Comparative sequence analysis of the non-protein-coding mitochondrial DNA of inbred rat strains

PLoS ONE

Volumn 4, Issue 12, 2009, Pages

  Abhyankar, Avinash ^a   Park, Hee Bok ^a   Tonolo, Giancarlo ^a,b   Luthman, Holger ^a  

^a LUND UNIVERSITY   (Sweden)

^b Azienda USL 2 Olbia   (Italy)

Author keywords

[No Author keywords available]

Indexed keywords

MITOCHONDRIAL DNA; RIBOSOME RNA; RNA 12S; RNA 16S; TRANSFER RNA; UNTRANSLATED RNA;

ARTICLE; COMPARATIVE STUDY; CONTROLLED STUDY; FEEDBACK SYSTEM; GENETIC CONSERVATION; MITOCHONDRIAL GENOME; MITOCHONDRION; NONHUMAN; NUCLEOTIDE SEQUENCE; PROTEIN SECONDARY STRUCTURE; RAT; RAT STRAIN; SEQUENCE ANALYSIS; SERODIAGNOSIS; TRANSCRIPTION REGULATION; ANIMAL; CHEMISTRY; CONFORMATION; DNA SEQUENCE; GENETIC SELECTION; GENETICS; MOLECULAR GENETICS; OPEN READING FRAME;

MAMMALIA; RATTUS; RATTUS NORVEGICUS;

ANIMALS; BASE SEQUENCE; DNA, MITOCHONDRIAL; MOLECULAR SEQUENCE DATA; NUCLEIC ACID CONFORMATION; OPEN READING FRAMES; RATS; RATS, INBRED STRAINS; RNA, RIBOSOMAL; RNA, TRANSFER; SELECTION, GENETIC; SEQUENCE ANALYSIS, DNA;

EID: 77949539305     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0008148     Document Type: Article

References (44)

1. Dyall SD, Brown MT, Johnson PJ (2004) Ancient invasions: from endosymbionts to organelles. Science 304: 253-257.
2. Blier PU, Dufresne F, Burton RS (2001) Natural selection and the evolution of mtDNA-encoded peptides: evidence for intergenomic co-adaptation. Trends Genet 17: 400-406.
3. Wu Z, Puigserver P, Andersson U, Zhang C, Adelmant G, et al. (1999) Mechanisms controlling mitochondrial biogenesis and respiration through the thermogenic coactivator PGC-1. Cell 98: 115-124.
4. Scarpulla RC (2006) Nuclear control of respiratory gene expression in mammalian cells. J Cell Biochem 97: 673-683.
5. Castillo-Davis CI, Hartl DL, Achaz G (2004) Cis-regulatory and protein evolution in orthologous and duplicate genes. Genome Res 14: 1530-1536.
6. Mears JA, Sharma MR, Gutell RR, McCook AS, Richardson PE, et al. (2006) A structural model for the large subunit of the mammalian mitochondrial ribosome. J Mol Biol 358: 193-212.
7. Springer MS, Douzery E (1996) Secondary structure and patterns of evolution among mammalian mitochondrial 12S rRNA molecules. J Mol Evol 43: 357-373.
8. Helm M, Brule H, Friede D, Giege R, Putz D, et al. (2000) Search for characteristic structural features of mammalian mitochondrial tRNAs. RNA 6: 1356-1379.
9. Cantatore P, Daddabbo L, Fracasso F, Gadaleta MN (1995) Identification by in organello footprinting of protein contact sites and of single-stranded DNA sequences in the regulatory region of rat mitochondrial DNA. Protein binding sites and single-stranded DNA regions in isolated rat liver mitochondria. J Biol Chem 270: 25020-25027.
10. Roberti M, Musicco C, Polosa PL, Milella F, Gadaleta MN, et al. (1998) Multiple protein-binding sites in the TAS-region of human and rat mitochondrial DNA. Biochem Biophys Res Commun 243: 36-40.
11. 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.
12. Larizza A, Pesole G, Reyes A, Sbisà E, Saccone C (2002) Lineage specificity of the evolutionary dynamics of the mtDNA D-loop region in rodents. J Mol Evol 54: 145-155.
13. Patel VB, Cunningham CC, Hantgan RR (2001) Physiochemical properties of rat liver mitochondrial ribosomes. J Biol Chem 276: 6739-6746.
14. Smits P, Smeitink JAM, van den Heuvel LP, Huynen MA, Ettema TJG (2007) Reconstructing the evolution of the mitochondrial ribosomal proteome. Nucl Acids Res 35: 4686-4703.
15. Kraft A, Lutz C, Lingenhel A, Grobner P, Piendl W (1999) Control of ribosomal protein L1 synthesis in mesophilic and thermophilic archaea. Genetics 152: 1363-1372.
16. Mayer C, Kohrer C, Grobner P, Piendl W (1998) MvaL1 autoregulates the synthesis of the three ribosomal proteins encoded on the MvaL1 operon of the archaeon Methanococcus vannielii by inhibiting its own translation before or at the formation of the first peptide bond. Mol Microbiol 27: 455-468.
17. Branlant C, Krol A, Machatt A, Ebel J-P (1981) The secondary structure of the protein L1 binding region of ribosomal 23S RNA. Homologies with putative secondary structures of the L11 mRNA and of a region of mitochondrial 16S rRNA. Nucleic Acids Res 9: 293-307.
18. Hixson JE, Wong TW, Clayton DA (1986) Both the conserved stem-loop and divergent 59-flanking sequences are required for initiation at the human mitochondrial origin of light- strand DNA replication. J Biol Chem 261: 2384-2390.
19. Tapper DP, Clayton DA (1981) Mechanism of replication of human mitochondrial DNA. Localization of the 59 ends of nascent daughter strands. J Biol Chem 256: 5109-5115.
20. Martens PA, Clayton DA (1979) Mechanism of mitochondrial DNA replication in mouse L-cells: localization and sequence of the light-strand origin of replication. J Mol Biol 135: 327-351.
21. Bogenhagen D, Clayton DA (1978) Mechanism of mitochondrial DNA replication in mouse L-cells: kinetics of synthesis and turnover of the initiation sequence. J Mol Biol 119: 49-68.
22. 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 U S A 78: 6116-6120.
23. Brown TA, Clayton DA (2002) Release of replication termination controls mitochondrial DNA copy number after depletion with 29,39-dideoxycytidine. Nucleic Acids Res 30: 2004-2010.
24. Kai Y, Miyako K, Muta T, Umeda S, Irie T, et al. (1999) Mitochondrial DNA replication in human T lymphocytes is regulated primarily at the H-strand termination site. Biochim Biophys Acta 1446: 126-134.
25. 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.
26. Ruiz-Pesini E, Lott MT, Procaccio V, Poole JC, Brandon MC, et al. (2007) An enhanced mitomap with a global mtDNA mutational phylogeny. Nucleic Acids Res 35: D823-828.
27. Stoneking M (2000) Hypervariable sites in the mtDNA control region are mutational hotspots. Am J Hum Genet 67: 1029-1032.
28. Ewing B, Green P (1998) Base-calling of automated sequencer traces using Phred. II. Error probabilities. Genome Res 8: 186-194.
29. Ewing B, Hillier L, Wendl MC, Green P (1998) Base-calling of automated sequencer traces using Phred. I. Accuracy assessment. Genome Res 8: 175-185.
30. Staden R (1996) The staden sequence analysis package. Mol Biotechnol 5: 233-241.
31. Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA, et al. (2007) Clustal W and Clustal X version 2.0. Bioinformatics 23: 2947-2948.
32. Rozas J, Sanchez-DelBarrio JC, Messeguer X, Rozas R (2003) DnaSP, DNA polymorphism analyses by the coalescent and other methods. Bioinformatics 19: 2496-2497.
33. Cavdar Koc E, Burkhart W, Blackburn K, Moseley A, Spremulli LL (2001) The small subunit of the mammalian mitochondrial ribosome. Identification of the full complement of ribosomal proteins present. J Biol Chem 276: 19363-19374.
34. Burk A, Douzery EJP, Springer MS (2002) The secondary structure of mammalian mitochondrial 16S rRNA molecules: refinements based on a comparative phylogenetic approach. J Mamm Evol 9: 225-252.
35. Zuker M (2003) Mfold web server for nucleic acid folding and hybridization prediction. Nucl Acids Res 31: 3406-3415.
36. Tajima F (1989) Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics 123: 585-595.
37. Fu YX, Li WH (1993) Statistical tests of neutrality of mutations. Genetics 133: 693-709.
38. Fu YX (1997) Statistical tests of neutrality of mutations against population growth, hitchhiking and background selection. Genetics 147: 915-925.
39. Ramos-Onsins SE, Rozas J (2002) Statistical properties of new neutrality tests against population growth. Mol Biol Evol 19: 2092-2100.
40. Gibbs RA, Weinstock GM, Metzker ML, Muzny DM, Sodergren EJ, et al. (2004) Genome sequence of the Brown Norway rat yields insights into mammalian evolution. Nature 428: 493-521.
41. Pak JW, Vang F, Johnson C, McKenzie D, Aiken JM (2005) MtDNA point mutations are associated with deletion mutations in aged rat. Exp Gerontol 40: 209-218.
42. Schlick NE, Jensen-Seaman MI, Orlebeke K, Kwitek AE, Jacob HJ, et al. (2006) Sequence analysis of the complete mitochondrial DNA in 10 commonly used inbred rat strains. Am J Physiol Cell Physiol 291: C1183-1192.
43. Nilsson MA, Gullberg A, Spotorno AE, Arnason U, Janke A (2003) Radiation of extant marsupials after the K/T boundary: evidence from complete mitochondrial genomes. J Mol Evol 57 Suppl 1: S3-12.
44. Gadaleta G, Pepe G, De Candia G, Quagliariello C, Sbisa E, et al. (1989) The complete nucleotide sequence of the Rattus norvegicus mitochondrial genome: cryptic signals revealed by comparative analysis between vertebrates. J Mol Evol 28: 497-516.