Characterization, prediction and evolution of plant peroxisomal targeting signals type 1 (PTS1s)

Our knowledge of the proteome of plant peroxisomes and their functional plasticity is far from being complete, primarily due to major technical challenges in experimental proteome research of the fragile cell organelle. Several unexpected novel plant peroxisome functions, for instance in biotin and phylloquinone biosynthesis, have been uncovered recently. Nevertheless, very few regulatory and membrane proteins of plant peroxisomes have been identified and functionally described up to now. To define the matrix proteome of plant peroxisomes, computational methods have emerged as important powerful tools. Novel prediction approaches of high sensitivity and specificity have been developed for peroxisome targeting signals type 1 (PTS1) and have been validated by in vivo subcellular targeting analyses and thermodynamic binding studies with the cytosolic receptor, PEX5. Accordingly, the algorithms allow the correct prediction of many novel peroxisome-targeted proteins from plant genome sequences and the discovery of additional organelle functions. In this review, we provide an overview of methodologies, capabilities and accuracies of available prediction algorithms for PTS1 carrying proteins. We also summarize and discuss recent quantitative, structural and mechanistic information of the interaction of PEX5 with PTS1 carrying proteins in relation to in vivo import efficiency. With this knowledge, we develop a model of how proteins likely evolved peroxisomal targeting signals in the past and still nowadays, in which order the two import pathways might have evolved in the ancient eukaryotic cell, and how the secondary loss of the PTS2 pathway probably happened in specific organismal groups.

The emerging role of photorespiration and non-photorespiratory peroxisomal metabolism in pathogen defence

Photorespiration represents one of the major highways of primary plant metabolism and is the most prominent example of metabolic cell organelle integration, since the pathway requires the concerted action of plastidial, peroxisomal, mitochondrial and cytosolic enzymes and organellar transport proteins. Oxygenation of ribulose-1,5-bisphosphate by Rubisco leads to the formation of large amounts of 2-phosphoglycolate, which are recycled to 3-phosphoglycerate by the photorespiratory C2 cycle, concomitant with stoichiometric production rates of H2 O2 in peroxisomes. Apart from its significance for agricultural productivity, a secondary function of photorespiration in pathogen defence has emerged only recently. Here, we summarise literature data supporting the crosstalk between photorespiration and pathogen defence and perform a meta-expression analysis of photorespiratory genes during pathogen attack. Moreover, we screened Arabidopsis proteins newly predicted using machine learning methods to be targeted to peroxisomes, the central H2 O2 -producing organelle of photorespiration, for homologues of known pathogen defence proteins and analysed their expression during pathogen infection. The analyses further support the idea that photorespiration and non-photorespiratory peroxisomal metabolism play multi-faceted roles in pathogen defence beyond metabolism of reactive oxygen species.

Evolution of the biochemistry of the photorespiratory C2 cycle

Oxygenic photosynthesis would not be possible without photorespiration in the present day O2 -rich atmosphere. It is now generally accepted that cyanobacteria-like prokaryotes first evolved oxygenic photosynthesis, which was later conveyed via endosymbiosis into a eukaryotic host, which then gave rise to the different groups of algae and streptophytes. For photosynthetic CO2 fixation, all these organisms use RubisCO, which catalyses both the carboxylation and the oxygenation of ribulose 1,5-bisphosphate. One of the reaction products of the oxygenase reaction, 2-phosphoglycolate (2PG), represents the starting point of the photorespiratory C2 cycle, which is considered largely responsible for recapturing organic carbon via conversion to the Calvin-Benson cycle (CBC) intermediate 3-phosphoglycerate, thereby detoxifying critical intermediates. Here we discuss possible scenarios for the evolution of this process toward the well-defined 2PG metabolism in extant plants. While the origin of the C2 cycle core enzymes can be clearly dated back towards the different endosymbiotic events, the evolutionary scenario that allowed the compartmentalised high flux photorespiratory cycle is uncertain, but probably occurred early during the algal radiation. The change in atmospheric CO2 /O2 ratios promoting the acquisition of different modes for inorganic carbon concentration mechanisms, as well as the evolutionary specialisation of peroxisomes, clearly had a dramatic impact on further aspects of land plant photorespiration.

The structural properties of plant peroxisomes and their metabolic significance

Plant peroxisomes can be isolated by Percoll density gradient centrifugation at high purity and metabolic competence as well as in relatively large quantities. According to biochemical and electrophysiological analyses, plant peroxisomes have recently been shown to differ from other cell organelles in essential structural properties. Unlike mitochondria or plastids, compartmentalization of plant peroxisomal metabolism is in major parts not caused by a boundary function of the membrane but is primarily due to the specific structure of the protein matrix. The enzymes of the photorespiratory C2 cycle of leaf peroxisomes are arranged as multienzyme complexes that allow efficient metabolic channelling with high flux rates and minimum leakage of reactive oxygen species from the organelle. Transfer of metabolites, such as carboxylates, proceeds across the peroxisomal membrane via a porin-like channel, which represents a relatively unspecific but highly efficient transport system. Because all variants of peroxisomes, which all contain only a single boundary membrane, are confronted with the task of transporting a large group of metabolites while preventing the escape of reactive intermediates, it is reasonable to speculate that the unique compartmentalization feature of leaf peroxisomes also applies to peroxisomes from fungi and mammals.

The endosymbiotic origin of the protein import machinery of chloroplastic envelope membranes

Chloroplasts have evolved a complex proteinaceous machinery to import nuclear-encoded proteins. The origin of this machinery, following the endosymbiotic events leading to chloroplasts, is an intriguing, unresolved problem. Given that cyanobacteria are the probable ancestors of chloroplasts, the genome sequence of Synechocystis sp. PCC 6803 offers a valuable resource to identify putative homologs for components of this protein import machinery and to gain insights into its possibly endosymbiotic origin. Detailed computational sequence analysis reveals that Synechocystis sp. PCC 6803 has homologs of three of the known membrane proteins of the chloroplastic translocon, namely Toc75, Tic20 and Tic22, as well as a homolog of the putative component Tic55. Thus, the chloroplastic protein import machinery is mainly derived from the endosymbiotic cyanobacterium, but, interestingly, not from any of the four main protein secretion systems of prokaryotes. The relatively high sequence variability between chloroplastic and Synechocystis proteins suggests that the ancestral proteins had different physiological roles and were modified significantly to fulfill the new demand of importing proteins into the evolving chloroplast. The fact that some chloroplastic protein import components are not related to any Synechocystis proteins (Toc159, Tic110 and Toc34) indicates that the chloroplastic protein import apparatus is of a dual evolutionary origin.

The evolutionary origin of the protein-translocating channel of chloroplastic envelope membranes: identification of a cyanobacterial homolog

The known envelope membrane proteins of the chloroplastic protein import apparatus lack sequence similarity to proteins of other eukaryotic or prokaryotic protein transport systems. However, we detected a putative homolog of the gene encoding Toc75, the protein-translocating channel from the outer envelope membrane of pea chloroplasts, in the genome of the cyanobacterium Synechocystis sp. PCC 6803. We investigated whether the low sequence identity of 21% reflects a structural and functional relationship between the two proteins. We provide evidence that the cyanobacterial protein is also localized in the outer membrane. From this information and the similarity of the predicted secondary structures, we conclude that Toc75 and the cyanobacterial protein, referred to as SynToc75, are structural homologs. synToc75 is essential, as homozygous null mutants were not recovered after directed mutagenesis. Sequence analysis indicates that SynToc75 belongs to a family of outer membrane proteins from Gram-negative bacteria whose function is not yet known. However, we demonstrate that these proteins are related to a specific group of prokaryotic secretion channels that transfer virulence factors, such as hemolysins and adhesins, across the outer membrane.

Participation of mitochondrial metabolism in photorespiration. Reconstituted system of peroxisomes and mitochondria from spinach leaves

In this study the interplay of mitochondria and peroxisomes in photorespiration was simulated in a reconstituted system of isolated mitochondria and peroxisomes from spinach (Spinacia oleracea L.) leaves. The mitochondria oxidizing glycine produced serine, which was reduced in the peroxisomes to glycerate. The required reducing equivalents were provided by the mitochondria via the malate-oxaloacetate (OAA) shuttle, in which OAA was reduced in the mitochondrial matrix by NADH generated during glycine oxidation. The rate of peroxisomal glycerate formation, as compared with peroxisomal protein, resembled the corresponding rate required during leaf photosynthesis under ambient conditions. When the reconstituted system produced glycerate at this rate, the malate-to-OAA ratio was in equilibrium with a ratio of NADH/NAD of 8. 8 x 10(-3). This low ratio is in the same range as the ratio of NADH/NAD in the cytosol of mesophyll cells of intact illuminated spinach leaves, as we had estimated earlier. This result demonstrates that in the photorespiratory cycle a transfer of redox equivalents from the mitochondria to peroxisomes, as postulated from separate experiments with isolated mitochondria and peroxisomes, can indeed operate under conditions of the very low reductive state of the NADH/NAD system prevailing in the cytosol of mesophyll cells in a leaf during photosynthesis.

Permeability properties of the porin of spinach leaf peroxisomes

The membrane of spinach leaf peroxisomes contains an anion-selective channel. Reconstitution experiments were performed with lipid bilayer membranes to study its permeability properties. A variety of different monovalent inorganic and organic anions were found to be permeable through the porin channel. Its single-channel conductance for these different ions suggested that the channel has a minimum diameter of about 0.6 nm. From selectivity measurement in KCl solution a ratio of the anion permeability to cation permeability of less than 0.04 was determined, indicating an almost ideal selectivity of the peroxisomal channel for chloride. The permeation of chloride through the peroxisomal channel could be blocked efficiently by the addition of increasing concentrations of organic anions to the aqueous phase. The results are consistent with a binding site for dicarboxylic anions inside the peroxisomal channel. A particular high stability constant for the binding was obtained for peroxisomal metabolites such as malate, oxaloacetate, succinate, and 2-oxoglutarate, which have to cross the membrane of plant peroxisomes in vivo. Among these solutes maximal binding affinity was determined for C4 dicarboxylic anions. The results indicate that the peroxisomal channel does not form a general diffusion pore similarly to known eukaryotic porins, but has specific properties comparable to specific and inducible porins, which have been characterized in some gram-negative bacteria.

Evidence for the Presence of a Porin in the Membrane of Glyoxysomes of Castor Bean

Glyoxysomes of endosperm tissue of castor bean (Ricinus communis L.) seedlings were solubilized in a detergent and added to a lipid bilayer. Conductivity measurements revealed that the glyoxysomal preparation contained a porin-like channel. Using an electrophysiological method, which we established for semiquantitative determination of porin activity, we were able to demonstrate that glyoxysomal membranes purified by sucrose density gradient centrifugation contain an integral membrane protein with porin activity. The porin of glyoxysomes was shown to have a relatively small single-channel conductance of about 330 picosiemens in 1 M KCl and to be strongly anion selective. Thus, the glyoxysomal porin differs from the other previously characterized porins in the outer membrane of mitochondria or plastids, but is similar to the porin of spinach (Spinacia oleracea L.) leaf peroxisomes. Our results suggest that, in analogy to the porin of leaf peroxisomes, the glyoxysomal porin facilitates the passage of small metabolites, such as succinate, citrate, malate, and aspartate, through the membrane.

The membrane of leaf peroxisomes contains a porin-like channel

Spinach leaf peroxisomes were purified by Percoll density gradient centrifugation. After several freeze-thaw cycles, the peroxisomal membranes were separated from the matrix enzymes by sucrose density gradient centrifugation. The purity of the peroxisomal membranes was checked by measuring the activities of marker enzymes and by using antibodies. Lipid bilayer membrane experiments with the purified peroxisomal membranes, solubilized with a detergent, demonstrated that the membranes contain a channel-forming component, which may represent the major permeability pathway of these membranes. Control experiments with membranes of other cell organelles showed that the peroxisomal channel was not caused by the contamination of the peroxisomes with mitochondria or chloroplasts. The peroxisomal channel had a comparatively small single channel conductance of 350 pS in 1 M KCl as compared with channels from other cell organelles. The channel is slightly anion selective, which is in accordance with its physiological function. The single channel conductance was found to be only moderately dependent on the salt concentration in the aqueous phase. This may be explained by the presence of positive point net charges in or near the channel or by the presence of a saturable binding site inside the channel. The possible role of the channel in peroxisomal metabolism is discussed.