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RNA editing and modifications of RNAs might have favoured the evolution of the triplet genetic code from an ennuplet code
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RNA editing and modifications of RNAs might have favoured the evolution of the triplet genetic code from an ennuplet code Massimo Di Giulio a,n, Marco Moracci b, Beatrice Cobucci-Ponzano b a b
Early Evolution of Life Laboratory, Institute of Biosciences and Bioresources, CNR, Via P. Castellino 111, 80131 Naples, Italy Glycobiology Laboratory, Institute of Biosciences and Bioresources, CNR, Via P. Castellino 111, 80131 Naples, Italy
H I G H L I G H T S
For the origin of the genetic code we consider credible the transition from ennuplet codes to the triplet code. We maintain that an extensive modification of RNAs has been crucial for this transition. RNA editing and post-transcriptional modifications of RNAs are retained vestiges of these modifications and of this transition. Trans-translation and ribosomal frameshifting are also considered by this hypothesis.
art ic l e i nf o
a b s t r a c t
Article history: Received 22 January 2014 Received in revised form 21 May 2014 Accepted 27 May 2014
Here we suggest that the origin of the genetic code, that is to say, the birth of first mRNAs has been triggered by means of a widespread modification of all RNAs (proto-mRNAs and proto-tRNAs), as today observed in the RNA editing and in post-transcriptional modifications of RNAs, which are considered as fossils of this evolutionary stage of the genetic code origin. We consider also that other mechanisms, such as the trans-translation and ribosome frameshifting, could have favoured the transition from an ennuplet code to a triplet code. Therefore, according to our hypothesis all these mechanisms would be reflexive of this period of the evolutionary history of the genetic code. & 2014 Published by Elsevier Ltd.
Keywords: Molecular fossils tmRNA Ribosome frameshifting Genetic code origin
1. Introduction and hypothesis One of the merits of the stereochemical theory of the origin of the genetic code is that it resolves the problem of the origin of the triplet genetic code, suggesting that there was an interaction between codons or anticodons and amino acids (Shimizu, 1982; Szathmary, 1993; Di Giulio, 1997a; Yarus, 1998; Yarus et al., 2009). On the contrary, the models that deny the validity of the stereochemical theory (Wong, 1991; Di Giulio, 1998, 2003, 2008a, 2008b) – suggesting that the triplet code originated from a code having a coding system larger of three bases (ennuplet codes) – have to explain how the reading system has been “reshaped”, moving, for instance, from a reading involving several bases (larger of three) to a triplet code. In particular, one of these models suggests that there has been a very long evolutionary stage that starting from a rudimentary protein synthesis resulted in the triplet genetic code, using intermediate evolutionary stages of ennuplet coding with a number of bases also greater than three
n
Corresponding author. Tel.: þ 39 816132369; fax: þ 39 816132706. E-mail address: [email protected] (M. Di Giulio).
(Di Giulio, 2003; see Fig. 1 in Di Giulio, 2008b). As also highlighted by Crick (1968), this transition is very difficult to realise because, for instance, if a quadruplet code was evolving suddenly to a triplet code, this would be impossible because all messages of the quadruplet code would lose sense if translated by means of the coding system of the triplet code. In other words, this transition would break the evolutionary continuity principle. Therefore, although there are simulations that seem to support an evolution of this kind (Baranov et al., 2009), the difficulty to transform a code that uses a reading system greater than three bases to that of three bases remains. However, this difficulty might be reduced or even eliminated if a set of mechanisms were evolved that favoured the transformation of an ennuplet code to a triplet code. For example, this might have been represented by a mechanism of reading that would have had success to overcome the obstacles deriving from an excessive slowdown or termination of reading, by means of, for instance, the intervention of molecules that restore the translation or were able to shift the protoribosome obtaining the reactivation of translation. In these hypothetical mechanisms of rescue of translation we can see a similarity with some known molecular mechanisms as, for instance, the trans-translation (Muto et al., 1998). Therefore,
http://dx.doi.org/10.1016/j.jtbi.2014.05.037 0022-5193/& 2014 Published by Elsevier Ltd.
Please cite this article as: Di Giulio, M., et al., RNA editing and modifications of RNAs might have favoured the evolution of the triplet genetic code from an ennuplet code. J. Theor. Biol. (2014), http://dx.doi.org/10.1016/j.jtbi.2014.05.037i
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in the certainty that the triplet genetic code originated from an improperly defined ennuplet code (Di Giulio, 2003; see Fig. 1 in Di Giulio, 2008b), we have decided to analyse all those mechanisms that might have favoured the birth of the first messenger RNAs using triplets from an ennuplet code.
2. RNA editing and modifications of RNAs The term “RNA editing” originally described an unusual form of post-transcriptional processing involving the insertion of uridylate (U) residues into an mRNA in the mitochondria of some protozoans (Gray, 2012). Later the mitochondria mRNA editing was found within kinetoplastida affecting many mRNAs, and involving deletions as well as insertions of U (Gray, 2012). Today, the RNA editing has become a generic term used to identify several posttranscriptional processes whose effect is to change the nucleotide sequence of a mature RNA species relative to the encoding DNA sequence (Gray, 2012). RNA editing excludes 50 capping, splicing, and 30 polyadenylation of mRNAs, as well as formation of modified nucleosides in RNA, although the distinction between “editing” and “modification” is somewhat not clear (Gray, 2012). For instance, an editing type involves deamination of adenosine (A) residues to form inosine (I), resulting in the conversion of the 6-aminopurine ring of A to 6-oxopurine in I (Gray, 2012). When this change occurs within the coding region of a mRNA, the edited site (I) is recognised as G during translation (Gray, 2012). However, A residues in the first position of tRNA anticodon also undergo deamination to I, which similarly results in a change in the anticodon pairing properties. Thus at a certain level, editing and modification may be regarded as two sides of the same coin (Gray, 2012). RNA editing has been described in mitochondria, chloroplasts, nuclear and viral genes, although C-to-U editing of tRNAs has been recently observed in Archaea (Randau et al., 2009; Gray, 2012). On the contrary, the modifications of tRNAs, for example, have been described in all the domains of life (Laforest et al., 2004; Heinemann et al., 2012; Machnicka et al., 2013). RNA editing has been considered both as a derived and as an ancestral trait. For instance, Lynch et al. (2006) maintain that RNA editing has been introduced by means of the genetic drift and would be therefore a derived trait. However, the presence of RNA editing among archaea seems to indicate that this interpretation might be false given that archaea have a huge population size that would have made the genetic drift not operative. Gray (2012) too considers RNA editing as a derived trait originated by means of a neutral evolutionary process. On the contrary, other authors have considered RNA editing as an ancestral trait (Landweber and Gilbert, 1994; Di Giulio, 2003, 2008b). The presence of posttranscriptional modifications in all domains of life, as for instance observed in tRNAs, would indicate that they are an ancestral trait. Here, we suggest that RNA editing and more in general all modifications of RNAs, would have had the crucial role to extend and to improve the catalytic performances of RNAs into the RNA world (see also: White, 1976; Reanney, 1977; Wong, 1991; Wong and Xue, 2002; Di Giulio, 1996a, 1996b, 1997b, 2003, 2008b). Both RNA editing and post-transcriptional modifications of RNAs would seem to have to do with the hypothesis here maintained. The G at the 1 position of histidine tRNAs is inserted by means of RNA editing (Heinemann et al., 2012). This position is also the main determinant of the identity of histidine tRNAs (Heinemann et al., 2012). Therefore we can see directly that this RNA editing has had to do with the genetic code origin, because that insertion of one base determines what amino acid will be charged on a specific species of the tRNA, determining the meeting between RNAs and amino acids, that is to say, the genetic code.
More in general, we could say that the insertion, deletion or base modification should have favoured the origin of first mRNAs with triplets, because such events might have created new open reading frames which might have been successfully selected from proto-mRNAs that cannot be read or read correctly. It is possible that the systematic insertion of three bases may have favoured the addition in growing polypeptides of certain amino acids that might have stabilised all polypeptides at high temperature, for instance (Di Giulio, 2003). Furthermore, there is an evolutionary argument even more general and persuasive that is related to the origin of the tRNA molecule. Following a model of the origin of the tRNA molecule, the first anticodons originated in hairpin RNA structures near their 30 end (Hopfield, 1978; de Duve 1988; Moller and Janssen, 1990, 1992; Schimmel et al., 1993; Schimmel and Henderson, 1994; Di Giulio, 1992, 1995, 1997b, 1999, 2004, 2006a, 2006b, 2008c, 2009a, 2009b; Widmann et al., 2005; Rodin et al., 1993, 1996, 2011). This suggestion is in accordance, for instance, with the position that several identity determinants have, exactly in the acceptor stem of tRNA molecules (Schimmel et al., 1993; Xue et al., 1993; Schimmel and Henderson, 1994; Heinemann et al., 2012). It has also been suggested that in this position the identity determinants would remind the existence of a code – called the second genetic code – which is considered more ancient than the genetic code (Hopfield, 1978; de Duve 1988; Moller and Janssen, 1990, 1992; Schimmel et al., 1993; Schimmel and Henderson, 1994; Di Giulio, 1992, 1995, 1997b, 1999, 2004, 2006a, 2006b, 2008c, 2009a, 2009b; Rodin et al., 1993, 1996, 2011). The observation that, for instance, the G at the 1 position is inserted by means of editing in the very acceptor stem of histidine tRNAs, would seem not only to be expression of this second genetic code but, above all, would reflect the position in which the anticodons originated. Therefore, establishing a relationship between the identity determinants and the origin of anticodons (Di Giulio, 1995, 2006a). Ultimately, all this argument would put the editing to the very origin of anticodons and consequently to the origin of the genetic code. The post-transcriptional modification of the CAU anticodon for isoleucine – in which the C (in 34 position) is modified by means of lysine to form lysidine, a modified nucleotide, which is involved both in the recognition of a new anticodon and as identity determinant for the isoleucine tRNA (Muramatsu et al., 1988) – Q4 indicates in a clear way to have been involved in the evolution of the genetic code. For this reason, also all the modifications of anticodons that are widespread in all domains of life (Laforest et al., 2004; Heinemann et al., 2012; Machnicka et al., 2013) would have had to do with the evolution of the genetic code, and in particular with the origin of the triplet code, being these modifications implied also in the codon–anticodon interaction. Therefore, the involvement of these modifications in the origin of the triplet code is evident. On the other hand, for those modifications (or equivalently for RNA editing) that might have altered the sequences of protomRNAs, these might have represented, within the proto-mRNA pool, variants on which natural selection could have operated, selecting for example mutants with crude catalytic activity in their products. In particular, there is a strong evidence that the first proto-mRNAs might have used only G starting codons (Eigen and Winkler-Oswatitsch, 1981; Ikehara, 2002; Di Giulio, 2008a; Higgs and Pudritz, 2009; Francis, 2013). For instance, according to the extended coevolution theory of the genetic code origin, being the majority of amino acids at the head of biosynthetic pathways codified by G starting codons (Di Giulio, 2008a), then it might have occurred that a subset of proto-mRNAs may have been made exactly by this type of codons (for introduction see: Di Giulio, 2003, 2008a, 2008b). Indeed, it is possible to conjecture that the evolutionary passage from the ennuplet code to the triplet code
Please cite this article as: Di Giulio, M., et al., RNA editing and modifications of RNAs might have favoured the evolution of the triplet genetic code from an ennuplet code. J. Theor. Biol. (2014), http://dx.doi.org/10.1016/j.jtbi.2014.05.037i
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might have been favoured, for instance, by a modification of a subset of proto-mRNAs in which many nucleotides in their sequences were transformed to a G every three bases. For example, if several of the developing triplet anticodons would have started to behave like guides used to edit many protomRNAs, then there might have been a partial coevolution between the birth of evolving anticodons and that of codons of first protomRNAs. In other words, the birth of proto-mRNAs containing G (or I) in the first position of codons may have been favoured by means of insertions of G (and/or I) in an editing mechanism in which developing anticodons containing C were used as guide. Furthermore, it might also have occurred an A-to-I editing as today observed into nuclear transcripts of animals (Gray, 2012). Crick (1968) has discussed the possibility that the primitive nucleic acids have initially I in place of G. These modifications might have represented, if positively selected, the crucial passage that would have led to the origin of the genetic code through the coding of all amino acids at the head of the biosynthetic pathways, by means of G starting codons (see Di Giulio, 2003, 2008a, 2008b). The observation that the anticodons are modified by amino acids is reported to be statistically significant (Di Giulio, 1998). This would seem to imply a close evolutionary interaction between amino acids and anticodons for the origin of the genetic code (Di Giulio, 1998; see also below). If this has happened for anticodons then a similar mechanism might have occurred for codons too. Thus the hypothesis that the early phases of the origin of the genetic code, that it to say, the one that led to the birth of first mRNAs, might have been favoured by means of a widespread modification of RNAs (proto-mRNAs and proto-tRNAs), seems to be truly fascinating.
3. tmRNA The transfer-messenger RNA (tmRNA) has a tRNA-like structure at its 50 and 30 termini, and presents a reading frame encoding a “tag” peptide (Muto et al., 1998). The double structure of this molecule as tRNA and mRNA is such to facilitate a transtranslational reaction (Muto et al., 1998). In this reaction the ribosome can switch between the translation of a truncated mRNA and the tmRNA’s tag sequence. The result is a chimerical protein with the tag peptide attached to the C-terminus end of the truncated peptide that can be thus degraded (Muto et al., 1998). The tmRNA is present in all the bacterial domain and viruses, therefore it seems to be a very ancient molecule. This and other features are such to make to believe that it was part of the primitive protein synthesis; that is to say, it is a molecular fossil of an evolutionary stage of the ancestral protein synthesis (Di Giulio, 2003, 2008b). The tmRNA seems to be in relationship with the hypothesis here maintained, for the following reasons. Being the tmRNA able to reactivate the translation of a truncated mRNA, it would have been able during the genetic code evolution to remove all translations that were abortive in some way, therefore setting free the proto-ribosome from deleterious pauses. In addition, it might have had the capacity to reactivate the translation of a mRNA, inserting for instance only alanine, and following the rescue of translation of mRNAs more downstream of the site that presented translational problems. Moreover, this proto-tmRNA might have been able to attach a “tag” sequence that would have conferred stability, in more general sense, to all polypeptides that were synthesised or to codify hydrophobic tails such to address the polypeptides towards the membrane. It is also clear that these simple properties of the proto-tmRNA would have favoured the reading of all proto-mRNAs, following the selection of mutants of proto-mRNAs particularly adaptive. This might have
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led to the synthesis not only of non functional polypeptides but also, although at very low frequency of polypeptides that gained a crude but very useful catalytic activity. Obviously, the prototmRNA might have worked in combination with some other of mechanisms discussed here as, for example, the ribosome frameshifting. It is worth specifying that at this evolutionary stage of the origin of the genetic code, it would be easy to expect that the most relevant part of synthesised polypeptides was not functional but only a very small part of them was operative (Di Giulio, 1996a, 1996b, 1997a, 1997b, 2003, 2008a, 2008b; see Fig. 1 in Di Giulio, 2008b).
4. Programmed ribosomal frameshifting (translational frameshifting) Given the triplet nature of codons, each mRNA contains three potential translational reading frames and one of the central questions is to understand how the ribosome initially chooses the “correct” reading frame, and how it maintains reading frame throughout the course of translating mRNAs. Having established a translational reading frame on an mRNA, the ribosome must maintain it throughout the remaining course of translation, the bulk of which is termed the elongation phase. While it is obvious that the translational apparatus needs to faithfully maintain reading frame, altering translational fidelity could be advantageous in special circumstances. Indeed, many viruses employ a molecular mechanism of translational recoding (Baranov et al., 2002) that Q5 direct elongating ribosomes to shift into an alternate reading frame, to utilise alternative start sites, and bypassing or recoding termination codons (Atkins and Gesteland, 2010). Q6 Our understanding of programmed 1 ribosomal frameshifting ( 1 PRF) arises from studies of RNA viruses. The relatively large number of viral 1 PRF signals has enabled definition of some of the parameters constituting a 1 PRF signal. The best defined 1 PRFs are directed by an mRNA sequence motif composed of three important elements: (i) a “slippery site” composed of seven nucleotides where the translational shift in reading frame actually takes place; (ii) a short spacer sequence of usually less than 12 nucleotides; and (iii) a downstream stimulatory structure (usually an mRNA pseudoknot). It is generally accepted that the downstream structure causes elongating ribosomes to pause with tRNAs positioned at the slippery site. The nature of the slippery sequence enables re-pairing of the nonwobble bases of both the aa- and peptidyl-tRNAs with the 1 frame codons. While it is also accepted that mRNA pseudoknots are the most common type of downstream stimulatory elements, other mRNA structures are capable of filling this role as well (for a review see Dinman, 2012). In contrast to 1 PRF where the translational reading frame is recoded by one nucleotide toward the 50 direction of the mRNA, the elongating ribosome is induced to bypass one nucleotide towards 30 direction in þ 1 PRF. þ1 PRF has been observed in the translation of prfB to produce release factor 2 (RF2) of Escherichia coli and in the yeast Saccharomyces cerevisiae two retrotransposable elements and three genes use þ1 PRF. The expression of the mammalian equivalent of yeast OAZ1, ornithine decarboxylase antizyme (i.e. OAZ), has also been shown to involve þ1 PRF (for a review see Dinman, 2012). Unlike 1 PRF, where there is only one general type of frameshift signal, þ1 PRF signals appear case specific. However, it is clear that þ1 PRF is also driven by cis-acting elements that cause elongating ribosomes to slip into the þ1 frame, and that slippage of P-site tRNA appear to be the most important parameter. However, the precise mechanisms are different for different þ 1 PRF signals (for a review see Dinman 2012). It has been also described a 2 PRF (Fanga et al., 2012).
Please cite this article as: Di Giulio, M., et al., RNA editing and modifications of RNAs might have favoured the evolution of the triplet genetic code from an ennuplet code. J. Theor. Biol. (2014), http://dx.doi.org/10.1016/j.jtbi.2014.05.037i
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Although first described in viruses, it is now clear that PRF is much more widespread and is employed by organisms representing the three domains of life (for reviews see Baranov et al., 2002; Cobucci-Ponzano et al., 2005). The ribosomal frameshifting seems to be related to the hypothesis suggested here because it could have permitted the exploration, building and selection of alternative frames from the proto-mRNAs. This would have allowed the birth of the first mRNAs with the coding limited to the amino acids at the head of biosynthetic pathways, which is to say, the one codified by G starting codons (Di Giulio, 2008a). Indeed, it is likely that very early on the protoribosome could have selected the proto-mRNAs based only on the criterion of their base composition (Crick et al., 1976; Eigen and Winkler-Oswatitsch, 1981; Shepherd, 1981; Ikehara, 2002; Di Giulio, 2008a; Higgs and Pudritz, 2009; Francis, 2013). That is to say, only proto-mRNAs might have been translated that would have had, for instance, G starting codons. In that sense, the proto-ribosome might have continuously shifted on the proto-mRNAs looking for sequences containing above of all G (or I) starting codons. In other words and more in general, the programmed ribosomal frameshifting might remind the evolutionary stage in which the slipping of reading may have created evolutionary opportunities not determinable by means of simple mutations even if multiple; therefore this would allow the making of reading variants whose polypeptides would have been better codified and/or conceivably with improved catalytic capabilities. Definitively, the ribosomal frameshifting might have been selected for the very reason that it helped the birth of first mRNAs, codifying only for few amino acids.
5. Conclusion We retain crucial that in one phase of the transition between ennuplet codes to the actual triplet genetic code has intervened an extensive editing, that is to say, an extensive modification of all RNAs. Indeed the possibility, for instance, of a coevolution between the origin of triplet anticodons and the origin of codons, in which the anticodons were used as guide in an editing mechanism for the birth of G starting codons, could really solve the huge problem of evolution of first mRNAs. The fact that today the anticodons are modified, and in particular modified by means of amino acids in a statistically significant way (Di Giulio, 1998), would make to presume in: (i) an intimate evolutionary relationship between amino acids and anticodons for the origin of the genetic code; (ii) an evolutionary maturation of anticodons that would seem really to imply the possibility that anticodons could have adapted, by means of modification, to the creation/identification of codons, and that (iii) codons might have been even them modified allowing the emergence of I (or G) rich proto-mRNAs, as the nuclear editing from A-to-I would testify to. Also other mechanisms as the trans-translation and ribosomal frameshifting might have favoured the evolution of the triplet genetic code. Obviously, other mechanisms as, for example, that represented by some present-day tRNAs that would seem to read quadruplet codons (Seligmann, 2012a, 2012b, 2013a, 2013b, 2013c, 2013d, 2014; Seligmann and Labra, 2013) might be vestiges, if confirmed, of this evolutionary stage of the origin of the genetic code.
Uncited references Di Giulio (2002).
References Atkins, J.F., Gesteland, R.F., 2010. Recoding: Expansion of Decoding Rules Enriches Gene Expression. Springer, New York. Baranov, P.V., Gesteland, R.F., Atkins, J.F., 2002. Recoding: translational bifurcations in gene expression. Gene 286, 187–201. Baranov, P., Venin, V., Provan, G., M., 2009. Codon size reduction as the origin of the triplet genetic code. PLoS One 4 (5), e5708. Cobucci-Ponzano, B., Rossi, M., Moracci, M., 2005. Recoding in archaea. Mol. Microbiol. 55, 339–348. Crick, F.H.C., 1968. The origin of the genetic code. J. Mol. Biol. 38, 367–379. Crick, F.H.C., Brenner, S., Klug, A., Pieczenik, G., 1976. A speculation on the origin of protein synthesis. Origins Life 7, 389–397. de Duve, C., 1988. The second genetic code. Nature, Lond 333 (ll7-118). Di Giulio, M., 1992. On the origin of the transfer RNA molecule. J. Theor. Biol. 159, 199–214. Di Giulio, M., 1995. Was it an ancient gene codifyng for a hairpin RNA that, by means of direct duplication, gave rise to the primitive tRNA molecule? J. Theor. Biol. 177, 95–101. Di Giulio, M., 1996a. The β-sheets of proteins, the biosynthetic relationshipsbetween amino acids, and the origin of the genetic code. Origins Life Evol. Biosphere 26, 589–609. Di Giulio, M., 1996b. The origin of protein synthesis: on some molecular fossils identified through comparison of protein sequences. Biosystems 39, 159–169. Di Giulio, M., 1997a. On the origin of the genetic code. J. Theor. Biol. 187, 573–581. Di Giulio, M., 1997b. On the RNA world: evidence in favor of an early ribonucleopeptide world. J. Mol. Evol. 45, 571–578. Di Giulio, M., 1998. Reflections on the origin of the genetic code: a hypothesis. J. Theor. Biol. 191, 191–196. Di Giulio, M., 1999. The non-monophyletic origin of tRNA molecule. J. Theor. Biol. 197, 403–414. Di Giulio, M., 2002. Genetic code origin: are the pathways of type Glu-tRNA(Gln)Gln-tRNA(Gln) molecular fossils or not? J. Mol. Evol. 55, 616–622. Di Giulio, M., 2003. The early phases of genetic code origin: conjectures on the evolution of coded catalysis. Origins Life Evol. Biosphere 33, 479–489. Di Giulio, M., 2004. The origin of the tRNA molecule: implications for the origin of protein synthesis. J. Theor. Biol. 226, 89–93. Di Giulio, M., 2006a. The non-monophyletic origin of the tRNA molecule and the origin of genes only after the evolutionary stage of the last universal Common Ancestor (LUCA). J. Theor. Biol. 240, 343–352. Di Giulio, M., 2006b. Nanoarchaeum equitans is a living fossil. J. Theor. Biol. 242, 257–260. Di Giulio, M., 2008a. An extension of the coevolution theory of the origin of the genetic code. Biol. Direct 3, 37. Di Giulio, M., 2008b. Why the genetic code originated. Implications for the origin of protein synthesis. The Codes of Life: The Rules of Macroevolution Chapter 4, 59–67. Di Giulio, M., 2008c. Split genes, ancestral genes. In: Tze-Fei Wong, J., lazcano, A. (Eds.), Prebiotic Evolution and Astrobiology. Landes Bioscience Publisher, Texas, USA (Chapter 13). Di Giulio, M., 2009a. A comparison among the models proposed to explain the origin of the tRNA molecule: a syn thesis. J. Mol. Evol. 69, 1–9. Di Giulio, M., 2009b. Formal proof tht the split genes of tRNAs of Nanoarchaeum equitans are an ancestral character. J. Mol. Evol. 69, 505–511. Dinman, J.D., 2012. Mechanisms and implications of programmed translational frameshifting. Wiley Interdiscip. Rev. RNA 3, 661–673. Eigen, M., Winkler-Oswatitsch, R., 1981. Transfer-RNA, an early gene? Naturwissenschaften 68, 217–228. Fanga, Y., Treffers, E.E., Lia, Tasc, Y.A., Suna, Z., van der Meerc, Y., de Rud, A.H., van Veelend, P.A., Atkinse, J.F., Snijderc, E.J., Firthf, A.F., 2012. Efficient -2 frameshifting by mammalian ribosomes to synthesize an additional arterivirus protein. Proc. Nat. Acad. Sci. U.S.A. 109, E2920–E2928. Francis, B.R., 2013. Evolution of the genetic code by incorporation that improved or changed protein function. J. Mol. Evol. 77, 134–158. Gray, M.W., 2012. Evolutionary origin of RNA editing. Biochemistry 51, 5235–5242. Heinemann, I.U., Nakamura, A., O’Donoghie, P., Eiler, D., Soll, D., 2012. tRNAHis -guanylyltransferase establishes tRNAHis identity. Nucl. Acids. Res. 40, 333–344. Higgs, P.G., Pudritz, R.E., 2009. A thermodynamic basis for prebiotic amino acid synthesis and the nature of the first genetic code. Astrobiology 9, 483–490. Hopfield, J.J., 1978. Origin of the genetic code: a testable hypothesis based on tRNA structure, sequence and kinetic proofreading. Proc. Nat. Acad. Sci. U.S.A. 75, 4334–4338. Ikehara, K., 2002. Origins of gene, genetic code, protein and life: comprehensive view of life systems from a GNC–SNS primitive genetic code hypothesis. J. Biosci. 27, 165–186. Laforest, M.J., Bullerwell, C.E., Forget, L., Lang, B.F., 2004. Origin, evolution, and mechanism of % tRNA editing in chytridiomycete fungi. RNA 10, 1191–1199. Landweber, L.F., Gilbert, W., 1994. Phylogenetic analysis of RNA editing: a primitive genetic phenomenon. Proc. Nat. Acad. Sci. U.S.A. 91, 918–921. Lynch, M., Koskella, B., Schaack, S., 2006. Mutation pressure and the evolution of organelle genomic architecture. Science 311, 1727–1730. Machnicka, M.A., Milanowska, K., Osman Oglou, O., Purta, E., Kurkowska, M., Olchowik, A., Januszewski, W., Kalinowski, S., Dunin-Horkawicz, S., Rother, K.M., Helm, M., Bujnicki, J.M., Grosjean, H., 2013. MODOMICS: a database of RNA modification pathways–2013 update. Nucleic Acids Res. 41, D262–D267.
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Moller, W., Janssen, G.M.C., 1990. Transfer RNAs for primordial amino acids contains remnants of a primitive code at position 3 to 5. Biochimie 72, 361–368. Moller, W., Janssen, G.M.C., 1992. Statistical evidence for remnants of primordial code in the acceptor stem of prokaryotic transfer RNA. J. Mol. Evol. 34, 471–477. Muramatsu, T., Nishikawa, K., Nemoto, F., Kuchino, Y., Nishimura, S., Miyazawa, T., Yokoyama, S., 1988. Codon and amino acid specificities of a transfer RNA are converted by a single post-transcriptional modification. Nature 336, 179–181. Muto, A., Ushida, C., Himeno, H., 1998. A bacterial RNA that functions as both a tRNA and an mRNA. Trends Biochem. Sci. 23, 25–29. Randau, L., Stanley, B.J., Kohlway, A., Mechta, S., Xiong, Y., Soll, D., 2009. A cytidine deaminase edits C to U in transfer RNAs in Archaea. Science 324, 657–659. Reanney, D.C., 1977. Aminoacyl thiol esters and the origins of genetic specificity. J. Theor. Biol. 65, 555–569. Rodin, S., Ohno, S., Rodin, A., 1993. Transfer RNA with complementary anticodon: could they reflect early evolution of discriminative genetic code adaptors? Proc. Nat. Acad. Sci. U.S.A. 90, 4723–4727. Rodin, S., Rodin, A., Ohno, S., 1996. The presence of codon–anticodon pairs in the acceptor stem of tRNAs. Proc. Nat. Acad. Sci. U.S.A. 93, 4537–4542. Rodin, S., Szathmary, E., Rodin, A., 2011. On origin of the genetic code and tRNA before translation. Biol. Direct 6, 4. Schimmel, P., Giegé, R., Morras, D., Yokoyama, S., 1993. An operational RNA code for amino acids and possible relationship to genetic code. Proc. Nat. Acad. Sci. U.S. A. 90, 8763–8768. Schimmel, P., Henderson, B., 1994. Possible role of aminoacyl-RNA complex in noncoded peptide synthesis and origin of codedsynthesis. Proc. Nat. Acad. Sci. U.S.A. 91, 11283–11286. Seligmann, H., 2012a. Putative mitochondrial polypeptides coded by expanded quadruplet codons, decoded by antisense tRNAs with unusual anticodons. Biosystems 110, 84–106. Seligmann, H., 2012b. Overlapping genes coded in the 30 -to-50 -direction in mitochondrial genes and 30 -to-50 polymerization of non-complementary RNA by an ‘invertase’. J. Theor. Biol. 315, 38–52. Seligmann, H., 2013a. Pocketknife tRNA hypothesis: anticodons in mammal mitochondrial tRNA side-arm loops translate proteins? Biosystems 113, 165–176.
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Seligmann, H., 2013b. Systematic asymmetric nucleotide exchanges produce human mitochondrial RNAs cryptically encoding for overlapping protein coding genes. J. Theor. Biol. 324, 1–20. Seligmann, H., 2013c. Polymerization of non-complementary RNA: systematic symmetric nucleotide exchanges mainly involving uracil produce mitochondrial RNA transcripts coding for cryptic overlapping genes. Biosystems 111, 156–174. Seligmann, H., 2013d. Triplex DNA:RNA, 30 -to-50 inverted RNA and protein coding in mitochondrial genomes. J. Comput. Biol. 20 (9), 660–671. Seligmann, H., 2014. Putative anticodons in mitochondrial tRNA sidearm loops: pocketknife tRNAs? J. Theor. Biol. 340, 155–163. Seligmann, H., Labra, A., 2013. Tetracoding increases with body temperature in Lepidosauria. Biosystems 114, 155–163. Shepherd, J.C., 1981. Periodic correlations in DNA sequences and evidence suggesting their evolutionary origin in a comma-less genetic code. J. Mol. Evol. 17, 94–102. Shimizu, M., 1982. Molecular basis for the genetic code. J. Mol. Evol. 18, 297–303. Szathmary, E., 1993. Coding coenzyme handles: a hypothesis for the origin of the genetic code. Proc. Nat. Acad. Sci. U.S.A. 90, 9916–9920. Xue, H., Shen, W., Giegé, R., Wong, J.T., 1993. Identity elements of tRNA(Trp). Identification and evolutionary conservation. J. Biol. Chem. 268, 9316–9322. White III, H.B., 1976. Coenzymes as fossils of an earlier metabolic state. J. Mol. Evol. 7, 101–104. Widmann, J., Di Giulio, M., Yarus, M., Knight, R., 2005. tRNA creation by hairpin duplication. J. Mol. Evol. 61, 524–530. Wong, J.T., 1991. Origin of genetically encoded protein synthesis a model based on selection for RNA peptidation. Origins Life Evol. Biosphere 21, 165–176. Wong, J.T., Xue, H., 2002. Self-perfecting Evolution of Heteropolymer Building Blocks and Sequences as the Basis of Life, in Fundamentals of Life. Editions Scientifiques et Medicales Elsevier SAS. Yarus, M., 1998. Amino acids as RNA ligands: a direct-RNA-template theory for the code’s origin. J. Mol. Evol. 47, 109–117. Yarus, M., Widmann, J.J., Knight, R., 2009. RNA-amino acid binding: a stereochemical era for the genetic code. J. Mol. Evol. 69, 406–429.
Please cite this article as: Di Giulio, M., et al., RNA editing and modifications of RNAs might have favoured the evolution of the triplet genetic code from an ennuplet code. J. Theor. Biol. (2014), http://dx.doi.org/10.1016/j.jtbi.2014.05.037i
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Journal of Theoretical Biology journal homepage: www.elsevier.com/locate/yjtbi
RNA editing and modifications of RNAs might have favoured the evolution of the triplet genetic code from an ennuplet code Massimo Di Giulio a,n, Marco Moracci b, Beatrice Cobucci-Ponzano b a b
Early Evolution of Life Laboratory, Institute of Biosciences and Bioresources, CNR, Via P. Castellino 111, 80131 Naples, Italy Glycobiology Laboratory, Institute of Biosciences and Bioresources, CNR, Via P. Castellino 111, 80131 Naples, Italy
H I G H L I G H T S
For the origin of the genetic code we consider credible the transition from ennuplet codes to the triplet code. We maintain that an extensive modification of RNAs has been crucial for this transition. RNA editing and post-transcriptional modifications of RNAs are retained vestiges of these modifications and of this transition. Trans-translation and ribosomal frameshifting are also considered by this hypothesis.
art ic l e i nf o
a b s t r a c t
Article history: Received 22 January 2014 Received in revised form 21 May 2014 Accepted 27 May 2014
Here we suggest that the origin of the genetic code, that is to say, the birth of first mRNAs has been triggered by means of a widespread modification of all RNAs (proto-mRNAs and proto-tRNAs), as today observed in the RNA editing and in post-transcriptional modifications of RNAs, which are considered as fossils of this evolutionary stage of the genetic code origin. We consider also that other mechanisms, such as the trans-translation and ribosome frameshifting, could have favoured the transition from an ennuplet code to a triplet code. Therefore, according to our hypothesis all these mechanisms would be reflexive of this period of the evolutionary history of the genetic code. & 2014 Published by Elsevier Ltd.
Keywords: Molecular fossils tmRNA Ribosome frameshifting Genetic code origin
1. Introduction and hypothesis One of the merits of the stereochemical theory of the origin of the genetic code is that it resolves the problem of the origin of the triplet genetic code, suggesting that there was an interaction between codons or anticodons and amino acids (Shimizu, 1982; Szathmary, 1993; Di Giulio, 1997a; Yarus, 1998; Yarus et al., 2009). On the contrary, the models that deny the validity of the stereochemical theory (Wong, 1991; Di Giulio, 1998, 2003, 2008a, 2008b) – suggesting that the triplet code originated from a code having a coding system larger of three bases (ennuplet codes) – have to explain how the reading system has been “reshaped”, moving, for instance, from a reading involving several bases (larger of three) to a triplet code. In particular, one of these models suggests that there has been a very long evolutionary stage that starting from a rudimentary protein synthesis resulted in the triplet genetic code, using intermediate evolutionary stages of ennuplet coding with a number of bases also greater than three
n
Corresponding author. Tel.: þ 39 816132369; fax: þ 39 816132706. E-mail address: [email protected] (M. Di Giulio).
(Di Giulio, 2003; see Fig. 1 in Di Giulio, 2008b). As also highlighted by Crick (1968), this transition is very difficult to realise because, for instance, if a quadruplet code was evolving suddenly to a triplet code, this would be impossible because all messages of the quadruplet code would lose sense if translated by means of the coding system of the triplet code. In other words, this transition would break the evolutionary continuity principle. Therefore, although there are simulations that seem to support an evolution of this kind (Baranov et al., 2009), the difficulty to transform a code that uses a reading system greater than three bases to that of three bases remains. However, this difficulty might be reduced or even eliminated if a set of mechanisms were evolved that favoured the transformation of an ennuplet code to a triplet code. For example, this might have been represented by a mechanism of reading that would have had success to overcome the obstacles deriving from an excessive slowdown or termination of reading, by means of, for instance, the intervention of molecules that restore the translation or were able to shift the protoribosome obtaining the reactivation of translation. In these hypothetical mechanisms of rescue of translation we can see a similarity with some known molecular mechanisms as, for instance, the trans-translation (Muto et al., 1998). Therefore,
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Please cite this article as: Di Giulio, M., et al., RNA editing and modifications of RNAs might have favoured the evolution of the triplet genetic code from an ennuplet code. J. Theor. Biol. (2014), http://dx.doi.org/10.1016/j.jtbi.2014.05.037i
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in the certainty that the triplet genetic code originated from an improperly defined ennuplet code (Di Giulio, 2003; see Fig. 1 in Di Giulio, 2008b), we have decided to analyse all those mechanisms that might have favoured the birth of the first messenger RNAs using triplets from an ennuplet code.
2. RNA editing and modifications of RNAs The term “RNA editing” originally described an unusual form of post-transcriptional processing involving the insertion of uridylate (U) residues into an mRNA in the mitochondria of some protozoans (Gray, 2012). Later the mitochondria mRNA editing was found within kinetoplastida affecting many mRNAs, and involving deletions as well as insertions of U (Gray, 2012). Today, the RNA editing has become a generic term used to identify several posttranscriptional processes whose effect is to change the nucleotide sequence of a mature RNA species relative to the encoding DNA sequence (Gray, 2012). RNA editing excludes 50 capping, splicing, and 30 polyadenylation of mRNAs, as well as formation of modified nucleosides in RNA, although the distinction between “editing” and “modification” is somewhat not clear (Gray, 2012). For instance, an editing type involves deamination of adenosine (A) residues to form inosine (I), resulting in the conversion of the 6-aminopurine ring of A to 6-oxopurine in I (Gray, 2012). When this change occurs within the coding region of a mRNA, the edited site (I) is recognised as G during translation (Gray, 2012). However, A residues in the first position of tRNA anticodon also undergo deamination to I, which similarly results in a change in the anticodon pairing properties. Thus at a certain level, editing and modification may be regarded as two sides of the same coin (Gray, 2012). RNA editing has been described in mitochondria, chloroplasts, nuclear and viral genes, although C-to-U editing of tRNAs has been recently observed in Archaea (Randau et al., 2009; Gray, 2012). On the contrary, the modifications of tRNAs, for example, have been described in all the domains of life (Laforest et al., 2004; Heinemann et al., 2012; Machnicka et al., 2013). RNA editing has been considered both as a derived and as an ancestral trait. For instance, Lynch et al. (2006) maintain that RNA editing has been introduced by means of the genetic drift and would be therefore a derived trait. However, the presence of RNA editing among archaea seems to indicate that this interpretation might be false given that archaea have a huge population size that would have made the genetic drift not operative. Gray (2012) too considers RNA editing as a derived trait originated by means of a neutral evolutionary process. On the contrary, other authors have considered RNA editing as an ancestral trait (Landweber and Gilbert, 1994; Di Giulio, 2003, 2008b). The presence of posttranscriptional modifications in all domains of life, as for instance observed in tRNAs, would indicate that they are an ancestral trait. Here, we suggest that RNA editing and more in general all modifications of RNAs, would have had the crucial role to extend and to improve the catalytic performances of RNAs into the RNA world (see also: White, 1976; Reanney, 1977; Wong, 1991; Wong and Xue, 2002; Di Giulio, 1996a, 1996b, 1997b, 2003, 2008b). Both RNA editing and post-transcriptional modifications of RNAs would seem to have to do with the hypothesis here maintained. The G at the 1 position of histidine tRNAs is inserted by means of RNA editing (Heinemann et al., 2012). This position is also the main determinant of the identity of histidine tRNAs (Heinemann et al., 2012). Therefore we can see directly that this RNA editing has had to do with the genetic code origin, because that insertion of one base determines what amino acid will be charged on a specific species of the tRNA, determining the meeting between RNAs and amino acids, that is to say, the genetic code.
More in general, we could say that the insertion, deletion or base modification should have favoured the origin of first mRNAs with triplets, because such events might have created new open reading frames which might have been successfully selected from proto-mRNAs that cannot be read or read correctly. It is possible that the systematic insertion of three bases may have favoured the addition in growing polypeptides of certain amino acids that might have stabilised all polypeptides at high temperature, for instance (Di Giulio, 2003). Furthermore, there is an evolutionary argument even more general and persuasive that is related to the origin of the tRNA molecule. Following a model of the origin of the tRNA molecule, the first anticodons originated in hairpin RNA structures near their 30 end (Hopfield, 1978; de Duve 1988; Moller and Janssen, 1990, 1992; Schimmel et al., 1993; Schimmel and Henderson, 1994; Di Giulio, 1992, 1995, 1997b, 1999, 2004, 2006a, 2006b, 2008c, 2009a, 2009b; Widmann et al., 2005; Rodin et al., 1993, 1996, 2011). This suggestion is in accordance, for instance, with the position that several identity determinants have, exactly in the acceptor stem of tRNA molecules (Schimmel et al., 1993; Xue et al., 1993; Schimmel and Henderson, 1994; Heinemann et al., 2012). It has also been suggested that in this position the identity determinants would remind the existence of a code – called the second genetic code – which is considered more ancient than the genetic code (Hopfield, 1978; de Duve 1988; Moller and Janssen, 1990, 1992; Schimmel et al., 1993; Schimmel and Henderson, 1994; Di Giulio, 1992, 1995, 1997b, 1999, 2004, 2006a, 2006b, 2008c, 2009a, 2009b; Rodin et al., 1993, 1996, 2011). The observation that, for instance, the G at the 1 position is inserted by means of editing in the very acceptor stem of histidine tRNAs, would seem not only to be expression of this second genetic code but, above all, would reflect the position in which the anticodons originated. Therefore, establishing a relationship between the identity determinants and the origin of anticodons (Di Giulio, 1995, 2006a). Ultimately, all this argument would put the editing to the very origin of anticodons and consequently to the origin of the genetic code. The post-transcriptional modification of the CAU anticodon for isoleucine – in which the C (in 34 position) is modified by means of lysine to form lysidine, a modified nucleotide, which is involved both in the recognition of a new anticodon and as identity determinant for the isoleucine tRNA (Muramatsu et al., 1988) – Q4 indicates in a clear way to have been involved in the evolution of the genetic code. For this reason, also all the modifications of anticodons that are widespread in all domains of life (Laforest et al., 2004; Heinemann et al., 2012; Machnicka et al., 2013) would have had to do with the evolution of the genetic code, and in particular with the origin of the triplet code, being these modifications implied also in the codon–anticodon interaction. Therefore, the involvement of these modifications in the origin of the triplet code is evident. On the other hand, for those modifications (or equivalently for RNA editing) that might have altered the sequences of protomRNAs, these might have represented, within the proto-mRNA pool, variants on which natural selection could have operated, selecting for example mutants with crude catalytic activity in their products. In particular, there is a strong evidence that the first proto-mRNAs might have used only G starting codons (Eigen and Winkler-Oswatitsch, 1981; Ikehara, 2002; Di Giulio, 2008a; Higgs and Pudritz, 2009; Francis, 2013). For instance, according to the extended coevolution theory of the genetic code origin, being the majority of amino acids at the head of biosynthetic pathways codified by G starting codons (Di Giulio, 2008a), then it might have occurred that a subset of proto-mRNAs may have been made exactly by this type of codons (for introduction see: Di Giulio, 2003, 2008a, 2008b). Indeed, it is possible to conjecture that the evolutionary passage from the ennuplet code to the triplet code
Please cite this article as: Di Giulio, M., et al., RNA editing and modifications of RNAs might have favoured the evolution of the triplet genetic code from an ennuplet code. J. Theor. Biol. (2014), http://dx.doi.org/10.1016/j.jtbi.2014.05.037i
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might have been favoured, for instance, by a modification of a subset of proto-mRNAs in which many nucleotides in their sequences were transformed to a G every three bases. For example, if several of the developing triplet anticodons would have started to behave like guides used to edit many protomRNAs, then there might have been a partial coevolution between the birth of evolving anticodons and that of codons of first protomRNAs. In other words, the birth of proto-mRNAs containing G (or I) in the first position of codons may have been favoured by means of insertions of G (and/or I) in an editing mechanism in which developing anticodons containing C were used as guide. Furthermore, it might also have occurred an A-to-I editing as today observed into nuclear transcripts of animals (Gray, 2012). Crick (1968) has discussed the possibility that the primitive nucleic acids have initially I in place of G. These modifications might have represented, if positively selected, the crucial passage that would have led to the origin of the genetic code through the coding of all amino acids at the head of the biosynthetic pathways, by means of G starting codons (see Di Giulio, 2003, 2008a, 2008b). The observation that the anticodons are modified by amino acids is reported to be statistically significant (Di Giulio, 1998). This would seem to imply a close evolutionary interaction between amino acids and anticodons for the origin of the genetic code (Di Giulio, 1998; see also below). If this has happened for anticodons then a similar mechanism might have occurred for codons too. Thus the hypothesis that the early phases of the origin of the genetic code, that it to say, the one that led to the birth of first mRNAs, might have been favoured by means of a widespread modification of RNAs (proto-mRNAs and proto-tRNAs), seems to be truly fascinating.
3. tmRNA The transfer-messenger RNA (tmRNA) has a tRNA-like structure at its 50 and 30 termini, and presents a reading frame encoding a “tag” peptide (Muto et al., 1998). The double structure of this molecule as tRNA and mRNA is such to facilitate a transtranslational reaction (Muto et al., 1998). In this reaction the ribosome can switch between the translation of a truncated mRNA and the tmRNA’s tag sequence. The result is a chimerical protein with the tag peptide attached to the C-terminus end of the truncated peptide that can be thus degraded (Muto et al., 1998). The tmRNA is present in all the bacterial domain and viruses, therefore it seems to be a very ancient molecule. This and other features are such to make to believe that it was part of the primitive protein synthesis; that is to say, it is a molecular fossil of an evolutionary stage of the ancestral protein synthesis (Di Giulio, 2003, 2008b). The tmRNA seems to be in relationship with the hypothesis here maintained, for the following reasons. Being the tmRNA able to reactivate the translation of a truncated mRNA, it would have been able during the genetic code evolution to remove all translations that were abortive in some way, therefore setting free the proto-ribosome from deleterious pauses. In addition, it might have had the capacity to reactivate the translation of a mRNA, inserting for instance only alanine, and following the rescue of translation of mRNAs more downstream of the site that presented translational problems. Moreover, this proto-tmRNA might have been able to attach a “tag” sequence that would have conferred stability, in more general sense, to all polypeptides that were synthesised or to codify hydrophobic tails such to address the polypeptides towards the membrane. It is also clear that these simple properties of the proto-tmRNA would have favoured the reading of all proto-mRNAs, following the selection of mutants of proto-mRNAs particularly adaptive. This might have
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led to the synthesis not only of non functional polypeptides but also, although at very low frequency of polypeptides that gained a crude but very useful catalytic activity. Obviously, the prototmRNA might have worked in combination with some other of mechanisms discussed here as, for example, the ribosome frameshifting. It is worth specifying that at this evolutionary stage of the origin of the genetic code, it would be easy to expect that the most relevant part of synthesised polypeptides was not functional but only a very small part of them was operative (Di Giulio, 1996a, 1996b, 1997a, 1997b, 2003, 2008a, 2008b; see Fig. 1 in Di Giulio, 2008b).
4. Programmed ribosomal frameshifting (translational frameshifting) Given the triplet nature of codons, each mRNA contains three potential translational reading frames and one of the central questions is to understand how the ribosome initially chooses the “correct” reading frame, and how it maintains reading frame throughout the course of translating mRNAs. Having established a translational reading frame on an mRNA, the ribosome must maintain it throughout the remaining course of translation, the bulk of which is termed the elongation phase. While it is obvious that the translational apparatus needs to faithfully maintain reading frame, altering translational fidelity could be advantageous in special circumstances. Indeed, many viruses employ a molecular mechanism of translational recoding (Baranov et al., 2002) that Q5 direct elongating ribosomes to shift into an alternate reading frame, to utilise alternative start sites, and bypassing or recoding termination codons (Atkins and Gesteland, 2010). Q6 Our understanding of programmed 1 ribosomal frameshifting ( 1 PRF) arises from studies of RNA viruses. The relatively large number of viral 1 PRF signals has enabled definition of some of the parameters constituting a 1 PRF signal. The best defined 1 PRFs are directed by an mRNA sequence motif composed of three important elements: (i) a “slippery site” composed of seven nucleotides where the translational shift in reading frame actually takes place; (ii) a short spacer sequence of usually less than 12 nucleotides; and (iii) a downstream stimulatory structure (usually an mRNA pseudoknot). It is generally accepted that the downstream structure causes elongating ribosomes to pause with tRNAs positioned at the slippery site. The nature of the slippery sequence enables re-pairing of the nonwobble bases of both the aa- and peptidyl-tRNAs with the 1 frame codons. While it is also accepted that mRNA pseudoknots are the most common type of downstream stimulatory elements, other mRNA structures are capable of filling this role as well (for a review see Dinman, 2012). In contrast to 1 PRF where the translational reading frame is recoded by one nucleotide toward the 50 direction of the mRNA, the elongating ribosome is induced to bypass one nucleotide towards 30 direction in þ 1 PRF. þ1 PRF has been observed in the translation of prfB to produce release factor 2 (RF2) of Escherichia coli and in the yeast Saccharomyces cerevisiae two retrotransposable elements and three genes use þ1 PRF. The expression of the mammalian equivalent of yeast OAZ1, ornithine decarboxylase antizyme (i.e. OAZ), has also been shown to involve þ1 PRF (for a review see Dinman, 2012). Unlike 1 PRF, where there is only one general type of frameshift signal, þ1 PRF signals appear case specific. However, it is clear that þ1 PRF is also driven by cis-acting elements that cause elongating ribosomes to slip into the þ1 frame, and that slippage of P-site tRNA appear to be the most important parameter. However, the precise mechanisms are different for different þ 1 PRF signals (for a review see Dinman 2012). It has been also described a 2 PRF (Fanga et al., 2012).
Please cite this article as: Di Giulio, M., et al., RNA editing and modifications of RNAs might have favoured the evolution of the triplet genetic code from an ennuplet code. J. Theor. Biol. (2014), http://dx.doi.org/10.1016/j.jtbi.2014.05.037i
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Although first described in viruses, it is now clear that PRF is much more widespread and is employed by organisms representing the three domains of life (for reviews see Baranov et al., 2002; Cobucci-Ponzano et al., 2005). The ribosomal frameshifting seems to be related to the hypothesis suggested here because it could have permitted the exploration, building and selection of alternative frames from the proto-mRNAs. This would have allowed the birth of the first mRNAs with the coding limited to the amino acids at the head of biosynthetic pathways, which is to say, the one codified by G starting codons (Di Giulio, 2008a). Indeed, it is likely that very early on the protoribosome could have selected the proto-mRNAs based only on the criterion of their base composition (Crick et al., 1976; Eigen and Winkler-Oswatitsch, 1981; Shepherd, 1981; Ikehara, 2002; Di Giulio, 2008a; Higgs and Pudritz, 2009; Francis, 2013). That is to say, only proto-mRNAs might have been translated that would have had, for instance, G starting codons. In that sense, the proto-ribosome might have continuously shifted on the proto-mRNAs looking for sequences containing above of all G (or I) starting codons. In other words and more in general, the programmed ribosomal frameshifting might remind the evolutionary stage in which the slipping of reading may have created evolutionary opportunities not determinable by means of simple mutations even if multiple; therefore this would allow the making of reading variants whose polypeptides would have been better codified and/or conceivably with improved catalytic capabilities. Definitively, the ribosomal frameshifting might have been selected for the very reason that it helped the birth of first mRNAs, codifying only for few amino acids.
5. Conclusion We retain crucial that in one phase of the transition between ennuplet codes to the actual triplet genetic code has intervened an extensive editing, that is to say, an extensive modification of all RNAs. Indeed the possibility, for instance, of a coevolution between the origin of triplet anticodons and the origin of codons, in which the anticodons were used as guide in an editing mechanism for the birth of G starting codons, could really solve the huge problem of evolution of first mRNAs. The fact that today the anticodons are modified, and in particular modified by means of amino acids in a statistically significant way (Di Giulio, 1998), would make to presume in: (i) an intimate evolutionary relationship between amino acids and anticodons for the origin of the genetic code; (ii) an evolutionary maturation of anticodons that would seem really to imply the possibility that anticodons could have adapted, by means of modification, to the creation/identification of codons, and that (iii) codons might have been even them modified allowing the emergence of I (or G) rich proto-mRNAs, as the nuclear editing from A-to-I would testify to. Also other mechanisms as the trans-translation and ribosomal frameshifting might have favoured the evolution of the triplet genetic code. Obviously, other mechanisms as, for example, that represented by some present-day tRNAs that would seem to read quadruplet codons (Seligmann, 2012a, 2012b, 2013a, 2013b, 2013c, 2013d, 2014; Seligmann and Labra, 2013) might be vestiges, if confirmed, of this evolutionary stage of the origin of the genetic code.
Uncited references Di Giulio (2002).
References Atkins, J.F., Gesteland, R.F., 2010. Recoding: Expansion of Decoding Rules Enriches Gene Expression. Springer, New York. Baranov, P.V., Gesteland, R.F., Atkins, J.F., 2002. Recoding: translational bifurcations in gene expression. Gene 286, 187–201. Baranov, P., Venin, V., Provan, G., M., 2009. Codon size reduction as the origin of the triplet genetic code. PLoS One 4 (5), e5708. Cobucci-Ponzano, B., Rossi, M., Moracci, M., 2005. Recoding in archaea. Mol. Microbiol. 55, 339–348. Crick, F.H.C., 1968. The origin of the genetic code. J. Mol. Biol. 38, 367–379. Crick, F.H.C., Brenner, S., Klug, A., Pieczenik, G., 1976. A speculation on the origin of protein synthesis. Origins Life 7, 389–397. de Duve, C., 1988. The second genetic code. Nature, Lond 333 (ll7-118). Di Giulio, M., 1992. On the origin of the transfer RNA molecule. J. Theor. Biol. 159, 199–214. Di Giulio, M., 1995. Was it an ancient gene codifyng for a hairpin RNA that, by means of direct duplication, gave rise to the primitive tRNA molecule? J. Theor. Biol. 177, 95–101. Di Giulio, M., 1996a. The β-sheets of proteins, the biosynthetic relationshipsbetween amino acids, and the origin of the genetic code. Origins Life Evol. Biosphere 26, 589–609. Di Giulio, M., 1996b. The origin of protein synthesis: on some molecular fossils identified through comparison of protein sequences. Biosystems 39, 159–169. Di Giulio, M., 1997a. On the origin of the genetic code. J. Theor. Biol. 187, 573–581. Di Giulio, M., 1997b. On the RNA world: evidence in favor of an early ribonucleopeptide world. J. Mol. Evol. 45, 571–578. Di Giulio, M., 1998. Reflections on the origin of the genetic code: a hypothesis. J. Theor. Biol. 191, 191–196. Di Giulio, M., 1999. The non-monophyletic origin of tRNA molecule. J. Theor. Biol. 197, 403–414. Di Giulio, M., 2002. Genetic code origin: are the pathways of type Glu-tRNA(Gln)Gln-tRNA(Gln) molecular fossils or not? J. Mol. Evol. 55, 616–622. Di Giulio, M., 2003. The early phases of genetic code origin: conjectures on the evolution of coded catalysis. Origins Life Evol. Biosphere 33, 479–489. Di Giulio, M., 2004. The origin of the tRNA molecule: implications for the origin of protein synthesis. J. Theor. Biol. 226, 89–93. Di Giulio, M., 2006a. The non-monophyletic origin of the tRNA molecule and the origin of genes only after the evolutionary stage of the last universal Common Ancestor (LUCA). J. Theor. Biol. 240, 343–352. Di Giulio, M., 2006b. Nanoarchaeum equitans is a living fossil. J. Theor. Biol. 242, 257–260. Di Giulio, M., 2008a. An extension of the coevolution theory of the origin of the genetic code. Biol. Direct 3, 37. Di Giulio, M., 2008b. Why the genetic code originated. Implications for the origin of protein synthesis. The Codes of Life: The Rules of Macroevolution Chapter 4, 59–67. Di Giulio, M., 2008c. Split genes, ancestral genes. In: Tze-Fei Wong, J., lazcano, A. (Eds.), Prebiotic Evolution and Astrobiology. Landes Bioscience Publisher, Texas, USA (Chapter 13). Di Giulio, M., 2009a. A comparison among the models proposed to explain the origin of the tRNA molecule: a syn thesis. J. Mol. Evol. 69, 1–9. Di Giulio, M., 2009b. Formal proof tht the split genes of tRNAs of Nanoarchaeum equitans are an ancestral character. J. Mol. Evol. 69, 505–511. Dinman, J.D., 2012. Mechanisms and implications of programmed translational frameshifting. Wiley Interdiscip. Rev. RNA 3, 661–673. Eigen, M., Winkler-Oswatitsch, R., 1981. Transfer-RNA, an early gene? Naturwissenschaften 68, 217–228. Fanga, Y., Treffers, E.E., Lia, Tasc, Y.A., Suna, Z., van der Meerc, Y., de Rud, A.H., van Veelend, P.A., Atkinse, J.F., Snijderc, E.J., Firthf, A.F., 2012. Efficient -2 frameshifting by mammalian ribosomes to synthesize an additional arterivirus protein. Proc. Nat. Acad. Sci. U.S.A. 109, E2920–E2928. Francis, B.R., 2013. Evolution of the genetic code by incorporation that improved or changed protein function. J. Mol. Evol. 77, 134–158. Gray, M.W., 2012. Evolutionary origin of RNA editing. Biochemistry 51, 5235–5242. Heinemann, I.U., Nakamura, A., O’Donoghie, P., Eiler, D., Soll, D., 2012. tRNAHis -guanylyltransferase establishes tRNAHis identity. Nucl. Acids. Res. 40, 333–344. Higgs, P.G., Pudritz, R.E., 2009. A thermodynamic basis for prebiotic amino acid synthesis and the nature of the first genetic code. Astrobiology 9, 483–490. Hopfield, J.J., 1978. Origin of the genetic code: a testable hypothesis based on tRNA structure, sequence and kinetic proofreading. Proc. Nat. Acad. Sci. U.S.A. 75, 4334–4338. Ikehara, K., 2002. Origins of gene, genetic code, protein and life: comprehensive view of life systems from a GNC–SNS primitive genetic code hypothesis. J. Biosci. 27, 165–186. Laforest, M.J., Bullerwell, C.E., Forget, L., Lang, B.F., 2004. Origin, evolution, and mechanism of % tRNA editing in chytridiomycete fungi. RNA 10, 1191–1199. Landweber, L.F., Gilbert, W., 1994. Phylogenetic analysis of RNA editing: a primitive genetic phenomenon. Proc. Nat. Acad. Sci. U.S.A. 91, 918–921. Lynch, M., Koskella, B., Schaack, S., 2006. Mutation pressure and the evolution of organelle genomic architecture. Science 311, 1727–1730. Machnicka, M.A., Milanowska, K., Osman Oglou, O., Purta, E., Kurkowska, M., Olchowik, A., Januszewski, W., Kalinowski, S., Dunin-Horkawicz, S., Rother, K.M., Helm, M., Bujnicki, J.M., Grosjean, H., 2013. MODOMICS: a database of RNA modification pathways–2013 update. Nucleic Acids Res. 41, D262–D267.
Please cite this article as: Di Giulio, M., et al., RNA editing and modifications of RNAs might have favoured the evolution of the triplet genetic code from an ennuplet code. J. Theor. Biol. (2014), http://dx.doi.org/10.1016/j.jtbi.2014.05.037i
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Moller, W., Janssen, G.M.C., 1990. Transfer RNAs for primordial amino acids contains remnants of a primitive code at position 3 to 5. Biochimie 72, 361–368. Moller, W., Janssen, G.M.C., 1992. Statistical evidence for remnants of primordial code in the acceptor stem of prokaryotic transfer RNA. J. Mol. Evol. 34, 471–477. Muramatsu, T., Nishikawa, K., Nemoto, F., Kuchino, Y., Nishimura, S., Miyazawa, T., Yokoyama, S., 1988. Codon and amino acid specificities of a transfer RNA are converted by a single post-transcriptional modification. Nature 336, 179–181. Muto, A., Ushida, C., Himeno, H., 1998. A bacterial RNA that functions as both a tRNA and an mRNA. Trends Biochem. Sci. 23, 25–29. Randau, L., Stanley, B.J., Kohlway, A., Mechta, S., Xiong, Y., Soll, D., 2009. A cytidine deaminase edits C to U in transfer RNAs in Archaea. Science 324, 657–659. Reanney, D.C., 1977. Aminoacyl thiol esters and the origins of genetic specificity. J. Theor. Biol. 65, 555–569. Rodin, S., Ohno, S., Rodin, A., 1993. Transfer RNA with complementary anticodon: could they reflect early evolution of discriminative genetic code adaptors? Proc. Nat. Acad. Sci. U.S.A. 90, 4723–4727. Rodin, S., Rodin, A., Ohno, S., 1996. The presence of codon–anticodon pairs in the acceptor stem of tRNAs. Proc. Nat. Acad. Sci. U.S.A. 93, 4537–4542. Rodin, S., Szathmary, E., Rodin, A., 2011. On origin of the genetic code and tRNA before translation. Biol. Direct 6, 4. Schimmel, P., Giegé, R., Morras, D., Yokoyama, S., 1993. An operational RNA code for amino acids and possible relationship to genetic code. Proc. Nat. Acad. Sci. U.S. A. 90, 8763–8768. Schimmel, P., Henderson, B., 1994. Possible role of aminoacyl-RNA complex in noncoded peptide synthesis and origin of codedsynthesis. Proc. Nat. Acad. Sci. U.S.A. 91, 11283–11286. Seligmann, H., 2012a. Putative mitochondrial polypeptides coded by expanded quadruplet codons, decoded by antisense tRNAs with unusual anticodons. Biosystems 110, 84–106. Seligmann, H., 2012b. Overlapping genes coded in the 30 -to-50 -direction in mitochondrial genes and 30 -to-50 polymerization of non-complementary RNA by an ‘invertase’. J. Theor. Biol. 315, 38–52. Seligmann, H., 2013a. Pocketknife tRNA hypothesis: anticodons in mammal mitochondrial tRNA side-arm loops translate proteins? Biosystems 113, 165–176.
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Seligmann, H., 2013b. Systematic asymmetric nucleotide exchanges produce human mitochondrial RNAs cryptically encoding for overlapping protein coding genes. J. Theor. Biol. 324, 1–20. Seligmann, H., 2013c. Polymerization of non-complementary RNA: systematic symmetric nucleotide exchanges mainly involving uracil produce mitochondrial RNA transcripts coding for cryptic overlapping genes. Biosystems 111, 156–174. Seligmann, H., 2013d. Triplex DNA:RNA, 30 -to-50 inverted RNA and protein coding in mitochondrial genomes. J. Comput. Biol. 20 (9), 660–671. Seligmann, H., 2014. Putative anticodons in mitochondrial tRNA sidearm loops: pocketknife tRNAs? J. Theor. Biol. 340, 155–163. Seligmann, H., Labra, A., 2013. Tetracoding increases with body temperature in Lepidosauria. Biosystems 114, 155–163. Shepherd, J.C., 1981. Periodic correlations in DNA sequences and evidence suggesting their evolutionary origin in a comma-less genetic code. J. Mol. Evol. 17, 94–102. Shimizu, M., 1982. Molecular basis for the genetic code. J. Mol. Evol. 18, 297–303. Szathmary, E., 1993. Coding coenzyme handles: a hypothesis for the origin of the genetic code. Proc. Nat. Acad. Sci. U.S.A. 90, 9916–9920. Xue, H., Shen, W., Giegé, R., Wong, J.T., 1993. Identity elements of tRNA(Trp). Identification and evolutionary conservation. J. Biol. Chem. 268, 9316–9322. White III, H.B., 1976. Coenzymes as fossils of an earlier metabolic state. J. Mol. Evol. 7, 101–104. Widmann, J., Di Giulio, M., Yarus, M., Knight, R., 2005. tRNA creation by hairpin duplication. J. Mol. Evol. 61, 524–530. Wong, J.T., 1991. Origin of genetically encoded protein synthesis a model based on selection for RNA peptidation. Origins Life Evol. Biosphere 21, 165–176. Wong, J.T., Xue, H., 2002. Self-perfecting Evolution of Heteropolymer Building Blocks and Sequences as the Basis of Life, in Fundamentals of Life. Editions Scientifiques et Medicales Elsevier SAS. Yarus, M., 1998. Amino acids as RNA ligands: a direct-RNA-template theory for the code’s origin. J. Mol. Evol. 47, 109–117. Yarus, M., Widmann, J.J., Knight, R., 2009. RNA-amino acid binding: a stereochemical era for the genetic code. J. Mol. Evol. 69, 406–429.
Please cite this article as: Di Giulio, M., et al., RNA editing and modifications of RNAs might have favoured the evolution of the triplet genetic code from an ennuplet code. J. Theor. Biol. (2014), http://dx.doi.org/10.1016/j.jtbi.2014.05.037i