Ubiquitylation by the GID/CTLH complex regulates the metabolic and innate immune response of macrophages to infection by Mycobacterium tuberculosis

Abstract

The GID/CTLH E3 ligase complex is implicated in several biological processes, yet its full substrate repertoire remains poorly defined. We recently identified the complex as a broad modulator of macrophage responses to Mycobacterium tuberculosis (Mtb) infection. Here, we use label-free proteomics and diGly capture analysis of Mtb-infected macrophages to define the GID/CTLH-dependent ubiquitylome. We identify thousands of dynamically altered ubiquitylation sites, with strong enrichment among proteins involved in cellular metabolism and innate immune signaling. Concurrent proteome analysis revealed extensive rewiring in GID/CTLH-deficient macrophages, with >90% of enriched pathways among increased proteins consisting of metabolic targets. Notably, inhibitory phosphatases (PTEN, INPP5D) also emerged as candidate substrates. Functional studies revealed proteasome-dependent stabilization of PTEN and INPP5D in GID/CTLH-deficient macrophages with each phosphatase individually exerting an influence on Mtb intracellular survival. Together, our study defines a GID/CTLH-dependent ubiquitylome in macrophages and identifies the complex as a central regulator of metabolism and antimicrobial immunity. Author summaryMycobacterium tuberculosis (Mtb), the bacterium that causes tuberculosis (TB), survives and replicates within macrophages, key immune cells that normally eliminate pathogens. How macrophages control their internal cellular environment in response to infection remains incompletely understood. One such important cellular control system is ubiquitylation, in which proteins are tagged with ubiquitin to determine their functional fate or target them for degradation. We recently identified the GID/CTLH E3 ligase ubiquitylation complex as a critical modulator of macrophage antimicrobial responses to Mtb. Here, we used proteomics approaches to define the proteins controlled by the GID/CTLH complex in Mtb-infected macrophages. We found that this complex ubiquitylates a broad network of proteins involved in cellular metabolism and immune signaling. When the complex is disrupted, macrophages undergo extensive metabolic reprogramming, particularly increased mitochondrial energy production, while showing reduced inflammatory signaling. Despite this dampened immune response, these cells are better able to restrict Mtb growth. We also identified the phosphatases PTEN and INPP5D as targets controlled by the GID/CTLH complex that independently influence intracellular bacterial survival. Our findings demonstrate that the GID/CTLH complex is a critical regulator of metabolism and immune function, shaping the outcomes of Mtb infection.