Modular organization of inteins and C-terminal autocatalytic domains

Protein Science

Volumn 7, Issue 1, 1998, Pages 64-71

  Pietrokovski, Shmuel ^a  

^a USA   (United States)

Author keywords

C terminal autocatalytic domains; Charge relay system; HO endonuclease; Homing endonucleases; Inteins; Protein splicing

Indexed keywords

ENDONUCLEASE;

ARTICLE; CARBOXY TERMINAL SEQUENCE; GENE SEQUENCE; GENETIC CONSERVATION; HEDGEHOG; PRIORITY JOURNAL; PROTEIN PROCESSING;

EID: 0031938897     PISSN: 09618368     EISSN: None     Source Type: Journal    
DOI: 10.1002/pro.5560070106     Document Type: Article

References (51)

1. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. 1990. Basic local alignment search tool. J Mol Biol 215:403-410.
2. Altwood TK, Beck ME, Bleashy AJ, Parry-Smith DJ. 1994. PRINTS - A database of protein motif fingerprints. Nucleic Acids Res 22:3590-3596.
3. Bailey TL, Elkan C. 1994. Fitting a mixture model by expectation maximization to discover motifs in hiopolymers. In: Proceedings of Second International Conference on Intelligent Systems for Molecular Biology. Menlo Park, California: AAAI Press. pp 28-36.
4. Belfort M, Perlman PS. 1995. Mechanisms of intron mobility. J Biol Chem 270:30237-30240.
5. Belfort M, Reaban ME, Coetzee T, Dalgaard JZ. 1995, Prokaryotic introns and inteins: A panoply of form and function. J Bacteriol 177:3897-3903.
6. Belfort M, Roberts R. 1997. Homing endonucleases - Keeping the house in order. Nucleic Acids Res 25:3379-3388.
7. Bernstein FC, Koetzle TF, Williams GJB, Meyer EF Jr, Brice MD, Rodgers JR, Kennard O, Shimanouchi T, Tasumi M. 1977. The Protein Data Bank: A computer-based archival file for macromolecular structures. J Mol Biol 112:535-542.
8. Bull CJ, While O, Olsen GJ, Zhou L, Fleischmann RD, Sutton GG, Blake JA, FitzGerald LM, Clayton RA, Gocayne JD, Kerlavage AR, Dougherty BA, Tomb JF, Adams MD, Reich CI, Overheek R, Kirkness EF, Weinstock KG, Merrick JM, Glodek A, Scott JL, Geoghagen NSM, Weidman JF, Fuhrmann JL, Presley EA, Nguyen D, Utterback TR, Kelley JM, Peterson JD, Sadow PW, Hanna MC, Cotton MD, Hurst MA, Roberts KM, Kaine BP, Borodovsky M, Klenk HP, Fraser CM, Smith HO, Woese CR, Venter JC. 1996. Complete genome sequence of the methanogenic archaeon, Methanococcus jannaschii. Science 273:1058-1073.
9. Burglin TR. 1996. Warthog and groundhog, novel families related to hedgehog. Curr Biol 6:1047-1050.
10. Chong S, Shao Y, Paulus H, Benner J, Perler FB, Xu MQ. 1996. Protein splicing involving the Saccharomyces cerevisiae VMA intein: The steps in the splicing pathway, side reactions leading to protein cleavage, and establishment of an in vitro splicing system. J Biol Chem 271:22159-22168.
11. Chong S, Xu MQ. 1997. Protein splicing of the Saccharomyces cerevisiae VMA intein without the endonuclease motifs. J Biol Chem 272:15587-15590.
12. Cooper AA, Chen YJ, Lindorfer MA, Stevens TH. 1993. Protein splicing of the yeast TFP1 intervening protein sequence: A model for self-excision. EMBO J 12(6):2575-2583.
13. Crick F. 1979. Split genes and RNA splicing. Science 204:264-271.
14. Dalgaard JZ, Moser MJ, Hughey R, Mian IS. 1997. Statistical modeling, phylogenetic analysis and structure prediction of a protein splicing domain common to inteins and hedgehog proteins. J Comput Biol 4:193-214.
15. Davis EO, Thangaraj HS, Brooks PC, Colston MJ. 1994. Evidence of selection for protein introns in the recAs of pathogenic mycobacteria. EMBO J 13:699-703.
16. Derbyshire V, Wood DW, Wu W, Dansereau J, Dalgaard JZ, Belfort M. 1997. Genetic definition of a protein splicing domain: Functional mini-inteins support structure predictions and a model for intein evolution. Proc Natl Acad Sci USA 94:11466-11471.
17. Duan X, Gimble FS, Quiocho FA. 1997. Crystal structure of PI-SceI, a homing endonuclease with protein splicing activity. Cell 89:555-564.
18. Fsihi H, Vincent V, Cole ST. 1996. Homing events in the gyrA gene of some mycobacteria. Proc Natl Acad Sci USA 93:3410-3415.
19. Gimble FS, Stephens BW. 1995. Substitutions in conserved dodecapeptide motifs that uncouple the DNA binding and DNA cleavage activities of PI-SceI endonuclease. J Biol Chem 270:5849-5856.
20. Gimble FS, Thorner J. 1992. Homing of a DNA endonuclease gene by meiotic gene conversion in Saccharomyces cerevisiae. Nature 357:301-306.
21. Gorbalenya AE. 1994. Self-splicing group I and group II introns encode homologous (putative) DNA endonucleases of a new family. Protein Sci 3:1117-1120.
22. Hammerschmidt M, Brook A, McMahon AP. 1997. The world according to hedgehog. Trends Genet 13:14-21.
23. Henikoff S, Henikoff JG. 1994. Protein family classification based on searching a database of blocks. Genomics 19:97-107.
24. Henikoff S, Henikoff JG, Alford WJ, Pietrokovski S. 1995. Automated construction and graphical presenlation of protein blocks from unaligned sequences. Gene 163:GC 17-26.
25. Hirata R, Anraku Y. 1992. Mutations at the putative junction sites of the yeast VMA1 protein, the catalytic subunit of the vacuolar membrane H(+)-ATPase, inhibit its processing by protein splicing. Biochem Biophys Res Commun 188:40-47.
26. Hirata R, Ohsumk Y, Nakano A, Kawasaki H, Suzuki K, Anraku Y. 1990. Molecular structure of a gene, VMA1, encoding the catalytic subunit of H(+)-translocating adenosine triphosphatase from vacuolar membranes of Saccharomyces cerevisiae. J Biol Chem 265:6726-6733.
27. Hodges RA, Perler FB, Noren JN, Jack WE. 1992. Protein splicing removes intervening sequences in an archaea DNA polymerase. Nucleic Acids Res 20:6153-6157.
28. Kaneko T, Sato S, Kotani H, Tanaka A, Asamizu E, Nakamura Y, Miyajima N, Hirosawa M, Sugiura M, Sasamoto S, Kimura T, Hosouchi T, Matsuno A, Raki A, Nakazaki N, Naruo K, Okumura S, Shimpo S, Takeuchi C, Wada T, Watanabe A, Yamada M, Yasuda M, Tabata S. 1996. Sequence analysis of the genome of the unicellular cyanobacterium Svnechocystis sp. strain PCC6803. II. Sequence determination of the entire genome and assignment of potential protein-coding regions. DNA Res 3:109-136.
29. Kawasaki M, Nogami S, Satow Y, Ohya Y, Anraku Y. 1997. Identification of three core regions essential for protein splicing of the yeast vmal protozyme. A random mutagenesis study of the entire VMA1-derived endonuclease sequence. J Biol Chem 272:15668-15674.
30. Koonin EV. 1995. A protein splice-junction motif in hedgehog family proteins. Trends Biochem Sci 20:141-142.
31. Lee JJ, Ekker SC, von KDP, Porter JA, Sun BI, Beachy PA. 1994. Autoproteolysis in hedgehog protein biogenesis. Science 266:1528-1537.
32. Liu XQ, Hu Z. 1997. Identification and characterization of a cyanobacterial DnaX intein. FEBS Lett 408:311-314.
33. Martinez C, Nicolas A, van Tilbeurgh H, Egloff MP, Cudrey C, Verger R, Cambillau C. 1994. Cutinase, a lipolytic enzyme with a preformed oxyanion hole. Biochemistry 33:83-89.
34. Navas J. 1996. Genetic tools in pathogenic nocardioform actinomycetes. Microbiologia 12:297-304.
35. Ollis DL, Cheah E, Cygler M, Dijkstra B, Frolow F, Franken SM, Harel M, Remington SJ, Silman I, Schrag J, Sussman JL, Verschueren KHG, Goldman A. 1992. The alpha/beta hydrolase fold. Protein Eng 5:197-211.
36. Perler FB, Comb DG, Jack WE, Moran LS, Qiang B, Kucera RB, Benner J, Slatko BE, Nwankwo DO, Hempstead SK, Carlow CKS, Jannasch H. 1992. Intervening sequences in an Archaea DNA polymerase gene. Proc Natl Acad Sci USA 89:5577-5581.
37. Perler FB, Olsen GJ, Adam E. 1997. Compilation and analysis of intein sequences. Nucleic Acids Res 25:1087-1093.
38. Pietrokovski S. 1994. Conserved sequence features of inteins (protein introns) and their use in identifying new inteins and related proteins. Protein Sci 3(12):2340-2350.
39. Pietrokovski S. 1996a. A new intein in Cyanobacteria and its significance for the spread of inteins. Trends Genet 12:287-288.
40. Pietrokovski S. 1996b. Searching databases of conserved sequence regions by aligning protein multiple-alignments. Nucleic Adds Res 24:3836-3845.
41. Porter JA, Ekker SC, Park WJ, von Kessler DP, Young KE, Chen CH, Ma Y, Woods AS, Cotter RJ, Koonin EV, Beachy PA. 1996a. Hedgehog patterning activity: Role of a lipophilic modification mediated by the carboxy-terminal autoprocessing domain. Cell 86:21-34.
42. Porter JA, Young KE, Beachy PA. 1996b. Cholesterol modification of hedgehog signaling proteins in animal development. Science 274:255-259.
43. Rawlings ND, Barrett AJ. 1994. Families of serine peptidases. Methods Enzvmol 244:19-61.
44. Riera J, Robb FT, Weiss R, Fontecave M. 1997. Ribonucleotide reductase in the archaeon Pyrococcus furiosus: A critical enzyme in the evolution of DNA genomes? Proc Natl Acad Sci USA 94:475-478.
45. Schuler GD, Altschul SF, Lipman DJ. 1991. A workbench for multiple alignment construction and analysis. Proteins Struct Funct Genet 9:180-190.
46. Shub D, Goodrich-Blair H, Eddy S. 1994. Amino acid sequence motif of group I intron endonucleases is conserved in open reading frames of group II introns. Trends Biochem Sci 19:402-404.
47. Smith DR, Doucette-Stamm LA, Deloughery C, Lee H, Dubois J, Aldredge T, Bashirzadeh R, Blakely D, Cook R, Gilbert K, Harrison D, Hoang L, Keagle P, Lumm W, Pothier B, Qiu D, Spadafora R, Vicaire R, Wang Y, Wierzbowski J, Gibson R, Jiwani N, Caruso A, Bush D, Safer H, Patwell D, Prabhakar S, McDougall S, Shimer G, Goyal A, Pietrokovski S, Church GM, Daniels CJ, Mao JI, Rice P, Nölling J, Reeve JN. 1997. Complete genome sequence of Methanobacterium thermoautotrophicum strain H: Functional analysis and comparative genomics. J Bacteriology 179:7135-7155.
48. Tanaka Hall TM, Porter JA, Young KE, Koonin EV, Beachy PA, Leahy DJ. 1997. Crystal structure of a hedgehog autoprocessing domain: Homology between hedgehog and self-splicing proteins. Cell 91:85-97.
49. Telenti A, Southworth M, Daugelat S, Alcaide F, Jacobs WRJ, Perler FB. 1997. The Mycobacterium xenopi gyrA intein: Characterization of a minimal intein. J Bacteriology 179:6378-6382.
50. Valentini RP, Brookhiser WT, Park J, Yang T, Briggs J, Dressler G, Holzman LB. 1997. Post-translational processing and renal expression of mouse Indian hedgehog. J Biol Chem 272:8466-8473.
51. Xu MQ, Perler FB. 1996. The mechanism of protein splicing and its modulation by mutation. EMBO J 15:5146-5153.