Comparative and functional analysis of the archaeal cell cycle

Cell Cycle

Volumn 9, Issue 4, 2010, Pages 795-806

  Bernander, Rolf ^a   Lundgren, Magnus ^a,b   Ettema, Thijs J G ^a  

^a UPPSALA UNIVERSITY   (Sweden)

^b UPPSALA UNIVERSITY   (Sweden)

Author keywords

Archaea; Caulobacter; Cell cycle; Cell division; Chromosome replication; Crenarchaeota; Cytokinesis; Genome segregation; Mitosis; Saccharomyces; Sulfolobus

Indexed keywords

HELICASE; NUCLEASE; PROTEIN KINASE; TRANSCRIPTION FACTOR; ARCHAEAL PROTEIN; CELL CYCLE PROTEIN;

ARCHAEBACTERIUM; ARTICLE; BACTERIAL GENOME; CELL CYCLE; CELL CYCLE PROGRESSION; COMPARATIVE STUDY; DNA RECOMBINATION; DNA REPAIR; DNA REPLICATION; GENE EXPRESSION; GENETIC CONSERVATION; GENETIC TRANSCRIPTION; METABOLISM; MICROORGANISM; NONHUMAN; AMINO ACID SEQUENCE; CLASSIFICATION; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENETICS; MOLECULAR GENETICS; SEQUENCE ALIGNMENT;

ARCHAEA; CAULOBACTER; CRENARCHAEOTA; EUKARYOTA; SACCHAROMYCES; SULFOLOBUS; SULFOLOBUS ACIDOCALDARIUS;

AMINO ACID SEQUENCE; ARCHAEA; ARCHAEAL PROTEINS; CELL CYCLE; CELL CYCLE PROTEINS; DNA REPLICATION; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, ARCHAEAL; MOLECULAR SEQUENCE DATA; SEQUENCE ALIGNMENT; TRANSCRIPTION FACTORS;

EID: 77953165295     PISSN: 15384101     EISSN: 15514005     Source Type: Journal    
DOI: 10.4161/cc.9.4.10674     Document Type: Article

References (67)

1. Woese CR, Kandler O, Wheelis ML. Towards a natural system of organisms: proposal for the domains Archaea, Bacteria and Eucarya. Proc Natl Acad Sci USA 1990; 87:4576-9.
2. Brochier-Armanet C, Boussau B, Gribaldo S, Forterre P. Mesophilic Crenarchaeota: proposal for a third archaeal phylum, the Thaumarchaeota. Nat Rev Microbiol 2008; 6:245-52.
3. Bernander R. The cell cycle of Sulfolobus. Mol Microbiol 2007; 66:557-62.
4. Duggin IG, Bell SD. The chromosome replication machinery of the archaeon Sulfolobus solfataricus. J Biol Chem 2006; 281:15029-32.
5. Lundgren M, Bernander R. Archaeal cell cycle progress. Curr Opin Microbiol 2005; 8:662-8.
6. Lundgren M, Malandrin L, Eriksson S, Huber H, Bernander R. Cell cycle characteristics of crenarchaeota: unity among diversity. J Bacteriol 2008; 190:5362-7.
7. Lindås AC, Karlsson EA, Lindgren MT, Ettema TJ, Bernander R. A unique cell division machinery in the Archaea. Proc Natl Acad Sci USA 2008; 105:18942-6.
8. Samson RY, Obita T, Freund SM, Williams RL, Bell SD. A role for the ESCRT system in cell division in archaea. Science 2008; 322:1710-3.
9. Lundgren M, Bernander R. Genome-wide transcription map of an archaeal cell cycle. Proc Natl Acad Sci USA 2007; 104:2939-44. (Pubitemid 46327982)
10. Laub MT, McAdams HH, Feldblyum T, Fraser CM, Shapiro L. Global analysis of the genetic network controlling a bacterial cell cycle. Science 2000; 290:2144-8. (Pubitemid 32001594)
11. Cho RJ, Campbell MJ, Winzeler EA, Steinmetz L, Conway A, Wodicka L, et al. A genome-wide transcriptional analysis of the mitotic cell cycle. Mol Cell 1998; 2:65-73. (Pubitemid 128378967)
12. Spellman PT, Sherlock G, Zhang MQ, Iyer VR, Anders K, Eisen MB, et al. Comprehensive identification of cell cycle-regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization. Mol Biol Cell 1998; 9:3273-97.
13. Jensen LJ, Jensen TS, de Lichtenberg U, Brunak S, Bork P. Co-evolution of transcriptional and post-translational cell cycle regulation. Nature 2006; 443:594-7. (Pubitemid 44527297)
14. McAdams HH, Shapiro L. A bacterial cell cycle regulatory network operating in time and space. Science 2003; 301:1874-7. (Pubitemid 37221385)
15. Klevecz RR, Bolen J, Forrest G, Murray DB. A genomewide oscillation in transcription gates DNA replication and cell cycle. Proc Natl Acad Sci USA 2004; 101:1200-5. (Pubitemid 38182666)
16. Tu BP, Kudlicki A, Rowicka M, McKnight SL. Logic of the yeast metabolic cycle: temporal compartmentalization of cellular processes. Science 2005; 310:1152-8. (Pubitemid 41681736)
17. Chen Z, Odstrcil EA, Tu BP, McKnight SL. Restriction of DNA replication to the reductive phase of the metabolic cycle protects genome integrity. Science 2007; 316:1916-9. (Pubitemid 47025794)
18. Janniere L, Canceill D, Suski C, Kanga S, Dalmais B, Lestini R, et al. Genetic evidence for a link between glycolysis and DNA replication. PLoS ONE 2007; 2:447.
19. Wang JD, Sanders GM, Grossman AD. Nutritional control of elongation of DNA replication by (p)ppGpp. Cell 2007; 128:865-75.
20. Weart RB, Lee AH, Chien AC, Haeusser DP, Hill NS, Levin PA. A metabolic sensor governing cell size in bacteria. Cell 2007; 130:335-47.
21. Erzberger JP, Pirruccello MM, Berger JM. The structure of bacterial DnaA: implications for general mechanisms underlying DNA replication initiation. EMBO J 2002; 21:4763-73.
22. Johnson A, O'Donnell M. Cellular DNA replicases: components and dynamics at the replication fork. Annu Rev Biochem 2005; 74:283-315. (Pubitemid 40995509)
23. Tye BK. MCM proteins in DNA replication. Annu Rev Biochem 1999; 68:649-86.
24. Robinson NP, Bell SD. Extrachromosomal element capture and the evolution of multiple replication origins in archaeal chromosomes. Proc Natl Acad Sci USA 2007; 104:5806-11.
25. de Lichtenberg U, Jensen LJ, Brunak S, Bork P. Dynamic complex formation during the yeast cell cycle. Science 2005; 307:724-7. (Pubitemid 40194642)
26. Berthon J, Cortez D, Forterre P. Genomic context analysis in Archaea suggests previously unrecognized links between DNA replication and translation. Genome Biol 2008; 9:71. (Pubitemid 351974306)
27. Ettema TJ, de Vos WM, van der Oost J. Discovering novel biology by in silico archaeology. Nat Rev Microbiol 2005; 3:859-69. (Pubitemid 41693181)
28. Jensen LJ, Kuhn M, Stark M, Chaffron S, Creevey C, Muller J, et al. STRING 8 - a global view on proteins and their functional interactions in 630 organisms. Nucleic Acids Res 2009; 37:412-6.
29. Zhang R, Zhou M, Gu M, Joachimiak A. The crystal structure of a protein of unknown function from Archaeoglobus fulgidus DSM 4304. Midwest Center for Structural Genomics (MCSG) 2008.
30. Dalhus B, Arvai AS, Rosnes I, Olsen OE, Backe PH, Alseth I, et al. Structures of endonuclease V with DNA reveal initiation of deaminated adenine repair. Nat Struct Mol Biol 2009; 16:138-43.
31. Aravind L, Koonin EV. DNA-binding proteins and evolution of transcription regulation in the archaea. Nucleic Acids Res 1999; 27:4658-70.
32. Paredes CJ, Alsaker KV, Papoutsakis ET. A comparative genomic view of clostridial sporulation and physiology. Nat Rev Microbiol 2005; 3:969-78.
33. Brinkman AB, Ettema TJ, de Vos WM, van der Oost J. The Lrp family of transcriptional regulators. Mol Microbiol 2003; 48:287-94.
34. Holtzendorff J, Hung D, Brende P, Reisenauer A, Viollier PH, McAdams HH, Shapiro L. Oscillating global regulators control the genetic circuit driving a bacterial cell cycle. Science 2004; 304:983-7. (Pubitemid 38638090)
35. Schmid AK, Reiss DJ, Pan M, Koide T, Baliga NS. A single transcription factor regulates evolutionarily diverse but functionally linked metabolic pathways in response to nutrient availability. Mol Syst Biol 2009; 5:282.
36. Gordon GS, Wright A. DNA segregation in bacteria. Annu Rev Microbiol 2000; 54:681-708.
37. Figge RM, Easter J, Gober JW. Productive interaction between the chromosome partitioning proteins, ParA and ParB, is required for the progression of the cell cycle in Caulobacter crescentus. Mol Microbiol 2003; 47:1225-37. (Pubitemid 36307848)
38. Iyer LM, Makarova KS, Koonin EV, Aravind L. Comparative genomics of the FtsK-HerA superfamily of pumping ATPases: implications for the origins of chromosome segregation, cell division and viral capsid packaging. Nucleic Acids Res 2004; 32:5260-79. (Pubitemid 39445514)
39. Louarn JM, Quentin Y. FtsK controls metastable recombination provoked by an extra Ter site in the Escherichia coli chromosome terminus. Mol Microbiol 2007; 64:207-19.
40. D'Amours D, Jackson SP. The Mre11 complex: at the crossroads of dna repair and checkpoint signalling. Nat Rev Mol Cell Biol 2002; 3:317-27. (Pubitemid 34619266)
41. Manzan A, Pfeiffer G, Hefferin ML, Lang CE, Carney JP, Hopfner KP. MlaA, a hexameric ATPase linked to the Mre11 complex in archaeal genomes. EMBO Rep 2004; 5:54-9. (Pubitemid 38228528)
42. Ren B, Kuhn J, Meslet-Cladiere L, Briffotaux J, Norais C, Lavigne R, et al. Structure and function of a novel endonuclease acting on branched DNA substrates. EMBO J 2009; 28:2479-89.
43. Ettema TJ, Bernander R. Cell division and the ESCRT complex: A surprise from the Archaea. Commun Integr Biol 2009; 2:86-8.
44. Carr-Schmid A, Pfund C, Craig EA, Kinzy TG. Novel G-protein complex whose requirement is linked to the translational status of the cell. Mol Cell Biol 2002; 22:2564-74. (Pubitemid 34262979)
45. Doma MK, Parker R. Endonucleolytic cleavage of eukaryotic mRNAs with stalls in translation elongation. Nature 2006; 440:561-4.
46. Passos DO, Doma MK, Shoemaker CJ, Muhlrad D, Green R, Weissman J, et al. Analysis of Dom34 and Its Function in No-Go Decay. Mol Biol Cell 2009.
47. Robinson LC, Bradley C, Bryan JD, Jerome A, Kweon Y, Panek HR. The Yck2 yeast casein kinase 1 isoform shows cell cycle-specific localization to sites of polarized growth and is required for proper septin organization. Mol Biol Cell 1999; 10:1077-92.
48. Bernander R. Archaea and the cell cycle. Mol Microbiol 1998; 29:955-61.
49. Downey M, Houlsworth R, Maringele L, Rollie A, Brehme M, Galicia S, et al. A genome-wide screen identifies the evolutionarily conserved KEOPS complex as a telomere regulator. Cell 2006; 124:1155-68.
50. Hecker A, Lopreiato R, Graille M, Collinet B, Forterre P, Libri D, van Tilbeurgh H. Structure of the archaeal Kae1/Bud32 fusion protein MJ1130: a model for the eukaryotic EKC/KEOPS subcomplex. EMBO J 2008; 27:2340-51.
51. Hecker A, Graille M, Madec E, Gadelle D, Le Cam E, van Tilbergh H, Forterre P. The universal Kae1 protein and the associated Bud32 kinase (PRPK), a mysterious protein couple probably essential for genome maintenance in Archaea and Eukarya. Biochem Soc Trans 2009; 37:29-35.
52. Roberts JA, Bell SD, White MF. An archaeal XPF repair endonuclease dependent on a heterotrimeric PCNA. Mol Microbiol 2003; 48:361-71.
53. Hutton RD, Roberts JA, Penedo JC, White MF. PCNA stimulates catalysis by structure-specific nucleases using two distinct mechanisms: substrate targeting and catalytic step. Nucleic Acids Res 2008; 36:6720-7.
54. Lu S, Epner DE. Molecular mechanisms of cell cycle block by methionine restriction in human prostate cancer cells. Nutr Cancer 2000; 38:123-30.
55. Schweingruber AM, Hilti N, Edenharter E, Schweingruber ME. Methionine induces sexual development in the fission yeast Schizosaccharomyces pombe via an ste11-dependent signalling pathway. J Bacteriol 1998; 180:6338-41.
56. Vignols F, Brehelin C, Surdin-Kerjan Y, Thomas D, Meyer Y. A yeast two-hybrid knockout strain to explore thioredoxin-interacting proteins in vivo. Proc Natl Acad Sci USA 2005; 102:16729-34.
57. Fujikane R, Shinagawa H, Ishino Y. The archaeal Hjm helicase has recQ-like functions, and may be involved in repair of stalled replication fork. Genes Cells 2006; 11:99-110.
58. Richards JD, Johnson KA, Liu H, McRobbie AM, McMahon S, Oke M, et al. Structure of the DNA repair helicase hel308 reveals DNA binding and auto-inhibitory domains. J Biol Chem 2008; 283:5118-26.
59. Li Z, Lu S, Hou G, Ma X, Sheng D, Ni J, Shen Y. Hjm/ Hel308A DNA helicase from Sulfolobus tokodaii promotes replication fork regression and interacts with Hjc endonuclease in vitro. J Bacteriol 2008; 190:3006-17.
60. Tatusov RL, Koonin EV, Lipman DJ. A genomic perspective on protein families. Science 1997; 278:631-7.
61. Lassmann T, Sonnhammer EL. Kalign - an accurate and fast multiple sequence alignment algorithm. BMC Bioinformatics 2005; 6:298.
62. Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, et al. The Protein Data Bank. Nucleic Acids Res 2000; 28:235-42.
63. Kaplan W, Littlejohn TG. Swiss-PDB Viewer (Deep View). Brief Bioinform 2001; 2:195-7.
64. Barry ER, Bell SD. DNA replication in the archaea. Microbiol Mol Biol Rev 2006; 70:876-87.
65. Sclafani RA, Holzen TM. Cell cycle regulation of DNA replication. Annu Rev Genet 2007.
66. Guindon S, Gascuel O. A simple, fast and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst Biol 2003; 52:696-704.
67. Marchler-Bauer A, Anderson JB, Chitsaz F, Derbyshire MK, DeWeese-Scott C, Fong JH, et al. CDD: specific functional annotation with the Conserved Domain Database. Nucleic Acids Res 2009; 37:205-10.