title: The Molecular Basis for Ubiquitin and Ubiquitin-like Specificities in Bacterial Effector Proteases.
abstract: Pathogenic bacteria rely on secreted effector proteins to manipulate host signaling pathways, often in creative ways. CE clan proteases, specific hydrolases for ubiquitin-like modifications (SUMO and NEDD8) in eukaryotes, reportedly serve as bacterial effector proteins with deSUMOylase, deubiquitinase, or, even, acetyltransferase activities. Here, we characterize bacterial CE protease activities, revealing K63-linkage-specific deubiquitinases in human pathogens, such as Salmonella, Escherichia, and Shigella, as well as ubiquitin/ubiquitin-like cross-reactive enzymes in Chlamydia, Rickettsia, and Xanthomonas. Five crystal structures, including ubiquitin/ubiquitin-like complexes, explain substrate specificities and redefine relationships across the CE clan. Importantly, this work identifies novel family members and provides key discoveries among previously reported effectors, such as the unexpected deubiquitinase activity in Xanthomonas XopD, contributed by an unstructured ubiquitin binding region. Furthermore, accessory domains regulate properties such as subcellular localization, as exemplified by a ubiquitin-binding domain in Salmonella Typhimurium SseL. Our work both highlights and explains the functional adaptations observed among diverse CE clan proteins.
authors.affiliation: Division of Protein and Nucleic Acid Chemistry, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK.
authors.forename: Jonathan N
authors.initials: JN
authors.lastname: Pruneda
authors.affiliation: Section of Microbiology, MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London SW7 2AZ, UK.
authors.forename: Charlotte H
authors.initials: CH
authors.lastname: Durkin
authors.affiliation: Division of Cell Biology, Netherlands Cancer Institute, Plesmanlaan 121, 1066 Amsterdam, the Netherlands.
authors.forename: Paul P
authors.initials: PP
authors.lastname: Geurink
authors.affiliation: Division of Cell Biology, Netherlands Cancer Institute, Plesmanlaan 121, 1066 Amsterdam, the Netherlands.
authors.forename: Huib
authors.initials: H
authors.lastname: Ovaa
authors.affiliation: Division of Structural Studies, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK.
authors.forename: Balaji
authors.initials: B
authors.lastname: Santhanam
authors.affiliation: Section of Microbiology, MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London SW7 2AZ, UK.
authors.forename: David W
authors.initials: DW
authors.lastname: Holden
authors.affiliation: Division of Protein and Nucleic Acid Chemistry, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK. Electronic address: dk@mrc-lmb.cam.ac.uk.
authors.forename: David
authors.initials: D
authors.lastname: Komander
mesh_terms: D000595:Amino Acid Sequence; D001419:Bacteria / Q000201:enzymology* / Q000235:genetics; D001426:Bacterial Proteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D002692:Chlamydia trachomatis / Q000201:enzymology; D019295:Computational Biology; D017124:Conserved Sequence; D030562:Databases, Protein; D004926:Escherichia coli / Q000201:enzymology; D006367:HeLa Cells; D006801:Humans; D007875:Legionella / Q000201:enzymology; D008958:Models, Molecular; D009154:Mutation; D010802:Phylogeny; D011487:Protein Conformation; D012281:Rickettsia / Q000201:enzymology; D012486:Salmonella typhimurium / Q000201:enzymology; D012763:Shigella flexneri / Q000201:enzymology; D013329:Structure-Activity Relationship; D013379:Substrate Specificity; D025801:Ubiquitin / Q000378:metabolism*; D064570:Ubiquitin-Specific Proteases / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D054875:Ubiquitination; D016959:Xanthomonas campestris / Q000201:enzymology
chemical_list: D001426:Bacterial Proteins; D025801:Ubiquitin; D064570:Ubiquitin-Specific Proteases