Raymond F. Gesteland, Ph.D.
Distinguished Professor
Vice President for Research

Contribution to Society

The newly described phenomenon of recoding is an essential mechanism for controlled gene expression and is used by all organisms. The genetic code itself is specifically altered for regulatory purposes. An understanding of the mechanisms provides insight into the code itself, into replication of RNA viruses such as HIV, and into complex regulatory pathways in cells.

Recoding opens up new prospects for gene control. Undoubtedly there will be a wide variety of ways in which this bag of tricks has been put to use. We do not yet know enough of the rules to search for genes requiring recoding, but continued examination of new examples will be revealing.

Research Summary

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 (γ) and tau (τ) 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.

Recent Publications

Howard MT, Gesteland RF and Atkins JF (2004) Efficient stimulation of site-specific ribosomal frameshifting by antisense oligonucleotides. RNA 10:1653-1661.

Mejlhede N, Licznar P, Prère M-F, Wills NM, Gesteland RF, Atkins JF and Fayet O (2004) -1 Frameshifting at a CGA AAG hexanucleotide site is required for transposition of insertion sequence IS1222. J. Bacteriol. 186:3274-3277.

Herr AJ, Wills NM, Nelson CC, Gesteland RF and Atkins JF (2004) Factors that influence selection of coding resumption sites in translational bypassing: Minimal conventional peptidyl-tRNA:mRNA pairing can suffice. J. Molec. Bio. 279:11081-11087.

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.

Ivanov IP, Anderson C, Gesteland RF and Atkins JF (2004) Identification of a new antizyme mRNA +1 frameshifting stimulatory pseudoknot in a subset of diverse invertebrates and its apparent absence in intermediate species. Jour. of Molecular Biology 339:495-504.

Howard MT, Anderson CB, Fass U, Khatri S, Gesteland RF, Atkins JF and Flanigan KM (2004) Readthrough of dystrophin stop codon mutations induced by aminoglycosides. Annals of Neurology 55:422-426.

Baranov PV, Gesteland RF and Atkins JF (2004) P-site tRNA is a crucial initiator of ribosomal frameshifting. RNA 10:221-230.

Gurvich OL, Baranov PV, Zhou J, Hammer AW, Gesteland RF and Atkins JF (2003) Sequences that direct significant levels of frameshifting are frequent in coding regions of E. coli. EMBO J. 22:5941-5950.

Licznar P, Mejlhede N, Prère M-F, Wills N, Gesteland RF, Atkins JF and Fayet O (2003) Programmed translational -1 frameshifting and the wobble properties of tRNAs. EMBO J. 22:4770-4778.

Matveeva OV, Shabalina SA, Nemtsov VA, Tsodikov AD, Gesteland RF and Atkins JF (2003) Thermodynamic calculations and statistical correlations for oligo-probes design. Nucl. Acids Res. 31:4211-4217.

Ivanov IP, Gurvich OL, Gesteland RF and Atkins JF (2003) Recoding: Site- or mRNA-specific alteration of genetic readout utilized for gene expression. Chapter 22 in Translation Mechanisms, eds. J. Lapointe and L. Brakier-Gingras. pp.354-369. Landes Bioscience, Eurekah.com. Kluwer Academic/Plenum Publishers. New York.

Matveeva OV, Mathews DH, Tsodikov AD, Shabalina SA, Gesteland RF, Atkins JF and Freier SM (2003) Thermodynamic criteria for high hit rate antisense oligonucleotide design. Nuc. Acids Res. 17:4989-4994.

Hansen TM, Baranov PV, Ivanov IP, Gesteland RF, and Atkins JF (2003) Maintenance of the correct open reading frame by the ribosome. EMBO Reports 4:499-504.

Hill KE, Zhou J, McMahan WJ, Motley AK, Atkins JF, Gesteland RF, and Burk RF (2003). Deletion of selenoprotein P alters distribution of selenium in the mouse. J. Biol. Chem. 278:13640-13646.

Baranov PV, Gurvich OL, Hammer AW, Gesteland RF, and Atkins JF (2003). Recode (2003). Nuc. Acids Res. 31:87-89.

Giddings MC, Shah AA, Gesteland RF, and Moore MB (2003). Genome-based peptide fingerprint scanning. PNAS 100:20-25.

Shah AA, Giddings MC, Parvaz, J.B., Gesteland RF, Atkins JF, and Ivanov IP (2002) Computational identification of putative programmed translational frameshift sites in protein-encoding nucleotide sequences. Bioinformatics 18:1046-1053.

Giddings MC, Shah AA, Freier, S, Atkins JF, Gesteland RF, and Matveeva OV (2002) Artificial neural network prediction of antisense oligodeoxynucleotide activity. NAR 30:4295-4304.

Wang Y, Wills N, Du Z, Rangan A, Atkins JF, Gesteland RF, and 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.

Atkins JF, Gesteland RF (2002) Biochemistry: The 22nd amino acid. Science. 296(5572):1409-10 (Commentary).

Atkins JF, Baranov PV, Fayet O, Herr AJ, Howard MT, Ivanov IP, Matsufuji, S., Miller, W.A., Moore MB, Prere MF, Wills NM, Zhou J, and Gesteland RF (2001) Overriding standard decoding: Implications of recoding for ribosome function and enrichment of gene expression. Cold Spring Harbor Symposia on Quantitative Biology. Volume LXVI: 217-232.

Baranov PV, Gesteland RF, Atkins JF (2002) Release factor 2 frameshifting sites in different bacteria. EMBO Rep. 3(4):373-7.

Baranov PV, Gesteland RF, Atkins JF (2002) Recoding: translational bifurcations in gene expression. Gene. 286(2):187-201. Review.

Bertrand C, Prere MF, Gesteland RF, Atkins JF, and Fayet O (2002) Influence of the stacking potential of the base 3' of tandem shift codons on -1 ribosomal frameshifting used for gene expression. RNA 8, 16-28.

Giddings MC, Matveeva OV, Atkins JF, and Gesteland RF (2000) ODNBase ú A web database for antisense oligonucleotide effectiveness studies. Bioinformatics 16:843-844.

Baranov PV, Gurvich OL, Fayet O, Prere MF, Miller WA, Gesteland RF, Atkins JF, and Giddings MC (2001) Recode: A database of frameshifting, bypassing and codon redefinition utilized for gene expression. Nuc. Acids Res. 29:264-267.

Felden B, Massire C, Westhof E, Atkins JF, and Gesteland RF (2001) Phylogenetic analysis of tmRNA genes within a bacterial subgroup reveals a specific structural signature. NAR 29:1602-1607.

Herr AJ, Nelson CC, Wills NM, Gesteland RF, and Atkins JF (2001) Analysis of the roles of tRNA structure, ribosomal protein L9, and the bacteriophage T4 gene 60 bypassing signals during ribosome slippage on mRNA. J. Mol. Biol. 309: 1029-1048.

Herr AJ, Wills NM, Nelson CC, Gesteland RF, and Atkins JF (2001) Drop-off during ribosome hopping. J. Molec. Biol. 311:445-452.

Howard MT, Shirts BH, Zhou J, Carlson CL, Matsufuji S, Gesteland RF, Weeks RS, and Atkins JF (2001) Cell culture analysis of the regulatory frameshift event required for the expression of mammalian antizymes. Genes to Cells 6:931-941.

Larsen B, Wills NM, Nelson C, Atkins JF, and Gesteland RF (2000) Non-linearity in genetic decoding: Homologous DNA replicase genes use alternatives of transcriptional slippage or translational frameshifting. PNAS 97:1683-1688.

Atkins JF, Herr AJ, Massiere C, O’Connor M, Ivanov I and Gesteland RF (2000) Poking a hole in the sanctity of the triplet code: Inferences for framing. pp369-383. in The Ribosome, eds. R.A. Garrett, S.R. Douthwaite, A. Liljas, A.T. Matheson, P.B. Moore, and H.F. Noller, ASM Press, Washington DC.

Herr AJ, Gesteland RF, and Atkins JF (2000) One protein from two open reading frames: mechanism of a 50 nt translational bypass. EMBO 19:2671-2680.

Ivanov IP, Rohrwasser A, Terreros DA, Gesteland RF, and Atkins JF (2000) Discovery of a spermatogenesis, stage specific, ornithine decarboxylase antizyme: Antizyme 3. PNAS 97:4808-4813. Accompanying commentary by P. Coffino: PNAS 97:4421-4423.

Ivanov IP, Matsufuji S, Murakami Y, Gesteland RF and Atkins JF (2000) Conservation of polyamine regulation by translational frameshifting from yeast to mammals. EMBO J. 19, 1907-1917. (See Editors Choice: Highlights of recent literature. Molecular Biology: Translational trickery and polyamines. Science 288, [May 5]).

Moore B, Persson B, Nelson CC, Gesteland RF, and Atkins JF (2000) Quadruplet codons: Implications for code expansion and the specification of translation step size. J. Mol. Bio. 298:195-209.

Lieberman KR, Firpo MA, Herr AJ, Nguyenle T, Atkins JF, Gesteland RF, and Noller HF (2000) The 23S rRNA environment of ribosomal protein L9 in the 50S ribosomal subunit. J. Mol. Bio. 297:1129-1143.

Matveeva OV, Tsodikov AD, Giddings M, Freier SM, Wyatt JR, Spiridonov AN, Shabalina SA, Gesteland RF, and Atkins JF (2000) Identification of sequence motifs in oligonucleotides whose presence is correlated with antisense activity. NAR 28:2862-2865.

Howard MT, Shirts BH, Petros LM, Flanigan KM, Gesteland RF, and Atkins JF (2000) Sequence specificity of aminoglycoside induced stop codon readthrough: Implications for treatment of Duchenne Muscular Dystrophy. Annals of Neurology 48:164-169.

Ivanov IP, Gesteland RF, and Atkins JF (2000) Antizyme expression: A subversion of triplet decoding, which is remarkably conserved by evolution, is a sensor for an autoregulatory circuit. NAR 17:3185-3196.

Atkins JF and Gesteland RF (2000) The twenty- first amino acid. Nature 407:463-465 (News and Views).

Moore MB, Nelson CC, Persson BC, Gesteland RF, and Atkins JF (2000) Decoding of tandem quadruplets by adjacent tRNAs with eight-base anticodon loops. NAR 28:3615-3624.

Herr AJ, Atkins JF, and Gesteland RF (2000) Coupling of open reading frames by translational bypassing. Ann. Rev. of Biochemistry 69:343-372.

Several articles on genetic code related topics in The Encyclopedia of Molecular Biology, ed. Thomas Crieghton, John Wiley & Sons, Inc.:

• Atkins JF, Gesteland RF, and Watanabe K (1999) Genetic Code. pp. 993-998.
• Atkins JF and Gesteland RF (1999) Start Codons. pp. 2429-2430.
• Atkins JF and Gesteland RF (1999) Stop Codons. pp. 2444-2445.
• Atkins JF and Gesteland RF (1999) Degeneracy of the genetic code. p.632.

Gesteland RF, Cech TR, Atkins JF – editors: “The RNA World – Second Edition, The Nature of Modern RNA Suggests a Prebiotic RNA World.” (1999) Cold Spring Harbor Laboratory Press. 709 pages.

Atkins JF, Bock A, Matsufuji S, and Gesteland RF (1999) Dynamics of the Genetic Code. In The RNA World – Second Edition. (Gesteland RF, Cech, T., Atkins JF, editors). Cold Spring Harbor Laboratory Press, Chp. 24, pp.637-673.

Gesteland RF, Cech TR, Atkins JF – editors: “The RNA World – Second Edition, The Nature of Modern RNA Suggests a Prebiotic RNA World.” (1999) Cold Spring Harbor Laboratory Press. 709 pages.

Atkins JF, Bock A, Matsufuji S, and Gesteland RF (1999) Dynamics of the Genetic Code. In The RNA World – Second Edition. (Gesteland RF, Cech, T., Atkins JF, editors). Cold Spring Harbor Laboratory Press, Chp. 24, pp.637-673.