An HD-domain phosphodiesterase mediates cooperative hydrolysis of c-di-AMP to affect bacterial growth and virulence

The nucleotide cyclic di-3′,5′- adenosine monophosphate (c-di-AMP) was recently identified as an essential and widespread second messenger in bacterial signaling. Among c-di-AMP–producing bacteria, altered nucleotide levels result in several physiological defects and attenuated virulence. Thus, a detailed molecular understanding of c-di-AMP metabolism is of both fundamental and practical interest. Currently, c-di-AMP degradation is recognized solely among DHH-DHHA1 domain-containing phosphodiesterases. Using chemical proteomics, we identified the Listeria monocytogenes protein PgpH as a molecular target of c-di-AMP. Biochemical and structural studies revealed that the PgpH His-Asp (HD) domain bound c-di-AMP with high affinity and specifically hydrolyzed this nucleotide to 5′-pApA. PgpH hydrolysis activity was inhibited by ppGpp, indicating a cross-talk between c-di-AMP signaling and the stringent response. Genetic analyses supported coordinated regulation of c-di-AMP levels in and out of the host. Intriguingly, a L. monocytogenes mutant that lacks c-di-AMP phosphodiesterases exhibited elevated c-di-AMP levels, hyperinduced a host type-I IFN response, and was significantly attenuated for infection. Furthermore, PgpH homologs, which belong to the 7TMR-HD family, are widespread among hundreds of c-di-AMP synthesizing microorganisms. Thus, PgpH represents a broadly conserved class of c-di-AMP phosphodiesterase with possibly other physiological functions in this crucial signaling network.

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Elucidating cyclic AMP signaling in subcellular domains with optogenetic tools and fluorescent biosensors

Biochemical Society Transactions ◽

10.1042/bst20190246 ◽

2019 ◽

Vol 47 (6) ◽

pp. 1733-1747 ◽

Cited By ~ 3

Author(s):

Christina Klausen ◽

Fabian Kaiser ◽

Birthe Stüven ◽

Jan N. Hansen ◽

Dagmar Wachten

Keyword(s):

Cyclic Amp ◽

Adenosine Monophosphate ◽

Adenylyl Cyclases ◽

Temporal Precision ◽

Fluorescent Biosensors ◽

Subcellular Domains ◽

Spatio Temporal ◽

Hydrolysis Of ◽

Shed Light ◽

Cyclic Amp Signaling

The second messenger 3′,5′-cyclic nucleoside adenosine monophosphate (cAMP) plays a key role in signal transduction across prokaryotes and eukaryotes. Cyclic AMP signaling is compartmentalized into microdomains to fulfil specific functions. To define the function of cAMP within these microdomains, signaling needs to be analyzed with spatio-temporal precision. To this end, optogenetic approaches and genetically encoded fluorescent biosensors are particularly well suited. Synthesis and hydrolysis of cAMP can be directly manipulated by photoactivated adenylyl cyclases (PACs) and light-regulated phosphodiesterases (PDEs), respectively. In addition, many biosensors have been designed to spatially and temporarily resolve cAMP dynamics in the cell. This review provides an overview about optogenetic tools and biosensors to shed light on the subcellular organization of cAMP signaling.

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Kinetics and Mechanistic Study of Hydrolysis of Adenosine Monophosphate Disodium Salt (AMPNa2) in Acidic and Alkaline Media

Open Chemistry ◽

10.1515/chem-2019-0044 ◽

2019 ◽

Vol 17 (1) ◽

pp. 544-556

Author(s):

Yoke-Leng Sim ◽

Beljit Kaur

Keyword(s):

Rate Constant ◽

Adenosine Monophosphate ◽

Disodium Salt ◽

Second Order ◽

Information Storage ◽

Alkaline Media ◽

Basic Medium ◽

Mechanistic Study ◽

Phosphate Ester ◽

Hydrolysis Of

AbstractPhosphate ester hydrolysis is essential in signal transduction, energy storage and production, information storage and DNA repair. In this investigation, hydrolysis of adenosine monophosphate disodium salt (AMPNa2) was carried out in acidic, neutral and alkaline conditions of pH ranging between 0.30-12.71 at 60°C. The reaction was monitored spectrophotometrically. The rate ranged between (1.20 ± 0.10) × 10-7 s-1 to (4.44 ± 0.05) × 10-6 s-1 at [NaOH] from 0.0008 M to 1.00M recorded a second-order base-catalyzed rate constant, kOH as 4.32 × 10-6 M-1 s-1. In acidic conditions, the rate ranged between (1.32 ± 0.06) × 10-7 s-1 to (1.67 ± 0.10) × 10-6 s-1 at [HCl] from 0.01 M to 1.00 M. Second-order acid-catalyzed rate constant, kH obtained was 1.62 × 10-6 M-1 s-1. Rate of reaction for neutral region, k0 was obtained from graphical method to be 10-7 s-1. Mechanisms were proposed to involve P-O bond cleavage in basic medium while competition between P-O bond and N-glycosidic cleavage was observed in acidic medium. In conclusion, this study has provided comprehensive information on the kinetic parameters and mechanism of cleavage of AMPNa2 which mimicked natural AMP cleavage and the action of enzymes that facilitate its cleavage.

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Crosstalk Between Autophagy and the cGAS–STING Signaling Pathway in Type I Interferon Production

Frontiers in Cell and Developmental Biology ◽

10.3389/fcell.2021.748485 ◽

2021 ◽

Vol 9 ◽

Author(s):

Kunli Zhang ◽

Sutian Wang ◽

Hongchao Gou ◽

Jianfeng Zhang ◽

Chunling Li

Keyword(s):

Signaling Pathway ◽

Adenosine Monophosphate ◽

Degradation Process ◽

Guanosine Monophosphate ◽

Type I Interferons ◽

Research Progress ◽

Type I ◽

Type I Ifn ◽

Major Pathway ◽

Sting Pathway

Innate immunity is the front-line defense against infectious microorganisms, including viruses and bacteria. Type I interferons are pleiotropic cytokines that perform antiviral, antiproliferative, and immunomodulatory functions in cells. The cGAS–STING pathway, comprising the main DNA sensor cyclic guanosine monophosphate/adenosine monophosphate synthase (cGAS) and stimulator of IFN genes (STING), is a major pathway that mediates immune reactions and is involved in the strong induction of type I IFN production, which can fight against microbial infections. Autophagy is an evolutionarily conserved degradation process that is required to maintain host health and facilitate capture and elimination of invading pathogens by the immune system. Mounting evidence indicates that autophagy plays an important role in cGAS–STING signaling pathway-mediated type I IFN production. This review briefly summarizes the research progress on how autophagy regulates the cGAS–STING pathway, regulating type I IFN production, with a particular focus on the crosstalk between autophagy and cGAS–STING signaling during infection by pathogenic microorganisms.

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Chemical Proteomics and Phenotypic Profiling Identifies the Aryl Hydrocarbon Receptor as a Molecular Target of the Utrophin Modulator Ezutromid

Angewandte Chemie International Edition ◽

10.1002/anie.201912392 ◽

2020 ◽

Vol 59 (6) ◽

pp. 2420-2428 ◽

Cited By ~ 4

Author(s):

Isabel V. L. Wilkinson ◽

Kelly J. Perkins ◽

Hannah Dugdale ◽

Lee Moir ◽

Aini Vuorinen ◽

...

Keyword(s):

Aryl Hydrocarbon Receptor ◽

Molecular Target ◽

Chemical Proteomics ◽

Aryl Hydrocarbon

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PROTEIN C : ROUEN - A NEW HEREDITARY PROTEIN C ABNORMALITY WITH LOW ANTICOAGULANT BUT NORMAL AMIDOLYTIC ACTIVITIES

10.1055/s-0038-1644306 ◽

1987 ◽

Author(s):

J Y Borg ◽

M Vasse ◽

M Monconduit

Keyword(s):

Protein C ◽

Anticoagulant Activity ◽

Protein S ◽

Functional Assay ◽

Type I ◽

Functional Abnormality ◽

Oral Anticoagulant Treatment ◽

Crossed Immunoelectrophoresis ◽

Deficiency Type ◽

Hydrolysis Of

During the last three years, we could detect hereditary quantitative protein C (PC) deficiency in 43 patients belonging to 18 families. In those defects type I without oral anticoagulant treatment, the values of PC measured either by an ELISA method (PC:Ag) or by a chronometric functional assay were very closed and well correlated. (Results expressed in % of normal pooled plasmas PC:Ag m=44,l %, SD = 15,3 ; PC : activity m = 49,5, SD = 13,5 - correlation r = 0,82). In a 32 year#old man with a severe thrombo-embolic disease and in 11 related people, we could diagnose a hereditary qualitative PC deficiency type II, because of a discrepancy between normal PC:Ag levels (m = 105 %, SD = 20,3, range = 78-143) and low PC anticoagulant activities (m = 46 %, SD = 9,5, range = 30-60). FunctionalpC studies included assays, with or without preliminary adsorption on baryum citrate or aluminium hydroxide, with various PC activators (thrombin, PROTAC venom), in chronometric and amidolytic assays.(Normal protein S levelswere first tested).As shown by those results, PC activity is normal in amidolytic assays even after preliminary adsorption whatever the activation is. On the contrary, the PC anticoagulant activity is reduced in any technique. We can conclude that the activation is normal. Crossed immunoelectrophoresis (CIE) with or without calcium showed normal migration as compared to controls. Normal adsorption on insoluble salts and normal Ca-binding in CIE allow us to say that the abnormal PC is not completely acarboxylated. As amidolytic assays (normal in patients) do not assess the ability of activated PC to interact with protein S (PS) and phospholipids via calcium, 3 hypothesis can explain the functional abnormality:- abnormal binding to PS- abnormal binding to phospholipids due to partially carboxylated glutamic acids (which would be sufficient to promote adsorption)- defective inhibition of Va and Villa because a conformational change allowing only hydrolysis of little synthetic peptides.

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Comparison of haplotype-based tests for detecting gene–environment interactions with rare variants

Briefings in Bioinformatics ◽

10.1093/bib/bbz031 ◽

2019 ◽

Vol 21 (3) ◽

pp. 851-862 ◽

Cited By ~ 1

Author(s):

Charalampos Papachristou ◽

Swati Biswas

Keyword(s):

Lung Cancer ◽

Rare Variants ◽

Practical Interest ◽

Serum Triglyceride ◽

Error Rates ◽

Type I ◽

Rare Haplotype ◽

Data Set ◽

Cancer Data ◽

Gene Environment

Abstract Dissecting the genetic mechanism underlying a complex disease hinges on discovering gene–environment interactions (GXE). However, detecting GXE is a challenging problem especially when the genetic variants under study are rare. Haplotype-based tests have several advantages over the so-called collapsing tests for detecting rare variants as highlighted in recent literature. Thus, it is of practical interest to compare haplotype-based tests for detecting GXE including the recent ones developed specifically for rare haplotypes. We compare the following methods: haplo.glm, hapassoc, HapReg, Bayesian hierarchical generalized linear model (BhGLM) and logistic Bayesian LASSO (LBL). We simulate data under different types of association scenarios and levels of gene–environment dependence. We find that when the type I error rates are controlled to be the same for all methods, LBL is the most powerful method for detecting GXE. We applied the methods to a lung cancer data set, in particular, in region 15q25.1 as it has been suggested in the literature that it interacts with smoking to affect the lung cancer susceptibility and that it is associated with smoking behavior. LBL and BhGLM were able to detect a rare haplotype–smoking interaction in this region. We also analyzed the sequence data from the Dallas Heart Study, a population-based multi-ethnic study. Specifically, we considered haplotype blocks in the gene ANGPTL4 for association with trait serum triglyceride and used ethnicity as a covariate. Only LBL found interactions of haplotypes with race (Hispanic). Thus, in general, LBL seems to be the best method for detecting GXE among the ones we studied here. Nonetheless, it requires the most computation time.

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ORDERING IN DENSE FIBER BUNDLES, THE PHYLLOTACTIC SOLUTION AND ITS APPLICATION TO COLLAGEN FIBRILS

Biophysical Reviews and Letters ◽

10.1142/s179304801350001x ◽

2013 ◽

Vol 08 (01n02) ◽

pp. 33-49 ◽

Cited By ~ 4

Author(s):

JEAN CHARVOLIN ◽

JEAN-FRANÇOIS SADOC

Keyword(s):

Long Range ◽

Cross Section ◽

Type I Collagen ◽

Radial Symmetry ◽

Collagen Fibrils ◽

Fiber Bundles ◽

Type I ◽

High Symmetry ◽

Structural Studies ◽

Packing Efficiency

The shape of the cross section of a dense fiber bundle is related to the symmetry of its molecular packing. However, this statement might be belied by type I collagen fibrils which have a rounded section of high symmetry while structural studies suggest that their molecules are assembled with a long range lateral order of lower symmetry. We examine how phyllotaxis, which is a nonconventional crystallographic solution to packing efficiency in situations of high radial symmetry, can establish a link between those two apparently conflicting points. The lateral order imposed by the algorithm of phyllotaxis, which implies an enlargement of the notion of long range lateral order beyond that used for classical crystals, provides a basis for a new analysis of the experimental data.

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