Nuclear protein LEDGF/p75 recognizes supercoiled DNA by a novel DNA-binding domain

Abstract

Lens epithelium-derived growth factor (LEDGF) or p75 is a co-activator of general transcription and also involved in insertion of human immunodeficiency virus type I (HIV-1) cDNA into host cell genome, which occurs preferentially to active transcription units. These phenomena may share an underlying molecular mechanism in common. We report here that LEDGF/p75 binds negatively supercoiled DNA selectively over unconstrained DNA. We identified a novel DNA-binding domain in the protein and termed it ‘supercoiled DNA-recognition domain’ (SRD). Recombinant protein fragments containing SRD showed a preferential binding to supercoiled DNA in vitro. SRD harbors a characteristic cluster of lysine and glutamic/aspartic acid residues. A polypeptide mimicking the cluster (K9E9K9) also showed this specificity, suggesting that the cluster is an essential element for the supercoil recognition. eGFP-tagged LEDGF/p75 expressed in the nucleus distributed partially in transcriptionally active regions that were identified by immunostaining of methylated histone H3 (H3K4me3) or incorporation of Br-UTP. This pattern of localization was observed with SRD alone but abolished if the protein lacked SRD. Thus, these results imply that LEDGF/p75 guides its binding partners, including HIV-1 integrase, to the active transcription site through recognition of negative supercoils generated around it.

Role of the PWWP Domain of Lens Epithelium-derived Growth Factor (LEDGF)/p75 Cofactor in Lentiviral Integration Targeting

“…3) (19,36,37,68), and loss of interaction with mitotic chromatin (19,37). The PWWP domain of LEDGF/p75 appears to exert a dominant effect on the protein intranuclear localization, excluding it from the nucleoli (19,46,68,74). Nucleolar localization is not a default pathway; current understanding suggests that interaction with nucleolar hub proteins is required (75,76).…”

Epigenetic repression of LEDGF during UVB exposure by recruitment of SUV39H1 and HDAC1 to the Sp1-responsive elements within LEDGF promoter CpG island

“…20 Recently, LEDGF was found to selectively bind to supercoiled DNA and to recruit its binding partners to active transcription units. 21 In addition, LEDGF also exerts biological activity by interacting with many proteins such as Myc-interacting protein JPO2 22 and mixed-lineage leukemia (MLL)/menin complex, 23 a domesticated transposase PogZ (pogo transposable element derived protein with zinc finger), 24 Cdc7-activator of S-phase kinase (ASK), 25 methyl CpG Binding Protein MeCP2 26 and its integrase binding domain (IBD; residues 347 to 429) to integrase. 1 More recently, sumoylation has been identified in LEDGF protein.…”

Lessons Learned: HIV Points the Way Towards Precision Treatment of Mixed-Lineage Leukemia

“…PSIP1 (PC4-and SFRS-interacting protein 1), the gene encoding LEDGF/ p75, also codes for an alternative splice variant (p52) sharing its N-terminal region [amino acids (aa) 1-325] with LEDGF/p75. This region comprises the PWWP domain, the nuclear localization signal (NLS), the A/T hook-like elements, and the supercoil recognition domain (SRD) (Figure 1) [8,13,14]. The unique C-terminal portion of LEDGF/p75 contains an additional 205 aa [1,15].…”