Raymond Gesteland
Distinguished Professor of Human Genetics
B.S. University of Wisconsin
Ph.D. Harvard University
Research
The genetic code is dynamic – it, or its readout, can be specifically changed by mRNA signals that modify the behavior of on-board ribosomes. Many viruses use recoding to maximize utilization of information in small genomes, and probably all organisms use recoding in at least some genes for expanding the regulatory repertoire. We are studying specific recoding examples to understand the mechanisms and the mRNA signals. These include: frameshift dependent decoding of E. coli dnaX to synthesize the gamma (t) and tau (t) subunits of DNA polymerase III; encoding of the 21st amino acid, selenocysteine, by UGA stop codons; bypassing of 50 mRNA nucleotides to make bacteriophage T4 gene 60 product; and the polyamine dependent frameshift for the synthesis of mammalian antizyme. We use biochemical and genetic approaches to identify and study the cellular factors involved in recoding. The signals in mRNA that dictate recoding often include complex folded structures of the RNA, which we are studying by a combination of genetics, biochemical and NMR approaches.
A new major effort is to investigate the genome wide complexity for protein products. What is the contribution of translational diversity and post-translational modification to complexity of the proteome? New high throughput mass spectrometry technology can identify proteins with gene open reading frames and can lead to specification of how each protein species arose. The goal is to define how many and which protein products come from each mRNA in a cell.
References
1. Baranov PV, Henderson CM, Anderson CB, Gesteland RF, Atkins JF, Howard MT (2005) Programmed ribosomal frameshifting in decoding the SARS-CoV genome. Virology 332:498-510
2. Matveeva OV, Foley BT, Nemtsov VA, Gesteland RF, Matsufuji S, Atkins JF, Ogurtsov AY, Shabalina SA (2004) Identification of regions in multiple sequence alignments thermodynamically suitable for targeting by consensus oligonucleotides: application to HIV genome. BMC Bioinformatics 5(1):44-51
3. Howard MT, Anderson CB, Fass U, Khatri S, Gesteland RF, Atkins JF, Flanigan KM (2004) Readthrough of dystrophin stop codon mutations induced by aminoglycosides. Annals of Neurology 55:422-426
4. Licznar P, Mejlhede N, Prère M-F, Wills N, Gesteland RF, Atkins JF, Fayet O (2003) Programmed translational -1 frameshifting and the wobble properties of tRNAs. EMBO J. 22:4770-4778
5. Hill KE, Zhou J, McMahan WJ, Motley AK, Atkins JF, Gesteland RF, Burk RF (2003) Deletion of selenoprotein P alters distribution of selenium in the mouse. J. Biol. Chem. 278:13640-13646
6. Giddings MC, Shah AA, Gesteland RF, Moore MB (2003) Genome-based peptide fingerprint scanning. PNAS 100:20-25
7. Wang Y, Wills N, Du Z, Rangan A, Atkins JF, Gesteland RF, Hoffman DW (2002) Comparative studies of frameshifting and non-frameshifting RNA pseudoknots: A mutational and NMR investigation of pseudoknots derived from the bacteriophage T2 gene 32 mRNA and the retroviral gag-pro frameshift site. RNA 8:981-996
8. Shah AA, Giddings MC, Parvaz JB, Gesteland RF, Atkins JF, Ivanov IP (2002) Computational identification of putative programmed translational frameshift sites. Bioinformatics 18:1046-1053
9. Felden B, Massire C, Westhof E, Atkins JF, Gesteland RF (2001) Phylogenetic analysis of tmRNA genes within a bacterial subgroup reveals a specific structural signature. NAR 29:1602-1607
10. Atkins JF, Gesteland RF (2001) mRNA readout at 40. Nature 414:693
11. Giddings MC, Matveeva OV, Atkins JF, Gesteland RF (2000) ODNBase - A web database for antisense oligonucleotide effectiveness studies. Bioinformatics 16:843-844
12. Herr AJ, Atkins JF, Gesteland RF (2000) Coupling of open reading frames by translational bypassing. Ann. Rev. of Biochemistry 69:343-372
13. Larsen B, Wills NM, Nelson C, Atkins JF, Gesteland RF (2000) Non-linearity in genetic decoding: Homologous DNA replicase genes use alternatives of transcriptional slippage or translational frameshifting. PNAS 97:1683-1688
