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Genome diversity, metagenomics and lateral gene transfer
Genome sequences have now been completed for more than 500 microbial genomes.
Perhaps one of the most surprising findings from the genomics era is the apparent extent of lateral gene transfer
in shaping microbial genomes, and the amount of genomic variability between even closely related strains of the same species.
In pursuing these issues, I have led the sequencing of more than twenty microbial genomes. Some of my groups' recent efforts
have focused on lateral gene transfer and niche adaptation in the marine cyanobacterium Synechococcus. In collaboration with
Dr. Brian Palenik at Scripps Institute of Oceanography we have sequenced four complete Synechococcus genomes,
and comparison of these genomes has identified a variety of novel genomic islands. Microarray expression analysis has been used
to investigate differences in gene regulation between these strains and to investigate functions of genes encoded within novel
islands, and comparative genome hybridization has been used to examine conservation of genomic islands amongst different isolates.
Recently, we have started to apply a targeted metagenomic approach, by undertaking 454 sequencing of the metagenomes of
Synechococcus cyanobacteria sorted from a complex community by flow cytometry and compare these data to the completed genomes
of strains previously isolated from these environments to gain a better insight into cyanobacterial genome diversity in the
"real world".
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Systems Biology analysis of membrane transport and metabolism
The deluge of genome data has lead to an ever increasing reliance on bioinformatic predictions, but the accuracy
of such predictions remains unclear. My group has been applying "high throughput" functional genomics to characterize the functional
of novel transport and metabolic genes, with the objectives of 1) validating the accuracy of our bioinformatics predictions,
and 2) developing a complete "systems biology" understanding of microbial physiology.
We have developed an annotation pipeline for automatically identifying and classifying membrane transporters
in sequenced genomes and have systematically analyzed every available complete genome. These analyses are available in our
relational database, TransportDB, which is publicly accessible at www.membranetransport.org. We have applied these analyses
to metabolic reconstruction to build models of the metabolic and transport networks for a variety of sequenced genomes.
My group has also been pursuing ways of validating such models through the use of gene knockouts and microarrays.
We have utilized Biolog Phenotype Microrrays to identify phenotypes of gene knockout mutants in a relatively high throughput fashion.
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Applying Genomics to Medicine
I have also been interested in utilizing genome sequence data for direct practical applications. One example has been
in using genomes for vaccine development using reverse vaccinology approaches: the bioinformatic identification of potential vaccine
candidates, followed by high throughput cloning, protein purification and screening offers an attractive approach for the rapid
development of vaccines or diagnostics. For instance, we have applied such an approach to vaccine development for the human and
animal pathogen Brucella suis in collaboration with Dr. Tom Ding at the Walter Reed Army Institute of Research.
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Selected Publications
1. Myers, G. S, Parker, D., Al-Hasani, K., Kennan, R. M., Seemann, T., Ren, Q., Badger, J. H., Selengut, J. D., Deboy, R. T., Tettelin, H., Boyce, J. D., McCarl, V. P., Han, X., Nelson, W. C., Madupu, R., Mohamoud, Y., Holley, T., Fedorova, N., Khouri, H., Bottomley, S. P., Whittington, R. J., Adler, B., Songer, J. G., Rood, J. I, and Paulsen, I. T. (2007) Genome sequence and identification of candidate vaccine antigens from the animal pathogen Dichelobacter nodosus. Nature Biotechnology 25:569-575.
2. Ren, Q., Chen, K., and Paulsen, I. T. (2007) TransportDB: a comprehensive database resource for cytoplasmic membrane transport systems and outer membrane channels. Nucleic Acids Research 35: D274-279.
3. Palenik, B., Ren, Q., Dupont, C. L., Myers, G. S., Heidelberg, J. F., Badger, J. H., Madupu, R., Nelson, W. C., Brinkac, L. M., Dodson, R. J., Durkin, A. S., Daugherty, S. C., Sullivan, S. A., Khouri, H., Mahamoud, Y., Halpin, R., and Paulsen, I. T. (2006) Genome sequence of Synechococcus CC9311: Insights into adaptation to a coastal environment. Proceedings of the National Academy of Sciences, USA 103: 13555-13559.
4. Myers, G. S. A, Rasko, D. A., Cheung, J., Ravel, J., Seshadri, R., DeBoy, R., Varga, J., Awad, M., Brinkac, L., Daugherty, S., Dodson, B., Madupu, R., Nelson, W., Rosovitz, M. J., Sullivan, S., Khouri, H., Dimitrov, G., Watkins, K., Mulligan, S., Benton, J., Fisher, D. J., Atkins, H. S., Hiscox, T., Jost, H., Billington, S., Songer, J. G., McClane, B. A., Titball, R. W., Rood, J. I., Melville, S., and Paulsen, I. T. (2006) Skewed distribution of genomic variability in strains of the toxigenic bacterial pathogen, Clostridium perfringens. Genome Research 16: 1031-1040.
5. Ding, X. Z., Paulsen, I. T., Bhattacharjee, A., Nikolich, M. P., Myers, G. and Hoover, D. L. (2006) A high efficiency cloning and expression system for proteomic analysis. Proteomics 6: 4038-4044.
6. Keseler, I. M., Collado-Vides, J., Gama-Castro, S., Ingraham, J., Paley, S., Paulsen, I. T., Peralta-Gil, M., and Karp, P. D. (2005) EcoCyc: a comprehensive database resource for Escherichia coli. Nucleic Acids Research 33: D334-337.
7. Paulsen, I. T., Press, C., Ravel, J., Kobayashi, D.Y., Myers, G.S.A., Mavrodi, D.V., DeBoy, R.T., Seshadri, R., Ren, Q., Madupu, R., Dodson, R.J., Durkin, A.S., Brinkac, L.M., Daugherty, S.C., Sullivan, S.A., Rosovitz, M.J., Gwinn, M.L., Zhou, L., Nelson, W.C., Weidman, J., Watkins, K., Tran, K., Khouri, H., Pierson, E.A., Pierson, L.S., III, Thomashow, L.S., and Loper, J.E. (2005) Complete genome sequence of the plant commensal Pseudomonas fluorescens Pf-5: insights into the biological control of plant disease. Nature Biotechnology 23: 873-878.
8. Ren, Q. and Paulsen, I. T. (2005) Comparative Analyses of Fundamental Differences in Membrane Transport Capabilities in Prokaryotes and Eukaryotes. PLOS Computational Biology 1: 190-201
9. Ren, Q., Kang, K., and Paulsen, I. T. TransportDB: a relational database of cellular membrane transport systems (2004) Nucleic Acids Research 32: 284-288.
10. Seshadri, R., Myers, G. S., Tettelin. H., Eisen, J. A., Heidelberg, J. F., Dodson, R. J., Davidsen, T. M., DeBoy, R. T., Fouts, D. E., Haft, D. H., Selengut, J., Ren, Q., Brinkac, L. M., Madupu, R., Kolonay, J., Durkin, S. A., Daugherty, S. C., Shetty, J., Shvartsbeyn, A., Gebregeorgis, E., Geer, K., Tsegaye, G., Malek, J., Ayodeji, B., Shatsman, S., McLeod, M. P., Smajs, D., Howell, J. K., Pal, S., Amin, A., Vashisth, P., McNeill, T. Z., Xiang, Q., Sodergren, E., Baca, E., Weinstock, G. M., Norris, S. J., Fraser, C. M., and Paulsen, I. T. (2004) Comparison of the genome of the oral pathogen Treponema denticola with other spirochete genomes. Proceedings of the National Academy of Sciences, USA 101: 5646-5651.
11. Venter, J. C., Remington, K., Heidelberg, J. F., Halpern, A. L., Rusch, D., Eisen, J. A., Wu, D., Paulsen, I., Nelson, K. E., Nelson, W., Fouts, D. E., Levy, S., Knap, A. H., Lomas, M. W., Nealson, K., White, O., Peterson, J., Hoffman, J., Parsons, R., Baden-Tillson, H., Pfannkoch, C., Rogers, Y. H., and Smith, H. O. (2004). Environmental genome shotgun sequencing of the Sargasso Sea. Science 304: 66-74.
12. Paulsen, I. T., Banerjei, L., Myers, G. S., Nelson, K. E., Seshadri, R., Read, T. D., Fouts, D. E., Eisen, J. A., Gill, S. R., Heidelberg, J. F., Tettelin, H., Dodson, R. J., Umayam, L., Brinkac, L., Beanan, M., Daugherty, S., DeBoy, R. T., Durkin, S., Kolonay, J., Madupu, R., Nelson, W., Vamathevan, J., Tran, B., Upton, J., Hansen, T., Shetty, J., Khouri, H., Utterback, T., Radune, D., Ketchum, K. A., Dougherty, B. A., and Fraser, C. M. Role of mobile DNA in the evolution of vancomycin-resistant Enterococcus faecalis. (2003) Science 299: 2071-2074.
13. Paulsen, I. T. (2003) Multidrug efflux pumps and resistance: regulation and evolution. Current Opinion in Microbiology 6: 446-451.
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