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Ribozymes

Ribozymes

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.
Ribozymes can...

Bacterial RNA Polymerase

Bacterial RNA Polymerase

Unlike eukaryotes, bacteria use a single RNA Polymerase (RNAP) to transcribe all genes. The different subunits of bacterial RNAPhave distinct functions. The multisubunit structure of the bacterial RNAP helps the enzyme to maintain catalytic function, facilitate assembly, interact with DNA and RNA, and self-regulate its activity.
In most genes, the transcription site is a single base present upstream of the coding sequence. Though RNAP is a catalytically efficient enzyme, it does not recognize...

Riboswitches

Riboswitches

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.
The aptamer has high specificity for a particular metabolite which allows riboswitches to specifically regulate...

Ribosomal RNA Synthesis

Ribosomal RNA Synthesis

Bacterial Transcription

Bacterial Transcription

RNA polymerase (RNAP) carries out DNA-dependent RNA synthesis in both bacteria and eukaryotes. Bacteria do not have a membrane-bound nucleus. So, transcription and translation occur simultaneously, on the same DNA template.
Transcription can be divided into three main stages, each involving distinct DNA sequences to guide the polymerase. These are:

Leaky Scanning

Leaky Scanning

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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Related Experiment Video

Updated: Sep 10, 2025

Chemical Triphosphorylation of Oligonucleotides

Chemical Triphosphorylation of Oligonucleotides

Published on: June 2, 2022

Exploring the space of self-reproducing ribozymes using generative models.

Camille N Lambert¹, Vaitea Opuu^1,2, Francesco Calvanese^1,3

¹Laboratoire de Biophysique et Evolution, UMR CNRS-ESPCI 8231 Chimie Biologie Innovation, ESPCI Paris, Université PSL, Paris, France.

Nature Communications

|August 22, 2025

Summary

This study explores RNA self-reproduction, crucial for origin-of-life theories. Researchers found over 10^39 self-reproducing ribozymes, expanding our understanding of abiogenesis.

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Area of Science:

Origin of Life Studies
Molecular Biology
Biochemistry

Background:

RNA self-reproduction is key to understanding abiogenesis.
Few catalytic RNAs have demonstrated this property.
Exploring RNA sequence space is essential for origin-of-life research.

Purpose of the Study:

To compare models for their generative power in diversifying a reference ribozyme.
To experimentally test model predictions using high-throughput sequencing.
To quantitatively assess the potential for RNA self-reproduction in abiogenesis.

Main Methods:

Statistical covariation and secondary structure prediction were used to model RNA diversification.
High-throughput sequencing was employed to experimentally validate model predictions.
Statistical physics methods were utilized to compute the number of self-reproducing ribozymes.

Main Results:

Over 10^39 ribozymes capable of autocatalytic self-reproduction were computed.
Sequences up to 65 mutations from the original and 99 mutations apart were identified.
This demonstrates a vast potential for RNA sequence space exploration.

Conclusions:

An efficient method for exploring RNA sequence space was demonstrated.
Quantitative data on self-reproducing RNA were provided.
The findings illuminate potential pathways to abiogenesis.