Kenneth E. Rudd

Associate Professor of Biochemistry and Molecular Biology

Ph.D. (1981) University of California at Berkeley

Bacterial Genetics, Bioinformatics, Functional Genomics, Small Proteins in E. coli

Tel: (305) 243-6055, Fax: (305) 243-3065

krudd@miami.edu

Our laboratory is engaged in the functional characterization of a selected set of genes and gene products of Escherichia coli. The 4.6 Mb genome of E. coli is now completely sequenced and contains over 4100 protein-encoding genes. Less than half of these genes have been functionally characterized. Most protein sequences can be organized into families based upon homologous relationships. Paralogous families have multiple members encoded in the E. coli genome; orthologous families have only one member in E. coli, but genes of similar function, orthologs, exist in other species. Some families are restricted to the bacterial domain of life whereas others contain Ancient Conserved Regions (ACRs) and are present in both bacteria and eucaryotes, including some human genes. Cloistered paralogous families do not have homologs in any other organisms, but do have homologs (paralogs) within E. coli. Loner proteins do not appear to have any homologs whatsoever, apparently having drifted far away from their ancestor proteins. All of the protein sequences derived from the E. coli genome are being organized into classes based upon types of homologous family relationships and functional predictions that can be associated with a family.

Our characterization of E. coli ORFs of unknown biological function is directed at selected proteins that fall into the different categories of homologous relationships. In some cases, a functional prediction can be made based on functions attributed to homologs in E. coli or other species. Sometimes, the functional prediction is limited to a general activity associated with a common protein motif. In other cases, no functions are attributed to any member of the homologous family, even though the family might be quite widespread in nature. Our approach includes determining the phenotype associated with mutations in the genes of interest as well as localizing, cloning, overproducing and purifying the proteins of interest. We are particularly interested in proteins of less than 150 amino acids in length as they are among the most difficult to analyze using bioinformatic approaches alone. Some of the proteins we are characterizing have predicted functions that include protein phosphorylation, nucleotide binding, protein-protein interactions, and protease activity. Other proteins have no function predicted, but appear to be soluble proteins with signal peptides that would localize them to the periplasm. We hope that this selective top-down approach to functional genomics will illuminate important new functions, not just in E. coli, but in organisms with related proteins as well.

The EcoGene database of sequences and annotations for all E. coli genes is available on a website:

http://bmb.med.miami.edu/EcoGene/EcoWeb

Representative Publications

1.    Horiuchi T, Keseler IM, Kosuge T, Mori H, Perna NT, Plunkett G 3rd, Rudd KE, Serres MH, Thomas GH, Thomson NR, Wishart D, Wanner BL, Escherichia coli K-12: a cooperatively developed annotation snapshot—2005, Nucleic Acids Res., 34:1-9, 2006

2.    Basturea G.N., Rudd K.E., Deutscher M.P., Identification and characterization of RsmE, the founding member of a new RNA base methyltransferase family, RNA, 12:426-434, 2006

3.    Gonnet, P., Rudd, K.E., and Lisacek, F., Fine-tuning the prediction if sequences cleaved by signal peptidase II: a curated set of proven and predicted lipoproteins of E. coli K-12, Proteomics, 4:1597-1613, 2004

4.    Shultzaberger, R.K., Bucheimer, R.E., Rudd, K.E., and Schneider, T.D., Anatomy of Escherichia coli ribosome binding sites, J. Mol. Biol., 313:231-244, 2001

5.    Sarkar, S., Rudd, K.E. and Oliver, D., Revised translation start site for secM defines an atypical signal peptide that regulates Escherichia coli secA expression, J. Bacteriol., 182:5592-5595, 2000

Honors and Professional Activities

Member, American Society for Microbiology

Member, Genetics Society of America.

Member, Amemican Association for the Advancement of Science

Editorial Board, Journal of Bacteriology, 1992-2000