PGFinder, a novel analysis pipeline for the consistent, reproducible, and high-resolution structural analysis of bacterial peptidoglycans

eLife

Robert D Turner¹  Milena M Awad²  Dena Lyras³  Ivo Gomperts Boneca⁴  Aline Rifflet⁴  Andrew Nichols⁵  Marshall Bern⁵  Stéphane Mesnage⁶  Ankur V Patel⁶  Mark O Collins⁷  Adelina E Acosta-Martin⁸ 

[1] Department of Computer Science, University of Sheffield, Sheffield, United Kingdom;Infection and Immunity Program, Monash Biomedicine Discovery Institute, Clayton, Australia;Infection and Immunity Program, Monash Biomedicine Discovery Institute, Clayton, Australia;Department of Microbiology, Monash University, Clayton, Australia;Institut Pasteur, Unité Biologie et Génétique de la Paroi Bactérienne, Paris, France;INSERM, Équipe Avenir, Paris, France;CNRS, UMR 2001 "Microbiologie intégrative et moléculaire", Paris, France;Protein Metrics Inc, Cupertino, United States;School of Biosciences, University of Sheffield, Sheffield, United Kingdom;School of Biosciences, University of Sheffield, Sheffield, United Kingdom;biOMICS Facility, Faculty of Science Mass Spectrometry Centre, University of Sheffield, Sheffield, United Kingdom;biOMICS Facility, Faculty of Science Mass Spectrometry Centre, University of Sheffield, Sheffield, United Kingdom;

关键词: peptigoglycan;    clostridium difficile;    peptidoglycan structure;    software;    open source;    jupyter notebook;    E. coli;    C. difficile;   

DOI  :  10.7554/eLife.70597

来源: eLife Sciences Publications, Ltd

【 摘 要 】

Many software solutions are available for proteomics and glycomics studies, but none are ideal for the structural analysis of peptidoglycan (PG), the essential and major component of bacterial cell envelopes. It icomprises glycan chains and peptide stems, both containing unusual amino acids and sugars. This has forced the field to rely on manual analysis approaches, which are time-consuming, labour-intensive, and prone to error. The lack of automated tools has hampered the ability to perform high-throughput analyses and prevented the adoption of a standard methodology. Here, we describe a novel tool called PGFinder for the analysis of PG structure and demonstrate that it represents a powerful tool to quantify PG fragments and discover novel structural features. Our analysis workflow, which relies on open-access tools, is a breakthrough towards a consistent and reproducible analysis of bacterial PGs. It represents a significant advance towards peptidoglycomics as a full-fledged discipline.

【 授权许可】

CC BY