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How amino acids and peptides shaped the RNA world.

van der Gulik PT, Speijer D - Life (Basel) (2015)

Bottom Line: Though the oldest center of the ribosome seems "RNA only", we cannot conclude from this that it ever functioned in an environment without amino acids and/or peptides.In this article, we try to bring the role of the peptide component of early life back into focus.We argue that an RNA world completely independent of amino acids never existed.

View Article: PubMed Central - PubMed

Affiliation: Centrum Wiskunde & Informatica, Science Park 123, 1098 SJ Amsterdam, The Netherlands. Peter.van.der.Gulik@cwi.nl.

ABSTRACT
The "RNA world" hypothesis is seen as one of the main contenders for a viable theory on the origin of life. Relatively small RNAs have catalytic power, RNA is everywhere in present-day life, the ribosome is seen as a ribozyme, and rRNA and tRNA are crucial for modern protein synthesis. However, this view is incomplete at best. The modern protein-RNA ribosome most probably is not a distorted form of a "pure RNA ribosome" evolution started out with. Though the oldest center of the ribosome seems "RNA only", we cannot conclude from this that it ever functioned in an environment without amino acids and/or peptides. Very small RNAs (versatile and stable due to basepairing) and amino acids, as well as dipeptides, coevolved. Remember, it is the amino group of aminoacylated tRNA that attacks peptidyl-tRNA, destroying the bond between peptide and tRNA. This activity of the amino acid part of aminoacyl-tRNA illustrates the centrality of amino acids in life. With the rise of the "RNA world" view of early life, the pendulum seems to have swung too much towards the ribozymatic part of early biochemistry. The necessary presence and activity of amino acids and peptides is in need of highlighting. In this article, we try to bring the role of the peptide component of early life back into focus. We argue that an RNA world completely independent of amino acids never existed.

No MeSH data available.


Related in: MedlinePlus

How to get a tRNA precursor. Two (identical) hairpin-loop structures (red and blue) can form one extended RNA molecule upon unfolding. Regions in this precursor are compared to a schematized version of a present day tRNA. 1: CCA acceptor stem; 2: D-arm; 3: T-arm; 4: Anticodon containing loop. The dotted line indicates the schematized separation between acceptor-TψC stem-loop and anticodon-D stem-Biloop [52]. The anticodon and the discriminator nucleotide U are shown in bold face. Hydrogen bonds are shown as stripes. * In the anticodon containing loop further insertions and deletions are needed. Here two identical molecules (accepting glycine) are depicted, however the extended molecule can also be formed by slightly different non-identical molecules. For further details see text.
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life-05-00230-f001: How to get a tRNA precursor. Two (identical) hairpin-loop structures (red and blue) can form one extended RNA molecule upon unfolding. Regions in this precursor are compared to a schematized version of a present day tRNA. 1: CCA acceptor stem; 2: D-arm; 3: T-arm; 4: Anticodon containing loop. The dotted line indicates the schematized separation between acceptor-TψC stem-loop and anticodon-D stem-Biloop [52]. The anticodon and the discriminator nucleotide U are shown in bold face. Hydrogen bonds are shown as stripes. * In the anticodon containing loop further insertions and deletions are needed. Here two identical molecules (accepting glycine) are depicted, however the extended molecule can also be formed by slightly different non-identical molecules. For further details see text.

Mentions: We could thus envisage two relatively small hairpin sequences basepair, forming a primitive tRNA precursor. If we begin with two “Shimizu” RNA stem loop molecules (C4N structures), each with a 5' anticodon-stem loop stem-discriminator nucleotide-CCA 3' structure (see Figure 1) and allow them to basepair after “opening up” their original stem loops, eventual ligation on one side of the molecule (where the differently colored sequences meet in Figure 1) would lead to a new RNA species. This molecule has both an anticodon in the middle and a discriminator nucleotide-CCA at its 3' end, and would start resembling a modern tRNA. Three major aspects should be stressed here.


How amino acids and peptides shaped the RNA world.

van der Gulik PT, Speijer D - Life (Basel) (2015)

How to get a tRNA precursor. Two (identical) hairpin-loop structures (red and blue) can form one extended RNA molecule upon unfolding. Regions in this precursor are compared to a schematized version of a present day tRNA. 1: CCA acceptor stem; 2: D-arm; 3: T-arm; 4: Anticodon containing loop. The dotted line indicates the schematized separation between acceptor-TψC stem-loop and anticodon-D stem-Biloop [52]. The anticodon and the discriminator nucleotide U are shown in bold face. Hydrogen bonds are shown as stripes. * In the anticodon containing loop further insertions and deletions are needed. Here two identical molecules (accepting glycine) are depicted, however the extended molecule can also be formed by slightly different non-identical molecules. For further details see text.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4390850&req=5

life-05-00230-f001: How to get a tRNA precursor. Two (identical) hairpin-loop structures (red and blue) can form one extended RNA molecule upon unfolding. Regions in this precursor are compared to a schematized version of a present day tRNA. 1: CCA acceptor stem; 2: D-arm; 3: T-arm; 4: Anticodon containing loop. The dotted line indicates the schematized separation between acceptor-TψC stem-loop and anticodon-D stem-Biloop [52]. The anticodon and the discriminator nucleotide U are shown in bold face. Hydrogen bonds are shown as stripes. * In the anticodon containing loop further insertions and deletions are needed. Here two identical molecules (accepting glycine) are depicted, however the extended molecule can also be formed by slightly different non-identical molecules. For further details see text.
Mentions: We could thus envisage two relatively small hairpin sequences basepair, forming a primitive tRNA precursor. If we begin with two “Shimizu” RNA stem loop molecules (C4N structures), each with a 5' anticodon-stem loop stem-discriminator nucleotide-CCA 3' structure (see Figure 1) and allow them to basepair after “opening up” their original stem loops, eventual ligation on one side of the molecule (where the differently colored sequences meet in Figure 1) would lead to a new RNA species. This molecule has both an anticodon in the middle and a discriminator nucleotide-CCA at its 3' end, and would start resembling a modern tRNA. Three major aspects should be stressed here.

Bottom Line: Though the oldest center of the ribosome seems "RNA only", we cannot conclude from this that it ever functioned in an environment without amino acids and/or peptides.In this article, we try to bring the role of the peptide component of early life back into focus.We argue that an RNA world completely independent of amino acids never existed.

View Article: PubMed Central - PubMed

Affiliation: Centrum Wiskunde & Informatica, Science Park 123, 1098 SJ Amsterdam, The Netherlands. Peter.van.der.Gulik@cwi.nl.

ABSTRACT
The "RNA world" hypothesis is seen as one of the main contenders for a viable theory on the origin of life. Relatively small RNAs have catalytic power, RNA is everywhere in present-day life, the ribosome is seen as a ribozyme, and rRNA and tRNA are crucial for modern protein synthesis. However, this view is incomplete at best. The modern protein-RNA ribosome most probably is not a distorted form of a "pure RNA ribosome" evolution started out with. Though the oldest center of the ribosome seems "RNA only", we cannot conclude from this that it ever functioned in an environment without amino acids and/or peptides. Very small RNAs (versatile and stable due to basepairing) and amino acids, as well as dipeptides, coevolved. Remember, it is the amino group of aminoacylated tRNA that attacks peptidyl-tRNA, destroying the bond between peptide and tRNA. This activity of the amino acid part of aminoacyl-tRNA illustrates the centrality of amino acids in life. With the rise of the "RNA world" view of early life, the pendulum seems to have swung too much towards the ribozymatic part of early biochemistry. The necessary presence and activity of amino acids and peptides is in need of highlighting. In this article, we try to bring the role of the peptide component of early life back into focus. We argue that an RNA world completely independent of amino acids never existed.

No MeSH data available.


Related in: MedlinePlus