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Zhang Y, Li X, Ba Z, Lou J, Gaertner KE, Zhu T, Lin X, Ye AY, Alt FW, Hu H. Molecular basis for differential Igk versus Igh V(D)J joining mechanisms. Nature 2024; 630:189-197. [PMID: 38811728 PMCID: PMC11153149 DOI: 10.1038/s41586-024-07477-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Accepted: 04/26/2024] [Indexed: 05/31/2024]
Abstract
In developing B cells, V(D)J recombination assembles exons encoding IgH and Igκ variable regions from hundreds of gene segments clustered across Igh and Igk loci. V, D and J gene segments are flanked by conserved recombination signal sequences (RSSs) that target RAG endonuclease1. RAG orchestrates Igh V(D)J recombination upon capturing a JH-RSS within the JH-RSS-based recombination centre1-3 (RC). JH-RSS orientation programmes RAG to scan upstream D- and VH-containing chromatin that is presented in a linear manner by cohesin-mediated loop extrusion4-7. During Igh scanning, RAG robustly utilizes only D-RSSs or VH-RSSs in convergent (deletional) orientation with JH-RSSs4-7. However, for Vκ-to-Jκ joining, RAG utilizes Vκ-RSSs from deletional- and inversional-oriented clusters8, inconsistent with linear scanning2. Here we characterize the Vκ-to-Jκ joining mechanism. Igk undergoes robust primary and secondary rearrangements9,10, which confounds scanning assays. We therefore engineered cells to undergo only primary Vκ-to-Jκ rearrangements and found that RAG scanning from the primary Jκ-RC terminates just 8 kb upstream within the CTCF-site-based Sis element11. Whereas Sis and the Jκ-RC barely interacted with the Vκ locus, the CTCF-site-based Cer element12 4 kb upstream of Sis interacted with various loop extrusion impediments across the locus. Similar to VH locus inversion7, DJH inversion abrogated VH-to-DJH joining; yet Vκ locus or Jκ inversion allowed robust Vκ-to-Jκ joining. Together, these experiments implicated loop extrusion in bringing Vκ segments near Cer for short-range diffusion-mediated capture by RC-based RAG. To identify key mechanistic elements for diffusional V(D)J recombination in Igk versus Igh, we assayed Vκ-to-JH and D-to-Jκ rearrangements in hybrid Igh-Igk loci generated by targeted chromosomal translocations, and pinpointed remarkably strong Vκ and Jκ RSSs. Indeed, RSS replacements in hybrid or normal Igk and Igh loci confirmed the ability of Igk-RSSs to promote robust diffusional joining compared with Igh-RSSs. We propose that Igk evolved strong RSSs to mediate diffusional Vκ-to-Jκ joining, whereas Igh evolved weaker RSSs requisite for modulating VH joining by RAG-scanning impediments.
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Affiliation(s)
- Yiwen Zhang
- Howard Hughes Medical Institute, Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Xiang Li
- Howard Hughes Medical Institute, Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Zhaoqing Ba
- Howard Hughes Medical Institute, Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- National Institute of Biological Sciences, Beijing, China
| | - Jiangman Lou
- Howard Hughes Medical Institute, Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Copenhagen University, Copenhagen, Denmark
| | - K Elyse Gaertner
- Howard Hughes Medical Institute, Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Georgetown University, Washington, DC, USA
| | - Tammie Zhu
- Howard Hughes Medical Institute, Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Xin Lin
- Howard Hughes Medical Institute, Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Adam Yongxin Ye
- Howard Hughes Medical Institute, Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Frederick W Alt
- Howard Hughes Medical Institute, Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, USA.
- Department of Genetics, Harvard Medical School, Boston, MA, USA.
| | - Hongli Hu
- Howard Hughes Medical Institute, Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, USA.
- Department of Genetics, Harvard Medical School, Boston, MA, USA.
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2
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Sharma S, Luo M, Patel H, Mueller DM, Liao M. Conformational ensemble of yeast ATP synthase at low pH reveals unique intermediates and plasticity in F 1-F o coupling. Nat Struct Mol Biol 2024; 31:657-666. [PMID: 38316880 DOI: 10.1038/s41594-024-01219-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Accepted: 01/05/2024] [Indexed: 02/07/2024]
Abstract
Mitochondrial adenosine triphosphate (ATP) synthase uses the proton gradient across the inner mitochondrial membrane to synthesize ATP. Structural and single molecule studies conducted mostly at neutral or basic pH have provided details of the reaction mechanism of ATP synthesis. However, pH of the mitochondrial matrix is slightly acidic during hypoxia and pH-dependent conformational changes in the ATP synthase have been reported. Here we use single-particle cryo-EM to analyze the conformational ensemble of the yeast (Saccharomyces cerevisiae) ATP synthase at pH 6. Of the four conformations resolved in this study, three are reaction intermediates. In addition to canonical catalytic dwell and binding dwell structures, we identify two unique conformations with nearly identical positions of the central rotor but different catalytic site conformations. These structures provide new insights into the catalytic mechanism of the ATP synthase and highlight elastic coupling between the catalytic and proton translocating domains.
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Affiliation(s)
- Stuti Sharma
- Department of Cell Biology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA.
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY, USA.
| | - Min Luo
- Department of Cell Biology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
- Department of Biological Sciences, Faculty of Science, National University of Singapore, Singapore, Singapore
| | - Hiral Patel
- Center for Genetic Diseases, The Chicago Medical School, Rosalind Franklin University, North Chicago, IL, USA
| | - David M Mueller
- Center for Genetic Diseases, The Chicago Medical School, Rosalind Franklin University, North Chicago, IL, USA.
| | - Maofu Liao
- Department of Cell Biology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA.
- Department of Chemical Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China.
- Institute for Biological Electron Microscopy, Southern University of Science and Technology, Shenzhen, China.
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3
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Kutnowski N, Ghanim GE, Lee Y, Rio DC. Activity of zebrafish THAP9 transposase and zebrafish P element-like transposons. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.22.586318. [PMID: 38562726 PMCID: PMC10983969 DOI: 10.1101/2024.03.22.586318] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Transposable elements are mobile DNA segments that are found ubiquitously across the three domains of life. One family of transposons, called P elements, were discovered in the fruit fly Drosophila melanogaster. Since their discovery, P element transposase-homologous genes (called THAP-domain containing 9 or THAP9) have been discovered in other animal genomes. Here, we show that the zebrafish (Danio rerio) genome contains both an active THAP9 transposase (zfTHAP9) and mobile P-like transposable elements (called Pdre). zfTHAP9 transposase can excise one of its own elements (Pdre2) and Drosophila P elements. Drosophila P element transposase (DmTNP) is also able to excise the zebrafish Pdre2 element, even though it's distinct from the Drosophila P element. However, zfTHAP9 cannot transpose Pdre2 or Drosophila P elements, indicating partial transposase activity. Characterization of the N-terminal THAP DNA binding domain of zfTHAP9 shows distinct DNA binding site preferences from DmTNP and mutation of the zfTHAP9, based on known mutations in DmTNP, generated a hyperactive protein,. These results define an active vertebrate THAP9 transposase that can act on the endogenous zebrafish Pdre and Drosophila P elements.
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Affiliation(s)
- Nitzan Kutnowski
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
- California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA, USA
| | - George E Ghanim
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
- California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA, USA
| | - Yeon Lee
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
- California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA, USA
| | - Donald C Rio
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
- California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA, USA
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4
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Lin YC, Swendeman S, Moreira IS, Ghosh A, Kuo A, Rosário-Ferreira N, Guo S, Culbertson A, Levesque MV, Cartier A, Seno T, Schmaier A, Galvani S, Inoue A, Parikh SM, FitzGerald GA, Zurakowski D, Liao M, Flaumenhaft R, Gümüş ZH, Hla T. Designer high-density lipoprotein particles enhance endothelial barrier function and suppress inflammation. Sci Signal 2024; 17:eadg9256. [PMID: 38377179 PMCID: PMC10954247 DOI: 10.1126/scisignal.adg9256] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 01/31/2024] [Indexed: 02/22/2024]
Abstract
High-density lipoprotein (HDL) nanoparticles promote endothelial cell (EC) function and suppress inflammation, but their utility in treating EC dysfunction has not been fully explored. Here, we describe a fusion protein named ApoA1-ApoM (A1M) consisting of apolipoprotein A1 (ApoA1), the principal structural protein of HDL that forms lipid nanoparticles, and ApoM, a chaperone for the bioactive lipid sphingosine 1-phosphate (S1P). A1M forms HDL-like particles, binds to S1P, and is signaling competent. Molecular dynamics simulations showed that the S1P-bound ApoM moiety in A1M efficiently activated EC surface receptors. Treatment of human umbilical vein ECs with A1M-S1P stimulated barrier function either alone or cooperatively with other barrier-enhancing molecules, including the stable prostacyclin analog iloprost, and suppressed cytokine-induced inflammation. A1M-S1P injection into mice during sterile inflammation suppressed neutrophil influx and inflammatory mediator secretion. Moreover, systemic A1M administration led to a sustained increase in circulating HDL-bound S1P and suppressed inflammation in a murine model of LPS-induced endotoxemia. We propose that A1M administration may enhance vascular endothelial barrier function, suppress cytokine storm, and promote resilience of the vascular endothelium.
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Affiliation(s)
- Yueh-Chien Lin
- Vascular Biology Program, Boston Children’s Hospital and Department of Surgery, Harvard Medical School, Boston, MA, 02115, USA
| | - Steven Swendeman
- Vascular Biology Program, Boston Children’s Hospital and Department of Surgery, Harvard Medical School, Boston, MA, 02115, USA
| | - Irina S. Moreira
- Department of Life Sciences, University of Coimbra, Calçada Martim de Freitas, 3000-456, Coimbra, Portugal
- CNC - Center for Neuroscience and Cell Biology, Center for Innovative Biomedicine and Biotechnology, University of Coimbra, 3000-456, Coimbra, Portugal
| | - Avishek Ghosh
- Vascular Biology Program, Boston Children’s Hospital and Department of Surgery, Harvard Medical School, Boston, MA, 02115, USA
| | - Andrew Kuo
- Vascular Biology Program, Boston Children’s Hospital and Department of Surgery, Harvard Medical School, Boston, MA, 02115, USA
| | - Nícia Rosário-Ferreira
- CNC - Center for Neuroscience and Cell Biology, Center for Innovative Biomedicine and Biotechnology, University of Coimbra, 3000-456, Coimbra, Portugal
| | | | - Alan Culbertson
- Department of Cell Biology, Harvard Medical School, Boston, MA, 02115, USA
| | - Michel V. Levesque
- Vascular Biology Program, Boston Children’s Hospital and Department of Surgery, Harvard Medical School, Boston, MA, 02115, USA
| | - Andreane Cartier
- Vascular Biology Program, Boston Children’s Hospital and Department of Surgery, Harvard Medical School, Boston, MA, 02115, USA
| | - Takahiro Seno
- Vascular Biology Program, Boston Children’s Hospital and Department of Surgery, Harvard Medical School, Boston, MA, 02115, USA
| | - Alec Schmaier
- Division of Cardiovascular Medicine, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, MA, 02115, USA
| | - Sylvain Galvani
- Vascular Biology Program, Boston Children’s Hospital and Department of Surgery, Harvard Medical School, Boston, MA, 02115, USA
| | - Asuka Inoue
- Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, Miyagi 980-8578, Japan
| | - Samir M. Parikh
- Division of Nephrology and Department of Medicine, Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, Texas, 75235, USA
| | - Garret A. FitzGerald
- Institute for Translational Medicine and Therapeutics, University of Pennsylvania School of Medicine, Philadelphia, PA, 19104, USA
| | - David Zurakowski
- Department of Anesthesia and Surgery, Boston Children’s Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Maofu Liao
- Department of Cell Biology, Harvard Medical School, Boston, MA, 02115, USA
- Department of Chemical Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, 518055, China
- Institute for Biological Electron Microscopy, Southern University of Science and Technology, Shenzhen, 518055, China
| | | | - Zeynep H. Gümüş
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA and Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Timothy Hla
- Vascular Biology Program, Boston Children’s Hospital and Department of Surgery, Harvard Medical School, Boston, MA, 02115, USA
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5
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Shin YC, Latorre-Muro P, Djurabekova A, Zdorevskyi O, Bennett CF, Burger N, Song K, Xu C, Sharma V, Liao M, Puigserver P. Structural basis of respiratory complexes adaptation to cold temperatures. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.16.575914. [PMID: 38293190 PMCID: PMC10827213 DOI: 10.1101/2024.01.16.575914] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2024]
Abstract
In response to cold, mammals activate brown fat for respiratory-dependent thermogenesis reliant on the electron transport chain (1, 2). Yet, the structural basis of respiratory complex adaptation to cold remains elusive. Herein we combined thermoregulatory physiology and cryo-EM to study endogenous respiratory supercomplexes exposed to different temperatures. A cold-induced conformation of CI:III 2 (termed type 2) was identified with a ∼25° rotation of CIII 2 around its inter-dimer axis, shortening inter-complex Q exchange space, and exhibiting different catalytic states which favor electron transfer. Large-scale supercomplex simulations in lipid membrane reveal how unique lipid-protein arrangements stabilize type 2 complexes to enhance catalytic activity. Together, our cryo-EM studies, multiscale simulations and biochemical analyses unveil the mechanisms and dynamics of respiratory adaptation at the structural and energetic level.
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6
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Wang S, Wang K, Song K, Li P, Li D, Sun Y, Mei Y, Xu C, Liao M. Structures of the essential efflux pump EfpA from Mycobacterium tuberculosis reveal the mechanisms of substrate transport and small-molecule inhibition. RESEARCH SQUARE 2024:rs.3.rs-3740027. [PMID: 38260587 PMCID: PMC10802681 DOI: 10.21203/rs.3.rs-3740027/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
As the first identified multidrug efflux pump in Mycobacterium tuberculosis (Mtb), EfpA is an essential protein and promising drug target. However, the functional and inhibitory mechanisms of EfpA are poorly understood. Herein we report cryo-EM structures of EfpA in outward-open conformation, either bound to three endogenous lipids or the inhibitor BRD-8000.3. Three lipids inside EfpA span from the inner leaflet to the outer leaflet of the membrane. BRD-8000.3 occupies one lipid site at the level of inner membrane leaflet, competitively inhibiting lipid binding. EfpA resembles the related lysophospholipid transporter MFSD2A in both overall structure and lipid binding sites, and may function as a lipid flippase. Combining AlphaFold-predicted EfpA structure, which is inward-open, we propose a complete conformational transition cycle for EfpA. Together, our results provide a structural and mechanistic foundation to comprehend EfpA function and develop EfpA-targeting anti-TB drugs.
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Affiliation(s)
- Shuhui Wang
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
- Present address: Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, USA
| | - Kun Wang
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
- Department of Molecular Metabolism, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Kangkang Song
- Department of Biochemistry & Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester, MA, USA
- Cryo-EM Core Facility, University of Massachusetts Medical School, Worcester, MA, USA
| | - Pengfei Li
- Single Particle, LLC, San Diego, CA, USA
| | - Dongying Li
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
- Present address: Cryo-electron microscopy center, Southern University of Science and Technology, Shenzhen, China
| | - Yajie Sun
- Cancer Center, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Ye Mei
- State Key Laboratory of Precision Spectroscopy, School of Physics and Electronic Science, East China Normal University, Shanghai, China
| | - Chen Xu
- Department of Biochemistry & Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester, MA, USA
- Cryo-EM Core Facility, University of Massachusetts Medical School, Worcester, MA, USA
| | - Maofu Liao
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
- Present address: Institute for Biological Electron Microscopy, Southern University of Science and Technology, Shenzhen, China
- Present address: Department of Chemical Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
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7
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Tang D, Kang R, Zeh HJ, Lotze MT. The multifunctional protein HMGB1: 50 years of discovery. Nat Rev Immunol 2023; 23:824-841. [PMID: 37322174 DOI: 10.1038/s41577-023-00894-6] [Citation(s) in RCA: 43] [Impact Index Per Article: 43.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/16/2023] [Indexed: 06/17/2023]
Abstract
Fifty years since the initial discovery of HMGB1 in 1973 as a structural protein of chromatin, HMGB1 is now known to regulate diverse biological processes depending on its subcellular or extracellular localization. These functions include promoting DNA damage repair in the nucleus, sensing nucleic acids and inducing innate immune responses and autophagy in the cytosol and binding protein partners in the extracellular environment and stimulating immunoreceptors. In addition, HMGB1 is a broad sensor of cellular stress that balances cell death and survival responses essential for cellular homeostasis and tissue maintenance. HMGB1 is also an important mediator secreted by immune cells that is involved in a range of pathological conditions, including infectious diseases, ischaemia-reperfusion injury, autoimmunity, cardiovascular and neurodegenerative diseases, metabolic disorders and cancer. In this Review, we discuss the signalling mechanisms, cellular functions and clinical relevance of HMGB1 and describe strategies to modify its release and biological activities in the setting of various diseases.
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Affiliation(s)
- Daolin Tang
- Department of Surgery, UT Southwestern Medical Center, Dallas, TX, USA.
| | - Rui Kang
- Department of Surgery, UT Southwestern Medical Center, Dallas, TX, USA
| | - Herbert J Zeh
- Department of Surgery, UT Southwestern Medical Center, Dallas, TX, USA
| | - Michael T Lotze
- Departments of Surgery, Immunology and Bioengineering, University of Pittsburgh, Pittsburgh, PA, USA.
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8
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Yu L, Xu X, Chua WZ, Feng H, Ser Z, Shao K, Shi J, Wang Y, Li Z, Sobota RM, Sham LT, Luo M. Structural basis of peptide secretion for Quorum sensing by ComA. Nat Commun 2023; 14:7178. [PMID: 37935699 PMCID: PMC10630487 DOI: 10.1038/s41467-023-42852-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Accepted: 10/23/2023] [Indexed: 11/09/2023] Open
Abstract
Quorum sensing (QS) is a crucial regulatory mechanism controlling bacterial signalling and holds promise for novel therapies against antimicrobial resistance. In Gram-positive bacteria, such as Streptococcus pneumoniae, ComA is a conserved efflux pump responsible for the maturation and secretion of peptide signals, including the competence-stimulating peptide (CSP), yet its structure and function remain unclear. Here, we functionally characterize ComA as an ABC transporter with high ATP affinity and determined its cryo-EM structures in the presence or absence of CSP or nucleotides. Our findings reveal a network of strong electrostatic interactions unique to ComA at the intracellular gate, a putative binding pocket for two CSP molecules, and negatively charged residues facilitating CSP translocation. Mutations of these residues affect ComA's peptidase activity in-vitro and prevent CSP export in-vivo. We demonstrate that ATP-Mg2+ triggers the outward-facing conformation of ComA for CSP release, rather than ATP alone. Our study provides molecular insights into the QS signal peptide secretion, highlighting potential targets for QS-targeting drugs.
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Affiliation(s)
- Lin Yu
- Department of Biological Sciences, Faculty of Science, National University of Singapore, Singapore, 117543, Singapore
- Institute of Translational Medicine, Medical College, Yangzhou University, Yangzhou, 225001, Jiangsu, China
| | - Xin Xu
- Department of Biological Sciences, Faculty of Science, National University of Singapore, Singapore, 117543, Singapore
| | - Wan-Zhen Chua
- Infectious Diseases Translational Research Programme and Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117545, Singapore
| | - Hao Feng
- Department of Biological Sciences, Faculty of Science, National University of Singapore, Singapore, 117543, Singapore
| | - Zheng Ser
- Functional Proteomics Laboratory, SingMass National Laboratory, Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), Singapore, 138673, Singapore
| | - Kai Shao
- Department of Biological Sciences, Faculty of Science, National University of Singapore, Singapore, 117543, Singapore
| | - Jian Shi
- Department of Biological Sciences, Faculty of Science, National University of Singapore, Singapore, 117543, Singapore
- Center for Bioimaging Sciences, Department of Biological Sciences, National University of Singapore, Singapore, 117543, Singapore
| | - Yumei Wang
- Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Science, Beijing, 100190, China
| | - Zongli Li
- Harvard Cryo-EM Center for Structural Biology, Harvard Medical School, Boston, MA, 02115, USA
| | - Radoslaw M Sobota
- Functional Proteomics Laboratory, SingMass National Laboratory, Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), Singapore, 138673, Singapore
| | - Lok-To Sham
- Infectious Diseases Translational Research Programme and Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117545, Singapore.
| | - Min Luo
- Department of Biological Sciences, Faculty of Science, National University of Singapore, Singapore, 117543, Singapore.
- Center for Bioimaging Sciences, Department of Biological Sciences, National University of Singapore, Singapore, 117543, Singapore.
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9
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Martin EC, Le Targa L, Tsakou-Ngouafo L, Fan TP, Lin CY, Xiao J, Huang Z, Yuan S, Xu A, Su YH, Petrescu AJ, Pontarotti P, Schatz DG. Insights into RAG Evolution from the Identification of "Missing Link" Family A RAGL Transposons. Mol Biol Evol 2023; 40:msad232. [PMID: 37850912 PMCID: PMC10629977 DOI: 10.1093/molbev/msad232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Revised: 09/28/2023] [Accepted: 10/10/2023] [Indexed: 10/19/2023] Open
Abstract
A series of "molecular domestication" events are thought to have converted an invertebrate RAG-like (RAGL) transposase into the RAG1-RAG2 (RAG) recombinase, a critical enzyme for adaptive immunity in jawed vertebrates. The timing and order of these events are not well understood, in part because of a dearth of information regarding the invertebrate RAGL-A transposon family. In contrast to the abundant and divergent RAGL-B transposon family, RAGL-A most closely resembles RAG and is represented by a single orphan RAG1-like (RAG1L) gene in the genome of the hemichordate Ptychodera flava (PflRAG1L-A). Here, we provide evidence for the existence of complete RAGL-A transposons in the genomes of P. flava and several echinoderms. The predicted RAG1L-A and RAG2L-A proteins encoded by these transposons intermingle sequence features of jawed vertebrate RAG and RAGL-B transposases, leading to a prediction of DNA binding, catalytic, and transposition activities that are a hybrid of RAG and RAGL-B. Similarly, the terminal inverted repeats (TIRs) of the RAGL-A transposons combine features of both RAGL-B transposon TIRs and RAG recombination signal sequences. Unlike all previously described RAG2L proteins, RAG2L-A proteins contain an acidic hinge region, which we demonstrate is capable of efficiently inhibiting RAG-mediated transposition. Our findings provide evidence for a critical intermediate in RAG evolution and argue that certain adaptations thought to be specific to jawed vertebrates (e.g. the RAG2 acidic hinge) actually arose in invertebrates, thereby focusing attention on other adaptations as the pivotal steps in the completion of RAG domestication in jawed vertebrates.
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Affiliation(s)
- Eliza C Martin
- Department of Immunobiology, Yale School of Medicine, New Haven, CT 06520-8011, USA
| | - Lorlane Le Targa
- Aix-Marseille Université, IRD, APHM, MEPHI, IHU Méditerranée Infection, Marseille 13005, France
| | - Louis Tsakou-Ngouafo
- Aix-Marseille Université, IRD, APHM, MEPHI, IHU Méditerranée Infection, Marseille 13005, France
| | - Tzu-Pei Fan
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei 11529, Taiwan
| | - Che-Yi Lin
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei 11529, Taiwan
| | - Jianxiong Xiao
- Department of Immunobiology, Yale School of Medicine, New Haven, CT 06520-8011, USA
| | - Ziwen Huang
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Pharmaceutical Functional Genes, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Shaochun Yuan
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Pharmaceutical Functional Genes, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
| | - Anlong Xu
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Pharmaceutical Functional Genes, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
- School of Life Sciences, Beijing University of Chinese Medicine, Beijing 100029, China
| | - Yi-Hsien Su
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei 11529, Taiwan
| | - Andrei-Jose Petrescu
- Department of Bioinformatics and Structural Biochemistry, Institute of Biochemistry of the Romanian Academy, 060031 Bucharest, Romania
| | - Pierre Pontarotti
- Aix-Marseille Université, IRD, APHM, MEPHI, IHU Méditerranée Infection, Marseille 13005, France
- CNRS SNC 5039, 13005 Marseille, France
| | - David G Schatz
- Department of Immunobiology, Yale School of Medicine, New Haven, CT 06520-8011, USA
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10
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Martin EC, Le Targa L, Tsakou-Ngouafo L, Fan TP, Lin CY, Xiao J, Su YH, Petrescu AJ, Pontarotti P, Schatz DG. Insights into RAG evolution from the identification of "missing link" family A RAGL transposons. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.20.553239. [PMID: 37645967 PMCID: PMC10462144 DOI: 10.1101/2023.08.20.553239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/31/2023]
Abstract
A series of "molecular domestication" events are thought to have converted an invertebrate RAG-like (RAGL) transposase into the RAG1-RAG2 (RAG) recombinase, a critical enzyme for adaptive immunity in jawed vertebrates. The timing and order of these events is not well understood, in part because of a dearth of information regarding the invertebrate RAGL-A transposon family. In contrast to the abundant and divergent RAGL-B transposon family, RAGL-A most closely resembles RAG and is represented by a single orphan RAG1-like (RAG1L) gene in the genome of the hemichordate Ptychodera flava (PflRAG1L-A). Here, we provide evidence for the existence of complete RAGL-A transposons in the genomes of P. flava and several echinoderms. The predicted RAG1L-A and RAG2L-A proteins encoded by these transposons intermingle sequence features of jawed vertebrate RAG and RAGL-B transposases, leading to a prediction of DNA binding, catalytic, and transposition activities that are a hybrid of RAG and RAGL-B. Similarly, the terminal inverted repeats (TIRs) of the RAGL-A transposons combine features of both RAGL-B transposon TIRs and RAG recombination signal sequences. Unlike all previously described RAG2L proteins, PflRAG2L-A and echinoderm RAG2L-A contain an acidic hinge region, which we demonstrate is capable of efficiently inhibiting RAG-mediated transposition. Our findings provide evidence for a critical intermediate in RAG evolution and argue that certain adaptations thought to be specific to jawed vertebrates (e.g., the RAG2 acidic hinge) actually arose in invertebrates, thereby focusing attention on other adaptations as the pivotal steps in the completion of RAG domestication in jawed vertebrates.
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Affiliation(s)
- Eliza C. Martin
- Department of Immunobiology, Yale School of Medicine, 300 Cedar Street, Box 208011, New Haven, CT, 06520-8011, United States
| | - Lorlane Le Targa
- Aix-Marseille Université, IRD, APHM, MEPHI, IHU Méditerranée Infection, Marseille France
| | - Louis Tsakou-Ngouafo
- Aix-Marseille Université, IRD, APHM, MEPHI, IHU Méditerranée Infection, Marseille France
| | - Tzu-Pei Fan
- Institute of Cellular and Organismic Biology, Academia Sinica, 128 Academia Rd., Sec. 2, Nankang, Taipei 11529, Taiwan
| | - Che-Yi Lin
- Institute of Cellular and Organismic Biology, Academia Sinica, 128 Academia Rd., Sec. 2, Nankang, Taipei 11529, Taiwan
| | - Jianxiong Xiao
- Department of Immunobiology, Yale School of Medicine, 300 Cedar Street, Box 208011, New Haven, CT, 06520-8011, United States
| | - Yi Hsien Su
- Institute of Cellular and Organismic Biology, Academia Sinica, 128 Academia Rd., Sec. 2, Nankang, Taipei 11529, Taiwan
| | - Andrei-Jose Petrescu
- Department of Bioinformatics and Structural Biochemistry, Institute of Biochemistry of the Romanian Academy, Splaiul Independentei 296, 060031, Bucharest, Romania
| | - Pierre Pontarotti
- Aix-Marseille Université, IRD, APHM, MEPHI, IHU Méditerranée Infection, Marseille France
- CNRS SNC 5039, 13005 Marseille, France
| | - David G. Schatz
- Department of Immunobiology, Yale School of Medicine, 300 Cedar Street, Box 208011, New Haven, CT, 06520-8011, United States
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11
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Del Pozo-Yauner L, Herrera GA, Perez Carreon JI, Turbat-Herrera EA, Rodriguez-Alvarez FJ, Ruiz Zamora RA. Role of the mechanisms for antibody repertoire diversification in monoclonal light chain deposition disorders: when a friend becomes foe. Front Immunol 2023; 14:1203425. [PMID: 37520549 PMCID: PMC10374031 DOI: 10.3389/fimmu.2023.1203425] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Accepted: 06/20/2023] [Indexed: 08/01/2023] Open
Abstract
The adaptive immune system of jawed vertebrates generates a highly diverse repertoire of antibodies to meet the antigenic challenges of a constantly evolving biological ecosystem. Most of the diversity is generated by two mechanisms: V(D)J gene recombination and somatic hypermutation (SHM). SHM introduces changes in the variable domain of antibodies, mostly in the regions that form the paratope, yielding antibodies with higher antigen binding affinity. However, antigen recognition is only possible if the antibody folds into a stable functional conformation. Therefore, a key force determining the survival of B cell clones undergoing somatic hypermutation is the ability of the mutated heavy and light chains to efficiently fold and assemble into a functional antibody. The antibody is the structural context where the selection of the somatic mutations occurs, and where both the heavy and light chains benefit from protective mechanisms that counteract the potentially deleterious impact of the changes. However, in patients with monoclonal gammopathies, the proliferating plasma cell clone may overproduce the light chain, which is then secreted into the bloodstream. This places the light chain out of the protective context provided by the quaternary structure of the antibody, increasing the risk of misfolding and aggregation due to destabilizing somatic mutations. Light chain-derived (AL) amyloidosis, light chain deposition disease (LCDD), Fanconi syndrome, and myeloma (cast) nephropathy are a diverse group of diseases derived from the pathologic aggregation of light chains, in which somatic mutations are recognized to play a role. In this review, we address the mechanisms by which somatic mutations promote the misfolding and pathological aggregation of the light chains, with an emphasis on AL amyloidosis. We also analyze the contribution of the variable domain (VL) gene segments and somatic mutations on light chain cytotoxicity, organ tropism, and structure of the AL fibrils. Finally, we analyze the most recent advances in the development of computational algorithms to predict the role of somatic mutations in the cardiotoxicity of amyloidogenic light chains and discuss the challenges and perspectives that this approach faces.
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Affiliation(s)
- Luis Del Pozo-Yauner
- Department of Pathology, University of South Alabama-College of Medicine, Mobile, AL, United States
| | - Guillermo A. Herrera
- Department of Pathology, University of South Alabama-College of Medicine, Mobile, AL, United States
| | | | - Elba A. Turbat-Herrera
- Department of Pathology, University of South Alabama-College of Medicine, Mobile, AL, United States
- Mitchell Cancer Institute, University of South Alabama-College of Medicine, Mobile, AL, United States
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12
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Sui X, Wang K, Song K, Xu C, Song J, Lee CW, Liao M, Farese RV, Walther TC. Mechanism of action for small-molecule inhibitors of triacylglycerol synthesis. Nat Commun 2023; 14:3100. [PMID: 37248213 PMCID: PMC10227072 DOI: 10.1038/s41467-023-38934-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Accepted: 05/23/2023] [Indexed: 05/31/2023] Open
Abstract
Inhibitors of triacylglycerol (TG) synthesis have been developed to treat metabolism-related diseases, but we know little about their mechanisms of action. Here, we report cryo-EM structures of the TG-synthesis enzyme acyl-CoA:diacylglycerol acyltransferase 1 (DGAT1), a membrane bound O-acyltransferase (MBOAT), in complex with two different inhibitors, T863 and DGAT1IN1. Each inhibitor binds DGAT1's fatty acyl-CoA substrate binding tunnel that opens to the cytoplasmic side of the ER. T863 blocks access to the tunnel entrance, whereas DGAT1IN1 extends further into the enzyme, with an amide group interacting with more deeply buried catalytic residues. A survey of DGAT1 inhibitors revealed that this amide group may serve as a common pharmacophore for inhibition of MBOATs. The inhibitors were minimally active against the related MBOAT acyl-CoA:cholesterol acyltransferase 1 (ACAT1), yet a single-residue mutation sensitized ACAT1 for inhibition. Collectively, our studies provide a structural foundation for developing DGAT1 and other MBOAT inhibitors.
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Affiliation(s)
- Xuewu Sui
- Department of Molecular Metabolism, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
- Department of Biochemistry and Biophysics, College of Agriculture and Life Sciences, Texas A&M University, College Station, TX, USA
| | - Kun Wang
- Department of Molecular Metabolism, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
| | - Kangkang Song
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester, MA, USA
- Cryo-EM Core Facility, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Chen Xu
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester, MA, USA
- Cryo-EM Core Facility, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Jiunn Song
- Department of Molecular Metabolism, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
| | - Chia-Wei Lee
- Department of Molecular Metabolism, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
| | - Maofu Liao
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA.
- School of Life Sciences, Southern University of Science and Technology, Shenzhen, China.
| | - Robert V Farese
- Department of Molecular Metabolism, Harvard T.H. Chan School of Public Health, Boston, MA, USA.
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Cell Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
| | - Tobias C Walther
- Department of Molecular Metabolism, Harvard T.H. Chan School of Public Health, Boston, MA, USA.
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Cell Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
- Howard Hughes Medical Institute, Boston, MA, USA.
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13
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Spínola-Amilibia M, Araújo-Bazán L, de la Gándara Á, Berger JM, Arias-Palomo E. IS21 family transposase cleaved donor complex traps two right-handed superhelical crossings. Nat Commun 2023; 14:2335. [PMID: 37087515 PMCID: PMC10122671 DOI: 10.1038/s41467-023-38071-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Accepted: 04/14/2023] [Indexed: 04/24/2023] Open
Abstract
Transposases are ubiquitous enzymes that catalyze DNA rearrangement events with broad impacts on gene expression, genome evolution, and the spread of drug-resistance in bacteria. Here, we use biochemical and structural approaches to define the molecular determinants by which IstA, a transposase present in the widespread IS21 family of mobile elements, catalyzes efficient DNA transposition. Solution studies show that IstA engages the transposon terminal sequences to form a high-molecular weight complex and promote DNA integration. A 3.4 Å resolution structure of the transposase bound to transposon ends corroborates our biochemical findings and reveals that IstA self-assembles into a highly intertwined tetramer that synapses two supercoiled terminal inverted repeats. The three-dimensional organization of the IstA•DNA cleaved donor complex reveals remarkable similarities with retroviral integrases and classic transposase systems, such as Tn7 and bacteriophage Mu, and provides insights into IS21 transposition.
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Affiliation(s)
- Mercedes Spínola-Amilibia
- Department of Structural & Chemical Biology, Centro de Investigaciones Biológicas Margarita Salas, CSIC, Madrid, 28040, Spain
| | - Lidia Araújo-Bazán
- Department of Structural & Chemical Biology, Centro de Investigaciones Biológicas Margarita Salas, CSIC, Madrid, 28040, Spain
| | - Álvaro de la Gándara
- Department of Structural & Chemical Biology, Centro de Investigaciones Biológicas Margarita Salas, CSIC, Madrid, 28040, Spain
| | - James M Berger
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Ernesto Arias-Palomo
- Department of Structural & Chemical Biology, Centro de Investigaciones Biológicas Margarita Salas, CSIC, Madrid, 28040, Spain.
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14
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Zhang Y, Li Q, Luo L, Duan C, Shen J, Wang Z. Application of germline antibody features to vaccine development, antibody discovery, antibody optimization and disease diagnosis. Biotechnol Adv 2023; 65:108143. [PMID: 37023966 DOI: 10.1016/j.biotechadv.2023.108143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Revised: 03/26/2023] [Accepted: 03/29/2023] [Indexed: 04/08/2023]
Abstract
Although the efficacy and commercial success of vaccines and therapeutic antibodies have been tremendous, designing and discovering new drug candidates remains a labor-, time- and cost-intensive endeavor with high risks. The main challenges of vaccine development are inducing a strong immune response in broad populations and providing effective prevention against a group of highly variable pathogens. Meanwhile, antibody discovery faces several great obstacles, especially the blindness in antibody screening and the unpredictability of the developability and druggability of antibody drugs. These challenges are largely due to poorly understanding of germline antibodies and the antibody responses to pathogen invasions. Thanks to the recent developments in high-throughput sequencing and structural biology, we have gained insight into the germline immunoglobulin (Ig) genes and germline antibodies and then the germline antibody features associated with antigens and disease manifestation. In this review, we firstly outline the broad associations between germline antibodies and antigens. Moreover, we comprehensively review the recent applications of antigen-specific germline antibody features, physicochemical properties-associated germline antibody features, and disease manifestation-associated germline antibody features on vaccine development, antibody discovery, antibody optimization, and disease diagnosis. Lastly, we discuss the bottlenecks and perspectives of current and potential applications of germline antibody features in the biotechnology field.
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Affiliation(s)
- Yingjie Zhang
- National Key Laboratory of Veterinary Public Health Security, Beijing Key Laboratory of Detection Technology for Animal-Derived Food, College of Veterinary Medicine, China Agricultural University, 100193 Beijing, People's Republic of China
| | - Qing Li
- National Key Laboratory of Veterinary Public Health Security, Beijing Key Laboratory of Detection Technology for Animal-Derived Food, College of Veterinary Medicine, China Agricultural University, 100193 Beijing, People's Republic of China
| | - Liang Luo
- National Key Laboratory of Veterinary Public Health Security, Beijing Key Laboratory of Detection Technology for Animal-Derived Food, College of Veterinary Medicine, China Agricultural University, 100193 Beijing, People's Republic of China
| | - Changfei Duan
- National Key Laboratory of Veterinary Public Health Security, Beijing Key Laboratory of Detection Technology for Animal-Derived Food, College of Veterinary Medicine, China Agricultural University, 100193 Beijing, People's Republic of China
| | - Jianzhong Shen
- National Key Laboratory of Veterinary Public Health Security, Beijing Key Laboratory of Detection Technology for Animal-Derived Food, College of Veterinary Medicine, China Agricultural University, 100193 Beijing, People's Republic of China
| | - Zhanhui Wang
- National Key Laboratory of Veterinary Public Health Security, Beijing Key Laboratory of Detection Technology for Animal-Derived Food, College of Veterinary Medicine, China Agricultural University, 100193 Beijing, People's Republic of China.
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15
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Kenter AL, Priyadarshi S, Drake EB. Locus architecture and RAG scanning determine antibody diversity. Trends Immunol 2023; 44:119-128. [PMID: 36706738 PMCID: PMC10128066 DOI: 10.1016/j.it.2022.12.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 12/07/2022] [Accepted: 12/08/2022] [Indexed: 01/27/2023]
Abstract
Diverse mammalian antibody repertoires are produced via distant genomic contacts involving immunoglobulin Igh variable (V), diversity (D), and joining (J) gene segments and result in V(D)J recombination. How such interactions determine V gene usage remains unclear. The recombination-activating gene (RAG) chromatin scanning model posits that RAG recombinase bound to the recombination center (RC) linearly tracks along chromatin by means of cohesin-mediated loop extrusion; a proposition supported by cohesin depletion studies. A mechanistic role for chromatin loop extrusion has also been implicated for Igh locus contraction. In this opinion, we provide perspective on how loop extrusion interfaces with the 3D conformation of the Igh locus and newly identified enhancers that regionally regulate VH gene usage during V(D)J recombination, shaping the preselected repertoire.
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Affiliation(s)
- Amy L Kenter
- Department of Microbiology and Immunology, University of Illinois College of Medicine, Chicago, IL 60612-7344, USA.
| | - Saurabh Priyadarshi
- Department of Microbiology and Immunology, University of Illinois College of Medicine, Chicago, IL 60612-7344, USA
| | - Ellen B Drake
- Department of Microbiology and Immunology, University of Illinois College of Medicine, Chicago, IL 60612-7344, USA
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16
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Yakovenko I, Tobi D, Ner-Gaon H, Oren M. Different sea urchin RAG-like genes were domesticated to carry out different functions. Front Immunol 2023; 13:1066510. [PMID: 36726993 PMCID: PMC9885083 DOI: 10.3389/fimmu.2022.1066510] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Accepted: 12/29/2022] [Indexed: 01/18/2023] Open
Abstract
The closely linked recombination activating genes (RAG1 and RAG2) in vertebrates encode the core of the RAG recombinase that mediates the V(D)J recombination of the immunoglobulin and T-cell receptor genes. RAG1 and RAG2 homologues (RAG1L and RAG2L) are present in multiple invertebrate phyla, including mollusks, nemerteans, cnidarians, and sea urchins. However, the function of the invertebrates' RAGL proteins is yet unknown. The sea urchins contain multiple RAGL genes that presumably originated in a common ancestral transposon. In this study, we demonstrated that two different RAG1L genes in the sea urchin Paracentrutus lividus (PlRAG1La and PlRAG1Lb) lost their mobility and, along with PlRAG2L, were fully domesticated to carry out different functions. We found that the examined echinoid RAGL homologues have distinct expression profiles in early developmental stages and in adult tissues. Moreover, the predicted structure of the proteins suggests that while PlRAG1La could maintain its endonuclease activity and create a heterotetramer with PlRAG2L, the PlRAG1Lb adopted a different function that does not include an interaction with DNA nor a collaboration with PlRAG2L. By characterizing the different RAG homologues in the echinoid lineage, we hope to increase the knowledge about the evolution of these genes and shed light on their domestication processes.
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Affiliation(s)
- Iryna Yakovenko
- Department of Molecular Biology, Ariel University, Ariel, Israel,*Correspondence: Matan Oren, ; Iryna Yakovenko,
| | - Dror Tobi
- Department of Molecular Biology, Ariel University, Ariel, Israel,Department of Computer Sciences, Ariel University, Ariel, Israel
| | - Hadas Ner-Gaon
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Matan Oren
- Department of Molecular Biology, Ariel University, Ariel, Israel,*Correspondence: Matan Oren, ; Iryna Yakovenko,
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17
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AKDENİZ FATMATUBA, AKBULUT ZEYNEP, VAYVADA MUSTAFA, KALAMANOĞLU BALCI MERİH, YEGİNSU ALİ, YANIKKAYA DEMİREL GULDEREN, KUTLU CEMALASIM. Monitoring T-Cell Kinetics in the Early Recovery Period of Lung Transplantation Cases by Copy Number Levels of T-Cell Receptor Excision Circle. In Vivo 2023; 37:310-319. [PMID: 36593057 PMCID: PMC9843769 DOI: 10.21873/invivo.13081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 10/21/2022] [Accepted: 11/10/2022] [Indexed: 01/04/2023]
Abstract
BACKGROUND/AIM Lung transplantation is a life-saving procedure for patients with end-stage lung diseases. T-Cell receptor excision circle (TREC) is circular DNA produced during T-cell receptor gene rearrangement in the thymus and indicates naive T-cell migration from the thymus. Therefore, its levels represent thymic T-cell output. Post-transplant lymphocyte kinetics correlate with graft tolerance. The aim of this study was to investigate T-lymphocyte kinetics in the early recovery period after lung transplantation. For this purpose, copy numbers of TREC were determined in patients with a lung transplant. In addition, TREC copy numbers were evaluated according to age, diagnosis and the forced expiratory volume in 1 second (FEV1) of lung transplant patients. MATERIALS AND METHODS Peripheral blood samples were taken from patients aged 23 to 59 years who underwent lung transplantation at the Thoracic Surgery Clinic, Kartal-Koşuyolu High Specialization Educational and Research Hospital. This study included peripheral blood samples from 11 lung transplant patients (comprising four with chronic obstructive pulmonary disease, three with idiopathic pulmonary fibrosis, one with cystic fibrosis, one with silicosis and two with bronchiectasis; three females in total). Samples were taken at three different timepoints: Before transplant, and 24 hours and 7 days post transplant. TREC copy numbers were analyzed with real time reverse transcriptase-polymerase chain reaction. RESULTS Post-transplant TREC numbers and density values were higher compared to pre-transplant values, although these differences were statistically insignificant. TREC copy numbers were found to be significantly higher in patients younger than 45 years compared to patients older than 45 years. At 24 hours after the transplant, the average TREC copy number/peripheral blood mononuclear cells of the cases with an FEV1 value of or below 50% was found to be statistically significantly higher than that of cases with an FEV1 value above 50% (p=0.046). There was no statistically significant difference in TREC copy numbers between male and female patients or by diagnostic group. CONCLUSION TREC copy numbers can be evaluated as a prognostic marker for lung transplantation. There is a need for multicenter studies with more patients.
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Affiliation(s)
- FATMA TUBA AKDENİZ
- Department of Medical Biology, Faculty of Medicine, Yeditepe University, Istanbul, Turkey
| | - ZEYNEP AKBULUT
- Department of Medical Biology and Genetic, Faculty of Medicine, Maltepe University, Istanbul, Turkey
| | - MUSTAFA VAYVADA
- Thoracic Surgery Clinic, Kartal-Koşuyolu High Specialization Educational and Research Hospital, Istanbul, Turkey
| | | | - ALİ YEGİNSU
- Thoracic Surgery Clinic, Liv Hospital Vadi, Istanbul, Turkey
| | | | - CEMAL ASIM KUTLU
- Department of Chest Disease, Faculty of Medicine, Bahçeşehir University, Istanbul, Turkey
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18
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Hoolehan W, Harris JC, Byrum JN, Simpson DA, Rodgers K. An updated definition of V(D)J recombination signal sequences revealed by high-throughput recombination assays. Nucleic Acids Res 2022; 50:11696-11711. [PMID: 36370096 PMCID: PMC9723617 DOI: 10.1093/nar/gkac1038] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Revised: 10/18/2022] [Accepted: 10/24/2022] [Indexed: 11/13/2022] Open
Abstract
In the adaptive immune system, V(D)J recombination initiates the production of a diverse antigen receptor repertoire in developing B and T cells. Recombination activating proteins, RAG1 and RAG2 (RAG1/2), catalyze V(D)J recombination by cleaving adjacent to recombination signal sequences (RSSs) that flank antigen receptor gene segments. Previous studies defined the consensus RSS as containing conserved heptamer and nonamer sequences separated by a less conserved 12 or 23 base-pair spacer sequence. However, many RSSs deviate from the consensus sequence. Here, we developed a cell-based, massively parallel assay to evaluate V(D)J recombination activity on thousands of RSSs where the 12-RSS heptamer and adjoining spacer region contained randomized sequences. While the consensus heptamer sequence (CACAGTG) was marginally preferred, V(D)J recombination was highly active on a wide range of non-consensus sequences. Select purine/pyrimidine motifs that may accommodate heptamer unwinding in the RAG1/2 active site were generally preferred. In addition, while different coding flanks and nonamer sequences affected recombination efficiency, the relative dependency on the purine/pyrimidine motifs in the RSS heptamer remained unchanged. Our results suggest RAG1/2 specificity for RSS heptamers is primarily dictated by DNA structural features dependent on purine/pyrimidine pattern, and to a lesser extent, RAG:RSS base-specific interactions.
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Affiliation(s)
- Walker Hoolehan
- Department of Biochemistry and Molecular Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
| | - Justin C Harris
- Department of Biochemistry and Molecular Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
| | - Jennifer N Byrum
- Department of Biochemistry and Molecular Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
| | - Destiny A Simpson
- Department of Biochemistry and Molecular Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
| | - Karla K Rodgers
- To whom correspondence should be addressed. Tel: +1 405 271 2227 (Ext 61248);
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19
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The role of chromatin loop extrusion in antibody diversification. Nat Rev Immunol 2022; 22:550-566. [PMID: 35169260 PMCID: PMC9376198 DOI: 10.1038/s41577-022-00679-3] [Citation(s) in RCA: 43] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/12/2022] [Indexed: 12/15/2022]
Abstract
Cohesin mediates chromatin loop formation across the genome by extruding chromatin between convergently oriented CTCF-binding elements. Recent studies indicate that cohesin-mediated loop extrusion in developing B cells presents immunoglobulin heavy chain (Igh) variable (V), diversity (D) and joining (J) gene segments to RAG endonuclease through a process referred to as RAG chromatin scanning. RAG initiates V(D)J recombinational joining of these gene segments to generate the large number of different Igh variable region exons that are required for immune responses to diverse pathogens. Antigen-activated mature B cells also use chromatin loop extrusion to mediate the synapsis, breakage and end joining of switch regions flanking Igh constant region exons during class-switch recombination, which allows for the expression of different antibody constant region isotypes that optimize the functions of antigen-specific antibodies to eliminate pathogens. Here, we review recent advances in our understanding of chromatin loop extrusion during V(D)J recombination and class-switch recombination at the Igh locus.
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20
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Park JU, Tsai AWL, Chen TH, Peters JE, Kellogg EH. Mechanistic details of CRISPR-associated transposon recruitment and integration revealed by cryo-EM. Proc Natl Acad Sci U S A 2022; 119:e2202590119. [PMID: 35914146 PMCID: PMC9371665 DOI: 10.1073/pnas.2202590119] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 06/04/2022] [Indexed: 11/18/2022] Open
Abstract
CRISPR-associated transposons (CASTs) are Tn7-like elements that are capable of RNA-guided DNA integration. Although structural data are known for nearly all core transposition components, the transposase component, TnsB, remains uncharacterized. Using cryo-electron microscopy (cryo-EM) structure determination, we reveal the conformation of TnsB during transposon integration for the type V-K CAST system from Scytonema hofmanni (ShCAST). Our structure of TnsB is a tetramer, revealing strong mechanistic relationships with the overall architecture of RNaseH transposases/integrases in general, and in particular the MuA transposase from bacteriophage Mu. However, key structural differences in the C-terminal domains indicate that TnsB's tetrameric architecture is stabilized by a different set of protein-protein interactions compared with MuA. We describe the base-specific interactions along the TnsB binding site, which explain how different CAST elements can function on cognate mobile elements independent of one another. We observe that melting of the 5' nontransferred strand of the transposon end is a structural feature stabilized by TnsB and furthermore is crucial for donor-DNA integration. Although not observed in the TnsB strand-transfer complex, the C-terminal end of TnsB serves a crucial role in transposase recruitment to the target site. The C-terminal end of TnsB adopts a short, structured 15-residue "hook" that decorates TnsC filaments. Unlike full-length TnsB, C-terminal fragments do not appear to stimulate filament disassembly using two different assays, suggesting that additional interactions between TnsB and TnsC are required for redistributing TnsC to appropriate targets. The structural information presented here will help guide future work in modifying these important systems as programmable gene integration tools.
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Affiliation(s)
- Jung-Un Park
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853
| | - Amy Wei-Lun Tsai
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853
| | - Tiffany H Chen
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853
| | - Joseph E Peters
- Department of Microbiology, Cornell University, Ithaca, NY 14853
| | - Elizabeth H Kellogg
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853
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21
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Laffleur B, Batista CR, Zhang W, Lim J, Yang B, Rossille D, Wu L, Estrella J, Rothschild G, Pefanis E, Basu U. RNA exosome drives early B cell development via noncoding RNA processing mechanisms. Sci Immunol 2022; 7:eabn2738. [PMID: 35658015 DOI: 10.1126/sciimmunol.abn2738] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
B cell development is linked to successful V(D)J recombination, allowing B cell receptor expression and ultimately antibody secretion for adaptive immunity. Germline noncoding RNAs (ncRNAs) are produced at immunoglobulin (Ig) loci during V(D)J recombination, but their function and posttranscriptional regulation are incompletely understood. Patients with trichohepatoenteric syndrome, characterized by RNA exosome pathway component mutations, exhibit lymphopenia, thus demonstrating the importance of ncRNA surveillance in B cell development in humans. To understand the role of RNA exosome in early B cell development in greater detail, we generated mouse models harboring a B cell-specific cre allele (Mb1cre), coupled to conditional inversion-deletion alleles of one RNA exosome core component (Exosc3) or RNase catalytic subunits (Exosc10 or Dis3). We noticed increased expression of RNA exosome subunits during V(D)J recombination, whereas a B cell developmental blockade at the pro-B cell stage was observed in the different knockout mice, overlapping with a lack of productive rearrangements of VDJ genes at the Ig heavy chain (Igh). This unsuccessful recombination prevented differentiation into pre-B cells, with accumulation of ncRNAs and up-regulation of the p53 pathway. Introduction of a prearranged Igh VDJ allele partly rescued the pre-B cell population in Dis3-deficient cells, although V-J recombination defects were observed at Ig light chain kappa (Igκ), preventing subsequent B cell development. These observations demonstrated that the RNA exosome complex is important for Igh and Igκ recombination and establish the relevance of RNA processing for optimal diversification at these loci during B cell development.
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Affiliation(s)
- Brice Laffleur
- Department of Microbiology and Immunology, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA
| | - Carolina R Batista
- Department of Microbiology and Immunology, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA
| | - Wanwei Zhang
- Department of Microbiology and Immunology, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA
| | - Junghyun Lim
- Department of Microbiology and Immunology, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA
| | - Biao Yang
- Department of Microbiology and Immunology, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA
| | - Delphine Rossille
- Universite of Rennes, INSERM, EFS Bretagne, CHU Rennes, UMR 1236, Rennes, France
| | - Lijing Wu
- Department of Microbiology and Immunology, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA
| | - Jerson Estrella
- Department of Microbiology and Immunology, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA
| | - Gerson Rothschild
- Department of Microbiology and Immunology, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA
| | | | - Uttiya Basu
- Department of Microbiology and Immunology, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA
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22
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Structural insights into the evolution of the RAG recombinase. Nat Rev Immunol 2022; 22:353-370. [PMID: 34675378 DOI: 10.1038/s41577-021-00628-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/09/2021] [Indexed: 11/09/2022]
Abstract
Adaptive immunity in jawed vertebrates relies on the assembly of antigen receptor genes by the recombination activating gene 1 (RAG1)-RAG2 (collectively RAG) recombinase in a reaction known as V(D)J recombination. Extensive biochemical and structural evidence indicates that RAG and V(D)J recombination evolved from the components of a RAG-like (RAGL) transposable element through a process known as transposon molecular domestication. This Review describes recent advances in our understanding of the functional and structural transitions that occurred during RAG evolution. We use the structures of RAG and RAGL enzymes to trace the evolutionary adaptations that yielded a RAG recombinase with exquisitely regulated cleavage activity and a multilayered array of mechanisms to suppress transposition. We describe how changes in modes of DNA binding, alterations in the dynamics of protein-DNA complexes, single amino acid mutations and a modular design likely enabled RAG family enzymes to survive and spread in the genomes of eukaryotes. These advances highlight the insight that can be gained from viewing evolution of vertebrate immunity through the lens of comparative genome analyses coupled with structural biology and biochemistry.
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23
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Luo S, Qiao R, Zhang X. DNA Damage Response and Repair in Adaptive Immunity. Front Cell Dev Biol 2022; 10:884873. [PMID: 35663402 PMCID: PMC9157429 DOI: 10.3389/fcell.2022.884873] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2022] [Accepted: 03/31/2022] [Indexed: 11/16/2022] Open
Abstract
The diversification of B-cell receptor (BCR), as well as its secreted product, antibody, is a hallmark of adaptive immunity, which has more specific roles in fighting against pathogens. The antibody diversification is from recombination-activating gene (RAG)-initiated V(D)J recombination, activation-induced cytidine deaminase (AID)-initiated class switch recombination (CSR), and V(D)J exon somatic hypermutation (SHM). The proper repair of RAG- and AID-initiated DNA lesions and double-strand breaks (DSBs) is required for promoting antibody diversification, suppressing genomic instability, and oncogenic translocations. DNA damage response (DDR) factors and DSB end-joining factors are recruited to the RAG- and AID-initiated DNA lesions and DSBs to coordinately resolve them for generating productive recombination products during antibody diversification. Recently, cohesin-mediated loop extrusion is proposed to be the underlying mechanism of V(D)J recombination and CSR, which plays essential roles in promoting the orientation-biased deletional end-joining . Here, we will discuss the mechanism of DNA damage repair in antibody diversification.
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Affiliation(s)
- Sha Luo
- Biomedical Pioneering Innovation Center, Innovation Center for Genomics, Peking University, Beijing, China
- Academy for Advanced Interdisciplinery Studies, Peking University, Beijing, China
| | - Ruolin Qiao
- Biomedical Pioneering Innovation Center, Innovation Center for Genomics, Peking University, Beijing, China
- Academy for Advanced Interdisciplinery Studies, Peking University, Beijing, China
| | - Xuefei Zhang
- Biomedical Pioneering Innovation Center, Innovation Center for Genomics, Peking University, Beijing, China
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24
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Treder KP, Huang C, Kim JS, Kirkland AI. Applications of deep learning in electron microscopy. Microscopy (Oxf) 2022; 71:i100-i115. [DOI: 10.1093/jmicro/dfab043] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Revised: 08/30/2021] [Accepted: 11/08/2021] [Indexed: 12/25/2022] Open
Abstract
Abstract
We review the growing use of machine learning in electron microscopy (EM) driven in part by the availability of fast detectors operating at kiloHertz frame rates leading to large data sets that cannot be processed using manually implemented algorithms. We summarize the various network architectures and error metrics that have been applied to a range of EM-related problems including denoising and inpainting. We then provide a review of the application of these in both physical and life sciences, highlighting how conventional networks and training data have been specifically modified for EM.
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Affiliation(s)
- Kevin P Treder
- Department of Materials, University of Oxford, Oxford, Oxfordshire OX1 3PH, UK
| | - Chen Huang
- Rosalind Franklin Institute, Harwell Research Campus, Didcot, Oxfordshire OX11 0FA, UK
| | - Judy S Kim
- Department of Materials, University of Oxford, Oxford, Oxfordshire OX1 3PH, UK
- Rosalind Franklin Institute, Harwell Research Campus, Didcot, Oxfordshire OX11 0FA, UK
| | - Angus I Kirkland
- Department of Materials, University of Oxford, Oxford, Oxfordshire OX1 3PH, UK
- Rosalind Franklin Institute, Harwell Research Campus, Didcot, Oxfordshire OX11 0FA, UK
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25
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Jin YB, Cao X, Shi CW, Feng B, Huang HB, Jiang YL, Wang JZ, Yang GL, Yang WT, Wang CF. Lactobacillus rhamnosus GG Promotes Early B Lineage Development and IgA Production in the Lamina Propria in Piglets. THE JOURNAL OF IMMUNOLOGY 2021; 207:2179-2191. [PMID: 34497150 DOI: 10.4049/jimmunol.2100102] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Accepted: 08/04/2021] [Indexed: 01/04/2023]
Abstract
Gut microbes play an important role in the development of host B cells. It has been controversial whether GALT is the development site of B cells in pigs. By investigating the relationship between gut microbes and the development of B cells in the GALT of piglets, we found, to our knowledge for the first time, that early B cells exist in the gut lamina propria (LP) in pigs at different ages. We further used Lactobacillus rhamnosus GG (LGG) to treat piglets. The results showed that LGG promotes the development of the early B lineage, affects the composition of the Ig CDR3 repertoires of B cells, and promotes the production of IgA in the intestinal LP. Additionally, we found that the p40 protein derived from LGG can activate the EGFR/AKT and NF-κB signaling pathways, inducing porcine intestinal epithelial cells (IPEC-J2) to secrete a proliferation-inducing ligand (APRIL), which promotes IgA production in B cells. Finally, we identified ARF4 and DIF3 as candidates for p40 receptors on IPEC-J2 by GST pull-down, liquid chromatography-mass spectrometry/mass spectrometry analysis, and coimmunoprecipitation. In conclusion, LGG could promote early B cell differentiation and development in the intestinal LP in piglets and might contribute to promoting IgA production via secretion of p40, which interacts with the membrane receptors on IPEC-J2 and induces them to secrete APRIL. Our study will provide insight to aid in better utilization of probiotics to increase human health.
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Affiliation(s)
- Yu-Bei Jin
- College of Animal Science and Technology, Jilin Provincial Engineering Research Center of Animal Probiotics, Key Laboratory of Animal Production and Product Quality Safety of Ministry of Education, Jilin Agricultural University, Changchun, China; and.,Guangdong Key Laboratory of Regional Immunity and Diseases, Department of Pathogen Biology, Shenzhen University School of Medicine, Shenzhen, China
| | - Xin Cao
- College of Animal Science and Technology, Jilin Provincial Engineering Research Center of Animal Probiotics, Key Laboratory of Animal Production and Product Quality Safety of Ministry of Education, Jilin Agricultural University, Changchun, China; and
| | - Chun-Wei Shi
- College of Animal Science and Technology, Jilin Provincial Engineering Research Center of Animal Probiotics, Key Laboratory of Animal Production and Product Quality Safety of Ministry of Education, Jilin Agricultural University, Changchun, China; and
| | - Bo Feng
- College of Animal Science and Technology, Jilin Provincial Engineering Research Center of Animal Probiotics, Key Laboratory of Animal Production and Product Quality Safety of Ministry of Education, Jilin Agricultural University, Changchun, China; and
| | - Hai-Bin Huang
- College of Animal Science and Technology, Jilin Provincial Engineering Research Center of Animal Probiotics, Key Laboratory of Animal Production and Product Quality Safety of Ministry of Education, Jilin Agricultural University, Changchun, China; and
| | - Yan-Long Jiang
- College of Animal Science and Technology, Jilin Provincial Engineering Research Center of Animal Probiotics, Key Laboratory of Animal Production and Product Quality Safety of Ministry of Education, Jilin Agricultural University, Changchun, China; and
| | - Jian-Zhong Wang
- College of Animal Science and Technology, Jilin Provincial Engineering Research Center of Animal Probiotics, Key Laboratory of Animal Production and Product Quality Safety of Ministry of Education, Jilin Agricultural University, Changchun, China; and
| | - Gui-Lian Yang
- College of Animal Science and Technology, Jilin Provincial Engineering Research Center of Animal Probiotics, Key Laboratory of Animal Production and Product Quality Safety of Ministry of Education, Jilin Agricultural University, Changchun, China; and
| | - Wen-Tao Yang
- College of Animal Science and Technology, Jilin Provincial Engineering Research Center of Animal Probiotics, Key Laboratory of Animal Production and Product Quality Safety of Ministry of Education, Jilin Agricultural University, Changchun, China; and
| | - Chun-Feng Wang
- College of Animal Science and Technology, Jilin Provincial Engineering Research Center of Animal Probiotics, Key Laboratory of Animal Production and Product Quality Safety of Ministry of Education, Jilin Agricultural University, Changchun, China; and
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26
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Gan T, Wang Y, Liu Y, Schatz DG, Hu J. RAG2 abolishes RAG1 aggregation to facilitate V(D)J recombination. Cell Rep 2021; 37:109824. [PMID: 34644584 DOI: 10.1016/j.celrep.2021.109824] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Revised: 02/09/2021] [Accepted: 09/21/2021] [Indexed: 11/26/2022] Open
Abstract
RAG1 and RAG2 form a tetramer nuclease to initiate V(D)J recombination in developing T and B lymphocytes. The RAG1 protein evolves from a transposon ancestor and possesses nuclease activity that requires interaction with RAG2. Here, we show that the human RAG1 aggregates in the nucleus in the absence of RAG2, exhibiting an extremely low V(D)J recombination activity. In contrast, RAG2 does not aggregate by itself, but it interacts with RAG1 to disrupt RAG1 aggregates and thereby activate robust V(D)J recombination. Moreover, RAG2 from mouse and zebrafish could not disrupt the aggregation of human RAG1 as efficiently as human RAG2 did, indicating a species-specific regulatory mechanism for RAG1 by RAG2. Therefore, we propose that RAG2 coevolves with RAG1 to release inert RAG1 from aggregates and thereby activate V(D)J recombination to generate diverse antigen receptors in lymphocytes.
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Affiliation(s)
- Tingting Gan
- The MOE Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Yuhong Wang
- The MOE Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Yang Liu
- The MOE Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - David G Schatz
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06519, USA
| | - Jiazhi Hu
- The MOE Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China.
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27
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Sharma S, Zhou R, Wan L, Feng S, Song K, Xu C, Li Y, Liao M. Mechanism of LolCDE as a molecular extruder of bacterial triacylated lipoproteins. Nat Commun 2021; 12:4687. [PMID: 34344901 PMCID: PMC8333309 DOI: 10.1038/s41467-021-24965-1] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Accepted: 07/16/2021] [Indexed: 02/07/2023] Open
Abstract
Lipoproteins are important for bacterial growth and antibiotic resistance. These proteins use lipid acyl chains attached to the N-terminal cysteine residue to anchor on the outer surface of cytoplasmic membrane. In Gram-negative bacteria, many lipoproteins are transported to the outer membrane (OM), a process dependent on the ATP-binding cassette (ABC) transporter LolCDE which extracts the OM-targeted lipoproteins from the cytoplasmic membrane. Lipid-anchored proteins pose a unique challenge for transport machinery as they have both hydrophobic lipid moieties and soluble protein component, and the underlying mechanism is poorly understood. Here we determined the cryo-EM structures of nanodisc-embedded LolCDE in the nucleotide-free and nucleotide-bound states at 3.8-Å and 3.5-Å resolution, respectively. The structural analyses, together with biochemical and mutagenesis studies, uncover how LolCDE recognizes its substrate by interacting with the lipid and N-terminal peptide moieties of the lipoprotein, and identify the amide-linked acyl chain as the key element for LolCDE interaction. Upon nucleotide binding, the transmembrane helices and the periplasmic domains of LolCDE undergo large-scale, asymmetric movements, resulting in extrusion of the captured lipoprotein. Comparison of LolCDE and MacB reveals the conserved mechanism of type VII ABC transporters and emphasizes the unique properties of LolCDE as a molecule extruder of triacylated lipoproteins.
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Affiliation(s)
- Stuti Sharma
- grid.38142.3c000000041936754XDepartment of Cell Biology, Blavatnik Institute, Harvard Medical School, Boston, MA USA
| | - Ruoyu Zhou
- grid.494629.40000 0004 8008 9315Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, China
| | - Li Wan
- grid.494629.40000 0004 8008 9315Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, China
| | - Shan Feng
- grid.494629.40000 0004 8008 9315Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, China
| | - KangKang Song
- grid.168645.80000 0001 0742 0364Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA USA ,grid.168645.80000 0001 0742 0364Cryo-EM Core Facility, University of Massachusetts Medical School, Worcester, MA USA
| | - Chen Xu
- grid.168645.80000 0001 0742 0364Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA USA ,grid.168645.80000 0001 0742 0364Cryo-EM Core Facility, University of Massachusetts Medical School, Worcester, MA USA
| | - Yanyan Li
- grid.494629.40000 0004 8008 9315Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, China
| | - Maofu Liao
- grid.38142.3c000000041936754XDepartment of Cell Biology, Blavatnik Institute, Harvard Medical School, Boston, MA USA
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28
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Wood CAP, Zhang J, Aydin D, Xu Y, Andreone BJ, Langen UH, Dror RO, Gu C, Feng L. Structure and mechanism of blood-brain-barrier lipid transporter MFSD2A. Nature 2021; 596:444-448. [PMID: 34349262 PMCID: PMC8884080 DOI: 10.1038/s41586-021-03782-y] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Accepted: 06/29/2021] [Indexed: 02/07/2023]
Abstract
MFSD2A is a sodium-dependent lysophosphatidylcholine symporter that is responsible for the uptake of docosahexaenoic acid into the brain1,2, which is crucial for the development and performance of the brain3. Mutations that affect MFSD2A cause microcephaly syndromes4,5. The ability of MFSD2A to transport lipid is also a key mechanism that underlies its function as an inhibitor of transcytosis to regulate the blood-brain barrier6,7. Thus, MFSD2A represents an attractive target for modulating the permeability of the blood-brain barrier for drug delivery. Here we report the cryo-electron microscopy structure of mouse MFSD2A. Our structure defines the architecture of this important transporter, reveals its unique extracellular domain and uncovers its substrate-binding cavity. The structure-together with our functional studies and molecular dynamics simulations-identifies a conserved sodium-binding site, reveals a potential lipid entry pathway and helps to rationalize MFSD2A mutations that underlie microcephaly syndromes. These results shed light on the critical lipid transport function of MFSD2A and provide a framework to aid in the design of specific modulators for therapeutic purposes.
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Affiliation(s)
- Chase A P Wood
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA
| | - Jinru Zhang
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA
| | - Deniz Aydin
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA.,Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA.,Department of Computer Science, Stanford University, Stanford, CA, USA.,Institute for Computational and Mathematical Engineering, Stanford University, Stanford, CA, USA
| | - Yan Xu
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA
| | | | - Urs H Langen
- Department of Neurobiology, Harvard Medical School, Boston, MA, USA
| | - Ron O Dror
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA.,Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA.,Department of Computer Science, Stanford University, Stanford, CA, USA.,Institute for Computational and Mathematical Engineering, Stanford University, Stanford, CA, USA
| | - Chenghua Gu
- Department of Neurobiology, Harvard Medical School, Boston, MA, USA
| | - Liang Feng
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA. .,Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA.
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29
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Yarema NM, Boyarchuk OR, Chornomydz IB, Panasiuk YV. Numerical and Structural Chromosomal Abnormalities Associated with Immunodeficiency. CYTOL GENET+ 2021. [DOI: 10.3103/s0095452721040137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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30
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Chen X, Gellert M, Yang W. Inner workings of RAG recombinase and its specialization for adaptive immunity. Curr Opin Struct Biol 2021; 71:79-86. [PMID: 34245989 DOI: 10.1016/j.sbi.2021.05.014] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 05/31/2021] [Indexed: 01/03/2023]
Abstract
RAG1/2 (RAG) is an RNH-type DNA recombinase specially evolved to initiate V(D)J gene rearrangement for generating the adaptive immune response in jawed vertebrates. After decades of frustration with little mechanistic understanding of RAG, the crystal structure of mouse RAG recombinase opened the flood gates in early 2015. Structures of three different chordate RAG recombinases, including protoRAG, and the evolutionarily preceding transib transposase have been determined in complex with various DNA substrates. Biochemical studies along with the abundant structural data have shed light on how RAG has evolved from an ordinary transposase to a specialized recombinase in initiating gene rearrangement. RAG has also become one of the best characterized RNH-type recombinases, illustrating how a single active site can cleave the two antiparallel DNA strands of a double helix.
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Affiliation(s)
- Xuemin Chen
- Laboratory of Molecular Biology, NIDDK, National Institutes of Health, Bethesda, MD 20892, USA
| | - Martin Gellert
- Laboratory of Molecular Biology, NIDDK, National Institutes of Health, Bethesda, MD 20892, USA
| | - Wei Yang
- Laboratory of Molecular Biology, NIDDK, National Institutes of Health, Bethesda, MD 20892, USA.
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31
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Yuan M, Wang Y, Qin M, Zhao X, Chen X, Li D, Miao Y, Otieno Odhiambo W, Liu H, Ma Y, Ji Y. RAG enhances BCR-ABL1-positive leukemic cell growth through its endonuclease activity in vitro and in vivo. Cancer Sci 2021; 112:2679-2691. [PMID: 33949040 PMCID: PMC8253288 DOI: 10.1111/cas.14939] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Revised: 04/15/2021] [Accepted: 04/30/2021] [Indexed: 12/14/2022] Open
Abstract
BCR-ABL1 gene fusion associated with additional DNA lesions involves the pathogenesis of chronic myelogenous leukemia (CML) from a chronic phase (CP) to a blast crisis of B lymphoid (CML-LBC) lineage and BCR-ABL1+ acute lymphoblastic leukemia (BCR-ABL1+ ALL). The recombination-activating gene RAG1 and RAG2 (collectively, RAG) proteins that assemble a diverse set of antigen receptor genes during lymphocyte development are abnormally expressed in CML-LBC and BCR-ABL1+ ALL. However, the direct involvement of dysregulated RAG in disease progression remains unclear. Here, we generate human wild-type (WT) RAG and catalytically inactive RAG-expressing BCR-ABL1+ and BCR-ABL1- cell lines, respectively, and demonstrate that BCR-ABL1 specifically collaborates with RAG recombinase to promote cell survival in vitro and in xenograft mice models. WT RAG-expressing BCR-ABL1+ cell lines and primary CD34+ bone marrow cells from CML-LBC samples maintain more double-strand breaks (DSB) compared to catalytically inactive RAG-expressing BCR-ABL1+ cell lines and RAG-deficient CML-CP samples, which are measured by γ-H2AX. WT RAG-expressing BCR-ABL1+ cells are biased to repair RAG-mediated DSB by the alternative non-homologous end joining pathway (a-NHEJ), which could contribute genomic instability through increasing the expression of a-NHEJ-related MRE11 and RAD50 proteins. As a result, RAG-expressing BCR-ABL1+ cells decrease sensitivity to tyrosine kinase inhibitors (TKI) by activating BCR-ABL1 signaling but independent of the levels of BCR-ABL1 expression and mutations in the BCR-ABL1 tyrosine kinase domain. These findings identify a surprising and novel role of RAG in the functional specialization of disease progression in BCR-ABL1+ leukemia through its endonuclease activity.
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MESH Headings
- Acid Anhydride Hydrolases/metabolism
- Animals
- Blast Crisis/genetics
- Blast Crisis/metabolism
- Cell Line, Tumor
- Cell Proliferation
- Cell Survival
- DNA Breaks, Double-Stranded
- DNA End-Joining Repair
- DNA-Binding Proteins/deficiency
- DNA-Binding Proteins/genetics
- DNA-Binding Proteins/metabolism
- Disease Progression
- Endonucleases/metabolism
- Fusion Proteins, bcr-abl/genetics
- Fusion Proteins, bcr-abl/metabolism
- Genomic Instability
- Heterografts
- Histones/analysis
- Homeodomain Proteins/genetics
- Homeodomain Proteins/metabolism
- Humans
- In Vitro Techniques
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/genetics
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/metabolism
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/pathology
- MRE11 Homologue Protein/metabolism
- Mice
- Mice, Inbred NOD
- Mice, SCID
- Nuclear Proteins/deficiency
- Nuclear Proteins/genetics
- Nuclear Proteins/metabolism
- Precursor Cell Lymphoblastic Leukemia-Lymphoma/genetics
- Precursor Cell Lymphoblastic Leukemia-Lymphoma/metabolism
- Protein Kinase Inhibitors/therapeutic use
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Affiliation(s)
- Meng Yuan
- Department of Pathogenic Biology and Immunology, School of Basic Medical SciencesXi’an Jiaotong University Health Science CenterXi’anChina
| | - Yang Wang
- Department of Pathogenic Biology and Immunology, School of Basic Medical SciencesXi’an Jiaotong University Health Science CenterXi’anChina
| | - Mengting Qin
- Department of Pathogenic Biology and Immunology, School of Basic Medical SciencesXi’an Jiaotong University Health Science CenterXi’anChina
| | - Xiaohui Zhao
- Department of Pathogenic Biology and Immunology, School of Basic Medical SciencesXi’an Jiaotong University Health Science CenterXi’anChina
| | - Xiaodong Chen
- Department of Pathogenic Biology and Immunology, School of Basic Medical SciencesXi’an Jiaotong University Health Science CenterXi’anChina
| | - Dandan Li
- Department of Pathogenic Biology and Immunology, School of Basic Medical SciencesXi’an Jiaotong University Health Science CenterXi’anChina
| | - Yinsha Miao
- Department of Pathogenic Biology and Immunology, School of Basic Medical SciencesXi’an Jiaotong University Health Science CenterXi’anChina
- Department of Clinical laboratoryXi’an No. 3 HospitalThe Affiliated Hospital of Northwest UniversityXi’anChina
| | - Wood Otieno Odhiambo
- Department of Pathogenic Biology and Immunology, School of Basic Medical SciencesXi’an Jiaotong University Health Science CenterXi’anChina
| | - Huasheng Liu
- Department of HematologyThe First Affiliated Hospital of Xi’an Jiaotong UniversityXi’anChina
| | - Yunfeng Ma
- Department of Pathogenic Biology and Immunology, School of Basic Medical SciencesXi’an Jiaotong University Health Science CenterXi’anChina
| | - Yanhong Ji
- Department of Pathogenic Biology and Immunology, School of Basic Medical SciencesXi’an Jiaotong University Health Science CenterXi’anChina
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32
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Ku70 suppresses alternative end joining in G1-arrested progenitor B cells. Proc Natl Acad Sci U S A 2021; 118:2103630118. [PMID: 34006647 DOI: 10.1073/pnas.2103630118] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Classical nonhomologous end joining (C-NHEJ) repairs DNA double-strand breaks (DSBs) throughout interphase but predominates in G1 phase when homologous recombination is unavailable. Complexes containing the Ku70/80 ("Ku") and XRCC4/ligase IV (Lig4) core C-NHEJ factors are required, respectively, for sensing and joining DSBs. While XRCC4/Lig4 are absolutely required for joining RAG1/2 endonuclease ("RAG")-initiated DSBs during V(D)J recombination in G1-phase progenitor lymphocytes, cycling cells deficient for XRCC4/Lig4 also can join chromosomal DSBs by alternative end-joining (A-EJ) pathways. Restriction of V(D)J recombination by XRCC4/Lig4-mediated joining has been attributed to RAG shepherding V(D)J DSBs exclusively into the C-NHEJ pathway. Here, we report that A-EJ of DSB ends generated by RAG1/2, Cas9:gRNA, and Zinc finger endonucleases in Lig4-deficient G1-arrested progenitor B cell lines is suppressed by Ku. Thus, while diverse DSBs remain largely as free broken ends in Lig4-deficient G1-arrested progenitor B cells, deletion of Ku70 increases DSB rejoining and translocation levels to those observed in Ku70-deficient counterparts. Correspondingly, while RAG-initiated V(D)J DSB joining is abrogated in Lig4-deficient G1-arrested progenitor B cell lines, joining of RAG-generated DSBs in Ku70-deficient and Ku70/Lig4 double-deficient lines occurs through a translocation-like A-EJ mechanism. Thus, in G1-arrested, Lig4-deficient progenitor B cells are functionally end-joining suppressed due to Ku-dependent blockage of A-EJ, potentially in association with G1-phase down-regulation of Lig1. Finally, we suggest that differential impacts of Ku deficiency versus Lig4 deficiency on V(D)J recombination, neuronal apoptosis, and embryonic development results from Ku-mediated inhibition of A-EJ in the G1 cell cycle phase in Lig4-deficient developing lymphocyte and neuronal cells.
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Lugo-Reyes SO, Pastor N, González-Serrano E, Yamazaki-Nakashimada MA, Scheffler-Mendoza S, Berron-Ruiz L, Wakida G, Nuñez-Nuñez ME, Macias-Robles AP, Staines-Boone AT, Venegas-Montoya E, Alaez-Verson C, Molina-Garay C, Flores-Lagunes LL, Carrillo-Sanchez K, Niemela J, Rosenzweig SD, Gaytan P, Yañez JA, Martinez-Duncker I, Notarangelo LD, Espinosa-Padilla S, Cruz-Munoz ME. Clinical Manifestations, Mutational Analysis, and Immunological Phenotype in Patients with RAG1/2 Mutations: First Cases Series from Mexico and Description of Two Novel Mutations. J Clin Immunol 2021; 41:1291-1302. [PMID: 33954879 DOI: 10.1007/s10875-021-01052-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Accepted: 04/20/2021] [Indexed: 11/25/2022]
Abstract
Mutations in recombinase activating genes 1 and 2 (RAG1/2) result in human severe combined immunodeficiency (SCID). The products of these genes are essential for V(D)J rearrangement of the antigen receptors during lymphocyte development. Mutations resulting in null-recombination activity in RAG1 or RAG2 are associated with the most severe clinical and immunological phenotypes, whereas patients with hypomorphic mutations may develop leaky SCID, including Omenn syndrome (OS). A group of previously unrecognized clinical phenotypes associated with granulomata and/or autoimmunity have been described as a consequence of hypomorphic mutations. Here, we present six patients from unrelated families with missense variants in RAG1 or RAG2. Phenotypes observed in these patients ranged from OS to severe mycobacterial infections and granulomatous disease. Moreover, we report the first evidence of two variants that had not been associated with immunodeficiency. This study represents the first case series of RAG1- or RAG2-deficient patients from Mexico and Latin America.
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Affiliation(s)
| | - Nina Pastor
- Centro de Investigación en Dinámica Celular, Universidad Autónoma del Estado de Morelos, Cuernavaca, Mexico
| | | | | | | | - Laura Berron-Ruiz
- Laboratorio de Inmunodeficiencias, Instituto Nacional de Pediatría, Mexico City, Mexico
| | - Guillermo Wakida
- Laboratorio de Inmunodeficiencias, Instituto Nacional de Pediatría, Mexico City, Mexico
| | | | | | | | - Edna Venegas-Montoya
- Unidad Médica de Alta Especialidad 25, Instituto Mexicano del Seguro Social, Mexico City, Mexico
| | | | | | | | | | - Julie Niemela
- Laboratory of Clinical Immunology and Microbiology, National Institute of Health, Mexico City, Mexico
| | - Sergio D Rosenzweig
- Laboratory of Clinical Immunology and Microbiology, National Institute of Health, Mexico City, Mexico
| | - Paul Gaytan
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Jorge A Yañez
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Ivan Martinez-Duncker
- Centro de Investigación en Dinámica Celular, Universidad Autónoma del Estado de Morelos, Cuernavaca, Mexico
| | - Luigi D Notarangelo
- Laboratory of Clinical Immunology and Microbiology, National Institute of Health, Mexico City, Mexico
| | - Sara Espinosa-Padilla
- Laboratorio de Inmunodeficiencias, Instituto Nacional de Pediatría, Mexico City, Mexico.
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34
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Bosticardo M, Pala F, Notarangelo LD. RAG deficiencies: Recent advances in disease pathogenesis and novel therapeutic approaches. Eur J Immunol 2021; 51:1028-1038. [PMID: 33682138 PMCID: PMC8325549 DOI: 10.1002/eji.202048880] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Revised: 01/13/2021] [Accepted: 03/03/2021] [Indexed: 12/26/2022]
Abstract
The RAG1 and RAG2 proteins initiate the process of V(D)J recombination and therefore play an essential role in adaptive immunity. While null mutations in the RAG genes cause severe combined immune deficiency with lack of T and B cells (T- B- SCID) and susceptibility to life-threatening, early-onset infections, studies in humans and mice have demonstrated that hypomorphic RAG mutations are associated with defects of central and peripheral tolerance resulting in immune dysregulation. In this review, we provide an overview of the extended spectrum of RAG deficiencies and their associated clinical and immunological phenotypes in humans. We discuss recent advances in the mechanisms that control RAG expression and function, the effects of perturbed RAG activity on lymphoid development and immune homeostasis, and propose novel approaches to correct this group of disorders.
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Affiliation(s)
- Marita Bosticardo
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Francesca Pala
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Luigi D Notarangelo
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
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35
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Wu GS, Yang-Iott KS, Klink MA, Hayer KE, Lee KD, Bassing CH. Poor quality Vβ recombination signal sequences stochastically enforce TCRβ allelic exclusion. J Exp Med 2021; 217:151853. [PMID: 32526772 PMCID: PMC7478721 DOI: 10.1084/jem.20200412] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Revised: 05/06/2020] [Accepted: 05/12/2020] [Indexed: 12/15/2022] Open
Abstract
The monoallelic expression of antigen receptor (AgR) genes, called allelic exclusion, is fundamental for highly specific immune responses to pathogens. This cardinal feature of adaptive immunity is achieved by the assembly of a functional AgR gene on one allele, with subsequent feedback inhibition of V(D)J recombination on the other allele. A range of epigenetic mechanisms have been implicated in sequential recombination of AgR alleles; however, we now demonstrate that a genetic mechanism controls this process for Tcrb. Replacement of V(D)J recombinase targets at two different mouse Vβ gene segments with a higher quality target elevates Vβ rearrangement frequency before feedback inhibition, dramatically increasing the frequency of T cells with TCRβ chains derived from both Tcrb alleles. Thus, TCRβ allelic exclusion is enforced genetically by the low quality of Vβ recombinase targets that stochastically restrict the production of two functional rearrangements before feedback inhibition silences one allele.
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Affiliation(s)
- Glendon S Wu
- Immunology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA.,Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Katherine S Yang-Iott
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Morgann A Klink
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Katharina E Hayer
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Kyutae D Lee
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Craig H Bassing
- Immunology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA.,Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
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36
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Zhong ED, Bepler T, Berger B, Davis JH. CryoDRGN: reconstruction of heterogeneous cryo-EM structures using neural networks. Nat Methods 2021; 18:176-185. [PMID: 33542510 PMCID: PMC8183613 DOI: 10.1038/s41592-020-01049-4] [Citation(s) in RCA: 222] [Impact Index Per Article: 74.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Accepted: 12/18/2020] [Indexed: 12/18/2022]
Abstract
Cryo-electron microscopy (cryo-EM) single-particle analysis has proven powerful in determining the structures of rigid macromolecules. However, many imaged protein complexes exhibit conformational and compositional heterogeneity that poses a major challenge to existing three-dimensional reconstruction methods. Here, we present cryoDRGN, an algorithm that leverages the representation power of deep neural networks to directly reconstruct continuous distributions of 3D density maps and map per-particle heterogeneity of single-particle cryo-EM datasets. Using cryoDRGN, we uncovered residual heterogeneity in high-resolution datasets of the 80S ribosome and the RAG complex, revealed a new structural state of the assembling 50S ribosome, and visualized large-scale continuous motions of a spliceosome complex. CryoDRGN contains interactive tools to visualize a dataset's distribution of per-particle variability, generate density maps for exploratory analysis, extract particle subsets for use with other tools and generate trajectories to visualize molecular motions. CryoDRGN is open-source software freely available at http://cryodrgn.csail.mit.edu .
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Affiliation(s)
- Ellen D Zhong
- Computational and Systems Biology, Massachusetts Institute of Technology, Cambridge, MA, USA.,Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Tristan Bepler
- Computational and Systems Biology, Massachusetts Institute of Technology, Cambridge, MA, USA.,Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Bonnie Berger
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA, USA. .,Department of Mathematics, Massachusetts Institute of Technology, Cambridge, MA, USA.
| | - Joseph H Davis
- Computational and Systems Biology, Massachusetts Institute of Technology, Cambridge, MA, USA. .,Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA.
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37
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Shi B, Dong X, Ma Q, Sun S, Ma L, Yu J, Wang X, Pan J, He X, Su D, Yao X. The Usage of Human IGHJ Genes Follows a Particular Non-random Selection: The Recombination Signal Sequence May Affect the Usage of Human IGHJ Genes. Front Genet 2020; 11:524413. [PMID: 33363565 PMCID: PMC7753069 DOI: 10.3389/fgene.2020.524413] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Accepted: 11/06/2020] [Indexed: 12/02/2022] Open
Abstract
The formation of the B cell receptor (BCR) heavy chain variable region is derived from the germline V(D)J gene rearrangement according to the “12/23” rule and the “beyond 12/23” rule. The usage frequency of each V(D)J gene in the peripheral BCR repertoires is related to the initial recombination, self-tolerance selection, and the clonal proliferative response. However, their specific differences and possible mechanisms are still unknown. We analyzed in-frame and out-of-frame BCR-H repertoires from human samples with normal physiological and various pathological conditions by high-throughput sequencing. Our results showed that IGHJ gene frequency follows a similar pattern which is previously known, where IGHJ4 is used at high frequency (>40%), IGHJ6/IGHJ3/IGHJ5 is used at medium frequencies (10∼20%), and IGH2/IGHJ1 is used at low frequency (<4%) under whether normal physiological or various pathological conditions. However, our analysis of the recombination signal sequences suggested that the conserved non-amer and heptamer and certain 23 bp spacer length may affect the initial IGHD-IGHJ recombination, which results in different frequencies of IGHJ genes among the initial BCR-H repertoire. Based on this “initial repertoire,” we recommend that re-evaluation and further investigation are needed when analyzing the significance and mechanism of IGHJ gene frequency in self-tolerance selection and the clonal proliferative response.
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Affiliation(s)
- Bin Shi
- Department of Laboratory Medicine, Affiliated Hospital of Zunyi Medical University, Zunyi, China.,School of Laboratory Medicine, Zunyi Medical University, Zunyi, China
| | - Xiaoheng Dong
- Department of Immunology, Center of Immunomolecular Engineering, Innovation & Practice Base for Graduate Students Education, Zunyi Medical University, Zunyi, China
| | - Qingqing Ma
- Department of Immunology, Center of Immunomolecular Engineering, Innovation & Practice Base for Graduate Students Education, Zunyi Medical University, Zunyi, China
| | - Suhong Sun
- Department of Breast Surgery, Affiliated Hospital of Zunyi Medical University, Zunyi, China
| | - Long Ma
- Department of Immunology, Center of Immunomolecular Engineering, Innovation & Practice Base for Graduate Students Education, Zunyi Medical University, Zunyi, China
| | - Jiang Yu
- Department of Immunology, Center of Immunomolecular Engineering, Innovation & Practice Base for Graduate Students Education, Zunyi Medical University, Zunyi, China
| | - Xiaomei Wang
- Department of Immunology, Center of Immunomolecular Engineering, Innovation & Practice Base for Graduate Students Education, Zunyi Medical University, Zunyi, China
| | - Juan Pan
- Department of Immunology, Center of Immunomolecular Engineering, Innovation & Practice Base for Graduate Students Education, Zunyi Medical University, Zunyi, China
| | - Xiaoyan He
- Department of Immunology, Center of Immunomolecular Engineering, Innovation & Practice Base for Graduate Students Education, Zunyi Medical University, Zunyi, China
| | - Danhua Su
- Department of Immunology, Center of Immunomolecular Engineering, Innovation & Practice Base for Graduate Students Education, Zunyi Medical University, Zunyi, China
| | - Xinsheng Yao
- Department of Immunology, Center of Immunomolecular Engineering, Innovation & Practice Base for Graduate Students Education, Zunyi Medical University, Zunyi, China
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38
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Ghanim GE, Rio DC, Teixeira FK. Mechanism and regulation of P element transposition. Open Biol 2020; 10:200244. [PMID: 33352068 PMCID: PMC7776569 DOI: 10.1098/rsob.200244] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Accepted: 11/26/2020] [Indexed: 12/05/2022] Open
Abstract
P elements were first discovered in the fruit fly Drosophila melanogaster as the causative agents of a syndrome of aberrant genetic traits called hybrid dysgenesis. This occurs when P element-carrying males mate with females that lack P elements and results in progeny displaying sterility, mutations and chromosomal rearrangements. Since then numerous genetic, developmental, biochemical and structural studies have culminated in a deep understanding of P element transposition: from the cellular regulation and repression of transposition to the mechanistic details of the transposase nucleoprotein complex. Recent studies have revealed how piwi-interacting small RNA pathways can act to control splicing of the P element pre-mRNA to modulate transposase production in the germline. A recent cryo-electron microscopy structure of the P element transpososome reveals an unusual DNA architecture at the transposon termini and shows that the bound GTP cofactor functions to position the transposon ends within the transposase active site. Genome sequencing efforts have shown that there are P element transposase-homologous genes (called THAP9) in other animal genomes, including humans. This review highlights recent and previous studies, which together have led to new insights, and surveys our current understanding of the biology, biochemistry, mechanism and regulation of P element transposition.
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Affiliation(s)
- George E. Ghanim
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
- California Institute for Quantitative Biosciences, University of California, Berkeley, CA 94720, USA
| | - Donald C. Rio
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
- California Institute for Quantitative Biosciences, University of California, Berkeley, CA 94720, USA
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39
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Mastio J, Saeed MB, Wurzer H, Krecke M, Westerberg LS, Thomas C. Higher Incidence of B Cell Malignancies in Primary Immunodeficiencies: A Combination of Intrinsic Genomic Instability and Exocytosis Defects at the Immunological Synapse. Front Immunol 2020; 11:581119. [PMID: 33240268 PMCID: PMC7680899 DOI: 10.3389/fimmu.2020.581119] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Accepted: 10/09/2020] [Indexed: 12/11/2022] Open
Abstract
Congenital defects of the immune system called primary immunodeficiency disorders (PID) describe a group of diseases characterized by a decrease, an absence, or a malfunction of at least one part of the immune system. As a result, PID patients are more prone to develop life-threatening complications, including cancer. PID currently include over 400 different disorders, however, the variety of PID-related cancers is narrow. We discuss here reasons for this clinical phenotype. Namely, PID can lead to cell intrinsic failure to control cell transformation, failure to activate tumor surveillance by cytotoxic cells or both. As the most frequent tumors seen among PID patients stem from faulty lymphocyte development leading to leukemia and lymphoma, we focus on the extensive genomic alterations needed to create the vast diversity of B and T lymphocytes with potential to recognize any pathogen and why defects in these processes lead to malignancies in the immunodeficient environment of PID patients. In the second part of the review, we discuss PID affecting tumor surveillance and especially membrane trafficking defects caused by altered exocytosis and regulation of the actin cytoskeleton. As an impairment of these membrane trafficking pathways often results in dysfunctional effector immune cells, tumor cell immune evasion is elevated in PID. By considering new anti-cancer treatment concepts, such as transfer of genetically engineered immune cells, restoration of anti-tumor immunity in PID patients could be an approach to complement standard therapies.
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Affiliation(s)
- Jérôme Mastio
- Department of Oncology, Cytoskeleton and Cancer Progression, Luxembourg Institute of Health, Luxembourg City, Luxembourg
| | - Mezida B Saeed
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Hannah Wurzer
- Department of Oncology, Cytoskeleton and Cancer Progression, Luxembourg Institute of Health, Luxembourg City, Luxembourg
| | - Max Krecke
- Department of Oncology, Cytoskeleton and Cancer Progression, Luxembourg Institute of Health, Luxembourg City, Luxembourg
| | - Lisa S Westerberg
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Clément Thomas
- Department of Oncology, Cytoskeleton and Cancer Progression, Luxembourg Institute of Health, Luxembourg City, Luxembourg
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40
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Safonova Y, Pevzner PA. V(DD)J recombination is an important and evolutionarily conserved mechanism for generating antibodies with unusually long CDR3s. Genome Res 2020; 30:1547-1558. [PMID: 32948615 PMCID: PMC7605257 DOI: 10.1101/gr.259598.119] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Accepted: 09/15/2020] [Indexed: 12/20/2022]
Abstract
The V(DD)J recombination is currently viewed as an aberrant and inconsequential variant of the canonical V(D)J recombination. Moreover, since the classical 12/23 rule for the V(D)J recombination fails to explain the V(DD)J recombination, the molecular mechanism of tandem D-D fusions has remained unknown since they were discovered three decades ago. Revealing this mechanism is a biomedically important goal since tandem fusions contribute to broadly neutralizing antibodies with ultralong CDR3s. We reveal previously overlooked cryptic nonamers in the recombination signal sequences of human IGHD genes and demonstrate that these nonamers explain the vast majority of tandem fusions in human repertoires. We further reveal large clonal lineages formed by tandem fusions in antigen-stimulated immunosequencing data sets, suggesting that such data sets contain many more tandem fusions than previously thought and that about a quarter of large clonal lineages with unusually long CDR3s are generated through tandem fusions. Finally, we developed the SEARCH-D algorithm for identifying D genes in mammalian genomes and applied it to the recently completed Vertebrate Genomes Project assemblies, nearly doubling the number of mammalian species with known D genes. Our analysis revealed cryptic nonamers in RSSs of many mammalian genomes, thus demonstrating that the V(DD)J recombination is not a "bug" but an important feature preserved throughout mammalian evolution.
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Affiliation(s)
- Yana Safonova
- Computer Science and Engineering Department, University of California San Diego, La Jolla, California 92093, USA
| | - Pavel A Pevzner
- Computer Science and Engineering Department, University of California San Diego, La Jolla, California 92093, USA
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41
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Zhang Y, Corbett E, Wu S, Schatz DG. Structural basis for the activation and suppression of transposition during evolution of the RAG recombinase. EMBO J 2020; 39:e105857. [PMID: 32945578 DOI: 10.15252/embj.2020105857] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Revised: 08/17/2020] [Accepted: 08/20/2020] [Indexed: 11/09/2022] Open
Abstract
Jawed vertebrate adaptive immunity relies on the RAG1/RAG2 (RAG) recombinase, a domesticated transposase, for assembly of antigen receptor genes. Using an integration-activated form of RAG1 with methionine at residue 848 and cryo-electron microscopy, we determined structures that capture RAG engaged with transposon ends and U-shaped target DNA prior to integration (the target capture complex) and two forms of the RAG strand transfer complex that differ based on whether target site DNA is annealed or dynamic. Target site DNA base unstacking, flipping, and melting by RAG1 methionine 848 explain how this residue activates transposition, how RAG can stabilize sharp bends in target DNA, and why replacement of residue 848 by arginine during RAG domestication led to suppression of transposition activity. RAG2 extends a jawed vertebrate-specific loop to interact with target site DNA, and functional assays demonstrate that this loop represents another evolutionary adaptation acquired during RAG domestication to inhibit transposition. Our findings identify mechanistic principles of the final step in cut-and-paste transposition and the molecular and structural logic underlying the transformation of RAG from transposase to recombinase.
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Affiliation(s)
- Yuhang Zhang
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Elizabeth Corbett
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Shenping Wu
- Department of Pharmacology, Yale School of Medicine West Haven, New Haven, CT, USA
| | - David G Schatz
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
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42
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Yao R, Qian J, Huang Q. Deep-learning with synthetic data enables automated picking of cryo-EM particle images of biological macromolecules. Bioinformatics 2020; 36:1252-1259. [PMID: 31584618 DOI: 10.1093/bioinformatics/btz728] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Revised: 08/28/2019] [Accepted: 09/26/2019] [Indexed: 11/13/2022] Open
Abstract
MOTIVATION Single-particle cryo-electron microscopy (cryo-EM) has become a powerful technique for determining 3D structures of biological macromolecules at near-atomic resolution. However, this approach requires picking huge numbers of macromolecular particle images from thousands of low-contrast, high-noisy electron micrographs. Although machine-learning methods were developed to get rid of this bottleneck, it still lacks universal methods that could automatically picking the noisy cryo-EM particles of various macromolecules. RESULTS Here, we present a deep-learning segmentation model that employs fully convolutional networks trained with synthetic data of known 3D structures, called PARSED (PARticle SEgmentation Detector). Without using any experimental information, PARSED could automatically segment the cryo-EM particles in a whole micrograph at a time, enabling faster particle picking than previous template/feature-matching and particle-classification methods. Applications to six large public cryo-EM datasets clearly validated its universal ability to pick macromolecular particles of various sizes. Thus, our deep-learning method could break the particle-picking bottleneck in the single-particle analysis, and thereby accelerates the high-resolution structure determination by cryo-EM. AVAILABILITY AND IMPLEMENTATION The PARSED package and user manual for noncommercial use are available as Supplementary Material (in the compressed file: parsed_v1.zip). SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Ruijie Yao
- State Key Laboratory of Genetic Engineering, MOE Engineering Research Center of Gene Technology, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Jiaqiang Qian
- State Key Laboratory of Genetic Engineering, MOE Engineering Research Center of Gene Technology, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Qiang Huang
- State Key Laboratory of Genetic Engineering, MOE Engineering Research Center of Gene Technology, School of Life Sciences, Fudan University, Shanghai 200438, China.,Multiscale Research Institute of Complex Systems, Fudan University, Shanghai 201203, China
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43
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Liu S, Yuan S, Gao X, Tao X, Yu W, Li X, Chen S, Xu A. Functional regulation of an ancestral RAG transposon ProtoRAG by a trans-acting factor YY1 in lancelet. Nat Commun 2020; 11:4515. [PMID: 32908127 PMCID: PMC7481187 DOI: 10.1038/s41467-020-18261-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Accepted: 08/09/2020] [Indexed: 01/04/2023] Open
Abstract
The discovery of ancestral RAG transposons in early deuterostomia reveals the origin of vertebrate V(D)J recombination. Here, we analyze the functional regulation of a RAG transposon, ProtoRAG, in lancelet. We find that a specific interaction between the cis-acting element within the TIR sequences of ProtoRAG and a trans-acting factor, lancelet YY1-like (bbYY1), is important for the transcriptional regulation of lancelet RAG-like genes (bbRAG1L and bbRAG2L). Mechanistically, bbYY1 suppresses the transposition of ProtoRAG; meanwhile, bbYY1 promotes host DNA rejoins (HDJ) and TIR-TIR joints (TTJ) after TIR-dependent excision by facilitating the binding of bbRAG1L/2 L to TIR-containing DNA, and by interacting with the bbRAG1L/2 L complex. Our data thus suggest that bbYY1 has dual functions in fine-tuning the activity of ProtoRAG and maintaining the genome stability of the host.
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Affiliation(s)
- Song Liu
- State Key Laboratory of Biocontrol, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, School of Life Sciences, Sun Yat-sen University, 510275, Guangzhou, People's Republic of China
| | - Shaochun Yuan
- State Key Laboratory of Biocontrol, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, School of Life Sciences, Sun Yat-sen University, 510275, Guangzhou, People's Republic of China.
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, 266237, Qingdao, People's Republic of China.
| | - Xiaoman Gao
- State Key Laboratory of Biocontrol, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, School of Life Sciences, Sun Yat-sen University, 510275, Guangzhou, People's Republic of China
| | - Xin Tao
- State Key Laboratory of Biocontrol, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, School of Life Sciences, Sun Yat-sen University, 510275, Guangzhou, People's Republic of China
| | - Wenjuan Yu
- State Key Laboratory of Biocontrol, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, School of Life Sciences, Sun Yat-sen University, 510275, Guangzhou, People's Republic of China
| | - Xu Li
- State Key Laboratory of Biocontrol, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, School of Life Sciences, Sun Yat-sen University, 510275, Guangzhou, People's Republic of China
| | - Shangwu Chen
- State Key Laboratory of Biocontrol, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, School of Life Sciences, Sun Yat-sen University, 510275, Guangzhou, People's Republic of China
| | - Anlong Xu
- State Key Laboratory of Biocontrol, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, School of Life Sciences, Sun Yat-sen University, 510275, Guangzhou, People's Republic of China.
- School of Life Sciences, Beijing University of Chinese Medicine, 100029, Beijing, People's Republic of China.
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44
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Chi X, Fan Q, Zhang Y, Liang K, Wan L, Zhou Q, Li Y. Structural mechanism of phospholipids translocation by MlaFEDB complex. Cell Res 2020; 30:1127-1135. [PMID: 32884137 PMCID: PMC7784689 DOI: 10.1038/s41422-020-00404-6] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2020] [Accepted: 08/14/2020] [Indexed: 12/16/2022] Open
Abstract
In Gram-negative bacteria, phospholipids are major components of the inner membrane and the inner leaflet of the outer membrane, playing an essential role in forming the unique dual-membrane barrier to exclude the entry of most antibiotics. Understanding the mechanisms of phospholipid translocation between the inner and outer membrane represents one of the major challenges surrounding bacterial phospholipid homeostasis. The conserved MlaFEDB complex in the inner membrane functions as an ABC transporter to drive the translocation of phospholipids between the inner membrane and the periplasmic protein MlaC. However, the mechanism of phospholipid translocation remains elusive. Here we determined three cryo-EM structures of MlaFEDB from Escherichia coli in its nucleotide-free and ATP-bound conformations, and performed extensive functional studies to verify and extend our findings from structural analyses. Our work reveals unique structural features of the entire MlaFEDB complex, six well-resolved phospholipids in three distinct cavities, and large-scale conformational changes upon ATP binding. Together, these findings define the cycle of structural rearrangement of MlaFEDB in action, and suggest that MlaFEDB uses an extrusion mechanism to extract and release phospholipids through the central translocation cavity.
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Affiliation(s)
- Ximin Chi
- Center for Infectious Disease Research, Zhejiang Provincial Laboratory of Life Sciences and Biomedicine, Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, 310024, China.,Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, Zhejiang, 310024, China
| | - Qiongxuan Fan
- Center for Infectious Disease Research, Zhejiang Provincial Laboratory of Life Sciences and Biomedicine, Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, 310024, China.,Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, Zhejiang, 310024, China
| | - Yuanyuan Zhang
- Center for Infectious Disease Research, Zhejiang Provincial Laboratory of Life Sciences and Biomedicine, Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, 310024, China.,Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, Zhejiang, 310024, China
| | - Ke Liang
- Center for Infectious Disease Research, Zhejiang Provincial Laboratory of Life Sciences and Biomedicine, Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, 310024, China.,Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, Zhejiang, 310024, China
| | - Li Wan
- Center for Infectious Disease Research, Zhejiang Provincial Laboratory of Life Sciences and Biomedicine, Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, 310024, China.,Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, Zhejiang, 310024, China
| | - Qiang Zhou
- Center for Infectious Disease Research, Zhejiang Provincial Laboratory of Life Sciences and Biomedicine, Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, 310024, China. .,Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, Zhejiang, 310024, China.
| | - Yanyan Li
- Center for Infectious Disease Research, Zhejiang Provincial Laboratory of Life Sciences and Biomedicine, Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, 310024, China. .,Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, Zhejiang, 310024, China.
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45
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Ortiz S, Stanisic L, Rodriguez BA, Rampp M, Hummer G, Cossio P. Validation tests for cryo-EM maps using an independent particle set. J Struct Biol X 2020; 4:100032. [PMID: 32743544 PMCID: PMC7385033 DOI: 10.1016/j.yjsbx.2020.100032] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Cryo-electron microscopy (cryo-EM) has revolutionized structural biology by providing 3D density maps of biomolecules at near-atomic resolution. However, map validation is still an open issue. Despite several efforts from the community, it is possible to overfit 3D maps to noisy data. Here, we develop a novel methodology that uses a small independent particle set (not used during the 3D refinement) to validate the maps. The main idea is to monitor how the map probability evolves over the control set during the 3D refinement. The method is complementary to the gold-standard procedure, which generates two reconstructions at each iteration. We low-pass filter the two reconstructions for different frequency cutoffs, and we calculate the probability of each filtered map given the control set. For high-quality maps, the probability should increase as a function of the frequency cutoff and the refinement iteration. We also compute the similarity between the densities of probability distributions of the two reconstructions. As higher frequencies are included, the distributions become more dissimilar. We optimized the BioEM package to perform these calculations, and tested it over systems ranging from quality data to pure noise. Our results show that with our methodology, it possible to discriminate datasets that are constructed from noise particles. We conclude that validation against a control particle set provides a powerful tool to assess the quality of cryo-EM maps.
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Affiliation(s)
- Sebastian Ortiz
- Biophysics of Tropical Diseases, Max Planck Tandem Group, University of Antioquia UdeA, Calle 70 No. 52-21, Medellín, Colombia
| | - Luka Stanisic
- Max Planck Computing and Data Facility, 85748 Garching, Germany
| | - Boris A Rodriguez
- Grupo de Fósica Atómica y Molecular, Instituto de Física, Facultad de Ciencias Exactas y Naturales, Universidad de Antioquia UdeA, Calle 70 No. 52-21, Medellín, Colombia
| | - Markus Rampp
- Max Planck Computing and Data Facility, 85748 Garching, Germany
| | - Gerhard Hummer
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, 60438 Frankfurt am Main, Germany
- Institute of Biophysics, Goethe University, 60438 Frankfurt am Main, Germany
| | - Pilar Cossio
- Biophysics of Tropical Diseases, Max Planck Tandem Group, University of Antioquia UdeA, Calle 70 No. 52-21, Medellín, Colombia
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, 60438 Frankfurt am Main, Germany
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46
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Hirokawa S, Chure G, Belliveau NM, Lovely GA, Anaya M, Schatz DG, Baltimore D, Phillips R. Sequence-dependent dynamics of synthetic and endogenous RSSs in V(D)J recombination. Nucleic Acids Res 2020; 48:6726-6739. [PMID: 32449932 PMCID: PMC7337519 DOI: 10.1093/nar/gkaa418] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 04/20/2020] [Accepted: 05/07/2020] [Indexed: 12/25/2022] Open
Abstract
Developing lymphocytes of jawed vertebrates cleave and combine distinct gene segments to assemble antigen-receptor genes. This process called V(D)J recombination that involves the RAG recombinase binding and cutting recombination signal sequences (RSSs) composed of conserved heptamer and nonamer sequences flanking less well-conserved 12- or 23-bp spacers. Little quantitative information is known about the contributions of individual RSS positions over the course of the RAG-RSS interaction. We employ a single-molecule method known as tethered particle motion to track the formation, lifetime and cleavage of individual RAG-12RSS-23RSS paired complexes (PCs) for numerous synthetic and endogenous 12RSSs. We reveal that single-bp changes, including in the 12RSS spacer, can significantly and selectively alter PC formation or the probability of RAG-mediated cleavage in the PC. We find that some rarely used endogenous gene segments can be mapped directly to poor RAG binding on their adjacent 12RSSs. Finally, we find that while abrogating RSS nicking with Ca2+ leads to substantially shorter PC lifetimes, analysis of the complete lifetime distributions of any 12RSS even on this reduced system reveals that the process of exiting the PC involves unidentified molecular details whose involvement in RAG-RSS dynamics are crucial to quantitatively capture kinetics in V(D)J recombination.
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Affiliation(s)
- Soichi Hirokawa
- Department of Applied Physics, California Institute of Technology, Pasadena, CA 91125, USA
| | - Griffin Chure
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Nathan M Belliveau
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Geoffrey A Lovely
- National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA
| | - Michael Anaya
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - David G Schatz
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06520, USA
| | - David Baltimore
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Rob Phillips
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
- Department of Physics, California Institute of Technology, Pasadena, CA 91125, USA
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47
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May MR, Bettridge JT, Desiderio S. Binding and allosteric transmission of histone H3 Lys-4 trimethylation to the recombinase RAG-1 are separable functions of the RAG-2 plant homeodomain finger. J Biol Chem 2020; 295:9052-9060. [PMID: 32414844 PMCID: PMC7335790 DOI: 10.1074/jbc.ra120.014382] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Revised: 05/15/2020] [Indexed: 11/06/2022] Open
Abstract
V(D)J recombination is initiated by the recombination-activating gene protein (RAG) recombinase, consisting of RAG-1 and RAG-2 subunits. The susceptibility of gene segments to cleavage by RAG is associated with gene transcription and with epigenetic marks characteristic of active chromatin, including histone H3 trimethylated at lysine 4 (H3K4me3). Binding of H3K4me3 by a plant homeodomain (PHD) in RAG-2 induces conformational changes in RAG-1, allosterically stimulating substrate binding and catalysis. To better understand the path of allostery from the RAG-2 PHD finger to RAG-1, here we employed phylogenetic substitution. We observed that a chimeric RAG-2 protein in which the mouse PHD finger is replaced by the corresponding domain from the shark Chiloscyllium punctatum binds H3K4me3 but fails to transmit an allosteric signal, indicating that binding of H3K4me3 by RAG-2 is insufficient to support recombination. By substituting residues in the C. punctatum PHD with the corresponding residues in the mouse PHD and testing for rescue of allostery, we demonstrate that H3K4me3 binding and transmission of an allosteric signal to RAG-1 are separable functions of the RAG-2 PHD finger.
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Affiliation(s)
- Meiling R May
- Department of Molecular Biology and Genetics and Institute for Cell Engineering, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - John T Bettridge
- Department of Molecular Biology and Genetics and Institute for Cell Engineering, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Stephen Desiderio
- Department of Molecular Biology and Genetics and Institute for Cell Engineering, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA; Division of Hematology, Department of Medicine, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA.
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48
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Sui X, Wang K, Gluchowski NL, Elliott SD, Liao M, Walther TC, Farese RV. Structure and catalytic mechanism of a human triacylglycerol-synthesis enzyme. Nature 2020; 581:323-328. [PMID: 32433611 PMCID: PMC7398557 DOI: 10.1038/s41586-020-2289-6] [Citation(s) in RCA: 63] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Accepted: 03/17/2020] [Indexed: 12/12/2022]
Abstract
Triglycerides (triacylglycerols, TGs) store metabolic energy in organisms and have industrial uses for foods and fuels. Excessive accumulation of TGs in humans causes obesity and is associated with metabolic diseases1. TG synthesis is catalyzed by acyl-CoA:diacylglycerol acyltransferase (DGAT) enzymes2–4 whose structures and catalytic mechanisms are unknown. Here we determined the structure of dimeric human DGAT1, a member of the membrane-bound O-acyltransferase (MBOAT) family, by cryo-electron microscopy at 3.0-Å resolution. DGAT1 forms a homodimer through N-terminal segments and a hydrophobic interface, with putative active sites within the membrane region. A structure obtained with oleoyl-CoA substrate resolved at 3.2-Å shows that the CoA moiety binds DGAT1 on the cytosolic side and the acyl group lies deep within a hydrophobic channel, positioning the acyl-CoA thioester bond near an invariant catalytic histidine residue. The reaction center is located inside a large cavity, which opens laterally to the membrane bilayer, providing lipid access to the active site. A lipid-like density, possibly an acyl-acceptor molecule, is located within the reaction center, orthogonal to acyl-CoA. Insights provided by the DGAT1 structures, together with mutagenesis and functional studies, give rise to a model of catalysis for DGAT’s generation of TGs.
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Affiliation(s)
- Xuewu Sui
- Department of Molecular Metabolism, Harvard T. H. Chan School of Public Health, Boston, MA, USA.,Department of Cell Biology, Harvard Medical School, Boston, MA, USA
| | - Kun Wang
- Department of Molecular Metabolism, Harvard T. H. Chan School of Public Health, Boston, MA, USA.,Department of Cell Biology, Harvard Medical School, Boston, MA, USA
| | - Nina L Gluchowski
- Department of Molecular Metabolism, Harvard T. H. Chan School of Public Health, Boston, MA, USA.,Department of Cell Biology, Harvard Medical School, Boston, MA, USA.,Department of Gastroenterology, Hepatology, and Nutrition, Boston Children's Hospital, Boston, MA, USA
| | - Shane D Elliott
- Department of Molecular Metabolism, Harvard T. H. Chan School of Public Health, Boston, MA, USA.,Department of Cell Biology, Harvard Medical School, Boston, MA, USA
| | - Maofu Liao
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA.
| | - Tobias C Walther
- Department of Molecular Metabolism, Harvard T. H. Chan School of Public Health, Boston, MA, USA. .,Department of Cell Biology, Harvard Medical School, Boston, MA, USA. .,Broad Institute of MIT and Harvard, Cambridge, MA, USA. .,Howard Hughes Medical Institute, Boston, MA, USA.
| | - Robert V Farese
- Department of Molecular Metabolism, Harvard T. H. Chan School of Public Health, Boston, MA, USA. .,Department of Cell Biology, Harvard Medical School, Boston, MA, USA. .,Broad Institute of MIT and Harvard, Cambridge, MA, USA.
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49
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Orlando BJ, Liao M. ABCG2 transports anticancer drugs via a closed-to-open switch. Nat Commun 2020; 11:2264. [PMID: 32385283 PMCID: PMC7210939 DOI: 10.1038/s41467-020-16155-2] [Citation(s) in RCA: 123] [Impact Index Per Article: 30.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Accepted: 04/16/2020] [Indexed: 12/18/2022] Open
Abstract
ABCG2 is an ABC transporter that extrudes a variety of compounds from cells, and presents an obstacle in treating chemotherapy-resistant cancers. Despite recent structural insights, no anticancer drug bound to ABCG2 has been resolved, and the mechanisms of multidrug transport remain obscure. Such a gap of knowledge limits the development of novel compounds that block or evade this critical molecular pump. Here we present single-particle cryo-EM studies of ABCG2 in the apo state, and bound to the three structurally distinct chemotherapeutics. Without the binding of conformation-selective antibody fragments or inhibitors, the resting ABCG2 adopts a closed conformation. Our cryo-EM, biochemical, and functional analyses reveal the binding mode of three chemotherapeutic compounds, demonstrate how these molecules open the closed conformation of the transporter, and establish that imatinib is particularly effective in stabilizing the inward facing conformation of ABCG2. Together these studies reveal the previously unrecognized conformational cycle of ABCG2. ABCG2 is a human ABC transporter that actively extrudes a wide variety of compounds from cells but the mechanisms of multidrug transport remain obscure. Here authors present cryo-EM structures of ABCG2 in the apo state, and bound to the three structurally distinct chemotherapeutics and demonstrate how these molecules open the closed conformation of the transporter.
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Affiliation(s)
- Benjamin J Orlando
- Department of Cell Biology, Harvard Medical School, Boston, MA, 02115, USA
| | - Maofu Liao
- Department of Cell Biology, Harvard Medical School, Boston, MA, 02115, USA.
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50
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Martin EC, Vicari C, Tsakou-Ngouafo L, Pontarotti P, Petrescu AJ, Schatz DG. Identification of RAG-like transposons in protostomes suggests their ancient bilaterian origin. Mob DNA 2020; 11:17. [PMID: 32399063 PMCID: PMC7204232 DOI: 10.1186/s13100-020-00214-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Accepted: 04/14/2020] [Indexed: 12/27/2022] Open
Abstract
Background V(D) J recombination is essential for adaptive immunity in jawed vertebrates and is initiated by the RAG1-RAG2 endonuclease. The RAG1 and RAG2 genes are thought to have evolved from a RAGL (RAG-like) transposon containing convergently-oriented RAG1-like (RAG1L) and RAG2-like (RAG2L) genes. Elements resembling this presumptive evolutionary precursor have thus far only been detected convincingly in deuterostomes, leading to the model that the RAGL transposon first appeared in an early deuterostome. Results We have identified numerous RAGL transposons in the genomes of protostomes, including oysters and mussels (phylum Mollusca) and a ribbon worm (phylum Nemertea), and in the genomes of several cnidarians. Phylogenetic analyses are consistent with vertical evolution of RAGL transposons within the Bilateria clade and with its presence in the bilaterian ancestor. Many of the RAGL transposons identified in protostomes are intact elements containing convergently oriented RAG1L and RAG2L genes flanked by terminal inverted repeats (TIRs) and target site duplications with striking similarities with the corresponding elements in deuterostomes. In addition, protostome genomes contain numerous intact RAG1L-RAG2L adjacent gene pairs that lack detectable flanking TIRs. Domains and critical active site and structural amino acids needed for endonuclease and transposase activity are present and conserved in many of the predicted RAG1L and RAG2L proteins encoded in protostome genomes. Conclusions Active RAGL transposons were present in multiple protostome lineages and many were likely transmitted vertically during protostome evolution. It appears that RAGL transposons were broadly active during bilaterian evolution, undergoing multiple duplication and loss/fossilization events, with the RAGL genes that persist in present day protostomes perhaps constituting both active RAGL transposons and domesticated RAGL genes. Our findings raise the possibility that the RAGL transposon arose earlier in evolution than previously thought, either in an early bilaterian or prior to the divergence of bilaterians and non-bilaterians, and alter our understanding of the evolutionary history of this important group of transposons.
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Affiliation(s)
- Eliza C Martin
- 1Department of Bioinformatics and Structural Biochemistry, Institute of Biochemistry of the Romanian Academy, Splaiul Independentei 296, 060031 Bucharest, Romania
| | - Célia Vicari
- 2Evolutionary biology team, Aix Marseille Université IRD, APHM, MEPHI, IHU Méditerranée Infection, Marseille, France
| | - Louis Tsakou-Ngouafo
- 2Evolutionary biology team, Aix Marseille Université IRD, APHM, MEPHI, IHU Méditerranée Infection, Marseille, France
| | - Pierre Pontarotti
- 2Evolutionary biology team, Aix Marseille Université IRD, APHM, MEPHI, IHU Méditerranée Infection, Marseille, France.,SNC5039 CNRS, 19-21 Boulevard Jean Moulin, 13005 Marseille, France
| | - Andrei J Petrescu
- 1Department of Bioinformatics and Structural Biochemistry, Institute of Biochemistry of the Romanian Academy, Splaiul Independentei 296, 060031 Bucharest, Romania
| | - David G Schatz
- 4Department of Immunobiology, Yale School of Medicine, 300 Cedar Street, Box 208011, New Haven, CT 06520-8011 USA
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