Michael P. Weir

Professor
Ph.D. (biology) University of Pennsylvania

Campus Extension: 2402
Room #: Hall-Atwater Labs 112
E-Mail: MWEIR@WESLEYAN.EDU

Drosophila developmental genetics; bioinformatics.

Gene Regulation Through Protein Degradation 

Understanding the mechanisms of gene regulation in developing embryos is a central problem in biology. In addition to regulation of mRNA transcription, gene expression is controlled at many other levels, including regulation of protein expression through targeted protein degradation. The ubiquitin-mediated protein degradation machinery has many shared general components as well as specificity factors that determine which proteins are ubiquitinated and degraded. The specificity factors include the recently-discovered family of F-box proteins, each of which targets a set of proteins for degradation. F-box proteins form bridges between the proteins to be degraded and the ubiquitination machinery. Understanding the relationships between different protein substrates that share the same F-box protein, and the relationships between different F-box proteins that share the same general degradation machinery, are primary goals of our research group.

 We are using the early Drosophila embryo as a model system to address these questions. In a yeast two-hybrid screen, we discovered one of the Drosophila F-box proteins, Partner of paired (Ppa), which targets the PAX transcription factor Paired for degradation. Paired is one of a number of segmentation proteins expressed in zebra stripes in the embryo which together provide combinatorial information for patterned development of the embryo. Strikingly, ppa mRNA is also expressed in zebra stripes (see Figure 1), but Ppa protein is not expressed in stripes. Instead, Ppa protein is expressed fairly uniformly, with enriched expression in dividing cells (Figure 2).

 The disparity between the distributions of ppa mRNA and protein expression presents a puzzle. Presumably there is post-transcriptional regulation, which we suspect acts at the level of protein degradation. Identification of the different substrate proteins that Ppa targets for ubiquitination is providing clues about the post-transcriptional regulation. Ppa substrates include both segmentation proteins and proteins involved in cell division. What are the relationships between these different substrates, and how do these substrates feed back on the expression of ppa mRNA and protein? Preliminary results suggest that increased expression of individual substrates leads to increased levels of Ppa protein, but not of ppa mRNA. This leads to the model that F-box proteins are up-regulated in cells requiring their ubiquitination function - i.e. only in cells with high levels of substrate to be degraded; however, when not required, the F-box proteins would be down-regulated, probably through rapid turn-over. This tuning of F-box protein levels would ensure that F-box proteins do not unnecessarily monopolize the shared ubiquitination machinery.

 If individual substrates can increase expression of a given F-box protein, how does this affect ubiquitination and degradation of the other substrates of that F-box protein? Does this feedback system define a regulatory network linking substrates that share the same F-box protein? We are addressing these and related questions using the powerful molecular genetics and genomics of the Drosophila experimental system.

 Bioinformatic Analysis of Drosophila cDNAs

An important ongoing effort of the Berkeley Drosophila Genome Project is to assemble the sequences for a large set of Drosophila cDNAs.  By comparing these sequences with their corresponding genomic sequences, we have computed a set of over 24,000 splice sites.  In collaboration with Professor Michael Rice (Department of Mathematics and Computer Science), we are using information-theoretic approaches to analyze the splice sites, using relational databases as an framework for our analysis. We find that the sequence conservation at splice sites depends upon the lengths of introns and exons in the neighborhood. By examining sets of splice sites where the spliceosome machine is strained, we are gaining insights into the mechanisms that govern splicing.

Funding: National Institutes of Health

Links:

• Selected publications
• Weir courses
• Integrative Genomic Science at Wesleyan University