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Origin and Evolution of Inteins and Other Hint Domains

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Book cover Homing Endonucleases and Inteins

Part of the book series: Nucleic Acids and Molecular Biology ((NUCLEIC,volume 16))

Abstract

Intein protein-splicing domains are part of the Hint superfamily. This superfamily includes three other characterized families: Hog-Hint and two types of Bacterial intein-like (BIL) domains. Hint domains share the same structure fold and common sequence features, and have similar biochemical activities. They post-translationally auto-process the proteins in which they are present by protein-splicing, self-cleavage or ligation activities. Yet, each Hint family apparently has its own distinct biological role. We discuss the evolution of the different Hint families, the origin of primordial Hint domains themselves, and their possible activities and biological functions.

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References

  • Abrahamsen M, Templeton T, Enomoto S, Abrahante J, Zhu G, Lancto C, Deng M, Liu C, Widmer G, Tzipori S, Buck G, Xu P, Bankier A, Dear P, Konfortov B, Spriggs H, Iyer L, Anantharaman V, Aravind L, Kapur V (2004) Complete genome sequence of the apicomplexan, Cryptosporidium parvum. Science 304:441–445

    Article  PubMed  CAS  Google Scholar 

  • Amitai G, Belenkiy O, Pietrokovski S (2003) Distribution and function of new bacterial intein-like protein domains. Mol Microbiol 47:61–73

    Article  PubMed  CAS  Google Scholar 

  • Amitai G, Dassa D, Pietrokovski S (2004) Protein-splicing of inteins with atypical glutamine and aspartate C-terminal residues. J Biol Chem 279:3121–3131

    PubMed  CAS  Google Scholar 

  • Aspock G, Kagoshima H, Niklaus G, Burglin TR (1999) Caenorhabditis elegans has scores of hedgehog-related genes: sequence and expression analysis. Genome Res 9:909–923

    Article  PubMed  CAS  Google Scholar 

  • Belfort M, Roberts RJ (1997) Homing endonucleases: keeping the house in order. Nucleic Acids Res 25:3379–3388

    Article  PubMed  CAS  Google Scholar 

  • Butler G, Kenny C, Fagan A, Kurischko C, Gaillardin C, Wolfe KH (2004) Evolution of the MAT locus and its Ho endonuclease in yeast species. Proc Natl Acad Sci USA 101:1632–1637

    PubMed  CAS  Google Scholar 

  • Caspi J, Amitai G, Belenkiy O, Pietrokovski S (2003) Distribution of split DnaE inteins in cyanobacteria. Mol Microbiol 50:1569–1577

    Article  PubMed  CAS  Google Scholar 

  • Dalgaard JZ, Klar AJ, Moser MJ, Holley WR, Chatterjee A, Mian IS (1997) Statistical modeling and analysis of the LAGLIDADG family of site-specific endonucleases and identification of an intein that encodes a site-specific endonuclease of the HNH family. Nucleic Acids Res 25:4626–4638

    Article  PubMed  CAS  Google Scholar 

  • Dassa B, Haviv H, Amitai G, Pietrokovski S (2004a) Protein-splicing and auto-cleavage of bacterial intein-like domains lacking a C′-flanking nucleophilic residue. J Biol Chem 279:32001–32007

    Article  PubMed  CAS  Google Scholar 

  • Dassa B, Yanai I, Pietrokovski S (2004b) New type of poly ubiquitin-like genes with inteinlike autoprocessing domains. Trends Genet 20:538–542

    Article  PubMed  CAS  Google Scholar 

  • Duan X, Gimble FS, Quiocho FA (1997) Crystal structure of PI-SceI, a homing endonuclease with protein-splicing activity. Cell 89:555–564

    Article  PubMed  CAS  Google Scholar 

  • Duchaud E, Rusniok C, Frangeul L, Buchrieser C, Givaudan A, Taourit S, Bocs S, Boursaux-Eude C, Chandler M, Charles J, Dassa E, Derose R, Derzelle S, Freyssinet G, Gaudriault S, Medigue C, Lanois A, Powell K, Siguier P, Vincent R, Wingate V, Zouine M, Glaser P, Boemare N, Danchin A, Kunst F (2003) The genome sequence of the entomopathogenic bacterium Photorhabdus luminescens. Nat Biotechnol 21:1307–1313

    Article  PubMed  CAS  Google Scholar 

  • Fsihi H, Vincent V, Cole ST (1996) Homing events in the gyrA gene of some mycobacteria. Proc Natl Acad Sci USA 93:3410–3415

    Article  PubMed  CAS  Google Scholar 

  • Gimble FS (2000) Invasion of a multitude of genetic niches by mobile endonuclease genes. FEMS Microbiol Lett 185:99–107

    Article  PubMed  CAS  Google Scholar 

  • Gimble FS (2001) Degeneration of a homing endonuclease and its target sequence in a wild yeast strain. Nucleic Acids Res 29(20):4215–4223

    Article  PubMed  CAS  Google Scholar 

  • Gogarten JP, Senejani AG, Zhaxybayeva O, Olendzenski L, Hilario E (2002) Inteins: structure, function, and evolution. Annu Rev Microbiol 56:263–287

    Article  PubMed  CAS  Google Scholar 

  • Haber J (1998) Mating-type gene switching in Saccharomyces cerevisiae. Annu Rev Genet 32:561–599

    Article  PubMed  CAS  Google Scholar 

  • 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

    Article  PubMed  CAS  Google Scholar 

  • Hammerschmidt M, Brook A, McMahon AP (1997) The world according to hedgehog. Trends Genet 13:14–21

    Article  PubMed  CAS  Google Scholar 

  • 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

    PubMed  CAS  Google Scholar 

  • Isabelle S, Mamadou D, Jean-Michel M (2001) Distribution of GyrA intein in non-tuberculous mycobacteria and genomic heterogeneity of Mycobacterium gastri. FEBS Lett 508:121–125

    Article  PubMed  CAS  Google Scholar 

  • Janssen R, Prpic NM, Damen WG (2004) Gene expression suggests decoupled dorsal and ventral segmentation in the millipede Glomeris marginata (Myriapoda: Diplopoda). Dev Biol 268:89–104

    Article  PubMed  CAS  Google Scholar 

  • Jentsch S, Pyrowolakis G (2000) Ubiquitin and its kin: how close are the family ties? Trends Cell Biol 10:335–342

    Article  PubMed  CAS  Google Scholar 

  • Kang D, Huang F, Li D, Shankland M, Gaffield W, Weisblat DA (2003) A hedgehog homolog regulates gut formation in leech (Helobdella). Development 130:1645–1657

    Article  PubMed  CAS  Google Scholar 

  • Koonin EV (1995) A protein splice-junction motif in hedgehog family proteins. Trends Biochem Sci 20:141–142

    PubMed  CAS  Google Scholar 

  • Koufopanou V, Goddard MR, Burt A (2002) Adaptation for horizontal transfer in a homing endonuclease. Mol Biol Evol 19:239–246

    PubMed  CAS  Google Scholar 

  • Liu XQ (2000) Protein-splicing intein: genetic mobility, origin, and evolution. Annu Rev Genet 34:61–76

    Article  PubMed  CAS  Google Scholar 

  • Mann R, Beachy P (2004) Novel lipid modifications of secreted protein signals. Annu Rev Biochem 73:891–923

    Article  PubMed  CAS  Google Scholar 

  • Matsuzaki M, Misumi O, Shin IT, Maruyama S, Takahara M, Miyagishima SY, Mori T, Nishida K, Yagisawa F, Yoshida Y, Nishimura Y, Nakao S, Kobayashi T, Momoyama Y, Higashiyama T, Minoda A, Sano M, Nomoto H, Oishi K, Hayashi H, Ohta F, Nishizaka S, Haga S, Miura S, Morishita T, Kabeya Y, Terasawa K, Suzuki Y, Ishii Y, Asakawa S, Takano H, Ohta N, Kuroiwa H, Tanaka K, Shimizu N, Sugano S, Sato N, Nozaki H, Ogasawara N, Kohara Y, Kuroiwa T (2004) Genome sequence of the ultrasmall unicellular red alga Cyanidioschyzon merolae 10D. Nature 428:653–657

    Article  PubMed  CAS  Google Scholar 

  • Mills KV, Manning JS, Garcia AM, Wuerdeman LA (2004) Protein-splicing of a Pyrococcus abyssi intein with a C-terminal glutamine. J Biol Chem 279:20685–20691

    PubMed  CAS  Google Scholar 

  • Nederbragt AJ, van Loon AE, Dictus WJ (2002) Evolutionary biology: hedgehog crosses the snail’s midline. Nature 417:811–812

    Article  PubMed  CAS  Google Scholar 

  • Okuda Y, Sasaki D, Nogami S, Kaneko Y, Ohya Y, Anraku Y (2003) Occurrence, horizontal transfer and degeneration of VDE intein family in Saccharomycete yeasts. Yeast 20:563–573

    Article  PubMed  CAS  Google Scholar 

  • Paulus H (2000) Protein-splicing and related forms of protein autoprocessing. Annu Rev Biochem 69:447–496

    Article  PubMed  CAS  Google Scholar 

  • Perler FB (1999) A natural example of protein trans-splicing. Trends Biochem Sci 24:209–211

    Article  PubMed  CAS  Google Scholar 

  • Perler FB, Olsen GJ, Adam E (1997) Compilation and analysis of intein sequences. Nucleic Acids Res 25:1087–1093

    Article  PubMed  CAS  Google Scholar 

  • Pietrokovski S (1994) Conserved sequence features of inteins (protein introns) and their use in identifying new inteins and related proteins. Protein Sci 3:2340–2350

    Article  PubMed  CAS  Google Scholar 

  • Pietrokovski S (1998) Modular organization of inteins and C-terminal autocatalytic domains. Protein Sci 7:64–71

    PubMed  CAS  Google Scholar 

  • Pietrokovski S (2001) Intein spread and extinction in evolution. Trends Genet 17:465–472

    Article  PubMed  CAS  Google Scholar 

  • Porter JA, Ekker SC, Park WJ, von Kessler DP, Young KE, Chen CH, Ma Y, Woods AS, Cotter RJ, Koonin EV, Beachy PA (1996) Hedgehog patterning activity: role of a lipophilic modification mediated by the carboxy-terminal autoprocessing domain. Cell 86:21–34

    Article  PubMed  CAS  Google Scholar 

  • Romanelli A, Shekhtman A, Cowburn D, Muir TW (2004) Semisynthesis of a segmental isotopically labeled protein-splicing precursor: NMR evidence for an unusual peptide bond at the N-extein-intein junction. Proc Natl Acad Sci USA 101:6397–6402

    Article  PubMed  CAS  Google Scholar 

  • Saves I, Laneelle MA, Daffe M, Masson JM (2000) Inteins invading mycobacterial RecA proteins. FEBS Lett 480:221–225

    Article  PubMed  CAS  Google Scholar 

  • Shimeld S (1999) The evolution of the hedgehog gene family in chordates: insights from amphioxus hedgehog. Dev Genes Evol 209:40–47

    Article  PubMed  CAS  Google Scholar 

  • Shingledecker K, Jiang S-Q, Paulus H (1998) Molecular dissection of the Mycobacterium tuberculosis RecA intein: design of a minimal intein and of a trans-splicing system involving two intein fragments. Gene 207:187–195

    Article  PubMed  CAS  Google Scholar 

  • Southworth MW, Adam E, Panne D, Byer R, Kautz R, Perler FB (1998) Control of proteinsplicing by intein fragment reassembly. EMBO J 17:918–926

    Article  PubMed  CAS  Google Scholar 

  • Southworth MW, Benner J, Perler FB (2000) An alternative protein-splicing mechanism for inteins lacking an N-terminal nucleophile. EMBO J 19(18):5019–5026

    Article  PubMed  CAS  Google Scholar 

  • Sun W, Yang J, Liu X-Q (2004) Synthetic two-piece and three-piece split inteins for protein trans-splicing. J Biol Chem 279:35281–35286

    PubMed  CAS  Google Scholar 

  • Takatori N, Satou Y, Satoh N (2002) Expression of hedgehog genes in Ciona intestinalis embryos. Mech Dev 116:235–238

    Article  PubMed  CAS  Google Scholar 

  • Vigneron N, Stroobant V, Chapiro J, Ooms A, Degiovanni G, Morel S, van der Bruggen P, Boon T, van den Eynde B (2004) An antigenic peptide produced by peptide splicing in the proteasome. Science 304:587–590

    Article  PubMed  CAS  Google Scholar 

  • Waters E, Hohn MJ, Ahel I, Graham DE, Adams MD, Barnstead M, Beeson KY, Bibbs L, Bolanos R, Keller M, Kretz K, Lin X, Mathur E, Ni J, Podar M, Richardson T, Sutton GG, Simon M, Soll D, Stetter KO, Short JM, Noordewier M (2003) The genome of Nanoarchaeum equitans: insights into early archaeal evolution and derived parasitism. Proc Natl Acad Sci USA 100:12984–12988

    Article  PubMed  CAS  Google Scholar 

  • Wu H, Hu Z, Liu X-Q (1998) Protein trans-splicing by a split intein encoded in a split DnaE gene of Synechocystis sp. PCC6803. Proc Natl Acad Sci USA 95:9226–9231

    PubMed  CAS  Google Scholar 

  • Ziebuhr W, Ohlsen K, Karch H, Korhonen T, Hacker J (1999) Evolution of bacterial pathogenesis. Cell Mol Life Sci 56:719–728

    Article  PubMed  CAS  Google Scholar 

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Author information

Authors and Affiliations

  1. Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, 76100, Israel

    Bareket Dassa & Shmuel Pietrokovski

Authors
  1. Bareket Dassa
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  2. Shmuel Pietrokovski
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Editors and Affiliations

  1. Wadsworth Center/NYSDOH, Center for Medical Science, 150 New Scotland Ave, Albany, NY, 12208, USA

    Marlene Belfort  & Victoria Derbyshire  & 

  2. Dept. of Chemical Engineering, Princeton University, A417 Engineering Quadrangle, Princeton, NJ, 08544, USA

    David W. Wood

  3. Fred Hutchinson Cancer Research, Center Institute, 1100 Fairview Ave. N. Mailstop A3-023, Seattle, WA, 98109, USA

    Barry L. Stoddard

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© 2005 Springer-Verlag Berlin Heidelberg

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Dassa, B., Pietrokovski, S. (2005). Origin and Evolution of Inteins and Other Hint Domains. In: Belfort, M., Wood, D.W., Stoddard, B.L., Derbyshire, V. (eds) Homing Endonucleases and Inteins. Nucleic Acids and Molecular Biology, vol 16. Springer, Berlin, Heidelberg. https://doi.org/10.1007/3-540-29474-0_13

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