Linking gene and function through comparative genomic and experimental approaches

University Of Florida, Gainesville FL

Investigators

Abstract

One of the challenges of the post-genomic era is to elucidate the function of the encoded proteomes. Even in widely studied model organisms such as Escherichia coli K12 or fission yeast, around 30% of the genes have yet to be linked to a function but this number rises to 50-70% in most non-model organisms. Since 1995, I have pioneered the use comparative genomic methods combined with experimental validations to identify the function of unknowns. This body of work has led to identifying the function of over 65 gene families resulting in over 160 publications since I started my independent group in 2004. The MIRA R35 mechanism will allow me to fully take advantage of the exploratory type of research driven by comparative genomic approaches that have often led our research program into unforeseen directions to discover novel enzymes and pathways, some conserved from bacteria to humans. Our research currently focuses mainly on the synthesis and function of complex tRNA and DNA modifications and the study of pyridoxal phosphate homeostasis. Two projects were developed in more detail in the proposal. The first focuses on the identification of missing tRNA modification genes including the transporters for the Queuosine (Q) micronutrient and the second on the role of orphan PLP binding enzyme families (YggS and YdcR). The importance of tRNA modifications in health and humans is currently emerging and to fully understand their roles, it is critical to identify all the corresponding genes at least in the major model organisms. One of the major gaps in knowledge that we will tackle is the missing Q precursor transporters in eukaryotes. This modification of the wobble base is important for translation accuracy and its absence can lead to memory defects in mammals. Eukaryotes salvage Q or its precursor base queuine (q). Identifying the missing Q/q transporter will allow us to better understand how this micronutrient is salvaged from the food and microbiota. YggS is a member of a very conserved protein family. Our group was the first to link this family to vitamin B6 homeostasis in E. coli and humans. This finding has now been confirmed in many other organisms by other groups. Mutations in the human homolog PLPBP lead to an inherited treatable form of vitamin B6-dependent early-onset epileptic encephalopathy. However, the exact molecular function of this protein family is still unknown. Recent findings from our laboratory on the E. coli YggS revealed an RNA binding role and genetic interactions with the predicted regulator PLP-binding regulator YdcR and the pyridoxal kinase PdxY, which will be further characterized as a novel window into the function of this enigmatic protein family.