Annotation of protein domains reveals remarkable conservation in the functional make up of proteomes across superkingdoms

Genes

Volumn 2, Issue 4, 2011, Pages 869-911

  Nasir, Arshan ^a   Naeem, Aisha ^a   Khan, Muhammad Jawad ^a   Lopez Nicora, Horacio D ^a   Caetano Anollés, Gustavo ^a  

^a UNIVERSITY OF ILLINOIS AT URBANA CHAMPAIGN   (United States)

Author keywords

Fold superfamily; Functional annotation; Molecular function; Protein domain; SCOP; Structure; Superkingdom

Indexed keywords

PROTEOME; TOXIN;

ARCHAEBACTERIUM; ARTICLE; BACTERIUM; CELL ADHESION; CHLAMYDIA; EUKARYOTE; GENE SEQUENCE; GUILLARDIA THETA; IMMUNE RESPONSE; INSECT; METABOLISM; MOLLICUTES; NANOARCHAEUM EQUITANS; NONHUMAN; PLANCTOMYCETES; PROTEIN DOMAIN; PROTEIN FUNCTION; PROTEIN STRUCTURE; PROTEOBACTERIA; SIGNAL TRANSDUCTION; SYMBIONT; VERRUCOMICROBIA;

EID: 84055190820     PISSN: None     EISSN: 20734425     Source Type: Journal    
DOI: 10.3390/genes2040869     Document Type: Article

References (52)

1. Caetano-Anolles, D.; Kim, K.M.; Mittenthal, J.E.; Caetano-Anolles, G. Proteome evolution andthe metabolic origins of translation and cellular life. J. Mol. Evol. 2011, 72, 14-33.
2. Lesk, A.M. Introduction to Protein Architecture; Oxford University Press: New York, NY, USA,2001.
3. Cordes, M.H.; Davidson, A.R.; Sauer, R.T. Sequence space, folding and protein design. Curr. Opin. Struct. Biol. 1996, 6, 3-10.
4. Linderstrom-Lang, K.U.; Schellman, J.A. The Enzymes; Academic Press: New York, NY, USA,1959; pp. 443-510.
5. Wang, M.; Caetano-Anolles, G. The evolutionary mechanics of domain organization in proteomesand the rise of modularity in the protein world. Structure 2009, 17, 66-78.
6. Vogel, C.; Bashton, M.; Kerrison, N.D.; Chothia, C.; Teichmann, S.A. Structure, function andevolution of multidomain proteins. Curr. Opin. Struct. Biol. 2004, 14, 208-216.
7. Wang, M.; Yafremava, L.S.; Caetano-Anolles, D.; Mittenthal, J.E.; Caetano-Anolles, G. Reductive evolution of architectural repertoires in proteomes and the birth of the tripartite world. Genome Res. 2007, 17, 1572-1585.
8. Gerstein, M.; Hegyi, H. Comparing genomes in terms of protein structure: Surveys of a finiteparts list. FEMS Microbiol. Rev. 1998, 22, 277-304.
9. Chothia, C.; Gough, J.; Vogel, C.; Teichmann, S.A. Evolution of the protein repertoire. Science 2003, 300, 1701-1703.
10. Murzin, A.G.; Brenner, S.E.; Hubbard, T.; Chothia, C. Scop: A structural classification of proteinsdatabase for the investigation of sequences and structures. J. Mol. Biol. 1995, 247, 536-540.
11. Orengo, C.A.; Michie, A.D.; Jones, S.; Jones, D.T.; Swindells, M.B.; Thornton, J.M. Cath-Ahierarchic classification of protein domain structures. Structure 1997, 5, 1093-1108.
12. Riley, M.; Labedan, B. Protein evolution viewed through escherichia coli protein sequences:Introducing the notion of a structural segment of homology, the module. J. Mol. Biol. 1997, 268,857-868.
13. Ponting, C.P.; Russell, R.R. The natural history of protein domains. Annu. Rev. Biophys. Biomol. Struct. 2002, 31, 45-71.
14. Andreeva, A.; Howorth, D.; Chandonia, J.M.; Brenner, S.E.; Hubbard, T.J.; Chothia, C.; Murzin, A.G. Data growth and its impact on the scop database: New developments. Nucleic AcidsRes. 2008, 36, D419-D425.
15. Caetano-Anolles, G.; Wang, M.; Caetano-Anolles, D.; Mittenthal, J.E. The origin, evolution andstructure of the protein world. Biochem. J. 2009, 417, 621-637.
16. Gough, J.; Karplus, K.; Hughey, R.; Chothia, C. Assignment of homology to genome sequencesusing a library of hidden markov models that represent all proteins of known structure. J. Mol. Biol. 2001, 313, 903-919.
17. Wilson, D.; Madera, M.; Vogel, C.; Chothia, C.; Gough, J. The superfamily database in 2007:Families and functions. Nucleic Acids Res. 2007, 35, D308-D313.
18. Karplus, K. Sam-t08, hmm-based protein structure prediction. Nucleic Acids Res. 2009, 37,W492-W497.
19. Kim, K.M.; Caetano-Anolles, G. The proteomic complexity and rise of the primordial ancestor ofdiversified life. BMC Evol. Biol. 2011, 11, 140:1-140:24.
20. Vogel, C.; Berzuini, C.; Bashton, M.; Gough, J.; Teichmann, S.A. Supra-domains: Evolutionaryunits larger than single protein domains. J. Mol. Biol. 2004, 336, 809-823.
21. Vogel, C.; Teichmann, S.A.; Pereira-Leal, J. The relationship between domain duplication andrecombination. J. Mol. Biol. 2005, 346, 355-365.
22. Vogel, C.; Chothia, C. Protein family expansions and biological complexity. PLoS Comput. Biol. 2006, 2, e48:0370-e48:0382.
23. Vogel, C. Function annotation of SCOP domain superfamilies 1.73. Superfamily-HMM libraryand genome assignments server. Available online: http://supfam.cs.bris.ac.uk/SUPERFAMILY/function.html (accessed on 28 October 2011).
24. Moreira, D.; Lopez-Garcia, P. Ten reasons to exclude viruses from the tree of life. Nat. Rev. Microbiol. 2009, 7, 306-311.
25. Wang, M.; Kurland, C.G.; Caetano-Anolles, G. Reductive evolution of proteomes and proteinstructures. Proc. Natl. Acad. Sci. USA 2011, 108, 11954-11958.
26. Koonin, E.V.; Wolf, Y.I.; Nagasaki, K.; Dolja, V.V. The big bang of picorna-like virus evolutionantedates the radiation of eukaryotic supergroups. Nat. Rev. Microbiol. 2008, 6, 925-939.
27. Das, S.; Paul, S.; Bag, S.K.; Dutta, C. Analysis of nanoarchaeum equitans genome and proteomecomposition: Indications for hyperthermophilic and parasitic adaptation. BMC Genomics 2006, 7, 186:1-186:16.
28. Huber, H.; Hohn, M.J.; Rachel, R.; Fuchs, T.; Wimmer, V.C.; Stetter, K.O. A new phylum ofarchaea represented by a nanosized hyperthermophilic symbiont. Nature 2002, 417, 63-67.
29. Waters, E.; Hohn, M.J.; Ahel, I.; Graham, D.E.; Adams, M.D.; Barnstead, M.; Beeson, K.Y.; Bibbs, L.; Bolanos, R.; Keller, M.; Kretz, K.; Lin, X.; Mathur, E.; Ni, J.; Podar, M.; Richardson, T.; Sutton, G.G.; Simon, M.; Soll, D.; Stetter, K.O.; Short, J.M.; Noordewier, M. The genome ofNanoarchaeum equitans: Insights into early archaeal evolution and derived parasitism. Proc. Natl. Acad. Sci. USA 2003, 100, 12984-12988.
30. Randau, L.; Munch, R.; Hohn, M.J.; Jahn, D.; Soll, D. Nanoarchaeum equitans creates functionaltrnas from separate genes for their 5′- and 3′-halves. Nature 2005, 433, 537-541.
31. Randau, L.; Schroder, I.; Soll, D. Life without rnase p. Nature 2008, 453, 120-123.
32. Di Giulio, M. Nanoarchaeum equitans is a living fossil. J. Theor. Biol. 2006, 242, 257-260.
33. Di Giulio, M. The tree of life might be rooted in the branch leading to nanoarchaeota. Gene 2007,401, 108-113.
34. Kim, K.M.; Caetano-Anolles, G. The evolutionary history of protein fold families and proteomesconfirms Archaea is the most ancient superkingdom. Ms. submitted.
35. Woese, C.R.; Maniloff, J.; Zablen, L.B. Phylogenetic analysis of the mycoplasmas. Proc. Natl. Acad. Sci. USA 1980, 77, 494-498.
36. Chambaud, I.; Heilig, R.; Ferris, S.; Barbe, V.; Samson, D.; Galisson, F.; Moszer, I.; Dybvig, K.; Wróblewski, H.; Viari, A.; Rocha, E.P.; Blanchard, A. The complete genome sequence of themurine respiratory pathogen Mycoplasma pulmonis. Nucleic Acids Res. 2001, 29, 2145-2153.
37. Gibson, D.G.; Smith, H.O.; Hutchison, C.A., III.; Venter, J.C.; Merryman, C. Chemical synthesisof the mouse mitochondrial genome. Nat. Methods 2010, 7, 901-903.
38. Nakabachi, A.; Yamashita, A.; Toh, H.; Ishikawa, H.; Dunbar, H.E.; Moran, N.A.; Hattori, M. The 160-kilobase genome of the bacterial endosymbiont carsonella. Science 2006, 314, 267.
39. Forterre, P.; Gribaldo, S. Bacteria with a eukaryotic touch: A glimpse of ancient evolution? Proc. Natl. Acad. Sci. USA 2010, 107, 12739-12740.
40. Santarella-Mellwig, R.; Franke, J.; Jaedicke, A.; Gorjanacz, M.; Bauer, U.; Budd, A.; Mattaj, I.W.; Devos, D.P. The compartmentalized bacteria of the planctomycetes-verrucomicrobiachlamydiaesuperphylum have membrane coat-like proteins. PLoS Biol. 2010, 8, e1000281:1-e1000281:11.
41. Kamneva, O.K.; Liberles, D.A.; Ward, N.L. Genome-wide influence of indel substitutions onevolution of bacteria of the PVC superphylum, revealed using a novel computational method. Genome Biol. Evol. 2010, 2, 870-886.
42. Devos, D.P.; Reynaud, E.G. Evolution. Intermediate steps. Science 2010, 330, 1187-1188.
43. Katinka, M.D.; Duprat, S.; Cornillot, E.; Méténier, G.; Thomarat, F.; Prensier, G.; Barbe, V.; Peyretaillade, E.; Brottier, P.; Wincker, P.; Delbac, F.; El Alaoui, H.; Peyret, P.; Saurin, W.; Gouy, M.; Weissenbach, J.; Vivarès, C.P, Genome sequence and gene compaction of theeukaryote parasite Encephalitozoon cuniculi. Nature 2001, 414, 450-453.
44. Corradi, N.; Pombert, J.F.; Farinelli, L.; Didier, E.S.; Keeling, P.J. The complete sequence of thesmallest known nuclear genome from the microsporidian Encephalitozoon intestinalis. Nat. Commun. 2010, 1, 77, doi: 10.1038/ncomms1082.
45. Douglas, S.; Zauner, S.; Fraunholz, M.; Beaton, M.; Penny, S.; Deng, L.T.; Wu, X.; Reith, M.; Cavalier-Smith, T.; Maier, U.G. The highly reduced genome of an enslaved algal nucleus. Nature 2001, 410, 1091-1096.
46. Peyretaillade, E.; Biderre, C.; Peyret, P.; Duffieux, F.; Metenier, G.; Gouy, M.; Michot, B.; Vivares, C.P. Microsporidian encephalitozoon cuniculi, a unicellular eukaryote with an unusualchromosomal dispersion of ribosomal genes and a lsu rrna reduced to the universal core. NucleicAcids Res. 1998, 26, 3513-3520.
47. Martin, W.; Herrmann, R.G. Gene transfer from organelles to the nucleus: How much, whathappens, and why? Plant Physiol. 1998, 118, 9-17.
48. Keeling, P.J.; Slamovits, C.H. Causes and effects of nuclear genome reduction. Curr. Opin. Genet. Dev. 2005, 15, 601-608.
49. Welch, B.L.; The significance of the difference between two means when the populationvariances are unequal. Biometrika 1938, 29, 350-362.
50. Caetano-Anolles, G.; Kim, H.S.; Mittenthal, J.E. The origin of modern metabolic networks inferredfrom phylogenomic analysis of protein architecture. Proc. Natl. Acad. Sci. USA 2007, 104, 9358-9363.
51. Ingham, P.W.; Nokano, Y.; Seger, C. Mechanisms and functions of Hedgehog signalling acrossthe metazoa. Nat. Rev. Genet. 2011, 12, 393-406.
52. Bürglin, T.R. Evolution of hedgehog and hedgehog-related genes, their origin from Hog proteins inancestral eukaryotes and discovery of a novel Hint motif. BMC Genomics 2008, 9, 127:1-127:28.