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      The mitochondrial carrier SFXN1 is critical for complex III integrity and cellular metabolism

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          SUMMARY

          Mitochondrial carriers (MCs) mediate the passage of small molecules across the inner mitochondrial membrane (IMM), enabling regulated crosstalk between compartmentalized reactions. Despite MCs representing the largest family of solute carriers in mammals, most have not been subjected to a comprehensive investigation, limiting our understanding of their metabolic contributions. Here, we functionally characterize SFXN1, a member of the non-canonical, sideroflexin family. We find that SFXN1, an integral IMM protein with an uneven number of transmembrane domains, is a TIM22 complex substrate. SFXN1 deficiency leads to mitochondrial respiratory chain impairments, most detrimental to complex III (CIII) biogenesis, activity, and assembly, compromising coenzyme Q levels. The CIII dysfunction is independent of one-carbon metabolism, the known primary role for SFXN1 as a mitochondrial serine transporter. Instead, SFXN1 supports CIII function by participating in heme and α-ketoglutarate metabolism. Our findings highlight the multiple ways that SFXN1-based amino acid transport impacts mitochondrial and cellular metabolic efficiency.

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          In brief

          Acoba et al. show that the amino acid transporter SFXN1 is a cargo of the TIM22 translocon that is important for maintaining complex III function and supports coenzyme Q, heme, and α-ketoglutarate metabolism.

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          Most cited references116

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          Genome engineering using the CRISPR-Cas9 system.

          Targeted nucleases are powerful tools for mediating genome alteration with high precision. The RNA-guided Cas9 nuclease from the microbial clustered regularly interspaced short palindromic repeats (CRISPR) adaptive immune system can be used to facilitate efficient genome engineering in eukaryotic cells by simply specifying a 20-nt targeting sequence within its guide RNA. Here we describe a set of tools for Cas9-mediated genome editing via nonhomologous end joining (NHEJ) or homology-directed repair (HDR) in mammalian cells, as well as generation of modified cell lines for downstream functional studies. To minimize off-target cleavage, we further describe a double-nicking strategy using the Cas9 nickase mutant with paired guide RNAs. This protocol provides experimentally derived guidelines for the selection of target sites, evaluation of cleavage efficiency and analysis of off-target activity. Beginning with target design, gene modifications can be achieved within as little as 1-2 weeks, and modified clonal cell lines can be derived within 2-3 weeks.
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            RNA-guided human genome engineering via Cas9.

            Bacteria and archaea have evolved adaptive immune defenses, termed clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated (Cas) systems, that use short RNA to direct degradation of foreign nucleic acids. Here, we engineer the type II bacterial CRISPR system to function with custom guide RNA (gRNA) in human cells. For the endogenous AAVS1 locus, we obtained targeting rates of 10 to 25% in 293T cells, 13 to 8% in K562 cells, and 2 to 4% in induced pluripotent stem cells. We show that this process relies on CRISPR components; is sequence-specific; and, upon simultaneous introduction of multiple gRNAs, can effect multiplex editing of target loci. We also compute a genome-wide resource of ~190 K unique gRNAs targeting ~40.5% of human exons. Our results establish an RNA-guided editing tool for facile, robust, and multiplexable human genome engineering.
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              One-Carbon Metabolism in Health and Disease.

              One-carbon (1C) metabolism, mediated by the folate cofactor, supports multiple physiological processes. These include biosynthesis (purines and thymidine), amino acid homeostasis (glycine, serine, and methionine), epigenetic maintenance, and redox defense. Both within eukaryotic cells and across organs, 1C metabolic reactions are compartmentalized. Here we review the fundamentals of mammalian 1C metabolism, including the pathways active in different compartments, cell types, and biological states. Emphasis is given to recent discoveries enabled by modern genetics, analytical chemistry, and isotope tracing. An emerging theme is the biological importance of mitochondrial 1C reactions, both for producing 1C units that are exported to the cytosol and for making additional products, including glycine and NADPH. Increased clarity regarding differential folate pathway usage in cancer, stem cells, development, and adult physiology is reviewed and highlights new opportunities for selective therapeutic intervention.
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                Author and article information

                Journal
                101573691
                39703
                Cell Rep
                Cell Rep
                Cell reports
                2211-1247
                20 March 2021
                16 March 2021
                15 April 2021
                : 34
                : 11
                : 108869
                Affiliations
                [1 ]Department of Physiology, The Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
                [2 ]Department of Biological Chemistry, The Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
                [3 ]McKusick-Nathans Institute of Genetic Medicine, The Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
                [4 ]Departments of Pathology and Oncology, The Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
                [5 ]Department of Chemistry and Biochemistry and Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA
                [6 ]Department of Biochemistry and Nebraska Redox Biology Center, University of Nebraska, Lincoln, NE 68588, USA
                [7 ]Fred & Pamela Buffett Cancer Center, Omaha, NE 68198, USA
                [8 ]Present address: Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN 55905, USA
                [9 ]Present address: Nurix Therapeutics, San Francisco, CA 94158, USA
                [10 ]Lead contact
                Author notes

                AUTHOR CONTRIBUTIONS

                M.G.A. and S.M.C. conceptualized the research, interpreted results, and wrote the manuscript, with input and approval from all authors; M.G.A. designed and conducted most of the experiments; E.S.S.A. designed, performed, and analyzed the metabolite quantification and isotope tracing experiments; S.R. performed the SILAC studies; L.F.-d.-R. performed and analyzed the CoQ measurements; Y.-W.L. performed experiments for antibody generation; S.M.C., M.J.W., A.P., C.F.C., and O.K. contributed to the experimental design and data analysis and provided essential reagents.

                [* ]Correspondence: sclaypo1@ 123456jhmi.edu
                Article
                NIHMS1684394
                10.1016/j.celrep.2021.108869
                8048093
                33730581
                c3d473c0-a8f6-4ee4-8f16-aaa6351e7ef8

                This is an open access article under the CC BY-NC-ND license ( http://creativecommons.org/licenses/by-nc-nd/4.0/).

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                Cell biology
                Cell biology

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