Archaea: What can we learn from their sequences?

Current Opinion in Genetics and Development

Volumn 7, Issue 6, 1997, Pages 764-770

  Forterre, Patrick ^a  

^a CNRS   (France)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL DNA;

ARCHAEBACTERIUM; BACTERIAL GENETICS; EUKARYOTE; EVOLUTION; GENE SEQUENCE; GENOME; NONHUMAN; PHYLOGENY; PRIORITY JOURNAL; REVIEW;

EID: 0031445864     PISSN: 0959437X     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0959-437X(97)80038-X     Document Type: Article

References (53)

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15. Forterre P. Protein versus rRNA: rooting the universal tree of life. of special interest ASM News. 63:1997;89-95 This review emphasizes the pitfalls of molecular phylogeny in deciphering very ancient relationships. The problem of rooting the tree of life is critically analyzed. It is suggested that cladistic analysis is applied to slowly evolving positions in protein sequences to test the validity of this rooting (see also [19]). The conclusion of such analysis is that the rooting of the universal tree in the bacterial branch is not supported by present data.
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20. Yue DX, Maizels N, Weiner AM. CCA-adding enzymes and poly(A) polymerases are all members of the same nucleotidyltransferase superfamily: characterization of the CCA-adding enzyme from the archaeal hyperthermophile Sulfolobus shibatae. of special interest RNA. 2:1996;895-908 The purification of the first archaeal tRNA CCA-adding enzyme and cloning of its genes led the authors to define two subfamilies in the superfamily of nucleotidyl-transferases. They discuss the possibility of intraconversion of CCA-adding enzymes and polyA polymerases early in evolution.
21. Riera J, Robb FT, Weiss R, Fontecave M. Ribonucleotide reductase in the archaeon Pyrococcus furiosus: a critical enzyme in the evolution of DNA genomes? of outstanding interest Proc Natl Acad Sci USA. 94:1997;475-478 See annotation [22].
22. Tauer A, Benner SA. The B12-dependent ribonucleotide reductase from the archaebacterium Thermoplasma acidophila: an evolutionary solution to the ribonucleotide reductase conundrum. of outstanding interest Proc Natl Acad Sci USA. 94:1997;53-58 These two very interesting papers [21, 22] combine biochemical and sequence analyses (including secondary structure predictions) in studying the first archaeal ribonucleotide reductase (RNR) isolated to date. Both conclude that the archaeal enzymes exhibit similarities with the three previously known classes of RNR, suggesting strongly that all RNR are homologous.
23. Bergerat A, de Massy B, Gadelle D, Varoutas PC, Nicolas A, Forterre P. An atypical type II DNA topoisomerase from archaea with implication for meiotic recombination. of outstanding interest Nature. 386:1997;414-417 A piece of luck: the identification of a new archaeal DNA topoisomerase (Topo VI) helped in the database identification of the protein responsible for breaking the eukaryote chromosomes during meiotic recombination. Site-directed mutagenesis targeted at the only tyrosine conserved between the archaeal and the yeast protein inhibits the formation of the double-stranded breaks that initiate meiosis. This work also led to the identification of a new ATP module present in all type II DNA topoisomerases and proteins of the Hsp90 and MutL families.
24. Trent JD, Kagama HK, Yaoi T, Zaluzec N. Chaperonin filaments: the archaeal cytoskeleton? of outstanding interest Proc Natl Acad Sci USA. 94:1997;5383-5388 A very interesting and provocative paper. The authors showed that the archaeal chaperone TF55 can polymerize in vitro to form long filaments reminiscent of eukaryotic microtubules. They visualize similar filaments in Sulfolobus cells by electron microscopy and suggest that they are formed by TF55. This challenges the existing view about the role of some chaperones in vivo.
25. Baumann P, Jackson SP. An archaebacterial homologue of the essential eubacterial cell division protein FtsZ. of special interest Proc Natl Acad Sci USA. 93:1996;6726-6730 A GTP-binding protein from Pyrococcus wosei turned out the be an archaeal homologue of bacterial protein FtsZ.
26. Margolin W, Wang R, Kumar M. Isolation of an ftsZ homolog from the archaebacterium Halobacterium salinarium: implications for the evolution of FstZ and tubulin. of special interest J Bacteriol. 178:1996;1320-1327 Overexpression of the H. salinarium ftsZ gene induces significant morphological changes in this archaeon, leading to the loss of rod-shape. This suggests that FtsZ interacts in this archaeon with the components of a putative cytoskeleton. The absence of a close homologue of Archaeal and bacterial FtsZ in eukaryotes suggests a priori that either the prokaryotic mechanism of cell division was already present in LUCA or that Archaea and Bacteria are in fact sister groups. Further work, however, is required at the molecular level to exclude the possibility of convergent evolution in the two prokaryotic domains using the same protein.
27. Wang X, Lutkenhaus J. FtsZ ring: the eubacterial division apparatus conserved in archaebacteria. of outstanding interest Mol Microbiol. 21:1996;313-319 This paper demonstrates the ATPase activity of the archaeal FtsZ homologue and shows that this protein is localized to a ring, as in E. coli, that coincides with the division constriction in Haloferax volcanii.
28. Zillig W. Comparative biochemistry of Archaea and Bacteria. Curr Opin Genet Dev. 1:1991;544-551.
29. Reeve JN, Sandman K, Daniels CJ. Archaeal histones, nucleosomes, and transcription initiation. of special interest Cell. 89:1997;999-1002 This interesting review links our knowledge of archaeal histones to the transcription machinery with an emphasis on the histone fold shared by eukaryotic and archaeal histones, as well as by several eukaryotic transcription factors.
30. of outstanding interest Kleman-Leyer K, Armbruster DW, Daniels CJ. Properties of H. volcanii tRNA intron endonuclease reveal a relationship between the archaeal and eukaryal tRNA intron processing systems. of outstanding interest Cell. 89:1997;839-847 This is one of three papers [29, 30, 40] in the same issue of Cell dealing with tRNA processing systems in Archaea and Eukaryota. In this case, sequence analysis revealed a common origin between archaeal and eukaryotic tRNA introns despite major differences in recognition specificity of their processing endonucleases.
31. Grosjean H, Constantinesco F, Foiret D, Benachenhou N. A novel enzymatic pathway leading to 1-methylinosine modification in Haloferax volcanii tRNA. Nucleic Acids Res. 23:1995;4312-4319.
32. of outstanding interest Fitz-Gibbon S, Choi AJ, Miller JH, Stetter KO, Simon MI, Swanson R, Kim UJ. A fosmid-based genomic map and identification of 474 genes of the hyperthermophilic archaeon Pyrobaculum aerophilum. of special interest Extremophiles. 1:1997;36-51 Pyrobaculum aerophilum is a microaerophilic hyperthermophile which might become an interesting model in future genetic studies. The authors notice the absence of mutS and mutL-like genes in Archaea and suggest that they might lack mismatch repair genes and have a high rate of spontaneous mutation (however, see [13]).
33. Borges KM, Brummet SR, Bogert A, Davis MC, Hujer KM, Domke ST, Szasz J, Ravel J, Di Ruggiero J, Fuller C, et al. A survey of the genome of the hyperthermophilic archaeon, Pyrococcus furiosus. Genome Sci Technol. 1:1996;37-46.
34. Sensen CW, Klenk H-P, Singh RK, Allard G, Chan CC-Y, Liu QY, Penny SL, Young F, Schenk ME, Gaasterland T, et al. Organizational characteristics and information content of an archaeal genome: 156 kb of sequence from Sulfolobus solfataricus P2. Mol Microbiol. 21:1996;174-191.
35. Olsen GJ, Woese CR. Lessons from an archaeal genome: what are we Learning from Methanococcus jannaschii? Trends Genet. 12:1996;377-379.
36. Garrett RA. Genomes: Methanococcus jannaschii and the golden fleece. Curr Biol. 6:1996;1377-1380.
37. Edgell DR, Doolittle WF. Archaebacterial genomics: the complete genome sequence of Methanococcus jannaschii. of special interest Bioessays. 19:1997;1-4 In this nice review, the authors made several original observations in discussing the sequencing of M. jannaschii. They emphasized the divergence between bacterial and eukaryotic DNA replication apparatus.
38. of outstanding interest Olsen GJ, Woese CR. Archaeal genomics: an overview. of special interest Cell. 89:1997;991-994 An update of [35], this is one of six mini-reviews [29, 30, 38, 40, 41] in the same issue of Cell that cover most of archaeal molecular biology. The authors discuss essential evolutionary issues such as the nature of the most recent common ancestor. They favor the sisterhood of Archaea and Eukaryota and suggest an extensive loss of metabolic genes in the latter.
39. Edgell DR, Doolittle WF. Archaea and the origin(s) of DNA replication proteins. of special interest Cell. 89:1997;995-998 Here, the authors entirely dedicate their mini-review to archaeal DNA replication. A tour de force considering that only sequence data are presently available. They conclude that the last universal common ancestor belonged to the DNA world, as I had previously predicted [19].
40. Belfort M, Weiner A. Another bridge between kingdoms: tRNA splicing in archaea and eucaryotes. of outstanding interest Cell. 89:1997;1003-1006 This excellent mini-review presents a comparative analysis of the tRNA splicing mechanism in Archaea and Eukaryota; the evolutionary implications are discussed with caveats. The authors point out that the present data do not imply that tRNA introns are ancient and that a pre-existing endonuclease might have been recruited independently for different processing reactions.
41. Dennis P. Ancient ciphers: translation in Archaea. of special interest Cell. 89:1997;1007-1010 This nice mini-review emphasises the mixture of eukaryotic and bacterial features in the archaeal translation apparatus and lists the putative initiation translation factors identified in M. jannaschii. The authors suggest that only open reading frames with bona fide Shine-Dalgamo sequences in M. jannaschii are real protein encoding genes. Incidentally, we also learnt that a U3-like RNA previously detected in the archaeon Sulfolobus was in fact a PCR artefact!
42. Kyprides NC, Olsen GJ, Klenk H-P, White O, Woese CR. Methanococcus jannaschii genome revisited. Microbial Comp Genomics. 1:1996;329-338.
43. Jacobs KIL, Grogan DW. Rates of spontaneous mutations in an archaeon from geothermal environments. of special interest J Bacteriol. 179:1997;3298-3302 The authors show that the rate of forward mutation at pyrE and pyrF loci in Sulfolobus is close to corresponding rates reported in E. coli, suggesting the existence of an efficient mismatch repair system in this archaeon.
44. Rashid N, Morikawa M, Nagahisa K, Kanaya S, Imanaka T. Characterization of a RecA/RAD51 homologue from the hyperthermophillic archaeon Pyrococcus sp. KOD1. Nucleic Acids Res. 25:1997;719-726.
45. Elie C, Baucher MF, Fondrat C, Forterre P. A protein related to eukaryal and bacterial DNA-motor proteins in the hyperthermophilic archaeon Sulfolobus acidocaldarius. J Mol Evol. 45:1997;107-114.
46. of outstanding interest Mushegian AR, Koonin EV. A minimal gene set for cellular life derived by comparison of complete bacterial genomes. of special interest Proc Natl Acad Sci USA. 93:1996;10268-10273 The attempts to construct a minimal genome from the comparison of E. coli and Haemophilus was quite premature but, here, the authors introduced the interesting concept of non-orthologous replacement (see also [47]) which can, in fact, be used against their hypothesis of LUCA with an RNA genome! Non-orthologous replacement means that the same reaction is performed in two groups by enzymes which belong to different protein families.
47. Lang BF, Burger G, O'Kelly CJ, Cedergren R, Golding GB, Lemieux C, Sankoff D, Turmel M, Gray MW. An ancestral mitochondrial DNA resembling a eubacterial genome in miniature. of outstanding interest Nature. 387:1997;493-497 Complete sequencing of the largest mitochondrial DNA known to date. This genome has apparently retained many genes of the ancestral bacterial endosymbiont that have either been lost or replaced in other mitochondrial genomes. Especially interesting is the observation that this mitochondria contains genes encoding a bacterial-like RNA polymerase (as expected from the origin of mitochondria) whereas previously known mitochondrial RNA polymerases were surprisingly related to T7 RNA polymerase. I suggest that such non-orthologous replacement of a complex system (in this case, three polypeptides) by a simpler one (one polypeptide) occurred several times in the evolution from LUCA to the three present domains, suggesting that LUCA might have been more complex than present-day organisms in terms of molecular organization.
48. Robb FT, Place AR, Sowers KR, Shreier HJ, DasSarma S, Fleishmann EM. Archaea, A Laboratory Manual (3 volumes: Thermophiles, Halophiles, Methanogens). 1995;Cold Spring Harbor Laboratory press, Cold Spring Harbor, New York.
49. Antranikian G, Konings WN, De Vos WM. Papers presented at the first international congress on extremophiles. of special interest FEMS Microbiol Rev. 2-3:1996;89-288 This special-issue group of 16 papers are devoted to the molecular biology of extremophiles and their biotechnological applications with emphasis on hyperthermophilic archaea.
50. Richards FM, Eisenberg DS, Kim PS. Enzymes and proteins from hyperthermophilic microorganisms. of special interest Adv Protein Chem. 49:1996;1-501 This publication contains several chapters dealing in details with some hyperthermophilic archaeal proteins and enzymes. In particular, they cover heat-shock proteins, enzymes involved in central metabolism, DNA polymerases, and DNA binding proteins.
51. Smith DR, Doucette-Stamm LA, Deloughery C, Lee H, Dubois J, Aldredge T, Bashirzadeh R, Blakely D, Cook R, Gilbert K, et al. Complete genome sequence of Methanobacterium thermoautotrophicum DH: functional analysis and comparative genomics. of outstanding interest J Bacteriol. 1997;7135-7155 See annotation [52].
52. Klenk H-P, Clayton R, Tomb J-F, White O, Nelson KE, Ketchum KA, Dodson RJ, Gwinn M, Hickey EK, Peterson JD, et al. Complete genome sequence of the hyperthermophilic, sulphate reducing archaeon Archaeoglobus fulgidus. of outstanding interest Nature. 390:1997;364-370 These two papers [51, 52] underline the extensive divergence that occurred between the three archaeal genomes now sequenced, despite the fact that all three belong to the euryarchaeal branch. An extensive analysis of the putative metabolic capacities of these two species are presented. Genes involved in the central mechanisms of information processing appear to be conserved in all these archaea with a few intriguing exceptions. In particular, Archaeoglobus appears rich in DNA topoisomerases, as it contains gyrase, reverse gyrase, a type I DNA topoisomerase and topoisomerase VI, whereas Methanobacterium contains only the latter two. The presence of a MutS homologue is reported in Methanobacterium. In contrast to the M. jannaschii genome, which contains 18 inteins, the A. fulgidus genome contains no intein whereas the M. thermoautotrophicum genome contains only one.
53. Koonin EV, Mushegian AR, Galperin MY, Walker DR. Comparison of archaeal and bacterial genomes: computer analysis of protein sequences predicts novel function and suggests a chimeric origin for the archaea. of special interest Mol Microbiol. 25:1997;619-637 This paper shows that careful analysis of previously annotated genome significantly increases the number of genes with sequence similarity to proteins from other species. 73% of the M. Jannaschii putative proteins turned out to have significant similarity to other proteins. More of them have higher similarity to bacterial than to eukaryotic proteins. The authors conclude that archaea might be Bacteria/Eukarya chimeras. The same reasoning, however, would suggest a chimeric origin for the two other domains too! In contradiction with some previous claims, there is no specific relationship between Archaea and Gram-positive bacteria. Massive non-orthologous displacement of genes responsible for essential functions (such as replication and repair) can be detected.