Discipline: Biological Sciences
Thomas Hahn - University of Arkansas at Little Rock
Co-Author(s): Richard Segall and Fusheng Tang, Arkansas State University, Jonesboro, AR Helen Benes, University of Arkansas for Medical Sciences, Little Rock, AR
Purpose, Motivation and Hypothesis: The objective is to understand how sterol transport is affected by caloric restriction (CR) and aging. Sterol synthesis generally increases as cells age. Yet, despite this increase, the sterol content of selected organelle membranes, such as lysosomal membranes, declines with age and adversely affects cellular functions. We are interested in a better understanding of changes in sterol transport to membranes of vacuoles (the yeast counterparts of mammalian lysosomes) in response to anti-aging and pro-aging manipulations. Methods: The protein Erg6 is involved in sterol synthesis, while Atg15 is associated with autophagy, a process for degradation of damaged materials by vacuoles (or lysosomes). Wild Type (WT) cells have been found to live longer with CR, while the lifespan of the erg6Δ and atg15Δ mutants is significantly shortened by CR. In a comparison of microarray data from erg6Δ and atg15Δ mutants with WT during CR, we looked for changes in expression of genes that could be involved in lifespan extending mechanisms triggered by CR. We used microarray data to determine the responses to different combinations of mutations and food availability pairs to examine differential expression of those genes. We constructed “heat maps” using R to identify the relevant genes and determined their roles in biological pathways. Results: Our analysis show that the two genes with still unknown functions DR124W and YBR238 are less expressed and the gene SIP18 is much more expressed in the WT during CR than in any other evaluated combination of genotype and food availability. Hence, these genes could be involved in a still undiscovered lifespan extending mechanism triggered by CR in WT but not in erg15Δ or erg6Δ knockout mutants. In erg6-delta, more pathways are differentially regulated by CR than in atg15-delta. Cellular amino acid metabolic process, biosynthetic process, and sterol metabolic process are the top 3 pathways that are differentially modulated by CR compared to WT. Our discovery that erg6-delta cannot up-regulate the production of NADH/NADPH is likely the cause of the accumulation of Reactive Oxygen Species (ROS) in CR-treated cells. In support, atg15 is required for lifespan extension in longevity mutants mimicking CR. Thus, we propose that autophagy relieves the ROS-stress induced by CR and plays a key role in lifespan extension. Conclusions and further work: SIP18 is the most promising candidate gene because it is expressed much higher in the WT during CR than in any other condition thus making it very sensitive to CR and possibly causing the lifespan extension associated with CR. In addition, deletion of SIP18 leads to deformed vacuoles. Hence, SIP18 is a good candidate for involvement in both autophagy and the sterol synthesis pathway. In the future we plan to consider multiple publically available microarray datasets to cross-validate lifespan regulating candidate genes.
Funder Acknowledgement(s): This project was supported by the Arkansas INBRE program, with grants from the National Center for Research Resources - NCRR (P20RR016460) and the National Institute of General Medical Sciences - NIGMS (P20 GM103429) from the National Institutes of Health.
Faculty Advisor: Fusheng Tang, FXTang@UALR.edu
Role: I contributed all components, which could be generated with a computer, since most of its features can be made much more accessible, except for the wet-lab work, because unfortunately the limitations caused by my visual disability prevent me from performing such kinds of tasks. I did all analytical and computational work, pathway analysis, network construction, GO term enrichments, differential gene expression, integrating and mining very heterogeneous high dimensional data to discover new associations and correlations for building new models for inferring causal relationships.