The School of Molecular and Cellular Biology at the University of Illinois at Urbana-Champaign

Most of our research focuses on two areas: (1) gene expression in Archaea, and its relation to corresponding systems in Eucarya and Bacteria, and (2) genomics, with an emphasis on comparative genomics and genome evolution. Our approach is a combination of experimental work and computational analyses of genomes and proteins.

Archaeal gene expression. 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.

We have examined transcription initiation factors and their interactions with promoters. We are continuing this work with the experimental identification of promoters in archaeal genomes, and the analysis of transcription factor binding as a function of sequence variation in the promoters. This work is also being extended to regulatory proteins and their DNA binding sites. We also exploring the role of protein-protein interactions in regulation and in RNA polymerase recruitment.

Genome analysis. We are analyz-ing 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 Ron Swanson (Diversa Corp.), we participated in the analysis of the Aquifex aeolicus genome sequence. Current projects include sequencing and analyzing genomes of Salmonella enterica serovars, with Stanley Malloy (San Diego State University) and Rob Edwards (University of Tennessee), and sequencing and analyzing the genome of Giardia lamblia (a deeply branching eukaryote), with Mitchell Sogin (Woods Hole Marine Biology Laboratory) and several other groups.

These genome projects influence all of the work in the laboratory. They have motivated and guided much of the experimental work; they have led to insights into protein thermal adaptations; they have stimulated work on new computational tools for sequence analysis; and they have led to new thinking on the roles of gene transfer in evolution. The comparative analysis of Salmonella enterica genomes is being used to correlate differences in organism life-style with both genome contents (what is there, or not there) and genome evolutionary processes (e.g., gene gain and loss events, and pseudogene formation).

Lateral gene transfer. One of the profound changes in biological thinking the past several years has been the growing appreciation of the role of lateral gene transfer in evolution. Although its role in the spread of antibiotic resistance was well known, genomic analyses reveal that most of the genes in a genome can be acquired by transfer. Even genes that could be inherited vertically (e.g., aminoacyl-tRNA synthetases) are still being passed between lineages at observable frequencies. We are characterizing the rates of transfer in a variety of lineages and on a variety of time scales. This will reveal the dynamics of the process and its role in both early and more recent evolution.

Bioinformatics. New research often require new tools. The ability to extract information from genomes and gene sequences is limited by the existing set of analysis methods. One of our on-going activities is the development of new forms of data analysis. Past examples include contributions to phylogenetic analysis of nucleotide sequences and the identification of coding regions within a genome. Current efforts include better handling of sequence alignments and phylogenetic trees in an environment where sequence data increase incrementally (with each new genome), identification of horizontally transferred genes, and analysis of pseudogene formation in prokaryotes.