Briggs Lab

We are mapping the regulatory networks that enable human and mouse embryonic stem (ES) cell self-renewal. Whole cell proteome profiles using LC ESI MSMS are revealing new genes whose products are unique to ES cells. Whole phosphopeptide profiles have shown us that many of these regulators of self-renewal are phosphorylated. We are working to determine the significance of this phosphorylation and to identify the protein kinases that are responsible. Our aim is to bridge the gap between studies of transcriptional regulation and cell signaling in ES cells.

Our objective is to develop the sensitivity of genome-wide proteomics tools so they can be routinely used to obtain quantitative read-outs and sequence identifications of 10,000 or more proteins per sample. This capability is necessary to provide direct measures of relative protein amounts, rather than inferences from mRNA measures, and to identify proteins whose levels are uncoupled from mRNA levels because of post-transcriptional regulation. This objective will be met within the context of benchmarking the protein expression dynamics of 10,000 arabidopsis genes. We will compare the proteome composition of roots to cotyledons and mature leaves. We will observe changes in the relative quantity of proteins following infection by the root knot nematode, Meloidogyne incognita, and contrast this with our own and published changes in mRNAs. Proteins whose levels significantly change without a concomitant change in mRNA will be tested, using mutants, to determine whether they play a role in infection. We will search our mass spectra against nematode protein databases to determine whether pathogen protein dynamics can be correlated with the host protein dynamics during disease development. We will determine whether proteomics can be used to discover conserved gene networks by comparing the changes caused by inoculating diverse host species including arabidopsis, tomato, lotus, Medicago, and rice with M. incognita. Plant mutants have been found that affect colonization by nematodes. Some of these mutants also affect colonization by symbiotic, nitrogen-fixing, rhizobial bacteria and by symbiotic mycorrhizal fungi. It appears that all 3 types of microbes have evolved to use the same plant signaling pathway for colonization. Our discoveries of changes in the arabidopsis response to infection by nematodes may provide insights into their convergent evolution with Rhizobia and mycorrhiza for exploitation of a conserved plant pathway.