A family of unconventional deubiquitinases with modular chain specificity determinants

Hermanns, Thomas; Pichlo, C.; Woiwode, Ilka; Klopffleisch, Karsten; Witting, Katharina F.; Ovaa, Huib; Baumann, Ulrich; Hofmann, Kay

doi:10.1038/s41467-018-03148-5

Cited by 104 publications

(117 citation statements)

References 46 publications

(53 reference statements)

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“…Selectivity was tested in recombinant and cellular systems, with probes varying in linker length, positioning of electrophilic trap and stability to DUBs as well as compatibility requirements. Many probes have proven to be excellent tools to study these complex pathways and have already provided valuable insights into the mechanistic and structural features of target enzymes (Bekes et al, 2016;Hann et al, 2019;Paudel et al, 2019) as well in the characterization of new family members (Hermanns et al, 2018) and identification of potential disease markers in patient samples (Pao et al, 2016).…”

Section: Resultsmentioning

confidence: 99%

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Strategies to Target Specific Components of the Ubiquitin Conjugation/Deconjugation Machinery

Taylor

McGouran

2020

Front. Chem.

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The regulation of ubiquitination status in the cell is controlled by ubiquitin ligases acting in tandem with deubiquitinating enzymes. Ubiquitination controls many key processes in the cell from division to death making its tight regulation key to optimal cell function. Activity based protein profiling has emerged as a powerful technique to study these important enzymes. With around 100 deubiquitinating enzymes and 600 ubiquitin ligases in the human genome targeting a subclass of these enzymes or even a single enzyme is a compelling strategy to unpick this complex system. In this review we will discuss different approaches adopted, including activity-based probes centered around ubiquitin-protein, ubiquitin-peptide and mutated ubiquitin scaffolds. We examine challenges faced and opportunities presented to increase specificity in activity-based protein profiling of the ubiquitin conjugation/deconjugation machinery.

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Section: Resultsmentioning

confidence: 99%

“…Both were seen to display a restricted labeling pattern in comparison to the VME probe and were later used to characterize Cezanne . In addition to this, the probe was used to elucidate the linkage specificity of Mug105, which along with ZUSFP, was identified as a founding member of a novel family of DUBs (Hermanns et al, 2018).…”

Section: Diubiquitin Probesmentioning

confidence: 99%

Strategies to Target Specific Components of the Ubiquitin Conjugation/Deconjugation Machinery

Taylor

McGouran

2020

Front. Chem.

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“…For example, around 100 DUBs have been discovered in humans but only 20 DUBs in Saccharomyces cerevisiae [13]. In general, DUBs can be divided into seven distinct structural families [14]: ubiquitin-specific proteases (USPs, family C19), C-terminal hydrolyses (UCHs, family C12), ovarian tumor proteases (OTUs, family C65), JAB1/MPN/MOV34 metalloenzymes (JAMM/MPN+, family), Josephins, family C86, MINDY, family C115 [15] and the newly identified ZUFSP (zinc finger with UFM1-specific peptidase domain protein), family C78 [13,16]. Here we characterise DUBs of Leishmania and describe a Bar-seq CRISPR-Cas9 genome editing strategy that was used to evaluate the requirement for DUB activity in the Leishmania life cycle.…”

Section: Introductionmentioning

confidence: 99%

Essential roles for deubiquitination inLeishmanialife cycle progression

Damianou

Burge

Catta-Preta

et al. 2020

Preprint

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14 The parasitic protozoan Leishmania requires proteasomal, autophagic and lysosomal 15 proteolytic pathways to enact the extensive cellular remodelling that occurs during its life cycle.16 The proteasome is essential for parasite proliferation, yet little is known about the requirement 17 for ubiquitination/deubiquitination processes in growth and differentiation. Activity-based 18 protein profiling of L. mexicana C12, C19 and C65 deubiquitinating cysteine peptidases 19 (DUBs) revealed DUB activity remains relatively constant during differentiation of procyclic 20 promastigote to amastigote. However, when Bar-seq was applied to a pool of 16 DUB null 21 mutants created in promastigotes using CRISPR-Cas9, significant loss of fitness was 22 observed during differentiation and intracellular infection. DUBs 4, 7, and 13 are required for 23 successful transformation from metacyclic promastigote to amastigote and DUBs 3, 5, 6, 10, 24 11 and 14 are required for normal amastigote proliferation in mice. DUBs 1, 2, 12 and 16 are 25 essential for promastigote viability and the essential role of DUB2 in establishing infection was 26 demonstrated using DiCre inducible gene deletion in vitro and in vivo. DUB2 is found in the 2 27 nucleus and interacts with nuclear proteins associated with transcription/chromatin dynamics, 28 mRNA splicing and mRNA capping. DUB2 has broad linkage specificity, cleaving all the di-29 ubiquitin chains except for Lys27 and Met1. Our study demonstrates the crucial role that DUBs 30 play in differentiation and intracellular survival of Leishmania and that amastigotes are 31 exquisitely sensitive to disruption of ubiquitination homeostasis. 33Author Summary 34 Leishmania parasites require a variety of protein degradation pathways to enable the parasite 35 to transition through the various life cycle stages that occur in its insect and mammalian hosts.36 Several enzymes involved in protein degradation in Leishmania are known to be essential, 37 including a multi-protein complex, the proteasome, but little is known about how proteins are 38 targeted to the proteasome for degradation. Here, we analyse components of the 39 deubiqutination pathway, including twenty cysteine peptidases (DUBs) that remove the 40 posttranslational modifier ubiquitin from substrates tagged for proteasomal degradation. We 41 used chemical probes to measure active enzymes in parasite lysates and genome engineering 42 to create DUB gene deletion mutants. We identified some DUBs that are essential for parasite 43 viability and some that are required for life cycle progression. We carried out a detailed 44 analysis of the essential DUB2, which has broad deubiquitinase activity and is found in the 45 nucleus. This enzyme interacts with nuclear proteins associated with transcription/chromatin 46 dynamics, mRNA splicing and mRNA capping. This work demonstrates the important role that 47 DUBs play in Leishmania in vivo infection and further validates DUBs as potential drug targets 48 in this parasite. 49 50 3 51 Introduction 52 Leishma...

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“…On the other end of the spectrum, the process of ubiquitination can be reversed by deubiquitinating enzymes known as deubiquitinases (DUBs) (Zhang & Sidhu, 2014). Humans encode seven different structural families of DUBs, which comprise almost 100 proteins in total (Hermanns et al, 2018;Wertz & Wang, 2019). Ub-specific proteases (USPs) represent the largest and best studied family, with close to 60 USPs currently described (Yuan et al, 2018).…”

Section: Introductionmentioning

confidence: 99%

Emerging drug development technologies targeting ubiquitination for cancer therapeutics

Veggiani

Gerpe

Sidhu

et al. 2019

Pharmacology & Therapeutics

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a b s t r a c t a r t i c l e i n f o Development of effective cancer therapeutic strategies relies on our ability to interfere with cellular processes that are dysregulated in tumors. Given the essential role of the ubiquitin proteasome system (UPS) in regulating a myriad of cellular processes, it is not surprising that malfunction of UPS components is implicated in numerous human diseases, including many types of cancer. The clinical success of proteasome inhibitors in treating multiple myeloma has further stimulated enthusiasm for targeting UPS proteins for pharmacological intervention in cancer treatment, particularly in the precision medicine era. Unfortunately, despite tremendous efforts, the paucity of potent and selective UPS inhibitors has severely hampered attempts to exploit the UPS for therapeutic benefits. To tackle this problem, many groups have been working on technology advancement to rapidly and effectively screen for potent and specific UPS modulators as intracellular probes or early-phase therapeutic agents. Here, we review several emerging technologies for developing chemical-and protein-based molecules to manipulate UPS enzymatic activity, with the aim of providing an overview of strategies available to target ubiquitination for cancer therapy.

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A family of unconventional deubiquitinases with modular chain specificity determinants

Cited by 104 publications

References 46 publications

Strategies to Target Specific Components of the Ubiquitin Conjugation/Deconjugation Machinery

Strategies to Target Specific Components of the Ubiquitin Conjugation/Deconjugation Machinery

Essential roles for deubiquitination inLeishmanialife cycle progression

Emerging drug development technologies targeting ubiquitination for cancer therapeutics

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