Gary J. Olsen
Professor, Microbiology and Institute for Genomic Biology
University of Illinois
601 South Goodwin Avenue M/C 110
Urbana, IL 61801
- B.S. (Physics), University of California, Los Angeles, 1975
- M.S. (Physics), University of California, Los Angeles, 1976
- Ph.D. (Biophysics), University of Colorado Health Sciences Center, 1983
- Postdoctoral (Molecular and Cellular Biology), National Jewish Hospital and Research Center, 1983-1984
- Postdoctoral (Biology), Indiana University, 1984-1985
- Assistant Scientist (Biology), Indiana University, 1985-1988
Our research focuses on gene expression in Archaea, and its relation to corresponding systems in Eucarya and Bacteria. Our approach is a combination of experimental work and comparative analyses of genomes and proteins. Current emphasis is on the machineries of DNA repair, RNA synthesis and protein synthesis. Each of these areas is briefly outlined below.
DNA repair. Many Archaea are extreme thermophiles, suggesting that their DNA will be subject to high levels of chemical damage. To compensate, there must be very active DNA repair machineries. Archaeal genome sequences have revealed a number genes that are likely to be involved in DNA repair, though other familiar enzymes seem to be highly modified or absent. We are studying two proteins distantly related to bacterial RecA. One of these proteins, RadA, is particularly similar to the yeast DNA repair proteins RAD51 and DCM1, and is likely to be their homologue. Biochemical characterizations further support this conclusion. We are also attempting to crystallize this protein for X-ray crystallographic analyses.
RNA synthetic machineries. Transcription in Archaea is much more like that observed in Eucarya, than that seen in Bacteria. Promoter selection requires proteins related to eukaryotic TATA-binding protein and transcription factor IIB. The ternary complex of DNA plus these two proteins then recruits an RNA polymerase with as many as 15 subunits, nearly all of which clearly correspond to specific homologues in RNA polymerase II of eukaryotes. Some specific areas of study include the interactions of the transcription initiation factors with promoters and with other cellular proteins (e.g., regulatory proteins), and the interactions among RNA polymerase subunits. This latter work will help to defined an assembly pathway for RNA polymerase and its overall 3-dimensional structure.
Protein synthetic machineries. Protein synthesis in Archaea is also very similar to that observed in Eucarya. Most ribosomal proteins, translation factors and amino acyl-tRNA synthetases are most similar to their eukaryotic counterparts. Another interesting facet of the archaeal translation apparatus is the large number of posttranslational modifications to the tRNAs and rRNAs, especially among thermophilic Archaea. We are using a combined computational and experimental approach to finding novel RNA methylase genes in Methanococcus jannaschii that are responsible for posttranslational modifications to the tRNAs.
Genome analysis. We are analyzing genomic DNA sequences from a number of organisms, especially members of the Archaea. In collaboration with the laboratory of Carl Woese and The Institute for Genomic Research (TIGR), we participated in the complete genome sequencing of Methanococcus jannaschii (a hyperthermophilic methanogen) and Archaeoglobus fulgidus (a hyperthermophilic, sulfate-reducing archaeon). In collaboration with R. V. Swanson (Diversa Corp.), we participated in the analysis of the Aquifex aeolicus genome sequence. In a collaboration with M. L. Sogin (Woods Hole Marine Biology Laboratory) and other groups, we are currently analyzing the genome of Giardia lamblia (a deeply branching eukaryote).
- Aziz, R., Bartels, D., Best, A., DeJongh, M., Disz, T., Edwards, R., Formsma, K., Gerdes, S., Glass, E., Kubal, M., Meyer, F., Olsen, G. J., Olson, R., Osterman, A., Overbeek, R., McNeil, L., Paarmann, D., Paczian, T., Parrello, B., Pusch, G. D., Reich, C., Stevens, R., Vassieva, O., Vonstein, V., Wilke, A., and Zagnitko, O. 2008. The RAST Server: Rapid Annotations using Subsystems Technology. BMC Genomics 9: 75. [Abstract; Full Text]
- Davis, J. J., and Olsen, G. J. 2010. Modal codon usage: Assessing the typical codon usage of a genome. Mol. Biol. Evol. 27: 800–810. [Abstract; Full Text]
- Davis, J. J., and Olsen, G. J. 2011. Characterizing the native codon usages of a genome: An axis projection approach. Mol. Biol. Evol. 28: 211–221. [Abstract; Full Text]
- Frank, J. A., Reich, C. I., Sharma, S., Weisbaum, J. S., Wilson, B. A., and Olsen, G. J. 2008. Critical evaluation of two commonly-used primers for amplification of bacterial 16S rRNA genes. Appl. Environ. Microbiol. 74: 2461–2470. [Abstract; Full Text]
- Karberg, K. A., Olsen, G. J., and Davis, J. J. 2011. Similarity of strain-specific genes horizontally acquired by Escherichia coli and Salmonella enterica. Proc. Natl. Acad. Sci. USA 108: 20154-20159. [Abstract; Full Text]
- Kim, T. K., Thomas, S. M., Ho, M., Sharma, S., Reich, C. I., Frank, J. A., Yeater, K. M., Biggs, D., Nakamura, N., Stumpf, R., Leigh, S. R., Tapping, R. I., Blanke, S. R., Slauch, J. M., Gaskins, H. R., Weisbaum, J. S., Olsen, G. J., Hoyer, L. L., and Wilson, B. A. 2009. Heterogeneity of vaginal bacterial communities within individuals. J. Clin. Microbiol. 47: 1181–1189. [Abstract; Full Text]
- Li, E., Reich, C. I., and Olsen, G. J. 2008. A whole-genome approach to identifying protein binding sites: Promoters in Methanocaldococcus (Methanococcus) jannaschii. Nucleic Acids Res. 36: 6948–6958. [Abstract; Full Text]
- Morrison, H. G., McArthur, A. G., Gillin, F. D., Aley, S. B., Adam, R. D., Olsen, G. J., Reiner, D. S., Svard, S. G., Elmendorf, H. G., Hehl, A. B., Samuelson, J., Nixon, J. E. J., Passamaneck, N. E., Kim, U. U., Lasek-Nesselquist, E., Cipriano, M. J., Holder, M. E., Huse, S. M., Palm, D., Best, A. A., Reich, C. I., Manning, G., Nigam, A., Prabhu, A., Davids, B. J., and Sogin, M. L. 2007. Genomic minimalism in the early diverging, intestinal parasite, Giardia lamblia. Science 317: 1921–1926. [Abstract]
- Zhang, J., and Olsen, G. J. 2009. Messenger RNA processing in Methanocaldococcus (Methanococcus) jannaschii. RNA 15: 1909–1916. [Abstract; Full Text)
- Zhang, J., Li, E., and Olsen, G. J. 2009. Protein-coding gene promoters in Methanocaldococcus (Methanococcus) jannaschii. Nucleic Acids Res. 37: 3588–3601. [Abstract; Full Text]