N4BP1 uses tandem KH domains to associate with EDC4 and mRNA decapping factors in P-bodies

Processing bodies (P-bodies) are cytoplasmic, non-membrane-bound structures involved in mRNA decay. EDC4 serves as a key scaffold for the decapping complex within P-bodies. Here, we demonstrate that N4BP1 interacts with EDC4, as well as with DCP1A, DCP2, and XRN1 - key components of 5′-cap hydrolysis. Endogenous N4BP1 colocalizes with EDC4 in P-bodies, requiring both of its KH domains. Structural analysis revealed that N4BP1 contains a type-I KH fold but lacks the canonical GXXG motif required for single-stranded RNA binding. Deletion or mutation of KH domains non-canonical GXXG motifs disrupts the N4BP1-EDC4 complex. N4BP1 reduces HIV-1 transcript levels independently of its P-body localization or association with decapping components, implying the involvement of other host factors in regulating viral mRNAs. Similarly, for N4PB1-dependend negative regulation of endogenous transcripts in HaCaT keratinocytes, EDC4 is not essential. For both HIV-1 and endogenous transcripts, the reduction is associated with the activity of the NYN domain.