Heterogeneity of the Mitochondrial Proteome for Photosynthetic and Non-photosynthetic Arabidopsis Metabolism

Abstract

Heterogeneity of the mitochondrial proteome in plants underlies fundamental differences in the roles of these organelles in different tissues. We quantitatively compared the mitochondrial proteome isolated from a nonphotosynthetic cell culture model with more specialized mitochondria isolated from photosynthetic shoots. Differences in intact mitochondrial respiratory rates with various substrates and activities of specific enzymes provided a backdrop of the functional variation between these mitochondrial populations. Proteomics comparisons provided a deep insight into the different steadystate abundances of specific mitochondrial proteins. Combined these data showed the elevated level of the photorespiratory apparatus and its complex interplay with glycolate, cysteine, formate, and one-carbon metabolism as well as the decrease of selected parts of the tricarboxylic acid cycle, alterations in amino acid metabolism focused on 2-oxoglutarate generation, and degradation of branched chain amino acids. Comparisons with microarray analysis of these tissue types showed a positive, mild correlation between mRNA and mitochondrial protein abundance, a tighter correlation for specific biochemical pathways, but over 78% concordance in direction between changes in protein and transcript abundance in the two tissues. Overall these results indicated that the majority of the variation in the plant mitochondrial proteome occurred in the matrix, highlighted the constitutive nature of the respiratory apparatus, and showed the differences in substrate choice and/or availability during photosynthetic and non-photosynthetic metabolism. Molecular & Cellular Proteomics 7:1297-1316, 2008.Plant mitochondria have been traditionally purified from total cell extracts of storage organs, etiolated tissues, or cell cultures by differential centrifugation and density gradient centrifugation using sucrose or Percoll (1-4). These organelles are derived from tissues where sugars or fats are used as energy sources and mitochondria have a primary role in ATP production for cellular activity. The combination of Percoll and PVP 1 gradients has also enabled purification of mitochondria away from chloroplasts in extracts of photosynthetic shoot or leaf samples from plants (3). These organelles are known to have a range of additional roles including carbon skeleton provision for nitrogen assimilation (5) and the recycling of carbon in the photorespiratory cycle (6, 7).Early reports using 1D SDS-PAGE documented apparent differences between mitochondria isolated from leaves, petioles, and roots from spinach (8); roots, leaves, and flowers from sugar beet (9); and shoot, scutella, endosperm, and cob from developing maize (10). Remy et al. (11) performed the first comparative 2D IEF/SDS-PAGE study of pea mitochondrial protein profiles isolated from different organs and quantified differences in the abundance of glycine decarboxylase complex subunits using protein spot intensities. Similar studies to compare mitochondrial proteomes were also performed on pot...

Combined Noninvasive Imaging and Modeling Approaches Reveal Metabolic Compartmentation in the Barley Endosperm

“…Thus, achieving a higher flux through Ala-AT represents an advantageous alternative under conditions where the operation of the usual TCA cycle is inhibited. Similar conclusions were drawn from studies on photosynthetically active Arabidopsis tissues (Lee et al, 2008) and metabolic changes in response to waterlogging in Lotus japonicus (Rocha et al, 2010). By removing pyruvate, the activation of ethanol/lactate fermentation is inhibited ( Figure 4A), and the stimulation of alternative oxidase activity can be avoided (Oliver et al, 2008).…”

Refining the Definition of Plant Mitochondrial Presequences through Analysis of Sorting Signals, N-Terminal Modifications, and Cleavage Motifs

“…Alignment of the mammalian and plant mitochondrial GDHs indicates that the plant N-terminal regions that appear to be responsible for mitochondrial targeting are much shorter than the presequences of the mammalian GDH proteins (data not shown). We recently observed the two Arabidopsis mitochondrial GDHs (At5g07440 [GDH2] and At5g18170 [GDH1]) shifting pI or molecular mass on two-dimensional gels of mitochondrial extracts from shoots and cultured stem cells (Lee et al, 2008a). Reanalysis of peptide spectra from those gel spots has revealed that both had the intact N-terminal sequence with acetylated Met as shown in Table I, indicating that presequence processing is not the cause of these observed pI differences (data not shown).…”

Plant d-2-Hydroxyglutarate Dehydrogenase Participates in the Catabolism of Lysine Especially during Senescence

“…4A). Here, it is worth mentioning that D-2HGDH has already been found as a mitochondrial protein in both Arabidopsis leaves and cell cultures in proteomic studies using mass spectrometry (31). In this study, At4g36400 was described as a glycolate dehydrogenase because of its close relatedness to At5g06580, which has been previously annotated as a glycolate dehydrogenase (32).…”