Genetic Interactions between PEROXIN12 and Other Peroxisome-Associated Ubiquitination Components

Most eukaryotic cells require peroxisomes, organelles housing fatty acid β-oxidation and other critical metabolic reactions. Peroxisomal matrix proteins carry peroxisome-targeting signals that are recognized by one of two receptors, PEX5 or PEX7, in the cytosol. After delivering the matrix proteins to the organelle, these receptors are removed from the peroxisomal membrane or matrix. Receptor retrotranslocation not only facilitates further rounds of matrix protein import but also prevents deleterious PEX5 retention in the membrane. Three peroxisome-associated ubiquitin-protein ligases in the Really Interesting New Gene (RING) family, PEX2, PEX10, and PEX12, facilitate PEX5 retrotranslocation. However, the detailed mechanism of receptor retrotranslocation remains unclear in plants. We identified an Arabidopsis (Arabidopsis thaliana) pex12 Glu-to-Lys missense allele that conferred severe peroxisomal defects, including impaired β-oxidation, inefficient matrix protein import, and decreased growth. We compared this pex12-1 mutant to other peroxisome-associated ubiquitination-related mutants and found that RING peroxin mutants displayed elevated PEX5 and PEX7 levels, supporting the involvement of RING peroxins in receptor ubiquitination in Arabidopsis. Also, we observed that disruption of any Arabidopsis RING peroxin led to decreased PEX10 levels, as seen in yeast and mammals. Peroxisomal defects were exacerbated in RING peroxin double mutants, suggesting distinct roles of individual RING peroxins. Finally, reducing function of the peroxisome-associated ubiquitin-conjugating enzyme PEX4 restored PEX10 levels and partially ameliorated the other molecular and physiological defects of the pex12-1 mutant. Future biochemical analyses will be needed to determine whether destabilization of the RING peroxin complex observed in pex12-1 stems from PEX4-dependent ubiquitination on the pex12-1 ectopic Lys residue.Oilseed plants obtain energy for germination and early development by utilizing stored fatty acids (Graham, 2008). This β-oxidation of fatty acids to acetyl-CoA occurs in peroxisomes, organelles that also house other important metabolic reactions, including the glyoxylate cycle, several steps in photorespiration, and phytohormone production (Hu et al., 2012). For example, indole-3-butyric acid (IBA) is β-oxidized into the active auxin indole-3-acetic acid (IAA) in peroxisomes (Zolman et al., 2000, 2007, 2008; Strader et al., 2010; Strader and Bartel, 2011). Many peroxisomal metabolic pathways generate reactive oxygen species (Inestrosa et al., 1979; Hu et al., 2012), and peroxisomes also house antioxidative enzymes, like catalase and ascorbate peroxidase, to detoxify hydrogen peroxide (Wang et al., 1999; Mhamdi et al., 2012).Peroxisomes can divide by fission or be synthesized de novo from the endoplasmic reticulum (ER). Preperoxisomes with peroxisomal membrane proteins bud from the ER and fuse, allowing matrix proteins to be imported to form mature peroxisomes (van der Zand et al., 2012; Mayerhofer, 2016). Peroxin (PEX) proteins facilitate peroxisome biogenesis and matrix protein import. Most peroxins are involved in importing proteins destined for the peroxisome matrix, which are imported after recognition of a type 1 or type 2 peroxisome-targeting signal (PTS). The PTS1 is a tripeptide located at the C terminus of most peroxisome-bound proteins (Gould et al., 1989; Chowdhary et al., 2012). The less common PTS2 is a nonapeptide usually located near the N terminus (Swinkels et al., 1991; Reumann, 2004). PTS1 proteins are recognized by PEX5 (van der Leij et al., 1993; Zolman et al., 2000), PTS2 proteins are recognized by PEX7 (Marzioch et al., 1994; Braverman et al., 1997; Woodward and Bartel, 2005), and PEX7 binds to PEX5 to allow matrix protein delivery in plants and mammals (Otera et al., 1998; Hayashi et al., 2005; Woodward and Bartel, 2005). The cargo-receptor complex docks with the membrane peroxins PEX13 and PEX14 (Urquhart et al., 2000; Otera et al., 2002; Woodward et al., 2014), and PEX5 assists cargo translocation into the peroxisomal matrix (Meinecke et al., 2010) before dissociating from its cargo (Freitas et al., 2011).After cargo delivery, PEX5 is recycled to enable further rounds of cargo recruitment (Thoms and Erdmann, 2006). This process requires a set of peroxins that is implicated in ubiquitinating PEX5 so that it can be retrotranslocated back to the cytosol. PEX5 ubiquitination is best understood in yeast. In Saccharomyces cerevisiae, Pex5 is monoubiquitinated through the action of the peroxisome-tethered ubiquitin-conjugating enzyme Pex4 and the peroxisomal ubiquitin-protein ligase Pex12 (Platta et al., 2009) and returned to the cytosol with the assistance of a peroxisome-tethered ATPase complex containing Pex1 and Pex6 (Grimm et al., 2012). S. cerevisiae Pex5 also can be polyubiquitinated and targeted for proteasomal degradation (Kiel et al., 2005). The cytosolic ubiquitin-conjugating enzyme Ubc4 cooperates with the peroxisomal ubiquitin-protein ligase Pex2 to polyubiquitinate Pex5 (Platta et al., 2009). Pex10 has ubiquitin-protein ligase activity (Williams et al., 2008; Platta et al., 2009; El Magraoui et al., 2012), but whether Pex10 directly ubiquitinates Pex5 is controversial. Pex10 promotes Ubc4-dependent Pex5 polyubiquitination when Pex4 is absent (Williams et al., 2008); however, Pex10 is not essential for Pex5 mono- or polyubiquitination (Platta et al., 2009), but rather enhances both Pex4/Pex12- and Ubc4/Pex2-mediated ubiquitination (El Magraoui et al., 2012). Recycling of the PTS2 receptor PEX7 is less understood, although the Pex5 recycling pathways are implicated in shuttling and degrading Pex7 in Pichia pastoris (Hagstrom et al., 2014).Although PEX5 ubiquitination has not been directly demonstrated in plants, the implicated peroxins are conserved in Arabidopsis, and several have been connected to PEX5 retrotranslocation. The PEX4 ubiquitin-conjugating enzyme binds to PEX22, which is predicted to be a peroxisomal membrane protein based on ability to restore peroxisome function to yeast mutants (Zolman et al., 2005). The pex4-1 mutant displays increased membrane-associated PEX5 (Ratzel et al., 2011; Kao and Bartel, 2015), suggesting that ubiquitin supplied by PEX4 promotes PEX5 retrotranslocation. PEX1 and PEX6 are members of the ATPases associated with diverse cellular activities (AAA) family and are tethered to peroxisomes by the peroxisomal membrane protein PEX26 (Goto et al., 2011; Li et al., 2014). The pex6-1 mutant displays PTS1 import defects and decreased PEX5 levels (Zolman and Bartel, 2004), suggesting that impaired PEX5 recycling can lead to increased PEX5 degradation. Indeed, pex4-1 restores PEX5 levels in the pex6-1 mutant (Ratzel et al., 2011), suggesting that Arabidopsis PEX4 also is involved in PEX5 ubiquitination and degradation when retrotranslocation is impeded.In addition to allowing for further rounds of PTS1 cargo import, several lines of evidence suggest that in the absence of efficient retrotranslocation, PEX5 retention in the peroxisomal membrane impairs peroxisome function. Slightly reducing levels of the PEX13 docking peroxin ameliorates the physiological defects of pex4-1 without restoring matrix protein import (Ratzel et al., 2011), presumably because decreasing PEX5 docking reduces its accumulation in the peroxisomal membrane. In addition, overexpressing PEX5 exacerbates rather than ameliorates the peroxisomal defects of pex4-1 (Kao and Bartel, 2015), suggesting that pex4-1 defects are linked to excessive PEX5 lingering in the peroxisome membrane rather than a lack of PEX5 available for import.The three Really Interesting New Gene (RING) peroxins (PEX2, PEX10, and PEX12) from Arabidopsis each possesses in vitro ubiquitin-protein ligase activity (Kaur et al., 2013). Null mutations in the RING peroxin genes confer embryo lethality in Arabidopsis (Hu et al., 2002; Schumann et al., 2003; Sparkes et al., 2003; Fan et al., 2005; Prestele et al., 2010), necessitating other approaches to study the in vivo functions of these peroxins. Expressing RING peroxins with mutations in the C-terminal zinc-binding RING domains (ΔZn) confers matrix protein import defects for PEX2-ΔZn and photorespiration defects for PEX10-ΔZn but no apparent defects for PEX12-ΔZn (Prestele et al., 2010). Targeting individual RING peroxins using RNAi confers β-oxidation deficiencies and impairs PTS1 cargo import (Fan et al., 2005; Nito et al., 2007). A screen for delayed matrix protein degradation (Burkhart et al., 2013) uncovered a missense pex2-1 mutant and a splicing pex10-2 mutant that both display PTS1 import defects (Burkhart et al., 2014), suggesting roles in regulating the PTS1 receptor, PEX5. A missense pex12 mutant (aberrant peroxisome morphology 4, apm4) has defects in β-oxidation and PTS1 import and increased membrane-associated PEX5 (Mano et al., 2006). These findings highlight the essential roles of the RING peroxins in Arabidopsis development and peroxisomal functions, but the RING peroxin interactions and the individual roles of the RING peroxins in PEX5 retrotranslocation remain incompletely understood.In this study, we describe a missense pex12-1 mutant recovered from a forward genetic screen for β-oxidation deficient mutants. The pex12-1 mutant displayed severe peroxisomal defects, including reduced growth, β-oxidation deficiencies, matrix protein import defects, and inefficient processing of PTS2 proteins. Comparing single and double mutants with impaired RING peroxins revealed that each RING peroxin contributes to complex stability and influences PEX5 accumulation. Furthermore, decreasing PEX4 function ameliorated pex12-1 defects, suggesting that the Glu-to-Lys substitution in pex12-1 lures ubiquitination, perhaps by pex12-1 itself, leading to PEX4-dependent degradation of the mutant protein.     

Peroxisomal Ubiquitin-Protein Ligases Peroxin2 and Peroxin10 Have Distinct But Synergistic Roles in Matrix Protein Import and Peroxin5 Retrotranslocation in Arabidopsis

Peroxisomal matrix proteins carry peroxisomal targeting signals (PTSs), PTS1 or PTS2, and are imported into the organelle with the assistance of peroxin (PEX) proteins. From a microscopy-based screen to identify Arabidopsis (Arabidopsis thaliana) mutants defective in matrix protein degradation, we isolated unique mutations in PEX2 and PEX10, which encode ubiquitin-protein ligases anchored in the peroxisomal membrane. In yeast (Saccharomyces cerevisiae), PEX2, PEX10, and a third ligase, PEX12, ubiquitinate a peroxisome matrix protein receptor, PEX5, allowing the PEX1 and PEX6 ATP-hydrolyzing enzymes to retrotranslocate PEX5 out of the membrane after cargo delivery. We found that the pex2-1 and pex10-2 Arabidopsis mutants exhibited defects in peroxisomal physiology and matrix protein import. Moreover, the pex2-1 pex10-2 double mutant exhibited severely impaired growth and synergistic physiological defects, suggesting that PEX2 and PEX10 function cooperatively in the wild type. The pex2-1 lesion restored the unusually low PEX5 levels in the pex6-1 mutant, implicating PEX2 in PEX5 degradation when retrotranslocation is impaired. PEX5 overexpression altered pex10-2 but not pex2-1 defects, suggesting that PEX10 facilitates PEX5 retrotranslocation from the peroxisomal membrane. Although the pex2-1 pex10-2 double mutant displayed severe import defects of both PTS1 and PTS2 proteins into peroxisomes, both pex2-1 and pex10-2 single mutants exhibited clear import defects of PTS1 proteins but apparently normal PTS2 import. A similar PTS1-specific pattern was observed in the pex4-1 ubiquitin-conjugating enzyme mutant. Our results indicate that Arabidopsis PEX2 and PEX10 cooperate to support import of matrix proteins into plant peroxisomes and suggest that some PTS2 import can still occur when PEX5 retrotranslocation is slowed.Peroxisomes are dynamic organelles housing critical oxidative metabolic reactions while sequestering harmful reactive oxygen species from the rest of the cell. In Arabidopsis (Arabidopsis thaliana), these single membrane-bound organelles are the sole site of β-oxidation and are essential for normal development (for review, see Hu et al., 2012). Triacylglycerols stored in seeds are cleaved by lipases during germination, and the released fatty acids are β-oxidized in peroxisomes to provide energy for early seedling development (for review, see Graham, 2008). Similarly, an auxin precursor, indole-3-butyric acid (IBA), is β-oxidized to active indole-3-acetic acid (IAA) in peroxisomes (Zolman et al., 2000, 2007, 2008; Strader et al., 2010; Strader and Bartel, 2011; Strader et al., 2011). IBA application enhances rooting in many plants (Woodward and Bartel, 2005a), and IAA produced from endogenous IBA promotes hypocotyl elongation, cotyledon expansion, root hair elongation, and lateral root proliferation in Arabidopsis seedlings (Zolman et al., 2001; Strader et al., 2010, 2011; De Rybel et al., 2012).The enzymes needed for β-oxidation and other peroxisomal processes are imported into the peroxisome matrix from their site of synthesis in the cytosol using proteins known as peroxin (PEX) proteins. PEX5 and PEX7 are receptors that recognize peroxisomal targeting signals (PTSs) on proteins destined for the peroxisome matrix. PEX5 recognizes a three-amino acid C-terminal PTS1 (Keller et al., 1987), and PEX7 recognizes a nine-amino acid PTS2 located near the N terminus of the protein (Osumi et al., 1991; Swinkels et al., 1991). In plants, DEG15, a peroxisomal protease, cleaves the N-terminal PTS2 region after the protein enters the peroxisome (Helm et al., 2007; Schuhmann et al., 2008). Cargo-bound PEX5 and PEX7 associate with PEX13 and PEX14 on the peroxisomal membrane (for review, see Azevedo and Schliebs, 2006; Williams and Distel, 2006) and release their cargo into the peroxisome (Fig. 1A). In yeast (Saccharomyces cerevisiae), membrane-associated PEX5 is ubiquitinated, recognized by a complex of ATP-hydrolyzing enzymes comprised of PEX1 and PEX6, and retrotranslocated out of the peroxisome to be used in additional rounds of import (for review, see Fujiki et al., 2012; Grimm et al., 2012).Open in a separate windowFigure 1.Recombination mapping of pfl36 and pfl81 reveals mutations in PEX2 and PEX10. A, PEX proteins (numbered) implicated in matrix protein import serve as receptors (PEX5 and PEX7) recognizing PTS1 or PTS2 cargo proteins, dock receptors at the peroxisomal membrane (PEX13 and PEX14), or assist in PEX5 retrotranslocation (for review, see Hu et al., 2012). In yeast, the RING-finger proteins PEX2, PEX10, and PEX12 participate as heterooligomers in different modes of PEX5 ubiquitination (Ub; for review, see Platta et al., 2013). B, GFP-ICL fluorescence is detected in both 5- and 7-d-old pex10-2 (pfl81) seedlings carrying ICLp:GFP-ICL, whereas GFP-ICL is easily detected in 5- but not 7-d-old wild-type (Wt) ICLp:GFP-ICL seedlings. Hypocotyls of light-grown seedlings were imaged for GFP fluorescence using confocal microscopy. Bar = 20 µm. C, pfl36 was mapped to the bottom of chromosome 1 near the PEX2 gene using the phenotypes of prolonged GFP-ICL fluorescence accompanied by PMDH processing defects. The number of recombinants over the number of chromosomes scored is indicated for each marker assayed. D, A gene diagram of PEX2 depicting exons as rectangles and introns as lines. A missense mutation in the fourth exon of PEX2 in pfl36 (pex2-1) changes Arg161 to Lys. Three other pex2 alleles are indicated: pex2-2, ted3 (Hu et al., 2002), and the transfer DNA insertion allele Salk_033081 that confers embryo lethality (Hu et al., 2002). E, The locations of the lesions in viable pex2 alleles are indicated on a diagram depicting the PEX2 protein domains, which include two predicted transmembrane domains (TMDs) and a C-terminal RING domain. F, pfl81 was mapped using the IBA resistance phenotype to an interval on the lower arm of chromosome 2 that contained the PEX10 gene. The number of recombinants over the number of chromosomes scored is indicated for each marker assayed. G, pfl81 (pex10-2) carries a PEX10 splicing mutation in the last nucleotide of intron 8. Four other reported pex10 mutants are indicated on the gene diagram: the pex10-1 transfer DNA insertion allele (Schumann et al., 2003; Sparkes et al., 2003) and three Targeting Induced Local Lesions In Genomes (TILLING) alleles: pex10-G93E, pex10-P126S, and pex10-W313* (Prestele et al., 2010). H, The locations of the lesions in the two viable pex10 alleles are indicated on a diagram depicting the PEX10 protein domains, which include two predicted TMDs and a C-terminal RING domain.Yeast PEX5 ubiquitination involves the peroxisomal membrane ubiquitin-protein ligases PEX2, PEX10, and PEX12 (for review, see Platta et al., 2013). The PEX12 ubiquitin-protein ligase monoubiquitinates PEX5 with the assistance of the ubiquitin-conjugating enzyme PEX4 (Platta et al., 2009), allowing PEX5 to be recycled back to the cytosol (Fig. 1A). When PEX4 is absent, yeast ubiquitin-conjugating enzyme4 (Ubc4) works with PEX2 to polyubiquitinate PEX5, marking PEX5 for proteasomal degradation (for review, see Thoms and Erdmann, 2006; Platta et al., 2007, 2013). In yeast, the Really Interesting New Gene (RING) domain of PEX10 binds both PEX2 and PEX12 RING domains to form a trimer (El Magraoui et al., 2012). PEX10 enhances in vitro ubiquitination activity of both PEX2-Ubc4 and PEX12-PEX4 (El Magraoui et al., 2012). Similarly, mammalian PEX12 enhances the in vitro ubiquitination activity of PEX10 (Okumoto et al., 2014). These findings suggest that these RING-finger proteins might act in heteromeric pairs to polyubiquitinate or monoubiquitinate PEX5 (Fig. 1A).Arabidopsis PEX2, PEX10, and PEX12 each display zinc-dependent monoubiquitination activity in vitro (Kaur et al., 2013), but the comparative functions of the Arabidopsis RING-finger PEX proteins in PEX5 ubiquitination, recycling, and degradation have not been reported. This deficiency may, in part, reflect the fact that null alleles of the RING-finger PEX genes confer embryo lethality (Hu et al., 2002; Schumann et al., 2003; Sparkes et al., 2003; Fan et al., 2005; Prestele et al., 2010). RNA interference (RNAi) lines targeting PEX2, PEX10, or PEX12 inefficiently import matrix proteins, display the Suc dependence phenotype that typically accompanies fatty acid β-oxidation defects, and are resistant to 2,4-dichlorophenoxybutyric acid (Fan et al., 2005; Nito et al., 2007), a synthetic analog of IBA (Hayashi et al., 1998). Mutation of any one RING-finger PEX gene results in disassociation or reduced levels of the PEX2-PEX10-PEX12 complex in yeast (Hazra et al., 2002; Agne et al., 2003) and mammals (Okumoto et al., 2014). It is not known whether the defects of the Arabidopsis null and RNAi lines result directly from the loss of catalytic activity of the corresponding RING-finger protein or indirectly from destabilization of the complex and consequent loss of activity of one or both of the associated RING-finger PEX proteins.Only one mutant defective in a RING-finger PEX gene has emerged from forward genetic screens for peroxisome defects in Arabidopsis. A partial loss-of-function pex12 missense allele, aberrant peroxisome morphology4 (apm4), was isolated from a GFP-PTS1 mislocalization screen (Mano et al., 2006). In addition to partially cytosolic GFP-PTS1, apm4 displays a PTS2 processing defect, Suc dependence, and 2,4-dichlorophenoxybutyric acid resistance (Mano et al., 2006), suggesting that PEX12 facilitates peroxisome protein import.In addition to roles in matrix protein import suggested by analysis of RNAi lines (Nito et al., 2007), PEX2 and PEX10 may have plant-specific roles. A pex2 missense allele, ted3, was identified as a dominant suppressor of the photomorphogenic defects of the de-etiolated1 mutant and carries a mutation near the PEX2 RING-finger domain (Fig. 1, D and E; Supplemental Fig. S1; Hu et al., 2002). Moreover, PEX10 RNAi lines display pleiotropic phenotypes not commonly found in Arabidopsis pex mutants, including variegated leaves, reduced fertility (Nito et al., 2007), organ fusions, reduced cuticular wax deposition, and changes in endoplasmic reticulum structure (Kamigaki et al., 2009). Three pex10 alleles generated by TILLING have been reported (Fig. 1G; Supplemental Fig. S2): pex10-W313* truncates the RING-finger domain and is embryo lethal, pex10-G93E germinates but displays seedling lethality, and pex10-P126S displays reduced growth in both normal air and high CO₂ conditions (Prestele et al., 2010). Although GFP-PTS1 is localized in peroxisomes in the pex10-P126S mutant, Suc dependence and IBA resistance were not reported (Prestele et al., 2010).The consequences of overexpressing a mutant version of PEX10 carrying missense mutations in the RING-finger domain (ΔZn) in wild-type Arabidopsis also hint at plant-specific roles for PEX10. PEX10-ΔZn expression confers pleiotropic phenotypes, including smaller cells, serrated leaves, inefficient photorespiration, abnormal peroxisome size and shape, and reduced peroxisome-chloroplast association (Prestele et al., 2010). However, PEX10-ΔZn plants respond like the wild type to IBA and do not require Suc, suggesting that peroxisome metabolism is not dramatically impaired (Schumann et al., 2007; Prestele et al., 2010). In contrast, expressing PEX2-ΔZn in the wild type impairs GFP-PTS1 import without conferring morphological defects, and expressing PEX12-ΔZn confers no abnormal phenotypes (Prestele et al., 2010).Here, we describe the identification and characterization of two unique mutants carrying lesions in Arabidopsis RING-finger PEX genes. We isolated pex2-1 and pex10-2 in a forward genetic screen for genes promoting peroxisomal matrix protein degradation and used these mutants to explore the roles of the corresponding proteins in peroxisome function. We found that PEX2 and PEX10 have independent but related functions that together support PEX5 recycling and matrix protein import into plant peroxisomes.     

Proteome Analysis of Peroxisomes from Etiolated Arabidopsis Seedlings Identifies a Peroxisomal Protease Involved in β-Oxidation and Development

Plant peroxisomes are highly dynamic organelles that mediate a suite of metabolic processes crucial to development. Peroxisomes in seeds/dark-grown seedlings and in photosynthetic tissues constitute two major subtypes of plant peroxisomes, which had been postulated to contain distinct primary biochemical properties. Multiple in-depth proteomic analyses had been performed on leaf peroxisomes, yet the major makeup of peroxisomes in seeds or dark-grown seedlings remained unclear. To compare the metabolic pathways of the two dominant plant peroxisomal subtypes and discover new peroxisomal proteins that function specifically during seed germination, we performed proteomic analysis of peroxisomes from etiolated Arabidopsis (Arabidopsis thaliana) seedlings. The detection of 77 peroxisomal proteins allowed us to perform comparative analysis with the peroxisomal proteome of green leaves, which revealed a large overlap between these two primary peroxisomal variants. Subcellular targeting analysis by fluorescence microscopy validated around 10 new peroxisomal proteins in Arabidopsis. Mutant analysis suggested the role of the cysteine protease RESPONSE TO DROUGHT21A-LIKE1 in β-oxidation, seed germination, and growth. This work provides a much-needed road map of a major type of plant peroxisome and has established a basis for future investigations of peroxisomal proteolytic processes to understand their roles in development and in plant interaction with the environment.Peroxisomes, originally known as microbodies, are small and single-membrane eukaryotic organelles that compartmentalize various oxidative metabolic functions. Most peroxisomal matrix proteins carry a C-terminal tripeptide named PEROXISOME TARGETING SIGNAL TYPE1 (PTS1), and fewer contain an N-terminal nonapeptide, PTS2 (Lanyon-Hogg et al., 2010). PTS1 is further divided into major and minor PTS1s. Major PTS1 tripeptides, such as SKL> and SRL> (> represents the stop codon), are by themselves sufficient to direct a protein to the peroxisome (Reumann, 2004), whereas minor PTS1s are usually found in low-abundance proteins and require additional upstream elements for peroxisomal targeting (Kaur et al., 2009). Peroxisomes are highly variable morphologically and metabolically, as their size, shape, abundance, and enzymatic content can differ depending on the species, tissue and cell type, and prevailing environmental conditions (Beevers, 1979; van den Bosch et al., 1992; Kaur et al., 2009; Hu et al., 2012; Schrader et al., 2012).Plant peroxisomes participate in a wide range of metabolic processes, such as lipid metabolism, photorespiration, detoxification, biosynthesis of jasmonic acid, and metabolism of indole-3-butyric acid (IBA), nitrogen, sulfite, and polyamine (Kaur et al., 2009; Hu et al., 2012). Specific names had been given to certain types of peroxisomes due to their unique metabolic properties. For example, the term glyoxysome was coined when a new type of organelle that contained enzymes of the glyoxylate cycle was identified from the endosperm of castor bean (Ricinus communis; Breidenbach et al., 1968). It was later realized that glyoxysomes are in fact a type of peroxisome, and Beevers (1979) subsequently classified plant peroxisomes into three subtypes based on their primary biochemical functions. Glyoxysomes are located in storage organs such as fatty seedling tissues and play a major role in converting fatty acids to sugar; leaf peroxisomes are involved in photorespiration; and nonspecialized peroxisomes exist in other plant tissues and perform unknown functions.The primary function of leaf peroxisomes is the recycling of phosphoglycolate during photorespiration, a process coordinated by chloroplasts, peroxisomes, mitochondria, and the cytosol. In this pathway, phosphoglycolate produced by the oxygenase activity of Rubisco is ultimately converted to glycerate, which reenters the chloroplastic Calvin-Benson cycle (Foyer et al., 2009; Peterhansel et al., 2010). The peroxisome-localized enzymes glycolate oxidase (GOX), catalase, aminotransferase (serine:glyoxylate aminotransferase [SGT] and glutamate-glyoxylate aminotransferase [GGT]), HYDROXYPYRUVATE REDUCTASE1 (HPR1), and peroxisomal malate dehydrogenase (PMDH) are involved in the process (Reumann and Weber, 2006). On the other hand, lipid mobilization through fatty acid β-oxidation and the glyoxylate cycle is the main function for peroxisomes in seeds and germinating seedlings. In this process, fatty acids are first activated into fatty acyl-CoA esters by the acyl-activating enzyme (AAE)/acyl-CoA synthetase before entering the β-oxidation cycle, during which an acetyl-CoA is cleaved in each cycle by the successive action of acyl-CoA oxidase (ACX), multifunctional protein (MFP), and 3-keto-acyl-CoA thiolase (KAT). Acetyl-CoA, an end product of β-oxidation, is further converted to four-carbon carbohydrates by the glyoxylate cycle, in which isocitrate lyase (ICL) and malate synthase (MLS) are two key enzymes that function exclusively in this pathway. Products of the glyoxylate cycle exit the peroxisome, enter gluconeogenesis, and are further converted to hexose and Suc to fuel the postgerminative development of seedlings (Penfield et al., 2006).Immunocytochemical studies of germinating seeds from pumpkin (Cucurbita pepo), watermelon (Citrullis vulgaris), and cucumber (Cucumis sativus) demonstrated that seed peroxisomes (glyoxysomes) are directly transformed into leaf peroxisomes during greening of the cotyledons without de novo biogenesis of leaf peroxisomes (Titus and Becker, 1985; Nishimura et al., 1986; Sautter, 1986). This conversion was illustrated by the import of photorespiratory enzymes and their concomitant presence with glyoxylate cycle enzymes within the same organelle. Furthermore, the increase in abundance of photorespiratory enzymes coincided with the marked decrease, and subsequently the absence, of glyoxylate cycle enzymes (ICL and/or MLS) at the culmination of this process (Titus and Becker, 1985; Nishimura et al., 1986; Sautter, 1986). It was suggested that the specific names for plant peroxisomal variants should be eliminated because protein composition between leaf peroxisomes and glyoxysomes may differ by only two proteins (i.e. ICL and MLS) out of the over 100 total proteins in the peroxisome (Pracharoenwattana and Smith, 2008). This prediction needed to be tested. In addition, mutants lacking core peroxisome biogenesis factors or major β-oxidation enzymes are nonviable, suggesting that peroxisomes are essential to embryogenesis and seed germination (Hu et al., 2012). However, how peroxisomes contribute to seed germination and seedling establishment is not completely understood. In the past, studies have been successfully undertaken to catalog the proteome of mitochondria and plastids isolated from different plant tissues, which uncovered unique facets of organelle metabolism in various tissues (van Wijk and Baginsky, 2011; Havelund et al., 2013; Lee et al., 2013). As such, it was necessary to establish a protein atlas for peroxisomes in dark-grown seedlings.Proteomic analyses of leaf peroxisomes and peroxisomes from suspension-cultured, leaf-derived cells followed by protein subcellular localization studies confirmed a total of over 30 new peroxisomal proteins, uncovering additional metabolic functions for leaf peroxisomes (Fukao et al., 2002; Reumann et al., 2007, 2009; Eubel et al., 2008; Babujee et al., 2010; Kataya and Reumann, 2010; Quan et al., 2010). For Arabidopsis (Arabidopsis thaliana), around 100 peroxisomal proteins were shown to be present in leaves or leaf-derived cells. Compared with the over 80 bona fide peroxisomal proteins detected by leaf peroxisomal proteomics (Reumann et al., 2007, 2009), the number of proteins identified from peroxisomal proteomic studies on etiolated seedlings was significantly smaller, with less than 10 known peroxisomal proteins from Arabidopsis (Fukao et al., 2003) and approximately 31 from soybean (Glycine max; Arai et al., 2008a, 2008b). Thus, a more in-depth analysis of the proteome of peroxisomes from these tissues was highly needed.Here, we performed proteomic analysis of peroxisomes isolated from etiolated Arabidopsis seedlings and detected peroxisomal proteins that encompass most of the known plant peroxisomal metabolic pathways. Fluorescence microscopy verified the peroxisomal localization of a number of proteins newly identified in this study or detected from previous proteomics that had not been verified by independent means. Reverse genetic analysis demonstrated the role for a Cys protease in germination, β-oxidation, and growth.     

Peroxisomal ATP Import Is Essential for Seedling Development in Arabidopsis thaliana

Several recent proteomic studies of plant peroxisomes indicate that the peroxisomal matrix harbors multiple ATP-dependent enzymes and chaperones. However, it is unknown whether plant peroxisomes are able to produce ATP by substrate-level phosphorylation or whether external ATP fuels the energy-dependent reactions within peroxisomes. The existence of transport proteins that supply plant peroxisomes with energy for fatty acid oxidation and other ATP-dependent processes has not previously been demonstrated. Here, we describe two Arabidopsis thaliana genes that encode peroxisomal adenine nucleotide carriers, PNC1 and PNC2. Both proteins, when fused to enhanced yellow fluorescent protein, are targeted to peroxisomes. Complementation of a yeast mutant deficient in peroxisomal ATP import and in vitro transport assays using recombinant transporter proteins revealed that PNC1 and PNC2 catalyze the counterexchange of ATP with ADP or AMP. Transgenic Arabidopsis lines repressing both PNC genes were generated using ethanol-inducible RNA interference. A detailed analysis of these plants showed that an impaired peroxisomal ATP import inhibits fatty acid breakdown during early seedling growth and other β-oxidation reactions, such as auxin biosynthesis. We show conclusively that PNC1 and PNC2 are essential for supplying peroxisomes with ATP, indicating that no other ATP generating systems exist inside plant peroxisomes.The β-oxidation of fatty acids, a process that exclusively occurs within peroxisomes in plants and yeast, plays an important role in storage oil mobilization to support seedling establishment of oilseed plants, such as Arabidopsis thaliana (Graham and Eastmond, 2002; Baker et al., 2006; Graham, 2008). Upon germination, fatty acids are released from storage oil triacylglycerol (TAG) by lipolysis, degraded via β-oxidation in specialized peroxisomes, termed glyoxysomes, and subsequently converted to sucrose, which drives growth and development until seedlings become photoautotrophic (Graham and Eastmond, 2002; Baker et al., 2006; Graham, 2008). Before the fatty acids can enter β-oxidation, they are imported into peroxisomes by a peroxisomal ATP binding cassette (ABC) transporter, variously known as CTS (COMATOSE), At PXA1 (Arabidopsis peroxisomal ABC transporter), or PED3 (peroxisomal defective 3) and hereafter referred to as CTS (Zolman et al., 2001; Footitt et al., 2002; Hayashi et al., 2002). Subsequently, the imported fatty acids are activated by esterification to CoA. This ATP-dependent reaction within peroxisomes is catalyzed by long-chain acyl-CoA synthetases 6 and 7 (LACS6 and LACS7, respectively), which are named according to their substrate specificity for long-chain fatty acids, which are significant components of seed storage oil in Arabidopsis (Fulda et al., 2002, 2004).In Saccharomyces cerevisiae, two mechanisms exist for import and activation of fatty acids, depending on chain length (Hettema et al., 1996). Long-chain fatty acids (C16 and C18) are converted to acyl-CoA esters in the cytosol prior to transport by the heterodimeric peroxisomal ABC transporter, Pxa1p/Pxa2 (Hettema et al., 1996). By contrast, short- and medium-chain fatty acids (≤C14) that enter the peroxisomes by passive diffusion or by an unknown transport protein are activated within peroxisomes (Hettema et al., 1996). The possibility cannot be excluded, though, that CTS imports the corresponding CoA derivatives, as is the case for the yeast Pxa1p/Pxa2p heterodimer (Hettema et al., 1996; Verleur et al., 1997), implicating a cytosolic activation of the fatty acids, catalyzed by a hitherto unknown enzyme. The actual substrates transported by CTS in Arabidopsis have not yet been experimentally determined (Theodoulou et al., 2006). However, the sucrose-dependent seedling growth phenotype of the lacs6 lacs7 double knockout mutant demonstrated that peroxisomal activation is essential for lipid mobilization to provide energy for early seedling growth (Fulda et al., 2004). The lacs6 lacs7 mutant is impaired in the degradation of fatty acids, leading to growth arrest shortly after germination (Fulda et al., 2004).Besides fatty acid mobilization, β-oxidation is also involved in generation of signaling molecules, such as the phytohormones auxin and fatty acid–derived jasmonic acid (JA) (Zolman et al., 2000; Schaller et al., 2004; Delker et al., 2007). By analogy to fatty acids released from storage oil, the precursors of these signaling molecules require CoA esterification before they can enter β-oxidation (Baker et al., 2006; Goepfert and Poirier, 2007). While the enzymes responsible for ATP-dependent activation of natural auxin (indole butyric acid [IBA]) and proherbicide 2,4-dichlorophenoxybutyric acid (2,4-DB) are currently unknown, several enzymes belonging to the acyl-activating enzyme (AAE) family have been implicated in jasmonate biosynthesis (Schneider et al., 2005; Koo et al., 2006; Kienow et al., 2008). Moreover, several as yet uncharacterized members of the large AAE family carry a putative peroxisome targeting signal (PTS) and thus might be good candidates to activate the additional β-oxidation substrates within peroxisomes (Shockey et al., 2002, 2003).In the case where activation of fatty acids or other substrates takes place within peroxisomes, the question arises as to how these ATP-dependent reactions are supplied with ATP. It is currently unknown whether plant peroxisomes are able to produce ATP by substrate-level phosphorylation or whether they depend on external ATP to supply energy-dependent reactions within peroxisomes. So far, transport proteins that supply plant peroxisomes with energy for fatty acid oxidation have not been characterized. However, in bakers'' yeast, a peroxisomal adenine nucleotide transporter, ANT1, that is required for the ATP-dependent activation of medium-chain fatty acids inside peroxisomes has been characterized (Palmieri et al., 2001).ATP transport proteins play an important role in the distribution of the primary agent coupling endergonic and exergonic reactions in every cellular compartment (Winkler and Neuhaus, 1999). In Arabidopsis and other plants, various adenine nucleotide carriers have been identified at the molecular level. The mitochondrial ADP/ATP carrier mediates the export of ATP that is synthesized in the mitochondrion to provide energy for cellular metabolism (Heimpel et al., 2001; Haferkamp et al., 2002). The plastidial ATP/ADP transporter (nucleotide transporter) is involved in ATP uptake by both chloroplasts and heterotrophic plastids, to enable the nocturnal ATP supply required for chlorophyll biosynthesis (Reiser et al., 2004; Reinhold et al., 2007), as well as by heterotrophic plastids to drive starch biosynthesis (Batz et al., 1992; Tjaden et al., 1998). Yet another ATP/ADP antiporter located in the endoplasmic reticulum (ER) membrane provides energy by importing ATP into the ER for the accumulation of ER-related storage lipids and proteins (Leroch et al., 2008).In this study, we identified two novel peroxisomal adenine nucleotide carrier proteins (PNC1 and PNC2) from Arabidopsis. Colocalization studies demonstrated that these proteins are targeted to peroxisomes. Yeast complementation and in vitro ATP uptake assays showed that both PNC1 and PNC2 catalyze the counterexchange of ATP with AMP. Using an inducible RNA interference (RNAi) repression strategy, we further established several transgenic Arabidopsis lines with reduced expression levels of both PNC1 and PNC2. Our results showed that import of ATP into peroxisomes that is catalyzed by PNC1 and PNC2 is essential for activation of fatty acids during seedling germination and plays a role in other β-oxidation reactions in peroxisomes, such as auxin metabolism. Analysis of PNC1 and PNC2 repression lines further indicates that no other ATP generating systems exist inside plant peroxisomes and that ATP import is the only way to supply the peroxisomal matrix with ATP.     

Systematic Phenotypic Screen of Arabidopsis Peroxisomal Mutants Identifies Proteins Involved in β-Oxidation

Peroxisomes are highly dynamic and multifunctional organelles essential to development. Plant peroxisomes accommodate a multitude of metabolic reactions, many of which are related to the β-oxidation of fatty acids or fatty acid-related metabolites. Recently, several dozens of novel peroxisomal proteins have been identified from Arabidopsis (Arabidopsis thaliana) through in silico and experimental proteomic analyses followed by in vivo protein targeting validations. To determine the functions of these proteins, we interrogated their transfer DNA insertion mutants with a series of physiological, cytological, and biochemical assays to reveal peroxisomal deficiencies. Sugar dependence and 2,4-dichlorophenoxybutyric acid and 12-oxo-phytodienoic acid response assays uncovered statistically significant phenotypes in β-oxidation-related processes in mutants for 20 of 27 genes tested. Additional investigations uncovered a subset of these mutants with abnormal seed germination, accumulation of oil bodies, and delayed degradation of long-chain fatty acids during early seedling development. Mutants for seven genes exhibited deficiencies in multiple assays, strongly suggesting the involvement of their gene products in peroxisomal β-oxidation and initial seedling growth. Proteins identified included isoforms of enzymes related to β-oxidation, such as acyl-CoA thioesterase2, acyl-activating enzyme isoform1, and acyl-activating enzyme isoform5, and proteins with functions previously unknown to be associated with β-oxidation, such as Indigoidine synthase A, Senescence-associated protein/B12D-related protein1, Betaine aldehyde dehydrogenase, and Unknown protein5. This multipronged phenotypic screen allowed us to reveal β-oxidation proteins that have not been discovered by single assay-based mutant screens and enabled the functional dissection of different isoforms of multigene families involved in β-oxidation.Peroxisomes are small (approximately 0.1–1.0 µm) single-membrane eukaryotic organelles that are essential for the development of animals and plants by mediating a multitude of conserved and lineage-specific metabolic functions (Beevers, 1979; van den Bosch et al., 1992; Kaur et al., 2009; Hu et al., 2012; Schrader et al., 2012). Plant peroxisomes house metabolic processes, including β-oxidation of fatty acids; hormone biosynthesis; photorespiration; the glyoxylate cycle; detoxification of reactive oxygen, nitrogen, and sulfur species; and metabolism of branched amino acids, urate, and polyamines (PAs; Beevers, 1979; Kaur et al., 2009; Hu et al., 2012). Peroxisomes also generate signaling molecules with regulatory roles in plant development (Weber, 2002; Corpas et al., 2013; Sandalio et al., 2013).β-oxidation of fatty acids and related metabolites is a major function of peroxisomes throughout the lifecycle of a plant from seed germination to senescence. Mobilization of seed oil reserves during seed germination and postgerminative growth requires peroxisomal β-oxidation and the glyoxylate cycle. In this process, fatty acids are transported into the peroxisome, where they are activated into fatty acyl-CoAs and later, shortened by two carbons in each cycle of β-oxidation. The product, acetyl-CoA, is converted to four-carbon molecules by the glyoxylate cycle, and its products further undergo gluconeogenesis to provide energy for postgerminative development (Theodoulou and Eastmond, 2012). Using core β-oxidation enzymes as well as pathway-specific enzymes, 12-oxo-phytodienoic acid (OPDA), the jasmonic acid (JA) precursor that enters the peroxisome after being synthesized in the chloroplast, is converted to JA (Acosta and Farmer, 2010), and indole 3-butyric acid (IBA) is converted to the principal form of auxin, indole 3-acetic acid (IAA; Strader and Bartel, 2011). Other than the core β-oxidation pathway, which metabolizes straight-chain saturated fatty acids, auxiliary β-oxidation pathways also occur in the peroxisome to metabolize unsaturated fatty acids, in which case accessory enzymes are required (Goepfert and Poirier, 2007; Graham, 2008).To assess the full composition of this versatile organelle in plants, both in silico analysis and experimental proteomics have been used to identify peroxisomal proteins. Bioinformatic analysis of the Arabidopsis (Arabidopsis thaliana) genome using Peroxisomal Target Signal type1 (PTS1) and PTS2 sequences predicted a total of over 400 proteins to be potentially peroxisomal (Lingner et al., 2011). Experimental proteomics of Arabidopsis, spinach (Spinacia oleracea), and soybean (Glycine max) peroxisomes using different tissue/cell types and development stages together identified several dozens of peroxisomal proteins that had not been found previously to associate with peroxisomes after in vivo targeting verification (Fukao et al., 2002, 2003; Arai et al., 2008a, 2008b; Eubel et al., 2008; Reumann et al., 2009; Babujee et al., 2010; Quan et al., 2013). After the identification of peroxisomal proteins from etiolated Arabidopsis seedlings through proteomics and in vivo protein-targeting analysis, we used reverse genetics to analyze the mutants of five newly identified proteins and revealed the role of a Cys protease, RESPONSE TO DROUGHT21A-LIKE1, in seed germination, β-oxidation, and stress response (Quan et al., 2013; Cassin-Ross and Hu, 2014). However, many other recently identified peroxisomal proteins have not been characterized with respect to their functions in peroxisomal physiology and plant development.In this study, we interrogated the mutants of 27 recently identified peroxisomal genes with systematic phenotypic assays to analyze the function of the proteins in peroxisomal metabolism. Mutants for 20 of the tested genes showed statistically significant phenotypes in at least one of the assays. Additional analysis revealed that mutants for 7 of 20 genes displayed deficiencies in multiple assays, suggesting strongly that these seven proteins are involved in β-oxidation-related processes. This multifaceted screen enabled us to identify β-oxidation proteins that may not have been discovered otherwise by genetic screens based on single assays.     

Peroxisomes Are Required for in Vivo Nitric Oxide Accumulation in the Cytosol following Salinity Stress of Arabidopsis Plants

Peroxisomes are unique organelles involved in multiple cellular metabolic pathways. Nitric oxide (NO) is a free radical active in many physiological functions under normal and stress conditions. Using Arabidopsis (Arabidopsis thaliana) wild type and mutants expressing green fluorescent protein through the addition of peroxisomal targeting signal 1 (PTS1), which enables peroxisomes to be visualized in vivo, this study analyzes the temporal and cell distribution of NO during the development of 3-, 5-, 8-, and 11-d-old Arabidopsis seedlings and shows that Arabidopsis peroxisomes accumulate NO in vivo. Pharmacological analyses using nitric oxide synthase (NOS) inhibitors detected the presence of putative calcium-dependent NOS activity. Furthermore, peroxins Pex12 and Pex13 appear to be involved in transporting the putative NOS protein to peroxisomes, since pex12 and pex13 mutants, which are defective in PTS1- and PTS2-dependent protein transport to peroxisomes, registered lower NO content. Additionally, we show that under salinity stress (100 mm NaCl), peroxisomes are required for NO accumulation in the cytosol, thereby participating in the generation of peroxynitrite (ONOO⁻) and in increasing protein tyrosine nitration, which is a marker of nitrosative stress.Peroxisomes are single membrane-bound organelles whose basic enzymatic constituents are catalase and H₂O₂-producing flavin oxidases as their basic enzymatic and are found in virtually all eukaryotic cell types (Corpas et al., 2001; Hayashi and Nishimura, 2006; Reumann et al., 2007; Pracharoenwattana and Smith, 2008; Palma et al., 2009). These oxidative organelles are characterized by metabolic plasticity, as their enzymatic content can vary according to the organism, cell/tissue type, and environmental conditions (Mullen et al., 2001; Hayashi and Nishimura, 2003; Corpas et al., 2009a). In higher plants, peroxisomes contain a complex battery of antioxidative enzymes, such as catalase, superoxide dismutase, the components of the ascorbate-glutathione cycle, and the NADP-dehydrogenases of the pentose-P pathway (Corpas et al., 2009a). The generation of superoxide radicals has also been reported in the matrices and membranes of peroxisomes (López-Huertas et al., 1999; del Río et al., 2006). All these findings point to the important role played by peroxisomes in the cellular metabolism of reactive oxygen species (Corpas et al., 2001, 2009a; del Río et al., 2006).Nitric oxide (NO) is a free radical involved in many physiological functions under normal and stress conditions in both animal and plant cells (Arasimowicz and Floryszak-Wieczorek, 2007; Corpas et al., 2007a, 2008; Neill et al., 2008). Unlike animal systems, knowledge of NO generation and subcellular location in plants remains largely elusive, and the data are sometimes contradictory and ambiguous (Zemojtel et al., 2006; Jasid et al., 2006; Gas et al., 2009). In previous studies, we detected l-Arg-dependent nitric oxide synthase (NOS) activity in isolated pea (Pisum sativum) leaf peroxisomes (Barroso et al., 1999). In a later study, using electron paramagnetic resonance techniques, we demonstrated the presence of NO in these types of peroxisomes (Corpas et al., 2004). However, several issues, such as whether NO is released into the cytosol and the physiological function of this free radical, remain unresolved.In this study, we provide an in vivo demonstration that Arabidopsis peroxisomes are essential for NO accumulation in the cytosol, thus participating in the generation of nitrosative stress under salinity conditions. In addition, using Arabidopsis mutants pex12 and pex13, we also suggest that these peroxins are involved in importing into peroxisomes the enzyme responsible for NO generation.     

The nuclease activity of DNA2 promotes exonuclease 1–independent mismatch repair

The DNA mismatch repair (MMR) system is a major DNA repair system that corrects DNA replication errors. In eukaryotes, the MMR system functions via mechanisms both dependent on and independent of exonuclease 1 (EXO1), an enzyme that has multiple roles in DNA metabolism. Although the mechanism of EXO1-dependent MMR is well understood, less is known about EXO1-independent MMR. Here, we provide genetic and biochemical evidence that the DNA2 nuclease/helicase has a role in EXO1-independent MMR. Biochemical reactions reconstituted with purified human proteins demonstrated that the nuclease activity of DNA2 promotes an EXO1-independent MMR reaction via a mismatch excision-independent mechanism that involves DNA polymerase δ. We show that DNA polymerase ε is not able to replace DNA polymerase δ in the DNA2-promoted MMR reaction. Unlike its nuclease activity, the helicase activity of DNA2 is dispensable for the ability of the protein to enhance the MMR reaction. Further examination established that DNA2 acts in the EXO1-independent MMR reaction by increasing the strand-displacement activity of DNA polymerase δ. These data reveal a mechanism for EXO1-independent mismatch repair.

The mismatch repair (MMR) system has been conserved from bacteria to humans (1, 2). It promotes genome stability by suppressing spontaneous and DNA damage-induced mutations (1, 3, 4, 5, 6, 7, 8, 9, 10, 11). The key function of the MMR system is the correction of DNA replication errors that escape the proofreading activities of replicative DNA polymerases (1, 4, 5, 6, 7, 8, 9, 10, 12). In addition, the MMR system removes mismatches formed during strand exchange in homologous recombination, suppresses homeologous recombination, initiates apoptosis in response to irreparable DNA damage caused by several anticancer drugs, and contributes to instability of triplet repeats and alternative DNA structures (1, 4, 5, 7, 8, 9, 10, 11, 13, 14, 15, 16, 17, 18). The principal components of the eukaryotic MMR system are MutSα (MSH2-MSH6 heterodimer), MutLα (MLH1-PMS2 heterodimer in humans and Mlh1-Pms1 heterodimer in yeast), MutSβ (MSH2-MSH3 heterodimer), proliferating cell nuclear antigen (PCNA), replication factor C (RFC), exonuclease 1 (EXO1), RPA, and DNA polymerase δ (Pol δ). Loss-of-function mutations in the MSH2, MLH1, MSH6, and PMS2 genes of the human MMR system cause Lynch and Turcot syndromes, and hypermethylation of the MLH1 promoter is responsible for ∼15% of sporadic cancers in several organs (19, 20). MMR deficiency leads to cancer initiation and progression via a multistage process that involves the inactivation of tumor suppressor genes and action of oncogenes (21).MMR occurs behind the replication fork (22, 23) and is a major determinant of the replication fidelity (24). The correction of DNA replication errors by the MMR system increases the replication fidelity by ∼100 fold (25). Strand breaks in leading and lagging strands as well as ribonucleotides in leading strands serve as signals that direct the eukaryotic MMR system to remove DNA replication errors (26, 27, 28, 29, 30). MMR is more efficient on the lagging than the leading strand (31). The substrates for MMR are all six base–base mismatches and 1 to 13-nt insertion/deletion loops (25, 32, 33, 34). Eukaryotic MMR commences with recognition of the mismatch by MutSα or MutSβ (32, 34, 35, 36). MutSα is the primary mismatch-recognition factor that recognizes both base–base mismatches and small insertion/deletion loops whereas MutSβ recognizes small insertion/deletion loops (32, 34, 35, 36, 37). After recognizing the mismatch, MutSα or MutSβ cooperates with RFC-loaded PCNA to activate MutLα endonuclease (38, 39, 40, 41, 42, 43). The activated MutLα endonuclease incises the discontinuous daughter strand 5′ and 3′ to the mismatch. A 5'' strand break formed by MutLα endonuclease is utilized by EXO1 to enter the DNA and excise a discontinuous strand portion encompassing the mismatch in a 5''→3′ excision reaction stimulated by MutSα/MutSβ (38, 44, 45). The generated gap is filled in by the Pol δ holoenzyme, and the nick is ligated by a DNA ligase (44, 46, 47). DNA polymerase ε (Pol ε) can substitute for Pol δ in the EXO1-dependent MMR reaction, but its activity in this reaction is much lower than that of Pol δ (48). Although MutLα endonuclease is essential for MMR in vivo, 5′ nick-dependent MMR reactions reconstituted in the presence of EXO1 are MutLα-independent (44, 47, 49).EXO1 deficiency in humans does not seem to cause significant cancer predisposition (19). Nevertheless, it is known that Exo1^-/- mice are susceptible to the development of lymphomas (50). Genetic studies in yeast and mice demonstrated that EXO1 inactivation causes only a modest defect in MMR (50, 51, 52, 53). In agreement with these genetic studies, a defined human EXO1-independent MMR reaction that depends on the strand-displacement DNA synthesis activity of Pol δ holoenzyme to remove the mismatch was reconstituted (54). Furthermore, an EXO1-independent MMR reaction that occurred in a mammalian cell extract system without the formation of a gapped excision intermediate was observed (54). Together, these findings implicated the strand-displacement activity of Pol δ holoenzyme in EXO1-independent MMR.In this study, we investigated DNA2 in the context of MMR. DNA2 is an essential multifunctional protein that has nuclease, ATPase, and 5''→3′ helicase activities (55, 56, 57). Previous research ascertained that DNA2 removes long flaps during Okazaki fragment maturation (58, 59, 60), participates in the resection step of double-strand break repair (61, 62, 63), initiates the replication checkpoint (64), and suppresses the expansions of GAA repeats (65). We have found in vivo and in vitro evidence that DNA2 promotes EXO1-independent MMR. Our data have indicated that the nuclease activity of DNA2 enhances the strand-displacement activity of Pol δ holoenzyme in an EXO1-independent MMR reaction.     

Synaptic dysfunction,memory deficits and hippocampal atrophy due to ablation of mitochondrial fission in adult forebrain neurons

Well-balanced mitochondrial fission and fusion processes are essential for nervous system development. Loss of function of the main mitochondrial fission mediator, dynamin-related protein 1 (Drp1), is lethal early during embryonic development or around birth, but the role of mitochondrial fission in adult neurons remains unclear. Here we show that inducible Drp1 ablation in neurons of the adult mouse forebrain results in progressive, neuronal subtype-specific alterations of mitochondrial morphology in the hippocampus that are marginally responsive to antioxidant treatment. Furthermore, DRP1 loss affects synaptic transmission and memory function. Although these changes culminate in hippocampal atrophy, they are not sufficient to cause neuronal cell death within 10 weeks of genetic Drp1 ablation. Collectively, our in vivo observations clarify the role of mitochondrial fission in neurons, demonstrating that Drp1 ablation in adult forebrain neurons compromises critical neuronal functions without causing overt neurodegeneration.In addition to their crucial importance in energy conversion, mitochondria serve many other housekeeping functions, including calcium buffering, amino-acid and steroid biosynthesis as well as fatty acids beta-oxidation and regulation of cell death. During the past decade, it has become increasingly clear that processes regulating mitochondrial morphology and ultrastructure are influenced by specific cellular requirements upon which mitochondria, in a precisely regulated manner, undergo fusion and division events.¹ Maintaining this balance is especially important for highly energy-consuming, polarized cells such as neurons, where single organellar units sprouting from the mitochondrial network are transported along the cytoskeleton into dendrites and spines to meet local energy requirements.² In addition, elaborate quality-control mechanisms also rely on mitochondrial dynamics: whereas defective organelles are sequestered by fission, enabling their removal from the mitochondrial network,^{3, 4} fusion supports qualitative homogeneity of the syncytium through complementation.⁵Mitochondrial fusion and fission are mediated by large GTPases of the dynamin superfamily.⁶ The outer mitochondrial membrane mitofusins 1 (MFN1) and 2 (MFN2) tether mitochondrial membranes by homodimer or heterodimer formation,⁷ thereby initiating fusion of the organelles, a process that also involves the inner mitochondrial membrane-associated GTPase Optic Atrophy 1.⁸ In addition, MFN2 also mediates contacts between mitochondria and endoplasmic reticulum.⁹ The only known mammalian mitochondrial fission protein, Dynamin-Related Protein 1 (Drp1), translocates upon dephosphorylation by calcineurin¹⁰ to fission sites where it binds to mitochondrial fission factor.¹¹ Drp1 translocation is preceded by ER membranes wrapping around mitochondria to constrict the organelles,¹² thereby facilitating the formation of multimeric Drp1 complexes that, upon GTP hydrolysis, further tighten to complete the process of mitochondrial fission.¹³Genetic evidence in mice and humans indicates that mitochondrial dynamics are crucially important in neurons: in humans, a sporadic dominant-negative DRP1 mutation caused a lethal syndromic defect with abnormal brain development;¹⁴ similarly, constitutive Drp1 knockout in the mouse brain leads to lethal neurodevelopmental defects.^{15, 16} Although the crucial role of Drp1 during brain development is undisputed, studies on Drp1 function in postmitotic (adult) neurons are scarce; likewise, Drp1 ablation studies in primary cultures have so far failed to yield a conclusive picture. In vitro, Drp1 ablation is reported to lead to a super-elongated neuroprotective^{17, 18, 19, 20, 21, 22, 23, 24} or an aggregated mitochondrial phenotype associated with neurodegeneration.^{15, 16, 25, 26, 27} These discrepancies are probably due to different experimental conditions: neuronal health is indeed influenced by the onset and duration of Drp1 inhibition, which varies considerably among the cited reports,²⁸ and different types of neuronal cultures studied display different sensitivity to Drp1 inhibition. In vivo, Drp1 ablation in Purkinje cells results in oxidative stress and neurodegeneration,²⁹ demonstrating that Drp1 is essential for postmitotic neurons'' health. In contrast, transient pharmacological Drp1 inhibition is neuroprotective in several mouse ischemia models, indicating that temporarily blocking mitochondrial fission holds therapeutic potential.^{30, 31, 32}To elucidate the consequences of blocked mitochondrial fission in the central nervous system in vivo, we bypassed the critical role of Drp1 during brain development by generating Drp1^flx/flx mice¹⁵ expressing tamoxifen-inducible Cre recombinase under the control of the CaMKIIα promoter.³³ Upon induced Drp1 deletion in postmitotic adult mouse forebrain neurons, mice develop progressive, neuronal subtype-specific alterations in mitochondrial shape and distribution in the absence of overt neurodegeneration. In addition, respiratory capacity, ATP content, synaptic reserve pool vesicle recruitment as well as spatial working memory are impaired, demonstrating that severely dysregulated mitochondrial dynamics can compromise critical neuronal functions in vivo without causing neuronal cell death.     

Identification of Mitochondrial Coenzyme A Transporters from Maize and Arabidopsis

Plants make coenzyme A (CoA) in the cytoplasm but use it for reactions in mitochondria, chloroplasts, and peroxisomes, implying that these organelles have CoA transporters. A plant peroxisomal CoA transporter is already known, but plant mitochondrial or chloroplastic CoA transporters are not. Mitochondrial CoA transporters belonging to the mitochondrial carrier family, however, have been identified in yeast (Saccharomyces cerevisiae; Leu-5p) and mammals (SLC25A42). Comparative genomic analysis indicated that angiosperms have two distinct homologs of these mitochondrial CoA transporters, whereas nonflowering plants have only one. The homologs from maize (Zea mays; GRMZM2G161299 and GRMZM2G420119) and Arabidopsis (Arabidopsis thaliana; At1g14560 and At4g26180) all complemented the growth defect of the yeast leu5Δ mitochondrial CoA carrier mutant and substantially restored its mitochondrial CoA level, confirming that these proteins have CoA transport activity. Dual-import assays with purified pea (Pisum sativum) mitochondria and chloroplasts, and subcellular localization of green fluorescent protein fusions in transiently transformed tobacco (Nicotiana tabacum) Bright Yellow-2 cells, showed that the maize and Arabidopsis proteins are targeted to mitochondria. Consistent with the ubiquitous importance of CoA, the maize and Arabidopsis mitochondrial CoA transporter genes are expressed at similar levels throughout the plant. These data show that representatives of both monocotyledons and eudicotyledons have twin, mitochondrially located mitochondrial carrier family carriers for CoA. The highly conserved nature of these carriers makes possible their reliable annotation in other angiosperm genomes.CoA acts as an acyl carrier in many reactions of primary and secondary metabolism, and some 8% of the nearly 4,900 enzymes described in the Enzyme Commission database are CoA dependent (Bairoch, 2000). CoA occupies a central position in lipid metabolism, respiration, gluconeogenesis, and other pathways (Leonardi et al., 2005). It is present in all forms of life, but while all organisms can synthesize it from pantothenate (vitamin B₅), only prokaryotes, plants, and fungi are able to synthesize pantothenate; animals obtain pantothenate from the diet (Daugherty et al., 2002; Leonardi et al., 2005; Webb and Smith, 2011).In plants, the steps that convert pantothenate to CoA are almost certainly cytosolic (Webb and Smith, 2011; Gerdes et al., 2012). CoA, however, is required in mitochondria for the citric acid cycle, in chloroplasts for fatty acid synthesis, and in peroxisomes for β-oxidation. CoA, therefore, must be imported into these organelles from the cytosol, and indeed, early work demonstrated a CoA transport system in potato (Solanum tuberosum) mitochondria (Neuburger et al., 1984). Yeast (Saccharomyces cerevisiae) and mammalian mitochondria and peroxisomes likewise import CoA because they cannot make it (Fiermonte et al., 2009; Agrimi et al., 2012b). The compartmentation of CoA in all eukaryotes appears to be closely regulated, with cytosol and organelles maintaining separate CoA pools whose levels can modulate fluxes through CoA-dependent reactions (Hunt and Alexson, 2002; Leonardi et al., 2005; De Marcos Lousa et al., 2013).Mitochondrial CoA transporters belonging to the mitochondrial carrier family (MCF) have been identified in yeast (Leu-5p; Prohl et al., 2001) and human (SLC25A42; Fiermonte et al., 2009). Furthermore, peroxisomal CoA carriers from human (SLC25A17; Agrimi et al., 2012b) and Arabidopsis (Arabidopsis thaliana; peroxisomal CoA and NAD carrier [PXN]; Agrimi et al., 2012a) have also been identified. However, no transporters for CoA are known for plant mitochondria or chloroplasts (Palmieri et al., 2011; Gerdes et al., 2012).In this study, a comparative genomic analysis first identified close Arabidopsis and maize (Zea mays) homologs of the yeast and mammalian mitochondrial CoA carriers as candidates for the missing plant mitochondrial or chloroplast transporters. Experimental evidence then demonstrated that the candidate proteins transport CoA when expressed in yeast, that they are targeted to mitochondria in vitro and in planta, and that they are expressed throughout the plant.     

The Fcp1-Wee1-Cdk1 axis affects spindle assembly checkpoint robustness and sensitivity to antimicrotubule cancer drugs

To grant faithful chromosome segregation, the spindle assembly checkpoint (SAC) delays mitosis exit until mitotic spindle assembly. An exceedingly prolonged mitosis, however, promotes cell death and by this means antimicrotubule cancer drugs (AMCDs), that impair spindle assembly, are believed to kill cancer cells. Despite malformed spindles, cancer cells can, however, slip through SAC, exit mitosis prematurely and resist killing. We show here that the Fcp1 phosphatase and Wee1, the cyclin B-dependent kinase (cdk) 1 inhibitory kinase, play a role for this slippage/resistance mechanism. During AMCD-induced prolonged mitosis, Fcp1-dependent Wee1 reactivation lowered cdk1 activity, weakening SAC-dependent mitotic arrest and leading to mitosis exit and survival. Conversely, genetic or chemical Wee1 inhibition strengthened the SAC, further extended mitosis, reduced antiapoptotic protein Mcl-1 to a minimum and potentiated killing in several, AMCD-treated cancer cell lines and primary human adult lymphoblastic leukemia cells. Thus, the Fcp1-Wee1-Cdk1 (FWC) axis affects SAC robustness and AMCDs sensitivity.The spindle assembly checkpoint (SAC) delays mitosis exit to coordinate anaphase onset with spindle assembly. To this end, SAC inhibits the ubiquitin ligase Anaphase-Promoting Complex/Cyclosome (APC/C) to prevent degradation of the anaphase inhibitor securin and cyclin B, the major mitotic cyclin B-dependent kinase 1 (cdk1) activator, until spindle assembly.¹ However, by yet poorly understood mechanisms, exceedingly prolonging mitosis translates into cell death induction.^{2, 3, 4, 5, 6, 7} Although mechanistic details are still missing on how activation of cell death pathways is linked to mitosis duration, prolongation of mitosis appears crucial for the ability of antimicrotubule cancer drugs (AMCDs) to kill cancer cells.^{2, 3, 4, 5, 6, 7} These drugs, targeting microtubules, impede mitotic spindle assembly and delay mitosis exit by chronically activating the SAC. Use of these drugs is limited, however, by toxicity and resistance. A major mechanism for resistance is believed to reside in the ability of cancer cells to slip through the SAC and exit mitosis prematurely despite malformed spindles, thus resisting killing by limiting mitosis duration.^{2, 3, 4, 5, 6, 7} Under the AMCD treatment, cells either die in mitosis or exit mitosis, slipping through the SAC, without or abnormally dividing.^{2, 3, 4} Cells that exit mitosis either die at later stages or survive and stop dividing or proliferate, giving rise to resistance.^{2, 3, 4} Apart from a role for p53, what dictates cell fate is still unknown; however, it appears that the longer mitosis is protracted, the higher the chances for cell death pathway activation are.^{2, 3, 4, 5, 6, 7}Although SAC is not required per se for killing,⁶ preventing SAC adaptation should improve the efficacy of AMCD by increasing mitosis duration.^{2, 3, 4, 5, 6, 7} Therefore, further understanding of the mechanisms by which cells override SAC may help to improve the current AMCD therapy. Several kinases are known to activate and sustain SAC, and cdk1 itself appears to be of primary relevance.^{1, 8, 9} By studying mitosis exit and SAC resolution, we recently reported a role for the Fcp1 phosphatase to bring about cdk1 inactivation.^{10, 11} Among Fcp1 targets, we identified cyclin degradation pathway components, such as Cdc20, an APC/C co-activator, USP44, a deubiquitinating enzyme, and Wee1.^{10, 11} Wee1 is a crucial kinase that controls the G2 phase by performing inhibitory phosphorylation of cdk1 at tyr-15 (Y15-cdk1). Wee1 is also in a feedback relationship with cdk1 itself that, in turn, can phosphorylate and inhibit Wee1 in an autoamplification loop to promote the G2-to-M phase transition.¹² At mitosis exit, Fcp1 dephosphorylated Wee1 at threonine 239, a cdk1-dependent inhibitory phosphorylation, to dampen down the cdk1 autoamplification loop, and Cdc20 and USP44, to promote APC/C-dependent cyclin B degradation.^{10, 11, 12} In this study we analysed the Fcp1 relevance in SAC adaptation and AMCD sensitivity.     

The LRRK2 inhibitor GSK2578215A induces protective autophagy in SH-SY5Y cells: involvement of Drp-1-mediated mitochondrial fission and mitochondrial-derived ROS signaling

Mutations in the leucine-rich repeat kinase 2 (LRRK2) gene have been associated with Parkinson''s disease, and its inhibition opens potential new therapeutic options. Among the drug inhibitors of both wild-type and mutant LRRK2 forms is the 2-arylmethyloxy-5-subtitutent-N-arylbenzamide GSK257815A. Using the well-established dopaminergic cell culture model SH-SY5Y, we have investigated the effects of GSK2578215A on crucial neurodegenerative features such as mitochondrial dynamics and autophagy. GSK2578215A induces mitochondrial fragmentation of an early step preceding autophagy. This increase in autophagosome results from inhibition of fusion rather than increases in synthesis. The observed effects were shared with LRRK2-IN-1, a well-described, structurally distinct kinase inhibitor compound or when knocking down LRRK2 expression using siRNA. Studies using the drug mitochondrial division inhibitor 1 indicated that translocation of the dynamin-related protein-1 has a relevant role in this process. In addition, autophagic inhibitors revealed the participation of autophagy as a cytoprotective response by removing damaged mitochondria. GSK2578215A induced oxidative stress as evidenced by the accumulation of 4-hydroxy-2-nonenal in SH-SY5Y cells. The mitochondrial-targeted reactive oxygen species scavenger MitoQ positioned these species as second messengers between mitochondrial morphologic alterations and autophagy. Altogether, our results demonstrated the relevance of LRRK2 in mitochondrial-activated pathways mediating in autophagy and cell fate, crucial features in neurodegenerative diseases.Nowadays, Parkinson''s disease (PD) constitutes the main motor disorder and the second neurodegenerative disease after Alzheimer''s disease. Etiology of PD remains unknown, but both environmental and genetic factors have been implicated. Among the genes associated with PD is the leucine-rich repeat kinase 2 (LRRK2, PARK8, OMIM 607060) encoding gene encoded by PARK8. Indeed, LRRK2 mutations have been described in a substantial number of idiopathic late-onset PD patients without a known family history of the disease.^{1, 2, 3}The physiologic function remains unknown. It localizes in the cytosol as well as in specific membrane subdomains, including mitochondria, autophagosomes and autolysosomes,⁴ and interacts with a whole array of proteins, including both α- and β-tubulin,^{5, 6} tau,⁷ α-synuclein⁸ and F-actin.⁹ LRRK2 gene mutations, including the most common G2019S,³ are associated with increases in toxic putative kinase activity.^{1, 10} LRRK2 overexpression is toxic to cultured cells,^{11, 12} and LRRK2 loss did not cause neurodegenerative changes (for a review see Tong and Shen¹³). However, LRRK2 transgenic mice lack obvious PD-like behavioral phenotypes.¹⁴ LRRK2-associated PD patients show degeneration of dopaminergic neurons in the substantia nigra.¹⁵ Data from our own group and others have associated mitochondrial apoptotical pathways with PD,^{16, 17, 18} and, in this context, LRRK2 mutant-mediated toxicity could be due to mitochondria-dependent apoptosis.¹⁹ There is considerable evidence for impaired mitochondrial function and morphology in both early-onset, autosomal recessive inherited PD and late-onset sporadic PD.Mitochondrial dynamics include several mechanisms, such as fission, fusion and mitophagy.^{20, 21} Altered fission/fusion dynamics might be a common pathogenic pathway of neurodegenerative diseases. It is well documented that mitochondrial dynamics constitute a relevant issue in some experimental neurodegenerative models.^{20, 22, 23, 24, 25} Mitochondrial dynamics is tightly regulated by cellular pathways including those participated by the dynamin-related protein-1 (Drp1). Drp1 mostly locates in the cytoplasm, but is stimulated after fission stimuli to migrate to the mitochondria. Once there, Drp1 forms ring-like structures, which wrap around the scission site to constrict the mitochondrial membrane resulting in mitochondrial fission.^{26, 27} Interestingly, a functional interaction between PD-associated LRRK2 and members of the dynamin GTPase superfamily has been described.²⁸Macroautophagy (hereafter referred to as autophagy) is an active cellular response, which functions in the intracellular degradation system of cellular debris such as damaged organelles. Whether autophagy promotes cell death or enhances survival is still controversial.^{29, 30} It requires the formation of autophagosomes where cellular content is to be degraded by the action of lysosomal enzymatic content. Autophagosome formation is regulated by an orderly action of >30 autophagy-related (Atg) proteins. Among them is the microtubule-associated protein 1A/1B-light chain 3 (LC3), a homolog of Apg8p, which is essential for autophagy in yeast and is associated with autophagosome membranes.³¹ Interestingly, these vesicles are mostly highly mobile in the cytoplasm.³² Wild-type and mutant LRRK2 expression has been related to autophagy.^{4, 33, 34, 35, 36} Reactive oxygen species (ROS) function as relevant second messengers after several stimuli, including mitochondrial disruption. Exacerbated ROS increases might result in overactivation of antioxidant systems and yield harmful oxidative stress. Among oxidative stress hallmarks is the accumulation of α,β-unsaturated hydroxyalkenal 4-hydroxy-2-nonenal (4-HNE), whose accumulation has been reported in PD post-mortem patient brains,^{37, 38} thus giving a significant relevance to ROS in the pathogenesis of PD.All these results indicate LRRK2 as a promising pharmacologic target in PD treatment.³⁹ Several LRRK2 inhibitor drugs have been synthetized, such as the potent and highly selective 2-arylmethyloxy-5-substitutent-N-arylbenzamide (GSK2578215A). GSK2578215A exhibits biochemical IC₅₀s of 10.9 nM against wild-type LRRK2, and possesses a high ratio of brain to plasma distribution.⁴⁰ This study provides key insights into the mechanisms downstream of LRRK2 inhibition, and spreads light onto an underexplored, yet potentially tractable therapeutic target for treating LRRK2-associated PD. We demonstrate how inhibition of this kinase results in the activation of cellular death pathways such as the mitochondrial fission machinery, and how cells reply by activating a protective autophagic response. Our results show the presence of oxidative stress hallmarks, thus pointing to a key function for ROS, placed downstream of mitochondrial fission.     

In Vivo Quantification of Peroxisome Tethering to Chloroplasts in Tobacco Epidermal Cells Using Optical Tweezers

Peroxisomes are highly motile organelles that display a range of motions within a short time frame. In static snapshots, they can be juxtaposed to chloroplasts, which has led to the hypothesis that they are physically interacting. Here, using optical tweezers, we tested the dynamic physical interaction in vivo. Using near-infrared optical tweezers combined with TIRF microscopy, we were able to trap peroxisomes and approximate the forces involved in chloroplast association in vivo in tobacco (Nicotiana tabacum) and observed weaker tethering to additional unknown structures within the cell. We show that chloroplasts and peroxisomes are physically tethered through peroxules, a poorly described structure in plant cells. We suggest that peroxules have a novel role in maintaining peroxisome-organelle interactions in the dynamic environment. This could be important for fatty acid mobilization and photorespiration through the interaction with oil bodies and chloroplasts, highlighting a fundamentally important role for organelle interactions for essential biochemistry and physiological processes.A combination of genetically encoded fluorescent probes, advances in light microscopy, and interdisciplinary approaches has revolutionized our understanding of organelle transport. Organelle movement in highly vacuolated leaf epidermal cells appears erratic, with individual organelles undergoing a range of movements within a relatively short time frame: they stop-go, change direction (trajectory), and move at varying speeds. The use of pharmacological inhibitors indicated a role for actin, and therefore myosins, in this process; however, myosin-organelle specificity is poorly characterized (Madison and Nebenführ, 2013; Tamura et al., 2013; Buchnik et al., 2015). Therefore, we are still at a relatively rudimentary stage in the understanding of the molecular and physical control, and interaction, of organelles in plant cells compared with that known in other model systems (Hammer and Sellers, 2012; Prinz, 2014). However, it is clear that organelle movement plays important roles in physological processes in plants; reduced movement effects growth and development, and movement is correlated with responses to extracellular stresses such as pathogens and heavy metals (for refs., see Sparkes, 2011; Madison and Nebenführ, 2013; Buchnik et al., 2015). Organelle interactions in other systems have important roles in calcium and lipid exchange, setting a precedent for physiologically important roles in plants (Prinz, 2014). However, characterization of the molecular factors required to physically tether organelles, as opposed to those that function in the exchange of molecules at the interaction site, is challenging. Monitoring organelle interactions in highly vacuolated plant epidermal cells is further complicated by the constraints imposed by the large central vacuole. Static snapshots provided through electron microscopy of highly vacuolated cells, where the vacuole can effectively push organelles together, giving the impression of direct interaction between organelles, is not a suitable method to determine dynamic interactions. Other techniques, such as the laser-induced shockwave by explosion method used by Oikawa et al. (2015), works globally without directly manipulating the individual organelle. Here, using optical tweezers with submicron precision, we provide a means to assess and quantify the dynamic interaction between peroxisomes and chloroplasts in vivo in leaf epidermal cells.Peroxisomes are responsible for several biochemical reactions, including the glyoxylate cycle and β-oxidation, which provides an energy source for germination in oilseeds. They also produce and scavenge free radicals, synthesize jasmonic acid and indole-3-acetic acid, and are required for photorespiration (for refs., see Hu et al., 2012). The photorespiratory pathway spans peroxisomes, chloroplasts, and mitochondria, where phosphoglycolate produced in the chloroplast is converted back to 3-phosphoglycerate. It has been suggested that functional connectivity between these organelles accounts for the close association observed in ultrastructural micrographs (Frederick and Newcomb, 1969). Several Arabidopsis (Arabidopsis thaliana) pex10 (peroxisomal membrane protein) mutants show altered chloroplast-peroxisome juxtaposition with a defect in photorespiration, while others do not (Schumann et al., 2007; Prestele et al., 2010). Both CLUMPED CHLOROPLASTS1 (CLMP1) and CHLOROPLAST UNUSUAL POSITIONING1 (CHUP1) encode for proteins that localize to the chloroplast, with CHUP1 playing a role in chloroplast-actin formation (Oikawa et al., 2003, 2008; Schmidt von Braun and Schleiff, 2008; Yang et al., 2011). While CHUP1 and CLMP1 affect chloroplast positioning, they have differential effects on peroxisome and mitochondrial location; clmp1 causes chloroplast clustering without affecting mitochondria or peroxisome location (Yang et al., 2011), whereas chup1 was reported to affect peroxisome location (Oikawa et al., 2003). In vitro analysis through density centrifugation highlighted chloroplast sedimentation with peroxisomes under certain conditions (Schnarrenberger and Burkhard, 1977), although this does not necessarily reflect the organelle interaction in live cells. Peroxisome proteomics studies have been hampered by difficulties in isolating pure peroxisomal fractions (Bussell et al., 2013). This could be indicative of interaction, where associated membranes are isolated together, or sticky nonspecific contaminating chloroplast membranes. The work by Oikawa et al. (2015) provides insight into the physiological processes controlling peroxisome-chloroplast interaction (photosynthesis dependent), but they did not determine the effective baseline force required to move peroxisomes that were not next to chloroplasts under control or altered environmental conditions. Comparisons between the relative forces required to move peroxisomes next to chloroplasts versus those that are not next to chloroplasts are critical in understanding and probing the physical interaction between the two organelles, the hypothesis being that tethering would increase the force required to move peroxisomes compared with organelles that are not tethered. Since peroxisomes have diverse biochemical roles that affect a wide range of physiological processes throughout the plant life cycle (Hu et al., 2012), an understanding of if and how peroxisomes may interact with other subcellular structures is likely to be an important consideration for efficient peroxisome function.Peroxisomes are highly pleomorphic, dynamic organelles bounded by a single membrane (Hu et al., 2012), whose movement is driven by acto-myosin-dependent processes (Jedd and Chua, 2002; Mano et al., 2002; Mathur et al., 2002; Avisar et al., 2008; Sparkes et al., 2008). Tubular emanations termed peroxules (Scott et al., 2007) can extend from the main peroxisome body, yet it is unclear what function they may play. Formation is quite frequent in hypocotyl cells (Cutler et al., 2000; Mano et al., 2002; Sinclair et al., 2009), can occur around chloroplasts in cotyledonary leaf pavement cells (Sinclair et al., 2009), and is not always from the trailing edge of the peroxisome (Sinclair et al., 2009). Exogenous addition of hydroxyl reactive oxygen species (ROS), or exposure to UV light, induces peroxule formation (Sinclair et al., 2009). It has been suggested that they represent an increased surface area for increased biochemical function or might represent a morphological precursor for peroxisome division (Jedd and Chua, 2002). Based on subcellular coalignment, a retro-flow model for the potential exchange of luminal content between the endoplasmic reticulum (ER) and peroxisome through the peroxule has been suggested (Sinclair et al., 2009; Barton et al., 2013). However, these studies, as with many others, interpret the close association between organelles to indicate physical connectivity between organelles, whereas, in fact, in highly vacuolated leaf epidermal cells, organelles can be closely packed within the cytoplasm due to mere spatial constrictions generated through the large central vacuole. This is further complicated by the highly motile, and seemingly stochastic, nature of acto-myosin-driven organelle movement, resulting in frequent apparent organelle collisions that may not reflect a functional requirement for organelle interaction.Optical trapping provides a highly specific and sensitive means to measure physical connectivity between organelles. By focusing an infrared beam, it allows the user to trap objects that have a significantly different refractive index from the surrounding medium. Upon trapping, the user can then move the trapped object relative to its original position to gain an understanding of whether the movement affects the position and motion of other structures (such as other organelles) that may be physically attached to the trapped organelle. For example, unlike the ER, Golgi bodies are amenable to trapping. By trapping and micromanipulating (i.e. precisely moving) the Golgi, a physical association between the ER and the Golgi was determined in a qualitative manner (Sparkes et al., 2009b). Here, we have developed a system to generate quantitative measures for organelle interaction by standardizing and automating how far we move the trapped organelle (which we call the translation step) at a defined speed and assessing how trapping efficiency alters in response to the power of the laser trap itself. By using these parameters, we can then model the forces imparted on the organelle, providing further insight into the tethering processes.Our results indicate that peroxisomes are amenable to being trapped, that they physically interact with chloroplasts in leaf epidermal cells, and, surprisingly, that peroxisomes are also tethered to other unknown structures within the cell. This approach highlights that organelle interactions within plant cells are not random but regulated through tethering. In addition, we provide a novel role for peroxules and a simple biophysical model to describe peroxisome motion during the trapping process.     

miR-361-regulated prohibitin inhibits mitochondrial fission and apoptosis and protects heart from ischemia injury

Cardiovascular disease remains the leading cause of morbidity and mortality worldwide. Emerging evidences suggest that the abnormal mitochondrial fission participates in pathogenesis of cardiac diseases, including myocardial infarction (MI) and heart failure. However, the molecular components regulating mitochondrial network in the heart remain largely unidentified. Here we report that miR-361 and prohibitin 1 (PHB1) constitute an axis that regulates mitochondrial fission and apoptosis. The results show that PHB1 attenuates mitochondrial fission and apoptosis in response to hydrogen peroxide treatment in cardiomyocytes. Cardiac-specific PHB1 transgenic mice show reduced mitochondrial fission and myocardial infarction sizes after myocardial infarction surgery. MiR-361 is responsible for the dysfunction of PHB1 and suppresses the translation of PHB1. Knockdown of miR-361 reduces mitochondrial fission and apoptosis in vivo and in vitro. MiR-361 cardiac-specific transgenic mice represent elevated mitochondrial fission and myocardial infarction sizes upon myocardial ischemia injury. This study identifies a novel signaling pathway composed of miR-361 and PHB1 that regulates mitochondrial fission program and apoptosis. This discovery will shed new light on the therapy of myocardial infarction and heart failure.The heart drives the blood flow in the body and it has a large requirement of energy. Mitochondria meet the high energy demand of the heart by consistently providing large amounts of ATP through oxidative phosphorylation. Thus, mitochondrial malfunction is tightly related to cardiac diseases and contributes to cardiomyocyte injury, cardiomyopathy and heart failure. Mitochondria morphology is also associated with the function. Mitochondria constantly undergo fission and fusion. Fission leads to the formation of small round mitochondria and promotes cell apoptosis,^{1, 2, 3, 4, 5, 6, 7} whereas fusion results in mitochondria elongation and have a protective role in cardiomyocytes maintenance.⁸ The above findings strongly suggest that mitochondrial fission and fusion machinery is important for cardiac function. In addition, unveiling the mechanism of mitochondrial network regulation will provide a novel therapeutic strategy for heart failure.The mitochondrial prohibitin complex is a macromolecular structure at the inner mitochondrial membrane that is composed of prohibitin 1 (PHB1) and prohibitin 2 subunits.⁹ These two proteins comprise an evolutionary conserved and ubiquitously expressed family of membrane proteins and are implicated in several important cellular processes such as mitochondrial biogenesis and function, cell proliferation, replicative senescence, and cell death.^{10, 11} The first mammalian PHB1 was identified as a potential tumor suppressor with anti-proliferative activity.¹² Recent findings suggest that PHB1 has an important role in regulating mitochondrial morphology. Loss of PHB1 results in accumulation of fragmented mitochondria in MEFs and HeLa cells.^{13, 14} However, it is not yet clear whether PHB1 participates in the regulation of mitochondrial dynamics in cardiomyocytes.MicroRNAs (miRNAs) are a class of short single-stranded non-coding endogenous RNAs and act as negative regulators of gene expression by inhibiting mRNA translation or promoting mRNA degradation.^{15, 16} Although the function of miRNAs has been widely studied in apoptosis, development, differentiation and proliferation, few works have been focused on miRNAs in the mitochondrial network regulation. It has been reported that miR-30b targets to p53 and inhibits mitochondrial fission.¹⁷ In addition, other miRNAs also affect the function of mitochondria by targeting to mitochondrial calcium uniporter.¹⁸ The study of miRNA function in mitochondria may shed new light on the machinery that underlies mitochondrial regulation.This study unveils that PHB1 is involved in the regulation of mitochondrial network in cardiomyocytes. PHB1 inhibits mitochondrial fission and apoptosis in cardiomyocytes. In addition, PHB1 transgenic mice exhibit a reduced myocardial infarction sizes upon myocardial ischemia injury in vivo. In searching for the mechanism by which PHB1 is downregulated under pathologic condition, we identify miR-361 participates in the suppression of PHB1 translation. MiR-361 initiates mitochondrial fission, apoptosis and myocardial infarction through downregulating PHB1. Our results reveal a novel mitochondrial regulating model, which is composed of miR-361 and PHB1. Modulation of their levels may represent a novel approach for interventional treatment of myocardial infarction and heart failure.