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      A Chemical Genetic Screen Identifies ABHD12 as an Oxidized Phosphatidylserine Lipase

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          Abstract

          Reactive oxygen species (ROS) are transient, highly reactive intermediates or byproducts produced during oxygen metabolism. However, when innate mechanisms are unable to cope with sequestration of surplus ROS, it causes oxidative stress, where excess ROS damage biomolecules. Oxidized phosphatidylserine (PS), a pro-apoptotic “eat me” signal, is produced in response to elevated ROS, yet, little is known of its chemical composition and metabolism. Here, we report a small molecule that generates ROS in different mammalian cells, using which we detect, characterize and study oxidized PS in mammalian cells. We describe a chemical genetic screen to identify enzymes that regulate oxidized PS in mammalian cells, and find that the lipase ABHD12 hydrolyzes oxidized PS. We validate these findings in different physiological settings including primary peritoneal macrophages, and brains from Abhd12 –/– knockout mice under inflammatory stress, and in the process functionally annotate an enzyme capable of regulating oxidized PS in vivo.

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          Most cited references45

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          The distribution and function of phosphatidylserine in cellular membranes.

          Phosphatidylserine (PS) is the most abundant negatively charged phospholipid in eukaryotic membranes. PS directs the binding of proteins that bear C2 or gamma-carboxyglutamic domains and contributes to the electrostatic association of polycationic ligands with cellular membranes. Rather than being evenly distributed, PS is found preferentially in the inner leaflet of the plasma membrane and in endocytic membranes. The loss of PS asymmetry is an early indicator of apoptosis and serves as a signal to initiate blood clotting. This review discusses the determinants and functional implications of the subcellular distribution and membrane topology of PS.
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            Is Open Access

            LIPID MAPS online tools for lipid research

            The LIPID MAPS consortium has developed a number of online tools for performing tasks such as drawing lipid structures and predicting possible structures from mass spectrometry (MS) data. A simple online interface has been developed to enable an end-user to rapidly generate a variety of lipid chemical structures, along with corresponding systematic names and ontological information. The structure-drawing tools are available for six categories of lipids: (i) fatty acyls, (ii) glycerolipids, (iii) glycerophospholipids, (iv) cardiolipins, (v) sphingolipids and (vi) sterols. Within each category, the structure-drawing tools support the specification of various parameters such as chain lengths at a specific sn position, head groups, double bond positions and stereochemistry to generate a specific lipid structure. The structure-drawing tools have also been integrated with a second set of online tools which predict possible lipid structures from precursor-ion and product-ion MS experimental data. The MS prediction tools are available for three categories of lipids: (i) mono/di/triacylglycerols, (ii) glycerophospholipids and (iii) cardiolipins. The LIPID MAPS online tools are publicly available at www.lipidmaps.org/tools/.
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              Free radicals, oxidative stress, and antioxidants in human health and disease

              Free radicals and other reactive oxygen species (ROS) are constantly formed in the human body. Free-radical mechanisms have been implicated in the pathology of several human diseases, including cancer, atherosclerosis, malaria, and rheumatoid arthritis and neurodegenerative diseases. For example, the superoxide radical (O2 ·−) and hydrogen peroxide (H2O2) are known to be generated in the brain and nervous system in vivo, and several areas of the human brain are rich in iron, which appears to be easily mobilizable in a form that can stimulate free-radical reactions. Antioxidant defenses to remove O2 ·− and H2O2 exist. Superoxide dismutases (SOD) remove O2 ·− by greatly accelerating its conversion to H2O2. Catalases in peroxisomes convert H2O2 into water and O2 and help to dispose of H2O2 generated by the action of the oxidase enzymes that are located in these organelles. Other important H2O2-removing enzymes in human cells are the glutathione peroxidases. When produced in excess, ROS can cause tissue injury. However, tissue injury can itself cause ROS generation (e.g., by causing activation of phagocytes or releasing transition metal ions from damaged cells), which may (or may not, depending on the situation) contribute to a worsening of the injury. Assessment of oxidative damage to biomolecules by means of emerging technologies based on products of oxidative damage to DNA (e.g., 8-hydroxydeoxyguanosine), lipids (e.g., isoprostanes), and proteins (altered amino acids) would not only advance our understanding of the underlying mechanisms but also facilitate supplementation and intervention studies designed and conducted to test antioxidant efficacy in human health and disease.
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                Author and article information

                Journal
                101231976
                32624
                Nat Chem Biol
                Nat. Chem. Biol.
                Nature chemical biology
                1552-4450
                1552-4469
                14 November 2018
                14 January 2019
                February 2019
                14 July 2019
                : 15
                : 2
                : 169-178
                Affiliations
                [1 ]Department of Biology, Indian Institute of Science Education and Research (IISER), Dr. Homi Bhabha Road, Pashan, Pune
                [2 ]Department of Chemistry, Indian Institute of Science Education and Research (IISER), Dr. Homi Bhabha Road, Pashan, Pune
                Author notes
                [* ]To whom the correspondence should be made: siddhesh@ 123456iiserpune.ac.in
                Article
                EMS80470
                10.1038/s41589-018-0195-0
                6420073
                30643283
                ee805f4d-7a04-423a-9804-3d971ba7e149

                Users may view, print, copy, and download text and data-mine the content in such documents, for the purposes of academic research, subject always to the full Conditions of use: http://www.nature.com/authors/editorial_policies/license.html#terms

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                Biochemistry
                Biochemistry

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