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

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 suga...

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Autores principales:	Ankur V Patel, Robert D Turner, Aline Rifflet, Adelina E Acosta-Martin, Andrew Nichols, Milena M Awad, Dena Lyras, Ivo Gomperts Boneca, Marshall Bern, Mark O Collins, Stéphane Mesnage
Formato:	article
Lenguaje:	EN
Publicado:	eLife Sciences Publications Ltd 2021
Materias:	peptigoglycan clostridium difficile peptidoglycan structure software open source jupyter notebook Medicine R Science Q Biology (General) QH301-705.5
Acceso en línea:	https://doaj.org/article/dc8df51d605e44f7b13fa1ec6b79a43e
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spelling	oai:doaj.org-article:dc8df51d605e44f7b13fa1ec6b79a43e2021-12-01T12:14:41ZPGFinder, a novel analysis pipeline for the consistent, reproducible, and high-resolution structural analysis of bacterial peptidoglycans10.7554/eLife.705972050-084Xe70597https://doaj.org/article/dc8df51d605e44f7b13fa1ec6b79a43e2021-09-01T00:00:00Zhttps://elifesciences.org/articles/70597https://doaj.org/toc/2050-084XMany 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.Ankur V PatelRobert D TurnerAline RiffletAdelina E Acosta-MartinAndrew NicholsMilena M AwadDena LyrasIvo Gomperts BonecaMarshall BernMark O CollinsStéphane MesnageeLife Sciences Publications Ltdarticlepeptigoglycanclostridium difficilepeptidoglycan structuresoftwareopen sourcejupyter notebookMedicineRScienceQBiology (General)QH301-705.5ENeLife, Vol 10 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	peptigoglycan clostridium difficile peptidoglycan structure software open source jupyter notebook Medicine R Science Q Biology (General) QH301-705.5
spellingShingle	peptigoglycan clostridium difficile peptidoglycan structure software open source jupyter notebook Medicine R Science Q Biology (General) QH301-705.5 Ankur V Patel Robert D Turner Aline Rifflet Adelina E Acosta-Martin Andrew Nichols Milena M Awad Dena Lyras Ivo Gomperts Boneca Marshall Bern Mark O Collins Stéphane Mesnage PGFinder, a novel analysis pipeline for the consistent, reproducible, and high-resolution structural analysis of bacterial peptidoglycans
description	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.
format	article
author	Ankur V Patel Robert D Turner Aline Rifflet Adelina E Acosta-Martin Andrew Nichols Milena M Awad Dena Lyras Ivo Gomperts Boneca Marshall Bern Mark O Collins Stéphane Mesnage
author_facet	Ankur V Patel Robert D Turner Aline Rifflet Adelina E Acosta-Martin Andrew Nichols Milena M Awad Dena Lyras Ivo Gomperts Boneca Marshall Bern Mark O Collins Stéphane Mesnage
author_sort	Ankur V Patel
title	PGFinder, a novel analysis pipeline for the consistent, reproducible, and high-resolution structural analysis of bacterial peptidoglycans
title_short	PGFinder, a novel analysis pipeline for the consistent, reproducible, and high-resolution structural analysis of bacterial peptidoglycans
title_full	PGFinder, a novel analysis pipeline for the consistent, reproducible, and high-resolution structural analysis of bacterial peptidoglycans
title_fullStr	PGFinder, a novel analysis pipeline for the consistent, reproducible, and high-resolution structural analysis of bacterial peptidoglycans
title_full_unstemmed	PGFinder, a novel analysis pipeline for the consistent, reproducible, and high-resolution structural analysis of bacterial peptidoglycans
title_sort	pgfinder, a novel analysis pipeline for the consistent, reproducible, and high-resolution structural analysis of bacterial peptidoglycans
publisher	eLife Sciences Publications Ltd
publishDate	2021
url	https://doaj.org/article/dc8df51d605e44f7b13fa1ec6b79a43e
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PGFinder, a novel analysis pipeline for the consistent, reproducible, and high-resolution structural analysis of bacterial peptidoglycans

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