Origin and evolution of mitochondria: What have we learnt from red algae?

Current Genetics

Volumn 31, Issue 3, 1997, Pages 193-207

  Leblanc, C ^a   Richard, O ^a   Kloareg, B ^a   Viehmann, S ^b   Zetsche, K ^b   Boyen, C ^a  

^a STATION BIOLOGIQUE   (France)

^b JUSTUS LIEBIG UNIVERSITY   (Germany)

Author keywords

Evolution; Mitochondrial genome; Red algae

Indexed keywords

MITOCHONDRIAL DNA;

EVOLUTION; GENETIC ORGANIZATION; GENOME; INHERITANCE; MITOCHONDRION; NONHUMAN; PHYLOGENY; PRIORITY JOURNAL; RED ALGA; REVIEW;

ALGAE, RED; DNA, CIRCULAR; DNA, MITOCHONDRIAL; DNA, PLANT; DNA, PROTOZOAN; EUKARYOTIC CELLS; GENETIC CODE; GENOME; MITOCHONDRIA; PHYLOGENY; PLANT PROTEINS; PROTEIN BIOSYNTHESIS; RNA, PLANT; RNA, RIBOSOMAL; SEQUENCE HOMOLOGY;

ALGAE; RHODOPHYTA;

EID: 0030961691     PISSN: 01728083     EISSN: None     Source Type: Journal    
DOI: 10.1007/s002940050196     Document Type: Review

References (99)

1. Angata K, Kuroe K, Yanagisawa K, Tanaka Y (1995) Codon usage, genetic code and phylogeny of Dictyostelium discoideum mitochondrial DNA as deduced from a 7.3-kb region. Curr Genet 27:249-256
2. Ariztia EV, Andersen RA, Sogin ML (1991) A new phylogeny for chromophyte algae using 16s-like rRNA sequences from Mallomonas papillosa (Synurophyceae) and Tribonema aequale (Xan-thophyceae). J Phycol 27:428-436
3. Atlan A, Couvet D (1993) A model simulating the dynamics of plant mitochondrial genomes. Genetics 135:213-222
4. Bhattacharya D, Medlin L (1995) The phylogeny of plastids: a review based on comparisons of small-subunit ribosomal RNA coding regions. J Phycol 31:489-498
5. Bhattacharya D, Stickel SK (1994) Sequence analysis of duplicated actin genes in Lagenidium giganteum and Pythium irregulare (Oomycota). J Mol Evol 39:56-61
6. Bhattacharya D, Helmchen T, Bibeau C, Melkonian M (1995 a) Comparisons of nuclear-encoded small-subunit ribosomal RNAs reveal the evolutionary position of the Glaucocystophyta. Mol Biol Evol 12:415-420
7. Bhattacharya D, Helmchen T, Melkonian M (1995 b) Molecular evolutionary analyses of nuclear-encoded small subunit ribosomal RNA identify an independant rhizopod lineage containing the Euglyphina and the Chorarachniophyta. J Eukary Microbiol 42:65-69
8. Bonnard G, Gualberto J M, Lamattina L, Grienenberger J M (1992) RNA editing in plant mitochondria. Crit Rev Plant Sci 10:503-524
9. Bouget F-Y, Kerbourc'h C, Liaud MF, Loiseaux-de Goër S, Quatrano RS, Cerff R, Kloareg B (1995) Structural features and phylogeny of the actin gene of Chondrus crispus (Gigartinales, Rhodophyta). Curr Genet 28: 164-172
10. Boyen C, Leblanc C, Bonnard G, Grienenberger JM, Kloareg B (1994a) Nucleotide sequence of the cox3 gene from Chondrus crispus: evidence that UGA encodes tryptophan and evolutionary implications. Nucleic Acids Res 22: 1400-1403
11. Boyen C, Leblanc C, Kloareg B, Loiseaux-de Goër S (1994 b) Physical map and gene organization of the mitochondrial genome of Chondrus crispus (Rhodophyta, Gigartinales). Plant Mol Biol 26:691-697
12. Brennicke A, Grohmann L, Hiesel R, Knoop V, Schuster W (1993) The mitochondrial genome on its way to the nucleus: different stages of gene transfer in higher plants. FEBS Lett 325:140-145
13. Brown TA (1993) Mitochondrial genome of Aspergillus nidulans. In: O'Brien SJ (ed) Genetic maps. Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, pp 3.85-3.86
14. Burger G, Plante I, Lonergan KM, Gray MW, (1995) The mitochondrial DNA of the amoeboid protozoan, Acanthamoeba castellanii: complete sequence, gene content, and genome organization. J Mol Biol 245:522-537
15. Burger G, Lang BF, Reith M, Gray MW (1996) Genes encoding the same three subunits of respiratory complex II are present in the mitochondrial DNA of two phylogenetically distant eukaryotes. Proc Natl Acad Sci USA 93, 3:2328-2332
16. Cavalier-Smith T (1992) The number of symbiotic origins of organelles. BioSystems 28:91-106
17. Cavalier-Smith T (1993) Kingdom Protozoa and its 18 phyla. Microbiol Rev 57:953-994
18. Cerff R (1995) Tracing biological evolution in protein and gene structures, In: Mitiko Go (ed) Proc 2Oth Taniguchi Int Symp. Elsevier Science, Amsterdam, pp 205-227
19. Christen R, Ratto A, Baroin A, Perasso R, Grell KG, Adoutte A (1991) An analysis of the origin of metazoans, using comparisons of partial sequences of the 28s RNA, reveals an early emergence of triploblasts. EMBO J 10:499-503
20. Clark CG, Roger AJ (1995) Direct evidence for secondary loss of mitochondria in Entamoeba histolytica. Proc Natl Acad Sci USA 92:6518-6521
21. Clark-Walker GD (1992) Evolution of mitochondrial genomes in fungi. In: Wolstenholme DR, Jeon KW (eds) Mitochondrial genomes. Academic press, San Diego, pp 89-127
22. Cole RA, Williams KL (1994) The Dictyostelium discoideum mitochondrial genome: a primordial system using the universal code and encoding hydrophilic proteins atypical of metazoan mitochondrial DNA. J Mol Evol 39:579-588
23. Coleman AW, Goff LJ (1991) DNA analysis of eukaryotic algal species. J Phycol 27:463-473
24. Collins RA (1993) Neurospora crassa laboratory strain 74-OR23-1A: mitochondrial genes. In: O'Brien SJ (ed) Genetic maps. Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, pp 3.33-3.35
25. Cummings DJ (1992) Mitochondrial genomes of the ciliates. In: Wolstenholme DR, Jeon KW (eds) Mitochondrial genomes. Academic press, San Diego, pp 1-64
26. 560 subunit of respiratory complex II. J Biol Chem 269:15469-15472
27. Denovan-Wright EM, Lee RW (1992) Comparative analysis of the mitochondrial genomes of Chlamydomonas eugametos and Chlamydomonas moewusii. Curr Genet 21:197-202
28. Douglas SE, Murphy CA, Spencer DF, Gray MW (1991) Cryptomonad algae are evolutionary chimaeras of two phylogenetically distinct unicellular eukaryotes. Nature 350:148-151
29. Feagin JE, Werner E, Gardner MJ, Williamson DH, Wilson RJM (1992) Homologies between the contiguous and fragmented rRNAs of the two Plasmodium falciparum extra chromosomal DNAs are limited to core sequences. Nucleic Acids Res 20:879-887
30. Felsenstein J (1978) Cases in which parsimony and compatibility methods will be positively misleading. Systematic Zool 27:401-410
31. Fontaine JM, Rousvoal S, Leblanc C, Kloareg B, Loiseaux-de Goër S (1995 a) The mitochondrial LSU rRNA gene of the brown alga Pylaiella littoralis reveals α-proteobacterial features and is split by four group-IIB introns with an atypical phylogeny. J Mol Biol 251:378-389
32. Fontaine JM, Rousvoal S, Delaroque N, Loiseaux-de Goër S (1995 b) Characterization of the cox3, nad7 and atp7 genes from the mitochondrial genome of the brown alga Pylaiella littoralis. Plant Physiol Biochem 33:605-609
33. Galtier N, Gouy M (1995) Inferring phylogenies from DNA sequences of unequal base compositions. Proc Natl Acad Sci USA 92:11317-11321
34. Gajadhar AA, Marquardt WC, Hall R, Gunderson J, Ariztia-Carmona EV, Sogin ML (1991) Ribosomal RNA sequences of Sarcocystis muris, Theileria annulata and Crypthecodinium cohnii reveal evolutionary relationships among apicomplexans, dinoflagellates, and ciliates. Mol Biochem Parasitol 45:147-154
35. Gott JM, Visomirski LM, Hunter JL (1993) Substitutional and insertional RNA editing of the cytochrome c oxidase subunit 1 mRNA of Physarum polycephalum. J Biol Chem 268:25483-25486
36. Gray MW (1992) The endosymbiont hypothesis revisited. In: Wolstenholme DR, Jeon KW (eds) Mitochondrial genomes. Academic press, San Diego, pp 233-257
37. Gray MW (1993) Origin and evolution of organelle genomes. Curr Opin Genet Dev 3:884-890
38. Gray MW (1995) Mitochondrial evolution. In: Levings CSIII, Vasil IK (eds) The molecular biology of plant mitochondria. Kluwer Academic Publishers, Netherlands, pp 635-659
39. Gray MW, Doolittle WF (1982) Has the endosymbiont hypothesis been proven? Microbiol Rev 46:1-42
40. Gray MW, Cedergren R, Abel Y, Sankoff D (1989) On the evolutionary origin of the plant mitochondrion and its genome. Proc Natl Acad Sci USA 86:2267-2271
41. Grivell LA (1993) Mitochondrial DNA in the yeast Saccharomyces cerevisiae. In: O'Brien SJ (ed) Genetic maps. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York, pp 3.57-3.65
42. Gupta RS (1995) Evolution of the chaperonin families (Hsp60, Hsp10 and Tcp-1) of proteins and the origin of eukaryotic cells. Mol Microbiol 15:1-11
43. Hasegawa M, HashimotoT, Adachi J, Iwabe N, Miyata T (1993) Early branchings in the evolution of eukaryotes: ancient divergence of entamoeba that lacks mitochondria revealed by protein sequence data. J Mol Evol 36:380-388
44. Hashimoto T, Adachi J, Hasegawa M (1992) Phylogenetic place of Giardia lamblia, a protozoan that lacks mitochondria. Endocyt Cell Res 9:59-69
45. Hashimoto T, Nakamura Y, Nakamura F, Shirakura T, Adachi J, Goto N, Okamoto KI, Hasegawa M (1994) Protein phylogeny gives a robust estimation for early divergences of eukaryotes: phylogenetic place of a mitochondria-lacking protozoan, Giardia lamblia. Mol Biol Evol 11:65-71
46. Hayashi-Ishimaru Y, Ohama T, Kawatsu Y, Nakamura K, Osawa S (1996) UAG is a sense codon in several chlorophycean mitochondria. Curr Genet 30:29-33
47. Hendriks L, De Baere R, Van de Peer Y, Neefs J, Goris A (1991) The evolutionary position of the rhodophyte Porphyra umbilicalis and the basidiomycete Leucosporidium scottii among other eukaryotes as deduced from complete sequences of small ribosomal subunit RNA. J Mol Evol 32:167-177
48. Henze K, Badr A, Wettern M, Cerff R, Martin W (1995) A nuclear gene of eubacterial origin in Euglena gracilis reflects cryptic endosymbioses during protist evolution. Proc Natl Acad Sci USA 92:9122-9126
49. Hiesel R, Combettes B, Brennicke A (1994) Evidence for RNA editing in mitochondria of all major groups of land plants except the Bryophyta. Proc Natl Acad Sci USA 91:629-633
50. Hori H, Osawa S (1987) Origin and evolution of organisms as deduced from 5s ribosomal RNA sequences. Mol Biol Evol 4:445-472
51. Horner DS, Hirt RP, Kilvington S, Lloyd D, Embley TM (1996) Molecular data suggest an early acquisition of the mitochondrion endosymbiont. Proc R Soc Lond 263:1053-1059
52. Jukes TH, Osawa S (1993) Evolutionary changes in the genetic code. Comp Biochem Physiol 106B:489-494
53. Karlovsky P, Fartmann B (1992) Genetic code and phylogenetic origin of oomycetous mitochondria. J Mol Evol 34:254-258
54. Kessler U, Zetsche K (1995) Physical map and gene organization of the mitochondrial genome from the unicellular green alga Platymonas (Tetraselmis) subcordiformis (Prasinophyceae). Plant Mol Biol 29:1081-1086
55. Kurland CG (1992) Evolution of mitochondrial genomes and the genetic code. BioEssays 14:709-714
56. Lang BF (1993) The mitochondrial genome of Schizosaccharomyces pombe. In: O'Brien SJ (ed) Genetic maps. Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, pp 3.118-3.119
57. Lang BF, Forget L (1993) The mitochondrial genome of Phytophtora infestons. In: O'Brien SJ (ed) Genetic maps. Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, pp 3.133-3.135
58. Lang BF, Goff LJ, Gray MW (1996) A 5s rRNA gene is present in the mitochondrial genome of the protist, Reclinomonas americana, but is absent from red algal mitochondria DNA. J Mol Biol 261:607-613
59. Leblanc C, Boyen C, Richard O, Bonnard G, Grienenberger J M, Kloareg B (1995 a) Complete sequence of the mitochondrial DNA of the rhodophyte alga Chondrus crispus (Gigartinales). Gene content and genome organization. J Mol Biol 250:484-495
60. Leblanc C, Kloareg B, Loiseaux-de Goër S, Boyen C (1995 b) The mitochondrial small subunit rRNA from the red alga Chondrus crispus (Gigartinales, Rhodophytes): DNA sequence, structure and evolutionary implications. J Mol Evol 41:196-202
61. Leblanc C, Fontaine J M, Boyen C, Loiseaux-de Goër S (1995 c) DNA sequence and secondary structure of the mitochondrial large subunit rRNA from the red alga Chondrus crispus (Gigartinales, Rhodophytes). Plant Physiol, Plant Gene Register, PGR95-052
62. Leipe DD, Gunderson JH, Nerad TA, Sogin ML (1993) Small subunit ribosomal RNA of Hexamita inflata and the quest for the first branch in the eukaryotic tree. Mol Biochem Parasitol 59:41-48
63. Leipe DD, Wainright PO, Gunderson JH, Porter D, Patterson DJ, Valois F, Himmerich S, Sogin ML (1994) The stramenopiles from a molecular perspective: 16s-like rRNA sequences from Labyrinthuloides minuta and Cafeteria roenbergensis. Phycologia 33:369-377
64. Loiseaux-de Goër S (1994) Plastid lineages. In: Round E, Chapman DJ (eds) Progress in phycological research 10. Biopress Ltd, Bristol, pp 137-177
65. Lonsdale DM, Grienenberger JM (1992) The mitochondrial genome of plants. In: Herrmann RG (ed) Plant gene research Cell organelles. Springer-Verlag, Vienna, pp 183-218
66. Maréchal-Drouard L, Weil JH, Dietrich A (1993) Transfer RNAs and transfer RNA genes in plants. Annu Rev Plant Physiol Plant Mol Biol 44:13-32
67. McFadden GI, Gilson PR, Hill DRA (1994 a) Goniomonas: rRNA sequences indicate that this phagotrophic flagellate is a close relative of the host component of cryptomonads. Eur J Phycol 29:29-32
68. McFadden GI, Gilson PR, Hofmann CJB, Adcock GJ, Maier UG (1994 b) Evidence that an amoeba acquired a chloroplast by retaining part of an engulfed eukaryotic alga. Proc Natl Acad Sci USA 91:3690-3694
69. McFadden GI, Gilson PR, Waller RF (1995) Molecular phylogeny of Chlorarachniophytes based on plastid rRNA and rbcL sequences. Arch Protistenkd 145:231-239
70. Medlin LK, Lange M, Baumann MEM (1994) Genetic differentiation among three colony-forming species of Phaeocystis: further evidence for the phylogeny of the Prymnesiophyta. Phycologia 33:199-212
71. Nordnes S, Krauss S, Johansen T (1994) cDNA sequence of zebra-fish (Brachydanio rerio) translation elongation factor-1α: molecular phylogeny of eukaryotes based on elongation factor-1α protein sequences. Biochim Biophys Acta 1219:529-532
72. Oda K, Yamato K, Ohta E, Nakamura Y, Takemura M, Nozato N, Akashi K, Kanegae T, Ogura Y, Kohchi T, Ohyama K (1992 a) Gene organization deduced from the complete sequence of liverwort Marchantia polymorpha mitochondrial DNA, a primitive form of plant mitochondrial genome. J Mol Biol 223:1-7
73. Oda K, Yamato K, Ohta E, Nakamura Y, Takemura M, Nozato N, Akashi K, Ohyama K (1992b) Transfer RNA genes in the mitochondrial genome from a liverwort, Marchantia polymorpha: the absence of chloroplast-like tRNAs. Nucleic Acids Res 20:3773-3777
74. Olsen GJ, Woese CR, Overbeek R (1994) The winds of (evolutionary) change: breathing new life into microbiology. J Bacteriol 176:1-6
75. Osawa S, Jukes TH, Watanabe K, Muto A (1992) Recent evidence for evolution of the genetic code. Microbiol Rev 56:229-264
76. Paquin B, Lang BF (1996) The mitochondrial DNA of Allomyces macrogynus: the complete genomic sequence from an ancestral fungus. J Mol Biol 255:688-701
77. Paquin B, Forget L, Roewer I, Lang BF (1995 a) Molecular phylogeny of Allomyces macrogynus: congruency between nuclear ribosomal RNA- and mitochondrial protein-based trees. J Mol Evol 41:657-665
78. Paquin B, Roewer I, Wang Z, Lang BF (1995 b) A robust phylogeny using the mitochondrially encoded NAD5 protein sequence. Can J Bot 73:S180-S185
79. Pring D, Brennicke A, Schuster W (1993) RNA editing gives a meaning to the genetic information in mitochondria and chloroplasts. Plant Mol Biol 21:1163-1170
80. Ragan MA, Gutell RR (1995) Are red algae plants ? Bot J Linnean Soc 118:81-105
81. Ragan MA, Bird CJ, Rice ER, Gutell RR, Murphy CA, Singh RK (1994) A molecular phylogeny of the marine red algae (Rhodophyta) based on the nuclear small-subunit rRNA gene. Proc Natl Acad Sci USA 91:7276-7280
82. Recipon H, Perasso R, Adoutte A, Quétier F (1992) ATP synthase subunit c/III/9 gene sequences as a tool for interkingdom and metaphyte molecular phylogenies. J Mol Evol 34:292-303
83. Reith M (1995) Molecular biology of rhodophyte and chromophyte plastids. Annu Rev Plant Physiol Plant Mol Biol 46: 549-575
84. Sachay DJ, Hudspeth DSS, Nadler SA, Hudspeth MES (1993) Oomycete mtDNA: Phytophthora genes for cytochrome c oxidase use an unmodified genetic code and encode proteins most similar to those of plants. Exp Mycol 17:7-23
85. Schlegel M (1994) Molecular phylogeny of eukaryotes. Tree 9:330-335
86. Schuster W, Brennicke A (1994) The plant mitochondrial genome: physical structure, information content, RNA editing, and gene migration to the nucleus. Annu Rev Plant Physiol Plant Mol Biol 45:61-78
87. Sekito T, Okamoto K, Kitano H, Yoshida K (1995) The complete mitochondrial DNA sequence of Hansenula wingei reveals new characteristics of yeast mitochondria. Curr Genet 28:39-53
88. Sitte P (1993) Symbiogenetic evolution of complex cells and complex plastids. Eur J Protistol 29:131-143
89. Sogin ML (1991) Early evolution and the origin of eukaryotes. Curr Opin Genet Dev 1:457-463
90. Specht CA, Novotny CP, Ullrich RC (1992) Mitochondrial DNA of Schizophyllum commune: restriction map, genetic map, and mode of inheritance Curr Genet 22:129-134
91. Stuart K, Feagin JE (1992) Mitochondrial DNA of kinetoplastids. In: Wolstenholme DR, Jeon KW (eds) Mitochondrial genomes. Academic press, San Diego, pp 65-88
92. Takemura M, Oda K, Yamato K, Ohta E, Nakamura Y, Nozato N, Akashi K, Ohyama K (1992) Gene clusters for ribosomal proteins in the mitochondrial genome of a liverwort, Marchantia polymorpha. Nucleic Acids Res 20:3199-3205
93. Viehmann S, Richard O, Boyen C, Zetsche K (1996) Genes for two subunits of succinate dehydrogenase form a cluster on the mitochondrial genome of Rhodophyta. Curr Genet 29:199-201
94. Wainright PO, Hinkle G, Sogin ML, Stickel SK (1993) Monophyletic origins of the Metazoa: an evolutionary link with Fungi. Science 260:340-342
95. Wolff G, Burger G, Lang BF, Kÿck U (1993) Mitochondrial genes in the colourless alga Prototheca wickerhamii resemble plant genes in their exons but fungal genes in their introns. Nucleic Acids Res 21:719-726
96. Wolff G, Plante I, Lang BF, Kÿck U, Burger G (1994) Complete sequence of the mitochondrial DNA of the chlorophyte alga Prototheca wickerhamii. J Mol Biol 237:75-86
97. Wolstenholme DR (1992) Animal mitochondrial DNA: structure and evolution. In: Wolstenholme DR, Jeon W (eds) Mitochondrial genomes. Academic press, San Diego, pp 1-64
98. Wolters J (1991) The troublesome parasites - molecular and morphological evidence that Apicomplexa belong to the dinoflagellate-ciliate clade. BioSystems 25:75-83
99. Yang D, Oyaizu Y, Oyaizu H, Olsen GJ, Woese CR (1985) Mitochondrial origins. Proc Natl Acad Sci USA 82:4443-4447