Société Française de Bioinformatique

Mots-Clés

protein structure function

Description

Elucidating substrate specificity in a prenyltransferase family through large-scale structure-function correlation

Objectives: Identify the residues that control the substrate specificity in MenA family members using large-scale comparative structural analyses and coevolution patterns. Propose mutations to alter substrate specificity in MenA proteins for testing in an experimental setting.

Abstract: Isoprenoid quinones play a key role in the functioning of most organisms, including the production of ATP via electron transfer chains. Menaquinone (MK) is synthesised by a wide variety of bacteria via a multi-step biosynthetic pathway. We found that 15% of gut bacteria synthesising MK have lost the upper part of the biosynthesis pathway, retaining only the MenA prenyltransferase. Testing the function of 50 MenA proteins revealed that family members had diversified to utilise various precursors: DHNA or menadione. The objectives of the internship are: 1) to conduct a large-scale comparative analysis of MenA structural models to identify factors contributing to substrate specificity; 2) to use the recently developed COCOA-Tree package(a) to identify co-evolving residues likely to govern substrate specificity within MenA proteins; 3) to propose mutations that may be tested experimentally to change the substrate specificity of selected MenA proteins. Our results will enable us to reconstruct the evolutionary history of the functional properties of MenA proteins across bacteria. The internship will be co-supervised by TrEE team members F. Pierrel (biochemist) and N. Varoquaux (computational biologist), as well as J. Esque (protein modelling, TBI-Toulouse).

**Methods: ** Structural modeling by using AI-based method such as Alphafold2/3 b, Boltz2 to characterize substrate binding. Co-evolution analysis (e.g., SCA) of multiple sequence alignments and statistical analysis. E. coli cultures and quinone analysis by HPLC for characterization of mutant MenA (optional)

a Jullien et al., bioRxiv 2026, doi : 10.64898/2026.02.05.703816
b Launay et al., J Chem Inf Model. 2024, doi: 10.1021/acs.jcim.4c00304
Kazemzadeh et al., Mol. Biol. Evol. 2023, doi: 10.1093/molbev/msad219
Requested domains of expertise:
Structural modeling, Bioinformatics, Biochemistry, Phylogenetics (optional)