Acquisition of Equipment for Genomics Research

California Lutheran University, Thousand Oaks CA

Investigators

Abstract

Project Abstract A grant has been awarded to Drs. Revie and Marcey at California Lutheran University to purchase equipment to perform structural and functional genomics research. The project will meet four goals. First, the equipment will be used to more quickly sequence the genome of strain 122-1B2 of the archaeon Thermoplasma acidophilum. Archaea are a group of microorganisms that comprise a third branch of life, which are distinct from the other two branches: (1) bacteria and (2) eukaryotes, a group that includes yeast and multicellular organisms. Determining the sequence of bases in the genome of T. acidophilum will allow for the identification of proteins that are involved in respiration. Second, the equipment will be used by Dr. Marcey to study a protein involved in cellular signaling in the fruit fly Drosophila melanogaster. Third, the equipment will allow students to perform a wider variety of research projects in formal laboratory classes. For example, genomics research will be conducted in Genetics, Molecular Biology, Developmental Biology, and Recombinant DNA Techniques. Fourth, the equipment will allow Biology and Biochemistry students to engage in faculty-mentored research experiences in structural and functional genomics. The archaeon T. acidophilum can grow either aerobically under normal oxygen concentrations, under very low oxygen concentrations, or anaerobically in the presence of sulfur. The organism grows optimally at pH 1.7 and 59 degrees C, but interestingly, lacks a cell wall. Although it can reduce sulfur, little is known about this process. Even less is known about how the organism survives under very low oxygen conditions. Considering the hostile and extreme environment where T. acidophilum thrives, this flexibility of respiration is quite remarkable, making the study of its respiratory proteins an interesting and important part of the overall study of Archaea. In order to find and study the respiratory proteins, the equipment will more quickly determine the entire sequence of bases in the DNA. This will primarily be done by sequencing T. acidophilum DNA that has been cloned into a plasmid, then assembling the resulting pieces into one contiguous chromosome. The DNA will then be analyzed to determine the entire complement of genes in the organism. A gene, Dpez, that encodes a member of novel class of proteins involved in cellular communication, the FERM domain Protein Tyrosine Phosphatases (PTPs), will be studied in the model organism Drosophila melanogaster. Equipment funded by this grant will be used to determine the DNA sequences of genes encoding proteins that interact with Dpez. Also, the DNA sequences of genes that produce mutant forms of the Dpez protein will be determined. Spatial and temporal patterns of DPez expression will be investigated. Archaea are a distinct group of organisms. Many of them, including T. acidophilum, live in extreme environments such as high temperatures and low pH. This project will aid the study of proteins that enable the organism to thrive under the extreme conditions in which it grows. In addition, the ability of T. acidophilum to grow under a variety of respiratory conditions makes the study of these proteins even more interesting. Determining the entire sequence of bases in the organism will also allow for comparisons between T. acidophilum and other microorganisms that will increase knowledge of evolutionary processes. The balance between the opposite actions of protein tyrosine kinases (PTKs) and protein tyrosine phosphatases (PTPs) can regulate cell proliferation, differentiation, and morphology. PTPs have been cloned in large numbers from a variety of organisms and are targeted to subcellular locations and linked to specific signaling pathways. The Dpez protein is the first invertebrate FERM-PTP described. Investigations of the functions of DPez will be conducted with the goal of using the tractable genetics of Drosophila to discover the roles of the protein in the development and cell physiology of a model insect.