Protein families in multicellular organisms

Current Opinion in Structural Biology

Volumn 9, Issue 3, 1999, Pages 408-415

  Copley, Richard R ^a   Schultz, Jörg ^a   Ponting, Chris P ^b   Bork, Peer ^a  

^a EUROPEAN MOLECULAR BIOLOGY LABORATORY   (Germany)

^b NATIONAL INSTITUTES OF HEALTH   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CAENORHABDITIS ELEGANS; GENOME; HUMAN; NEMATODE; NONHUMAN; PHYLOGENY; PRIORITY JOURNAL; PROTEIN FAMILY; REVIEW; SEQUENCE ANALYSIS; SEQUENCE HOMOLOGY; YEAST;

CAENORHABDITIS ELEGANS;

EID: 0033150836     PISSN: 0959440X     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0959-440X(99)80055-4     Document Type: Article

References (61)

1. Koonin EV, Tatusov RL, Galperin MY: Beyond complete genomes: From sequence to structure and function. Curr Opin Struct Biol 1998, 8:355-363.
2. Bork P, Dandekar T, Diaz-Lazcoz Y, Eisenhaber F, Huynen M, Yuan Y: Predicting function: From genes to genomes and back. J Mol Biol 1998, 283:707-725.
3. The C. elegans sequencing consortium: Genome sequence of the nematode C. elegans: A platform for investigating biology. Science 1998, 282:2012-2018. The importance of this paper lies in the availability of the data that it describes - the first complete genome of a multicellular organism. For the time being, sequence analysis of all aspects of multicellularity will be reliant upon it. In addition, C. elegans represents one of the classic experimental models for developmental biology. Linking such experiments to sequences should facilitate the transfer of these data to other organisms.
4. Rubin GM: The Drosophila genome project: A progress report. Trends Genet 1998, 14:340-343.
5. Pennisi E: Fruit fly researchers sign pact with Celera. Science 1999, 283:767.
6. Meinke DW, Cherry JM, Dean C, Rounsley SD, Koorneef M: Arabidopsis thailiana: A model plant for genome analysis. Science 1998, 282:671-682.
7. Huynen MA, Bork P: Measuring genome evolution. Proc Natl Acad Sci USA 1998, 95:5849-5856.
8. Sidow A: Gen(om)e duplications in the evolution of early vertebrates. Curr Opin Genet Dev 1996, 6:715-722.
9. Wittbrodt J, Meyer A, Schartl M: More genes in fish? Bioessays 1998, 20:511-515.
10. Amores A, Force A, Yan Y, Joly L, Amemiya C, Fritz A, Ho RK, Langeland J, Prince V, Wang Y et al.: Zebrafish hox clusters and vertebrate genome evolution. Science 1998, 282:1711-1714.
11. Cooke J, Nowak MA, Boerlijst M, Maynard-Smith J: Evolutionary origins and maintenance of redundant gene expression during metazoan development. Trends Genet 1997, 13:360-364.
12. Gibson TJ, Spring J: Genetic redundancy in vertebrates: Polyploidy and persistence of genes encoding multidomain proteins. Trends Genet 1998, 14:46-49. Continuing the debate on paralogue persistence started in [11], the authors argue that some multidomain proteins may be inherently more resistant to decay by point mutation than single-domain proteins, owing to the existence of dominant negative phenotypes. See also the reply by Cooke following this article.
13. Mushegian AR, Garey JR, Martin J, Xiu LX: Large-scale taxonomic profiling of eukaryotic model organisms: A comparison of orthologous proteins encoded by the human, fly, nematode, and yeast genomes. Genome Res 1998, 8:590-598.
14. Chervitz SA, Aravind L, Sherlock G, Ball CA, Koonin EV, Dwight SS, Harris MA, Dolinski K, Mohr S, Smith T et al.: Comparison of the complete protein sets of worm and yeast: Orthology and divergence. Science 1998, 292:2022-2028. This work is significant as it represents the first general comparison of the complete protein sets of C. elegans and S. cerevisiae. For certain types of proteins carrying out 'core biological processes', one-to-one orthologous relationships are identifiable, whereas for proteins involved in signal transduction and regulatory control, many novel domains are found. Although the results are unsurprising, they represent the starting point from which further analyses may proceed.
15. Maleszka R, De Couet HG, Gabor Miklos GL: Data transferability from model organisms to human beings: Insights from the functional genomics of the flightless region of Drosophila. Proc Natl Acad Sci USA 1998, 95:3731-3736.
16. Schultz J, Milpetz F, Bork P, Ponting CP: SMART, a simple modular architecture research tool: Identification of signaling domains. Proc Natl Acad Sci USA 1998, 95:5857-5864. The modular architectures of many of the more interesting proteins in multicellular organisms can be difficult to analyse using conventional database searching techniques. Systems such as SMART [19], ProfileScan [17•] and Pfam [18•] represent the easiest ways of analysing proteins at the domain level. The SMART system focuses on the sensitive detection of the intracellular and extracellular domains involved in signal transduction using manually curated alignments. Pfam covers all types of protein modules, at the expense of some sensitivity.
17. Hofmann K, Bucher P, Falquet L, Bairoch A: The PROSITE database, its status in 1999. Nucleic Acids Res 1999, 27:215-219. See annotation to [16•].
18. Bateman A, Birney E, Durbin R, Eddy SR, Finn RD, Sonnhammer ELL: Pfam 3.1: 1313 multiple alignments and profile HMMs match the majority of proteins. Nucleic Acids Res 1999, 27:260-262. See annotation to [16•].
19. Ponting CP, Schultz J, Milpetz F, Bork P: SMART: Identification and annotation of domains from signalling and extracellular protein sequences. Nucleic Acids Res 1999, 27:229-232.
20. Leonard CJ, Aravind L, Koonin EV: Novel families of putative protein kinases in bacteria and archaea: Evolution of the eukaryotic protein kinase superfamily. Genome Res 1998, 8:1038-1047.
21. Fraser A, James C: Fermenting debate: Do yeast undergo apoptosis? Trends Cell Biol 1998, 8:219-221.
22. Uren AG, Coulson EJ, Vaux D: Conservation of baculovirus inhibitor of apoptosis repeat proteins (BIRPs) in viruses, nematodes, vertebrates and yeasts. Trends Biochem Sci 1998, 5:159-162.
23. Aravind L, Dixit VM, Koonin EV: The domains of death: Evolution of the apoptosis machinery. Trends Biochem Sci 1999, 24:47-53. This paper examines the phylogenetic distribution of protein domains found in the apoptotic machinery, in order to trace the evolutionary origins of this phenomenon. Apoptosis is an intriguing case study, involving many regulatory domains, some with apparently ancient origins, in a pathway that appears to have arisen relatively late in evolution.
24. Takayama S, Xie Z, Reed JC: An evolutionary conserved family of Hsp70/Hsc70 molecular chaperone regulators. J Biol Chem 1999, 274:781-786.
25. Jiang Y, Woronicz JD, Lin W, Goeddel DV: Prevention of constitutive TNF receptor 1 signaling by silencer of death domains. Science 1999, 283:543-546.
26. Chen J, Rawlings ND, Stevens RAE, Barrett AJ: Identification of the active site of legumain links it to caspases, clostripain and gingipains in a new clan of cysteine endopeptidases. FEBS Lett 1998, 441:361-365.
27. van der Biezen EA, Jones JDG: The NB-ARC domain: A novel motif shared by plant resistance gene products and regulators of cell death in animals. Curr Biol 1998, 8:R226-R227.
28. del Pozo O, Lam E: Caspases and programmed cell death in the hypersensitive response of plants to pathogens. Curr Biol 1998, 8:1129-1132.
29. Craven SE, Bredt DS: PDZ proteins organize synaptic signaling pathways. Cell 1998, 93:495-498.
30. Bargmann CI: Neurobiology of the Caenorhabditis elegans genome. Science 1998, 282:2028-2033.
31. Satterlee JS, Sussman MR: Unusual membrane-associated protein kinases in higher plants. J Membr Biol 1998, 164:205-213.
32. Birkeland NK: Cloning, molecular characterization, and expression of the genes encoding the lytic functions of lactococcal bacteriophage phi LC3: A dual lysis system of modular design. Can J Microbiol 1994, 40:658-665.
33. Nielson H, Engelbrecht J, Brunak S, von Heijne G: Identification of prokaryotic and eukaryotic signal peptides and prediction of their cleavage sites. Protein Eng 1997, 10:1-6.
34. Blaxter M: Caenorhabditis elegans is a nematode. Science 1998, 282:2041-2046.
35. Tudor JE, Pallaghy PK, Pennington MW, Norton RS: Solution structure of the ShK toxin, a novel potassium channel inhibitor from a sea anemone. Nat Struct Biol 1998, 3:317-320.
36. Kidd T, Brose K, Mitchell KJ, Fetter RD, Tessier-Lavigne M, Goodman CS, Tear G: Roundabout controls axon crossing of the CNS midline and defines a novel subfamily of evolutionary conserved guidance receptors. Cell 1998, 92:205-215.
37. Zallen JA, Yi BA, Bargmann CI: The conserved immunoglobulin superfamily member SAX-3/Robo directs multiple aspects of axon guidance in C. elegans. Cell 1998, 92:217-227.
38. Vacquier VD: Evolution of gamete recognition proteins. Science 1998, 281:1995-1998.
39. Gao Z, Garbers DL: Species diversity in the structure of zonadhesin, a sperm-specific membrane protein containing multiple cell adhesion molecule-like domains. J Biol Chem 1998, 273:3415-3421.
40. Peynet J, Beaudeux JL, Woimant F, FLourie F, Giraudeaux V, Vicaut E, Launay JM: Apolipoprotein(a) size polymorphism in young adults with ischemic stroke. Atherosclerosis 1999, 142:233-239.
41. Clarke ND, Berg JM. Zinc fingers in Caenorhabditis elegans: Finding families and probing pathways. Science 1998, 282:2018-2022.
42. Ruvkun G, Hobert O: The taxonomy of developmental control in Caenorhabditis elegans. Science 1998, 282:2033-2041. Many early analyses of complete genomes have been little more than exercises in counting numbers of proteins and domains. This paper presents the beginnings of a more focused approach, concerning transcription factors and regulatory genes in specific developmental pathways, and a comparison with other organisms.
43. Gibson TJ, Ramu C, Gemund C, Aasland R: The APECED polyglandular autoimmune syndrome protein, AIRE-1, contains the SAND domain and is probably a transcription factor. Trends Biochem Sci 1998, 7:242-244.
44. Kagaya K, Ohmiya K, Hattori OT: RAV1, a novel DNA-binding protein, binds to bipartite recognition sequence through two distinct DNA-binding domains uniquely found in higher plants. Nucleic Acids Res 1999, 27:470-478.
45. Bork PJ, Gibson TJ: Applying motif and profile searches. Methods Enzymol 1996, 266:162-184.
46. Pehrson JR, Fuji RN: Evolutionary conservation of histone macroH2A subtypes and domains. Nucleic Acids Res 1998, 26:2837-2842.
47. Smith ER, Belote JM, Schiltz RL, Yang X, Moore PA, Berger SL, Nakatani Y, Allis CD: Cloning of Drosophila GCN5: Conserved features among metazoan GCN5 family members. Nucleic Acids Res 1998, 26:2948-2954.
48. Beckmann G, Hanke J, Bork P, Reich JG: Merging extracellular domains: Fold prediction for laminin G-like and amino-terminal thrombospondin-like modules based on homology to pentraxins. J Mol Biol 1998, 275:725-730.
49. Callebaut I, Cossart P, Dehoux P: EVH1/WH1 domains of VASP and WASP proteins belong to a large family including Ran-binding domains of the RanBP1 family. FEBS Lett 1998, 441:181-185.
50. Huang B, Eberstadt M, Olejniczak ET, Meadows RP, Fesik SW: NMR structure and mutagenesis of the Fas (APO-1/CD95) death domain. Nature 1996, 384:638-641.
51. Hofmann K, Bucher P: The CARD domain: A new apoptotic signalling motif. Trends Biochem Sci 1997, 5:155-156.
52. Eberstadt M, Huang B, Chen Z, Meadows RP, Ng SC, Zheng L, Lenardo MJ, Fesik SW: NMR structure and mutagenesis of the FADD (Mort1) death-effector domain. Nature 1998, 392:941-945.
53. Chou JJ, Masuo H, Duan H, Wagner G. Solution structure of the RAIDD CARD and model for CARD/CARD interaction in caspase-2 and caspase-9 recruitment. Cell 1998, 94:171-180.
54. Shapiro L, Scherer PE: The crystal structure of a complement-1q family protein suggests an evolutionary link to tumor necrosis factor. Curr Biol 1998, 8:335-338.
55. Aravind L, Koonin EV: Fold prediction and evolutionary analysis of the POZ domain: Structural and evolutionary relationship with the potassium channel tetramerization domain. J Mol Biol 1999, 285:1353-1361.
56. Ahmed KF, Engel CK, Prive GG: Crystal structure of the BTB domain from PLZF. Proc Natl Acad Sci USA 1998, 95:12123-12128.
57. Stapleton D, Balan I, Pawson T, Sicheri F: The crystal structure of an Eph receptor SAM domain reveals a mechanism for modular dimerization. Nat Struct Biol 1999, 6:44-49.
58. Thanos CD, Goodwill KE, Bowie JU: Oligomeric structure of the human EphB2 receptor SAM domain. Science 1999, 283:833-836.
59. Himanen JP, Henkemeyer M, Nikolov DB: Crystal structure of the ligand-binding domain of the receptor tyrosine kinase EphB2. Nature 1998, 396:486-491.
60. George SE, Simokat K, Hardin J, Chisholm AD: The VAB-1 Eph receptor tyrosine kinase functions in neural and epithelial morphogenesis in C. elegans. Cell 1998, 92:633-643.
61. Porting CP, Aravind L, Schultz J, Bork P, Koonin EV: Eukaryotic signalling domain homologues in archaea and bacteria - ancient ancestry and horizontal gene transfer. J Mol Biol 1999, in press.