Host Protein General Information (ID: PT0205)
  Protein Name
ATP-dependent RNA helicase A (DHX9)
  Gene Name
DHX9
  Host Species
Homo sapiens
  Uniprot Entry Name
DHX9_HUMAN
  Protein Families
DEAD box helicase family
  EC Number
3.6.4.13
  Subcellular Location
Nucleus; nucleoplasm Nucleus
  External Link
NCBI Gene ID
1660
Uniprot ID
Q08211
Ensembl ID
ENSG00000135829
HGNC ID
HGNC:2750
  Function in Host
Multifunctional ATP-dependent nucleic acid helicase thatunwinds DNA and RNA in a 3' to 5' direction and that plays importantroles in many processes, such as DNA replication, transcriptionalactivation, post-transcriptional RNA regulation, mRNA translation andRNA-mediated gene silencing. Requires a 3'-single-stranded tailas entry site for acid nuclei unwinding activities as well as thebinding and hydrolyzing of any of the four ribo- or deoxyribo-nucleotide triphosphates (NTPs). Unwinds numerousnucleic acid substrates such as double-stranded (ds) DNA and RNA, DNA:RNA hybrids, DNA and RNA forks composed of either partiallycomplementary DNA duplexes or DNA:RNA hybrids, respectively, and alsoDNA and RNA displacement loops (D- and R-loops), triplex-helical DNA (H-DNA) structure and DNA and RNA-based G-quadruplexes. Binds dsDNA, single-stranded DNA (ssDNA), dsRNA, ssRNA and poly (A) -containing RNA. Binds also to circular dsDNA ordsRNA of either linear and/or circular forms and stimulates therelaxation of supercoiled DNAs catalyzed by topoisomerase TOP2A. Plays a role in DNA replication at origins ofreplication and cell cycle progression. Plays a roleas a transcriptional coactivator acting as a bridging factor betweenpolymerase II holoenzyme and transcription factors or cofactors, suchas BRCA1, CREBBP, RELA and SMN1. Binds to the CDKN2A promoter. Playsseveral roles in post-transcriptional regulation of gene expression. In cooperation with NUP98, promotespre-mRNA alternative splicing activities of a subset of genes. As component of a large PER complex, is involved in the negativeregulation of 3' transcriptional termination of circadian target genessuch as PER1 and NR1D1 and the control of the circadian rhythms. Acts also as a nuclear resolvase that is able to bind andneutralize harmful massive secondary double-stranded RNA structuresformed by inverted-repeat Alu retrotransposon elements that areinserted and transcribed as parts of genes during the process of genetransposition. Involved in the positive regulation ofnuclear export of constitutive transport element (CTE) -containingunspliced mRNA. Component of the coding region determinant (CRD) -mediated complex thatpromotes cytoplasmic MYC mRNA stability. Plays a rolein mRNA translation. Positively regulates translationof selected mRNAs through its binding to post-transcriptional controlelement (PCE) in the 5'-untranslated region (UTR). Involved with LARP6 in the translation stimulation of type I collagenmRNAs for CO1A1 and CO1A2 through binding of a specific stem-loopstructure in their 5'-UTRs. Stimulates LIN28A-dependent mRNA translation probably by facilitating ribonucleoproteinremodeling during the process of translation. Playsalso a role as a small interfering (siRNA) -loading factor involved inthe RNA-induced silencing complex (RISC) loading complex (RLC) assembly, and hence functions in the RISC-mediated gene silencingprocess. Binds preferentially to short double-stranded RNA, such as those produced during rotavirus intestinalinfection. This interaction may mediate NLRP9inflammasome activation and trigger inflammatory response, includingIL18 release and pyroptosis. Finally, mediates theattachment of heterogeneous nuclear ribonucleoproteins (hnRNPs) toactin filaments in the nucleus. [1-6]
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  3D Structure

Function of This Protein During Virus Infection
Virus NameSARS-COV-2 Protein Function Pro-viral [7]
Infected TissueColon Infection Time48 h
Infected CellCaco-2 cells (Human colorectal adenocarcinoma cell) Cellosaurus IDCVCL_0025 
Method DescriptionTo detect the role of host protein DHX9 in viral infection, DHX9 protein knockout Caco-2 cells were infected with SARS-COV-2 for 48 h , and the effects on infection was detected through qPCR.
ResultsIt is reported that Knockdown of DHX9 leads to the reduced the vRNA levels compared with control group.

Host Protein - Virus RNA Network

 Full List of Virus RNA Interacting with This Protien
            RNA Region: 3'-UTR (hCoV-19/Not Specified Virus Strain )
              RNA Region Details RNA Info Click to show the detail information of this RNA binding region [8]
              Strains Name
hCoV-19/Not Specified Virus Strain
              RNA Binding Region
3'-UTR
              Virus Name
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)
              Infection Cells Huh7 cells (human liver cell line); Calu-3 cells (human lung cancer cell line)  (CVCL_0336;CVCL_0609 )
              Cell Originated Tissue Liver; Lung
              Interaction Score P-value < 0.05
              Method Description RNA pull-down assays; liquid chromatography with tandem mass spectrometry (LC-MS/MS); Wilcoxon test; MS2 affinity purification coupled with liquid chromatography-mass spectrometry (MAMS)
           RNA Region: 3'-UTR (hCoV-19/IPBCAMS-YL01/2020 )
              RNA Region Details RNA Info Click to show the detail information of this RNA binding region [7]
              Strains Name
hCoV-19/IPBCAMS-YL01/2020
              Strains Family
Beta (B.1.351)
              RNA Binding Region
3'-UTR
              Virus Name
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)
              Interaction Type Potiential to be direct binder
              Interaction Binding Type double stranded RNA binding
              Infection Cells Huh7.5.1 cells (Hepatocyte derived cellular carcinoma cell) Huh7.5.1 cells (Hepatocyte derived cellular carcinoma cell)  (CVCL_E049 )
              Cell Originated Tissue Liver
              Infection Time 30 h
              Interaction Score MIST = 0.805456376
              Method Description comprehensive identification of RNA-binding proteins by massspectrometry (ChIRP-MS)
           RNA Region: 5'-UTR (hCoV-19/Not Specified Virus Strain )
              RNA Region Details RNA Info Click to show the detail information of this RNA binding region [8]
              Strains Name
hCoV-19/Not Specified Virus Strain
              RNA Binding Region
5'-UTR
              Virus Name
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)
              Infection Cells Huh7 cells (human liver cell line); Calu-3 cells (human lung cancer cell line) Huh7 cells (human liver cell line); Calu-3 cells (human lung cancer cell line)  (CVCL_0336;CVCL_0609 )
              Cell Originated Tissue Liver; Lung
              Interaction Score P-value < 0.05
              Method Description RNA pull-down assays; liquid chromatography with tandem mass spectrometry (LC-MS/MS); Wilcoxon test; MS2 affinity purification coupled with liquid chromatography-mass spectrometry (MAMS)
           RNA Region: ORF10 (hCoV-19/Not Specified Virus Strain )
              RNA Region Details RNA Info Click to show the detail information of this RNA binding region [8]
              Strains Name
hCoV-19/Not Specified Virus Strain
              RNA Binding Region
ORF10
              Virus Name
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)
              Infection Cells Huh7 cells (human liver cell line) Huh7 cells (human liver cell line)  (CVCL_0336 )
              Cell Originated Tissue Liver
              Interaction Score P-value < 0.05
              Method Description RNA pull-down assays; liquid chromatography with tandem mass spectrometry (LC-MS/MS); Wilcoxon test; MS2 affinity purification coupled with liquid chromatography-mass spectrometry (MAMS)
           RNA Region: ORF10 (hCoV-19/Not Specified Virus Strain )
              RNA Region Details RNA Info Click to show the detail information of this RNA binding region [8]
              Strains Name
hCoV-19/Not Specified Virus Strain
              Strains Family
Beta (B.1.351)
              RNA Binding Region
ORF10
              Virus Name
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)
              Infection Cells Huh7 cells (human liver cell line); Calu-3 cells (human lung cancer cell line) Huh7 cells (human liver cell line); Calu-3 cells (human lung cancer cell line)  (CVCL_0336;CVCL_0609 )
              Cell Originated Tissue Liver; Lung
              Interaction Score P-value < 0.05
              Method Description RNA pull-down assays; liquid chromatography with tandem mass spectrometry (LC-MS/MS); Wilcoxon test; MS2 affinity purification coupled with liquid chromatography-mass spectrometry (MAMS)
           RNA Region: Not Specified Virus Region (hCoV-19/USA/WA1/2020 )
              RNA Region Details RNA Info Click to show the detail information of this RNA binding region [9]
              Strains Name
hCoV-19/USA/WA1/2020
              Strains Family
Alpha (B.1.1.7)
              RNA Binding Region
Not Specified Virus Region
              Virus Name
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)
              Infection Cells Huh7.5 cells (Hepatocyte derived cellular carcinoma cell) Huh7.5 cells (Hepatocyte derived cellular carcinoma cell)  (CVCL_7927 )
              Cell Originated Tissue Liver
              Infection Time 48 h
              Interaction Score FDR ≤ 0.05
              Method Description comprehensive identification of RNA-binding proteins by massspectrometry (ChIRP-MS)
           RNA Region: Not Specified Virus Region (hCoV-19/France/IDF-220-95/2020 )
              RNA Region Details RNA Info Click to show the detail information of this RNA binding region [10]
              Strains Name
hCoV-19/France/IDF-220-95/2020
              RNA Binding Region
Not Specified Virus Region
              Virus Name
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)
              Interaction Type Direct interaction
              Infection Cells HEK293 Cells (Human embryonic kidney cell) HEK293 Cells (Human embryonic kidney cell)  (CVCL_0045 )
              Cell Originated Tissue Kidney
              Infection Time 48 h
              Interaction Score SAINT score ≥ 0.79
              Method Description comprehensive identification of RNA-binding proteins by massspectrometry (ChIRP-MS)

Differential Gene Expression During SARS-COV-2 Infection
GEO Accession: GSE152641
Sample Type: Blood
Samples Details: Healthy Control: 24; COVID-19: 62
Platform: GPL24676 Illumina NovaSeq 6000
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GEO Accession: GSE162835
Sample Type: Nasopharyngeal Swabs
Samples Details: COVID-19 (Mild Symptoms): 37; COVID-19 (Moderate Symptoms): 10; COVID-19 (Severe Symptoms): 3
Platform: GPL24676 Illumina NovaSeq 6000
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GEO Accession: GSE175779
Sample Type: Human Bronchial Epithelial Cells
Samples Details: Healthy Control: 4 (0, 24, 48, 72 and 96 h); COVID-19: 4 (24, 48, 72 and 96 h)
Platform: GPL18573 Illumina NextSeq 500
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Protein Phosphorylation after Virus Infection
S321 [11]
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S688 [11]
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S87 [11]
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T108 [11]
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T92 [11]
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T94 [11]
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T98 [11]
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Protein Sequence Information
MGDVKNFLYAWCGKRKMTPSYEIRAVGNKNRQKFMCEVQVEGYNYTGMGNSTNKKDAQSNAARDFVNYLVRINEIKSEEVPAFGVASPPPLTDTPDTTANAEGDLPTTMGGPLPPHLALKAENNSEVGASGYGVPGPTWDRGANLKDYYSRKEEQEVQATLESEEVDLNAGLHGNWTLENAKARLNQYFQKEKIQGEYKYTQVGPDHNRSFIAEMTIYIKQLGRRIFAREHGSNKKLAAQSCALSLVRQLYHLGVVEAYSGLTKKKEGETVEPYKVNLSQDLEHQLQNIIQELNLEILPPPEDPSVPVALNIGKLAQFEPSQRQNQVGVVPWSPPQSNWNPWTSSNIDEGPLAFATPEQISMDLKNELMYQLEQDHDLQAILQERELLPVKKFESEILEAISQNSVVIIRGATGCGKTTQVPQFILDDFIQNDRAAECNIVVTQPRRISAVSVAERVAFERGEEPGKSCGYSVRFESILPRPHASIMFCTVGVLLRKLEAGIRGISHVIVDEIHERDINTDFLLVVLRDVVQAYPEVRIVLMSATIDTSMFCEYFFNCPIIEVYGRTYPVQEYFLEDCIQMTHFVPPPKDKKKKDKDDDGGEDDDANCNLICGDEYGPETRLSMSQLNEKETPFELIEALLKYIETLNVPGAVLVFLPGWNLIYTMQKHLEMNPHFGSHRYQILPLHSQIPREEQRKVFDPVPVGVTKVILSTNIAETSITINDVVYVIDSCKQKVKLFTAHNNMTNYATVWASKTNLEQRKGRAGRVRPGFCFHLCSRARFERLETHMTPEMFRTPLHEIALSIKLLRLGGIGQFLAKAIEPPPLDAVIEAEHTLRELDALDANDELTPLGRILAKLPIEPRFGKMMIMGCIFYVGDAICTIAAATCFPEPFINEGKRLGYIHRNFAGNRFSDHVALLSVFQAWDDARMGGEEAEIRFCEHKRLNMATLRMTWEAKVQLKEILINSGFPEDCLLTQVFTNTGPDNNLDVVISLLAFGVYPNVCYHKEKRKILTTEGRNALIHKSSVNCPFSSQDMKYPSPFFVFGEKIRTRAISAKGMTLVTPLQLLLFASKKVQSDGQIVLVDDWIKLQISHEAAACITGLRAAMEALVVEVTKQPAIISQLDPVNERMLNMIRQISRPSAAGINLMIGSTRYGDGPRPPKMARYDNGSGYRRGGSSYSGGGYGGGYSSGGYGSGGYGGSANSFRAGYGAGVGGGYRGVSRGGFRGNSGGDYRGPSGGYRGSGGFQRGGGRGAYGTGYFGQGRGGGGY
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References
1 A new RNA helicase isolated from HeLa cells that catalytically translocates in the 3 to 5 direction. J Biol Chem. 1992 Mar 5;267(7):4398-407.
2 DHX9 helicase is involved in preventing genomic instability induced by alternatively structured DNA in human cells. Nucleic Acids Res. 2013 Dec;41(22):10345-57.
3 Human DHX9 helicase preferentially unwinds RNA-containing displacement loops (R-loops) and G-quadruplexes. DNA Repair (Amst). 2011 Jun 10;10(6):654-65.
4 Human DHX9 helicase unwinds triple-helical DNA structures. Biochemistry. 2010 Aug 24;49(33):6992-9.
5 Pre-mRNA and mRNA binding of human nuclear DNA helicase II (RNA helicase A). J Cell Sci. 1999 Apr;112 ( Pt 7):1055-64.
6 Domain structure of human nuclear DNA helicase II (RNA helicase A). J Biol Chem. 1997 Apr 25;272(17):11487-94.
7 Comparison of viral RNA-host protein interactomes across pathogenic RNA viruses informs rapid antiviral drug discovery for SARS-CoV-2. Cell Res. 2022 Jan;32(1):9-23.
8 Mapping the host protein interactome of non-coding regions in SARS-CoV-2 genome. bioRxiv. 2021 Jun; DOI:10.1101/2021.06.19.449092.
9 Discovery and functional interrogation of SARS-CoV-2 RNA-host protein interactions. Cell. 2021 Apr 29;184(9):2394-2411.e16.
10 Characterization and functional interrogation of the SARS-CoV-2 RNA interactome. Cell Rep. 2022 Apr 26;39(4):110744.
11 Multilevel proteomics reveals host perturbations by SARS-CoV-2 and SARS-CoV. Nature. 2021 Jun;594(7862):246-252.