The intein of the Thermoplasma A-ATPase A subunit: Structure, evolution and expression in E. coli

BMC Biochemistry

Volumn 2, Issue , 2001, Pages 1-10

  Senejani, Alireza G ^a   Hilario, Elena ^b   Gogarten, J Peter ^a  

^a UNIVERSITY OF CONNECTICUT   (United States)

^b THE NEW ZEALAND INSTITUTE FOR PLANT AND FOOD RESEARCH LIMITED   (New Zealand)

Author keywords

[No Author keywords available]

Indexed keywords

ADENOSINE TRIPHOSPHATASE; AMINO ACID; ENDONUCLEASE; INTEIN; TRANSFER RNA; VANILMANDELIC ACID;

ARTICLE; BACTERIAL GENOME; CODON; CONTROLLED STUDY; ENZYME ACTIVE SITE; ENZYME STRUCTURE; ESCHERICHIA COLI; GENE FREQUENCY; GENE IDENTIFICATION; GENE INSERTION; GENETIC CODE; MOLECULAR EVOLUTION; NONHUMAN; PROTEIN DOMAIN; PROTEIN EXPRESSION; PYROCOCCUS; PYROCOCCUS ABYSSI; PYROCOCCUS FURIOSUS; PYROCOCCUS HORIKOSHII; SACCHAROMYCES CEREVISIAE; SEQUENCE HOMOLOGY; THERMOPLASMA ACIDOPHILUM;

BACTERIA (MICROORGANISMS); ESCHERICHIA COLI; INSERTION SEQUENCES; PYROCOCCUS; PYROCOCCUS ABYSSI; PYROCOCCUS FURIOSUS; PYROCOCCUS HORIKOSHII; SACCHAROMYCES; SACCHAROMYCES CEREVISIAE; THERMOPLASMA; THERMOPLASMA ACIDOPHILUM;

EID: 3042813413     PISSN: 14712091     EISSN: None     Source Type: Journal    
DOI: 10.1186/1471-2091-2-13     Document Type: Article

References (48)

1. Liu XQ: Protein-splicing intein: Genetic mobility, origin, and evolution. Annu Rev Genet 2000, 34:61-76
2. Paulus H: Protein splicing and related forms of protein auto-processing. Annu Rev Biochem 2000, 69:447-496
3. Dujon B: Group I introns as mobile genetic elements: facts and mechanistic speculations - a review. Gene 1989, 82:91-114
4. Perler FB, Davis EO, Dean GE, Gimble FS, Jack WE, Neff N, Noren CJ, Thorner J, Belfort M: Protein splicing elements: inteins and exteins - a definition of terms and recommended nomenclature. Nucleic Acids Res 1994, 22:1125-1127
5. Cooper AA, Stevens TH: Protein splicing: self-splicing of genetically mobile elements at the protein level. Trends Biochem Sci 1995, 20:351-356
6. Hirata R, Ohsumk Y, Nakano A, Kawasaki H, Suzuki K, Anraku Y: Molecular structure of a gene, VMAI, encoding the catalytic subunit of H(+)-translocating adenosine triphosphatase from vacuolar membranes of Saccharomyces cerevisiae. J Biol Chem 1990, 265:6726-6733
7. Kane PM, Yamashiro CT, Wolczyk DF, Neff N, Goebl M, Stevens TH: Protein splicing converts the yeast TFPI gene product to the 69-kD subunit of the vacuolar H(+)-adenosine triphosphatase. Science 1990, 250:651-657
8. Chen L, Benner J, Perler FB: Protein splicing in the absence of an intein penultimate histidine. J Biol Chem 2000
9. Pietrokovski S: Intein spread and extinction in evolution. Trends Genet 2001, 17:465-472
10. Pietrokovski S: Modular organization of inteins and C-terminal autocatalytic domains. Protein Sci 1998, 7:64-71
11. Perler FB, Olsen GJ, Adam E: Compilation and analysis of intein sequences. Nucleic Acids Res 1997, 25:1087-1093
12. Dalgaard JZ, Moser MJ, Hughey R, Mian IS: Statistical modeling, phylogenetic analysis and structure prediction of a protein splicing domain common to inteins and hedgehog proteins. J Comput Biol 1997, 4:193-214
13. Duan X, Gimble FS, Quiocho FA: Crystal structure of PI-Scel, a homing endonuclease with protein splicing activity. Cell 1997, 89:555-564
14. Gimble FS, Thorner J: Homing of a DNA endonuclease gene by meiotic gene conversion in Saccharomyces cerevisiae. Nature 1992, 357:301-306
15. Chong S, Xu MQ: Protein splicing of the Saccharomyces cerevisiae VMA intein without the endonuclease motifs. J Biol Chem 1997, 272:15587-15590
16. Derbyshire V, Wood DW, Wu W, Dansereau JT, Dalgaard JZ, Belfort M: Genetic definition of a protein-splicing domain: functional mini-inteins support structure predictions and a model for intein evolution [published erratum appears in Proc Natl Acad Sci USA 1998 Jan 20;95(2):762]. Proc Natl Acad Sci U S A 1997, 94:11466-11471
17. Derbyshire V, Wood DW, Wu W, Dansereau JT, Dalgaard JZ, Belfort M: Genetic definition of a protein-splicing domain: functional mini-inteins support structure predictions and a model for intein evolution [published erratum appears in Proc Natl Acad Sci USA 1998 Jan 20;95(2):762]. Proc Natl Acad Sci U S A 1997, 94:11466-11471
18. Jurica MS, Stoddard BL: Homing endonucleases: structure, function and evolution. Cell Mol Life Sci 1999, 55:1304-1326
19. Perler FB: InBase, the Intein Database. Nucleic Acids Res 2000, 28:344-345
20. Searcy DG, Stein DB, Green GR: Phylogenetic affinities between eukaryotic cells and a thermophilic mycoplasma. Biosystems 1978, 10:19-28
21. Darland G, Brock TD, Samsonoff W, Conti SF: A thermophilic, acidophilic mycoplasma isolated from a coal refuse pile. Science 1970, 170:1416-1418
22. Searcy DG: Thermoplasma acidophilum: intracellular pH and potassium concentration. Biochim Biophys Acta 1976, 451:278-286
23. Gogarten JP, Starke T, Kibak H, Fishman J, Taiz L: Evolution and isoforms of V-ATPase subunits. J Exp Biol 1992, 172:137-147
24. Gu HH, Xu J, Gallagher M, Dean GE: Peptide splicing in the vacuolar ATPase subunit A from Candida tropicalis. J Biol Chem 1993, 268:7372-7381
25. Hilario E: The vacuolar H+-ATPase from Giardia lamblia: a potential model for the study of the evolution of the first eukaryotes. University of Connecticut, Storrs, CT 1998
26. Ruepp A, Graml W, Santos-Martinez ML, Koretke KK, Volker C, Mewes HW, Frishman D, Stocker S, Lupas AN, Baumeister W: The genome sequence of the thermoacidophilic scavenger Thermoplasma acidophilum. Nature 2000, 407:508-513
27. Kawashima T, Amano N, Koike H, Makino S, Higuchi S, Kawashima-Ohya Y, Watanabe K, Yamazaki M, Kanehori K, Kawamoto T, Nunoshiba T, Yamamoto Y, Aramaki H, Makino K, Suzuki M: Archaeal adaptation to higher temperatures revealed by genomic sequence of Thermoplasma volcanium. Proc Natl Acad Sci USA 2000, 97:14257-14262
28. Schaffer AA, Aravind L, Madden TL, Shavirin S, Spouge JL, Wolf YI, Koonin EV, Altschul SF: Improving the accuracy of PSI-BLAST protein database searches with composition-based statistics and other refinements. Nucleic Acids Res 2001, 29:2994-3005
29. Pietrokovski S: Conserved sequence features of inteins (protein introns) and their use in identifying new inteins and related proteins. Protein Sci 1994, 3:2340-2350
30. Pearson WR: Empirical statistical estimates for sequence similarity searches. J Mol Biol 1998, 276:71-84
31. Abrahams JP, Leslie AG, Lutter R, Walker JE: Structure at 2.8 A resolution of F1-ATPase from bovine heart mitochondria. Nature 1994, 370:621-628
32. Makrides SC: Strategies for achieving high-level expression of genes in Escherichia coli. Microbiol Rev 1996, 60:512-538
33. Zimniak L, Dittrich P, Gogarten JP, Kibak H, Taiz L: The cDNA sequence of the 69-kDa subunit of the carrot vacuolar H+- AT-Pase. Homology to the beta-chain of F0F1-ATPases. J Biol Chem 1988, 263:9102-9112
34. Padan E, Zilberstein D, Rottenberg H: The proton electrochemical gradient in Escherichia coli cells. Eur J Biochem 1976, 63:533-541
35. Doolittle WF: Lateral genomics. Trends Cell Biol 1999, 9:M5-8
36. Gogarten JP, Olendzenski L: Orthologs, paralogs and genome comparisons. Curr Opin Genet Dev 1999, 9:630-636
37. Lawrence JG: Gene transfer, speciation, and the evolution of bacterial genomes. Curr Opin Microbiol 1999, 2:519-523
38. Olendzenski L, Liu L, Zhaxybayeva O, Murphey R, Shin DG, Gogarten JP: Horizontal transfer of archaeal genes into the deinococcaceae: detection by molecular and computer-based approaches. J Mol Evol 2000, 51:587-599
39. Goddard MR, Burt A: Recurrent invasion and extinction of a selfish gene. Proc Natl Acad Sci USA 1999, 96:13880-13885
40. Searcy DG: Thermophiles: Culture of Thermoplasma acidophilum. Amherst, MA: Biology Dept., Univ. of Massachusetts, available through the author 1993
41. Sambrook J, Fritsch EF, Maniatis T: Molecular Cloning: A Laboratory Manual, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 1989
42. Ausubel FM, Brent R, Kingston RE, Moore DD, Seidman JG, Smith JA, Struhl K: Current Protocols in Molecular Biology. John Wiley and Sons Inc 2000
43. Schagger H, von Jagow G: Tricine-sodium dodecyl sulfate-polyacrylamide gel electrophoresis for the separation of proteins in the range from 1 to 100 kDa. Anal Biochem 1987, 166:368-379
44. Nakamura Y, Gojobori T, Ikemura T: Codon usage tabulated from international DNA sequence databases: status for the year 2000. Nucleic Acids Res 2000, 28:292
45. Maidak BL, Cole JR, Lilburn TG, Parker CT Jr, Saxman PR, Farris RJ, Garrity GM, Olsen GJ, Schmidt TM, Tiedje JM: The RDP-II (Ribosomal Database Project). Nucleic Acids Res 2001, 29:173-174
46. Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG: The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 1997, 25:4876-4882
47. Strimmer K, von Haeseler A: Quartet puzzling: A quartet maximum-likelihood method for reconstructing tree topologies. Molecular Biology and Evolution 1996964-969
48. Swofford D: PAUP* 4.0 beta version, Phylogenetic Analysis Using Parsimony (and Other Methods): Sinauer Associates, Inc., Sunderland, MA, USA 1998