Jeffrey W. Touchman
- Genomics, Evolution, & Bioinformatics |
- Translational Genomics Research Institute (TGen) |
- Touchman Lab
Comparative Microbial Genomics
My lab conducts research in the area of comparative genomics, which can be described as the study of genomes from different organisms to understand what, at the molecular level, distinguishes different life forms from each other, how the overall structures of genes and genomes have evolved, and what these findings tell us about gene expression and regulation. A particular research focus involves comparative genomics of photosynthetic bacteria.
The process of photosynthesis has had profound global-scale effects on Earth; however, its origin and evolution remain enigmatic. Primary production by photosynthetic organisms supports nearly all ecosystems. Oxygen, one of the by-products of photosynthesis by cyanobacteria and their descendants (including algae and higher plants), transformed the Precambrian Earth and made possible the development of more complex organisms that use aerobic metabolism. Understanding how this complex process works at a molecular, cellular and ecosystem level, as well as how it originated and evolved, are fundamental problems that are essential to obtaining the deep understanding required to yield improvements in bioenergy, agriculture, and the environment.
We are sequencing and studying the complete genomes of several phototrophic microbial species as part of our our ongoing 'phototrophic genome project'. Currently, we are focusing our attention on the genomes of seven organisms. They were chosen for a variety of reasons, however, in each case the organism selected has one or more unique aspect surrounding their metabolism, physiology, or ecology that differs in fundamental ways from sequenced genomes of any other phototroph. Obtaining genome sequences for these organisms will thus significantly expand the available database on the genomes of anoxygenic photosynthetic bacteria, including two quite distinct heliobacteria, a group which is the least sampled of the five traditional phyla, three proteobacteria with very different physiologies and ecology from any others whose genomes have been sequenced, and a cyanobacterium with the ability to shift into anoxygenic photosynthesis in the presence of sulfide, a possible evolutionary “missing link” between anoxygenic and oxygenic photosynthetic organisms.
There are important linkages of this work to the field of Astrobiology as well. It is clear that oxygen will be a central biosignature sought in the atmospheric spectra of planets beyond our solar system. Understanding the prevalence of oxygenic photosynthesis and its potential for interplanetary promiscuity will be important in interpreting these signatures if they are ever found, particularly in stellar systems that might have terrestrial-type rocky planets that could be capable of exchanging rocky material. Phototrophic extremophiles (organisms living in unusually harsh and exotic environments) are excellent model microbes for hypothesis-driven studies of interplanetary photosynthetic exchange. The exogenous arrival of oxygenic photosynthesis on a planet would profoundly change the direction of biological evolution on its surface. Thus a detailed molecular understanding of how phototrophs can push the boundaries of extreme-environment existence on our own planet will fill important gaps in our current understanding of extra-terrestrial potential for oxygen-evolving photosynthesis.
Recent Selected Publications
Swingley W.D., Chen M, Cheung P.C., Conrad A.L., Dejesa L.C., Hao J., Honchak B.M., Karbach L.E, Kurdoglu A., Lahiri S., Mastrian S.D., Miyashita H., Page L., Ramakrishna P., Satoh S., Sattley W.M., Shimada Y., Taylor H.L., Tomo T., Tsuchiya T., Wang Z.T., Raymond J., Mimuro M., Blankenship R.E., and Touchman J.W. Niche adaptation and genome expansion in the chlorophyll d-producing cyanobacterium Acaryochloris marina. Proc Natl Acad Sci USA 105(6):2005-10 (2008)
Trent J.M. and Touchman J.W. The gene topography of cancer. Science 318(5853):1079-80. (2007)
Carpten J.D. et al. A transforming mutation in the pleckstrin homology domain of AKT1 in cancer. Nature 448:439-444. (2007)
Touchman J. W., Wagner D. M., Hao J., Mastrian S. D., Shah M. K., Vogler A. J., Allender C. J., Clark E. A., Benitez D. S., Youngkin D. J., Girard J. M., Auerbach R. K., Beckstrom-Sternberg S. M., and Keim P. A North American Yersinia pestis Draft Genome Sequence: SNPs and Phylogenetic Analysis. PLoS ONE 2:e220. (2007)
Swingley W.D., Gholba S., Mastrian S.D., Matthies H.J., Hao J., Ramos H., Acharya C.R., Conrad A.L., Taylor H.L., Dejesa L.C., Shah M.K., O’Huallachain M.E., Lince M.T., Blankenship R.E., Beatty J.T., and Touchman J.W. The complete genome sequence of Roseobacter denitrificans reveals a mixotrophic rather than photosynthetic metabolism. J Bacteriol 189:683-690. (2007)
Wang T., Xue G., and Touchman J.W. Modeling gene functional linkages with two-level simulated annealing. Int J Bioinformatics Res and Applications 3(2): 170-186. (2007)
Verrelli, B. C., S. A. Tishkoff, A. C. Stone and Touchman J.W.
Contrasting Histories of G6PD Molecular Evolution and Malarial Resistance in Humans and Chimpanzees. Mol Biol Evol 23(8): 1592-160.
(2006)