Operational RNA Code for Amino Acids in Relation to Genetic Code in Evolution

aminoacyl-tRNA synthetase(s) base pair(s) The genetic code is based on the specific aminoacylation of transfer RNAs (tRNAs) by aminoacyl-tRNA synthetases (aaRS)1 (1Giegé R. Sissler M. Florentz C. Nucleic Acids Res. 1998; 26: 5017-5035Crossref PubMed Scopus (648) Google Scholar, 2Beuning P.J. Musier-Forsyth K. Biopolymers. 1999; 52: 1-28Crossref PubMed Scopus (128) Google Scholar). This reaction links anticodon triplets in tRNAs with specific amino acids. The specificity of the reaction is governed by tRNA identity elements that are recognized by the aminoacylating enzymes (2Beuning P.J. Musier-Forsyth K. Biopolymers. 1999; 52: 1-28Crossref PubMed Scopus (128) Google Scholar). The universal distribution and conservation of tRNAs and aaRS imply that they preceded the origin of the three kingdoms of life, Bacteria, Archae, and Eucarya (3Nagel G.M. Doolittle R.F. Proc. Natl. Acad. Sci. U. S. A. 1991; 88: 8121-8125Crossref PubMed Scopus (112) Google Scholar, 4Nagel G.M. Doolittle R.F. J. Mol. Evol. 1995; 40: 487-498Crossref PubMed Scopus (109) Google Scholar, 5Brown J.R. Doolittle W.F. Proc. Natl. Acad. Sci. U. S. A. 1995; 92: 2441-2445Crossref PubMed Scopus (315) Google Scholar). Significantly, nucleotide determinants other than the anticodon triplets are important for aminoacylation efficiency and specificity (6Musier-Forsyth K. Schimmel P. Acc. Chem. Res. 1999; 32: 368-375Crossref Scopus (41) Google Scholar, 7Martinis S.A. Schimmel P. Neidhart F. Escherichia coli and Salmonella. 1. American Society for Microbiology, Washington, D. C.1996: 887-901Google Scholar). It is these nucleotides (making up an operational RNA code) that are now seen as important for maintaining a universal genetic code. Typically, aminoacylation occurs in two steps. E+AA+ATP↔E(AA­AMP)+PPi E(AA­AMP)+tRNA↔E+AA­tRNA+AMP REACTIONS1AND2First, the enzyme (E) condenses its cognate amino acid (AA) with ATP to form a tightly bound aminoacyl adenylate (AA-AMP) with the release of pyrophosphate (PPi). The aminoacyl group is then transferred to the 3′-end of tRNA to give aminoacyl-tRNA (AA-tRNA) and release of AMP. In this way, a specific nucleotide triplet (anticodon) in the tRNA is physically connected (through the tRNA structure) with a particular amino acid. Transfer RNAs are usually comprised of 76 nucleotides arranged into a cloverleaf structure with four major arms. The acceptor stem is a helix of 7 bp that ends on the 3′-side with the universal tetranucleotide NCCA76, with the amino acid attachment site at A76. The dihydrouridine-, TψC-, and anticodon-stem-loop make up the other three arms (Fig. 1). The four arms are arranged in three dimensions into an L-shaped structure (8Kim S.H. Suddath F.L. Quigley G.J. McPherson A. Sussman J.L. Wang A.H. Seeman N.C. Rich A. Science. 1974; 185: 435-440Crossref PubMed Scopus (758) Google Scholar, 9Robertus J.D. Ladner J.E. Finch J.T. Rhodes D. Brown R.S. Clark B.F. Klug A. Nature. 1974; 250: 546-551Crossref PubMed Scopus (808) Google Scholar), where the acceptor and TψC stems stack together to make up a 12-bp hairpin known as the minihelix (ending in the TψC loop) (10Francklyn C. Schimmel P. Nature. 1989; 337: 478-481Crossref PubMed Scopus (280) Google Scholar). At right angles, the D- and anticodon stems fuse to give a 10-bp helix with the D-loop at one end and the anticodon loop at the other. Thus, the triplet of the code and its cognate amino acid are in distinct domains at opposite ends of the tRNA structure (Fig. 1). The minihelix domain terminating in the CCA trinucleotide is found as a regulatory element for replication of specific RNA genomes (11Maizels N. Weiner A.M. Proc. Natl. Acad. Sci. U. S. A. 1994; 91: 6729-6734Crossref PubMed Scopus (169) Google Scholar, 12Weiner A.M. Maizels N. Biol. Bull. 1999; 196: 327-330Crossref PubMed Scopus (31) Google Scholar). In the ribosome, the anticodon-containing and the minihelix domain bind to distinct rRNAs (13Cate J.H. Yusupov M.M. Yusupova G.Z. Earnest T.N. Noller H.F. Science. 1999; 285: 2095-2104Crossref PubMed Scopus (524) Google Scholar). This observation raises the possibility that the minihelix and anticodon-containing domains had separate origins. That an ancient minihelix duplicated and gave rise to the anticodon-containing domain and genetic code has also been proposed (14Noller H.F. Gesteland R.F. Atkins J.F. The RNA World. Cold Spring Harbor Laboratory, Cold Spring Harbor, NY1993: 137-156Google Scholar). In bacteria, there typically is one aaRS for each amino acid. In eukaryotes, distinct nuclear encoded cytoplasmic and mitochondrial enzymes carry out aminoacylations in their respective cellular compartments. Broadly speaking, the enzymes are comprised of two major domains. The historical, most ancient domain contains the catalytic site with determinants for binding the minihelix portion of the tRNA. These catalytic domains are limited to two folds that define two families known as classes I and II (15Webster T. Tsai H. Kula M. Mackie G.A. Schimmel P. Science. 1984; 226: 1315-1317Crossref PubMed Scopus (210) Google Scholar, 16Ludmerer S.W. Schimmel P. J. Biol. Chem. 1987; 262: 10801-10806Abstract Full Text PDF PubMed Google Scholar, 17Eriani G. Delarue M. Poch O. Gangloff J. Moras D. Nature. 1990; 347: 203-206Crossref PubMed Scopus (1190) Google Scholar, 18Moras D. Trends Biochem. Sci. 1992; 17: 159-164Abstract Full Text PDF PubMed Scopus (200) Google Scholar, 19Cusack S. Nat. Struct. Biol. 1995; 2: 824-831Crossref PubMed Scopus (201) Google Scholar). (With rare exceptions, each class contains enzymes specific for 10 different amino acids.) Most of the structural evolution that gave rise to the two classes of synthetases took place before the first split of the universal tree of life based on analyses of 16 S RNA sequences (4Nagel G.M. Doolittle R.F. J. Mol. Evol. 1995; 40: 487-498Crossref PubMed Scopus (109) Google Scholar, 5Brown J.R. Doolittle W.F. Proc. Natl. Acad. Sci. U. S. A. 1995; 92: 2441-2445Crossref PubMed Scopus (315) Google Scholar, 20Woese C.R. Microbiol. Rev. 1987; 51: 221-271Crossref PubMed Google Scholar). The synthetases also have a second major domain that, in many instances, interacts with the anticodon. The idiosyncratic structures of these domains, even for enzymes within the same class, suggest that the second domain was added later in evolution. An obvious way for an aaRS to relate a specific amino acid to a nucleotide triplet is through direct recognition of the tRNA anticodon. However, the anticodon is not used as the principal determinant for aminoacylation by alanyl-, seryl-, or leucyl-tRNA synthetases (1Giegé R. Sissler M. Florentz C. Nucleic Acids Res. 1998; 26: 5017-5035Crossref PubMed Scopus (648) Google Scholar). For example, bacterial and eukaryote cytoplasmic alanyl-tRNA synthetase throughout evolution rely on a specific G3:U70 base pair in the acceptor stem to define the identity of tRNAAla (21Hou Y.M. Schimmel P. Nature. 1988; 333: 140-145Crossref PubMed Scopus (516) Google Scholar, 22McClain W.H. Foss K. Science. 1988; 241: 1804-1807Crossref PubMed Scopus (114) Google Scholar, 23Hou Y.M. Schimmel P. Biochemistry. 1989; 28: 6800-6804Crossref PubMed Scopus (97) Google Scholar, 24Ripmaster T.L. Shiba K. Schimmel P. Proc. Natl. Acad. Sci. U. S. A. 1995; 92: 4932-4936Crossref PubMed Scopus (40) Google Scholar, 25Shiba K. Ripmaster T. Suzuki N. Nichols R. Plotz P. Noda T. Schimmel P. Biochemistry. 1995; 34: 10340-10349Crossref PubMed Scopus (35) Google Scholar) (Fig. 2). No physical contact is made by the enzyme with the anticodon (26Park S.J. Schimmel P. J. Biol. Chem. 1988; 263: 16527-16530Abstract Full Text PDF PubMed Google Scholar). As a consequence, a minihelix or even smaller helices (e.g.microhelices of 7 bp) that contain a G3:U70 base pair are robust substrates for aminoacylation by bacterial, yeast, and human enzymes (10Francklyn C. Schimmel P. Nature. 1989; 337: 478-481Crossref PubMed Scopus (280) Google Scholar, 24Ripmaster T.L. Shiba K. Schimmel P. Proc. Natl. Acad. Sci. U. S. A. 1995; 92: 4932-4936Crossref PubMed Scopus (40) Google Scholar, 25Shiba K. Ripmaster T. Suzuki N. Nichols R. Plotz P. Noda T. Schimmel P. Biochemistry. 1995; 34: 10340-10349Crossref PubMed Scopus (35) Google Scholar). Variants of these substrates with natural and non-natural base analogs have been useful for evaluating energetic contributions of the G3:U70 base pair (6Musier-Forsyth K. Schimmel P. Acc. Chem. Res. 1999; 32: 368-375Crossref Scopus (41) Google Scholar, 27Musier-Forsyth K. Usman N. Scaringe S. Doudna J. Green R. Schimmel P. Science. 1991; 253: 784-786Crossref PubMed Scopus (137) Google Scholar, 28Musier-Forsyth K. Schimmel P. Nature. 1992; 357: 513-515Crossref PubMed Scopus (106) Google Scholar, 29Musier-Forsyth K. Shi J.-P. Henderson B. Bald R. Fürste J.P. Erdmann V.A. Schimmel P. J. Am. Chem. Soc. 1995; 117: 7523-7524Crossref Scopus (32) Google Scholar). These observations are mirrored by numerous examples of tRNA synthetases that charge microhelices based on the sequences of the acceptor stems of their cognate tRNAs (6Musier-Forsyth K. Schimmel P. Acc. Chem. Res. 1999; 32: 368-375Crossref Scopus (41) Google Scholar, 7Martinis S.A. Schimmel P. Neidhart F. Escherichia coli and Salmonella. 1. American Society for Microbiology, Washington, D. C.1996: 887-901Google Scholar, 10Francklyn C. Schimmel P. Nature. 1989; 337: 478-481Crossref PubMed Scopus (280) Google Scholar, 30–44). Thus, despite synthetase contacts with the anticodon (45Saks M.E. Sampson J.R. Abelson J.N. Science. 1994; 263: 191-197Crossref PubMed Scopus (150) Google Scholar), the acceptor stem often contains determinants sufficient for specific aminoacylations. The sequences/structures in RNA oligonucleotides that mimic the acceptor stem and confer specific aminoacylations constitute an operational RNA code for amino acids (46Schimmel P. Giegé R. Moras D. Yokoyama S. Proc. Natl. Acad. Sci. U. S. A. 1993; 90: 8763-8768Crossref PubMed Scopus (352) Google Scholar) (also referred to as the “second genetic code” (47De Duve C. Blueprint for a Cell: The Nature and Origin of Life. Neil Patterson, Burlington, NC1991Google Scholar, 48de Duve C. Nature. 1988; 333: 117-118Crossref PubMed Scopus (138) Google Scholar)). These determinants typically are comprised of 1–3 bp and the N73 “discriminator” base. The operational RNA code may have predated the genetic code and according to some analyses was the progenitor of the genetic code (6Musier-Forsyth K. Schimmel P. Acc. Chem. Res. 1999; 32: 368-375Crossref Scopus (41) Google Scholar, 48de Duve C. Nature. 1988; 333: 117-118Crossref PubMed Scopus (138) Google Scholar, 49Moller W. Janssen G.M. J. Mol. Evol. 1992; 34: 471-477Crossref PubMed Scopus (53) Google Scholar, 50Dick T.P. Schamel W.A. J. Mol. Evol. 1995; 41: 1-9Crossref PubMed Scopus (46) Google Scholar, 51Rodin S. Rodin A. Ohno S. Proc. Natl. Acad. Sci. U. S. A. 1996; 93: 4537-4542Crossref PubMed Scopus (88) Google Scholar, 52Di Giulio M. J. Mol. Evol. 1997; 45: 571-578Crossref PubMed Scopus (68) Google Scholar). The tyrosine and glycine systems illustrate how the position of acceptor stem determinants for aminoacylation, but not the determinants themselves, have been conserved (1Giegé R. Sissler M. Florentz C. Nucleic Acids Res. 1998; 26: 5017-5035Crossref PubMed Scopus (648) Google Scholar, 2Beuning P.J. Musier-Forsyth K. Biopolymers. 1999; 52: 1-28Crossref PubMed Scopus (128) Google Scholar). For example, eubacterial TyrRS do not aminoacylate eukaryotic cytoplasmic tRNATyr (53Nair S. Ribas de Pouplana L. Houman F. Avruch A. Shen X. Schimmel P. J. Mol. Biol. 1997; 269: 1-9Crossref PubMed Scopus (25) Google Scholar). Conversely, eubacterial tRNATyr cannot be aminoacylated by eukaryotic TyrRS. This domain specificity correlates with the change of the conventional G1:C72 base pair found in most tRNAs to C1:G72 in eukaryotic and archaeal tRNATyrsequences. 2M. Sprinzl, K. S. Vassilenko, J. Emmerich, and F. Bauer, unpublished data. The 1:72 base pair was demonstrated to be important for aminoacylation of microhelices or tRNAs based on sequences of tyrosine acceptors inBacillus stearothermophilus (55Bedouelle H. Biochimie ( Paris ). 1990; 72: 589-598Crossref PubMed Scopus (68) Google Scholar), the eukaryote pathogenPneumocystis carinii (56Quinn C.L. Tao N. Schimmel P. Biochemistry. 1995; 34: 12489-12495Crossref PubMed Scopus (56) Google Scholar), the yeast Saccharomyces cerevisiae (56Quinn C.L. Tao N. Schimmel P. Biochemistry. 1995; 34: 12489-12495Crossref PubMed Scopus (56) Google Scholar), and humans (57Wakasugi K. Quinn C.L. Tao N. Schimmel P. EMBO J. 1998; 17: 297-305Crossref PubMed Scopus (93) Google Scholar). Indeed, changing G1:C72 to C1:G72 is sufficient to reverse the cross-domain specificity, that is to enable a synthetase from bacteria to charge a substrate based on the RNA sequence from an eukaryote or vice versa (Fig.3) (57Wakasugi K. Quinn C.L. Tao N. Schimmel P. EMBO J. 1998; 17: 297-305Crossref PubMed Scopus (93) Google Scholar). Remarkably, these aminoacylation barriers could be overcome through the generation of chimeric enzymes that contained a 39-amino acid fragment of the eukaryotic enzyme within the context of the eubacterial TyrRS (57Wakasugi K. Quinn C.L. Tao N. Schimmel P. EMBO J. 1998; 17: 297-305Crossref PubMed Scopus (93) Google Scholar). Conversely, incorporation of the bacterial peptide fragment into the body of the human enzyme enabled the latter to charge the bacterial substrate while losing its ability to charge the human RNA. These experiments illustrate that the position of a determinant important for aminoacylation was conserved and that coadaptations by the cognate synthetase maintain specific recognition. A similar principle presumably operates with glycyl-tRNA synthetases (Fig. 3) (58Shiba K. Schimmel P. Motegi H. Noda T. J. Biol. Chem. 1994; 269: 30049-30055Abstract Full Text PDF PubMed Google Scholar, 59Hipps D. Shiba K. Henderson B. Schimmel P. Proc. Natl. Acad. Sci. U. S. A. 1995; 92: 5550-5552Crossref PubMed Scopus (55) Google Scholar). Thus, acceptor-stem positions important for aminoacylation have been conserved across phyla, and variations at these positions can account for domain specificity of aminoacylation. Unlike most species, the archaebacterium Methanococcus jannaschii does not have a gene coding for a class II lysyl-tRNA synthetase (60Bult C.J. White O. Olsen G.J. Zhou L. Fleischmann R.D. Sutton G.G. Blake J.A. FitzGerald L.M. Clayton R.A. Gocayne J.D. Kerlavage A.R. Dougherty B.A. Tomb J.F. Adams M.D. Reich C.I. Overbeek R. Kirkness E.F. Weinstock K.G. Merrick J.M. Glodek A. Scott J.L. Geoghagen N.S.M. Venter J.C. Science. 1996; 273: 1058-1073Crossref PubMed Scopus (2290) Google Scholar). Instead, aminoacylation of tRNALys is catalyzed by a class I enzyme (61Ibba M. Morgan S. Curnow A.W. Pridmore D.R. Vothknecht U.C. Gardner W. Lin W. Woese C.R. Söll D. Science. 1997; 278: 1119-1122Crossref PubMed Scopus (174) Google Scholar). Phylogenetic analysis of the novel class I LysRS showed that its origin cannot be explained by a recent gene transfer event (62Ribas de Pouplana L. Turner R.J. Steer B.A. Schimmel P. Proc. Natl. Acad. Sci. U. S. A. 1998; 95: 11295-11300Crossref PubMed Scopus (65) Google Scholar). Analysis of sequences of tRNALys from all phylogenetic domains showed that tRNALys does not divide into two groups that follow the distribution of its two different aminoacylating enzymes (62Ribas de Pouplana L. Turner R.J. Steer B.A. Schimmel P. Proc. Natl. Acad. Sci. U. S. A. 1998; 95: 11295-11300Crossref PubMed Scopus (65) Google Scholar). The coherence of the tRNALys sequences implies that the identity of this tRNA was established independently (and probably before) the establishment of the two forms of LysRS (62Ribas de Pouplana L. Turner R.J. Steer B.A. Schimmel P. Proc. Natl. Acad. Sci. U. S. A. 1998; 95: 11295-11300Crossref PubMed Scopus (65) Google Scholar). This situation is unlike the case of glutaminyl- and asparaginyl-tRNA synthetases. These two aaRS appeared later in evolution as result of duplications of genes for glutamyl- and aspartyl-tRNA synthetases, respectively, that were laterally transferred across the phylogenetic tree (63Lamour V. Quevillon S. Diriong S. N′Guyen V.C. Lipinski M. Mirande M. Proc. Natl. Acad. Sci. U. S. A. 1994; 91: 8670-8674Crossref PubMed Scopus (135) Google Scholar, 64Woese C.R. Olsen G.J. Ibba M. Söll D. Microbiol. Mol. Biol. Rev. 2000; 64: PubMed Scopus Google Scholar). I tRNA synthetases the of the acceptor stem class II enzymes tRNA from the major D. Trends Biochem. Sci. 1992; 17: 159-164Abstract Full Text PDF PubMed Scopus (200) Google Scholar, Söll D. Science. 1989; PubMed Scopus Google Scholar, M. S. M. A. A. A. B. J.C. Moras D. Science. 1991; PubMed Scopus Google Scholar, C. S. C. J.L. Biochimie ( Paris ). 1995; PubMed Scopus Google Scholar). tRNALys contain an important and can be aminoacylated by class I and class II LysRS M. H. S. Söll D. Proc. Natl. Acad. Sci. U. S. A. 1999; PubMed Scopus Google Scholar). This result implies that opposite (and distinct of the same base pair are recognized by the two of In tRNALys from the that has a class I contains a base pair at position This base pair aminoacylation of tRNALys by class II Escherichia coli LysRS M. H. S. Söll D. Proc. Natl. Acad. Sci. U. S. A. 1999; PubMed Scopus Google Scholar). Thus, of the class II LysRS by its class I in was of a in the operational RNA code for that with class II LysRS M. H. S. Söll D. Proc. Natl. Acad. Sci. U. S. A. 1999; PubMed Scopus Google Scholar, P. Ribas de Pouplana L. Proc. Natl. Acad. Sci. U. S. A. 1999; PubMed Scopus Google Scholar) suggest that the evolution of identity elements in tRNAs may have been one of the for of forms of aminoacyl-tRNA synthetases. In to the conservation of G3:U70 to a tRNA for aminoacylation with (Fig. aspartyl-tRNA synthetase has a conserved for recognition of through with the anticodon triplet and the base (1Giegé R. Sissler M. Florentz C. Nucleic Acids Res. 1998; 26: 5017-5035Crossref PubMed Scopus (648) Google Scholar, J. J.D. Florentz C. Giegé R. Science. 1991; PubMed Scopus Google Scholar). A phylogenetic tree with that its distribution is with the tree of life H. L. G. D. Biochemistry. 2000; PubMed Scopus Google Scholar). and are the to the same C.R. Olsen G.J. Ibba M. Söll D. Microbiol. Mol. Biol. Rev. 2000; 64: PubMed Scopus Google Thus, be that an enzyme that a of universal identity elements transfer species, the of genes coding for has not been to gene across different that the of examples of may be to the ability of to the in For example, in a synthetase is The aminoacylation of with is through an of catalyzed by is by a catalyzed by a separate enzyme A. S. Söll D. Nature. 1988; PubMed Scopus Google archaeal contains the important archaeal has a recognition for the anticodon. In is to the base at position anticodon and L. S. T. J.C. Moras D. EMBO J. 1998; 17: PubMed Scopus Google Scholar). and eukaryotic do not this of they a that probably as a of an ancient The distribution of may in archaeal an enzyme of tRNA Thus, these cannot a bacterial or eukaryotic that not aminoacylate an that contains a and an the of transfer of an archaeal into This situation could an H. L. G. D. Biochemistry. 2000; PubMed Scopus Google Scholar). In from the aminoacylation of by to a of with the archaeal and later the into a reaction H. L. G. D. Biochemistry. 2000; PubMed Scopus Google Scholar). Indeed, the is found in T. D. Proc. Natl. Acad. Sci. U. S. A. 1998; 95: PubMed Scopus Google Scholar). At the of of the the operational RNA code had the to to the of of of RNA These tRNAs to cellular RNAs as that could and a tRNA elements in tRNA acceptor stems in different aminoacylations of many different These aminoacylation barriers genetic genes for tRNAs and their synthetases and were probably important to of the genetic code. In two distinct synthetases for the same amino acid are gene or of gene then can in one of while the other is It is that be but with tRNAs or tRNAs could the amino acid or tRNA specificity and in the acid S.J. R.D. Trends Biochem. Sci. 2000; Full Text Full Text PDF PubMed Scopus (35) Google Scholar). of the universal genetic code has in rare instances, but its conservation to the of its In this the operational RNA code for aminoacylation of tRNA as a of the code through This for tRNA recognition most tRNA synthetases in bacteria and are encoded by the for of the genetic code is The situation in is the A distinct gene is for a synthetase in each the and The of and eubacterial gave rise to the eukaryotic and and T. N. Acad. Sci. 1987; PubMed Scopus Google Scholar). The of these had to of their systems for aminoacylation. The to the duplicated systems could have been by the in the synthetases (and acceptor stem that were R.F. J. 1998; PubMed Scopus Google C.R. Olsen G.J. Ibba M. Söll D. Microbiol. Mol. Biol. Rev. 2000; 64: PubMed Scopus Google Scholar). two and that the same genetic code. For example, two genes for the same enzyme and are encoded by the genomes of The possibility for two of the same enzyme up in the same cellular is a mitochondrial enzyme to the same acceptor stem elements as its cytoplasmic the of two synthetases in the to the same acceptor to and the genetic code distinct recognition elements for the mitochondrial the of an is This may account in for acceptor stem elements for from their cytoplasmic than is typically seen for the same elements across domains. Thus, throughout evolution the G3:U70 base pair a tRNA for aminoacylation with (Fig. G3:U70 is often not found in mitochondrial G3:U70 is found in of other Analysis of identity elements for other mitochondrial tRNA sequences that tRNAAla is not an The variations in mitochondrial tRNA identity elements may also be in to a of In the of tRNA genes in mitochondrial genomes is coli contains tRNA and the human contains This that aaRS tRNA synthetases now have to a smaller of tRNA these the to maintain a of identity elements is In the genetic code is seen as throughout evolution all domains and in with their separate as a of in the identity elements in tRNA acceptor stems that constitute an operational RNA code. These are a of the to anticodon sequences to have a universal on the one and on the the to the and of This ancient RNA may have with the aminoacylation of of tRNAs by has the genetic code was established a of the code from tRNA synthetases with amino that from of the universal code. It also of its to to and of RNAs and the of that they