title: Freeze-quenched maize mesophyll and bundle sheath separation uncovers bias in previous tissue-specific RNA-Seq data.
abstract: The high efficiency of C4photosynthesis 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 C4tissues along a developing leaf gradient. This method treats both C4tissues 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 C4tissue 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 C4cycle 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.
authors.affiliation: Institute of Plant Biochemistry, Cluster of Excellence on Plant Sciences (CEPLAS), iGRAD-Plant Program, Heinrich-Heine-University, 40225 Düsseldorf, Germany.
authors.forename: Alisandra K
authors.initials: AK
authors.lastname: Denton
authors.affiliation: Institute of Informatics, Cluster of Excellence on Plant Sciences (CEPLAS), iGRAD-Plant Program, Heinrich-Heine University, 40225 Düsseldorf, Germany.
authors.forename: Janina
authors.initials: J
authors.lastname: Maß
authors.affiliation: Institute of Plant Biochemistry, Cluster of Excellence on Plant Sciences (CEPLAS), iGRAD-Plant Program, Heinrich-Heine-University, 40225 Düsseldorf, Germany.
authors.forename: Canan
authors.initials: C
authors.lastname: Külahoglu
authors.affiliation: Institute of Informatics, Cluster of Excellence on Plant Sciences (CEPLAS), iGRAD-Plant Program, Heinrich-Heine University, 40225 Düsseldorf, Germany.
authors.forename: Martin J
authors.initials: MJ
authors.lastname: Lercher
authors.affiliation: Institute of Plant Biochemistry, Cluster of Excellence on Plant Sciences (CEPLAS), iGRAD-Plant Program, Heinrich-Heine-University, 40225 Düsseldorf, Germany.|Network Analysis and Modeling Group, IPK Gatersleben, Corrensstrasse 3, D-06466 Stadt Seeland, Germany.
authors.forename: Andrea
authors.initials: A
authors.lastname: Bräutigam
authors.affiliation: Institute of Plant Biochemistry, Cluster of Excellence on Plant Sciences (CEPLAS), iGRAD-Plant Program, Heinrich-Heine-University, 40225 Düsseldorf, Germany andreas.weber@uni-duesseldorf.de.
authors.forename: Andreas P M
authors.identifier: 0000-0003-0970-4672
authors.initials: AP
authors.lastname: Weber
mesh_terms: D058503:Mesophyll Cells / Q000378:metabolism*; D055442:Metabolome; D010788:Photosynthesis; D059467:Transcriptome; D003313:Zea mays / Q000166:cytology / Q000378:metabolism*
keywords: C4
  ; cell separation; maize; meta-analysis; transcriptomics.