Origin and evolution of the peroxisomal proteome

Biology Direct

Volumn 1, Issue , 2006, Pages

  Gabaldón, Toni ^a,c   Snel, Berend ^a   van Zimmeren, Frank ^a   Hemrika, Wieger ^b   Tabak, Henk ^b   Huynen, Martijn A ^a  

^a RADBOUD UNIVERSITY MEDICAL CENTER   (Netherlands)

^b UTRECHT UNIVERSITY   (Netherlands)

^c CENTRO DE INVESTIGACIÓN PRÍNCIPE FELIPE   (Spain)

Author keywords

[No Author keywords available]

Indexed keywords

EUKARYOTA; PROTEOBACTERIA; RATTUS;

ARTICLE;

EID: 33747893546     PISSN: None     EISSN: 17456150     Source Type: Journal    
DOI: 10.1186/1745-6150-1-8     Document Type: Review

References (49)

1. de Duve D The peroxisome: A new cytoplasmic organelle Proc R Soc Lond B Biol Sci 1969 173 30 71-83
2. Subramani S Components involved in peroxisome import, biogenesis, proliferation, turnover, and movement Physiol Rev 1998 78 1 171-188 9457172
3. Latruffe N Vamecq J Evolutionary aspects of peroxisomes as cell organelles, and of genes encoding peroxisomal proteins Biol Cell 2000 92 6 389-395 10.1016/S0248-4900(00)01083-2 11132700
4. Lazarow PB Fujiki Y Biogenesis of peroxisomes Annu Rev Cell Biol 1985 1 489-530 10.1146/annurev.cb.01.110185.002421 3916321
5. Erdmann R Kunau WH A genetic approach to the biogenesis of peroxisomes in the yeast Saccharomyces cerevisiae Cell Biochem Funct 1992 10 3 167-174 10.1002/cbf.290100306 1423897
6. Hoepfner D Schildknegt D Braakman I Philippsen P Tabak HF Contribution of the endoplasmic reticulum to peroxisome formation Cell 2005 122 1 85-95 10.1016/j.cell.2005.04.025 16009135
7. Kurland CG Andersson SG Origin and evolution of the mitochondrial proteome Microbiol Mol Biol Rev 2000 64 4 786-820 99014 11104819 10.1128/ MMBR.64.4.786-820.2000
8. Gabaldón T Huynen MA Reconstruction of the proto-mitochondrial metabolism Science 2003 301 5633 609 10.1126/science.1085463 12893934
9. Schafer H Nau K Sickmann A Erdmann R Meyer HE Identification of peroxisomal membrane proteins of Saccharomyces cerevisiae by mass spectrometry Electrophoresis 2001 22 14 2955-2968 10.1002/ 1522-2683(200108)22:14<2955::AID-ELPS2955>3.0.CO;2-U 11565790
10. Yi EC Marelli M Lee H Purvine SO Aebersold R Aitchison JD Goodlett DR Approaching complete peroxisome characterization by gas-phase fractionation Electrophoresis 2002 23 18 3205-3216 10.1002/ 1522-2683(200209)23:18<3205::AID-ELPS3205>3.0.CO;2-Y 12298092
11. Kikuchi M Hatano N Yokota S Shimozawa N Imanaka T Taniguchi H Proteomic analysis of rat liver peroxisome: Presence of peroxisome-specific isozyme of Lon protease J Biol Chem 2004 279 1 421-428 10.1074/ jbc.M305623200 14561759
12. Jarosch E Lenk U Sommer T Endoplasmic reticulum-associated protein degradation Int Rev Cytol 2003 223 39-81 12641210
13. Rabinovich E Kerem A Frohlich KU Diamant N Bar-Nun S AAA-ATPase p97/ Cdc48p, a cytosolic chaperone required for endoplasmic reticulum-associated protein degradation Mol Cell Biol 2002 22 2 626-634 139744 11756557 10.1128/MCB.22.2.626-634.2002
14. Harper JW Burton JL Solomon MJ The anaphase-promoting complex: It's not just for mitosis any more Genes Dev 2002 16 17 2179-2206 10.1101/ gad.1013102 12208841
15. Platta HW Grunau S Rosenkranz K Girzalsky W Erdmann R Functional role of the AAA peroxins in dislocation of the cycling PTS1 receptor back to the cytosol Nat Cell Biol 2005 7 8 817-822 10.1038/ncb1281 16007078
16. Ye Y Shibata Y Yun C Ron D Rapoport TA A membrane protein complex mediates retro-translocation from the ER lumen into the cytosol Nature 2004 429 6994 841-847 10.1038/nature02656 15215856
17. Birschmann I Stroobants AK van den Berg M Schafer A Rosenkranz K Kunau WH Tabak HF Pex15p of Saccharomyces cerevisiae provides a molecular basis for recruitment of the AAA peroxin Pex6p to peroxisomal membranes Mol Biol Cell 2003 14 6 2226-2236 194873 12808025 10.1091/mbc.E02-11-0752
18. Erdmann R Schliebs W Peroxisomal matrix protein import: The transient pore model Nat Rev Mol Cell Biol 2005 6 9 738-742 16103872
19. Marelli M Smith JJ Jung S Yi E Nesvizhskii AI Christmas RH Saleem RA Tam YY Fagarasanu A Goodlett DR Aebersold R Rachubinski RA Aitchison JD Quantitative mass spectrometry reveals a role for the GTPase Rho1p in actin organization on the peroxisome membrane J Cell Biol 2004 167 6 1099-1112 10.1083/jcb.200404119 15596542
20. Hoepfner D van den Berg M Philippsen P Tabak HF Hettema EH A role for Vps1p, actin, and the Myo2p motor in peroxisome abundance and inheritance in Saccharomyces cerevisiae J Cell Biol 2001 155 6 979-990 10.1083/jcb.200107028 11733545
21. Sickmann A Reinders J Wagner Y Joppich C Zahedi R Meyer HE Schonfisch B Perschil I Chacinska A Guiard B Rehling P Pfanner N Meisinger C The proteome of Saccharomyces cerevisiae mitochondria Proc Natl Acad Sci U S A 2003 100 23 13207-13212 263752 14576278 10.1073/pnas.2135385100
22. Valadi A Granath K Gustafsson L Adler L Distinct intracellular localization of Gpd1p and Gpd2p, the two yeast isoforms of NAD+ glycerol-3-phosphate dehydrogenase, explains their different contributions to redox-driven glycerol production J Biol Chem 2004 279 38 39677-39685 10.1074/jbc.M403310200 15210723
23. Janssen U Fink T Lichter P Stoffel W Human mitochondrial 3,2-trans-enoyl-CoA isomerase (DCI): Gene structure and localization to chromosome 16p13.3 Genomics 1994 23 1 223-228 10.1006/geno.1994.1480 7829074
24. Abdelraheim SR Spiller DG McLennan AG Mammalian NADH diphosphatases of the Nudix family: Cloning and characterization of the human peroxisomal NUDT12 protein Biochem J 2003 374 Pt 2 329-335 1223609 12790796 10.1042/ BJ20030441
25. Scharfe C Zaccaria P Hoertnagel K Jaksch M Klopstock T Dembowski M Lill R Prokisch H Gerbitz KD Neupert W Mewes HW Meitinger T MITOP, the mitochondrial proteome database: 2000 update Nucleic Acids Res 2000 28 1 155-158 102491 10592209 10.1093/nar/28.1.155
26. Solaas K Ulvestad A Soreide O Kase BF Subcellular organization of bile acid amidation in human liver: A key issue in regulating the biosynthesis of bile salts J Lipid Res 2000 41 7 1154-1162 10884298
27. Elgersma Y van Roermund CW Wanders RJ Tabak HF Peroxisomal and mitochondrial carnitine acetyltransferases of Saccharomyces cerevisiae are encoded by a single gene Embo J 1995 14 14 3472-3479 394414 7628448
28. Koch A Yoon Y Bonekamp NA McNiven MA Schrader M A Role for Fis1 in Both Mitochondrial and Peroxisomal Fission in Mammalian Cells Mol Biol Cell 2005
29. Birdsey GM Lewin J Cunningham AA Bruford MW Danpure CJ Differential enzyme targeting as an evolutionary adaptation to herbivory in carnivora Mol Biol Evol 2004 21 4 632-646 10.1093/molbev/msh054 14739251
30. Danpure CJ Lumb MJ Birdsey GM Zhang X Alanine:glyoxylate aminotransferase peroxisome-to-mitochondrion mistargeting in human hereditary kidney stone disease Biochim Biophys Acta 2003 1647 1 2 70-75 12686111
31. Reumann S Ma C Lemke S Babujee L AraPerox. A database of putative Arabidopsis proteins from plant peroxisomes Plant Physiol 2004 136 1 2587-2608 523325 15333753 10.1104/pp.104.043695
32. Soares MJ De Souza W Cytoplasmic organelles of trypanosomatids: A cytochemical and stereological study J Submicrosc Cytol Pathol 1988 20 2 349-361 3135113
33. Thieringer R Kunau WH The beta-oxidation system in catalase-free microbodies of the filamentous fungus Neurospora crassa. Purification of a multifunctional protein possessing 2-enoyl-CoA hydratase, L-3-hydroxyacyl-CoA dehydrogenase, and 3-hydroxyacyl-CoA epimerase activities J Biol Chem 1991 266 20 13110-13117 1830048
34. Hannaert V Saavedra E Duffieux F Szikora JP Rigden DJ Michels PA Opperdoes FR Plant-like traits associated with metabolism of Trypanosoma parasites Proc Natl Acad Sci U S A 2003 100 3 1067-1071 298727 12552132 10.1073/pnas.0335769100
35. Schluter A Ripp R Fourcade S Mandel JL Poch O Pujol A The Evolutionary Origin of Peroxisomes: An ER-Peroxisome Connection Mol Biol Evol 2006 16452116
36. Saccharomyces Genome Database
37. Swissprot Swissprot http://www.ebi.ac.uk/swissprot
38. GeneBank GeneBank http://www.ncbi.nlm.nih.gov/Genbank
39. IPI IPI database http://www.ebi.ac.uk/IPI
40. Edgar RC MUSCLE: A multiple sequence alignment method with reduced time and space complexity BMC Bioinformatics 2004 5 1 113 517706 15318951 10.1186/1471-2105-5-113
41. Thompson JD Higgins DG Gibson TJ CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice Nucleic Acids Res 1994 22 22 4673-4680 308517 7984417
42. Guindon S Gascuel O A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood Syst Biol 2003 52 5 696-704 10.1080/10635150390235520 14530136
43. Kanehisa M Goto S KEGG: Kyoto encyclopedia of genes and genomes Nucleic Acids Res 2000 28 1 27-30 102409 10592173 10.1093/nar/28.1.27
44. material S Supplementary material Supplemantary material http://www.cmbi.ru.nl/~jagabald/peroxisome_trees.html
45. Letunic I Copley RR Schmidt S Ciccarelli FD Doerks T Schultz J Ponting CP Bork P SMART 4.0: Towards genomic data integration Nucleic Acids Res 2004 32 Database issue D142-4 10.1093/nar/gkh088
46. Soding J Protein homology detection by HMM-HMM comparison Bioinformatics 2005 21 7 951-960 10.1093/bioinformatics/bti125 15531603
47. Altschul SF Koonin EV Iterated profile searches with PSI-BLAST - a tool for discovery in protein databases Trends Biochem Sci 1998 23 11 444-447 10.1016/S0968-0004(98)01298-5 9852764
48. Shiozawa K Maita N Tomii K Seto A Goda N Akiyama Y Shimizu T Shirakawa M Hiroaki H Structure of the N-terminal domain of PEX1 AAA-ATPase. Characterization of a putative adaptor-binding domain J Biol Chem 2004 279 48 50060-50068 10.1074/jbc.M407837200 15328346
49. Baldauf SL Roger AJ Wenk-Siefert I Doolittle WF A kingdom-level phylogeny of eukaryotes based on combined protein data Science 2000 290 5493 972-977 10.1126/science.290.5493.972 11062127