An expansion of age constraints for microbial clades that lack a conventional fossil record using phylogenomic dating

Journal of Molecular Evolution

Volumn 73, Issue 3-4, 2011, Pages 188-208

  Blank, Carrine E ^a  

^a UNIVERSITY OF MONTANA   (United States)

Author keywords

Archaea; Chitin degradation; Chitinase; Lignin degradation; Microbial evolution; Phylogenomic dating; Relaxed molecular clock

Indexed keywords

ARCHAEAL PROTEIN; CHITIN; CHITIN SYNTHASE; CHITINASE; DIOXYGENASE; LIGNIN; OXYGEN;

AMINO ACID SEQUENCE; ARTICLE; BAYES THEOREM; BIOLOGICAL MODEL; COMPUTER SIMULATION; ENZYMOLOGY; EVOLUTION; GENETICS; HALOBACTERIALES; METABOLISM; OPERON; PHYLOGENY; SEQUENCE ANALYSIS; SPECIES DIFFERENTIATION; STATISTICAL MODEL; THERMOCOCCALES;

AMINO ACID SEQUENCE; ARCHAEAL PROTEINS; BAYES THEOREM; BIOLOGICAL EVOLUTION; CHITIN; CHITIN SYNTHASE; CHITINASE; COMPUTER SIMULATION; DIOXYGENASES; GENETIC SPECIATION; HALOBACTERIALES; LIGNIN; LIKELIHOOD FUNCTIONS; MODELS, GENETIC; OPERON; OXYGEN; PHYLOGENY; SEQUENCE ANALYSIS, PROTEIN; THERMOCOCCALES;

ARCHAEA; HALOBACTERIALES; SULFOLOBUS; SULFOLOBUS ISLANDICUS; SULFOLOBUS SOLFATARICUS; THERMOCOCCALES;

EID: 84856338450     PISSN: 00222844     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00239-011-9467-y     Document Type: Article

References (106)

1. Agarry SE, Durojaiye AO, Solomon BO (2008) Microbial degradation of phenols: a review. Int J Environ Pollut 32:12-28 (Pubitemid 351171359)
2. Andersson JO, Hirt RP, Foster PG, Roger AJ (2006) Evolution of four gene families with patchy phylogenetic distributions: influx of genes into protist genomes. BMC Evol Biol 6:27 (Pubitemid 43986501)
3. Badreddine I, Lafitte C, Heux L, Skandalis N, Spanou Z, Martinez Y, Esquerré-Tugayé M-T, Bulone V, Dumas B, Bottin A (2008) Cell wall chitosaccharides are essential components and exposed patterns of the phytopathogenic oomycete Aphanomyces euteiches. Eukaryot Cell 7:1980-1993
4. Baldauf SL (2008) An overview of the phylogeny and diversity of eukaryotes. J Syst Evol 46:263-273
5. Barns SM, Delwiche CF, Palmer JD, Pace NR (1996) Perspectives on archaeal diversity, thermophily and monophyly from environmental rRNA sequences. Proc Natl Acad Sci USA 93:9188-9193 (Pubitemid 26282757)
6. Bekker A, Holland HD, Wang P-L, Rumble D, Stein HJ, Hannah JL, Coetzee LL, Beukes NJ (2004) Dating the rise of atmospheric oxygen. Nature 427:117-120 (Pubitemid 38094946)
7. Blank CE (2009a) Phylogenomic dating-a method for constraining the age of microbial taxa that lack a conventional fossil record. Astrobiology 9:173-192
8. Blank CE (2009b) Phylogenomic dating-the relative antiquity of archaeal metabolic and physiological traits. Astrobiology 9:193-220
9. Blank CE (2009c) Not so old Archaea-the antiquity of biogeochemical processes in the archaeal domain of life. Geobiology 7:495-514
10. Blank CE, Sánchez-Baracaldo P (2010) Timing of morphological and ecological innovations in the Cyanobacteria-a key to understanding the rise in atmospheric oxygen. Geobiology 8:1-23
11. Boerjan W, Ralph J, Baucher M (2003) Lignin biosynthesis. Annu Rev Plant Biol 54:519-546 (Pubitemid 37400004)
12. Boll M, Fuchs G (2005) Unusual reactions involved in anaerobic metabolism of phenolic compounds. Biol Chem 386:989-997 (Pubitemid 41548731)
13. Brock TD (1978) Thermophilic microorganisms and life at high temperatures. Springer, New York
14. Campos-Gónora E, Ebert F, Willhoeft W, Said-Fernández S, Tannich E (2004) Characterization of chitin synthases from Entamoeba. Protist 155:323-330 (Pubitemid 39384654)
15. Castenholz RW (1988) Thermophilic cyanobacteria: special problems. Methods Enzymol 167:96-100
16. Cavalier-Smith T, Chao EE-Y (2003) Phylogeny of Choanozoa, Apusozoa, and other protozoa and early eukaryote megaevolution. J Mol Evol 56:540-563 (Pubitemid 36418983)
17. Chae JC, Kim E, Bini E, Zystra GJ (2007) Comparative analysis of the catechol 2,3-dioxygenase gene locus in thermoacidophilic archaeon Sulfolobus solfataricus strain 98/2. Biochem Biophy Res Commun 357:815-819 (Pubitemid 46653853)
18. Coronado JE, Mneimneh S, Epstein SL, Qiu W-G, Lipke PN (2007) Conserved processes and lineage-specific proteins in fungal cell wall evolution. Eukaryot Cell 6:2269-2277
19. Das S, Gillin FD (1991) Chitin synthase in encysting Entamoeba invadens. Biochem J 280:641-647
20. Das S, Van Dellen K, Bulik D, Magnelli P, Cui J, Head J, Robbins PW, Samuelson J (2006) The cyst wall of Entamoeba invadens contains chitosan (deacetylated chitin). Mol Biochem Parasitol 148:86-92 (Pubitemid 43795869)
21. Davies G, Henrissat B (1995) Structures and mechanisms of glycosyl hydrolases. Curr Biol 3:853-859
22. Delwiche CF, Graham LE, Thomson N (1989) Lignin-like compounds and sporopollenin in Coleochaete, an algal model for land plant ancestry. Science 245:399-401
23. Douzery EJP, Snell EA, Bapteste E, Delsuc F, Philippe H (2004) The timing of eukaryotic evolution: does a relaxed molecular clock reconcile proteins and fossils? Proc Natl Acad Sci USA 101:15386-15391 (Pubitemid 39441551)
24. Durkin CA, Mock T, Armbrust EV (2009) Chitin in diatoms and its association with the cell wall. Eukaryot Cell 8:1038-1050
25. Dutilh BE, van Noort V, van der Heijden RT, Boekhout T, Snel B, Huynen MA (2007) Assessment of phylogenomic and orthology approaches for phylogenetic inference. Bioinformatics 23(7):815-824 (Pubitemid 47049915)
26. Dutkiewicz A, Volk H, Ridley J, George S (2003) Biomarkers, brines, and oil in the Mesoproterozoic, Roper Superbasin, Australia. Geology 31:981-984 (Pubitemid 38000052)
27. Erickson M, Miksche GE (1974) On the occurrence of lignin or polyphenols in some mosses and liverworts. Phytochemistry 13:2295-2299
28. Espiñeira JM, Nono Uzal E, Gómex Ros LV, Carrión JS, Merino F, Ros Barceló A, Pomar F (2011) Distribution of lignin monomers and the evolution of lignification among lower plants. Plant Biol 13:59-68
29. Field CB, Behrenfeld MJ, Randerson JT, Falkowski P (2008) Primary production of the biosphere: integrating terrestrial and oceanic compartments. Science 281:237-240
30. Fuller MS, Clay RP (1993) Observations of Gonapodya in pure culture: growth, development and cell wall characterization. Mycologia 85:38-45
31. Gao J, Bauer MW, Shockley KR, Pysz MA, Kelly RM (2003) Growth of hyperthermophilic archaeon Pyrococcus furiosus on chitin involves two family 18 chitinases. Appl Environ Microbiol 69:3119-3128 (Pubitemid 36693312)
32. Gooday GW (1990) The ecology of chitin degradation. Adv Microb Ecol 11:387-430
33. Gunnison D, Alexander M (1975) Basis for the resistance of several algae to microbial decomposition. Appl Microbiol 29:729-738
34. Guo D-M, Ran J-H, Wang X-Q (2010) Evolution of the cinnamyl/sinapyl alcohol dehydrogenase (CAD/SAD) gene family: the emergence of real lignin is associated with the origin of bona fide CAD. J Mol Evol 71:202-218
35. Hayes JM, Des Marais DJ, Lambert ID, Strauss H, Summons RE (1992) Proterozoic biochemistry. In: Schopf JW, Klein C (eds) The Proterozoic biosphere. Cambridge University Press, New York, pp 81-134
36. Hinkle G, Morrison HG, Sogin ML (1997) Genes coding for reverse transcriptase, DNA-directed RNA polymerase, and chitin synthase from the microsporidian Spraguea lophii. Biol Bull 193:250-251 (Pubitemid 27526464)
37. Huber R, Stöhr J, Hohenhaus S, Rachel R, Burggraf S, Jannasch HW, Stetter KO (1995) Thermococcus chitonophagus sp. nov., a novel, chitin-degrading, hyperthermophilic archaeum from a deep-sea hydrothermal vent environment. Arch Microbiol 164:255-264
38. Huelsenbeck JP, Ronquist F (2001) MRBAYES: Bayesian inference of phylogeny. Bioinformatics 17:754-755
39. Hunt DE, Gevers D, Vahora NM, Polz MF (2008) Conservation of the chitin utilization pathway in the Vibrionaceae. Appl Environ Microbiol 74:44-51
40. Imanaka T, Fukui T, Fujiwara S (2001) Chitinase from Thermococcus kodakaraensis KOD1. Methods Enzymol 330:319-329 (Pubitemid 32107539)
41. Izzo V, Notomista E, Picardi A, Pennacchio F, Di Donato A (2005) The thermophilic archaeon Sulfolobus solfataricus is able to grow on phenol. Res Microbiol 156:677-689 (Pubitemid 40798509)
42. James TY, Kauff F, Schoch CL, Matheny PB, Hofstetter V et al (2006) Reconstructing the early evolution of fungi using a six-gene phylogeny. Nature 443:818-822 (Pubitemid 44622687)
43. Jockovic N, Andrade PB, Valentao P, Sabovljevic M (2008) HPLC-DAD of phenolics in bryophytes Lunularia cruciata, Brachytheciastrum velutinum and Kindbergia praelonga. J Serbian Chem Soc 73:1161-1167
44. Jones MDM, Forn I, Gadelha C, Egan MJ, Bass D, Massana R, Richards TA (2011) Discovery of novel intermediate forms redefines the fungal tree of life. Nature 474:200-203
45. Kakhki AM, Amoozegar MA, Khaledi EM (2011) Diversity of hydrolytic enzymes in haloarchaeal strains isolated from salt lake. Int J Environ Sci Technol 8:705-714
46. Karr CD, Jarroll EL (2004) Cyst wall synthase: N- acetylgalactosaminyltransferase activity is induced to form the novel N-acetylgalactosamine polysaccharide in the Giardia cyst wall. Microbiology SGM 150:1237-1243 (Pubitemid 38744726)
47. Keyhani NO, Roseman S (1999) Physiological aspects of chitin catabolism in marine bacteria. Biochim Biophys Acta 1473:108-122
48. Klejdus B, Kopechy J, Benesová L, Vacek J (2009) Solid-phase/supercritical-fluid extraction for liquid chromatography of phenolic compounds in freshwater microalgae and selected cyanobacterial species. J Chromatogr A 1216:763-771
49. Kneipp LF, Andrade AFB, de Souza W, Angluster J, Alviano CS, Travassos LR (1998) Trichomonas vaginalis and Tritrichomonas foetus: expression of chitin at the cell surface. Exp Parasitol 89:195-204 (Pubitemid 28380315)
50. Kovácik J, Klejdus B, Hedbavny J, Backor M (2010) Effect of copper and salicylic acid on phenolic metabolites and free amino acids in Scenedesmus quadricauda (Chlorophyceae). Plant Sci 178:307-311
51. LeCleir GR, Buchan A, Hollibaugh JT (2004) Chitinase gene sequences retrieved from diverse aquatic habitats reveal environment-specific distributions. Appl Environ Microbiol 70:6977-6983 (Pubitemid 39643758)
52. Lewis NG, Yamamoto E (1990) Lignin: Occurrence, biogenesis and degradation. Ann Rev Plant Physiol Plant Mol Biol 41:455-496
53. Li C, Peng P, Sheng G, Fu J, Yan Y (2003) A molecular and isotopic geochemical study of Meso- to Neoproterozoic (1.73-0.85 Ga) sediments from the Jixian section, Yanshan Basin, North China. Precambrian Res 125:337-356 (Pubitemid 37522273)
54. Ligrone R, Carafa A, Duckett JG, Renzaglia KS, Ruel K (2008) Immunocytochemical detection of lignin-related epitopes in cell walls in bryophytes and the charalean alga Nitella. Plant Sys Evol 270:257-272
55. Linder M, Winiecka-Krusnell J, Linder E (2002) Use of recombinant cellulose-binding domains of Trichoderma reesei cellulase as a selective immunocytochemical marker for cellulose in Protozoa. Appl Environ Microbiol 68:2503-2508 (Pubitemid 34477850)
56. Loftus B, Anderson I, Davies R, Alsmark UCM, Samuelson J et al (2005) The genome of the protist parasite Entamoeba histolytica. Nature 433:865-868 (Pubitemid 40314894)
57. Logan GA, Hinman MC, Walter MR, Summons RE (2001) Biogeochemistry of the 1640 Ma McArthur River (HYC) lead-zinc ore and host sediments, Northern Territory, Australia. Geochim Cosmochim Acta 65:2317-2336 (Pubitemid 32706899)
58. Lundell TK, Mäkelä MR, Hildén K (2010) Lignin-modifying enzymes in filamentous basidiomycetes-ecological, functional and phylogenetic review. J Basic Microbiol 50:5-20
59. Maddison WP, Maddison DR (2010) Mesquite: a modular system for evolutionary analysis. Version 2.73. www.mesquite.project.org
60. Maloof AC, Rose CV, Beach R, Samuels BM, Calmet CC et al (2010) Possible animal-body fossils in pre-Marinoan limestones from South Australia. Nat Geosci 3:653-659
61. Martone PT, Estevez JM, Lu F, Ruel K, Denny MW, Somerville C, Ralph J (2009) Discovery of lignin in seaweed reveals convergent evolution of cell-wall architecture. Curr Biol 19:169-175
62. Mendoza L, Taylor JW, Ajello L (2002) The class Mesomycetozoea: a heterogeneous group of microorganisms at the animal-fungal boundary. Ann Rev Microbiol 56:315-344 (Pubitemid 35217458)
63. Minge MA, Silberman JD, Orr RJS, Cavalier-Smith T, Shalchian-Tabrizi K, Burki F, Skjæveland Å, Jakobsen KS (2009) Evolutionary position of breviate amoebae and the primary eukaryote divergence. Proc R Soc Lond B 276:597-604
64. Moliner C, Fournier P-E, Raoult D (2010) Genome analysis of microorganisms living in amoebae reveals a melting pot of evolution. FEMS Microbiol Rev 34:281-294
65. Nakamura T, Mine S, Hagihara Y, Ishikawa K, Uegaki K (2007) Structure of the catalytic domain of the hyperthermophilic chitinase from Pyrococcus furiosus. Acta Crystallogr F 63:7-11 (Pubitemid 46067233)
66. Neaman A, Chorover J, Brantley SL (2005) Implications of the evolution of organic acid moieties for basalt weathering over geological time. Am J Sci 305:147-185 (Pubitemid 40696531)
67. Peterson DJ, Cotton JA, Gehling JG, Pisani D (2008) The Ediacaran emergence of bilaterians: congruence between the genetic and the geological fossil records. Philos Trans R Soc Lond B 363:1435-1443 (Pubitemid 351363986)
68. Rambaut A (2007) Sequence Alignment Editor Se-Al v2.0a11. Institute of Evolutionary Biology, University of Edinburgh, Edinburgh
69. Randall TA, Dwyer RA, Huitema E, Beyer K, Cvitanich C et al (2005) Large-scale gene discovery in the oomycete Phytophthora infestans reveals likely components of phytopathogenicity shared with tree fungi. Mol Plant Microbe Interact 18:229-243 (Pubitemid 40263618)
70. Roncero C (2002) The genetic complexity of chitin synthesis in fungi. Curr Genet 41:367-378 (Pubitemid 36075980)
71. Ruiz-Herrera J, Ortiz-Castellanos (2010) Analysis of the phylogenetic relationships and evolution of the cell walls from yeasts and fungi. FEMS Yeast Res 10:225-243
72. Ruiz-Herrera J, González-Prieto JM, Ruiz-Medrano R (2002) Evolution and phylogenetic relationships of chitin synthases from yeasts and fungi. FEMS Yeast Res 1:247-256 (Pubitemid 34442252)
73. Ruiz-Trillo I, Roger AJ, Burger G, Gray MW, Lang BF (2008) A phylogenomic investigation into the origin of metazoa. Mol Biol Evol 25:664-672 (Pubitemid 351398321)
74. Sánchez-Baracaldo P, Hayes PK, Blank CE (2005) Morphological and habitat evolution in the Cyanobacteria using a compartmentalization approach. Geobiology 3(3):145-165
75. Sanderson MJ (2002) Estimating absolute rates of molecular evolution and divergence times: a penalized likelihood approach. Mol Biol Evol 19:101-109 (Pubitemid 34008052)
76. Sanderson MJ (2003) r8s: inferring absolute rates of molecular evolution and divergence times in the absence of a molecular clock. Bioinformatics 19:301-302. http://loco.biosci.arizona.edu/r8s/
77. Shimodaira H, Hasegawa M (2001) CONSEL: For assessing the confidence of phylogenetic tree selection. Bioinformatics 17:1246-1247. http://www.is.titech. ac.jp/~shimo/prog/consel/
78. Siddiqui R, Khan NA, Jarroll EL (2009) The cyst wall carbohydrate composition of Balamuthia mandrillaris. Parisitol Res 104:1439-1443
79. Sims PA, Mann DG, Medlin LK (2006) Evolution of the diatoms: insights from fossil, biological and molecular data. Phycologia 45:361-402 (Pubitemid 44126962)
80. Spanggaard B, Skouboe P, Rossen L, Taylor JW (1996) Phylogenetic relationships of the intercellular fish pathogen Ichthyophonus hoferi and fungi, choanoflagellates and the rosette agent. Mar Biol 126:109-115 (Pubitemid 26397201)
81. Sperling EA, Robinson JM, Pisani D, Peterson KJ (2010) Where's the glass? Biomarkers, molecular clocks, and microRNAs suggest a 200-Myr missing Precambrian fossil record of siliceous sponge spicules. Geobiology 8:24-36
82. Steemans P, Le Hérissé A, Melvin J, Miller MA, Paris F, Verniers J, Wellman CH (2009) Origin and radiation of the earliest vascular land plants. Science 324:353
83. Swofford D (2001) PAUP. Phylogenetic analysis using parsimony (and other methods). versions 4.0b10. Sinauer Associates, Sunderland
84. Tanaka T, Fukui T, Atomi H, Imanaka T (2003) Characterization of an exo-β-D-glucosaminidase involved in a novel chitinolytic pathway from the hyperthermophilic archaeon Thermococcus kodakaraensis KOD1. J Bacteriol 185:5175-5181 (Pubitemid 37021979)
85. Tanaka T, Fukui T, Fujiwara S, Atomi H, Imanaka T (2004) Concerted action of diacetylchitobiose deacetylase and exo-β-D-glucosaminidase in a novel chitinolytic pathway in the hyperthermophilic archaeon Thermococcus kodakaraensis KOD1. J Biol Chem 279:30021-30027 (Pubitemid 38937922)
86. Tanaka T, Takahashi F, Fukui T, Fujiwara S, Atomi H, Imanaka T (2005) Characterization of a novel glucosamine-6-phosphate deaminase from a hyperthermophilic archaeon. J Bacteriol 187:7038-7044 (Pubitemid 41428880)
87. Teske A, Edgcomb V, Rivers AR, Thompson JR, de Vera Gomez A, Molyneaux SJ, Wirsen CO (2009) A molecular and physiological survey of a diverse collection of hydrothermal vent Thermococcus and Pyrococcus isolates. Extremophiles 13:905-915
88. Theriot EC, Cannone JJ, Gutell RR, Alverson AJ (2009) The limits of nuclear-encoded SSU rDNA for resolving the diatom phylogeny. Eur J Phycol 44:277-290
89. Thomas V, Greub G (2010) Amoeba/amoebal symbiont genetic transfers: lessons from giant virus neighbors. Intervirology 53:254-267
90. Tissot BP, Welte DH (1978) Petroleum formation and occurrence-a new approach to oil and gas exploration. Springer, New York
91. Van Dellen KL, Bulik DA, Specht CA, Robbins PW, Samuelson JC (2006) Heterologous expression of an Entamoeba histolytica chitin synthase in Saccharomyces cerevisiae. Eukaryot Cell 5:203-206 (Pubitemid 43113466)
92. Ventura GT, Kenig F, Reddy CM, Schieber J, Frysinger GS, Nelson RK, Dinel E, Gaines RB, Schaeffer P (2007) Molecular evidence of Late Archean archaea and the presence of a subsurface hydrothermal biosphere. Proc Natl Acad Sci USA 104:14260-14265 (Pubitemid 350003250)
93. Waldeck J, Meyer-Rammes H, Wieland S, Freesche J, Maurer KH, Meinhardt F (2007) Targeted deletion of genes encoding extracellular enzymes in Bacillus licheniformis and the impact on the secretion capability. J Biotechnol 130:124-132 (Pubitemid 46813175)
94. Ward HD, Alroy J, Lev BI, Keusch GT, Pereria MEA (1985) Identification of chitin as a structural component of Giardia cysts. Infect Immun 49:629-634 (Pubitemid 15021521)
95. Wellman CH, Osterloff PL, Mohluddin U (2003) Fragments of the earliest land plants. Nature 425:282-285 (Pubitemid 37158401)
96. Wilson MA, Sawyer J, Hatcher PG, Lerch HE III (1989) 1,3,5-Hydroxybenzene structures in mosses. Phytochemistry 28:1395-1400
97. Woese CR (1987) Bacterial evolution. Microbiol Rev 51:221-271 (Pubitemid 17082512)
98. Woese CR, Fox GE (1977) Phylogenetic structure of the prokaryotic domain: the primary kingdoms. Proc Natl Acad Sci USA 74:5088-5090 (Pubitemid 8241042)
99. Woese CR, Kandler O, Wheelis ML (1990) Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya. Proc Natl Acad Sci USA 87:4576-4579 (Pubitemid 20204145)
100. Wong DWS (2009) Structure and action mechanism of ligninolytic enzymes. Appl Biochem Biotechnol 157:174-209
101. Xu Z, Zhang D, Hu J, Zhou X, Ye X et al (2009) Comparative genome analysis of lignin biosynthesis gene families across the plant kingdom. BMC Bioinformatics 10(suppl 11):S3
102. Yang Z (2007) PAML 4: a program package for phylogenetic analysis by maximum likelihood. Mol Biol Evol 24:1586-1591. http://abacus.gene.ucl.ac.uk/ software/paml.html
103. Yoshinobu H, Motosuke S, Keita O, Rie Y, Kimiko E, Toshiaki F, Satoshi N (2006) Characterization of recombinant family 18 chitinase from extremely halophilic archaeon Halobacterium salinarum strain NRC-1. Chitin Chitosan Res 12:201
104. Zamani A, Jeihanipour A, Edebo L, Niklasson C, Taherzadeh MJ (2008) Determination of glucosamine and N-acetyl glucosamine in fungal cell walls. J Agric Food Chem 56:8314-8318
105. Zillig W, Reysenbach A-L (2001) Class IV. Thermococci. In: Boone DR, Catenholz RW (eds) Bergey's manual of systematic bacteriology, 2nd edn., vol 1. pp 341-348
106. Zillig W, Holz I, Janekovic D, Klenk HP, Imsel E, Trent J, Wunderl S, Forjaz VH, Coutinho R, Ferreira T (1990) Hyperthermus butylicus, a hyperthermophilic sulfur-reducing archaebacterium that ferments peptides. J Bacteriol 172:3959-3965 (Pubitemid 20213380)