Pathways of nucleic acid metabolism and innate immune sensing (Homo sapiens)

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DNA damageDNAreplicationNucleotideexcision repairRibonucleotideexcision repairByproducts of DNA repairType I IFN activiationNucleusRNA degradationDegradationDNA sensing pathway led by cGASUV lightmRNAOAS1DDX58RNase LdsDNADNASAMHD1MAVSdNTP poolsIRF3RNase H2subunit AdsRNATMEM173IFIH1RetroelementcGASIFNBSTINGTREX1ADARAdenosine12, 3cDNAMDA5RIG-IdNssDNAssDNADNATRTRNase H2subunit BRNase H2subunit CDNARssDNAssDNASAMHD1dsRNAAdsRNAIdsRNAInosineshortdsRNAfragmentsRNA sensing pathways led by MDA5 and RIG-IIRF3PISGs


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Bibliography

  1. Cho DS, Yang W, Lee JT, Shiekhattar R, Murray JM, Nishikura K; ''Requirement of dimerization for RNA editing activity of adenosine deaminases acting on RNA.''; J Biol Chem, 2003 PubMed Europe PMC Scholia
  2. Patterson JB, Samuel CE; ''''; , PubMed Europe PMC Scholia
  3. Deininger PL, Batzer MA; ''Mammalian retroelements.''; Genome Res, 2002 PubMed Europe PMC Scholia

History

View all...
CompareRevisionActionTimeUserComment
128779view23:35, 21 February 2024EweitzUse standard shape for clickable pathways
128778view23:32, 21 February 2024EweitzRemove unnecessary background color, standardize case
123423view06:18, 26 July 2022EgonwMade a pathway clickable
119081view08:58, 16 June 2021DeSlUpdated sNTP pools ID
119080view05:36, 16 June 2021EgonwNot a mim-conversion
119064view07:46, 14 June 2021DeSlConverted last DNA and retroelement to RNA DataNodes
119063view07:44, 14 June 2021DeSlConverted some more Metabolites to RNA
119062view07:42, 14 June 2021DeSlUpdated some metabolites to RNA
118976view05:14, 6 June 2021EgonwdsRna is Rna
110737view09:55, 30 May 2020EgonwNot a mim-conversion
110687view13:32, 28 May 2020LaurentUpdated types of data nodes where type was missing
107300view12:13, 19 September 2019DeSlModified description
107299view12:12, 19 September 2019DeSlAdded missing IDs
107298view12:06, 19 September 2019DeSlOntology Term : 'altered DNA repair pathway' added !
107297view12:06, 19 September 2019DeSlOntology Term : 'signaling pathway in the innate immune response' added !
107296view12:05, 19 September 2019DeSlModified description
107295view12:00, 19 September 2019DeSlAdded rRNA part
107294view11:50, 19 September 2019DeSlAdded background colours, added Lysosome
107293view11:43, 19 September 2019DeSlAdded IFNB and ISGs
107291view11:37, 19 September 2019DeSlAdded phosphorylation of the transcription factor interferon regulatory factor 3 (IRF3)
107290view11:33, 19 September 2019DeSlCompleted right hand side of PW
107286view08:35, 19 September 2019DeSlAdded more details on dsRNA interaction with MDA5
107183view14:27, 17 September 2019MaintBotChEBI identifier normalization
106678view15:09, 16 September 2019DeSlAdded more details on NER and RER
106677view14:35, 16 September 2019DeSlNew pathway

External references

DataNodes

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NameTypeDatabase referenceComment
ADARProteinP55265 (Uniprot-TrEMBL) Catalyzes the hydrolytic deamination of adenosine to inosine in double-stranded RNA (dsRNA) referred to as A-to-I RNA editing
AdenosineMetabolite74411 (ChEBI)
DDX58GeneProductENSG00000107201 (Ensembl)
DNA replicationPathwayWP466 (WikiPathways)
DNA sensing pathway led by cGASPathway
DNAQ7430 (Wikidata)
IFIH1GeneProductENSG00000115267 (Ensembl)
IFNBGeneProductENSG00000171855 (Ensembl)
IRF3ProteinQ14653 (Uniprot-TrEMBL)
ISGsProteinIPR000471 (InterPro) interferon-responsive genes
InosineMetabolite82852 (ChEBI)
MAVSProteinQ7Z434 (Uniprot-TrEMBL) mitochondrial antiviral signaling (MAVS)
MDA5ProteinQ9BYX4 (Uniprot-TrEMBL)
  • Cytosolic RNA sensor
  • Activating mutations in RIG-I and MDA5 increase receptor affinity resulting in constitutive type I IFN signaling.
Nucleotide

excision

repair		PathwayWP1980 (WikiPathways) The presence of ribonucleotides in genomic DNA enhances photodimerization of adjacent pyrimidines, which are repaired by nucleotide excision repair
OAS1ProteinP00973 (Uniprot-TrEMBL)
RIG-IProteinO95786 (Uniprot-TrEMBL)
  • cytosolic RNA sensor
  • Activating mutations in RIG-I and MDA5 increase receptor affinity resulting in constitutive type I IFN signaling.
RNA sensing pathways led by MDA5 and RIG-IPathway
RNase H2 subunit AProteinO75792 (Uniprot-TrEMBL) Catalytic subunit
RNase H2 subunit BProteinQ5TBB1 (Uniprot-TrEMBL) Noncatalytic subunit
RNase H2 subunit CProteinNoncatalytic subunit
RNase LProteinQ05823 (Uniprot-TrEMBL)
RetroelementQ1473344 (Wikidata)
SAMHD1ProteinQ9Y3Z3 (Uniprot-TrEMBL) SAMHD1 has also ribonuclease activity, suggesting that a loss of SAMHD1 may lead to RNA accumulation.
STINGProteinQ86WV6 (Uniprot-TrEMBL)
TMEM173GeneProductcGAS which signals via STING (encoded by TMEM173)
TREX1ProteinQ9NSU2 (Uniprot-TrEMBL) Cytosolic deoxyribonuclease anchored in the outer nuclear membrane. A lack of TREX1 causes DNA accumulation, both within the nucleus and the cytosol.
cDNAQ283478 (Wikidata) Single-stranded complementary DNA synthesized from an RNA template by the action of RNA-dependent DNA polymerase.
cGASProteinQ8N884 (Uniprot-TrEMBL) DNA sensor
dNMetaboliteCHEBI:18274 (ChEBI)
dNTP poolsMetaboliteCHEBI:46149 (ChEBI)
dsDNAQ55978910 (Wikidata)
dsRNAQ2819370 (Wikidata)
mRNAQ188928 (Wikidata)
short

dsRNA

fragments		Q2819370 (Wikidata)
ssDNAQ10906438 (Wikidata) single-stranded DNA

Annotated Interactions

SourceTargetTypeDatabase referenceComment
dNTP poolsdNmim-conversion46149 (Rhea) SAMHD1 degrades deoxynucleoside triphosphates (dNTP)
dsRNAdsRNAmim-conversion10121 (Rhea) ADAR modifies dsRNA through deamination of adenosine to inosine
Retrieved from "https://classic.wikipathways.org/index.php/Pathway:WP4705"
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