thermodynamics. Proc Natl Acad Sci USA. 95:1460-1465.
32. Sbisa E, Tanzariello F, Reyes A, Pesole G, Saccone C. 1997. Mammalian mitochondrial D-loop region structural analysis: identification of new conserved sequences and their functional and evolutionary implications. Gene. 205:125-140.
33. Seffens W, Digby D. 1999. mRNAs have greater negative folding free energies than shuffled or codon choice randomized sequences. Nucleic Acids Res. 27:1578-1584.
34. Shadel GS, Clayton DA. 1997. Mitochondrial DNA maintenance in vertebrates. Annu Rev Biochem. 66:409-435.
35. Slomovic S, Laufer D, Geiger D, Schuster G. 2005. Polyadenylation and degradation of human mitochondrial RNA: the prokaryotic past leaves its mark. Mol Cell Biol. 225:6427-6435.
36. Spelbrink JN. 2003. Replication, repair, and recombination of mitochondrial DNA. In: Holt I, editor. Genetics of mitochondrial diseases. Oxford: Oxford Medical Publications. p. 3-25.
37. Stothard P. 2000. The sequence manipulation suite: JavaScript programs for analyzing and formatting protein and DNA sequences. Biotechniques. 28:1102-1104.
38. Taanman JW. 1999. The mitochondrial genome: structure, transcription, translation and replication. Biochim Biophys Acta. 1410:103-123.
39. Tajima F. 1989. Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics. 123:585-595.
40. Walberg MW, Clayton DA. 1981. Sequence and properties of the human KB cell and mouse L cell D-loop regions of mitochondrial DNA. Nucleic Acids Res. 9:5411-5421.
41. Washietl S, Hofacker IL. 2004. Consensus folding of aligned sequences as a new measure for the detection of functional RNAs by comparative genomics. J Mol Biol. 342:19-30.
42. Workman C, Krogh A. 1999. No evidence that mRNAs have lower folding free energies than random sequences with the same dinucleotide distribution. Nucleic Acids Res. 27:4816-4822.
43. Wright BE. 2000. A biochemical mechanism for nonrandom mutations and evolution. J Bacteriol. 182:2993-3001.
44. Wright BE, Reimers JM, Schmidt KH, Reschke DK. 2002. Hypermutable bases in the p53 cancer gene are at vulnerable positions in DNA secondary structures. Cancer Res. 62:5641-5644.
45. Wright BE, Reschke DK, Schmidt KH, Reimers JM, Knight W. 2003. Predicting mutation frequencies in stem-loop structures of derepressed genes: implications for evolution. Mol Microbiol. 48:429-441.
46. Yasukawa T, Yang MY, Jacobs HT, Holt IJ. 2005. A bidirectional origin of replication maps to the major noncoding region of human mitochondrial DNA. Mol Cell. 18:651-662.
47. Yui R, Matsuura ET. 2006. Detection of deletions flanked by short direct repeats in mitochondrial DNA of aging Drosophila. Mutat Res. 594:155-161.
48. Zuker M. 2000. Calculating nucleic acid secondary structure. Curr Opin Struct Biol. 10:303-310.