The molecular basis for selective assembly of the UBAP1-containing, endosome-specific ESCRT-I complex

Abstract

ESCRT-I is essential for the multivesicular body (MVB) sorting of ubiquitylated cargo such as epidermal growth factor receptor, as well as for several cellular functions, such as cell division and retroviral budding. ESCRT-I has four subunits; TSG101, VPS28, VPS37 and MVB12. There are several members of VPS37 and MVB12 families in mammalian cells, and their differential incorporation into ESCRT-I could provide function-specific variants of the complex. However, it remains unclear whether these different forms of VPS37 and MVB12 combine randomly or generate selective pairings within ESCRT-I, and what the mechanistic basis for such pairing would be. Here, we show that the incorporation of two MVB12 members, UBAP1 and MVB12A, into ESCRT-I is highly selective with respect to their VPS37 partners. We map the region mediating selective assembly of UBAP1–VPS37A to the core ESCRT-I-binding domain of VPS37A. In contrast, selective integration of UBAP1 requires both the minimal ESCRT-I-binding region and a neighbouring predicted helix. The biochemical specificity in ESCRT-I assembly is matched by functional specialisation as siRNA-mediated depletion of UBAP1, but not MVB12A and MVB12B, disrupts ubiquitin-dependent sorting at the MVB.

Structural Basis for Selective Interaction between the ESCRT Regulator HD-PTP and UBAP1

“…In contrast, HD-PTP function is largely restricted to the early endosome (Doyotte et al., 2008, Parkinson et al., 2015) where it acts in close cooperation with ESCRT-0 (Ali et al., 2013) and UBAP1 (ESCRT-I) to downregulate multiple ubiquitinated cargoes (Agromayor et al., 2012, Kharitidi et al., 2015). UBAP1 is an ubiquitin-binding ESCRT-I subunit that acts exclusively in MVB sorting (Stefani et al., 2011, Wunderley et al., 2014) and, like for HD-PTP (Cheng et al., 1998, Toyooka et al., 2000), haploinsufficiency of UBAP1 is linked to nasopharyngeal carcinoma (Qian et al., 2001). UBAP1 is also a risk factor for familial frontotemporal lobar degeneration (Rollinson et al., 2009).…”

Truncating variants in UBAP1 associated with childhood‐onset nonsyndromic hereditary spastic paraplegia

“…It is a component of the endosome‐specific endosomal sorting complexes required for transport‐I (ESCRT‐I) complex that functions to sort ubiquitylated cargo such as epidermal growth factor receptor to the multivesicular body (MVB) and for endosomal ubiquitin homeostasis (Stefani et al, ). There are two functionally critical domains in UBAP1—the UMA (UBAP1‐MVB12‐associated) domain for ESCRT‐I binding near the N‐terminus (de Souza & Aravind, ; Wunderley, Brownhill, Stefani, Tabernero, & Woodman, ), and the solenoid of overlapping ubiquitin‐associated (SOUBA) domains for ubiquitin interaction near the C‐terminus (Agromayor et al, ; Figure a). The two predicted truncated proteins reported in this study and all proteins reported by Farazi Fard et al have an intact UMA domain while lacking the SOUBA domains.…”

Concurrent depletion of Vps37 proteins evokes ESCRT-I destabilization and profound cellular stress responses

“…We speculated that the type and magnitude of transcriptional responses after individual and concurrent silencing of VPS37 paralogs might be attributed to distinct ESCRT-I stability. It was previously shown that knockdown of some ESCRT-I core components induced partial or complete degradation of other complex subunits (Stefani et al, 2011;Wunderley et al, 2014); yet, a detailed characterization of all ESCRT-I subunits after individual and concurrent Vps37 proteins depletion has not been performed so far.…”

“…ESCRT-I is a heterotetramer composed of three core components (Tsg101, Vps28 and one of four Vps37 family members) and a single auxiliary protein (UBAP-1, Mvb12A or Mvb12B) (Stefani et al, 2011;Wunderley et al, 2014). At least under some conditions two of its subunits (Tsg101 and Vps37A) have been identified as putative tumor suppressors (Li and Cohen, 1996;Moberg et al, 2005;Xu et al, 2003).…”