Download Suppl. Table S3

Table S3: Ustilago maydis theoretical peroxisomal protein inventory
PEXs
Accn no.
Name
Function
PTS1
PTS2
MTS
um04191
Pex1
AAA ATPase involved recycling/undocking of Pex5
n.a.
n.a.
n.a.
um00325
Pex2
E(3) ligase required involved in the polyubiquitination of Pex5
n.a.
n.a.
n.a.
um06200
Pex3
Docking factor for Pex19, vesicle assembly during de novo formation
n.a.
n.a.
n.a.
um11354
Pex4
Ubiquitin-conjugating enzyme required for monoubiquitination of Pex5
n.a.
n.a.
n.a.
um02528,
Pex5
Peroxisomal matrix protein import PTS1-receptor
n.a.
n.a.
n.a.
um02421
Pex6
AAA ATPase involved recycling/undocking of Pex5
n.a.
n.a.
n.a.
um03596
Pex7
Peroxisomal matrix protein import PTS2-receptor
n.a.
n.a.
n.a.
um02887
Pex8
Involved in the assembly of the Po matrix protein importomer
n.a.
n.a.
n.a.
um02641
Pex10
E(3) ligase for Ubc4p-dependent ubiquitination of Pex5p
n.a.
n.a.
n.a.
um04294
Pex11α/β
Peroxisome elongation, membrane bending for subsequent division
n.a.
n.a.
n.a.
um00440
Pex11γ
Peroxisome elongation, membrane bending for subsequent division
n.a.
n.a.
n.a.
um00297
Pex12
E(3) ligase required for Pex4-dependent monoubiquitination of Pex5p
n.a.
n.a.
n.a.
um03165
Pex13
Part of the peroxisomal membrane docking complex for Pex5 and Pex7
n.a.
n.a.
n.a.
um02323
Pex14
Part of the peroxisomal membrane docking complex for Pex5 and Pex7
n.a.
n.a.
n.a.
um06341
Pex16
Recruitment of Pex3 to the Po membrane, required for de novo formation
n.a.
n.a.
n.a.
um10731
Pex19
Po membrane protein import receptor, required for de novo formation
n.a.
n.a.
n.a.
um10172
Pex5/20 fusion protein
Unknown, according to the Pex20 domain possible PTS2 co-receptor
n.a.
n.a.
n.a.
um01564
Pex23
Required for peroxisome assembly/ peroxisomal matrix protein import
n.a.
n.a.
n.a.
um10336
Pex24
Required for peroxisome assembly and protein import
n.a.
n.a.
n.a.
um12204
Pex26
Pex1/Pex6 anchor protein at the peroxisomal membrane
n.a.
n.a.
n.a.
um00755
Pex33
Pex14/17 fusion protein, part of the membrane docking complex for Pex5
n.a.
n.a.
n.a.
Peroxins
Other proteins involved in peroxisome biogenesis
um03919
Related to FIS1
Involved in mitochondrial/peroxisomal division, possible adaptor for DNM1
n.a.
n.a.
n.a.
um05378
Mitochondrial fission factor DNM1
Organelle fission, member of the dynamin family of GTPases
n.a.
n.a.
n.a.
um03498
Related to CAF4 - CCR4 associated factor
Involved in DNM1-dependent mitochondrial/peroxisomal division
n.a.
n.a.
n.a.
um15047
Probable VPS1
Organelle fission, member of the dynamin family of GTPases
n.a.
n.a.
n.a.
um02719
Related to DnaJ-like protein1 - DJP1
Involved in peroxisomal matrix protein import in yeast
n.a.
n.a.
n.a.
um05734
Probable GTPase Rho1
Required for peroxisome proliferation in yeasts; organization of the actin
n.a.
n.a.
n.a.
um10663
Probable RHO1 GTP-binding protein
cytoskeleton attached to the peroxisomal membrane
n.a.
n.a.
n.a.
Lipid metabolism – fatty acid transport/activation
um01105
Peroxisomal half ABC transporter PXA2
ABC membrane transporter, fatty acid import
n.a.
n.a.
um03945
Peroxisomal half ABC transporter PXA1
ABC membrane transporter, fatty acid import
n.a.
n.a.

um05450
Rel. to Long-chain-fatty-acid-CoA ligase 6
Fatty acid activation by coupling to coenzyme A
 PKL
um02583
Rel. to Very-long-chain fatty acid-CoA synth.
Fatty acid activation by coupling to coenzyme A
 VRL
um03228
FACL-like2/long-chain fatty acid coA ligase
Fatty acid activation by coupling to coenzyme A
 PRL


um11659
PCS60 - AMP-binding protein, peroxisomal
High similarities to E. coli Long-chain acyl-CoA synthase
 AKL
um02235
Rel. to Acyl-CoA synthetase
Fatty acid activation by coupling to coenzyme A
 SKL
um05869
Rel. to mito. carnitine/acyl carnitine carrier
Export of fatty acids from peroxisomes?
n.a.
um11660
Carnitine O-acetyltransferase (CRAT)
Export of fatty acids from peroxisomes
 SKL
um11938
Peroxisomal SCP2-like protein A
Fatty acid/Steroid binding/transport
 AKL
um01850
Peroxisomal SCP2-like protein B
Fatty acid/Steroid binding/transport
 AKL
um11277
Oleate induced Po lipid transfer protein
Fatty acid/Steroid binding/transport (SCP2 domain)
 ARL

n.a.

Lipid metabolism – fatty acid β-oxidation
um00122
AidB-like ACAD
Fatty acid β-oxidation, first step?
 SHL
um10665
Related to ACAD with CytB5 domain
Fatty acid β-oxidation, first step?
 SKF
um01466
CytB5 domain bearing ACAD
Fatty acid β-oxidation, first step?
 ARL
um06400
ACAD11n
Fatty acid β-oxidation, first step
 SHL


um06422
ACAD11c, N-terminal domain
Unknown
 SKL
um01966
Acyl-CoA oxidase ACOX1-like A
Fatty acid β-oxidation, first step
 SNL
um02028
Acyl-CoA oxidase ACOX1-like B
Fatty acid β-oxidation, first step
 ARL
um02208
Acyl-CoA oxidase ACOX1-like C
Fatty acid β-oxidation, first step
 AKL
um04324
Acyl-CoA oxidase POX1
Fatty acid β-oxidation, first step
um02097
Peroxisomal enoyl-CoA hydratase
Fatty acid β-oxidation, second step
 SKL
um11001
Peroxisomal enoyl-CoA hydratase
Fatty acid β-oxidation, second step
 SNL
um01747
MFE-2 like enoyl-CoA hydratase
Fatty acid β-oxidation, second step
 AKL

um10825
3-Hydroxyacyl-CoA dehydrogenase type 2
Fatty acid β-oxidation, third step
 GKL

um10038
Peroxisomal multifunctional enzyme MFE2
Fatty acid β-oxidation, second & third step
um01090
POT1 - acetyl-CoA C-acyltransferase
Fatty acid β-oxidation, fourth step
um02715
POT1-like - acetyl-CoA C-acyltransferase
Fatty acid β-oxidation, fourth step
um01986
Peroxisomal sterol carrier protein SCPx
Fatty acid β-oxidation, fourth step



Lipid metabolism – fatty acid α-oxidation
um05961
α-Methylacyl-CoA racemase (AMACR)
Conversion of pristanoyl-CoA and C27-bile acyl-CoA to (S)-stereoisomers
um03994
2-Hydroxyacyl-CoA lyase 1 (HPCL2)
Conversion 2-hydroxyphytanoyl-CoA to pristanal
um11241
Fatty aldehyde dehydrogenase (AL3A2)
Conversion of pristanal to pristanic acid
 SKL
Lipid metabolism – degradation of polyunsaturated fatty acids
um03158
Rel. to Δ3,Δ2-enoyl-CoA isomerase ECI2
Isomerization of 3-trans,5-cis-dienoyl-CoA to 2-trans,4-trans-dienoyl-CoA
 SKL
um01599
Rel. to Δ3,Δ2-enoyl-CoA isomerase ECI2
Isomerization of 3-trans,5-cis-dienoyl-CoA to 2-trans,4-trans-dienoyl-CoA
 HKL
um10273
Rel. to Δ3,Δ2-enoyl-CoA isomerase ECH1
Isomerization of 3-trans,5-cis-dienoyl-CoA to 2-trans,4-trans-dienoyl-CoA
 AKL
um10183
Peroxisomal 2,4-dienoyl-CoA reductase
Catalyzes the reduction of 2,4-dienoyl-CoA to trans-3-enoyl-CoA
 SRL
Lipid metabolism – miscellaneous proteins
um00334
Peroxisomal acyl-CoA thioester hydrolase
Regulation of intraorganellar CoA-SH levels
 PKL
um01415
Hypothetical thioester hydrolase
Unknown
 PKL
um11630
Hypothetical thioester hydrolase
Unknown
 SKL

um06465
Hypothetical thioester hydrolase
Unknown
 SQL
um11350
Rel. to Short chain acyl-CoA synthetase 3
Activation of acetate to acetyl-CoA
 CKL
um10088
Related to Acetoacetyl-CoA synthetase
Generation of acetoacetyl-CoA from 2 acetyl-CoA
 AKL
um02182
Rel. to Dehydrogenase/reductase SDR 4
NADPH-dependent beta-ketoacyl reductase
 PRL
um02023
Rel.to Long chain fatty alcohol oxidase FAO1
Involved in the omega-oxidation pathway of lipid degradation
 ARL
um02862
Rel. to Ectomycorrhiza-regulated esterase
Unknown
 SRL
um10545
Rel. to Ectomycorrhiza-regulated esterase
Unknown
 ARL

Lipid metabolism – etherlipid synthesis*
um11632
Rel. to DHAP acyltransferase
Synthesis of acyl-DHAP from DHAP and acyl-CoA
 AQL

um02491
Glyceraldehyde 3-phosphate dehydrogenase
Conversion of glyceraldehyde 3-phosph. into 3-phospho-glyceroyl phosph.
 SRL

um05422
Similar to FAR1
Fatty alcohol synthesis
n.a.
n.a.
um05893
Rel. to acyl DHAP reductase
Conversion of acyl dihydroxyacetone-phosphate (DHAP) into glycerolipids
n.a.
n.a.
Lipid metabolism –synthesis of mannosylerythritol lipids (MEL)
um03116
MAC1
Transfer of fatty acids to C-2 and C-3 positions of mannosylerythritol
 ARL
um10636
MAC2
Transfer of fatty acids to C-2 and C-3 positions of mannosylerythritol
 AKL
Amino acid metabolism
um02001
Hydroxymethylglutaryl-CoA lyase
Terminal step in leucine metabolism
 AKL
um05247
Rel. to methylcrotonyl-CoA carboxylase β
Leucine degradation
 SRM
um06326
Rel. to fumarylacetoacetate hydrolase
Tyrosine degradation
 PKL
um05703
Rel. to D-amino-acid oxidase
Degradation of D-amino acids
 SRL
um11649
Rel. to D-amino acid oxidase
Degradation of D-amino acids
 LKL
um03935
Rel. to sarcosine oxidase
Oxidation of L-pipecolate and L-proline
 ARL
um03239
Probable acetolactate synthase
Catalyzes the first step in valine, isoleucine biosynthesis


Glycolate/glyoxylate metabolism
um10682
Rel. to Hydoxyacid oxidase 1
Degradation of glycolate to glyoxylate
 NKL
um12269
Rel. to Hydoxyacid oxidase 1
Degradation of glycolate to glyoxylate
 GRL

um01329
Isocitrate dehydrogenase subunit 1, IDH1
Isocitrate + NAD+ = 2-oxoglutarate + CO2 + NADH
NAD+
= 2-oxoglutarate + CO2 + NADH
 SNL

 SRL


um01328
Isocitrate dehydrogenase subunit 2, IDH2
Isocitrate +
um06111
Isocitrate dehydrogenase, IDP1/2
Isocitrate + NADP+ = 2-oxoglutarate + CO2 + NADPH
 GKL
um15004
Probable malate synthase, glyoxysomal
Acetyl-CoA + H2O + glyoxylate = (S)-malate + CoA.
 ARI
um11161
Probable MDH1 - malate dehydrogenase
(S)-malate + NAD+ = oxaloacetate + NADH
 ANL
Oxygen metabolism and oxidation of redox equivalents
um04063
Related to Epoxide hydrolase 2
C-terminal dom.: epoxide hydrolase, N-terminal domain: lipid phosphatase
 SKL
um01852
Related to Epoxide hydrolase 1
Catalyzes the hydrolysis of arene and aliphatic epoxides dihydrodiols
 SKI
um10746
Similar to Epoxide hydrolase
Catalyzes the hydrolysis of arene and aliphatic epoxides dihydrodiols
 AKL
um05678
Related to Glutathione S-transferase κ
RX + glutathione = HX + R-S-glutathione
 AKL
Um02610
Related to Glutathione S-transferase
RX + glutathione = HX + R-S-glutathione
 AKL
um11067
Probable Catalase 2
Degradation of hydogen peroxide: 2 H2O2 = O2 + 2 H2O
 ARF
um10331
Rel. to peroxisomal PMP20, PRDX5
Reduction of hydrogen peroxide and alkyl hydroperoxides
 AKL
um01947
Related to cytochrome-c peroxidase
2 ferrocytochrome c + H2O2 = 2 ferricytochrome c + 2 H2O
 AKL
Purine and pyrimidine metabolism
um00672
Probable urate oxidase (uricase)
Conversion of uric acid to allantoin
 AKL
um03264
Probable xanthine dehydrogenase/oxidase
Conversion of hypoxanthine to uric acid
n.a.
Carbohydrate metabolism
um00555
Glycerol-3-phosphate dehydrogenase (NAD)
Regulation of the NAD+/NADH coenzyme equilibrium
 SRL
um04930
Prob. Glucose 6-phosphate dehydrogenase
Conversion of glucose-6-phosphate to D-glucono-1,5-lactone-6-phosphate
 GKM
um00674
Probable Fructose-bisphosphate aldolase
Condensation of DHAP + glyceraldehyde-3-phosphate to FBP
 GKL
um11953
Related to STE23
Mammalian insulin-degrading enzyme homolog, unknown function in Po
 ANL
um05558
Related to mammalian Lon protease Lon2p
Cleavage of PTS2, degradation of misfolded polypeptides in Po
 SRL
Regulation of intracellular polyamine concentration
 SRL
Proteases
Amine and polyamine metabolism
um03524
Rel. to Po amine oxidase (Cu-containing)

um05850
Rel. to Po amine oxidase
Regulation of intracellular polyamine concentration
 NKL
Oxidizes L-gulono-1,4-lactone to H2O2 and L-xylo-hexulonolactone
 SRL
Condensation of pimeloyl-CoA and L-alanine to 8-amino-7-oxononanoate
 SKL
Ascorbate biosynthesis
um10013
Related to l-gulonolactone oxidase
Biotin biosynthesis
um01197
Rel.to 8-amino-7-oxononanoate synthase
Possible alcohol metabolism
um01872
Related to gmc type oxidoreductase
Probable peroxisomal alcohol oxidase or polyamine biosynthesis
 SHL
um05407
Rel. to Betaine aldehyde dehydrogenase
(Acet)aldehyde degradation or polyamine biosynthesis
 AKL
 PKL

Cleavage of Cofactors
um01332
Related to CoA diphosphatase (NUDT7)
Regulation of CoA and acyl-CoA levels in response to metabolic demands
um06194
Rel. to NADH pyrophosphatase NUDT12
Regulation of NADH levels levels in response to metabolic demands
um03979
Rel. to Nudix motif 19 (NUDT19)
Regulation of CoA and acyl-CoA levels in response to metabolic demands
 AKL
Further acyl-activating enzymes
um15048
Related to 4-coumarate-CoA ligase 1
Unknown
 AKL
um06153
Related to 4-coumarate--CoA ligase 1
Unknown
 ANL
um04479
Related to 4-coumarate--CoA ligase
Unknown
 AKL
Miscellaneous proteins with unknown function
um01189
Probable translation elongation factor eEF1β
EF1B catalyzes the exchange of GDP bound to the G-protein for GTP
 AKI
um10014
Rel. to Ribonuclease UK114
Unknown function in Po metabolism (Antonenkov et al. 2007)
 SNL
um01286
Related to PTC5 - 2C protein phosphatase
Sim. to metazoan mitochondrial pyruvate dehydrogenase phosphatase 1
 AKL
um11368
Probable cytochrome b5
Electron acceptor protein
 AKL
um11567
Related to Histidine triad protein
Superfamily of nucleotide-binding and -hydrolyzing enzymes
 AKL
um00154
Related to Para-nitrobenzyl esterase
Possible carboxylesterase
 AKL
um01881
Related to Oxidoreductase
SDR short-chain dehydrogenase
 SHL
um03451
Related to 2-Nitropropane dioxygenase
Denitrification of nitroalkanes to their corresponding carbonyl compounds
 ARL
um11382
Related to 2-Nitropropane dioxygenase
Denitrification of nitroalkanes to their corresponding carbonyl compounds
 SKL

um11901
Rel. to Lactamase, beta 2
Unknown
 SAL
um00045
Related to soluble Quinone reductase
Detoxification of quinones
 HKL
um11449
Related to Phenol 2-monooxygenase
Detoxification of phenol compounds
 TRL
um10538
Related to 2-Dehydropantoate-2 reductase
Panthotenate (vitamin b5) synthesis
 ANL
um02920
Histidine phosphatase domain containing p.
Unknown
 TKL
um01941
Uncharacterized α/β hydrolase
Unknown
 TKL
um02502
Uncharacterized α/β hydrolase
Unknown
 SKL
um12002
Uncharacterized α/β hydrolase
Unknown
 AKL
um06455
Uncharacterized α/β hydrolase
Unknown
 SRL
um04482
Uncharacterized α/β hydrolase
Unknown, “toxin biosynthesis protein”
 SRL
um01771
Uncharacterized protein (CoA-binding fold)
Unknown
 GKL
um12171
Uncharacterized protein
Unknown
 SKL
um03250
Uncharacterized protein
Unknown
 SKL
um12308
Uncharacterized protein
Unknown
 ANL
um11300
Uncharacterized protein
Unknown
 SKL
um02990
Hydroxysteroid dehydrogenase-like 2
Unknown


Miscellaneous peroxisomal membrane proteins
um03207
Rel. to MPV17-like 2
Unknown
n.a.
n.a.
um03019
Rel. to MPV17-like 2
Unknown
n.a.
n.a.
um05390
Rel. to PXMP4 (PMP24)
Unknown
n.a.
n.a.
um00984
Rel. to Mosc2
Reduction of N-hydroxylated drugs in mitochondria, Po function unknown
n.a.
n.a.
um01257
Related to ANT1 - Peroxisomal ATP carrier
Import/export of ATP/AMP
n.a.
n.a.
um04444
Related to ANT1 – Peroxisomal ATP carrier
Import/export of ATP/AMP
n.a.
n.a.
um01782
Related PMP47/PMP34
Import/export of ATP/AMP
n.a.
n.a.
um02959
Rel. to ACBD5
Pexophagy
n.a.
n.a.
Proteins with a conserved PTS1 found only in Ustilaginomycetes**
um11593
Related to PYC2 - pyruvate carboxylase 2
Gluconeogenesis: ATP + pyruvate + HCO3- = ADP + P + oxaloacetate
 PHL
um05747
Related to SEC31 -
Component of the COPII coat of ER-Golgi vesicles
 SRL
um10552
Related to Prolyl endopeptidase
Unknown
 SRL
um00952
Related to RTS2/Kin17
Basic zinc-finger protein, DNA/RNA-binding
 SRF
um00037
Sim. to Monodehydroascorbate reductase
Detoxification of organic radical compounds
 AKI
um00438
Related to 50S ribosomal protein L35
Translational regulation
 PSL
um00589
Similar to Glyoxalase
Removal of the toxic metabolite methylglyoxal and related compounds
 ANI
um00740
Related to 2-Dehydropantoate 2-reductase
Panthotenate (vitamin b5) synthesis
 GRL
um11303
Related to paraoxonase
Protection from lipid peroxidation
 CKL
um10872
Rleated to Nudix hydrolase Nudt5
hydrolysis of ADP-to AMP and ribose-5-phosphate
 GRL
um01904
Related to Succinyl-coa ligase 2 β-chain
Ligation of succinate and CoA to succinyl-CoA (tricarboxylic acid cycle)
 GHL
um03128
Uncharacterized α/β hydrolase
Unknown
 AHL
um03699
Prob. Phosphopantothenoylcysteine synth.
Catalyzes the first step in the biosynthesis of coenzyme A
 ARI
um15025
Prob. NADP-depndt. alcohol dehydrogenase
Alcohol metabolism
 ANL
um12289
Probable Dephospho-CoA kinase
Catalyzes the fifth step in the biosynthesis of coenzyme A from vitamin B5
 SKL
um11572
Related to Rab geranylgeranyltransferase α
Transfer of a geranylgeranyl moeiety to Rab proteins
 AHF
um10945
Uncharacterized α/β hydrolase
Unknown
 PKL
um10582
Uncharacterized α/β hydrolase
Unknown
 PKL
um03638
Uncharacterized protein
Unknown
 ARF
um04796
Uncharacterized protein
Unknown
 SHF



PTS1/2, peroxisomal targeting signal 1/2; MTS, mitochondrial targeting signal; n.a. - not applicable
 - predicted strong targeting signal,  - predicted weak targeting signal
*ADHAP, the key enzyme of peroxisomal ether lipid synthesis is not found in fungi, whereas homologs of all remaining proteins of the peroxisomal part of this
pathway were identified
** Proteins with an often unusual PTS1 only found among Ustilaginomycetes. The targeting signal of many proteins in this group may not be functional