1
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Igamberdiev AU, Gordon R. Macroevolution, differentiation trees, and the growth of coding systems. Biosystems 2023; 234:105044. [PMID: 37783374 DOI: 10.1016/j.biosystems.2023.105044] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Revised: 09/27/2023] [Accepted: 09/28/2023] [Indexed: 10/04/2023]
Abstract
An open process of evolution of multicellular organisms is based on the rearrangement and growth of the program of differentiation that underlies biological morphogenesis. The maintenance of the final (adult) stable non-equilibrium state (stasis) of a developmental system determines the direction of the evolutionary process. This state is achieved via the sequence of differentiation events representable as differentiation trees. A special type of morphogenetic code, acting as a metacode governing gene expression, may include electromechanical signals appearing as differentiation waves. The excessive energy due to the incorporation of mitochondria in eukaryotic cells resulted not only in more active metabolism but also in establishing the differentiation code for interconnecting cells and forming tissues, which fueled the evolutionary process. The "invention" of "continuing differentiation" distinguishes multicellular eukaryotes from other organisms. The Janus-faced control, involving both top-down control by differentiation waves and bottom-up control via the mechanical consequences of cell differentiations, underlies the process of morphogenesis and results in the achievement of functional stable final states. Duplications of branches of the differentiation tree may be the basis for continuing differentiation and macroevolution, analogous to gene duplication permitting divergence of genes. Metamorphoses, if they are proven to be fusions of disparate species, may be classified according to the topology of fusions of two differentiation trees. In the process of unfolding of morphogenetic structures, microevolution can be defined as changes of the differentiation tree that preserve topology of the tree, while macroevolution represents any change that alters the topology of the differentiation tree.
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Affiliation(s)
- Abir U Igamberdiev
- Department of Biology, Memorial University of Newfoundland, St. John's, NL, Canada.
| | - Richard Gordon
- Gulf Specimen Marine Laboratory & Aquarium, 222 Clark Drive, Panacea, FL, 32346, USA.
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2
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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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3
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Hoolehan W, Harris JC, Rodgers KK. Molecular Mechanisms of DNA Sequence Selectivity in V(D)J Recombination. ACS OMEGA 2023; 8:34206-34214. [PMID: 37779976 PMCID: PMC10536018 DOI: 10.1021/acsomega.3c05601] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Accepted: 09/07/2023] [Indexed: 10/03/2023]
Abstract
Antigen receptor (AgR) diversity is central to the ability of adaptive immunity in jawed vertebrates to protect against pathogenic agents. The production of highly diverse AgR repertoires is initiated during B and T cell lymphopoiesis by V(D)J recombination, which assembles the receptor genes from component gene segments in a cut-and-paste recombination reaction. Recombination activating proteins, RAG1 and RAG2 (RAG1/2), catalyze V(D)J recombination by cleaving adjacent to recombination signal sequences (RSSs) that flank AgR 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, and the molecular mechanism for semiselective V(D)J recombination specificity is unknown. The modulation of chromatin structure during V(D)J recombination is essential in the formation of diverse AgRs in adaptive immunity while also reducing the likelihood for off-target recombination events that can result in chromosomal aberrations and genomic instability. Here we review what is presently known regarding mechanisms that facilitate assembly of RAG1/2 with RSSs, the ensuing conformational changes required for DNA cleavage activity, and how the readout of the RSS sequence affects reaction efficiency.
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Affiliation(s)
- Walker Hoolehan
- Department
of Biochemistry and Molecular Biology, Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma 73104, United States
| | - Justin C. Harris
- Department
of Biochemistry and Molecular Biology, Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma 73104, United States
| | - Karla K. Rodgers
- Department
of Biochemistry and Molecular Biology, Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma 73104, United States
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4
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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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5
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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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6
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Devaux CA, Pontarotti P, Nehari S, Raoult D. 'Cannibalism' of exogenous DNA sequences: The ancestral form of adaptive immunity which entails recognition of danger. Front Immunol 2022; 13:989707. [PMID: 36618387 PMCID: PMC9816338 DOI: 10.3389/fimmu.2022.989707] [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: 07/08/2022] [Accepted: 12/05/2022] [Indexed: 12/24/2022] Open
Abstract
Adaptive immunity is a sophisticated form of immune response capable of retaining the molecular memory of a very great diversity of target antigens (epitopes) as non-self. It is capable of reactivating itself upon a second encounter with an immunoglobulin or T-cell receptor antigen-binding site with a known epitope that had previously primed the host immune system. It has long been considered that adaptive immunity is a highly evolved form of non-self recognition that appeared quite late in speciation and complemented a more generalist response called innate immunity. Innate immunity offers a relatively non-specific defense (although mediated by sensors that could specifically recognize virus or bacteria compounds) and which does not retain a memory of the danger. But this notion of recent acquisition of adaptive immunity is challenged by the fact that another form of specific recognition mechanisms already existed in prokaryotes that may be able to specifically auto-protect against external danger. This recognition mechanism can be considered a primitive form of specific (adaptive) non-self recognition. It is based on the fact that many archaea and bacteria use a genome editing system that confers the ability to appropriate viral DNA sequences allowing prokaryotes to prevent host damage through a mechanism very similar to adaptive immunity. This is indistinctly called, 'endogenization of foreign DNA' or 'viral DNA predation' or, more pictorially 'DNA cannibalism'. For several years evidence has been accumulating, highlighting the crucial role of endogenization of foreign DNA in the fundamental processes related to adaptive immunity and leading to a change in the dogma that adaptive immunity appeared late in speciation.
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Affiliation(s)
- Christian A. Devaux
- Aix-Marseille University, Institut de recherche pour le développement (IRD), Assistance Publique Hôpitaux de Marseille (APHM), MEPHI, Institut Hospitalo-universitaire (IHU)-Méditerranée Infection, Marseille, France,Department of Biological Sciences, Centre National de la Recherche Scientifique, Centre National de la Recherche Scientifique (CNRS)-SNC5039, Marseille, France,*Correspondence: Christian A. Devaux,
| | - Pierre Pontarotti
- Aix-Marseille University, Institut de recherche pour le développement (IRD), Assistance Publique Hôpitaux de Marseille (APHM), MEPHI, Institut Hospitalo-universitaire (IHU)-Méditerranée Infection, Marseille, France,Department of Biological Sciences, Centre National de la Recherche Scientifique, Centre National de la Recherche Scientifique (CNRS)-SNC5039, Marseille, France
| | - Sephora Nehari
- Aix-Marseille University, Institut de recherche pour le développement (IRD), Assistance Publique Hôpitaux de Marseille (APHM), MEPHI, Institut Hospitalo-universitaire (IHU)-Méditerranée Infection, Marseille, France
| | - Didier Raoult
- Aix-Marseille University, Institut de recherche pour le développement (IRD), Assistance Publique Hôpitaux de Marseille (APHM), MEPHI, Institut Hospitalo-universitaire (IHU)-Méditerranée Infection, Marseille, France
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7
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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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8
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Tao X, Huang Z, Chen F, Wang X, Zheng T, Yuan S, Xu A. The RAG key to vertebrate adaptive immunity descended directly from a bacterial ancestor. Natl Sci Rev 2022; 9:nwac073. [PMID: 36060303 PMCID: PMC9435367 DOI: 10.1093/nsr/nwac073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 03/11/2022] [Accepted: 04/13/2022] [Indexed: 11/24/2022] Open
Affiliation(s)
- Xin Tao
- 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
- Center for Infection and Immunity, School of Medicine, Sun Yat-sen University, Guangzhou, 510275, China
| | - 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
| | - Fan Chen
- 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
| | - Xinli Wang
- 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
| | - Tingting Zheng
- Shanghai Institute of Immunology, College of Basic Medical Sciences, Shanghai Jiao Tong University School of Medicine, 200025 Shanghai, 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, 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
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9
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Pradhan RK, Ramakrishna W. Transposons: Unexpected players in cancer. Gene 2022; 808:145975. [PMID: 34592349 DOI: 10.1016/j.gene.2021.145975] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 09/19/2021] [Accepted: 09/24/2021] [Indexed: 12/21/2022]
Abstract
Transposons are repetitive DNA sequences encompassing about half of the human genome. They play a vital role in genome stability maintenance and contribute to genomic diversity and evolution. Their activity is regulated by various mechanisms considering the deleterious effects of these mobile elements. Various genetic risk factors and environmental stress conditions affect the regulatory pathways causing alteration of transposon expression. Our knowledge of the biological role of transposons is limited especially in various types of cancers. Retrotransposons of different types (LTR-retrotransposons, LINEs and SINEs) regulate a plethora of genes that have a role in cell reprogramming, tumor suppression, cell cycle, apoptosis, cell adhesion and migration, and DNA repair. The regulatory mechanisms of transposons, their deregulation and different mechanisms underlying transposon-mediated carcinogenesis in humans focusing on the three most prevalent types, lung, breast and colorectal cancers, were reviewed. The modes of regulation employed include alternative splicing, deletion, insertion, duplication in genes and promoters resulting in upregulation, downregulation or silencing of genes.
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10
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Frock RL, Sadeghi C, Meng J, Wang JL. DNA End Joining: G0-ing to the Core. Biomolecules 2021; 11:biom11101487. [PMID: 34680120 PMCID: PMC8533500 DOI: 10.3390/biom11101487] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Revised: 10/05/2021] [Accepted: 10/06/2021] [Indexed: 12/28/2022] Open
Abstract
Humans have evolved a series of DNA double-strand break (DSB) repair pathways to efficiently and accurately rejoin nascently formed pairs of double-stranded DNA ends (DSEs). In G0/G1-phase cells, non-homologous end joining (NHEJ) and alternative end joining (A-EJ) operate to support covalent rejoining of DSEs. While NHEJ is predominantly utilized and collaborates extensively with the DNA damage response (DDR) to support pairing of DSEs, much less is known about A-EJ collaboration with DDR factors when NHEJ is absent. Non-cycling lymphocyte progenitor cells use NHEJ to complete V(D)J recombination of antigen receptor genes, initiated by the RAG1/2 endonuclease which holds its pair of targeted DSBs in a synapse until each specified pair of DSEs is handed off to the NHEJ DSB sensor complex, Ku. Similar to designer endonuclease DSBs, the absence of Ku allows for A-EJ to access RAG1/2 DSEs but with random pairing to complete their repair. Here, we describe recent insights into the major phases of DSB end joining, with an emphasis on synapsis and tethering mechanisms, and bring together new and old concepts of NHEJ vs. A-EJ and on RAG2-mediated repair pathway choice.
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11
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Beilinson HA, Glynn RA, Yadavalli AD, Xiao J, Corbett E, Saribasak H, Arya R, Miot C, Bhattacharyya A, Jones JM, Pongubala JM, Bassing CH, Schatz DG. The RAG1 N-terminal region regulates the efficiency and pathways of synapsis for V(D)J recombination. J Exp Med 2021; 218:e20210250. [PMID: 34402853 PMCID: PMC8374863 DOI: 10.1084/jem.20210250] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Revised: 06/30/2021] [Accepted: 07/30/2021] [Indexed: 11/29/2022] Open
Abstract
Immunoglobulin and T cell receptor gene assembly depends on V(D)J recombination initiated by the RAG1-RAG2 recombinase. The RAG1 N-terminal region (NTR; aa 1-383) has been implicated in regulatory functions whose influence on V(D)J recombination and lymphocyte development in vivo is poorly understood. We generated mice in which RAG1 lacks ubiquitin ligase activity (P326G), the major site of autoubiquitination (K233R), or its first 215 residues (Δ215). While few abnormalities were detected in R1.K233R mice, R1.P326G mice exhibit multiple features indicative of reduced recombination efficiency, including an increased Igκ+:Igλ+ B cell ratio and decreased recombination of Igh, Igκ, Igλ, and Tcrb loci. Previous studies indicate that synapsis of recombining partners during Igh recombination occurs through two pathways: long-range scanning and short-range collision. We find that R1Δ215 mice exhibit reduced short-range Igh and Tcrb D-to-J recombination. Our findings indicate that the RAG1 NTR regulates V(D)J recombination and lymphocyte development by multiple pathways, including control of the balance between short- and long-range recombination.
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Affiliation(s)
- Helen A. Beilinson
- Department of Immunobiology, Yale School of Medicine, Yale University, New Haven, CT
| | - Rebecca A. Glynn
- Cell and Molecular Biology 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
| | - Anurupa Devi Yadavalli
- Department of Immunobiology, Yale School of Medicine, Yale University, New Haven, CT
- Department of Animal Biology, School of Life Sciences, University of Hyderabad, Hyderabad, India
| | - Jianxiong Xiao
- Department of Immunobiology, Yale School of Medicine, Yale University, New Haven, CT
| | - Elizabeth Corbett
- Department of Immunobiology, Yale School of Medicine, Yale University, New Haven, CT
| | - Huseyin Saribasak
- Department of Immunobiology, Yale School of Medicine, Yale University, New Haven, CT
| | - Rahul Arya
- Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Charline Miot
- Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Anamika Bhattacharyya
- Department of Biochemistry and Molecular & Cellular Biology, Georgetown University, Washington, DC
| | - Jessica M. Jones
- Department of Biochemistry and Molecular & Cellular Biology, Georgetown University, Washington, DC
| | - Jagan M.R. Pongubala
- Department of Animal Biology, School of Life Sciences, University of Hyderabad, Hyderabad, India
| | - Craig H. Bassing
- Cell and Molecular Biology 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
| | - David G. Schatz
- Department of Immunobiology, Yale School of Medicine, Yale University, New Haven, CT
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT
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12
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Yakovenko I, Agronin J, Smith LC, Oren M. Guardian of the Genome: An Alternative RAG/Transib Co-Evolution Hypothesis for the Origin of V(D)J Recombination. Front Immunol 2021; 12:709165. [PMID: 34394111 PMCID: PMC8355894 DOI: 10.3389/fimmu.2021.709165] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Accepted: 07/05/2021] [Indexed: 11/13/2022] Open
Abstract
The appearance of adaptive immunity in jawed vertebrates is termed the immunological 'Big Bang' because of the short evolutionary time over which it developed. Underlying it is the recombination activating gene (RAG)-based V(D)J recombination system, which initiates the sequence diversification of the immunoglobulins and lymphocyte antigen receptors. It was convincingly argued that the RAG1 and RAG2 genes originated from a single transposon. The current dogma postulates that the V(D)J recombination system was established by the split of a primordial vertebrate immune receptor gene into V and J segments by a RAG1/2 transposon, in parallel with the domestication of the same transposable element in a separate genomic locus as the RAG recombinase. Here, based on a new interpretation of previously published data, we propose an alternative evolutionary hypothesis suggesting that two different elements, a RAG1/2 transposase and a Transib transposon invader with RSS-like terminal inverted repeats, co-evolved to work together, resulting in a functional recombination process. This hypothesis offers an alternative understanding of the acquisition of recombinase function by RAGs and the origin of the V(D)J system.
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Affiliation(s)
- Iryna Yakovenko
- Department of Molecular Biology, Ariel University, Ariel, Israel
| | - Jacob Agronin
- Department of Biological Sciences, George Washington University, Washington, DC, United States
| | - L. Courtney Smith
- Department of Biological Sciences, George Washington University, Washington, DC, United States
| | - Matan Oren
- Department of Molecular Biology, Ariel University, Ariel, Israel
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13
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Ghorbani A, Quinlan EM, Larijani M. Evolutionary Comparative Analyses of DNA-Editing Enzymes of the Immune System: From 5-Dimensional Description of Protein Structures to Immunological Insights and Applications to Protein Engineering. Front Immunol 2021; 12:642343. [PMID: 34135887 PMCID: PMC8201067 DOI: 10.3389/fimmu.2021.642343] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 04/06/2021] [Indexed: 01/02/2023] Open
Abstract
The immune system is unique among all biological sub-systems in its usage of DNA-editing enzymes to introduce targeted gene mutations and double-strand DNA breaks to diversify antigen receptor genes and combat viral infections. These processes, initiated by specific DNA-editing enzymes, often result in mistargeted induction of genome lesions that initiate and drive cancers. Like other molecules involved in human health and disease, the DNA-editing enzymes of the immune system have been intensively studied in humans and mice, with little attention paid (< 1% of published studies) to the same enzymes in evolutionarily distant species. Here, we present a systematic review of the literature on the characterization of one such DNA-editing enzyme, activation-induced cytidine deaminase (AID), from an evolutionary comparative perspective. The central thesis of this review is that although the evolutionary comparative approach represents a minuscule fraction of published works on this and other DNA-editing enzymes, this approach has made significant impacts across the fields of structural biology, immunology, and cancer research. Using AID as an example, we highlight the value of the evolutionary comparative approach in discoveries already made, and in the context of emerging directions in immunology and protein engineering. We introduce the concept of 5-dimensional (5D) description of protein structures, a more nuanced view of a structure that is made possible by evolutionary comparative studies. In this higher dimensional view of a protein's structure, the classical 3-dimensional (3D) structure is integrated in the context of real-time conformations and evolutionary time shifts (4th dimension) and the relevance of these dynamics to its biological function (5th dimension).
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Affiliation(s)
- Atefeh Ghorbani
- Program in Immunology and Infectious Diseases, Department of Biomedical Sciences, Faculty of Medicine, Memorial University of Newfoundland, St. John's, NL, Canada.,Department of Molecular Biology and Biochemistry, Faculty of Science, Simon Fraser University, Burnaby, BC, Canada
| | - Emma M Quinlan
- Program in Immunology and Infectious Diseases, Department of Biomedical Sciences, Faculty of Medicine, Memorial University of Newfoundland, St. John's, NL, Canada
| | - Mani Larijani
- Program in Immunology and Infectious Diseases, Department of Biomedical Sciences, Faculty of Medicine, Memorial University of Newfoundland, St. John's, NL, Canada.,Department of Molecular Biology and Biochemistry, Faculty of Science, Simon Fraser University, Burnaby, BC, Canada
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14
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Morimoto R, Swann J, Nusser A, Trancoso I, Schorpp M, Boehm T. Evolution of thymopoietic microenvironments. Open Biol 2021; 11:200383. [PMID: 33622100 PMCID: PMC8061691 DOI: 10.1098/rsob.200383] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
In vertebrates, the development of lymphocytes from undifferentiated haematopoietic precursors takes place in so-called primary lymphoid organs, such as the thymus. Therein, lymphocytes undergo a complex differentiation and selection process that culminates in the generation of a pool of mature T cells that collectively express a self-tolerant repertoire of somatically diversified antigen receptors. Throughout this entire process, the microenvironment of the thymus in large parts dictates the sequence and outcome of the lymphopoietic activity. In vertebrates, direct genetic evidence in some species and circumstantial evidence in others suggest that the formation of a functional thymic microenvironment is controlled by members of the Foxn1/4 family of transcription factors. In teleost fishes, both Foxn1 and Foxn4 contribute to thymopoietic activity, whereas Foxn1 is both necessary and sufficient in the mammalian thymus. The evolutionary history of Foxn1/4 genes suggests that an ancient Foxn4 gene lineage gave rise to the Foxn1 genes in early vertebrates, raising the question of the thymopoietic capacity of the ancestor common to all vertebrates. Recent attempts to reconstruct the early events in the evolution of thymopoietic tissues by replacement of the mouse Foxn1 gene by Foxn1-like genes isolated from various chordate species suggest a plausible scenario. It appears that the primordial thymus was a bi-potent lymphoid organ, supporting both B cell and T cell development; however, during the course of vertebrate, evolution B cell development was gradually diminished converting the thymus into a site specialized in T cell development.
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Affiliation(s)
- Ryo Morimoto
- Department of Developmental Immunology, Max Planck Institute of Immunobiology and Epigenetics, Stuebeweg 51, 79108 Freiburg, Germany
| | - Jeremy Swann
- Department of Developmental Immunology, Max Planck Institute of Immunobiology and Epigenetics, Stuebeweg 51, 79108 Freiburg, Germany
| | - Anja Nusser
- Department of Developmental Immunology, Max Planck Institute of Immunobiology and Epigenetics, Stuebeweg 51, 79108 Freiburg, Germany
| | - Inês Trancoso
- Department of Developmental Immunology, Max Planck Institute of Immunobiology and Epigenetics, Stuebeweg 51, 79108 Freiburg, Germany
| | - Michael Schorpp
- Department of Developmental Immunology, Max Planck Institute of Immunobiology and Epigenetics, Stuebeweg 51, 79108 Freiburg, Germany
| | - Thomas Boehm
- Department of Developmental Immunology, Max Planck Institute of Immunobiology and Epigenetics, Stuebeweg 51, 79108 Freiburg, Germany
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15
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Lees-Miller JP, Cobban A, Katsonis P, Bacolla A, Tsutakawa SE, Hammel M, Meek K, Anderson DW, Lichtarge O, Tainer JA, Lees-Miller SP. Uncovering DNA-PKcs ancient phylogeny, unique sequence motifs and insights for human disease. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2020; 163:87-108. [PMID: 33035590 PMCID: PMC8021618 DOI: 10.1016/j.pbiomolbio.2020.09.010] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/19/2020] [Revised: 09/12/2020] [Accepted: 09/29/2020] [Indexed: 01/26/2023]
Abstract
DNA-dependent protein kinase catalytic subunit (DNA-PKcs) is a key member of the phosphatidylinositol-3 kinase-like (PIKK) family of protein kinases with critical roles in DNA-double strand break repair, transcription, metastasis, mitosis, RNA processing, and innate and adaptive immunity. The absence of DNA-PKcs from many model organisms has led to the assumption that DNA-PKcs is a vertebrate-specific PIKK. Here, we find that DNA-PKcs is widely distributed in invertebrates, fungi, plants, and protists, and that threonines 2609, 2638, and 2647 of the ABCDE cluster of phosphorylation sites are highly conserved amongst most Eukaryotes. Furthermore, we identify highly conserved amino acid sequence motifs and domains that are characteristic of DNA-PKcs relative to other PIKKs. These include residues in the Forehead domain and a novel motif we have termed YRPD, located in an α helix C-terminal to the ABCDE phosphorylation site loop. Combining sequence with biochemistry plus structural data on human DNA-PKcs unveils conserved sequence and conformational features with functional insights and implications. The defined generally progressive DNA-PKcs sequence diversification uncovers conserved functionality supported by Evolutionary Trace analysis, suggesting that for many organisms both functional sites and evolutionary pressures remain identical due to fundamental cell biology. The mining of cancer genomic data and germline mutations causing human inherited disease reveal that robust DNA-PKcs activity in tumors is detrimental to patient survival, whereas germline mutations compromising function are linked to severe immunodeficiency and neuronal degeneration. We anticipate that these collective results will enable ongoing DNA-PKcs functional analyses with biological and medical implications.
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Affiliation(s)
- James P Lees-Miller
- Department of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, Alberta, T2N 4N1, Canada
| | - Alexander Cobban
- Department of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, Alberta, T2N 4N1, Canada
| | - Panagiotis Katsonis
- Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Albino Bacolla
- Departments of Cancer Biology and of Molecular and Cellular Oncology, University of Texas MD Anderson Cancer Center, 6767 Bertner Avenue, Houston, TX, 77030, USA
| | - Susan E Tsutakawa
- Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Michal Hammel
- Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Katheryn Meek
- College of Veterinary Medicine, Department of Microbiology & Molecular Genetics, And Department of Pathobiology & Diagnostic Investigation, Michigan State University, East Lansing, MI, 48824, USA
| | - Dave W Anderson
- Department of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, Alberta, T2N 4N1, Canada
| | - Olivier Lichtarge
- Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - John A Tainer
- Departments of Cancer Biology and of Molecular and Cellular Oncology, University of Texas MD Anderson Cancer Center, 6767 Bertner Avenue, Houston, TX, 77030, USA; Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.
| | - Susan P Lees-Miller
- Department of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, Alberta, T2N 4N1, Canada.
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16
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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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17
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Swiatczak B. Genomic Stress Responses Drive Lymphocyte Evolvability: An Ancient and Ubiquitous Mechanism. Bioessays 2020; 42:e2000032. [PMID: 32767393 DOI: 10.1002/bies.202000032] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2020] [Revised: 07/03/2020] [Indexed: 12/15/2022]
Abstract
Somatic diversification of antigen receptor genes depends on the activity of enzymes whose homologs participate in a mutagenic DNA repair in unicellular species. Indeed, by engaging error-prone polymerases, gap filling molecules and altered mismatch repair pathways, lymphocytes utilize conserved components of genomic stress response systems, which can already be found in bacteria and archaea. These ancient systems of mutagenesis and repair act to increase phenotypic diversity of microbial cell populations and operate to enhance their ability to produce fit variants during stress. Coopted by lymphocytes, the ancient mutagenic processing systems retained their diversification functions instilling the adaptive immune cells with enhanced evolvability and defensive capacity to resist infection and damage. As reviewed here, the ubiquity and conserved character of specialized variation-generating mechanisms from bacteria to lymphocytes highlight the importance of these mechanisms for evolution of life in general.
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Affiliation(s)
- Bartlomiej Swiatczak
- Department of History of Science and Scientific Archeology, University of Science and Technology of China, 96 Jinzhai Rd., Hefei, 230026, China
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18
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Tsakou-Ngouafo L, Paganini J, Kaufman J, Pontarotti P. Origins of the RAG Transposome and the MHC. Trends Immunol 2020; 41:561-571. [PMID: 32467030 DOI: 10.1016/j.it.2020.05.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Revised: 05/04/2020] [Accepted: 05/06/2020] [Indexed: 01/12/2023]
Abstract
How innate immunity gave rise to adaptive immunity in vertebrates remains unknown. We propose an evolutionary scenario beginning with pathogen-associated molecular pattern(s) (PAMPs) being presented by molecule(s) on one cell to specific receptor(s) on other cells, much like MHC molecules and T cell receptors (TCRs). In this model, mutations in MHC-like molecule(s) that bound new PAMP(s) would not be recognized by original TCR-like molecule(s), and new MHC-like gene(s) would be lost by neutral drift. Integrating recombination activating gene (RAG) transposon(s) in a TCR-like gene would result in greater recognition diversity, with new MHC-like variants recognized and selected, along with a new RAG/TCR-like system. MHC genes would be selected to present many peptides, through multigene families, allelic polymorphism, and peptide-binding promiscuity.
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Affiliation(s)
- Louis Tsakou-Ngouafo
- Aix Marseille University IRD, APHM, MEPHI, IHU Méditerranée Infection, Marseille France 3, 19-21 Boulevard Jean Moulin, 13005 Marseille, France
| | | | - Jim Kaufman
- University of Cambridge, Department of Pathology, Tennis Court Road, Cambridge CB2 1QP, UK; University of Cambridge, Department of Veterinary Medicine, Madingley Road, Cambridge CB2 0ES, UK; University of Edinburgh, Institute for Immunology and Infection Research, Charlotte Auerbach Road, Edinburgh EH9 3FL, UK.
| | - Pierre Pontarotti
- Aix Marseille University IRD, APHM, MEPHI, IHU Méditerranée Infection, Marseille France 3, 19-21 Boulevard Jean Moulin, 13005 Marseille, France; SNC5039 CNRS, 19-21 Boulevard Jean Moulin, 13005 Marseilles, France.
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