ODH like search (private)

In this project, I attempted to find ODH-type candidates by combining MMseqs2 homology search, MAFFT/FastTree phylogeny, ColabFold structure prediction (with MSA), and structure-based confirmation via Foldseek/TM-align, plus inspection of the active site/pocket in PyMOL relative to 6XUU

Author

Affiliation

Corentin Maslard, PhD

UniNE

Abstract

Oligosaccharide dehydrogenases (ODHs) are flavin-dependent oxidoreductases involved in carbohydrate oxidation, yet their occurrence and diversification in grasses remain poorly characterized. Here, we sought to identify and validate ODH-like homologs in Brachypodium distachyon using an integrated sequence- and structure-based strategy starting from the fungal ODH reference structure 6XUU. Candidate proteins were first retrieved by sequence similarity searches and clustered to obtain representative hits. Multiple sequence alignment and phylogenetic reconstruction highlighted a small subset of top candidates closely related to the reference. To obtain an orthogonal validation, we predicted 3D structures of the best candidates using AlphaFold/ColabFold with MSA generation, and quantified structural similarity to 6XUU using TM-align. Two Brachypodium proteins (BdiBd21-3.1G0418900 isoforms) showed high-confidence folds (pLDDT ~86; pTM ~0.86) and strong structural agreement with 6XUU (TM-score ~0.76 over ~485 aligned residues; RMSD ~2.7–2.8 Å), consistent with a conserved overall architecture. Mapping of ligand-proximal residues around the sugar-binding region of 6XUU revealed a largely conserved pocket geometry, supporting functional relatedness while leaving room for substrate specificity differences. Together, these results identify BdiBd21-3.1G0418900 as a robust ODH-like candidate in Brachypodium and establish a transferable workflow combining phylogeny and structure comparison for enzyme homolog discovery in plant genomes.

Preface

Contributors: Corentin Maslard / Kevin Bellande / Joop E.M Vermeer / Richard Sibout

This project is an extension of the research work carried out by the Laboratory of cell and molecular biology and the Laboratory working on Variability and quality of plant bioresources in relation to the cell wall PVPP

NoteGuide being written

This guide is still incomplete. The complete repository (documentation, data, script for analyse data, etc.) will be available shortly at this link: https://github.com/cmaslard/odh_like_search.

Grants and institutional support:

NoteMore informations about my work :

• Personal website
• Email
• Github
• Linkedin

• ORCID
• ResearchGate
• Google Scholar

• X (Twitter)
• HAL
• CV

Licence

This document is made available under the terms of the Licence Creative Commons Attribution - Non Commercial Use - Share Alike 4.0 International.

Package used in this quarto document

library(renv) # install.packages("renv")
library(dplyr)

deps <- renv::dependencies(path = ".", progress = F, quiet = T)

unique_packages <- unique(deps$Package)
writeLines(unique_packages, here::here("src/packages_use_in_this_quarto.txt"))

data.frame(
  Package = unique_packages,
  Version = sapply(unique_packages, function(pkg) {
    tryCatch(as.character(packageVersion(pkg)), error = function(e) NA)
  }),
  stringsAsFactors = FALSE
) %>% 
  #knitr::kable(caption = "List of packages used in this document", row.names = FALSE)
  DT::datatable(.,
  filter = "top",
  class = 'cell-border stripe',
  rownames = FALSE
)