Abiogenesis & Evolution

RNA world

RNA has been put forward as the chemical candidate for the transition from primordial soup to self-replicating cells.

RNA can:
- be transcribed into DNA
- self-replicate
- act as an enzyme (ribozyme) – peptide-bond formation is catalyzed solely by RNA

"The first stage of evolution proceeds, then, by RNA molecules performing the catalytic activities necessary to assemble themselves from a nucleotide soup. The RNA molecules evolve in self-replicating patterns, using recombination and mutation to explore new niches. ... they then develop an entire range of enzymic activities. At the next stage, RNA molecules began to synthesize proteins, first by developing RNA adaptor molecules that can bind activated amino acids and then by arranging them according to an RNA template using other RNA molecules such as the RNA core of the ribosome. This process would make the first proteins, which would simply be better enzymes than their RNA counterparts. ... These protein enzymes are ... built up of mini-elements of structure.Finally, DNA appeared on the scene, the ultimate holder of information copied from the genetic RNA molecules by reverse transcription. ... RNA is then relegated to the intermediate role it has today—no longer the center of the stage, displaced by DNA and the more effective protein enzymes."
Walter Gilbert, "The RNA world," p 618 v 319, Nature, 1986.
More links: RNA World Website

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protein catalysts and ribozymes

BIO.COM: Biotechnology & Pharmaceutical News, Jobs, Software, Reports, Books, Events: "Protein enzymes are polymer strings made up of the 20 different amino acid building blocks, many of which have reactive side chains that can participate in biocatalysis. RNA polymers are made up of only four different building blocks, the RNA nucleotides, which lack the chemical versatility and reactivity of the protein functional groups.

After the discovery that RNA could act as a biocatalyst, many scientists began to theorize and discuss the possibility of an RNA world, the notion that at one time the world was ruled by RNA-based life forms in which RNA enzymes were the chief catalytic molecules and RNA nucleotides were the building blocks that stored genetic information. This raised a number of questions, such as where catalysis came from and how the world transitioned from an RNA-based form to the current DNA-RNA-protein form."

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A primordial RNA modification enzyme: the case of tRNA (m1A) methyltransferase.

Entrez PubMed: "The modified nucleoside 1-methyladenosine (m(1)A) is found in the T-loop of many tRNAs from organisms belonging to the three domains of life (Eukaryota, Bacteria, Archaea). In the T-loop of eukaryotic and bacterial tRNAs, m(1)A is present at position 58, whereas in archaeal tRNAs it is present at position(s) 58 and/or 57, m(1)A57 being the obligatory intermediate in the biosynthesis of 1-methylinosine (m(1)I57). In yeast, the formation of m(1)A58 is catalysed by the essential tRNA (m(1)A58) methyltransferase (MTase), a tetrameric enzyme that is composed of two types of subunits (Gcd14p and Gcd10p), whereas in the bacterium Thermus thermophilus the enzyme is a homotetramer of the TrmI polypeptide. Here, we report that the TrmI enzyme from the archaeon Pyrococcus abyssi is also a homotetramer. However, unlike the bacterial site-specific TrmI MTase, the P.abyssi enzyme is region-specific and catalyses the formation of m(1)A at two adjacent positions (57 and 58) in the T-loop of certain tRNAs. The stabilisation of P.abyssi TrmI at extreme temperatures involves intersubunit disulphide bridges that reinforce the tetrameric oligomerisation, as revealed by biochemical and crystallographic evidences. The origin and evolution of m(1)A MTases is discussed in the context of different hypotheses of the tree of life."Roovers M, Wouters J, Bujnicki JM, Tricot C, Stalon V, Grosjean H, Droogmans L. A primordial RNA modification enzyme: the case of tRNA (m1A) methyltransferase. Nucleic Acids Res. 2004 Jan 22;32(2):465-76. Print 2004. Free Full Text article

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