Project description:RNA-directed DNA methylation (RdDM) in plants is a well-characterized example of RNA interference-related transcriptional gene silencing. To determine the relationships between RdDM and heterochromatin in the repeat-rich maize (Zea mays) genome, we performed whole-genome analyses of several heterochromatic features: dimethylation of lysine 9 and lysine 27 (H3K9me2 and H3K27me2), chromatin accessibility, DNA methylation, and small RNAs; we also analyzed two mutants that affect these processes, mediator of paramutation1 and zea methyltransferase2.
Project description:Whole Genome Metabolism of "Zea mays"
This is a whole genome metabolism model of Zea mays.
This model has been automatically generated by the SuBliMinaL Toolbox
and libAnnotationSBML using information coming from from KEGG (release 66, April 2013, accessed via the resource's web services interface) and, where relevant, augmented with metabolic pathway information extracted from MetaCyc (version 17.0, March 2013).
This model has been produced by the path2models
project and is currently hosted on BioModels Database
and identified by: BMID000000140835
Other models with the same genus include BMID000000025302 BMID000000025303 BMID000000025304 BMID000000025305 BMID000000025306 BMID000000025307 BMID000000025308 BMID000000025309 BMID000000025310 BMID000000025311 BMID000000025312 BMID000000025313 BMID000000025314 BMID000000025315 BMID000000025316 BMID000000025317 BMID000000025318 BMID000000025319 BMID000000025320 BMID000000025321 BMID000000025322 BMID000000025323 BMID000000025324 BMID000000025325 BMID000000025326 BMID000000025327 BMID000000025328 BMID000000025329 BMID000000025330 BMID000000025331 BMID000000132155 BMID000000132156 BMID000000132157 BMID000000132158 BMID000000132159 BMID000000132160 BMID000000132161 BMID000000132162 BMID000000132163 BMID000000132164 BMID000000132165 BMID000000132166 BMID000000132167 BMID000000132168 BMID000000132169 BMID000000132170 BMID000000132171 BMID000000132172 BMID000000132173 BMID000000132174 BMID000000132175 BMID000000132176 BMID000000132177 BMID000000132178 BMID000000132179 BMID000000132180 BMID000000132181 BMID000000132182 BMID000000132183 BMID000000132184 BMID000000132185 BMID000000132186 BMID000000132187 BMID000000132188 BMID000000132189 BMID000000132190 BMID000000132191 BMID000000132192 BMID000000132193 BMID000000132194 BMID000000132195 BMID000000132196 BMID000000132197 BMID000000132198 BMID000000132199 BMID000000132200 BMID000000132201 BMID000000132202 BMID000000132203 BMID000000132204 BMID000000132205 BMID000000132206 BMID000000132207 BMID000000132208 BMID000000132209 BMID000000132210 BMID000000132211 BMID000000132212 BMID000000132213 BMID000000132214 BMID000000132215 BMID000000132216 BMID000000132217 BMID000000132218 BMID000000132219 BMID000000132220 BMID000000132221 BMID000000132222 BMID000000132223 BMID000000132224 BMID000000132225 BMID000000132226 BMID000000132227 BMID000000132228 BMID000000132229 BMID000000132230 BMID000000132231 BMID000000132232 BMID000000132233 BMID000000132234 BMID000000132235 BMID000000132236 BMID000000132237 BMID000000132238 BMID000000132239 BMID000000132240 BMID000000132241 BMID000000132242 .
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.
Project description:Saha2011- Genome-scale metabolic network of
Zea mays (iRS1563)
This model is described in the article:
Zea mays iRS1563: a
comprehensive genome-scale metabolic reconstruction of maize
Saha R, Suthers PF, Maranas
PLoS ONE 2011; 6(7): e21784
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.
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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
Public Domain Dedication for more information.