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Research

Michael R. Sussman (Professor, Dept. of Biochemistry and Director, UW Biotechnology Center)

Michael R. Sussman, is also founder and supervisor of the UWBC's Mass Spectrometry Facility.  His research program has two main goals: (1) Development of novel technologies for global characterization of biological systems, and (2) Application of traditional genetics and biochemistry as well as novel technology to better understand the role of plasma membrane proteins in eukaryotic cell differentiation, with emphasis on the two model eukaryotes, Arabidopsis and yeast.  Within the realm of technology development, Sussman's laboratory has previously pioneered the development of a reverse genetic approach for performing functional genomics in Arabidopsis, as well as the development and use of new technologies for elucidating the downstream signaling components of plasma membrane hormone receptors. Transcriptome measurements using a maskless array synthesizer to create custom DNA tiling chips (Nimblegen) have identified clusters of genes whose changes in expression are correlated with particular hormone response pathways initiated at the plasma membrane. Since 1998, the Sussman laboratory has been implementing various strategies for isotope-assisted mass spectrometry-based techniques to monitor changes in protein and metabolite expression, as a compliment to the genomic technologies.  Applications of isotope-assisted proteomics are discussed below, followed by other more recent applications in metabolomics. 

Isotope-Assisted Proteomics: In recent years a variety of methods have been developed for introducing isotopic labels into proteomic samples, including in vitro methods such as ICAT, ITRAQ, and O-18 labeling, as well as in vivo methods such as SILAC and metabolic labeling.  The Sussman laboratory has implemented several of these technologies for the study of Arabidopsis and yeast, as well as other model organisms, with numerous collaborators on campus.  Their work has included optimization of isotopic incorporation for routine sample generation as well as development of fractionation techniques, optimization of instrument operation, and implementation of automated data processing and analysis algorithms for several of these labeling techniques.  Examples of work within the Sussman Laboratory using isotope-assisted proteomics techniques include: (1) use of N-15 metabolic labeling for the characterization of auxin response in intact Arabidopsis seedlings (link); (2) use of O-18 Labeling to evaluate a purification strategy of plasma membrane proteins in Arabidopsis (link);.(3) Implementation of new metabolic labeling strategies for comparative proteomics (link); (4) Identification of blood borne biomarkers of colorectal cancer using N-15 metabolic labeling of a mouse model, in collaboration with William F. Dove (link) (Depts. Genetics and Oncology). (link)

Isotope Assisted Metabolomics.  In addition to our proteomics work, we have applied metabolic labeling techniques to our metabolomic research efforts.  These have been largely supported by an NIH technology and resource development grant (R21 in the first year and R35 in the second year) establishing the Madison Metabolomics Consortium, in which Sussman is the PI and Lloyd Smith (Chemistry Dept.) and John Markley (Biochemistry Dept. and NMRFAM) are co-PI’s.  Smith’s contribution is in the development of new mass spectrometric hardware for increasing the sensitivity of metabolomic measurements and Markley’s is in (1) the use of NMR with N-15 and C-13 labeled material, for metabolome identification and quantification in mutants and (2) the development of NMR bioinformatics tools and databases for metabolome analysis, ultimately combining NMR and mass spectrometric observations.  The collaborative effort has resulted in the development of community metabolomics resources that are hosted by the Biological Magnetic Resonance Data Bank (BMRB).