Biology subjects

Akkermans, J. J. L. L.

Publications and source records attributed to Akkermans, J. J. L. L..

4 recordsLinked to original sources

bioRxiv2024

USP24 is an ISG15 cross-reactive deubiquitinasethat mediates IFN-I production by de-ISGylatingthe RNA helicase MOV10

The interferon-stimulated gene 15 (ISG15) is a ubiquitin-like modifier induced by type I Interferon (IFN-I) and plays a crucial role in the innate immune response against viral infections. ISG15 is conjugated to target proteins by an enzymatic cascade through a process called ISGylation. While ubiquitin-specific protease 18 (USP18) is a well-defined deISGylase counteracting ISG15 conjugation, ISG15 cross-reactive deubiquitylating enzymes (DUBs) have also been reported. Our study reports USP24 as a novel ISG15 cross-reactive DUB identified through activity-based protein profiling (ABPP). We demonstrate that recombinant USP24 processed pro-ISG15 and ISG15-linked synthetic substrates in vitro. Moreover, the depletion of USP24 significantly increased the accumulation of ISG15 conjugates upon IFN-{beta} stimulation. An extensive proteomic analysis of the USP24-dependent ISGylome, integrating total proteome, GG-peptidome, and ISG15 interactome data, identified the helicase Moloney leukemia virus 10 (MOV10) as a specific target of USP24 for deISGylation. Further validation in cells revealed that ISGylated MOV10 enhances IFN-{beta} production/secretion, whereas USP24 deISGylates MOV10 to negatively regulate the innate immune response. This study showcases USP24s novel roles in modulating ISGylation and modulation of the IFN-I-dependent immune responses, with potential therapeutic implications in infectious diseases, cancer, autoimmunity, and neuroinflammation.

biochemistry↗

bioRxiv2023

Colon cancer and cell transformation by clinical Salmonella strains are associated with bacterial virulence and intracellular fitness

Non-typhoidal Salmonella (NTS) are facultative intracellular pathogens that are associated epidemiologically and experimentally with colon cancer development. Yet, the driving factors of Salmonella-induced cell transformation are mostly unknown. We compared 30 (case) NTS clinical strains isolated from patients who were diagnosed with colon cancer >1 year after NTS infection, versus 30 (control) strains from patients who did not develop colon cancer. While we observed diverse cell invasion and transformation efficiencies among the 60 NTS strains, case strains showed higher transformation efficiency than matching control strains. Genomic and transcriptomic analyses showed that transformation efficiency could not be attributed to specific genomic features, but was associated with gene expression, particularly metabolic genes and regulons. Moreover, high-transforming NTS strains display increased capacity to utilize various nutrient sources, including carbohydrates and amino acids, and grow significantly faster intracellularly than low-transforming NTS. Our results link NTS intracellular virulence to cancer promotion. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=198 SRC="FIGDIR/small/562874v1_ufig1.gif" ALT="Figure 1"> View larger version (51K): org.highwire.dtl.DTLVardef@137c6bcorg.highwire.dtl.DTLVardef@d874c1org.highwire.dtl.DTLVardef@d94b22org.highwire.dtl.DTLVardef@1d3e11c_HPS_FORMAT_FIGEXP M_FIG C_FIG In briefNon-typhoidal Salmonella (NTS) infections can promote cell transformation and colon cancer progression. Yet, little is known about the driving factors of Salmonella-induced transformation. Stevenin et al. performed a multi-omic characterization of clinical NTS strains identified in a nation-wide epidemiological study as associated with colon cancer and revealed a link between bacterial virulence, intracellular fitness, and host cell transformation. Highlights- Cancer-associated clinical NTS generate more cell transformation than matching control NTS. - NTS transformation efficiency did not correlate with specific genetic features. - NTS transformation efficiency correlates with gene expression and bacterial metabolic needs. - High-transforming NTS display increased virulence and intracellular fitness.

microbiology↗

bioRxiv2023

USP16 is an ISG15 cross-reactive deubiquitinase targeting a subset of metabolic pathway-related proteins

The ubiquitin-like modifier ISG15 can modulate host and viral proteins to restrict viral and microbial infections, and act as a cytokine. Its expression and conjugation are strongly up-regulated by type I interferons. Here we identify the deubiquitinating enzyme USP16 as an ISG15 cross-reactive protease. Ubiquitin-specific protease 16 (USP16) was found to react with an ISG15 activity-based probe in pull-down experiments using chronic myeloid leukaemia-derived human cells (HAP1). Supporting this finding, recombinant USP16 cleaved pro-ISG15 and ISG15 iso-peptide linked model substrates in vitro, as well as ISGylated substrates present in cell lysates. Moreover, the interferon-induced stimulation of ISGylation in human HAP1 cells was increased by knockdown or knockout of USP16. Depletion of USP16 did not affect interferon signaling, and interferon treatment did not affect USP16 expression or enzymatic activity either. A USP16-dependent ISG15 interactome was established by anti-ISG15 immunoprecipitation mass spectrometry (IP-MS), which indicated that the deISGylating function of USP16 may regulate metabolic pathways involving GOT1, ALDOA, SOD1 and MDH1, all of which were further confirmed to be deISGylated by USP16 in HEK293T cells. Together, our results indicate that USP16 may contribute to regulating the ISGylation status of a subset of proteins related to metabolism during type I interferon responses.

biochemistry↗

bioRxiv2023

A lipid transfer protein knockout library reveals ORP9-ORP11 dimer mediating PS/PI(4)P exchange at the ER-trans Golgi contact site to promote sphingomyelin synthesis

Numerous lipids are heterogeneously distributed among organelles. Most lipid trafficking between organelles is achieved by a group of lipid transfer proteins (LTPs) that carry lipids using their hydrophobic cavities. The human genome encodes many intracellular LTPs responsible for lipid trafficking and the function of many LTPs in defining cellular lipid levels and distributions is unclear. Here, we created a gene knockout library targeting 90 intracellular LTPs and performed whole-cell lipidomics analysis. This analysis confirmed known lipid disturbances and identified new ones caused by loss of LTPs. Among these, we found major sphingolipid imbalances in ORP9 and ORP11 knockout cells, two proteins of previously unknown function in sphingolipid metabolism. ORP9 and ORP11 form a heterodimer to localize at the ER-trans Golgi membrane contact sites, where the dimer exchanges phosphatidylserine (PS) for phosphatidylinositol-4-phosphate (PI(4)P) between the two organelles. Consequently, loss of either protein causes phospholipid imbalances in the Golgi apparatus that result in lowered sphingomyelin synthesis at this organelle. Overall, our LTP knockout library toolbox identifies various proteins in control of cellular lipid levels, including the ORP9-ORP11 heterodimer, which exchanges PS and PI(4)P at the ER-Golgi membrane contact site as a critical step in sphingomyelin synthesis in the Golgi apparatus.

cell biology↗