Deep origin of plastid/parasite ATP/ADP translocases

Journal of Molecular Evolution

Volumn 56, Issue 2, 2003, Pages 137-150

  Amiri, Haleh ^a   Karlberg, Olof ^a   Andersson, Siv G E ^a,b  

^a UPPSALA UNIVERSITY   (Sweden)

^b Department of Molecular Evolution ^*  (Sweden)

Author keywords

ATP ADPtransporters; Chlamydia; Glycolysis; Horizontal transfer; Mitochondria; Plastids; Respiration; Rickettsia

Indexed keywords

ADENOSINE DIPHOSPHATE; ADENOSINE TRIPHOSPHATE; CARRIER PROTEIN;

AMINO ACID SEQUENCE; ARTICLE; CHLAMYDIA; ENZYME ANALYSIS; GENE DUPLICATION; GENE SEQUENCE; GENETIC VARIABILITY; GLYCOLYSIS; HORIZONTAL GENE TRANSFER; MICROBIAL RESPIRATION; MITOCHONDRION; NONHUMAN; NUCLEOTIDE SEQUENCE; PARASITE; PHYLOGENY; PLASTID; RICKETTSIA; SEQUENCE ANALYSIS;

AMINO ACID SEQUENCE; BACTERIAL PROTEINS; CHLAMYDIACEAE; EUKARYOTIC CELLS; EVOLUTION, MOLECULAR; GENE TRANSFER, HORIZONTAL; HOST-PARASITE RELATIONS; MITOCHONDRIA; MITOCHONDRIAL ADP, ATP TRANSLOCASES; MOLECULAR SEQUENCE DATA; PHYLOGENY; PLASTIDS; RICKETTSIA; RICKETTSIA RICKETTSII; RICKETTSIA TYPHI; SEQUENCE ANALYSIS; SEQUENCE HOMOLOGY, AMINO ACID;

CHLAMYDIA; EUKARYOTA; PROTOZOA; RICKETTSIA; RICKETTSIALES;

EID: 0037311465     PISSN: 00222844     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00239-002-2387-0     Document Type: Article

References (75)

1. Alexeyev MF, Winkler HH (2002) Transposable dual reporters for studying the structure-function relationships in membrane proteins: Permissive sites in R. prowazekii ATP/ADP translocase. Biochemistry 41:406-411
2. Altschul SF, Madden TL, Schäffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ (1997) Gapped BLAST and PSI-BLAST: A new generation of protein database search programs. Nucleic Acids Res 25:3389-3402
3. Amiri H, Alsmark CM, Andersson SGE (2002) Proliferation and deterioration of Rickettsia palindromic elements. Mol Biol Evol 19:1234-1243
4. Andersson SGE (1998) Bioenergetics of the obligate intracellular parasite Rickettsia prowazekii. Biochim Biophys Acta 1365:105-111
5. Andersson SGE, Kurland CG (1995) Genomic evolution drives the evolution of the translation system. Biochem Cell Biol 73:775-787
6. Andersson SGE, Kurland CG (1998) Reductive evolution of resident genomes. Trends Microbiol 6:263-268
7. Andersson SGE, Kurland CG (1999) Origin of mitochondria and hydrogenosomes. Curr Opin Microbiol 2:535-541
8. Andersson SGE, Sharp PM (1996) Codon usage and base composition in Rickettsia prowazekii. J Mol Evol 42:525-536
9. Andersson SGE, Zomorodipour A, Winkler HH, Kurland CG (1995) Unusual organization of the rRNA genes in Rickettsia prowazekii J Bacteriol 177:4171-4175
10. Andersson SGE, Zomorodipour A, Andersson JO, Sicheritz-Ponten T, Alsmark UCM, Podowski RM, Näslund AK, Winkler HH, Kurland CG (1998) The genome sequence of Rickettsia prowazekii and the origin of mitochondria. Nature 96:133-140
11. Aquila H, Link TA, Klingenberg M (1987) Solute carriers involved in energy transfer of mitochondria form a homologous protein family. FEBS Lett 212:1-9
12. Baldauf SL, Roger AJ, Wenk-Siefert I, Doolittle WF (2000) A kingdom-level phylogeny of eukaryotes based on combined protein data. Science 290:972-977
13. Brinkman FSL, Blanchard JL, Cherkasov A, Av-Gay Y, Brunham RC, Fernandez RC, Finlay BB, Oho SP, Ouellette BFF, Keeling PJ, Rose AM, Hancook REW, Jones SJM (2002) Evidence that plant-like genes in Chlamydia species reflect an ancestral relationship between Chlamydiaceae, Cyanobacteria, and the chloroplast. Genome Res 12:1159-1167
14. Cai J, Winkler HH (1996) Transcriptional regulation in the obligate intracytoplasmic bacterium Rickettsia prowazekii. J Bacteriol 178:5543-5545
15. Cammarano P, Palm P, Creti R, Ceccarelli E, Sanangelantoni, AM, Tiboni O (1992) Early evolutionary relationships among known life forms inferred from elongation factor EF-2/EF-G sequences: Phylogenetic coherence and structure of the archaeal domain. J Mol Evol 34:396-405
16. Canbäck B, Andersson SGE, Kurland CG (2002) The global phylogeny of glycolytic enzymes. Proc Natl Acad Sci USA 99:6097-6102
17. Creti R, Ceccarelli E, Bocchetta M, Sanangelantoni AM, Tiboni O, Palm P, Cammarano P (1994) Evolution of translational elongation factor (EF) sequences: Reliability of global phylogenies inferred from EF-1alpha(Tu) and EF-2(G) proteins. Proc Natl Acad Sci USA 91:3255-3259
18. Davids W, Amiri H, Andersson SGE (2002) Small RNAs in Rickettsia: Are they functional? Trends Genet 18:331-334
19. Ewing B, Green P (1998) Base-calling of automated sequencer traces using phred. II. Error probabilities. Genome Res 8:186-194
20. 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
21. Galtier N, Gouy M, Gautier C (1996) SeaView and Phylo_win, two graphic tools for sequence alignment and molecular phylogeny. Comput Appl Biosci 12:543-548
22. Germot A, Philippe H, Le Guyader H (1997) Evidence for loss of mitochondria in Microsporidia from a mitochondrial-type HSP70 in Nosema locustae. Mol Biochem Parasitol 87:159-168
23. Goldman N, Zhang Z (1994) A codon-based model of nucleotide substitutions for protein-coding DNA sequences. Mol Biol Evol 11:725-736
24. Gordon D, Abajian C, Green, P (1998) Consed: A graphical tool for sequence finishing. Genome Res 8:195-202
25. Gray MW, Burger G, Lang BF (1999) Mitochondrial evolution. Nature 283:233-357
26. Hackenberg H, Klingenberg M (1980) Molecular weight and hydrodynamic parameters of the adenosine 5′-diphosphateadenosine 5′-triphosphate carrier in Triton X-100. Biochemistry 19:548-555
27. Hall TA (1999) BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symp Ser 41:95-98
28. Hatch TP, Al-Houssaine E, Silvermann JA (1982) Adenine nucleotide and lysine transport in Chlamydia psittaci. J Bacteriol 150:662-670
29. Heldt HW (1969) Adenine nucleotide translocation in spinach chloroplasts. FEBS Lett 5:11-14
30. Hirt RP, Logsdon JM Jr, Healy B, Dorey MW, Doolittle WF, Embley TM (1999) Microsporidia are related to Fungi: Evidence from the largest subunit of RNA polymerase II and other proteins. Proc Natl Acad Sci USA 96:580-585
31. Iwabe N, Kuma KI, Haseagawa M, Osawa S, Takashi M (1989) Evolutionary relationship of archaebacteria, eubacteria, and eukaryotes inferred from phylogenetic trees of duplicated genes. Proc Natl Acad Sci USA 86:9355-9359
32. Kampfenkel K, Möhlmann T, Batz O, Van Montagu M, Inze D, Neuhaus HE (1995) Molecular characterisation of an Arabidopsis thaliana cDNA encoding a novel putative adenylate translocator of higher plants. FEBS Lett 374:351-355
33. Karlberg O, Canbäck B, Kurland CG, Andersson SGE (2000) The dual origin of the yeast mitochondrial proteome. Yeast 17:170-187
34. Katinka MD, Duprat S, Cornillot E, Metenier G, Thomarat F, Prensier G, Barbe V, Peyretaillade E, Brottier P, Wincker P, Delbac F, El Alaoui H, Peyret P, Saurin W, Gouy M, Weissenback J, Vivares CP (2001) Genome sequence and gene compaction of the eukaryotic parasite Encephalitozoon cuniculi. Nature 414:450-453
35. Keeling PJ, Luker MA, Palmer JD (2000) Evidence from beta-tubulin phylogeny that microsporidia evolved from within the fungi. Mol Biol Evol 17:23-31
36. Klingenberg M (1989) Molecular aspects of adenine nucleotide carrier from mitochondria. Arch Biochem Biophys 270:1-14
37. Klingenberg M (1993a) Dialectics in carrier research: The ADP/ATP carrier and the uncoupling protein. J Bioenerg Biomembr 25:447-457
38. Klingenberg M (1993b) Mitochondrial carrier family: ADP/ATP carrier as a carrier paradigm. Soc Gen Physiol Ser 48:201-212
39. Krogh A, Larsson B, von Heijne G, Sonnhammer ELL (2001) Predicting transmembrane protein topology with a hidden Markov model: Application to complete genomes. J Mol Biol 305:567-580
40. Kuan J, Saier MH (1993) The mitochondrial carrier family of transport proteins: Structural, functional, and evolutionary relationships. Crit Rev Biochem Mol Biol 28:209-233
41. Kurland CG, Andersson SGE (2000) Origin and evolution of the mitochondrial proteome. Microbiol Mol Biol Rev 64:786-820
42. Marc P, Margeot A, Devaux F, Blugeon C, Corral-Debrinski M, Jacq C. (2002) Genome-wide analysis of mRNAs targeted to yeast mitochondria. EMBO Rep 3:159-164
43. Martin W, Müller M (1998) The hydrogen hypothesis for the first eukaryote. Nature 391:37-41
44. Möhlmann T, Tjaden J, Schwöppe C, Winkler HH, Kampfenkel K, Neuhaus HE (1998) Occurrence of two plastidic ADP/ATP transporters in Arabidopsis thaliana. Eur J Biochem 252:353-359
45. Neuhaus HE, Henrichs G, Scheibe R (1993) Characterization of glucose-6-phosphate incorporation into starch by isolated intact cauliflower-bud plastids. Plant Physiol (Rock) 101:573-578
46. Ogata H, Audic S, Renesto-Audiffren P, Fournier PE, Barbe V, Samson D, Roux V, Cossart P, Weissenbach J, Claverie JM, Raoult D (2001) Mechanisms of evolution in Rickettsia conorii and R. prowazekii. Science 293:2093-2098
47. Pang H, Winkler HH (1993) Copy numbers of the 16S rRNA gene in Rickettsia prowazekii. J Bacteriol 175:3893-3896
48. Pfeiffer T, Schuster S, Bonhoeffer S (2001) Cooperation and competition in the evolution of ATP-producing pathways. Science 292:504-507
49. Plano GV, Winkler HH (1991) Identification and initial topological analysis of the Rickettsia prowazekii ADP/ATP translocase. J Bacteriol 173:3389-3396
50. Pozueta-Romero J, Frehner M, Viale AM, Akazawa T (1991) Direct transport of ADP glucose by an adenylate translocator is linked to starch biosynthesis in amyloplasts. Proc Natl Acad Sci USA 88:5769-5773
51. Pretzman CI, Rikihisa Y, Ralph D, Gordon JC, Nielsen SB (1987) Enzyme-linked immunosorbent assay for Potomac horse fever disease. J Clin Microbiol 25:31-36
52. Peyretaillade E, Biderre C, Peyret P, Duffieux F, Metenier G, Gouy M, Michot B, Vivares CP (1998) Microsporidian Encephalitozoon cuniculi, a unicellular eukaryote with an unusual chromosomal dispersion of ribosomal genes and a LSU rRNA reduced to the universal core. Nucleic Acids Res 126:3513-3520
53. Philippe H, Forterre P (1999) The rooting of the Universal Tree of Life is not reliable. J Mol Evol 49:509-523
54. Runswick MJ, Powell SJ, Nyren P, Walker JE (1987) Sequence of the bovine mitochondfial carrier protein: Structural relationship to ADP/ATP translocase and the brown fat mitochondria uncoupling protein. EMBO J 6:1367-1373
55. Saitou N, Nei M (1987) The neighbor-joining method: A new method for reconstructing phylogenedc trees. Mol Biol Evol 4:406-425
56. Saraste M, Walker JE (1982) Internal sequence repeats and the path of polypeptide in mitochondrial ADP/ATP translocase. FEBS Lett 144:250-254
57. Schunemann D, Borchert S, Flugge UI, Heldt HW (1993) ADP/ATP translocator from pea root plastids. Comparison with translocators from spinach chloroplasts and pea leaf mitochondria. Plant Physiol (Rock) 103:131-137
58. Sicheritz-Ponten T, Kurland CG, Andersson SGE (1998) A phylogenetic analysis of the cytochrome b and cytochrome c oxidase I genes supports an origin of mitochondria from within the Rickettsiaceae. Biochim Biophys Acta 1365:545-551
59. Sonnhammer ELL, von Heijne G, Krogh A (1998) A hidden Markov model for predicting transmembrane helices in protein sequences. In: Proceedings of the Sixth International Conference on Intelligent Systems for Molecular Biology. AAAI Press, Menlo Park, CA, pp 175-182
60. Stephens RS, Kalman S, Lammel C, Fan J, Marathe R, Aravind L, Mitchell W, Olinger L, Tatusov RL, Zhao Q, Koonin EV, Davis RW (1998) Genome sequence of an obligate intracellular pathogen of humans: Chlamydia trachomatis. Science 282:754-759
61. Strimmer K, von Haesler A (1996) Quartet puzzling: A quartet maximum likelihood method for reconstructing tree topologies. Mol Biol Evol 13:964-969
62. Swofford DL (2000) PAUP*. Phylogenetic analysis using parsimony (* and other methods). Version 4. Sinauer Associates, Sunderland, MA.
63. Syvänen A-C, Amiri H, Jamal A, Andersson SGE, Kurland CG (1996) A chimeric disposition of the elongation factor genes in Rickettsia prowazekii. J Bacteriol 178:6192-6199
64. Thompson JD, Higgins DG, Gibson TJ (1994) CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 22:4673-4680
65. Tjaden J, Winkler HH, Schwoppe C, Van der Laan MV, Möhlman T, Neuhaus HE (1999) Two nucleotide transport proteins in Chlamydia trachomatis, one for net nucleoside triphosphate uptake and the other for transport of energy. J Bacteriol 181:1196-1202
66. Trentman O, Decker C, Winkler HH, Neuahus HE (2000) Charged amino-acid residues in transmembrane domains of the plastidic ADP/ATP transporter from Arabidopsis are important for transport efficiency, substrate specificity and counter exchange properties. Eur J Biochem 267:4098-4105
67. Van der Giezen M, Slotboom DJ, Homer DS, Dyal PL, Harding M, Xue GP, Embley TM, Kunji ER (2002) Conserved properties of hydrogenosomal and mitochondrial ADP/ATP carriers: A common origin for both organelles. EMBO J 15:572-579
68. Viale A, Arakaki AK (1994) The chaperone connection to the origins of the eukaryotic organelles. FEBS Lett 341:146-151
69. Vignais PV (1976) Molecular and physiological aspects of adenine nucleotide transport in mitochondria. Biochim Biophys Acta 456:1-38
70. Voncken F, Boxma B, Tjaden J, Akhmanova A, Huynen M, Verbeek F, Tielens AGM, Haferkamp I, Neuhaus HE, Vogels G, Veenhuis M, Hackstein JHP (2002) Multiple origins of hydrogenosomes: Functional and phylogenetic evidence from ADP/ATP carrier of the anaerobic chytrid Neocallimastix sp. Mol Microbiol 44:1441-1454
71. Wilkinson M, Peres-Neto PR, Foster PG, Moncrieff CB (2002) Type 1 error rates of the parsimony permutation tail probability test. Syst Biol 51:524-527
72. Williamson LR, Plano GV, Winkler HH, Krause DC, Wood DO (1989) Nucleotide sequence of the Rickettsia prowazekii ADP/ATP translocase-encoding gene. Gene 80:269-278
73. Winkler HH (1976) Rickettsial permeability: An ADP-ATP transport system. J Biol Chem 251:389-396
74. Wolf YI, Aravind L, Koonin EV (1999) Rickettsiae and Chlamydiae: Evidence of horizontal transfer and gene exchange. Trends Genet 15:173-175
75. Yang Z (1997) PAML: A program for phylogenetic analysis by maximum likelihood. CABIOS 13:555-556