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Table 1 Summary of the C9orf72 and SMCR8 protein interactomes and selected functional categories

From: C9orf72-associated SMCR8 protein binds in the ubiquitin pathway and with proteins linked with neurological disease

Gene Name Protein Name Total # Spectra
RNase
- +
A. C9orf72-FL
 C9orf72 chromosome 9 open reading frame 72 108 103
TOP 20 C9orf72-INTERACTING PROTEINS
  SMCR8 Smith-Magenis syndrome chromosome region, candidate 8 165 217
  WDR41 WD repeat domain 41 69 85
  FLG2 filaggrin family member 2 33 6
  LRPPRC leucine rich pentatricopeptide repeat containing 23 25
  IARS isoleucyl-tRNA synthetase 21 22
  SERPINB3 serpin family B member 3 21 0
  CALML5 calmodulin like 5 20 0
  HADHA hydroxyacyl-CoA dehydrogenase/3-ketoacyl-CoA thiolase/enoyl-CoA hydratase, alpha subunit 18 14
  CDSN corneodesmosin 17 8
  EEF2 eukaryotic translation elongation factor 2 15 18
  FABP5 fatty acid binding protein 5 15 0
  COPB1 coatomer protein complex subunit beta 1 14 14
  DSC1 desmocollin 1 14 15
  U2AF2 U2 small nuclear RNA auxiliary factor 2 14 6
  LUC7L3 LUC7 like 3 pre-mRNA splicing factor 13 4
  EIF2S3 eukaryotic translation initiation factor 2 subunit gamma 12 10
  HNRNPH2 heterogeneous nuclear ribonucleoprotein H2 12 9
  KHDRBS1 KH RNA binding domain containing, signal transduction associated 1 12 6
  PSMC2 proteasome 26S subunit, ATPase 2 12 25
B. FL-SMCR8
 SMCR8 Smith-Magenis syndrome chromosome region, candidate 8 1135 1182
TOP 25 SMCR8-INTERACTING PROTEINS
  DNAJA1 DnaJ heat shock protein family member A1 70 76
  GTF2I general transcription factor IIi 55 61
  CAD carbamoyl-phosphate synthetase 2, aspartate transcarbamylase, and dihydroorotase 62 48
  ATP1A1 ATPase Na+/K+ transporting subunit alpha 1 38 46
  EPRS glutamyl-prolyl-tRNA synthetase 36 40
  MAGED1 MAGE family member D1 26 33
  WDR41 WD repeat domain 41 32 33
  DNAJC7 DnaJ heat shock protein family member C7 30 32
  SLC25A3 solute carrier family 25 member 3 22 32
  STUB1 STIP1 homology and U-box containing protein 1 30 31
  GCN1 GCN1, eIF2 alpha kinase activator homolog 37 30
  DDB1 damage specific DNA binding protein 1 31 29
  DYNC1H1 dynein cytoplasmic 1 heavy chain 1 38 29
  CHD4 chromodomain helicase DNA binding protein 4 13 28
  SLC25A11 solute carrier family 25 member 11 14 28
  RANBP2 RAN binding protein 2 29 25
  RUVBL2 RuvB like AAA ATPase 2 30 25
  ATP2A2 ATPase sarcoplasmic/endoplasmic reticulum Ca2+ transporting 2 19 22
  DNAJA3 DnaJ heat shock protein family member A3 19 22
  IARS isoleucyl-tRNA synthetase 18 22
  STIP1 stress induced phosphoprotein 1 37 22
  COPA coatomer protein complex subunit alpha 23 20
  HUWE1 HECT, UBA and WWE domain containing 1, E3 ubiquitin protein ligase 29 20
  AIFM1 apoptosis inducing factor, mitochondria associated 1 18 18
  C9orf72 chromosome 9 open reading frame 72 15 18
AMINOACYL-tRNA SYNTHESIS
  EPRS glutamyl-prolyl-tRNA synthetase 40 13
  IARS isoleucyl-tRNA synthetase 18 22
  DARS aspartyl-tRNA synthetase 11 8
  MARS methionyl-tRNA synthetase 10 6
  RARS arginyl-tRNA synthetase 9 8
  LARS leucyl-tRNA synthetase 9 14
  QARS glutaminyl-tRNA synthetase 8 7
  TARS2 threonyl-tRNA synthetase 2, mitochondrial (putative) 6 4
  TARS threonyl-tRNA synthetase 4 0
  FARSA phenylalanyl-tRNA synthetase alpha subunit 0 6
CELL CYCLE
  SMC3 structural maintenance of chromosomes 3 12 8
  CDK4 cyclin dependent kinase 4 5 0
  PCNA proliferating cell nuclear antigen 5 4
  MCM7 minichromosome maintenance complex component 7 4 6
  YWHAZ tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein zeta 4 9
  RAD21 RAD21 cohesin complex component 3 0
  CDC7 cell division cycle 7 3 0
  PLK1 polo like kinase 1 3 9
  PPP6C protein phosphatase 6 catalytic subunit 3 0
  CDKN2A cyclin dependent kinase inhibitor 2A 0 3
  MCM2 minichromosome maintenance complex component 2 0 4
  MCM5 minichromosome maintenance complex component 5 0 4
  SMC1A structural maintenance of chromosomes 1A 0 4
HEAT SHOCK PROTEINS / CHAPERONES
  DNAJA1 DnaJ heat shock protein family member A1 70 76
  DNAJC7 DnaJ heat shock protein family member C7 30 32
  DNAJA3 DnaJ heat shock protein family member A3 19 22
  DNAJA3 DnaJ heat shock protein family member A3 19 22
  HSPH1 heat shock protein family H member 1 19 8
  BAG5 BCL2 associated athanogene 5 18 11
  DNAJA2 DnaJ heat shock protein family member A2 15 16
  BAG2 BCL2 associated athanogene 2 11 16
  BAG6 BCL2 associated athanogene 6 11 8
  SERPINH1 serpin family H member 1 11 0
  HSPB1 heat shock protein family B member 1 10 9
  MDN1 midasin AAA ATPase 1 10 14
  FKBP8 FK506 binding protein 8 8 0
  DNAJB6 DnaJ heat shock protein family member B6 6 4
  PFDN2 prefoldin subunit 2 5 4
  DNAJB1 DnaJ heat shock protein family member B1 4 0
  HSPA4 heat shock protein family A member 4 4 3
  HSPA4 heat shock protein family A member 4 4 3
  RBBP7 RB binding protein 7, chromatin remodeling factor 3 4
  SERPINB3 serpin family B member 3 3 0
  BAG3 BCL2 associated athanogene 3 2 3
  UNC45A unc-45 myosin chaperone A 2 5
  DNAJB11 DnaJ heat shock protein family member B11 0 6
  DNAJC10 DnaJ heat shock protein family member C10 0 5
  PARK7 Parkinsonism associated deglycase 0 4
MISMATCH REPAIR
  RFC3 replication factor C subunit 3 5 0
  SSBP1 single stranded DNA binding protein 1 5 0
  MSH6 mutS homolog 6(MSH6) 5 5
  POLD3 DNA polymerase delta 3, accessory subunit 2 3
  PCNA proliferating cell nuclear antigen 0 4
  POLD1 DNA polymerase delta 1, catalytic subunit 0 3
PHAGOSOME/AUTOPHAGY
  DYNC1H1 dynein cytoplasmic 1 heavy chain 1 38 29
  SEC16A SEC16 homolog A, endoplasmic reticulum export factor 14 12
  TUBB4A tubulin beta 4A class IVa 11 10
  IRS4 insulin receptor substrate 4 10 13
  TUBB3 tubulin beta 3 class III 9 13
  TUBB6 tubulin beta 6 class V 9 18
  PPP2R1A protein phosphatase 2 scaffold subunit Aalpha 7 5
  CDK5 cyclin dependent kinase 5 7 0
  SEC61B Sec61 translocon beta subunit 6 0
  HLA-A major histocompatibility complex, class I, A 5 5
  ANKRD28 aminoadipate-semialdehyde dehydrogenase-phosphopantetheinyl transferase 5 5
  RAB1B RAB1B, member RAS oncogene family 5 0
  SLC3A2 solute carrier family 3 member 2 4 8
  SEC24C SEC24 homolog C, COPII coat complex component 4 3
  TFRC transferrin receptor 4 0
  AP3M1 adaptor related proteincomplex 3 Mu 1 subunit 3 0
  PPP6C protein phosphatase 6 catalytic subunit 3 0
  BAG3 BCL2 associated athanogene 3 2 3
  WDR5 WD repeat domain 5 0 5
  YME1L1 YME1 like 1 ATPase 0 4
  KEAP1 kelch like ECH associated protein 1 0 4
  DYNC1I2 dynein cytoplasmic 1 intermediate chain 2 0 4
  CDKN2A cyclin dependent kinase inhibitor 2A 0 3
  HLA-B major histocompatibility complex, class I, B 0 3
PROTEIN PROCESSING IN THE ENDOPLASMIC RETICULUM
  DNAJA1 DnaJ heat shock protein family (Hsp40) member A1 70 76
  STUB1 STIP1 homology and U-box containing protein 1 30 31
  HSPH1 heat shock protein family H (Hsp110) member 1 19 8
  DNAJA2 DnaJ heat shock protein family (Hsp40) member A2 15 16
  BAG2 BCL2 associated athanogene 2 11 16
  SEC61B Sec61 translocon beta subunit 6 0
  RPN1 ribophorin I 5 3
  TXNDC5 thioredoxin domain containing 5 5 2
  DNAJB1 DnaJ heat shock protein family (Hsp40) member B1 4 0
  SEC24C SEC24 homolog C, COPII coat complex component 4 3
  DDOST dolichyl-diphosphooligosaccharide--protein glycosyltransferase 48 kD subunit 3 4
  SSR4 signal sequence receptor subunit 4 2 3
  DNAJB11 DnaJ heat shock protein family (Hsp40) member B11 0 6
  DNAJC10 DnaJ heat shock protein family (Hsp40) member C10 0 5
  RRBP1 ribosome binding protein 1 0 3
PROTEOSOME
  PSMC2 proteasome 26S subunit, ATPase 2 22 18
  PSMD2 proteasome 26S subunit, non-ATPase 2 18 10
  PSMA7 proteasome subunit alpha 7 17 16
  PSMD11 proteasome 26S subunit, non-ATPase 11 14 9
  PSMC3 proteasome 26S subunit, ATPase 3 12 9
  PSMD3 proteasome 26S subunit, non-ATPase 3 12 8
  PSMA5 proteasome subunit alpha 5 11 6
  PSMC5 proteasome 26S Subunit, ATPase 5 10 10
  PSME3 proteasome activator subunit 3 10 11
  PSMA6 proteasome subunit alpha 6 9 0
  PSMD6 proteasome 26S subunit, non-ATPase 6 9 7
  PSMA3 proteasome subunit alpha 3 8 3
  PSMD1 proteasome 26S subunit, non-ATPase 1 8 8
  PSMA1 proteasome subunit alpha 1 7 7
  PSMB1 proteasome subunit beta 1 7 7
  PSMB5 proteasome subunit beta 5 6 6
  PSMC1 proteasome 26S subunit, ATPase 1 6 6
  PSMB2 proteasome subunit beta 2 5 5
  PSMB6 proteasome subunit beta 6 5 5
  PSMC4 proteasome 26S subunit, ATPase 4 5 0
  PSMC6 proteasome 26S subunit, ATPase 6 5 6
  PSMD12 proteasome 26S subunit, non-ATPase 12 4 2
  PSMD7 proteasome 26S subunit, non-ATPase 7 3 0
  PSMD13 proteasome 26S subunit, non-ATPase 13 0 3
  PSMD14 proteasome 26S subunit, non-ATPase 14 0 3
  PSMD8 proteasome 26S subunit, non-ATPase 8 0 6
RNA TRANSPORT
  RANBP2 RAN binding protein 2 29 25
  XPO1 exportin 1 13 13
  NUP93 nucleoporin 93 11 10
  NUP133 nucleoporin 133 10 15
  THOC2 THO complex 2 9 6
  RANGAP1 Ran GTPase activating protein 1 8 11
  KPNB1 karyopherin subunit beta 1 7 5
  KPNA2 karyopherin subunit alpha 2 6 4
  EIF4A1 eukaryotic translation initiation factor 4A1 5 4
  EIF4G1 eukaryotic translation initiation factor 4 gamma 1 5 4
  NUP155 nucleoporin 155 4 6
  NUP210 nucleoporin 210 4 0
  EIF3F eukaryotic translation initiation factor 3 subunit F 3 3
  FXR2 FMR1 autosomal homolog 2 3 0
  NUP160 nucleoporin 160 3 4
  NUP205 nucleoporin 205 3 4
  EIF3E eukaryotic translation initiation factor 3 subunit E 2 4
  FMR1 fragile X mental retardation 1 2 0
  NUP98 nucleoporin 98 2 5
  NUP153 nucleoporin 153 0 5
  THOC3 THO complex 3 0 4
  XPOT exportin for tRNA 0 4
UBIQUITINATION / SUMOYLATION
  STUB1 STIP1 homology and U-box containing protein 1 30 31
  HUWE1 HECT, UBA and WWE domain containing 1, E3 ubiquitin ligase 29 20
  RANBP2 RAN binding protein 2, E3 SUMO ligase 29 25
  RNF40 ring finger protein 40, E3 ubiquitin ligase 4 10
  USP7 ubiquitin specific peptidase 7 4 9
  USP9X ubiquitin specific peptidase 9, X-linked 4 5
  RNF2 ring finger protein 2, , E3 ubiquitin protein ligase 3 0
  UBR5 ubiquitin protein ligase E3 component n-recognin 5 3 12
  USP15 ubiquitin specific peptidase 15 3 0
  SUMO3 small ubiquitin-like modifier 3 0 3
  MKRN2 makorin ring finger protein 2, E3 ubiquitin ligase 0 3
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