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Michael Hampsey, PhD Lab Site

Research Description:

Our laboratory studies the regulation of gene expression and cell metabolism in eukaryotic organisms. We are especially interested in (i) the mechanism underlying the Warburg Effect, a metabolic change that occurs in all cancer cells; and (ii) transcription of protein-encoding genes by RNA polymerase II (Pol II).   The experimental organism used in most of our work is the yeast Saccharomyces cerevisiae, which enables us to use a powerful combination of classical genetics, molecular biology and modern biochemistry in our research.  


1) Cancer genetics.  Most cancer cells metabolize glucose by “aerobic fermentation” rather than by respiration.  Accordingly, glucose is metabolized to pyruvate, followed by reduction to lactate to regenerate NAD+, stopping short of complete oxidation of pyruvate to carbon dioxide in the citric acid cycle.  This process was discovered by Otto Warburg in 1923 and is referred to as the “Warburg effect” or “aerobic glycolysis.”  Remarkably, 90+ years after its discovery, we still do not understand why cancer cells ferment glucose, resulting in a 19-fold lower yield of ATP per glucose molecule, than by respiration to CO2. 
 

In the past 15 years there has been a resurgence of interest in the Warburg effect in an effort to understand why cancer cells metabolize glucose by the energy inefficient process of aerobic glycolysis.  Much of this work has focused on the utilization of metabolic intermediates in the glycolytic pathway.  Here we propose a different perspective on the Warburg effect: specifically, cancer cells acquire mutations in components of the respiratory machinery that enable cells to utilize metabolic intermediates to enhance fatty acid synthesis (FAS).  We have isolated mutants affecting the respiratory machinery as suppressors that enhance FAS and do so by bypassing the normal regulatory controls exerted on the rate-limiting step in FAS.  This result is especially interesting, and potentially relevant to understanding cancer biology, as the fatty acid requirement of rapidly proliferating cells is as much as 40% of their biomass.  


2) Role of “gene loops” in transcription.   Although Ssu72 is a component of the CPF 3' end processing complex, we first identified this protein based on genetic and physical interactions with TFIIB, a transcription initiation factor.   As such, Ssu72 defined an unexpected link between the Pol II initiation and termination machineries.   This suggested to us that the ends of gene might physically interact to form gene loops.   Our recent studies revealed that gene loops are a general feature of Pol II transcription. Looping is dependent upon transcription and requires specific components of the transcription initiation and 3'-end processing complexes, including the Ssu72 CTD phosphatase. We are now working (i) to define the factors and mechanisms involved in loop formation; and (ii) to determine the functional significance of gene loops with respect to regulation of gene expression.

 

3) Coupling of 3' end processing to Pol II transcription.   Nascent mRNA undergoes modifications that include 5' capping, splicing, 3' endonucleolytic cleavage and polyadenylation.   These processing events occur co-transcriptionally and involve recruitment and exchange of processing enzymes to the C-terminal domain (CTD) of the Rpb1 subunit of Pol II.   The CTD is phosphorylated and dephosphorylated at Ser2 and Ser5 during the transcription cycle.   We recently discovered that the Ssu72 protein is an integral component of the CPF 3'-end processing complex and is a CTD Ser5-P phosphatase.   We are now focused on (i) determining how Ssu72-mediated Ser5-P dephosphorylation affects Pol II progression through the transcription cycle; (ii) how Ssu72 is regulated by the transcriptional machinery; and (iii) how Ssu72 is regulated by 3' end processing factors.   These questions are being addressed in collaboration with Professor Claire Moore (Tufts Medical School ).  
 

A remarkable feature of cell metabolism and transcription is the extent to which these processes – and the proteins that facilitate them – are conserved among eukaryotic organisms.   Accordingly, we are able to exploit the extensive arsenal of experimental approaches available in yeast with the results directly applicable to human biology and medicine.