Biology subjects

Kong, K.-Y. E.

Publications and source records attributed to Kong, K.-Y. E..

3 recordsLinked to original sources

bioRxiv2026

Molecular basis for C-degron recognition by the SCFDas1 ubiquitin ligase

Selective protein degradation by the ubiquitin-proteasome system frequently involves substrate recognition via short linear motifs known as degradation signals or degrons. Whereas degrons located at protein N-termini (N-degrons) have been extensively studied, our understanding of C-terminal degrons (C-degrons) is comparatively limited. Previously, we showed that the yeast SCF ubiquitin ligase and one of its substrate receptor subunits, the F-box protein Das1, target a broad range of C-degrons and implicated SCFDas1 in orphan quality control. Here, we sought to determine how Das1 recognizes its substrates. By combining in vivo competition assays with structural modeling and mutational analysis, we demonstrate that distinct C-degrons compete for a common site on Das1, indicating a shared mode of recognition. We identify a positively charged pocket within the Das1 leucine-rich repeat domain as the C-degron binding site. Three basic residues at the base of this pocket are essential for Das1 function, likely mediating electrostatic interactions with the C-terminal carboxyl group of the degron, while additional residues contribute to substrate specificity. Comparative analysis reveals that this pocket and its function are conserved across the Saccharomycetaceae family, supporting a conserved role for Das1 in protein quality control.

biochemistry↗

bioRxiv2025

Bidirectional control of a metabolic transition by the GID ubiquitin ligase

The GID/CTLH ubiquitin ligase is a multisubunit E3 conserved across eukaryotes. GID/CTLH has been implicated in a variety of processes, including metabolic regulation, cell proliferation, embryonic development and cell differentiation. However, our understanding of substrate recognition by GID/CTLH remains incomplete. Here, we characterize the regulation, specificity and functions of the putative substrate receptor Gid11 in budding yeast. We find that upon its expression during the switch of carbon source from glucose to ethanol, Gid11 associates with the core GID complex, likely forming a large ring assembly. Through systematic mutagenesis, we identify a negatively charged pocket on Gid11 that binds substrates carrying N-terminal degrons starting with threonine and define the Thr/N-degron motif. Such Thr/N-degrons are exposed upon co-translational removal of the initiator methionine, while escaping N-terminal acetylation. Finally, we show that during the switch to ethanol, GIDGid11 targets for degradation factors linked to glycolysis, opposing the established role of GID in the degradation of gluconeogenic enzymes during the reverse switch from ethanol to glucose. Taken together, our results establish Gid11 as a bona fide GID substrate receptor and highlight GID as a regulator of metabolic transitions.

molecular biology↗

bioRxiv2023

Orphan quality control by an SCF ubiquitin ligase directed to pervasive C-degrons

Selective protein degradation typically involves substrate recognition via short linear motifs known as degrons. Various degrons can be found at protein termini from bacteria to mammals. While N-degrons have been extensively studied, our understanding of C-degrons is still limited. Towards a comprehensive understanding of eukaryotic C-degron pathways, we performed an unbiased survey of C-degrons in budding yeast. We identified over 5000 potential C-degrons by stability profiling of random peptide libraries and of the yeast C-terminome. Combining machine learning, high-throughput mutagenesis and genetic screens revealed that the SCF ubiquitin ligase targets [~]40% of degrons using a single F-box substrate receptor Das1. Although sequence-specific, Das1 is highly promiscuous, recognizing a variety of C-degron motifs. By screening for endogenous substrates, we implicate SCFDas1 in degradation of orphan protein complex subunits. Altogether, this work provides a comprehensive view of a eukaryotic C-degronome and uncovers how an SCF/C-degron pathway of broad specificity contributes to proteostasis.

molecular biology↗