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Ribozymes02:47

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The term ribozyme is used for RNA that can act as an enzyme. Ribozymes are mainly found in selected viruses, bacteria, plant organelles, and lower eukaryotes. Ribozymes were first discovered in 1982 when Tom Cech’s laboratory observed Group I introns acting as enzymes. This was shortly followed by the discovery of another ribozyme, Ribonulcease P, by Sid Altman’s laboratory. Both Cech and Altman received the Nobel Prize in chemistry in 1989 for their work on ribozymes.
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Riboswitches are non-coding mRNA domains that regulate the transcription and translation of downstream genes without the help of proteins. Riboswitches bind directly to a metabolite and can form unique stem-loop or hairpin structures in response to the amount of the metabolite present. They have two distinct regions – a metabolite-binding aptamer and an expression platform.
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Three main types of RNA are involved in protein synthesis: messenger RNA (mRNA), transfer RNA (tRNA), and ribosomal RNA (rRNA). These RNAs perform diverse functions and can be broadly classified as protein-coding or non-coding RNA. Non-coding RNAs play important roles in the regulation of gene expression in response to developmental and environmental changes. Non-coding RNAs in prokaryotes can be manipulated to develop more effective antibacterial drugs for human or animal use.
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Base complementarity between the three base pairs of mRNA codon and the tRNA anticodon is not a failsafe mechanism. Inaccuracies can range from a single mismatch to no correct base pairing at all. The free energy difference between the correct and nearly correct base pairs can be as small as 3 kcal/ mol. With complementarity being the only proofreading step, the estimated error frequency would be one wrong amino acid in every 100 amino acids incorporated. However, error frequencies observed in...
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During most eukaryotic translation processes, the small 40S ribosome subunit scans an mRNA from its 5' end until it encounters the first start AUG codon. The large 60S ribosomal subunit then joins the smaller one to initiate protein synthesis. The location of the translation initiation is largely determined by the nucleotides near the start codon as there may be multiple translation initiation sites present on the mRNA.  Marilyn Kozak discovered that the sequence RCCAUGG (where R...
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Weak effects of prebiotically plausible peptides on self-triphosphorylation ribozyme function.

Joshua T Arriola1, Shayan Poordian1, Estefanía Martínez Valdivia2

  • 1Department of Chemistry & Biochemistry, University of California, San Diego La Jolla CA 92093 USA ufmuller@ucsd.edu.

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Prebiotically plausible peptides did not significantly aid the emergence of catalytic RNA (ribozyme) activity in early life. This suggests specific peptide features, not just general presence, were crucial for ribozyme evolution.

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Area of Science:

  • Origin of Life Studies
  • Biochemistry
  • RNA World Hypothesis

Background:

  • Catalytic RNAs (ribozymes) likely played a key role in early life.
  • Amino acids and peptides can form under prebiotic conditions.
  • The influence of prebiotic peptides on ribozyme emergence is investigated.

Purpose of the Study:

  • To test if prebiotically plausible peptides could enhance ribozyme emergence.
  • To select self-triphosphorylation ribozymes in the presence of specific peptides.
  • To biochemically assess peptide benefits on selected ribozymes.

Main Methods:

  • In vitro selection of ribozymes from random sequences.
  • Use of ten different octapeptides composed of prebiotic amino acids (d- and l-isomers).
  • High-throughput sequencing and biochemical assays to evaluate peptide effects.

Main Results:

  • The strongest peptide benefit observed was a 2.6-fold enhancement in ribozyme activity.
  • This enhancement was comparable to a 0.5 unit increase in pH.
  • Four previously selected ribozymes showed no significant activity change with these peptides.

Conclusions:

  • Prebiotically plausible peptides, lacking optimized sequences and charged/aromatic side chains, did not strongly benefit ribozyme emergence.
  • This contrasts with the significant effects of polycationic peptides, peptide-hydrocarbon conjugates, and modern proteins.
  • The findings highlight the importance of specific peptide characteristics in the context of the origin of life.