Table 3

The 66 TUX-MS-identified host factors that have not been previously implicated in the enteroviral life cyclea

Protein nameDesignationAccession no.bMol mass (kDa)No. of unique peptidescTotal no. of spectradFold incorporatedeGene ontologyfCellular localizationgRelative abundancehInteractionReference(s)
VirusiIRESj
Non-POU domain-containing octamer-binding proteinNONOQ1523354.21421INFRRMN++++HIV-1, HDVc-Myc9092
Nucleolar RNA helicase 2DDX21Q9NR3087.31517INFRBPN+++BDV93
Ribosomal L1 domain-containing protein 1RSL1D1O7602155.01315INFRBPN/C+++
Ribonucleases P/MRP protein subunit POP1POP1Q99575114.71214INFRBPN/C++
Myb-binding protein 1AMYBBP1AQ9BQG0148.91212INFDBPN/C+++
SAFB-like transcription modulatorSLTMQ9NWH9117.2811INFRRMN++
KH domain-containing, RNA-binding, signal transduction-associated protein 1KHDRBS1Q0766648.21011INFRBPN++++HIV-194
TATA-binding protein-associated factor 2NTAF15Q9280461.8410INFRRMN/C+++
Cellular nucleic acid-binding protein (ZNF9)CNBPP6263319.579INFRBPN/C++++JCVODC9597
Putative rRNA methyltransferase NOP2NOP2P4608789.389INFRBPN++
Fragile X mental retardation syndrome-related protein 1FXR1P5111469.777INFRBPN/C+++
Fragile X mental retardation syndrome-related protein 2FXR2P5111674.247INFRBPN/C++
X-ray repair cross-complementing protein 5XRCC5P1301082.767INFDBPN/C++++
X-ray repair cross-complementing protein 6XRCC6P1295669.856INFDBPN/C++++PDGF2, VEGF98
Heterogeneous nuclear ribonucleoprotein L-likeHNRPLLQ8WVV960.145INFRRMN++
RNA-binding protein 28RBM28Q9NW1385.755INFRRMN/C++
Bcl-2-associated transcription factor 1BCLAF1Q9NYF8106.155INFDBPN/C+++
Histone H2B type 1-DHIST1H2BDP5887613.925INFDBPN+++++
RNA-binding protein EWSEWSR1Q0184468.545INFRRMN/C+++HCVHCV99
Splicing factor, arginine/serine-rich 5SFRS5Q1324331.334INFRRMN+++
Importin subunit alpha-2/karyopherin alpha 2KPNA2P5229257.944INFRBPN/C++++
A-kinase anchor protein 8AKAP8O4382376.144INFDBPN/C++
Nucleolysin TIA-1 isoform p40TIA1P3148343.0310INFRRMN/C++
RNA-binding protein FUSFUSP3563753.4122625.5RRMN/C+++
Polyubiquitin-BUBBP0CG4725.872525N/C++++
Splicing factor, proline- and glutamine-rich (PSF)SFPQP2324676.1152121.0RRMN++++HDVc-Myc92, 100
Zinc finger protein 326ZNF326Q5BKZ165.7101211.5DBPN+++
Zinc finger RNA-binding proteinZFRQ96KR1117.0101111.0RBPN/C++
Zinc finger protein 638ZNF638Q14966220.615188.8RRMN/C+
Heterogeneous nuclear ribonucleoprotein U-like protein 2HNRNPUL2Q1KMD385.115217.0RBPN+++
Heterogeneous nuclear ribonucleoprotein GRBMXP3815942.318355.8RRMN+++
Ras GTPase-activating protein-binding protein 2G3BP2Q9UN8654.1565.5RRMC+++
rRNA 2′-O-methyltransferase fibrillarinFBLP2208733.8565.5RBPN+++
Transcriptional activator protein Pur-alphaPURAQ0057734.9555.0DBPN/C+++
RNA-binding protein 4RBM4Q9BWF340.3894.3RRMN/C+++
Probable ATP-dependent RNA helicase DDX17DDX17Q9284172.423504.1RBPN+++
Heterogeneous nuclear ribonucleoprotein RHNRNPRO4339070.922654.0RRMN/C++++
Zinc finger CCCH-type antiviral protein 1ZC3HAV1Q7Z2W4101.411124.0RBPN/C+++RNA viruses65
Heterogeneous nuclear ribonucleoprotein U (SAF-A)HNRNPUQ0083990.5551383.8RBPN/C++++
Heterogeneous nuclear ribonucleoprotein LHNRNPLP1486664.1251023.5RRMN/C++++HDV, HSV, HCVHCV, Cat-16769, 91, 101
RNA-binding protein 39RBM39Q1449859.4443.5RRMN/C+++
Splicing factor 3B subunit 4SF3B4Q1542744.4343.5RRMN++
Heterogeneous nuclear ribonucleoprotein A0HNRNPA0Q1315130.89113.5RRMN++++
Protein FAM98AFAM98AQ8NCA555.4343.5+++
Peptidyl-prolyl cis-trans-isomerase APPIAP6293718.0343.5N/C+++++
Probable ATP-dependent RNA helicase DDX5DDX5P1784469.128513.4RBPN+++HCV, IAV66, 102
Heterogeneous nuclear ribonucleoprotein D0 (AUF1)HNRNPDQ1410338.417313.4RRMN/C++++
Ubiquitin-associated protein 2-likeUBAP2LQ14157114.59143.4DBPN+++
La-related protein 1LARP1Q6PKG0123.59103.3RBPN/C++
Serine/arginine-rich splicing factor 10SFRS13AO7549431.3573.3RRMN/C++
Splicing factor, arginine/serine-rich 7SFRS7Q1662927.38133.3RRMN++++HSV-1103
RNA-binding protein 47RBM47A0AV9664.1563.0RRMN+
Serine/arginine-rich splicing factor 2SFRS2Q0113025.5393.0RRMN+++
RNA-binding protein RalyRALYQ9UKM932.5563.0RRMN+++
Splicing factor, arginine/serine-rich 9SFRS9Q1324225.5692.8RRMN+++
Nuclease-sensitive element-binding protein 1YBX1P6780935.917512.6RBPN/C++++DENc-Myc92, 104
Splicing factor U2AF 65-kDa subunitU2AF2P2636853.5682.5RRMN++++
Nucleolysin TIARTIAL1Q0108541.613182.5RRMN/C+
Heterogeneous nuclear ribonucleoprotein D-likeHNRPDLO1497946.413292.4RRMN/C++++NRF105, 106
Heterogeneous nuclear ribonucleoprotein A3HNRNPA3P5199139.625432.4RRMN++++
Serine/arginine-rich splicing factor 1 (ASF-1, SF2-P33)SFRS1Q0795527.711192.3RRMN/C++++HDV91
Heterogeneous nuclear ribonucleoprotein U-like protein 1HNRNPUL1Q9BUJ296.015232.3RBPN+++Adenovirus107
Transformer-2 protein homolog betaTRA2BP6299533.7692.3RRMN+++
Serine/arginine-rich splicing factor 6SFRS6Q1324739.68112.2RRMN+++
Heterogeneous nuclear ribonucleoprotein QSYNCRIPO6050669.630642.2RRMN/C++++HCVHCV, BiP108110
Plasminogen activator inhibitor 1 RNA-binding proteinSERBP1Q8NC5145.017222.2RBPN/C++++
  • a The mass spectroscopy was performed on two poliovirus-infected samples, and the data presented represent an average of results between those data sets. The data sets were highly reproducible (see Data Set S1 in the supplemental material).

  • b UniProt-SwissProt accession number.

  • c Average number of unique peptides identified by MS.

  • d Average total number of spectra that were assigned to that protein from the MS analysis.

  • e Average fold increase in total spectra for PV-infected versus mock-infected control. For proteins only detected in the PV-infected samples, fold change is indicated as “infinite” (INF).

  • f Most of the identified host factors are RNA binding proteins (RBP) or have RNA recognition motifs (RRMs), which are indicated in the gene ontology column. Some are DNA binding proteins (DBP). Blank table cells indicate they are not known to bind either RNA or DNA to date.

  • g Cellular localization is indicated as nuclear (N) or cytoplasmic (C). N/C, proteins known to shuttle between the nucleus and the cytoplasm.

  • h Protein abundances according to the Protein Abundance Across Organisms Database (pax-db.org). Abundances are expressed relative to β-actin (5,120 ppm). +++++ represents the range of 9,999 to 1,000 ppm. Stepwise 10-fold decreases down to 0.99 to 0.1 ppm (+) are indicated.

  • i Viruses whose life cycle has been shown to be impacted in some manner by the host factor. HCV, hepatitis C virus; HDV, hepatitis D virus; BDV, Borna disease virus; JCV, JC virus; HSV, herpes simplex virus; IAV, influenza A virus; DEN, dengue virus.

  • j Host factors that have been implicated as an IRES-trans-acting factor (ITAF) for other IRESs are indicated. ODC, ornithine decarboxylase; PDGF2, platelet-derived growth factor 2; VEGF, vascular endothelial growth factor; NRF, nuclear respiratory factor.