Protein degradation – an alternative respiratory substrate for stressed plants  Wagner L. Araújo, Takayuki Tohge, Kimitsune Ishizaki, Christopher J. Leaver, Alisdair R. Fernie  Trends in Plant Science  Volume 16, Issue 9, Pages 489-498 (September 2011) DOI: 10.1016/j.tplants.2011.05.008 Copyright © 2011 Elsevier Ltd Terms and Conditions

Figure 1 Functional interactions between the major players in the process of protein degradation. In this simplified depiction, three main pathways, ubiquitinylation, autophagic processes and the TOR pathways, are indicated. Ubiquitinylation occurs in order to target proteins to the proteosome for degradation. The process of autophagy involves the degradation of the component sub-cellular compartments of the cell via the lysosomal machinery. The (downstream) operation of the TOR nutrient-sensing pathway involves the integration of nutrient-derived and growth factor-derived signals to control the cell growth machinery and protein synthesis. Crosstalk between the three mechanisms of protein degradation plays a key role in maximizing the catabolic processes for the benefit of the plant, particularly during stress conditions, and potentially provides alternative substrates for the mitochondrial electron transport chain. Trends in Plant Science 2011 16, 489-498DOI: (10.1016/j.tplants.2011.05.008) Copyright © 2011 Elsevier Ltd Terms and Conditions

Figure 2 Protein degradation feeding electrons to the mitochondrial electron transport chain. After protein degradation a range of amino acids are generated and further metabolized either into isovaleryl-CoA or HG. Isovaleryl-CoA can be produced by catabolism of the branched chain and aromatic amino acids and by both phytol and Lys degradation, whereas HG can be produced by aromatic amino acid degradation, either in the peroxysome or from the Lys derivative L-pipecolate, as in non-plants. The electrons generated are transferred to the respiratory chain through to the ubiquinol pool via an ETF/ETFQO system. In addition, some of the amino acids produced can proceed via two routes: (i) conversion to pyruvic acid or acetyl-CoA before entering the TCA cycle; or (ii) they might enter the TCA cycle directly after being converted into one of the intermediates such as 2-OG and direct electron supply to the ubiquinone pool of the mitochondrial electron transport chain in plants. Dotted arrows represent possible transport processes and multi enzymatic reactions. Abbreviations: e–, electron; ETF, electron transfer flavoprotein; ETFQO, ETF:ubiquinone oxidoreductase; HG, hydroxyglutarate; Lys, lysine; 3-MC-CoA, 3-methylcrotonyl-CoA; 2-OG, 2-oxoglutarate; TCA cycle, tricarboxylic acid cycle; UQ, ubiquinone. Trends in Plant Science 2011 16, 489-498DOI: (10.1016/j.tplants.2011.05.008) Copyright © 2011 Elsevier Ltd Terms and Conditions

Figure 3 Co-expression analysis as a tool to identify candidate genes involved in the provision of alternative substrates for the mitochondrial electron transport chain. Framework for co-regulation network analysis (r >0.6) of chlorophyll breakdown (4 genes), ubiquitination control (31), protein degradation (29), amino acid degradation and N mobilization (38) and autophagy (5 genes) using co-expression PRIMe database [134] (http://prime.psc.riken.jp/?action=coexpression_index) and Pajek software [135]. The candidate genes were listed by a combinatorial method of ‘intersection of sets’ and ‘interconnection of sets’ using the PRIMe website (http://prime.psc.riken.jp/?action=coexpression_index) following a procedure described in [84,130]. Candidate genes were found by an ‘intersection of sets’ search with a threshold value with a coefficient of r >0.75 queried by intraconnection between all query genes. A co-expression network, including candidate genes (47 genes) and queried genes (107 genes), was re-constructed by a ‘union of sets’ search with r >0.60 using the PRIMe database. The output files that were formatted with a ‘.net’ file from the PRIMe database and networks were drawn using Pajek software [135] (http://vlado.fmf.uni-lj.si/pub/networks/pajek/). For a complete description of the gene names see Supplementary Material Table S1. Trends in Plant Science 2011 16, 489-498DOI: (10.1016/j.tplants.2011.05.008) Copyright © 2011 Elsevier Ltd Terms and Conditions