An integrative approach to the identification of Arabidopsis and rice genes involved in xylan and secondary wall development.

Xylans constitute the major non-cellulosic component of plant biomass. Xylan biosynthesis is particularly pronounced in cells with secondary walls, implying that the synthesis network consists of a set of highly expressed genes in such cells. To improve the understanding of xylan biosynthesis, we pe...

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Autores principales:	Ai Oikawa, Hiren J Joshi, Emilie A Rennie, Berit Ebert, Chithra Manisseri, Joshua L Heazlewood, Henrik Vibe Scheller
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2010
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/b2a5bdb2ff2644c4b0e605773f6260f1
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spelling	oai:doaj.org-article:b2a5bdb2ff2644c4b0e605773f6260f12021-11-18T07:36:37ZAn integrative approach to the identification of Arabidopsis and rice genes involved in xylan and secondary wall development.1932-620310.1371/journal.pone.0015481https://doaj.org/article/b2a5bdb2ff2644c4b0e605773f6260f12010-11-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/21124849/?tool=EBIhttps://doaj.org/toc/1932-6203Xylans constitute the major non-cellulosic component of plant biomass. Xylan biosynthesis is particularly pronounced in cells with secondary walls, implying that the synthesis network consists of a set of highly expressed genes in such cells. To improve the understanding of xylan biosynthesis, we performed a comparative analysis of co-expression networks between Arabidopsis and rice as reference species with different wall types. Many co-expressed genes were represented by orthologs in both species, which implies common biological features, while some gene families were only found in one of the species, and therefore likely to be related to differences in their cell walls. To predict the subcellular location of the identified proteins, we developed a new method, PFANTOM (plant protein family information-based predictor for endomembrane), which was shown to perform better for proteins in the endomembrane system than other available prediction methods. Based on the combined approach of co-expression and predicted cellular localization, we propose a model for Arabidopsis and rice xylan synthesis in the Golgi apparatus and signaling from plasma membrane to nucleus for secondary cell wall differentiation. As an experimental validation of the model, we show that an Arabidopsis mutant in the PGSIP1 gene encoding one of the Golgi localized candidate proteins has a highly decreased content of glucuronic acid in secondary cell walls and substantially reduced xylan glucuronosyltransferase activity.Ai OikawaHiren J JoshiEmilie A RennieBerit EbertChithra ManisseriJoshua L HeazlewoodHenrik Vibe SchellerPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 5, Iss 11, p e15481 (2010)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Ai Oikawa Hiren J Joshi Emilie A Rennie Berit Ebert Chithra Manisseri Joshua L Heazlewood Henrik Vibe Scheller An integrative approach to the identification of Arabidopsis and rice genes involved in xylan and secondary wall development.
description	Xylans constitute the major non-cellulosic component of plant biomass. Xylan biosynthesis is particularly pronounced in cells with secondary walls, implying that the synthesis network consists of a set of highly expressed genes in such cells. To improve the understanding of xylan biosynthesis, we performed a comparative analysis of co-expression networks between Arabidopsis and rice as reference species with different wall types. Many co-expressed genes were represented by orthologs in both species, which implies common biological features, while some gene families were only found in one of the species, and therefore likely to be related to differences in their cell walls. To predict the subcellular location of the identified proteins, we developed a new method, PFANTOM (plant protein family information-based predictor for endomembrane), which was shown to perform better for proteins in the endomembrane system than other available prediction methods. Based on the combined approach of co-expression and predicted cellular localization, we propose a model for Arabidopsis and rice xylan synthesis in the Golgi apparatus and signaling from plasma membrane to nucleus for secondary cell wall differentiation. As an experimental validation of the model, we show that an Arabidopsis mutant in the PGSIP1 gene encoding one of the Golgi localized candidate proteins has a highly decreased content of glucuronic acid in secondary cell walls and substantially reduced xylan glucuronosyltransferase activity.
format	article
author	Ai Oikawa Hiren J Joshi Emilie A Rennie Berit Ebert Chithra Manisseri Joshua L Heazlewood Henrik Vibe Scheller
author_facet	Ai Oikawa Hiren J Joshi Emilie A Rennie Berit Ebert Chithra Manisseri Joshua L Heazlewood Henrik Vibe Scheller
author_sort	Ai Oikawa
title	An integrative approach to the identification of Arabidopsis and rice genes involved in xylan and secondary wall development.
title_short	An integrative approach to the identification of Arabidopsis and rice genes involved in xylan and secondary wall development.
title_full	An integrative approach to the identification of Arabidopsis and rice genes involved in xylan and secondary wall development.
title_fullStr	An integrative approach to the identification of Arabidopsis and rice genes involved in xylan and secondary wall development.
title_full_unstemmed	An integrative approach to the identification of Arabidopsis and rice genes involved in xylan and secondary wall development.
title_sort	integrative approach to the identification of arabidopsis and rice genes involved in xylan and secondary wall development.
publisher	Public Library of Science (PLoS)
publishDate	2010
url	https://doaj.org/article/b2a5bdb2ff2644c4b0e605773f6260f1
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An integrative approach to the identification of Arabidopsis and rice genes involved in xylan and secondary wall development.

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