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Evolutionary aspects of peroxisomes as cell organelles, and of genes encoding peroxisomal proteins
Biology of the Cell 92 (2000) 389−395 © 2000 Éditions scientifiques et médicales Elsevier SAS. All rights reserved S0248490000010832/REV
Review
Evolutionary aspects of peroxisomes as cell organelles, and of genes encoding peroxisomal proteins Norbert Latruffea*, Joseph Vamecqb a
Université de Bourgogne, LBMC, 6 boulevard Gabriel, 21000 Dijon, France
b
Inserm/département de neuropédiatrie, CHU Lille, 2 avenue Oscar-Lambret, 59037 Lille, France
Received 9 December 1999; accepted 28 July 2000
Peroxisomes are present in most eukaryotic cell types, and have different enzymatic content and metabolic functions throughout the life scale. The endosymbiotic origin of these DNA-devoid organelles is supported by evolutionary data concerning genes encoding not only most peroxisomal proteins, but also several transcriptional factors regulating their expression such as peroxisome proliferator-activated receptors. © 2000 Éditions scientifiques et médicales Elsevier SAS phylogeny / peroxisomes / evolution / mitochondria / microbodies
1. INTRODUCTION There are three key events in the history of peroxisomes: their appearance 1.5 billion years ago when eukaryotic cells appeared on earth, their discovery (Rhodin, 1954), and their characterisation (de Duve, 1983). Finally, plant peroxisomes were for the first time quoted in a textbook no earlier than 15 years ago (Becker, 1986), and they still remain an oddity for several cell biologists and some master textbooks.
2. MORPHOLOGY, ENZYMATIC CONTENT AND FUNCTION Peroxisomes are ubiquitous, roundish, single membrane-bound organelles (figure 1) belonging to the family of microbodies. On the basis of their enzymatic properties (Tolbert, 1981) and host cell types, members of this family are classified as 1) peroxisomes, which * Correspondence and reprints: tel: +33 380 396 237; fax: +33 380 396 250. E-mail address: [email protected] (N. Latruffe).
Phylogeny of peroxisomes
contain enzymes producing and destroying hydrogen peroxide; 2) leaves and seeds glyoxysomes which contain enzymes catalysing the glyoxylate cycle; 3) Trypanosoma brucei glycosomes containing glycolytic enzymes; and possibly 4) gerontosomes, involved in plant senescence (Vicentini and Matile, 1993). Trichomonas vaginalis hydrogenosomes endowed with hydrogen-producing enzymes and initially classified together with peroxisomes in the early 1970s (Lindmark and Müller, 1973; Müller, 1975), are now considered as related to mitochondria (Müller, 1997; Martin and Müller, 1998; Gray et al. 1999; Müller and Martin, 1999). Peroxisomes of many species (human excepted) contain an electron dense core of urate oxidase that catalyses the conversion of uric acid into allantoin with hydrogen peroxide production. In some animals, peroxisomes may also contain a marginal plate. From a metabolic point of view, peroxisomal functions show some kind of link with those performed by mitochondria and/or chloroplasts. In plants, glyoxysomes produce glyoxylic acid, which can be converted to glycolate and subsequently to 3-phosphoglyceric acid, which in turn is handled by chloroplasts as a precursor Latruffe and Vamecq
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Biology of the Cell 92 (2000) 389–395
Figure 1. Electron microscope view of peroxisomes stained by the DAB-alkaline phosphatase method in 3 adjacent guinea pig hepatocytes. The peroxisomes (P) are globular in the cell on the right and rather polyhaedric in the cell on the left; also seen are a bile canaliculus (C) and its microvilli (MV). Magnification × 12 000. From Dr. J.P. Zahnd (unpublished results), in collaboration with N. Latruffe’s laboratory and SterlingWinthrop laboratory, Dijon.
of carbohydrate in the Calvin–Benson cycle. In mammalian liver, peroxisomes shorten fatty acids carbon chains before their subsequent and complete breakdown by β-oxidation enzymes in mitochondria (Lindmark and Müller, 1973). Furthermore, peroxisomes can contribute to the NAD+/NADH balance (‘cellular redox state’) through the pyruvate/lactate cycling, carried out by the peroxisomal α-hydroxy-acid oxidase and the cytoplasmic lactate dehydrogenase.
3. BIOGENESIS OF PEROXISOMES – COMPARISON WITH MITOCHONDRIA Most of the studies conclude that the biogenesis of peroxisomes occurs through division of pre-existing organelles which are progressively enriched in lipidic and peptidic components synthesised in the cytosol. Recently however, several biochemical studies re-
Figure 2. Targeting sequences of neosynthesised polypeptides. a, b or c are the possible PTS (peroxisome targeting sequences), d is the NLS (nuclear localization sequence) and e is the main MTS (mitochondrial targeting sequence)/CTS (chloroplast targeting sequence).
Phylogeny of peroxisomes
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vealed close relations between peroxisomes and the endoplasmic reticulum, rather than any prokaryote (Kunau and Erdmann, 1998; Olsen, 1998; Titorenko and Rachubinski, 1998). Peroxisomal proteins are synthesised on free polyribosomes and their targeting into the organelle involves different tags and mechanisms (Aitchison et al., 1992) (figure 2). The most common addressing pathway is the PTS1 (peroxisome targeting sequence #1), consisting of a ‘SKL’ motif (seryl-lysylleucyl residues) located at the C-terminus; this protein tag recognized by the PTS1 receptor, is specific of peroxisomes, and is not found in any other targeting pathway. Several proteins are also sorted to the peroxisome via PTS2, a N-terminal signal, whose location and aminoacid composition (conserved hydrophobic and basic aminoacid residues) are similar to those found in chloroplastic targeting sequences. Finally, in a
restricted number of peroxisomal proteins, the signal PTS3 consists of a sequence of hydrophobic and basic aminoacid residues located inside the polypeptide chain, similar to the nuclear localization sequences (NLS). An indication of the possible common origin of peroxisomes and mitochondria comes from studies concerning the alanine glyoxylate aminotransferase (AGT), located in peroxisomes in humans and in mitochondria in other species (Danpure, 1993). In patients affected by primary hypoxaluria type I, AGT maintains its catalytic activity, but is mislocated into mitochondria as a result of a point mutation. In fact, the mitochondrial targeting sequence has become prominent over the peroxisomal one (Müller, 1997). In hyperoxaluria-affected humans, the inefficient removal of glyoxylic acid leads to an accumulation of oxalic acid (see figure 3). Enzyme mislocations between per-
A
B
Figure 3. Mislocation of the alanine glyoxylate aminotransferase (AGT) in mitochondria, resulting in the accumulation of calcium oxalate in the cytosol. A: AGT is imported into the peroxisome via the PTS receptor. In the peroxisome, the role of AGT is to convert glyoxylic acid to glycine in the presence of alanine with pyruvate formation. This conversion step prevents the local formation of oxalic acid (catalysed by peroxisomal glycolate oxidase) and its exit from the peroxisome with formation of a cytosolic pool of glyoxylic acid. In the cytosol, due to the abundance of lactate dehydrogenase, glyoxylic acid largely oxidized to oxalic acid, besides undergoing transamination into glycine, catalysed by the glyoxylate aminotransferase (GGT) in the presence of glutamate. The general (peroxisome + cytosol) result of liver glyoxylate disposition is, by far, in favour of glycine formation, despite a very active cytosolic lactate dehydrogenase. B: In patients affected by primary hyperoxaluria type I, AGT is mistargeted to mitochondria, as a consequence of a point mutation converting the PTS into a MTS. The loss of conversion of glyoxylic acid into glycine leads to a high increase in its cytosolic pool, and consequently, an extremely increased amount of oxalic acid. The removal of this excess of oxalic acid from liver into body fluids and urine is responsible for the occurrence of kidney stones in these patients. It is worth mentioning that for a long time primary hyperoxaluria type I was supposed to be caused by a deficient cytosolic GGT. Being now widely known that in humans the peroxisomal AGT plays a major role in this glycine formation step with respect to cytosolic GGT, it is now sufficiently clear why in the case of AGT mislocation the activity of this cytosolic aminotransferase is not sufficient to counterbalance the high rates of glyoxylic acid oxidation catalysed by lactate dehydrogenase.
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Biology of the Cell 92 (2000) 389–395
Table I. Structure of β-oxidation enzymes among three living particles, either organelles or organism (from Kunau et al., 1987)
corresponds to multifunctional enzymes.
oxisomes and mitochondria might have frequently occurred during evolution and might have resulted in the presence of analogue pathways in both organelles.
4. FATTY ACID β-OXIDATION ENZYMES: COMPARISON BETWEEN MITOCHONDRIA, PEROXISOMES AND BACTERIA In these three living entities, the catabolism of fatty acids is combined with a yield of ATP (mainly in mitochondria), and with heat production (mainly in peroxisomes). While the primary sequences of fatty acid oxidation enzymes show some conservation between the living entities, their tertiary and quaternary structures can differ (table I). The comparison of gene sequences supports the hypothesis of a common ancestor and suggests that peroxisomal enzymes might have diverged from mitochondrial enzymes about 400 millions years ago (Kanayama et al., 1994; Baumgart et al., 1996).
5. PEROXISOMES, MITOCHONDRIA AND CHLOROPLASTS, A COMMON ENDOSYMBIOTIC ORIGIN On the basis of 1) the widely accepted idea that mitochondria and chloroplasts originate from a comPhylogeny of peroxisomes
mon ancestral bacterium that colonised a proeukaryotic cell, and 2) the close metabolic similarities and interrelations between these two organelles and peroxisomes, the same endosymbiotic origin has been proposed for all these cellular particles (Rhodin, 1954; Cavalier-Smith, 1987; Cavalier-Smith, 1997). A possible explanation for the absence of DNA in peroxisomes could be that these organelles might have entered the eukaryotic cells earlier than mitochondria and chloroplasts. In latter particles, however only vestigial amounts of DNA are contained as compared to a bacterial genome (15 × 103 bp for human mitochondria DNA/4.7 × 106 bp for E.coli DNA). Microbodies may have first appeared as hydrogenosomes when the gaseous atmosphere on earth was still reducing (figure 4), before molecular oxygen appeared on the planet (Stabenau et al., 1998).
6. DIFFERENTIAL REGULATION OF PEROXISOMAL ENZYMES IN THE EUKARYOTIC LIFE SCALE In lower fungi and yeasts, genes encoding for peroxisomal fatty acid β-oxidation enzymes are upregulated by fatty acids (oleate) (Kamada, 1982) or methanol. In mammals, several xenobiotic compounds with hypolipidaemic properties (fibrates) act as powerful up-regulators of the same genes (Motojima et al., 1998), whereas in plants their expression may be stimulated in response to light exposure (Jiang et al. 1994). Latruffe and Vamecq
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peroxisome proliferator DNA response element) (Vamecq and Latruffe, 1999) (figure 5).
7. ORIGIN AND EVOLUTION OF PPAR GENES
Figure 4. Possible endosymbiotic origin of peroxisomes appearance in eukaryotic cells: comparison with mitochondria and chloroplasts in the eukaryotic cell.
The molecular mechanisms for these regulatory events consist in the interactions between transcription factors and DNA responsive sequences. Apparently, there is no relationship between the fungi and the mammalian systems (Einerhand et al., 1991), while the plant mechanism is not yet understood. In vertebrates, the key regulatory system is the PPAR/PPRE couple (peroxisome proliferator-activated nuclear receptor/
PPARs belong to the hormone nuclear receptor superfamily which is supposed to have appeared before the vertebrate/invertebrate evolutionary branching (Dreyer etal., 1993). Since in Drosophila a hormonerelated nuclear receptor superfamily (comprising genes such as fushi tarazu or the ecdysone receptor gene) has presumably appeared 400 millions years ago, it has been proposed that the diversity of the hormone receptors superfamily preceded the fish/mammalian evolutionary divergence occurring 200 millions years ago (table II). Since that period, PPARs evolved three times faster than other members of the hormone nuclear receptor superfamily, such as the thyroid hormone receptor (TR), the retinoic acid receptor (RAR) and the oestrogen receptor (ER), and exhibit now three isoforms (α, β/δ and γ). Biological activating ligands have been identified for each member of the nuclear steroid receptors superfamily with the exception of orphan receptors or temporary orphan receptors. Due to the fast evolutionary changes occurring in the dietary and environmental exposure of vertebrates, as well as to pharmaceutical research concerning PPARs in physiology and medicine, a high number of natural and synthetic ligands should be easily discovered in the near future.
Figure 5. Induction of mammalian gene transcription by PPAR (peroxisome proliferator-activated receptor) in presence of a ligand, for example a hypolipidaemic agent (CherkaouiMalki, 1990). X is a co-activator, usually RXR (retinoic acid receptor activated by 9-cis-retinoic acid).
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Table II. Life evolutionary tree with the possible place of peroxisomes.
Geologic period
Age
Living organisms
Quaternary Permian Devonian
present time 0 2 million years 280 million years 400 million years
first hominoids fish/mammalian divergence insects/vertebrates divergence
Precambrian Solar system formation Universe (big bang)
1.5 billion years 3.5 billion years 4.6 billion years 15 billion years
primitive eucaryotic cell first procaryotes
Peroxisome history
PPAR isoforms hormone receptor superfamily (PPAR ancestor) peroxisomes (hydrogenosomes)
8. OTHER DETERMINANTS OF PEROXISOMAL FUNCTIONS DURING EVOLUTION
example, an event of cellular enzymes being trapped inside a new type of particle with no link to the nucleus or endoplasmic reticulum.
Phenomena of intracellular protein mislocation might have occurred during evolutionary loss and acquirement of peroxisomal functions. By analogy with the AGT mistargeting in human primary hyperoxaluria type I (see figure 3), such mislocations derive from point mutations, and changes in peroxisomal enzymatic content. They might depend on sudden mutational events rather than progressive mutational mechanisms, including point mutations in DNA sequences other than those encoding protein-targeting signals responsible for the loss of urate oxidase in liver peroxisomes of humans and other primates. In fact in humans, two nonsense mutations are found in the urate oxidase gene (Wu et al., 1989; Yeldandi et al., 1990; Yeldandi et al., 1991), and consequently 1) the enzyme is not expressed, and 2) uric acid is not converted to the more soluble compound allantoin, and constitutes the end product of purines metabolism. In conditions where uric acid formation is increased, its low solubility in body fluids and tissues leads to the formation of kidney stones, as well as uric acid deposits (tophi), which deposition is favoured by the relative low local temperature in lower member extremities and external ear auricles. This is the pathological basis for the human gout, a disease completely absent in mammals that possess a functional peroxisomal urate oxidase.
REFERENCES
9. COMMENTS In conclusion, peroxisomes constitute an exciting example of intracellular organelle evolution. Experimental evidence and hypotheses deal with the endosymbiotic origin similar to that of mitochondria/ chloroplasts. Future advances should determine whether this endosymbiotic origin is confirmed or invalidated in favour of another theory, suggesting for Phylogeny of peroxisomes
Aitchison, J.D., Nuttley, W.M., Szilard, R.K., Brade, A.M., Glover, J.R., Rachunbinski, R.A., 1992. Peroxisome biogenesis in yeast. Mol. Microbiol. 6, 3455–3460. Baumgart, E., Vanhooren, J.C., Franzen, M., Marynen, P., Puype, M., Vanderkerhove, J., Leunissen, J.A., Fahimi, H.D., Mannaerts, G.P., Van Veldhoven, P.P., 1996. Molecular characterization of the human peroxisomal branched-chain acyl-CoA oxidase: cDNA cloning, chromosomal assignment tissue distribution, and evidence for the absence of the protein in Zellweger syndrome. Proc. Natl. Acad. Sci. USA 93, 13748–13755. Becker, W.H., 1986. The World of the Cell. The Benjamin/Cummings Publishing Co., Inc., San Francisco. Cavalier-Smith, T., 1987. The simultaneous symbiotic origin of mitochondria, chloroplasts and microbodies. Ann. N.Y. Acad. Sci. 503, 55–71. Cavalier-Smith, T., 1997. Cell and genome co-evolution: facultative anaerobiosis, glycosomes and kinetoplastan RNA editing. Trends Genet. 13, 6–9. Cherkaoui-Malki, M., Bardot, O., Lhuguenot, J.C., Latruffe, N., 1990. Expression of liver peroxisomal proteins as compared to other organelle marker enzymes in rats treated with hypolipidemic agents. Biol. Cell 69, 83–92. Danpure, C.J., 1993. Primary hyperoxaluria type 1 and peroxisome to mitochondrion mistargeting of alanine: glyoxylate aminotransferase. Biochimie 75, 309–315. de Duve, C., 1983. Les microcorpuscules de la cellule vivante. Pour la Science (Scientific American) 69, 80–91. Dreyer, C., Keller, H.J., Mahfoudi, A., Laudet, V., Krey, G., Wahli, W., 1993. Positive regulation of the peroxisomal β-oxidation pathway by fatty acid through activation of peroxisome proliferator-activated receptors (PPAR). Biol. Cell 77, 67–76. Einerhand, A.W.C., Voorn-Brouwer, T.M., Erdmann, R., Kunau, W.H., Tabak, H.F., 1991. Regulation of transcription of the gene coding for peroxisomal 3-oxoacyl-CoA thiolase of Saccharomyces cerevisae. Eur. J. Biochem. 200, 113–122. Gray, M.W., Burger, G., Lang, B.F., 1999. Mitochondrial evolution. Science 283, 1476–1481. Jiang, L.W., Bunkelmann, J., Towill, L., Kleff, S., Trelease, R.N., 1994. Identification of peroxisome membrane proteins (PMPs) in sunflower (Helianthus annuis L.) cotyledons and influence of light on the PMP developmental pattern. Plant Physiol. 106, 293–302. Kamada, Y., Ueda, M., Atomi, H., Oda, K., Kurihara, T., Naito, N., Ukita, R., Ramasawa, N., Osumi, M., Tanaka, A., 1982. Localization of
Latruffe and Vamecq
Biology of the Cell 92 (2000) 389–395 Candida tropicalis peroxisomal isocitrate lyase highly expressed in peroxisome proliferated Saccharomyces cerevisae. J. Ferment. Bioeng. 74, 368–371. Kanayama, N., Ueda, M., Atomi, H., Kurihara, T., Tanaka, A., 1994. Molecular evolution of yeast thiolase isozymes. J. Ferment. Bioeng. 78, 279–282. Kunau, W.H., Erdmann, R., 1998. Peroxisome biogenesis: back to the endoplasmic reticulum?. Curr. Biol. 89, R299–R302. Kunau, W.H., Kiouka, C., Ledebur, A., Mateblowski, M., Moreno de la Garza, M., Schultz-Borchard, U., Thieringer, R., Veenhuis, M., 1987. β-oxidation systems in eukaryotic microorganisms. In: Fahimi, H.D., Sies, H. (Eds.), Peroxisome in Biology and Medicine. Springer Verlag, New York, pp. 128–140. Lindmark, D.G., Müller, M., 1973. Hydrogenosome, a cytoplasmic organelle of the anaerobic flagellate, Trichomonas fœtus and its role in pyruvate metabolism. J. Biol. Chem. 248, 7724–7728. Martin, W., Müller, M., 1998. The hydrogen hypothesis of the first eukaryote. Nature 392, 37–41. Motojima, K., Passilly, P., Peters, J.M., Gonzalez, F.J., Latruffe, N., 1998. Expression of putative fatty acid transporter genes are regulated by peroxisome proliferator-activated receptor α and γ activators in a tissue- and inducer-specific manner. J. Biol. Chem. 273, 16710–16714. Müller, M., 1975. Biochemistry of protozoan microbodies: peroxisomes, α-glycerophosphate oxidase bodies, hydrogenosomes. Ann. Rev. Microbiol. 29, 467–483. Müller, M., 1997. The evolutionary origin of Trichonomonas hydrogenosomes. Parasitol. Today 13, 166–167. Müller, M., Martin, W., 1999. The genome of Rickettsia prowazekii and some thoughts on the origin of mitochondria and hydrogenosome. BioEssays 21, 377–381.
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395 Olsen, L.J., 1998. The surprising complexity of peroxisome biogenesis. Plant Biol. Mol. 38, 163–189. Rhodin, J., 1954. Correlation of ultrastructural organization and function in normal and experimentaly changed proximal convoluted tubule cells of the mouse kidney. PhD dissertation, Aktiebolaget Godvil, Stockholm. Stabenau, H., Winkler, U., Säftel, W., 1998. On the origin of microbodies in plants. University of Oldenburg, Oldenburg, Germany, pp. 3-8. Titorenko, V.I., Rachubinski, R.A., 1998. The endoplasmic reticulum plays an essential role in peroxisome biogenesis. Trends Biochem. Sci. 23, 231–233. Tolbert, N., 1981. Metabolic pathways in peroxisomes and glyoxysomes. Ann. Rev. Biochem. 50, 133–157. Vamecq, J., Latruffe, N., 1999. Medical significance of peroxisome proliferator-activated receptors. Lancet 354, 141–148. Vicentini, F., Matile, P., 1993. Gerontosomes, a multifunctional type of peroxisome in senescent leaves. J. Plant. Physiol. 142, 50–56. Wu, X.W., Lee, C.C., Musny, D.M., Caskey, C.T., 1989. Urate oxidase: primary structure and evolutionary implications. Proc. Natl. Acad. Sci. USA 86, 9412–9416. Yeldandi, A.V., Wang, X.D., Alvares, K., Kumar, S., Rao, M.S., Reddy, J.K., 1990. Human urate oxidase gene: cloning and partial sequence analysis reveal a stop codon within the fifth exon. Biochem. Biophys. Res. Commun. 171, 641–646. Yeldandi, A.V., Yeldandi, V., Kumar, S., Murthy, C.V., Wang, X.D., Alvares, K., Rao, M.S., Reddy, J.K., 1991. Molecular evolution of the urate oxidase-encoding gene in hominoid primates: nonsense mutations. Gene 109, 281–284.
Latruffe and Vamecq
Review
Evolutionary aspects of peroxisomes as cell organelles, and of genes encoding peroxisomal proteins Norbert Latruffea*, Joseph Vamecqb a
Université de Bourgogne, LBMC, 6 boulevard Gabriel, 21000 Dijon, France
b
Inserm/département de neuropédiatrie, CHU Lille, 2 avenue Oscar-Lambret, 59037 Lille, France
Received 9 December 1999; accepted 28 July 2000
Peroxisomes are present in most eukaryotic cell types, and have different enzymatic content and metabolic functions throughout the life scale. The endosymbiotic origin of these DNA-devoid organelles is supported by evolutionary data concerning genes encoding not only most peroxisomal proteins, but also several transcriptional factors regulating their expression such as peroxisome proliferator-activated receptors. © 2000 Éditions scientifiques et médicales Elsevier SAS phylogeny / peroxisomes / evolution / mitochondria / microbodies
1. INTRODUCTION There are three key events in the history of peroxisomes: their appearance 1.5 billion years ago when eukaryotic cells appeared on earth, their discovery (Rhodin, 1954), and their characterisation (de Duve, 1983). Finally, plant peroxisomes were for the first time quoted in a textbook no earlier than 15 years ago (Becker, 1986), and they still remain an oddity for several cell biologists and some master textbooks.
2. MORPHOLOGY, ENZYMATIC CONTENT AND FUNCTION Peroxisomes are ubiquitous, roundish, single membrane-bound organelles (figure 1) belonging to the family of microbodies. On the basis of their enzymatic properties (Tolbert, 1981) and host cell types, members of this family are classified as 1) peroxisomes, which * Correspondence and reprints: tel: +33 380 396 237; fax: +33 380 396 250. E-mail address: [email protected] (N. Latruffe).
Phylogeny of peroxisomes
contain enzymes producing and destroying hydrogen peroxide; 2) leaves and seeds glyoxysomes which contain enzymes catalysing the glyoxylate cycle; 3) Trypanosoma brucei glycosomes containing glycolytic enzymes; and possibly 4) gerontosomes, involved in plant senescence (Vicentini and Matile, 1993). Trichomonas vaginalis hydrogenosomes endowed with hydrogen-producing enzymes and initially classified together with peroxisomes in the early 1970s (Lindmark and Müller, 1973; Müller, 1975), are now considered as related to mitochondria (Müller, 1997; Martin and Müller, 1998; Gray et al. 1999; Müller and Martin, 1999). Peroxisomes of many species (human excepted) contain an electron dense core of urate oxidase that catalyses the conversion of uric acid into allantoin with hydrogen peroxide production. In some animals, peroxisomes may also contain a marginal plate. From a metabolic point of view, peroxisomal functions show some kind of link with those performed by mitochondria and/or chloroplasts. In plants, glyoxysomes produce glyoxylic acid, which can be converted to glycolate and subsequently to 3-phosphoglyceric acid, which in turn is handled by chloroplasts as a precursor Latruffe and Vamecq
390
Biology of the Cell 92 (2000) 389–395
Figure 1. Electron microscope view of peroxisomes stained by the DAB-alkaline phosphatase method in 3 adjacent guinea pig hepatocytes. The peroxisomes (P) are globular in the cell on the right and rather polyhaedric in the cell on the left; also seen are a bile canaliculus (C) and its microvilli (MV). Magnification × 12 000. From Dr. J.P. Zahnd (unpublished results), in collaboration with N. Latruffe’s laboratory and SterlingWinthrop laboratory, Dijon.
of carbohydrate in the Calvin–Benson cycle. In mammalian liver, peroxisomes shorten fatty acids carbon chains before their subsequent and complete breakdown by β-oxidation enzymes in mitochondria (Lindmark and Müller, 1973). Furthermore, peroxisomes can contribute to the NAD+/NADH balance (‘cellular redox state’) through the pyruvate/lactate cycling, carried out by the peroxisomal α-hydroxy-acid oxidase and the cytoplasmic lactate dehydrogenase.
3. BIOGENESIS OF PEROXISOMES – COMPARISON WITH MITOCHONDRIA Most of the studies conclude that the biogenesis of peroxisomes occurs through division of pre-existing organelles which are progressively enriched in lipidic and peptidic components synthesised in the cytosol. Recently however, several biochemical studies re-
Figure 2. Targeting sequences of neosynthesised polypeptides. a, b or c are the possible PTS (peroxisome targeting sequences), d is the NLS (nuclear localization sequence) and e is the main MTS (mitochondrial targeting sequence)/CTS (chloroplast targeting sequence).
Phylogeny of peroxisomes
Latruffe and Vamecq
Biology of the Cell 92 (2000) 389–395
391
vealed close relations between peroxisomes and the endoplasmic reticulum, rather than any prokaryote (Kunau and Erdmann, 1998; Olsen, 1998; Titorenko and Rachubinski, 1998). Peroxisomal proteins are synthesised on free polyribosomes and their targeting into the organelle involves different tags and mechanisms (Aitchison et al., 1992) (figure 2). The most common addressing pathway is the PTS1 (peroxisome targeting sequence #1), consisting of a ‘SKL’ motif (seryl-lysylleucyl residues) located at the C-terminus; this protein tag recognized by the PTS1 receptor, is specific of peroxisomes, and is not found in any other targeting pathway. Several proteins are also sorted to the peroxisome via PTS2, a N-terminal signal, whose location and aminoacid composition (conserved hydrophobic and basic aminoacid residues) are similar to those found in chloroplastic targeting sequences. Finally, in a
restricted number of peroxisomal proteins, the signal PTS3 consists of a sequence of hydrophobic and basic aminoacid residues located inside the polypeptide chain, similar to the nuclear localization sequences (NLS). An indication of the possible common origin of peroxisomes and mitochondria comes from studies concerning the alanine glyoxylate aminotransferase (AGT), located in peroxisomes in humans and in mitochondria in other species (Danpure, 1993). In patients affected by primary hypoxaluria type I, AGT maintains its catalytic activity, but is mislocated into mitochondria as a result of a point mutation. In fact, the mitochondrial targeting sequence has become prominent over the peroxisomal one (Müller, 1997). In hyperoxaluria-affected humans, the inefficient removal of glyoxylic acid leads to an accumulation of oxalic acid (see figure 3). Enzyme mislocations between per-
A
B
Figure 3. Mislocation of the alanine glyoxylate aminotransferase (AGT) in mitochondria, resulting in the accumulation of calcium oxalate in the cytosol. A: AGT is imported into the peroxisome via the PTS receptor. In the peroxisome, the role of AGT is to convert glyoxylic acid to glycine in the presence of alanine with pyruvate formation. This conversion step prevents the local formation of oxalic acid (catalysed by peroxisomal glycolate oxidase) and its exit from the peroxisome with formation of a cytosolic pool of glyoxylic acid. In the cytosol, due to the abundance of lactate dehydrogenase, glyoxylic acid largely oxidized to oxalic acid, besides undergoing transamination into glycine, catalysed by the glyoxylate aminotransferase (GGT) in the presence of glutamate. The general (peroxisome + cytosol) result of liver glyoxylate disposition is, by far, in favour of glycine formation, despite a very active cytosolic lactate dehydrogenase. B: In patients affected by primary hyperoxaluria type I, AGT is mistargeted to mitochondria, as a consequence of a point mutation converting the PTS into a MTS. The loss of conversion of glyoxylic acid into glycine leads to a high increase in its cytosolic pool, and consequently, an extremely increased amount of oxalic acid. The removal of this excess of oxalic acid from liver into body fluids and urine is responsible for the occurrence of kidney stones in these patients. It is worth mentioning that for a long time primary hyperoxaluria type I was supposed to be caused by a deficient cytosolic GGT. Being now widely known that in humans the peroxisomal AGT plays a major role in this glycine formation step with respect to cytosolic GGT, it is now sufficiently clear why in the case of AGT mislocation the activity of this cytosolic aminotransferase is not sufficient to counterbalance the high rates of glyoxylic acid oxidation catalysed by lactate dehydrogenase.
Phylogeny of peroxisomes
Latruffe and Vamecq
392
Biology of the Cell 92 (2000) 389–395
Table I. Structure of β-oxidation enzymes among three living particles, either organelles or organism (from Kunau et al., 1987)
corresponds to multifunctional enzymes.
oxisomes and mitochondria might have frequently occurred during evolution and might have resulted in the presence of analogue pathways in both organelles.
4. FATTY ACID β-OXIDATION ENZYMES: COMPARISON BETWEEN MITOCHONDRIA, PEROXISOMES AND BACTERIA In these three living entities, the catabolism of fatty acids is combined with a yield of ATP (mainly in mitochondria), and with heat production (mainly in peroxisomes). While the primary sequences of fatty acid oxidation enzymes show some conservation between the living entities, their tertiary and quaternary structures can differ (table I). The comparison of gene sequences supports the hypothesis of a common ancestor and suggests that peroxisomal enzymes might have diverged from mitochondrial enzymes about 400 millions years ago (Kanayama et al., 1994; Baumgart et al., 1996).
5. PEROXISOMES, MITOCHONDRIA AND CHLOROPLASTS, A COMMON ENDOSYMBIOTIC ORIGIN On the basis of 1) the widely accepted idea that mitochondria and chloroplasts originate from a comPhylogeny of peroxisomes
mon ancestral bacterium that colonised a proeukaryotic cell, and 2) the close metabolic similarities and interrelations between these two organelles and peroxisomes, the same endosymbiotic origin has been proposed for all these cellular particles (Rhodin, 1954; Cavalier-Smith, 1987; Cavalier-Smith, 1997). A possible explanation for the absence of DNA in peroxisomes could be that these organelles might have entered the eukaryotic cells earlier than mitochondria and chloroplasts. In latter particles, however only vestigial amounts of DNA are contained as compared to a bacterial genome (15 × 103 bp for human mitochondria DNA/4.7 × 106 bp for E.coli DNA). Microbodies may have first appeared as hydrogenosomes when the gaseous atmosphere on earth was still reducing (figure 4), before molecular oxygen appeared on the planet (Stabenau et al., 1998).
6. DIFFERENTIAL REGULATION OF PEROXISOMAL ENZYMES IN THE EUKARYOTIC LIFE SCALE In lower fungi and yeasts, genes encoding for peroxisomal fatty acid β-oxidation enzymes are upregulated by fatty acids (oleate) (Kamada, 1982) or methanol. In mammals, several xenobiotic compounds with hypolipidaemic properties (fibrates) act as powerful up-regulators of the same genes (Motojima et al., 1998), whereas in plants their expression may be stimulated in response to light exposure (Jiang et al. 1994). Latruffe and Vamecq
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peroxisome proliferator DNA response element) (Vamecq and Latruffe, 1999) (figure 5).
7. ORIGIN AND EVOLUTION OF PPAR GENES
Figure 4. Possible endosymbiotic origin of peroxisomes appearance in eukaryotic cells: comparison with mitochondria and chloroplasts in the eukaryotic cell.
The molecular mechanisms for these regulatory events consist in the interactions between transcription factors and DNA responsive sequences. Apparently, there is no relationship between the fungi and the mammalian systems (Einerhand et al., 1991), while the plant mechanism is not yet understood. In vertebrates, the key regulatory system is the PPAR/PPRE couple (peroxisome proliferator-activated nuclear receptor/
PPARs belong to the hormone nuclear receptor superfamily which is supposed to have appeared before the vertebrate/invertebrate evolutionary branching (Dreyer etal., 1993). Since in Drosophila a hormonerelated nuclear receptor superfamily (comprising genes such as fushi tarazu or the ecdysone receptor gene) has presumably appeared 400 millions years ago, it has been proposed that the diversity of the hormone receptors superfamily preceded the fish/mammalian evolutionary divergence occurring 200 millions years ago (table II). Since that period, PPARs evolved three times faster than other members of the hormone nuclear receptor superfamily, such as the thyroid hormone receptor (TR), the retinoic acid receptor (RAR) and the oestrogen receptor (ER), and exhibit now three isoforms (α, β/δ and γ). Biological activating ligands have been identified for each member of the nuclear steroid receptors superfamily with the exception of orphan receptors or temporary orphan receptors. Due to the fast evolutionary changes occurring in the dietary and environmental exposure of vertebrates, as well as to pharmaceutical research concerning PPARs in physiology and medicine, a high number of natural and synthetic ligands should be easily discovered in the near future.
Figure 5. Induction of mammalian gene transcription by PPAR (peroxisome proliferator-activated receptor) in presence of a ligand, for example a hypolipidaemic agent (CherkaouiMalki, 1990). X is a co-activator, usually RXR (retinoic acid receptor activated by 9-cis-retinoic acid).
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Table II. Life evolutionary tree with the possible place of peroxisomes.
Geologic period
Age
Living organisms
Quaternary Permian Devonian
present time 0 2 million years 280 million years 400 million years
first hominoids fish/mammalian divergence insects/vertebrates divergence
Precambrian Solar system formation Universe (big bang)
1.5 billion years 3.5 billion years 4.6 billion years 15 billion years
primitive eucaryotic cell first procaryotes
Peroxisome history
PPAR isoforms hormone receptor superfamily (PPAR ancestor) peroxisomes (hydrogenosomes)
8. OTHER DETERMINANTS OF PEROXISOMAL FUNCTIONS DURING EVOLUTION
example, an event of cellular enzymes being trapped inside a new type of particle with no link to the nucleus or endoplasmic reticulum.
Phenomena of intracellular protein mislocation might have occurred during evolutionary loss and acquirement of peroxisomal functions. By analogy with the AGT mistargeting in human primary hyperoxaluria type I (see figure 3), such mislocations derive from point mutations, and changes in peroxisomal enzymatic content. They might depend on sudden mutational events rather than progressive mutational mechanisms, including point mutations in DNA sequences other than those encoding protein-targeting signals responsible for the loss of urate oxidase in liver peroxisomes of humans and other primates. In fact in humans, two nonsense mutations are found in the urate oxidase gene (Wu et al., 1989; Yeldandi et al., 1990; Yeldandi et al., 1991), and consequently 1) the enzyme is not expressed, and 2) uric acid is not converted to the more soluble compound allantoin, and constitutes the end product of purines metabolism. In conditions where uric acid formation is increased, its low solubility in body fluids and tissues leads to the formation of kidney stones, as well as uric acid deposits (tophi), which deposition is favoured by the relative low local temperature in lower member extremities and external ear auricles. This is the pathological basis for the human gout, a disease completely absent in mammals that possess a functional peroxisomal urate oxidase.
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