This Article
Right arrow Full Text
Right arrow Full Text (PDF)
Right arrow Supplemental material
Right arrow Alert me when this article is cited
Right arrow Alert me if a correction is posted
Services
Right arrow Similar articles in this journal
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Download to citation manager
Right arrowReprints and Permissions
Right arrow Copyright Information
Right arrow Books from ASM Press
Right arrow MicrobeWorld
Citing Articles
Right arrow Citing Articles via HighWire
Right arrow Citing Articles via Google Scholar
Google Scholar
Right arrow Articles by Poole, F. L.
Right arrow Articles by Adams, M. W. W.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Poole, F. L., II
Right arrow Articles by Adams, M. W. W.

 Previous Article  |  Next Article 

Journal of Bacteriology, November 2005, p. 7325-7332, Vol. 187, No. 21
0021-9193/05/$08.00+0     doi:10.1128/JB.187.21.7325-7332.2005
Copyright © 2005, American Society for Microbiology. All Rights Reserved.

Defining Genes in the Genome of the Hyperthermophilic Archaeon Pyrococcus furiosus: Implications for All Microbial Genomes{dagger}

Farris L. Poole II, Brian A. Gerwe, Robert C. Hopkins, Gerrit J. Schut, Michael V. Weinberg, Francis E. Jenney Jr., and Michael W. W. Adams*

Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia 30602-7229

Received 16 May 2005/ Accepted 19 August 2005

The original genome annotation of the hyperthermophilic archaeon Pyrococcus furiosus contained 2,065 open reading frames (ORFs). The genome was subsequently automatically annotated in two public databases by the Institute for Genomic Research (TIGR) and the National Center for Biotechnology Information (NCBI). Remarkably, more than 500 of the originally annotated ORFs differ in size in the two databases, many very significantly. For example, more than 170 of the predicted proteins differ at their N termini by more than 25 amino acids. Similar discrepancies were observed in the TIGR and NCBI databases with the other archaeal and bacterial genomes examined. In addition, the two databases contain 60 (NCBI) and 221 (TIGR) ORFs not present in the original annotation of P. furiosus. In the present study we have experimentally assessed the validity of 88 previously unannotated ORFs. Transcriptional analyses showed that 11 of 61 ORFs examined were expressed in P. furiosus when grown at either 95 or 72°C. In addition, 7 of 54 ORFs examined yielded heat-stable recombinant proteins when they were expressed in Escherichia coli, although only one of the seven ORFs was expressed in P. furiosus under the growth conditions tested. It is concluded that the P. furiosus genome contains at least 17 ORFs not previously recognized in the original annotation. This study serves to highlight the discrepancies in the public databases and the problems of accurately defining the number and sizes of ORFs within any microbial genome.

* Corresponding author. Mailing address: Department of Biochemistry and Molecular Biol., Davison Life Sciences Complex, University of Georgia, Athens, GA 30602-7229. Phone: 706 542-2060. Fax: 706 542-0229. E-mail: adams{at}bmb.uga.edu.

{dagger} Supplemental material for this article may be found at http://jb.asm.org/.

Journal of Bacteriology, November 2005, p. 7325-7332, Vol. 187, No. 21
0021-9193/05/$08.00+0     doi:10.1128/JB.187.21.7325-7332.2005
Copyright © 2005, American Society for Microbiology. All Rights Reserved.



This article has been cited by other articles:

  • Menon, A. L., Poole, F. L. II, Cvetkovic, A., Trauger, S. A., Kalisiak, E., Scott, J. W., Shanmukh, S., Praissman, J., Jenney, F. E. Jr., Wikoff, W. R., Apon, J. V., Siuzdak, G., Adams, M. W. W. (2009). Novel Multiprotein Complexes Identified in the Hyperthermophilic Archaeon Pyrococcus furiosus by Non-denaturing Fractionation of the Native Proteome. Mol. Cell. Proteomics 8: 735-751 [Abstract] [Full Text]  
  • Santangelo, T. J., Cubonova, L., Reeve, J. N. (2008). Shuttle Vector Expression in Thermococcus kodakaraensis: Contributions of cis Elements to Protein Synthesis in a Hyperthermophilic Archaeon. Appl. Environ. Microbiol. 74: 3099-3104 [Abstract] [Full Text]  
  • Hu, G.-Q., Zheng, X., Yang, Y.-F., Ortet, P., She, Z.-S., Zhu, H. (2008). ProTISA: a comprehensive resource for translation initiation site annotation in prokaryotic genomes. Nucleic Acids Res 36: D114-D119 [Abstract] [Full Text]  
  • Schut, G. J., Bridger, S. L., Adams, M. W. W. (2007). Insights into the Metabolism of Elemental Sulfur by the Hyperthermophilic Archaeon Pyrococcus furiosus: Characterization of a Coenzyme A- Dependent NAD(P)H Sulfur Oxidoreductase. J. Bacteriol. 189: 4431-4441 [Abstract] [Full Text]  
  • Delcher, A. L., Bratke, K. A., Powers, E. C., Salzberg, S. L. (2007). Identifying bacterial genes and endosymbiont DNA with Glimmer. Bioinformatics 23: 673-679 [Abstract] [Full Text]  
  • Tran, T. T., Dam, P., Su, Z., Poole, F. L. II, Adams, M. W. W., Zhou, G. T., Xu, Y. (2007). Operon prediction in Pyrococcus furiosus. Nucleic Acids Res 35: 11-20 [Abstract] [Full Text]  
  • White, R. H. (2006). The difficult road from sequence to function.. J. Bacteriol. 188: 3431-3432 [Full Text]  


Copyright © 2009 by the American Society for Microbiology.   For an alternate route to Journals.ASM.org, visit: http://intl-journals.asm.org | More Info»