KatayaProject

Highlights

We have cataloged over 100 polypeptides as peroxisomal phospho-proteins using available phospho-proteomic datasets, fully establishing protein phosphorylation as a regulatory mechanism in peroxisomes.

Phospho-proteins have been identified as components of most peroxisomal processes, many functioning in the fatty acid β-oxidation pathway.

Peroxisomes perform essential roles in a range of cellular processes, highlighted by lipid metabolism, reactive species detoxification, and response to a variety of stimuli. The ability of peroxisomes to grow, divide, respond to changing cellular needs, interact with other organelles, and adjust their proteome as required, suggest that, like other organelles, their specialized roles are highly regulated. Similar to most other cellular processes, there is an emerging role for protein phosphorylation to regulate these events. In this review, we establish a knowledge framework of key players that control protein phosphorylation events in the plant peroxisome (i.e., the protein kinases and phosphatases), and highlight a vastly expanded set of (phospho)substrates.

b-Oxidation

The high degree of protein phosphorylation now observed for the steps of FA b-oxidation in peroxisomes hints that phosphorylation may be a key regulatory event for this process and is worthy of focused studies to explore this possibility.

Triacylglycerides (TAG) are broken down into FAs in lipid droplets. The b-oxidation pathway successively removes two carbon units from FAs in each b-oxidation cycle. In plants and yeast, b-oxidation is a peroxisomal process that leads to chain shortening of acyl-CoA esters to yield chain-shortened acyl-CoA and acetyl-CoA or enoyl-CoA, depending on the substrates. In oilseed plants, FA b-oxidation is essential to supply energy and carbon metabolites after seed germination. This energy pathway involves FA b-oxidation, the glyoxylate cycle, and gluconeogenesis. Peroxisomes have been shown to physically interact with lipid droplets in a sucrose-dependent fashion). Lipid droplet-derived FAs are transported into peroxisomes, putatively through the peroxisomal ABC transporter 1 (PXA1), also named peroxisome-deficient 3 (PED3) and comatose (CTS).

Phosphorylation of PXA1 has been observed, and is thought to fine-tune the transport of FAs into the peroxisome. It is fascinating that the anchor on peroxisomes for association with lipid droplets is in fact PXA1/PED3. After transport into peroxisomes, FAs are activated into their CoA form with the help of long-chain acyl-CoA synthetases. Three members of long-chain acyl- CoA synthetases (isoform 2, 5, and 6) are catalogued as phospho-proteins. Remarkably, select isoforms of all the b-oxidation enzymes are known to be phosphorylated, as are several glyoxylate cycle enzymes. Arabidopsis MFP2 and AIM1 catalyze the second step of b-oxidation and additional activities for some unsaturated FAs, and are experimentally validated to be phosphorylated. The 2- trans-enoyl-CoA hydratase motif of MFP2 was reported to be only active against C18:0 substrates, whereas the L3-hydroxyacyl-CoA dehydrogenase domain is active against C6:0, C12:0, and C18:0 substrates. Additionally, representative candidates such as delta (3) and delta (2)-enoyl CoA isomerase (ECIs) proposed to activate unsaturated FAs have shown phosphorylation status. Here, shortened FA-CoA and acetyl-CoA are the outcomes, which fed into another b-oxidation cycle and the glyoxylate cycle, respectively. Acetyl-CoA can be further metabolized in seedlings via the glyoxylate cycle, which has two phosphorylated enzymes (citrate synthase and isocitrate lyase). Although not yet detected as phospho-proteins in Arabidopsis, malate synthase and malate dehydrogenase have been reported to be phosphorylated in castor bean glyoxysomes and pea leaf peroxisomes (D.P. Mantilla, University of Granada, 2009).

Experimentally validated phosphorylated proteins (see online supplemental information Tables S1 and S2; kataya et al., 2019). The photorespiration scheme, including the crosstalk between chloroplast, mitochondria, and peroxisomes, are presented. Scheme of jasmonic acid (JA) biosynthesis displays the phosphorylation of most of the key enzymes involved from chloroplast and peroxisomes. Salicylic acid (SA), and indole-acetic acid (IAA) peroxisomal biosynthetic pathways are also represented. A brief overview of reactive oxygen species (ROS) biosynthesis and detoxification of key enzymes and their phosphorylation status are also shown, as are biogenesis factors affecting peroxisome abundance and content. This includes: (i) proteins involved in transporting of peroxisomal membrane proteins (PMPs) and matrix proteins; (ii) recycling of transporters (PEX5), induction of peroxule formation and proliferation; (iii) degradation of matrix proteins (ex. LON2); and (iv) pexophagy.