Dataset Information

RIP-Seq analysis of non-PPR editing factors OZ1, ORRM1, RIP9/MORF9

ABSTRACT: We provide sequences of maize chlroplast RNAs associated with non-PPR editing factors through immunoprecipitation. The accumulated sequences indicate expansive role in RNA processing and potential associations of OZ1-ORRM1 complexes with the ribosome and less efficiently translated mRNAs.

ORGANISM(S): Zea mays

PROVIDER: GSE151702 | GEO | 2021/12/31

REPOSITORIES: GEO

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Project description:Saha2011 - Genome-scale metabolic network of Arabidopsis thaliana (iRS1597) This model is described in the article: Zea mays iRS1563: a comprehensive genome-scale metabolic reconstruction of maize metabolism. Saha R, Suthers PF, Maranas CD. PLoS ONE 2011; 6(7): e21784 Abstract: The scope and breadth of genome-scale metabolic reconstructions have continued to expand over the last decade. Herein, we introduce a genome-scale model for a plant with direct applications to food and bioenergy production (i.e., maize). Maize annotation is still underway, which introduces significant challenges in the association of metabolic functions to genes. The developed model is designed to meet rigorous standards on gene-protein-reaction (GPR) associations, elementally and charged balanced reactions and a biomass reaction abstracting the relative contribution of all biomass constituents. The metabolic network contains 1,563 genes and 1,825 metabolites involved in 1,985 reactions from primary and secondary maize metabolism. For approximately 42% of the reactions direct literature evidence for the participation of the reaction in maize was found. As many as 445 reactions and 369 metabolites are unique to the maize model compared to the AraGEM model for A. thaliana. 674 metabolites and 893 reactions are present in Zea mays iRS1563 that are not accounted for in maize C4GEM. All reactions are elementally and charged balanced and localized into six different compartments (i.e., cytoplasm, mitochondrion, plastid, peroxisome, vacuole and extracellular). GPR associations are also established based on the functional annotation information and homology prediction accounting for monofunctional, multifunctional and multimeric proteins, isozymes and protein complexes. We describe results from performing flux balance analysis under different physiological conditions, (i.e., photosynthesis, photorespiration and respiration) of a C4 plant and also explore model predictions against experimental observations for two naturally occurring mutants (i.e., bm1 and bm3). The developed model corresponds to the largest and more complete to-date effort at cataloguing metabolism for a plant species. This model is hosted on BioModels Database and identified by: MODEL1507180011. To cite BioModels Database, please use: BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models. To the extent possible under law, all copyright and related or neighbouring rights to this encoded model have been dedicated to the public domain worldwide. Please refer to CC0 Public Domain Dedication for more information.

Dataset Information

RIP-Seq analysis of non-PPR editing factors OZ1, ORRM1, RIP9/MORF9

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