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Freeze-quenched maize mesophyll and bundle sheath separation uncovers bias in previous tissue-specific RNA-Seq data

The high efficiency of C(4) photosynthesis relies on spatial division of labor, classically with initial carbon fixation in the mesophyll and carbon reduction in the bundle sheath. By employing grinding and serial filtration over liquid nitrogen, we enriched C(4) tissues along a developing leaf grad...

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Autores principales: Denton, Alisandra K, Maß, Janina, Külahoglu, Canan, Lercher, Martin J, Bräutigam, Andrea, Weber, Andreas P M
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2017
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5853576/
https://www.ncbi.nlm.nih.gov/pubmed/28043950
http://dx.doi.org/10.1093/jxb/erw463
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author Denton, Alisandra K
Maß, Janina
Külahoglu, Canan
Lercher, Martin J
Bräutigam, Andrea
Weber, Andreas P M
author_facet Denton, Alisandra K
Maß, Janina
Külahoglu, Canan
Lercher, Martin J
Bräutigam, Andrea
Weber, Andreas P M
author_sort Denton, Alisandra K
collection PubMed
description The high efficiency of C(4) photosynthesis relies on spatial division of labor, classically with initial carbon fixation in the mesophyll and carbon reduction in the bundle sheath. By employing grinding and serial filtration over liquid nitrogen, we enriched C(4) tissues along a developing leaf gradient. This method treats both C(4) tissues in an integrity-preserving and consistent manner, while allowing complementary measurements of metabolite abundance and enzyme activity, thus providing a comprehensive data set. Meta-analysis of this and the previous studies highlights the strengths and weaknesses of different C(4) tissue separation techniques. While the method reported here achieves the least enrichment, it is the only one that shows neither strong 3′ (degradation) bias, nor different severity of 3′ bias between samples. The meta-analysis highlighted previously unappreciated observations, such as an accumulation of evidence that aspartate aminotransferase is more mesophyll specific than expected from the current NADP-ME C(4) cycle model, and a shift in enrichment of protein synthesis genes from bundle sheath to mesophyll during development. The full comparative dataset is available for download, and a web visualization tool (available at http://www.plant-biochemistry.hhu.de/resources.html) facilitates comparison of the the Z. mays bundle sheath and mesophyll studies, their consistencies and their conflicts.
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spelling pubmed-58535762018-07-25 Freeze-quenched maize mesophyll and bundle sheath separation uncovers bias in previous tissue-specific RNA-Seq data Denton, Alisandra K Maß, Janina Külahoglu, Canan Lercher, Martin J Bräutigam, Andrea Weber, Andreas P M J Exp Bot Research Paper The high efficiency of C(4) photosynthesis relies on spatial division of labor, classically with initial carbon fixation in the mesophyll and carbon reduction in the bundle sheath. By employing grinding and serial filtration over liquid nitrogen, we enriched C(4) tissues along a developing leaf gradient. This method treats both C(4) tissues in an integrity-preserving and consistent manner, while allowing complementary measurements of metabolite abundance and enzyme activity, thus providing a comprehensive data set. Meta-analysis of this and the previous studies highlights the strengths and weaknesses of different C(4) tissue separation techniques. While the method reported here achieves the least enrichment, it is the only one that shows neither strong 3′ (degradation) bias, nor different severity of 3′ bias between samples. The meta-analysis highlighted previously unappreciated observations, such as an accumulation of evidence that aspartate aminotransferase is more mesophyll specific than expected from the current NADP-ME C(4) cycle model, and a shift in enrichment of protein synthesis genes from bundle sheath to mesophyll during development. The full comparative dataset is available for download, and a web visualization tool (available at http://www.plant-biochemistry.hhu.de/resources.html) facilitates comparison of the the Z. mays bundle sheath and mesophyll studies, their consistencies and their conflicts. Oxford University Press 2017-01-21 2017-01-02 /pmc/articles/PMC5853576/ /pubmed/28043950 http://dx.doi.org/10.1093/jxb/erw463 Text en © The Author 2017. Published by Oxford University Press on behalf of the Society for Experimental Biology. http://creativecommons.org/licenses/by/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Research Paper
Denton, Alisandra K
Maß, Janina
Külahoglu, Canan
Lercher, Martin J
Bräutigam, Andrea
Weber, Andreas P M
Freeze-quenched maize mesophyll and bundle sheath separation uncovers bias in previous tissue-specific RNA-Seq data
title Freeze-quenched maize mesophyll and bundle sheath separation uncovers bias in previous tissue-specific RNA-Seq data
title_full Freeze-quenched maize mesophyll and bundle sheath separation uncovers bias in previous tissue-specific RNA-Seq data
title_fullStr Freeze-quenched maize mesophyll and bundle sheath separation uncovers bias in previous tissue-specific RNA-Seq data
title_full_unstemmed Freeze-quenched maize mesophyll and bundle sheath separation uncovers bias in previous tissue-specific RNA-Seq data
title_short Freeze-quenched maize mesophyll and bundle sheath separation uncovers bias in previous tissue-specific RNA-Seq data
title_sort freeze-quenched maize mesophyll and bundle sheath separation uncovers bias in previous tissue-specific rna-seq data
topic Research Paper
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5853576/
https://www.ncbi.nlm.nih.gov/pubmed/28043950
http://dx.doi.org/10.1093/jxb/erw463
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