Abstract
Thermodynamic stability and mutational robustness of secondary structure are critical to the function and evolutionary longevity of RNA molecules. We hypothesize that natural and artificial selection for functional molecules favors the formation of structures that are stable to both thermal and mutational perturbation. There is little direct evidence, however, that functional RNA molecules have been selected for their stability. Here we use thermodynamic secondary structure prediction algorithms to compare the thermal and mutational robustness of over 1000 naturally and artificially evolved molecules. Although we find evidence for the evolution of both types of stability in both sets of molecules, the naturally evolved functional RNA molecules were significantly more stable than those selected in vitro, and artificially evolved catalysts (ribozymes) were more stable than artificially evolved binding species (aptamers). The thermostability of RNA molecules bred in the laboratory is probably not constrained by a lack of suitable variation in the sequence pool but, rather, by intrinsic biases in the selection process.
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References
LW Ancel W Fontana (2000) ArticleTitlePlasticity, evolvability and modularity in RNA J Exp Zool (Mol Dev Evol) 288 242–283 Occurrence Handle10.1002/1097-010X(20001015)288:3<242::AID-JEZ5>3.0.CO;2-O Occurrence Handle1:CAS:528:DC%2BD3cXnsFChs70%3D
JM Bevilacqua PC Bevilacqua (1998) ArticleTitleThermodynamic analysis of an RNA combinatorial library contained in a short hairpin Biochemistry 37 15877–15884 Occurrence Handle10.1021/bi981732v Occurrence Handle1:CAS:528:DyaK1cXmsleitbs%3D Occurrence Handle9843393
E Bornberg-Bauer HS Chan (1999) ArticleTitleModeling evolutionary landscapes: Mutational stability, topology, and superfunnels in sequence space Proc Natl Acad Sci USA 96 10689–10694 Occurrence Handle10.1073/pnas.96.19.10689 Occurrence Handle1:CAS:528:DyaK1MXmtFKjsr4%3D Occurrence Handle10485887
HJ Bussemaker D Thirumalai JK Bhattacharjee (1997) ArticleTitleThermodynamic stability of folded proteins against mutations Phys Rev Lett 79 3530–3533 Occurrence Handle10.1103/PhysRevLett.79.3530 Occurrence Handle1:CAS:528:DyaK2sXntFGntLo%3D
A Calcagnile T Basic-Zaninovic F Plombo E Dogliotti (1996) ArticleTitleMisincorporation rate and type on the leading and lagging strands of UV-damaged DNA Nucleic Acids Res 15 3005–3009 Occurrence Handle10.1093/nar/24.15.3005
C Claesson T Samuelsson F Lustig T Boren (1990) ArticleTitleCodon reading properties of an unmodified transfer RNA FEBS Lett 273 173–176 Occurrence Handle10.1016/0014-5793(90)81077-2 Occurrence Handle1:CAS:528:DyaK3MXjslyktw%3D%3D Occurrence Handle2226850
EC Cox C Yanofsky (1967) ArticleTitleAltered base ratios in the DNA of an Escherichia coli mutator strain Proc Natl Acad Sci USA 58 1895–1902 Occurrence Handle1:CAS:528:DyaF1cXislKltQ%3D%3D Occurrence Handle4866980
W Gilbert (1986) ArticleTitleThe RNA world Nature . 319–618
PA Gottlieb Y Prasad JB Smith AP Williams G Dinter-Gottlieb (1994) ArticleTitleEvidence that alternate foldings of the hepatitis delta RNA confer varying rates of self-cleavage Biochemistry 33 2802–2808 Occurrence Handle10.1021/bi00176a008 Occurrence Handle1:CAS:528:DyaK2cXhsFOntrY%3D Occurrence Handle8130192
S Griffiths-Jones A Bateman M Marshall A Khanna SR Eddy (2003) ArticleTitleRfam: An RNA family database Nucleic Acids Res 31 439–441 Occurrence Handle10.1093/nar/gkg006 Occurrence Handle1:CAS:528:DC%2BD3sXhvFSls7w%3D Occurrence Handle12520045
F Guo TR Cech (2002) ArticleTitleEvolution of Tetrahymena ribozyme mutants with increased structural stability Nat Struct Biol 9 855–861 Occurrence Handle1:CAS:528:DC%2BD38XosFCjsLY%3D Occurrence Handle12368901
KM Harrington IA Nazarenko DB Dix RC Thompson OC Uhlenbeck (1993) ArticleTitleIn vitro analysis of translational rate and accuracy with an unmodified tRNA Biochemistry 32 7617–7622 Occurrence Handle10.1021/bi00081a003 Occurrence Handle1:CAS:528:DyaK3sXks1Grs74%3D Occurrence Handle7688564
IL Hofacker W Fontana PF Stadler LS Bonhoeffer M Tacker P Schuster (1994) ArticleTitleFast folding and comparison of RNA secondary structures Monatsh Chem 125 167–199 Occurrence Handle10.1007/BF00818163 Occurrence Handle1:CAS:528:DyaK2cXivFaht7k%3D
KD James AD Ellington (1999) ArticleTitleThe fidelity of template-directed oligonucleotide ligation and the inevitability of polymerase function Orig Life Evol Biosph 29 375–390 Occurrence Handle1:CAS:528:DyaK1MXlvF2hsLo%3D Occurrence Handle10472627
EC Lai (2003) ArticleTitleRNA sensors and riboswitches: Self-regulating messages Curr Biol 13 R285–R291 Occurrence Handle1:CAS:528:DC%2BD3sXislChsLY%3D Occurrence Handle12676109
J Lambert N Moran (1998) ArticleTitleDeleterious mutations destabilize ribosomal RNA in endosymbiotic bacteria Proc Natl Acad Sci USA 95 4458–4462 Occurrence Handle1:CAS:528:DyaK1cXis1Ogsr0%3D Occurrence Handle9539759
M Levy AD Ellington (2001) ArticleTitleThe descent of polymerization Nat Struct Biol 8 580–582 Occurrence Handle1:CAS:528:DC%2BD3MXkvFCrs74%3D Occurrence Handle11427883
TM Lowe SR Eddy (1997) ArticleTitletRNAscan-SE: A program for improved detection of transfer RNA genes in genomic sequence Nucleic Acids Res 25 955–964 Occurrence Handle1:CAS:528:DyaK2sXhvVahtrk%3D Occurrence Handle9023104
M Lynch (1996) ArticleTitleMutation accumulation in transfer RNAs: molecular evidence for Muller’s ratchet in mitochondrial genomes Mol Biol Evol 13 209–202 Occurrence Handle1:CAS:528:DyaK28XhtVylu7w%3D Occurrence Handle8583893
M Lynch (1997) ArticleTitleMutation accumulation in nuclear, organelle, and prokaryotic transfer RNA genes Mol Biol Evol 14 914–925 Occurrence Handle1:CAS:528:DyaK2sXlvVejurg%3D Occurrence Handle9287424
DH Mathews J Sabina M Zucker M Turner (1999) ArticleTitleExpanded sequence dependence of thermodynamic parameters provides robust prediction of RNA secondary structure J Mol Biol 288 911–940 Occurrence Handle1:CAS:528:DyaK1MXjtVers7Y%3D Occurrence Handle10329189
JS McCaskill (1990) ArticleTitleThe equilibrium partition function and base pair binding probabilities for RNA secondary structure Biopolymers 29 1105–1119 Occurrence Handle1:CAS:528:DyaK3cXkt1Snurk%3D Occurrence Handle1695107
EM Moody PC Bevilacqua (2003) ArticleTitleThermodynamic coupling of the loop and stem in unusually stable DNA hairpins closed by CG base pairs J Am Chem Soc 125 2032–2033 Occurrence Handle1:CAS:528:DC%2BD3sXnt1Krtg%3D%3D Occurrence Handle12590515
M Nakano EM Moody J Liang PC Bevilacqua (2002) ArticleTitleSelection for thermodynamically stable DNA tetraloops using temperature gradient gel electrophoresis reveals four motifs: d(cGNNAg), d(cGNABg), d(cCNNGg), and d(gCNNGc) Biochemistry 41 14281–14292 Occurrence Handle1:CAS:528:DC%2BD38XotlOmsLg%3D Occurrence Handle12450393
TV Pestova CU Hellen (2001) ArticleTitlePreparation and activity of synthetic unmodified mammalian tRNAi(Met) in initiation of translation in vitro RNA 7 1496–1505 Occurrence Handle1:CAS:528:DC%2BD3MXnvFSrsrk%3D Occurrence Handle11680854
DJ Proctor JE Schaak JM Bevilacqua CJ Falzone PC Bevilacqua (2002) ArticleTitleIsolation and characterization of a family of stable RNA tetraloops with the motif YNMG that participate in tertiary interactions Biochemistry 41 12062–12075 Occurrence Handle1:CAS:528:DC%2BD38XmvFKktL0%3D Occurrence Handle12356306
D Repsilber S Wiese M Rachen AW Schroder D Riesner G Steger (1999) ArticleTitleFormation of metastable RNA structures by sequential folding during transcription: time-resolved structural analysis of potato spindle tuber viroid (−)-stranded RNA by temperature-gradient gel electrophoresis RNA 5 574–584 Occurrence Handle1:CAS:528:DyaK1MXisVCisLo%3D Occurrence Handle10199573
E Rocha A Danchin (2002) ArticleTitleBase composition bias might result from competition for metabolic resources Trends Genet 18 291–294 Occurrence Handle1:CAS:528:DC%2BD38XktVCku7Y%3D Occurrence Handle12044357
K Salehi-Ashtiani JW Szostak (2001) ArticleTitleIn vitro evolution suggests multiple origins for the hammerhead ribozyme Nature 414 82–84 Occurrence Handle1:CAS:528:DC%2BD3MXot1aisbk%3D Occurrence Handle11689947
JR Sampson OC Uhlenbeck (1988) ArticleTitleBiochemical and physical characterization of an unmodified yeast phenylalanine transfer RNA transcribed in vitro Proc Natl Acad Sci USA 85 1033–1037 Occurrence Handle1:CAS:528:DyaL1cXkvVOhs7c%3D Occurrence Handle3277187
T Schmitt N Lehman (1999) ArticleTitleNon-unity molecular heritability demonstrated by continuous evolution in vitro Chem Biol 6 857–869 Occurrence Handle1:CAS:528:DyaK1MXotVygsrw%3D Occurrence Handle10631514
EA Schultes DP Bartel (2000) ArticleTitleOne sequence, two ribozymes: Implications for the emergence of new ribozyme folds Science 289 448–452 Occurrence Handle1:CAS:528:DC%2BD3cXlsV2gtLg%3D Occurrence Handle10903205
Z Shu PC Bevilacqua (1999) ArticleTitleIsolation and characterization of thermodynamically stable and unstable RNA hairpins from a triloop combinatorial library Biochemistry 38 15369–15379 Occurrence Handle1:CAS:528:DyaK1MXmslCksro%3D Occurrence Handle10563823
JB Smith PA Gottlieb G Dinter-Gottlieb (1992) ArticleTitleA sequence element necessary for self-cleavage of the antigenomic hepatitis delta RNA in 20 M formamide Biochemistry 31 9629–9635 Occurrence Handle1:CAS:528:DyaK38XlvVGrt7Y%3D Occurrence Handle1390740
M Szymanski MZ Barciszewska J Barciszewski VA Erdmann (2000) ArticleTitle5S ribosomal RNA database Y2K Nucleic Acids Res 28 166–167 Occurrence Handle1:CAS:528:DC%2BD3cXhvVKjsLc%3D Occurrence Handle10592212
K Takai H Takaku S Yokoyama (1996) ArticleTitleCodon-reading specificity of an unmodified form of Escherichia coli tRNA1Ser in cell-free protein synthesis Nucleic Acids Res 24 2894–2899 Occurrence Handle1:CAS:528:DyaK28XlsFChur4%3D Occurrence Handle8760870
E van Nimwegen JP Crutchfield MA Huynen (1999) ArticleTitleNeutral evoltuion of mutational robustness Proc Natl Acad Sci USA 96 9716–9720 Occurrence Handle1:CAS:528:DyaK1MXlsVymtrk%3D Occurrence Handle10449760
M Vendruscolo A Maritan JR Banavar (1997) ArticleTitleStability threshold as a selection principle for protein design Phys Rev Lett 78 3967–3970 Occurrence Handle1:CAS:528:DyaK2sXjtleku7s%3D
GP Wagner G Booth H Bagheri-Chaichian (1997) ArticleTitleA population genetic theory of canalization Evolution 51 329–347
A Walter D Turner J Kim M Lyttle P Müller D Mathews M Zuker (1994) ArticleTitleCoaxial stacking of helices enhances binding of oligoribonucleotides Proc Natl Acad Sci USA 91 9218–9222 Occurrence Handle1:CAS:528:DyaK2MXhtFWksbc%3D Occurrence Handle7524072
S Wuchty W Fontana IL Hofacker P Schuster (1999) ArticleTitleComplete suboptimal folding of RNA and the stability of secondary structures Biopolymers 49 145–165 Occurrence Handle1:CAS:528:DyaK1MXpsFOqsQ%3D%3D Occurrence Handle10070264
Acknowledgments
The authors thank Walter Fontana and Rob Knight for technical advice and Kourosh Salehi-Ashtiani and Jack Szostak at Mass General Hospital for providing selected ribozyme sequences. This work was supported in part by the Santa Fe Institute and grants from the NSF (Grant DEB-0303636) to L.A.M., grants from the NSF (Grant EIA-0218447) and the NIH–NIBIB (Grant 8R01EB002043) to A.D.E., and NSF-IGERT fellowships in computational phylogenetics to J.F.L and M.C.
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Meyers, L.A., Lee, J.F., Cowperthwaite, M. et al. The Robustness of Naturally and Artificially Selected Nucleic Acid Secondary Structures. J Mol Evol 58, 681–691 (2004). https://doi.org/10.1007/s00239-004-2590-2
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DOI: https://doi.org/10.1007/s00239-004-2590-2