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Unlocking conserved and diverged metabolic characteristics in cassava carbon assimilation via comparative genomics approach

Globally, cassava is an important source of starch, which is synthesized through carbon assimilation in cellular metabolism whereby harvested atmospheric carbon is assimilated into macromolecules. Although the carbon assimilation pathway is highly conserved across species, metabolic phenotypes could...

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Autores principales: Siriwat, Wanatsanan, Kalapanulak, Saowalak, Suksangpanomrung, Malinee, Saithong, Treenut
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Nature Publishing Group UK 2018
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6226483/
https://www.ncbi.nlm.nih.gov/pubmed/30413726
http://dx.doi.org/10.1038/s41598-018-34730-y
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author Siriwat, Wanatsanan
Kalapanulak, Saowalak
Suksangpanomrung, Malinee
Saithong, Treenut
author_facet Siriwat, Wanatsanan
Kalapanulak, Saowalak
Suksangpanomrung, Malinee
Saithong, Treenut
author_sort Siriwat, Wanatsanan
collection PubMed
description Globally, cassava is an important source of starch, which is synthesized through carbon assimilation in cellular metabolism whereby harvested atmospheric carbon is assimilated into macromolecules. Although the carbon assimilation pathway is highly conserved across species, metabolic phenotypes could differ in composition, type, and quantity. To unravel the metabolic complexity and advantage of cassava over other starch crops, in terms of starch production, we investigated the carbon assimilation mechanisms in cassava through genome-based pathway reconstruction and comparative network analysis. First, MeRecon — the carbon assimilation pathway of cassava was reconstructed based upon six plant templates: Arabidopsis, rice, maize, castor bean, potato, and turnip. MeRecon, available at http://bml.sbi.kmutt.ac.th/MeRecon, comprises 259 reactions (199 EC numbers), 1,052 proteins (870 genes) and 259 metabolites in eight sub-metabolisms. Analysis of MeRecon and the carbon assimilation pathways of the plant templates revealed the overall topology is highly conserved, but variations at sub metabolism level were found in relation to complexity underlying each biochemical reaction, such as numbers of responsible enzymatic proteins and their evolved functions, which likely explain the distinct metabolic phenotype. Thus, this study provides insights into the network characteristics and mechanisms that regulate the synthesis of metabolic phenotypes of cassava.
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spelling pubmed-62264832018-11-13 Unlocking conserved and diverged metabolic characteristics in cassava carbon assimilation via comparative genomics approach Siriwat, Wanatsanan Kalapanulak, Saowalak Suksangpanomrung, Malinee Saithong, Treenut Sci Rep Article Globally, cassava is an important source of starch, which is synthesized through carbon assimilation in cellular metabolism whereby harvested atmospheric carbon is assimilated into macromolecules. Although the carbon assimilation pathway is highly conserved across species, metabolic phenotypes could differ in composition, type, and quantity. To unravel the metabolic complexity and advantage of cassava over other starch crops, in terms of starch production, we investigated the carbon assimilation mechanisms in cassava through genome-based pathway reconstruction and comparative network analysis. First, MeRecon — the carbon assimilation pathway of cassava was reconstructed based upon six plant templates: Arabidopsis, rice, maize, castor bean, potato, and turnip. MeRecon, available at http://bml.sbi.kmutt.ac.th/MeRecon, comprises 259 reactions (199 EC numbers), 1,052 proteins (870 genes) and 259 metabolites in eight sub-metabolisms. Analysis of MeRecon and the carbon assimilation pathways of the plant templates revealed the overall topology is highly conserved, but variations at sub metabolism level were found in relation to complexity underlying each biochemical reaction, such as numbers of responsible enzymatic proteins and their evolved functions, which likely explain the distinct metabolic phenotype. Thus, this study provides insights into the network characteristics and mechanisms that regulate the synthesis of metabolic phenotypes of cassava. Nature Publishing Group UK 2018-11-09 /pmc/articles/PMC6226483/ /pubmed/30413726 http://dx.doi.org/10.1038/s41598-018-34730-y Text en © The Author(s) 2018 Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.
spellingShingle Article
Siriwat, Wanatsanan
Kalapanulak, Saowalak
Suksangpanomrung, Malinee
Saithong, Treenut
Unlocking conserved and diverged metabolic characteristics in cassava carbon assimilation via comparative genomics approach
title Unlocking conserved and diverged metabolic characteristics in cassava carbon assimilation via comparative genomics approach
title_full Unlocking conserved and diverged metabolic characteristics in cassava carbon assimilation via comparative genomics approach
title_fullStr Unlocking conserved and diverged metabolic characteristics in cassava carbon assimilation via comparative genomics approach
title_full_unstemmed Unlocking conserved and diverged metabolic characteristics in cassava carbon assimilation via comparative genomics approach
title_short Unlocking conserved and diverged metabolic characteristics in cassava carbon assimilation via comparative genomics approach
title_sort unlocking conserved and diverged metabolic characteristics in cassava carbon assimilation via comparative genomics approach
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6226483/
https://www.ncbi.nlm.nih.gov/pubmed/30413726
http://dx.doi.org/10.1038/s41598-018-34730-y
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