Porter Room B413B
This laboratory has engaged in three major types of scientific work:
- On the fundamental reactions of the translational apparatus, and the roles of particular tRNA and mRNA sequences in translational efficiency and accuracy.
- On the selection of particular RNA structures with binding or catalytic activity, and the relation of those activities to the origin of the genetic code, or translation in a larger sense.
- On the nature of RNA affinity for phospholipid bilayers and on the role of such membrane RNAs in biology.
Selected Publications
A recent group of ms on the origins of the near-universal genetic code
From initial RNA encoding to the Standard Genetic Code [Internet]. 2023 bioRxiv 2023.11.07.566042; doi: https://doi.org/10.1101/2023.11.07.566042.
The Genetic Code Assembles via Division and Fusion, Basic Cellular Events. Life Basel Switz 2023; 13:2069.
Order of events in a developing genetic code. RNA Biology Volume 21, 2024 - Issue 1; doi: 10.1080/15476286.2023.2299615
A crescendo of competent coding (c3) contains the Standard Genetic Code. RNA. 2022 Oct;28(10):1337-1347. doi: 10.1261/rna.079275.122.
Evolution and favored change: a principle of least selection, bioRxiv 2021.06.27.450095; doi: https://doi.org/10.1101/2021.06.27.450095
Optimal Evolution of the Standard Genetic Code. J Mol Evol. 2021 Feb;89(1-2):45-49. doi: 10.1007/s00239-020-09984-8. Epub 2021 Jan 24.
Fitting the standard genetic code into its triplet table. Proc Natl Acad Sci U S A. 2021 Sep 7;118(36):e2021103118. doi: 10.1073/pnas.2021103118.
Crick Wobble and Superwobble in Standard Genetic Code Evolution. J Mol Evol. 2021 Feb;89(1-2):50-61. doi: 10.1007/s00239-020-09985-7.
Evolution of the Standard Genetic Code. J Mol Evol. 2021 Feb;89(1-2):19-44. doi: 10.1007/s00239-020-09983-9.
A pop-science book for people interested in the significance of the RNA world:
Life from an RNA world. The ancestor within. Harvard University Press, Cambridge, Mass. 2010. 202 pages. ISBN 9780674056985.
The amino acid arginine site in the Tetrahymena self-splicing RNA
Selection of small molecules by the Tetrahymena catalytic center. Yarus M, Illangesekare M, Christian E. Nucleic Acids Res. 1991 Mar 25;19(6):1297-304. doi: 10.1093/nar/19.6.1297.
Stereoselective arginine binding is a phylogenetically conserved property of group I self-splicing RNAs. Hicke BJ, Christian EL, Yarus M. EMBO J. 1989 Dec 1;8(12):3843-51. doi: 10.1002/j.1460-2075.1989.tb08562.x.
A specific amino acid binding site composed of RNA. Science. 1988 Jun 24;240(4860):1751-8. doi: 10.1126/science.3381099.
Other amino acid binding sites in RNA; in particular, their cognate codon and anticodon content
Nucleotides that are essential but not conserved; a sufficient L-tryptophan site in RNA. Majerfeld I, Chocholousova J, Malaiya V, Widmann J, McDonald D, Reeder J, Iyer M, Illangasekare M, Yarus M, Knight R. RNA. 2010 Oct;16(10):1915-24. doi: 10.1261/rna.2220210.
Simple, recurring RNA binding sites for L-arginine. Janas T, Widmann JJ, Knight R, Yarus M. RNA. 2010 Apr;16(4):805-16. doi: 10.1261/rna.1979410.
Chiral histidine selection by D-ribose RNA. Illangasekare M, Turk R, Peterson GC, Lladser M, Yarus M. RNA. 2010 Dec;16(12):2370-83. doi: 10.1261/rna.2385310.
A diminutive and specific RNA binding site for L-tryptophan. Majerfeld I, Yarus M. Nucleic Acids Res. 2005 Sep 25;33(17):5482-93. doi: 10.1093/nar/gki861.
RNA affinity for molecular L-histidine; genetic code origins. Majerfeld I, Puthenvedu D, Yarus M. J Mol Evol. 2005 Aug;61(2):226-35. doi: 10.1007/s00239-004-0360-9.
Selection of the simplest RNA that binds isoleucine. Lozupone C, Changayil S, Majerfeld I, Yarus M. RNA. 2003 Nov;9(11):1315-22. doi: 10.1261/rna.5114503.
Phenylalanine-binding RNAs and genetic code evolution. Illangasekare M, Yarus M. J Mol Evol. 2002 Mar;54(3):298-311. doi: 10.1007/s00239-001-0045-6.
RNA-ligand chemistry: a testable source for the genetic code. RNA. 2000 Apr;6(4):475-84. doi: 10.1017/s1355838200002569.
Isoleucine:RNA sites w/ associated coding sequences. Majerfeld I, Yarus M. RNA. 1998 Apr;4(4):471-8.
An RNA pocket for the planar aromatic side chains of phenylalanine and tryptophane. Zinnen S, Yarus M. Nucleic Acids Symp Ser. 1995;(33):148-51.
The Genetic Code and RNA-Amino Acid Affinities. Life (Basel). 2017 Mar 23;7(2):13. doi: 10.3390/life7020013.
Origins of the genetic code: the escaped triplet theory. Yarus M, Caporaso JG, Knight R. Annu Rev Biochem. 2005;74:179-98. doi: 10.1146/annurev.biochem.74.082803.133119.
Genetic code origins. Yarus M, Christian EL. Nature. 1989 Nov 23;342(6248):349-50. doi: 10.1038/342349b0.
In vitro selection of RNA sites and catalysts
Size, constant sequences, and optimal selection. Legiewicz M, Lozupone C, Knight R, Yarus M. RNA. 2005 Nov;11(11):1701-9. doi: 10.1261/rna.2161305.
Acyl-CoAs from coenzyme ribozymes. Jadhav VR, Yarus M. Biochemistry. 2002 Jan 22;41(3):723-9. doi: 10.1021/bi011803h.
RNA-catalyzed amino acid activation. Kumar RK, Yarus M. Biochemistry. 2001 Jun 19;40(24):6998-7004. doi: 10.1021/bi010710x.
Diversity of oligonucleotide functions. Gold L, Polisky B, Uhlenbeck O, Yarus M. Annu Rev Biochem. 1995;64:763-97. doi: 10.1146/annurev.bi.64.070195.003555.
Selection of an RNA domain that binds Zn2+. Ciesiolka J, Gorski J, Yarus M. RNA. 1995 Jul;1(5):538-50.
RNA-catalyzed synthesis of aminoacyl-RNA, a 5-nt enzyme with a 4-nt substrate
Small aminoacyl transfer centers at GU within a larger RNA. Illangasekare M, Yarus M. RNA Biol. 2012 Jan;9(1):59-66. doi: 10.4161/rna.9.1.18039.
Catalyzed and spontaneous reactions on ribozyme ribose. Turk RM, Illangasekare M, Yarus M. J Am Chem Soc. 2011 Apr 20;133(15):6044-50. doi: 10.1021/ja200275h.
The meaning of a minuscule ribozyme. Philos Trans R Soc Lond B Biol Sci. 2011 Oct 27;366(1580):2902-9. doi: 10.1098/rstb.2011.0139.
Multiple translational products from a five-nucleotide ribozyme. Turk RM, Chumachenko NV, Yarus M. Proc Natl Acad Sci U S A. 2010 Mar 9;107(10):4585-9. doi: 10.1073/pnas.0912895107.
Aminoacyl-RNA synthesis catalyzed by an RNA. Illangasekare M, Sanchez G, Nickles T, Yarus M. Science. 1995 Feb 3;267(5198):643-7. doi: 10.1126/science.7530860. PMID: 7530860
Suitability of primordial conditions for biosynthesis – fluctuation effects
Efficient Heritable Gene Expression Readily Evolves in RNA Pools. J Mol Evol. 2017 Jun;84(5-6):236-252. doi: 10.1007/s00239-017-9800-1.
Biochemical Refinement Before Genetics: Chance Utility. J Mol Evol. 2016 Oct;83(3-4):89-92. doi: 10.1007/s00239-016-9757-5.
A ribonucleotide Origin for Life--fluctuation and near-ideal reactions. Orig Life Evol Biosph. 2013 Feb;43(1):19-30. doi: 10.1007/s11084-013-9325-6.
Templated synthesis of cofactor-like molecules; potential primordial gene and product
Non-Watson-Crick RNA synthesis suited to origin functions. Puthenvedu D, Majerfeld I, Yarus M. RNA. 2018 Jan;24(1):90-97. doi: 10.1261/rna.063974.117.
Cross-backbone templating; ribodinucleotides made on poly(C). Majerfeld I, Puthenvedu D, Yarus M. RNA. 2016 Mar;22(3):397-407. doi: 10.1261/rna.054866.115.
Poly(U) RNA-templated synthesis of AppA. Puthenvedu D, Janas T, Majerfeld I, Illangasekare M, Yarus M. RNA. 2015 Oct;21(10):1818-25. doi: 10.1261/rna.052696.115.
Evolution of alternate genetic codes
On malleability in the genetic code. Schultz DW, Yarus M. J Mol Evol. 1996 May;42(5):597-601. doi: 10.1007/BF02352290.
Transfer RNA mutation and the malleability of the genetic code. Schultz DW, Yarus M. J Mol Biol. 1994 Feb 4;235(5):1377-80. doi: 10.1006/jmbi.1994.1094.
Capping ribozymes – synthesis of cofactors by RNAs
Coenzymes as coribozymes. Jadhav VR, Yarus M. Biochimie. 2002 Sep;84(9):877-88. doi: 10.1016/s0300-9084(02)01404-9.
RNA-Catalyzed CoA, NAD, and FAD synthesis from phosphopantetheine, NMN, and FMN. Huang F, Bugg CW, Yarus M. Biochemistry. 2000 Dec 19;39(50):15548-55. doi: 10.1021/bi002061f.
5'-RNA self-capping from guanosine diphosphate. Huang F, Yarus M. Biochemistry. 1997 Jun 3;36(22):6557-63. doi: 10.1021/bi970475b.
RNA enzymes with two small-molecule substrates. Huang F, Yang Z, Yarus M. Chem Biol. 1998 Nov;5(11):669-78. doi: 10.1016/s1074-5521(98)90294-0.
A calcium-metalloribozyme with autodecapping and pyrophosphatase activities. Huang F, Yarus M. Biochemistry. 1997 Nov 18;36(46):14107-19. doi: 10.1021/bi971081n.
Membrane RNAs, with affinity for phospholipid layers, particularly structured layers
Human tRNA(Sec) associates with HeLa membranes, cell lipid liposomes, and synthetic lipid bilayers. Janas T, Janas T, Yarus M. RNA. 2012 Dec;18(12):2260-8. doi: 10.1261/rna.035352.112.
Specific RNA binding to ordered phospholipid bilayers. Janas T, Janas T, Yarus M. Nucleic Acids Res. 2006 Apr 26;34(7):2128-36. doi: 10.1093/nar/gkl220.
A membrane transporter for tryptophan composed of RNA. Janas T, Janas T, Yarus M. RNA. 2004 Oct;10(10):1541-9. doi: 10.1261/rna.7112704.
Visualization of membrane RNAs. Janas T, Yarus M. RNA. 2003 Nov;9(11):1353-61. doi: 10.1261/rna.5129803.
Binding and disruption of phospholipid bilayers by supramolecular RNA complexes. Vlassov A, Khvorova A, Yarus M. Proc Natl Acad Sci U S A. 2001 Jul 3;98(14):7706-11. doi: 10.1073/pnas.141041098. Epub 2001 Jun 26.
Codon context effects in bacterial mRNA
Sense codons are found in specific contexts. Yarus M, Folley LS. J Mol Biol. 1985 Apr 20;182(4):529-40. doi: 10.1016/0022-2836(85)90239-6.
Codon contexts from weakly expressed genes reduce expression in vivo. Folley LS, Yarus M. J Mol Biol. 1989 Oct 5;209(3):359-78. doi: 10.1016/0022-2836(89)90003-x.
Rates of translation of individual codons, by competition with a frameshift
Rates of aminoacyl-tRNA selection at 29 sense codons in vivo. Curran JF, Yarus M. J Mol Biol. 1989 Sep 5;209(1):65-77. doi: 10.1016/0022-2836(89)90170-8.
tRNA structure and function – extended anticodon, waggle theory
Natural selection is not required to explain universal compositional patterns in rRNA secondary structure categories. Smit S, Yarus M, Knight R. RNA. 2006 Jan;12(1):1-14. doi: 10.1261/rna.2183806.
A twisted tRNA intermediate sets the threshold for decoding. Yarus M, Valle M, Frank J. RNA. 2003 Apr;9(4):384-5. doi: 10.1261/rna.2184703.
tRNA structure and ribosomal function. I. tRNA nucleotide 27-43 mutations enhance first position wobble. Schultz DW, Yarus M. J Mol Biol. 1994 Feb 4;235(5):1381-94. doi: 10.1006/jmbi.1994.1095.
tRNA on the Ribosome: a Waggle Theory. Michael Yarus, Drew Smith. In tRNA: structure, biosynthesis and function. Book Editor(s):Dieter Söll, Uttam L. RajBhandary. 1994. https://doi.org/10.1128/9781555818333.ch22
tRNA-tRNA interactions within cellular ribosomes. Smith D, Yarus M. Proc Natl Acad Sci U S A. 1989 Jun;86(12):4397-401. doi: 10.1073/pnas.86.12.4397.
Mutation in the D arm enables a suppressor with a CUA anticodon to read both amber and ochre codons in Escherichia coli. Raftery LA, Bermingham JR Jr, Yarus M. J Mol Biol. 1986 Aug 5;190(3):513-7. doi: 10.1016/0022-2836(86)90020-3.
Construction of a systematic set of tRNA mutants by ligation of synthetic oligonucleotides into defined single-stranded gaps. Cline SW, Yarus M, Wier P. DNA. 1986 Feb;5(1):37-51. doi: 10.1089/dna.1986.5.37.
Site-specific mutagenesis of Escherichia coli gltT yields a weak, glutamic acid-inserting ochre suppressor. Raftery LA, Yarus M. J Mol Biol. 1985 Jul 20;184(2):343-5. doi: 10.1016/0022-2836(85)90385-7.
Translational efficiency of transfer RNA's: uses of an extended anticodon. Science. 1982 Nov 12;218(4573):646-52. doi: 10.1126/science.6753149.
Dual specificity of su+ 7 tRNA. Evidence for translational discrimination. Knowlton RG, Soll L, Yarus M. J Mol Biol. 1980 Jun 5;139(4):705-20. doi: 10.1016/0022-2836(80)90056-x.
Construction of a composite tRNA gene by anticodon loop transplant. Yarus M, McMillan C 3rd, Cline S, Bradley D, Snyder M. Proc Natl Acad Sci U S A. 1980 Sep;77(9):5092-6. doi: 10.1073/pnas.77.9.5092.
Control of ribosome synthesis and amber suppression
Mutations that overcome plasmid-mediated relaxation affect (p)ppGpp. Breeden L, Yarus M. Mol Gen Genet. 1980;179(1):119-24. doi: 10.1007/BF00268453.
A transition state analogue for the peptidyl transferase – key to the ribosomal active center
Peptidyl transferase: ancient and exiguous. Yarus M, Welch M. Chem Biol. 2000 Oct;7(10):R187-90. doi: 10.1016/s1074-5521(00)00027-2.
23S rRNA similarity from selection for peptidyl transferase mimicry. Welch M, Majerfeld I, Yarus M. Biochemistry. 1997 Jun 3;36(22):6614-23. doi: 10.1021/bi963135j.
An inhibitor of ribosomal peptidyl transferase using transition-state analogy. Welch M, Chastang J, Yarus M. Biochemistry. 1995 Jan 17;34(2):385-90. doi: 10.1021/bi00002a001.
Translational accuracy – aa-tRNA editing discovered (simultaneous with Paul Schimmel lab)
Proofreading, NTPases and translation: successful increase in specificity. Trends Biochem Sci. 1992 May;17(5):171-4. doi: 10.1016/0968-0004(92)90257-a.
Intrinsic precision of aminoacyl-tRNA synthesis enhanced through parallel systems of ligands. Nat New Biol. 1972 Sep 27;239(91):106-8. doi: 10.1038/newbio239106a0.
Solvent and specificity. Binding and isoleucylation of phenylalanine transfer ribonucleic acid (Escherichia coli) by isoleucyl transfer ribonucleic acid synthetase from Escherichia coli. Biochemistry. 1972 Jun 6;11(12):2352-61. doi: 10.1021/bi00762a022.
Phenylalanyl-tRNA synthetase and isoleucyl-tRNA Phe : a possible verification mechanism for aminoacyl-tRNA. Proc Natl Acad Sci U S A. 1972 Jul;69(7):1915-9. doi: 10.1073/pnas.69.7.1915.