Acetylation of the «-amino group of lysine (Lys) is a reversible posttranslational modification recently discovered to be widespread, occurring on proteins outside the nucleus, in most subcellular locations in mammalian cells. Almost nothing is known about this modification in plants beyond the well-studied acetylation of histone proteins in the nucleus. Here, we report that Lys acetylation in plants also occurs on organellar and cytosolic proteins. We identified 91 Lys-acetylated sites on 74 proteins of diverse functional classes. Furthermore, our study suggests that Lys acetylation may be an important posttranslational modification in the chloroplast, since four Calvin cycle enzymes were acetylated. The plastid-encoded large subunit of Rubisco stands out because of the large number of acetylated sites occurring at important Lys residues that are involved in Rubisco tertiary structure formation and catalytic function. Using the human recombinant deacetylase sirtuin 3, it was demonstrated that Lys deacetylation significantly affects Rubisco activity as well as the activities of other central metabolic enzymes, such as the Calvin cycle enzyme phosphoglycerate kinase, the glycolytic enzyme glyceraldehyde 3-phosphate dehydrogenase, and the tricarboxylic acid cycle enzyme malate dehydrogenase. Our results demonstrate that Lys acetylation also occurs on proteins outside the nucleus in Arabidopsis (Arabidopsis thaliana) and that Lys acetylation could be important in the regulation of key metabolic enzymes.

We describe the construction and analysis of a genome-scale metabolic model of Arabidopsis (Arabidopsis thaliana) primarily derived from the annotations in the Aracyc database. We used techniques based on linear programming to demonstrate the following: (1) that the model is capable of producing biomass components (amino acids, nucleotides, lipid, starch, and cellulose) in the proportions observed experimentally in a heterotrophic suspension culture; (2) that approximately only 15% of the available reactions are needed for this purpose and that the size of this network is comparable to estimates of minimal network size for other organisms; (3) that reactions may be grouped according to the changes in flux resulting from a hypothetical stimulus (in this case demand for ATP) and that this allows the identification of potential metabolic modules; and (4) that total ATP demand for growth and maintenance can be inferred and that this is consistent with previous estimates in prokaryotes and yeast.Historically, attempts to engineer plant metabolism for increased production of specific useful products have met with mixed success. Problems arise because of considerable metabolic redundancy that allows imposed genetic changes to be circumvented, because of an insufficiently detailed knowledge of the distribution of control of flux, and because the behavior of plant metabolism at the network level is not well described. While increasingly complex metabolic networks are now being characterized with steadystate stable isotope labeling experiments (Libourel and Shachar-Hill, 2008;Schwender, 2008;Kruger and Ratcliffe, 2009), the resulting flux maps still only cover a small percentage of the total metabolic network. The construction of a comprehensive plant metabolic model that includes the complete repertoire of catalyzed transformations represented within a specific genome (a genome-scale metabolic model) would represent a significant step forward in the development of a description of plant metabolic behavior at the network level.The aim of this work is to describe a genome-scale structural model of Arabidopsis (Arabidopsis thaliana) metabolism and to explore the utility of the model as a tool to characterize possible flux behavior states of the metabolic network. Arabidopsis is the logical choice for this exercise because of its well-annotated genome. Moreover, the translation of the Arabidopsis genome into a curated set of metabolic reactions is already well advanced, and the reaction lists are available through the Aracyc database (Mueller et al., 2003;Zhang et al., 2005). While this is an excellent starting point for metabolic modeling, uncritical use of such reaction lists is likely to generate models exhibiting a number of problems, the most fundamental of which is violation of mass conservation. Thus, considerable effort is required to generate a useful genome-scale metabolic model from these databases .Once a stoichiometrically balanced structural model is achieved, the investigator is then faced with the challenge o...

Most transcriptional repression pathways depend on the targeted deacetylation of histone tails. In this report, we characterize NIR, a novel transcriptional corepressor with inhibitor of histone acetyltransferase (INHAT) activity. NIR (Novel INHAT Repressor) is ubiquitously expressed throughout embryonic development and adulthood. NIR is a potent transcriptional corepressor that is not blocked by histone deacetylase inhibitors and is capable of silencing both basal and activator-driven transcription. NIR directly binds to nucleosomes and core histones and prevents acetylation by histone acetyltransferases, thus acting as a bona fide INHAT. Using a tandem affinity purification approach, we identified the tumor suppressor p53 as a NIR-interacting partner. Association of p53 and NIR was verified in vitro and in vivo. Upon recruitment by p53, NIR represses transcription of both p53-dependent reporters and endogenous target genes. Knock-down of NIR by RNA interference significantly enhances histone acetylation at p53-regulated promoters. Moreover, p53-dependent apoptosis is robustly increased upon depletion of NIR. In summary, our findings describe NIR as a novel INHAT that plays an important role in the control of p53 function.[Keywords: INHAT; transcription; HDAC-independent repression; p53] Supplemental material is available at http://www.genesdev.org.