Dataset Information

Cellular Targets and the Lysine Selectivity of the HERC5 ISG15 Ligase

ABSTRACT: ISG15 is a type I interferon-induced ubiquitin-like protein modifier that functions in innateimmune responses. The single major human ISG15 ligase is HERC5 (hHERC5), a ribosome-associated HECT E3s that broadly ISGylates proteins cotranslationally. Here, we characterized the hHERC5-dependent ISGylome and identified over 5,000 modified lysines in over 2,000 proteins. In parallel, we characterized the substrate selectivity of the major mouse ISG15 ligase, mHERC6, and analysis of sequences surrounding ISGylation sites revealed that hHERC5 and mHERC6 have distinct preferences for amino acid sequence context. Several features of the datasets were consistent with ISGylation of ribosome-tethered nascent chains, and mHERC6, like hHERC5, associated with polysomes and cotranslationally modified nascent polypeptides. Like many genes encoding innate immune effectors, the hHERC5 and mHERC6 genes are under positive genetic selection and we propose that the differing lysine selectivities of these ligases may reflect species-specific adaptations to pathogen challenges experienced over evolutionary timeframes.

INSTRUMENT(S): Orbitrap Fusion

ORGANISM(S): Homo Sapiens (human)

SUBMITTER: Peter Faull

LAB HEAD: Jon M Huibregtse

PROVIDER: PXD044834 | Pride | 2024-03-05

REPOSITORIES: Pride

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Publications

Cellular targets and lysine selectivity of the HERC5 ISG15 ligase.

Zhao Xu X Perez Jessica M JM Faull Peter A PA Chan Catherine C Munting Femke W FW Canadeo Larissa A LA Cenik Can C Huibregtse Jon M JM

iScience 20240109 2

ISG15 is a type I interferon-induced ubiquitin-like modifier that functions in innate immune responses. The major human ISG15 ligase is hHERC5, a ribosome-associated HECT E3 that broadly ISGylates proteins cotranslationally. Here, we characterized the hHERC5-dependent ISGylome and identified over 2,000 modified lysines in over 1,100 proteins in IFN-β-stimulated cells. In parallel, we compared the substrate selectivity hHERC5 to the major mouse ISG15 ligase, mHERC6, and analysis of sequences surr ...[more]

PMID: 38303729

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Project description:Maintaining the integrity of nucleic acids is an essential feature of all organisms. Unwanted modification of DNA, if left unrepaired, is deleterious to cellular homeostasis and could have far-reaching consequences that include genomic instability and accumulation of mutations. Similarly, accumulation of damaged RNA has been correlated with various neurodegenerative diseases. Given their inherent reactivity, nucleic acids are susceptible to damage from both endogenous and exogenous reactive oxygen species (ROS) as well as alkylation agents. We have recently begun to address how some of these modifications on mRNA impact the function of the ribosome and in particular the decoding process. We find that most modifications severely change the speed and accuracy of translation. These observations revealed that oxidation of RNA is most likely to stall the ribosome and necessitates the presence of quality-control processes to handle damaged mRNA. To this end, we have uncovered a connection between the process of no-go decay (NGD), which degrades mRNAs that stall translation, and chemical insults. In the absence of key NGD factors in yeast, the levels of damaged mRNA significantly increase and cells are rendered sensitive to oxidizing and alkylation agents. Furthermore, these agents activate ribosome quality control (RQC) of nascent peptides. Deletion of the E3 ligase responsible for the ubiquitination of the nascent peptides resulted in the accumulation of protein aggregates in the presence of oxidizing and alkylating agents. These observations suggest that chemical damage stalls translation, activating NGD and RQC. Interestingly, the addition of nucleic-acids-damaging agents was also found to result in K63-linked ubiquitination of ribosomal proteins. This signaling-mode of ubiquitination precedes DNA-damage marks, indicating that cells respond to RNA damage due to stalled ribosomes before DNA damage. Collectively our data highlights the burden of chemically-damaged mRNA on cellular homeostasis and suggests that organisms evolved ribosome-based mRNA-surveillance processes to rapidly degrade it.

Dataset Information

Cellular Targets and the Lysine Selectivity of the HERC5 ISG15 Ligase

Publications

Cellular targets and lysine selectivity of the HERC5 ISG15 ligase.

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