Functional-genomics-based identification and characterization of open reading frames encoding α-glucoside-processing enzymes in the hyperthermophilic archaeon Pyrococcus furiosus

Applied and Environmental Microbiology

Volumn 74, Issue 4, 2008, Pages 1281-1283

  Comfort, Donald A ^a,b   Chou, Chung Jung ^a   Conners, Shannon B ^a,c   VanFossen, Amy L ^a   Kelly, Robert M ^a  

^a North Carolina State University   (United States)

^b PFIZER INC   (United States)

^c SAS INSTITUTE INC   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

GLUCANS; TRANSCRIPTIONAL RESPONSE;

AMINO ACIDS; BIOINFORMATICS; GENE ENCODING; GROWTH KINETICS; TRANSCRIPTION;

BACTERIA;

BETA AMYLASE; BINDING PROTEIN; GLUCOSIDE; GLYCOSIDASE; OLIGO 1,6 GLUCOSIDASE; STARCH BINDING PROTEIN; UNCLASSIFIED DRUG;

ENZYME; ENZYME ACTIVITY; GENOMICS; IDENTIFICATION METHOD; THERMOPHILIC BACTERIUM;

AMINO ACID SEQUENCE; ARTICLE; BACTERIAL GENE; BACTERIAL GENOME; BACTERIAL GROWTH; BIOINFORMATICS; ENZYME ANALYSIS; GENETIC TRANSCRIPTION; GENOMICS; HUMAN; MULTIGENE FAMILY; OPEN READING FRAME; PYROCOCCUS FURIOSUS;

ALPHA-GLUCOSIDASES; BETA-AMYLASE; COMPUTATIONAL BIOLOGY; GENE EXPRESSION REGULATION, BACTERIAL; GENOMICS; OPEN READING FRAMES; PYROCOCCUS FURIOSUS;

ARCHAEA; PYROCOCCUS FURIOSUS;

EID: 39649089570     PISSN: 00992240     EISSN: None     Source Type: Journal    
DOI: 10.1128/AEM.01920-07     Document Type: Article

References (17)

1. Costantino, H. R., S. H. Brown, and R. M. Kelly. 1990. Purification and characterization of an α-glucosidase from a hyperthermophilic archaebacterium, Pyrococcus furiosus, exhibiting a temperature optimum of 105 to 115°C. J. Bacteriol. 172:3654-3660.
2. Crabb, W. D., and J. K. Shetty. 1999. Commodity scale production of sugars from starches. Curr. Opin. Microbiol. 2:252-256.
3. Dong, G., C. Vieille, and J. G. Zeikus. 1997. Cloning, sequencing, and expression of the gene encoding amylopullulanase from Pyrococcus furiosus and biochemical characterization of the recombinant enzyme. Appl. Environ. Microbiol. 63:3577-3584.
4. Ermolaeva, M. D., O. White, and S. L. Salzberg. 2001. Prediction of operons in microbial genomes. Nucleic Acids Res. 29:1216-1221.
5. Fiala, G., and K. O. Stetter. 1986. Pyrococcus furiosus sp. nov. represents a novel genus of marine heterotrophic archaebacteria growing optimally at 100 degrees C. Arch. Microbiol. 145:56-61.
6. Gerdes, K., S. K. Christensen, and A. Lobner-Olesen. 2005. Prokaryotic toxin-antitoxin stress response loci. Nat. Rev. Microbiol. 3:371-382.
7. Henrissat, B., and G. Davies. 1997. Structural and sequence-based classification of glycoside hydrolases. Curr. Opin. Struct. Biol. 7:637-644.
8. Lee, H.-S., K. R. Shockley, G. J. Schut, S. B. Conners, C. I. Montero, M. R. Johnson, C.-J. Chou, S. L. Bridger, N. Wigner, S. D. Brehm, F. E. Jenney, Jr., D. A. Comfort, R. M. Kelly, and M. W. W. Adams. 2006. Transcriptional and biochemical analysis of starch metabolism in the hyperthermophilic archaeon Pyrococcus furiosus. J. Bacteriol. 188:2115-2125.
9. Marchler-Bauer, A., J. B. Anderson, P. F. Cherukuri, C. DeWeese-Scott, L. Y. Geer, M. Gwadz, S. Q. He, D. I. Hurwitz, J. D. Jackson, Z. X. Ke, C. J. Lanczycki, C. A. Liebert, C. L. Liu, F. Lu, G. H. Marchler, M. Mullokandov, B. A. Shoemaker, V. Simonyan, J. S. Song, P. A. Thiessen, R. A. Yamashita, J. J. Yin, D. C. Zhang, and S. H. Bryant. 2005. CDD: a conserved domain database for protein classification. Nucleic Acids Res. 33:D192-D196.
10. Pfaffl, M. W. 2001. A new mathematical model for relative quantification in real-time RT-PCR. Nucleic Acids Res. 29:e45.
11. Rashid, N., J. Cornista, S. Ezaki, T. Fukui, H. Atomi, and T. Imanaka. 2002. Characterization of an archaeal cyclodextrin glucanotransferase with a novel C-terminal domain. J. Bacteriol. 184:777-784.
12. Schultz, J., F. Milpetz, P. Bork, and C. P. Ponting. 1998. SMART, a simple modular architecture research tool: identification of signaling domains. Proc. Natl. Acad. Sci. USA 95:5857-5864.
13. Shockley, K. R., D. E. Ward, S. R. Chhabra, S. B. Conners, C. I. Montero, and R. M. Kelly. 2003. Heat shock response by the hyperthermophilic archaeon Pyrococcus furiosus. Appl. Environ. Microbiol. 69:2365-2371.
14. Sonnhammer, E. L. L., S. R. Eddy, and R. Durbin. 1997. Pfam: a comprehensive database of protein domain families based on seed alignments. Proteins 28:405-420.
15. Tachdjian, S., and R. M. Kelly. 2006. Dynamic metabolic adjustments and genome plasticity are implicated in the heat shock response of the extremely thermoacidophilic archaeon Sulfolobus solfataricus. J. Bacteriol. 188:4553-4559.
16. Wolfinger, R. D., G. Gibson, E. D. Wolfinger, L. Bennett, H. Hamadeh, P. Bushel, C. Afshari, and R. S. Paules. 2001. Assessing gene significance from cDNA microarray expression data via mixed models. J. Comput. Biol. 8:625-637.
17. Zona, R., F. Chang-Pi-Hin, M. J. O'Donohue, and S. Janecek. 2004. Bioinformatics of the glycoside hydrolase family 57 and identification of catalytic residues in amylopullulanase from Thermococcus hydrothermalis. Eur. J. Biochem. 271:2863-2872.