Research Update

RNA polymerases are multi-subunit proteins that transcribe genes encoded in DNA to messenger RNA (mRNA). The mRNA is then translated into protein at the ribosome.

In a recent publication in Protein Science, iCOOL affiliate Claudia Alvarez Carreno, Co-I Anton Petrov, and PI Loren Williams describe, for the first time, the insertion of blocks of conserved sequence and structure into the catalytic subunits of RNA polymerase.

Interestingly, although the insertions, dubbed BEAN and HABAS, each represent a group of orthologs (descending from a common ancestor), their insertion positions within the catalytic subunits vary. Additionally, the BEAN insertion is found in the archaeal version of universally conserved ribosomal protein uL10 but not the bacterial version. Taken together, the results suggest discrete episodes of domain insertion around or after the last bacterial common ancestor.

Insertion of BEAN in the RNAP-β subunit of RNA polymerase.

October 20, 2024. In life on modern Earth, enzymes made of protein catalyze the formation of most other types of biopolymers. These enzymes have been evolving for billions of years and have become very efficient at assembling nucleic acid, carbohydrate, and lipid biopolymers from their monomer parts. The enzymes are biopolymers themselves, which presents an intriguing challenge for origins researchers.

If biopolymers are required to make other biopolymers, how did the first biopolymers emerge? To address this question, PI Loren Williams, Collaborator Moran Frenkel-Pinter and student Rotem Edri of the Hebrew University of Jerusalem have been reviewing the condensation-dehydration reactions that occur under oscillating water activity. These reactions are of interest because the enzymatic polymerization of monomers is a dehydration (or water producing) step.

In a new review in Accounts of Chemical Research, Edri and coauthors demonstrate how prebiotic catalysis by small molecules could have evolved and promoted chemical evolution, leading to increasing complexity and some of the core processes of contemporary biocatalysis. The role of water as a metabolite for promoting complexification over chemical evolution is highlighted.

Co-I Anton Petrov, PI Loren Williams, and students published RiboVision2, an open-source tool for understanding RNA structure and evolution. RiboVision2 is a web server designed to visualize the phylogenetic, structural, and evolutionary properties of ribosomal RNAs, simultaneously, at the levels of primary, secondary, and three-dimensional structure and in the context of full ribosomal complexes. RiboVision2 instantly computes and displays a broad variety of RNA data in the main user interface; enables saving of RNA visualizations as publication-quality images; supports visualization of any RNA molecule; and represents a major upgrade of the original RiboVision. It has no login requirements, is free for all users, and is available at https://ribovision2.chemistry.gatech.edu.