Edwards AM

References (3)

Title : Lipidome modulation by dietary omega-3 polyunsaturated fatty acid supplementation or selective soluble epoxide hydrolase inhibition suppresses rough LPS-accelerated glomerulonephritis in lupus-prone mice - Favor_2023_Front.Immunol_14_1124910
Author(s) : Favor OK , Chauhan PS , Pourmand E , Edwards AM , Wagner JG , Lewandowski RP , Heine LK , Harkema JR , Lee KSS , Pestka JJ
Ref : Front Immunol , 14 :1124910 , 2023
Abstract : INTRODUCTION: Lipopolysaccharide (LPS)-accelerated autoimmune glomerulonephritis (GN) in NZBWF1 mice is a preclinical model potentially applicable for investigating lipidome-modulating interventions against lupus. LPS can be expressed as one of two chemotypes: smooth LPS (S-LPS) or rough LPS (R-LPS) which is devoid of O-antigen polysaccharide sidechain. Since these chemotypes differentially affect toll-like receptor 4 (TLR4)-mediated immune cell responses, these differences may influence GN induction. METHODS: We initially compared the effects of subchronic intraperitoneal (i.p.) injection for 5 wk with 1) Salmonella S-LPS, 2) Salmonella R-LPS, or 3) saline vehicle (VEH) (Study 1) in female NZBWF1 mice. Based on the efficacy of R-LPS in inducing GN, we next used it to compare the impact of two lipidome-modulating interventions, omega-3 polyunsaturated fatty acid (PUFA) supplementation and soluble epoxide hydrolase (sEH) inhibition, on GN (Study 2). Specifically, effects of consuming omega-3 docosahexaenoic acid (DHA) (10 g/kg diet) and/or the sEH inhibitor 1-(4-trifluoro-methoxy-phenyl)-3-(1-propionylpiperidin-4-yl) urea (TPPU) (22.5 mg/kg diet = 3 mg/kg/day) on R-LPS triggering were compared. RESULTS: In Study 1, R-LPS induced robust elevations in blood urea nitrogen, proteinuria, and hematuria that were not evident in VEH- or S-LPS-treated mice. R-LPS-treated mice further exhibited kidney histopathology including robust hypertrophy, hyperplasia, thickened membranes, lymphocytic accumulation containing B and T cells, and glomerular IgG deposition consistent with GN that was not evident in VEH- or SLPS-treated groups. R-LPS but not S-LPS induced spleen enlargement with lymphoid hyperplasia and inflammatory cell recruitment in the liver. In Study 2, resultant blood fatty acid profiles and epoxy fatty acid concentrations reflected the anticipated DHA- and TPPU-mediated lipidome changes, respectively. The relative rank order of R-LPS-induced GN severity among groups fed experimental diets based on proteinuria, hematuria, histopathologic scoring, and glomerular IgG deposition was: VEH/CON< R-LPS/DHA = R-LPS/TPPU<<< R-LPS/TPPU+DHA = R-LPS/CON. In contrast, these interventions had modest-to- negligible effects on R-LPS-induced splenomegaly, plasma antibody responses, liver inflammation, and inflammation-associated kidney gene expression. DISCUSSION: We show for the first time that absence of O-antigenic polysaccharide in R-LPS is critical to accelerated GN in lupus-prone mice. Furthermore, intervention by lipidome modulation through DHA feeding or sEH inhibition suppressed R-LPS-induced GN; however, these ameliorative effects were greatly diminished upon combining the treatments.
ESTHER : Favor_2023_Front.Immunol_14_1124910
PubMedSearch : Favor_2023_Front.Immunol_14_1124910
PubMedID: 36875087

Title : Enzyme genomics: Application of general enzymatic screens to discover new enzymes - Kuznetsova_2005_FEMS.Microbiol.Rev_29_263
Author(s) : Kuznetsova E , Proudfoot M , Sanders SA , Reinking J , Savchenko A , Arrowsmith CH , Edwards AM , Yakunin AF
Ref : FEMS Microbiology Reviews , 29 :263 , 2005
Abstract : In all sequenced genomes, a large fraction of predicted genes encodes proteins of unknown biochemical function and up to 15% of the genes with "known" function are mis-annotated. Several global approaches are routinely employed to predict function, including sophisticated sequence analysis, gene expression, protein interaction, and protein structure. In the first coupling of genomics and enzymology, Phizicky and colleagues undertook a screen for specific enzymes using large pools of partially purified proteins and specific enzymatic assays. Here we present an overview of the further developments of this approach, which involve the use of general enzymatic assays to screen individually purified proteins for enzymatic activity. The assays have relaxed substrate specificity and are designed to identify the subclass or sub-subclasses of enzymes (phosphatase, phosphodiesterase/nuclease, protease, esterase, dehydrogenase, and oxidase) to which the unknown protein belongs. Further biochemical characterization of proteins can be facilitated by the application of secondary screens with natural substrates (substrate profiling). We demonstrate here the feasibility and merits of this approach for hydrolases and oxidoreductases, two very broad and important classes of enzymes. Application of general enzymatic screens and substrate profiling can greatly speed up the identification of biochemical function of unknown proteins and the experimental verification of functional predictions produced by other functional genomics approaches.
ESTHER : Kuznetsova_2005_FEMS.Microbiol.Rev_29_263
PubMedSearch : Kuznetsova_2005_FEMS.Microbiol.Rev_29_263
PubMedID: 15808744
Gene_locus related to this paper: ecoli-yafa , ecoli-ybff , ecoli-ycjy , ecoli-yeiG , ecoli-YFBB , ecoli-yjfp , ecoli-ypfh , ecoli-yqia , ecoli-yuar

Title : Integrating structure, bioinformatics, and enzymology to discover function: BioH, a new carboxylesterase from Escherichia coli - Sanishvili_2003_J.Biol.Chem_278_26039
Author(s) : Sanishvili R , Yakunin AF , Laskowski RA , Skarina T , Evdokimova E , Doherty-Kirby A , Lajoie GA , Thornton JM , Arrowsmith CH , Savchenko A , Joachimiak A , Edwards AM
Ref : Journal of Biological Chemistry , 278 :26039 , 2003
Abstract : Structural proteomics projects are generating three-dimensional structures of novel, uncharacterized proteins at an increasing rate. However, structure alone is often insufficient to deduce the specific biochemical function of a protein. Here we determined the function for a protein using a strategy that integrates structural and bioinformatics data with parallel experimental screening for enzymatic activity. BioH is involved in biotin biosynthesis in Escherichia coli and had no previously known biochemical function. The crystal structure of BioH was determined at 1.7 A resolution. An automated procedure was used to compare the structure of BioH with structural templates from a variety of different enzyme active sites. This screen identified a catalytic triad (Ser82, His235, and Asp207) with a configuration similar to that of the catalytic triad of hydrolases. Analysis of BioH with a panel of hydrolase assays revealed a carboxylesterase activity with a preference for short acyl chain substrates. The combined use of structural bioinformatics with experimental screens for detecting enzyme activity could greatly enhance the rate at which function is determined from structure.
ESTHER : Sanishvili_2003_J.Biol.Chem_278_26039
PubMedSearch : Sanishvili_2003_J.Biol.Chem_278_26039
PubMedID: 12732651
Gene_locus related to this paper: ecoli-bioh