People involved: Kirstin Dion, Ryan Garrick, Saverio Vicario, and Etsuko Moriyama
Our major research involving Drosophila is to understand the evolution of codon usage. Many organisms, including all species of Drosophila studied (reference 6 in list of publications), show very uneven usage of synonymous codons or codon usage bias (CUB). There are two plausible explanations for systematic CUB (the same bias for all genes in a genome, ruling out pure chance): mutation bias and/or selection, not mutually exclusive forces. Mutation bias, generally toward A+T, can account for CUB in genes residing in non-recombining regions of the Drosophila genome such as the “dot” chromosome, also known as Muller’s Element F. Elsewhere in the genome, generally G+C containing codons are favored, the opposite pattern produced by mutation bias, thus strongly implying selection for and against synonymous codons must be occurring. Our recent and ongoing work on this subject includes:
- Demonstration that post-translational modification of some tRNAs at the “wobble” position many account for a shift in preferred codons in the D. willistoni lineage (reference 19 in list of publications). This modification substitutes queuosine (Q) for G and changes the optimal de-coding from C in the mRNA wobble position to T. Amino acids in D. willistoni for which there are tRNAs that have Q modified bases favor T in the thrid position. In most species of Drosophila Q-modified tRNAs appear primarily old adult life. Unlike other Drosophila, in D. willistoni the gene that catalyzes the substitution of Q for G has its highest level of expression in young females that are producing eggs. Thus the presence of Q-modified tRNAs occurs likely earlier in D. willistoni development starting in the egg cytoplasm.
- Another relevant observation in the D. willistoni lineage is that the Element F chromosome has become fused with Element E and the genes in Element F are now in a recombining environment. We have studied D. wilistoni genes on Element F previously shown to be nearly monomorphic in species where this element is non-recombining. We observed moderately high levels of nucleotide polymorphism as well as a shift in codon usage more typical of recombining genes, as well as much less linkage disequilibrium. This confirms the importance of recombination as a factor affecting both levels and patterns of molecular variation as well as the pattern of codon usage (see reference 20 in list of publications).
- Our most recent and ongoing project is to develop an in vitro assay system to experimentally manipulate codon usage and to measure its effects on both transcription and translation. For this, we are developing a transfection vector with two distinguishable reporter lucerferases under the control of different promoters, tubulin and actin. We are attaching synthetic oligonucleotides to the lucerferase proteins. These oligos will consist of runs of a single codon for a particular amino acid, leucine being our first test amino acid. The two reporter genes will have different codons for leucine. We will then transfect Drosophila tissue culture cells with the vector and measure by RT-PCR rates of transcription of the two synthetic genes, and the different luciferase reporters will measure rates of translation. The two tested oligos will then be swapped between promoters. This will allow us the quantify the affect of codon usage on both transcription and translation for virtually any set of codons.
Relevant Powell lab publications prior to 2007
Powell, J. R. and E. N. Moriyama. 1997. Evolution of codon usage bias in Drosophila. Proceedings of the National Academy of Sciences, USA 94:7784-7790. (A general discussion of the issues and results up to that point.) Abstract
Moriyama, E. N. and J. R. Powell. Patterns of codon usage bias and tRNA pools in Drosophila. Journal of Molecular Evolution 45:514-523.
Moriyama, E. N. and J. R. Powell. 1998. Gene length and codon usage bias in Drosophila melanogaster, Saccharomyces cerevisiae, and Escherichia coli. Nucl. Acids Res. 26:3188-3193. An unexpected finding that gene length and level of codon usage bias are related in a number of species from diverse groups. (Possible explanations are discussed.) Abstract
Powell, J. R., E. Sezzi, E. N. Moriyama, J. M. Gleason, and A. Caccone. 2003. Analysis of a shift in codon usage in Drosophila. Journal of Molecular Evolution 57:S214-S225. (A more recent paper describing a particularly intriguing finding for a group of species of Drosophila and also contains several references to other papers.) Abstract