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Title : DPP9 sequesters the C terminus of NLRP1 to repress inflammasome activation - Hollingsworth_2021_Nature_592_778
Author(s) : Hollingsworth LR , Sharif H , Griswold AR , Fontana P , Mintseris J , Dagbay KB , Paulo JA , Gygi SP , Bachovchin DA , Wu H
Ref : Nature , 592 :778 , 2021
Abstract : Nucleotide-binding domain and leucine-rich repeat pyrin-domain containing protein 1 (NLRP1) is an inflammasome sensor that mediates the activation of caspase-1 to induce cytokine maturation and pyroptosis(1-4). Gain-of-function mutations of NLRP1 cause severe inflammatory diseases of the skin(4-6). NLRP1 contains a function-to-find domain that auto-proteolyses into noncovalently associated subdomains(7-9), and proteasomal degradation of the repressive N-terminal fragment of NLRP1 releases its inflammatory C-terminal fragment (NLRP1 CT)(10,11). Cytosolic dipeptidyl peptidases 8 and 9 (hereafter, DPP8/DPP9) both interact with NLRP1, and small-molecule inhibitors of DPP8/DPP9 activate NLRP1 by mechanisms that are currently unclear(10,12-14). Here we report cryo-electron microscopy structures of the human NLRP1-DPP9 complex alone and with Val-boroPro (VbP), an inhibitor of DPP8/DPP9. The structures reveal a ternary complex that comprises DPP9, full-length NLRP1 and the NLRPT CT. The binding of the NLRP1 CT to DPP9 requires full-length NLRP1, which suggests that NLRP1 activation is regulated by the ratio of NLRP1 CT to full-length NLRP1. Activation of the inflammasome by ectopic expression of the NLRP1 CT is consistently rescued by co-expression of autoproteolysis-deficient full-length NLRP1. The N terminus of the NLRP1 CT inserts into the DPP9 active site, and VbP disrupts this interaction. Thus, VbP weakens the NLRP1-DPP9 interaction and accelerates degradation of the N-terminal fragment(10) to induce inflammasome activation. Overall, these data demonstrate that DPP9 quenches low levels of NLRP1 CT and thus serves as a checkpoint for activation of the NLRP1 inflammasome.
ESTHER : Hollingsworth_2021_Nature_592_778
PubMedSearch : Hollingsworth_2021_Nature_592_778
PubMedID: 33731932
Gene_locus related to this paper: human-DPP9

Title : DPP9 directly sequesters the NLRP1 C-terminus to repress inflammasome activation - Hollingsworth_2020_Biorxiv__
Author(s) : Hollingsworth LR , Sharif H , Griswold AR , Fontana P , Mintseris J , Dagbay KB , Paulo JA , Gygi SP , Bachovchin DA , Wu
Ref : Biorxiv , : , 2020
Abstract : NLRP1 is a cytosolic inflammasome sensor that mediates activation of caspase-1, which in turn induces cytokine maturation and pyroptotic cell death1-6. Gain-of-function NLPR1 mutations cause skin inflammatory diseases including carcinoma, keratosis, and papillomatosis7-14. NLRP1 contains a unique function-to-find domain (FIIND) that autoproteolyzes into noncovalently associated subdomains15-18. Proteasomal degradation of the autoinhibitory N-terminal fragment (NT) activates NLRP1 by releasing the inflammatory C-terminal fragment (CT)19,20. Cytosolic dipeptidyl peptidases 8 and 9 (DPP8/9) interact with NLRP1, and small-molecule DPP8/9 inhibitors activate NLRP1 by poorly characterized mechanisms11,19,21. Here, we report cryo-EM structures of the human NLRP1-DPP9 complex, alone and in complex with the DPP8/9 inhibitor Val-boroPro (VbP). Surprisingly, the NLRP1-DPP9 complex is a ternary complex comprised of DPP9, one intact FIIND of a non-degraded full-length NLRP1 (NLRP1-FL) and one NLRP1-CT freed by NT degradation. The N-terminus of the NLRP1-CT unfolds and inserts into the DPP9 active site but is not cleaved by DPP9, and this binding is disrupted by VbP. Structure-based mutagenesis reveals that the binding of NLRP1-CT to DPP9 requires NLRP1-FL and vice versa, and inflammasome activation by ectopic NLRP1-CT expression is rescued by co-expressing autoproteolysis-deficient NLRP1-FL. Collectively, these data indicate that DPP9 functions as a 'bomb-diffuser' to prevent NLRP1-CTs from inducing inflammation during homeostatic protein turnover.
ESTHER : Hollingsworth_2020_Biorxiv__
PubMedSearch : Hollingsworth_2020_Biorxiv__
Gene_locus related to this paper: human-DPP9

Title : The paraoxonase-1 pathway is not a major bioactivation pathway of clopidogrel in vitro - Ancrenaz_2012_Br.J.Pharmacol_166_2362
Author(s) : Ancrenaz V , Desmeules J , James RW , Fontana P , Reny JL , Dayer P , Daali Y
Ref : British Journal of Pharmacology , 166 :2362 , 2012
Abstract : BACKGROUND AND PURPOSE: Clopidogrel is a prodrug bioactivated by cytochrome P450s (CYPs). More recently, paraoxonase-1 (PON1) has been proposed as a major contributor to clopidogrel metabolism. The purpose of this study was to assess the relative contribution of CYPs and PON1 to clopidogrel metabolism in vitro. EXPERIMENTAL APPROACH: Clopidogrel metabolism was studied in human serum, recombinant PON1 enzyme (rePON1), pooled human liver microsomes (HLMs), HLMs with the CYP2C19*1/*1 genotype and HLMs with the CYP2C19*2/*2 genotype. Inhibition studies were also performed using specific CYP inhibitors and antibodies. Clopidogrel and its metabolites were measured using LC/MS/MS method. KEY
RESULTS: PON1 activity was highest in the human serum and there was no difference in PON1 activity between any of the HLM groups. The production of clopidogrel's active metabolite (clopidogrel-AM) from 2-oxo-clopidogrel in pooled HLMs was approximately 500 times that in serum. When 2-oxo-clopidogrel was incubated with rePON1, clopidogrel-AM was not detected. Clopidogrel-AM production from 2-oxo-clopidogrel was lower in CYP2C19*2/*2 HLMs compared with CYP2C19*1/*1 HLMs, while PON1 activity in HLMs with both genotypes was similar. Moreover, incubation with inhibitors of CYP3A, CYP2B6 and CYP2C19 significantly reduced clopidogrel bioactivation while a PON1 inhibitor, EDTA, had only a weak inhibitory effect. CONCLUSION AND IMPLICATIONS: This in vitro study shows that the contribution of PON1 to clopidogrel metabolism is limited at clinically relevant concentrations. Moreover, CYP2C19, CYP2B6 and CYP3A play important roles in the bioactivation of clopidogrel.
ESTHER : Ancrenaz_2012_Br.J.Pharmacol_166_2362
PubMedSearch : Ancrenaz_2012_Br.J.Pharmacol_166_2362
PubMedID: 22428615

Title : Influence of the paraoxonase-1 Q192R genetic variant on clopidogrel responsiveness and recurrent cardiovascular events: a systematic review and meta-analysis - Reny_2012_J.Thromb.Haemost_10_1242
Author(s) : Reny JL , Combescure C , Daali Y , Fontana P
Ref : J Thromb Haemost , 10 :1242 , 2012
Abstract : BACKGROUND: A poor biological response to clopidogrel is associated with an increased risk of major cardiovascular ischemic events (MACE). Paraoxonase 1 (PON1) enzyme activity is modulated by the PON1-Q192R variant (rs662) and was recently suggested to be strongly involved in clopidogrel bioactivation, but the influence of the PON1-Q192R variant on the risk of MACE in clopidogrel-treated patients is controversial. OBJECTIVES: To determine whether the PON1-Q192R variant influences clopidogrel biological responsiveness and the risk of MACE in patients treated with clopidogrel.
METHODS: Systematic review and meta-analysis of studies of the association between the PON1-Q192R polymorphism and the biological response to clopidogrel and/or the risk of MACE during clopidogrel administration.
RESULTS: Seventeen studies were included. In the 12 studies of the biological response to clopidogrel (n = 5302 patients), there was no significant difference between 192QQ and 192QR + 192RR subjects, whatever the laboratory method used (global mean standardized difference = 0.10 [-0.06; 0.25], P = 0.22). Eleven studies assessed the risk of MACE, four using a case-control design (n = 2739 patients) and seven a prospective design (n = 5353 patients). Overall, MACE occurred in 19% of patients in case-control studies and in 6% of patients in prospective cohort studies, with no significant difference between 192QQ and 192QR + 192RR patients (OR = 1.28 [0.97; 1.68], P = 0.08). Similar results were obtained when study design was taken into account. Heterogeneity was mainly driven by one publication.
CONCLUSIONS: This meta-analysis suggests that the PON1-Q192R polymorphism has no major impact on the risk of MACE and does not alter the biological response to clopidogrel in clopidogrel-treated patients.
ESTHER : Reny_2012_J.Thromb.Haemost_10_1242
PubMedSearch : Reny_2012_J.Thromb.Haemost_10_1242
PubMedID: 22520065

Title : A high quality draft consensus sequence of the genome of a heterozygous grapevine variety - Velasco_2007_PLoS.One_2_e1326
Author(s) : Velasco R , Zharkikh A , Troggio M , Cartwright DA , Cestaro A , Pruss D , Pindo M , FitzGerald LM , Vezzulli S , Reid J , Malacarne G , Iliev D , Coppola G , Wardell B , Micheletti D , Macalma T , Facci M , Mitchell JT , Perazzolli M , Eldredge G , Gatto P , Oyzerski R , Moretto M , Gutin N , Stefanini M , Chen Y , Segala C , Davenport C , Dematte L , Mraz A , Battilana J , Stormo K , Costa F , Tao Q , Si-Ammour A , Harkins T , Lackey A , Perbost C , Taillon B , Stella A , Solovyev V , Fawcett JA , Sterck L , Vandepoele K , Grando SM , Toppo S , Moser C , Lanchbury J , Bogden R , Skolnick M , Sgaramella V , Bhatnagar SK , Fontana P , Gutin A , Van de Peer Y , Salamini F , Viola R
Ref : PLoS ONE , 2 :e1326 , 2007
Abstract : BACKGROUND: Worldwide, grapes and their derived products have a large market. The cultivated grape species Vitis vinifera has potential to become a model for fruit trees genetics. Like many plant species, it is highly heterozygous, which is an additional challenge to modern whole genome shotgun sequencing. In this paper a high quality draft genome sequence of a cultivated clone of V. vinifera Pinot Noir is presented. PRINCIPAL FINDINGS: We estimate the genome size of V. vinifera to be 504.6 Mb. Genomic sequences corresponding to 477.1 Mb were assembled in 2,093 metacontigs and 435.1 Mb were anchored to the 19 linkage groups (LGs). The number of predicted genes is 29,585, of which 96.1% were assigned to LGs. This assembly of the grape genome provides candidate genes implicated in traits relevant to grapevine cultivation, such as those influencing wine quality, via secondary metabolites, and those connected with the extreme susceptibility of grape to pathogens. Single nucleotide polymorphism (SNP) distribution was consistent with a diffuse haplotype structure across the genome. Of around 2,000,000 SNPs, 1,751,176 were mapped to chromosomes and one or more of them were identified in 86.7% of anchored genes. The relative age of grape duplicated genes was estimated and this made possible to reveal a relatively recent Vitis-specific large scale duplication event concerning at least 10 chromosomes (duplication not reported before). CONCLUSIONS: Sanger shotgun sequencing and highly efficient sequencing by synthesis (SBS), together with dedicated assembly programs, resolved a complex heterozygous genome. A consensus sequence of the genome and a set of mapped marker loci were generated. Homologous chromosomes of Pinot Noir differ by 11.2% of their DNA (hemizygous DNA plus chromosomal gaps). SNP markers are offered as a tool with the potential of introducing a new era in the molecular breeding of grape.
ESTHER : Velasco_2007_PLoS.One_2_e1326
PubMedSearch : Velasco_2007_PLoS.One_2_e1326
PubMedID: 18094749
Gene_locus related to this paper: vitvi-a5ajc4 , vitvi-a5ama3 , vitvi-a5ane2 , vitvi-a5ayn8 , vitvi-a5b3m9 , vitvi-a5b5p5 , vitvi-a5b6n6 , vitvi-a5b6r9 , vitvi-a5b7c0 , vitvi-a5b7e5 , vitvi-a5b8k1 , vitvi-a5b8l9 , vitvi-a5b8q6 , vitvi-a5bft8 , vitvi-a5bji4 , vitvi-a5bkl0 , vitvi-a5blq0 , vitvi-a5bm71 , vitvi-a5bub9 , vitvi-a5c1g2 , vitvi-a5c6e7 , vitvi-a5c8m8 , vitvi-a5c8p7 , vitvi-a5c9w6 , vitvi-a7pnb4 , vitvi-d7t940 , vitvi-d7tpk8 , vitvi-f6hhx5 , vitvi-f6hqf1 , vitvi-d7tum4 , vitvi-d7stm8 , vitvi-a5bej7 , vitvi-e0cv10 , vitvi-f6gtp7 , vitvi-a5bej5