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Kosek D, Hickman AB, Ghirlando R, He S, Dyda F. Structures of ISCth4 transpososomes reveal the role of asymmetry in copy-out/paste-in DNA transposition. EMBO J 2021; 40:e105666. [PMID: 33006208 PMCID: PMC7780238 DOI: 10.15252/embj.2020105666] [Citation(s) in RCA: 4] [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: 05/19/2020] [Revised: 08/07/2020] [Accepted: 09/10/2020] [Indexed: 01/23/2023] Open
Abstract
Copy-out/paste-in transposition is a major bacterial DNA mobility pathway. It contributes significantly to the emergence of antibiotic resistance, often by upregulating expression of downstream genes upon integration. Unlike other transposition pathways, it requires both asymmetric and symmetric strand transfer steps. Here, we report the first structural study of a copy-out/paste-in transposase and demonstrate its ability to catalyze all pathway steps in vitro. X-ray structures of ISCth4 transposase, a member of the IS256 family of insertion sequences, bound to DNA substrates corresponding to three sequential steps in the reaction reveal an unusual asymmetric dimeric transpososome. During transposition, an array of N-terminal domains binds a single transposon end while the catalytic domain moves to accommodate the varying substrates. These conformational changes control the path of DNA flanking the transposon end and the generation of DNA-binding sites. Our results explain the asymmetric outcome of the initial strand transfer and show how DNA binding is modulated by the asymmetric transposase to allow the capture of a second transposon end and to integrate a circular intermediate.
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Affiliation(s)
- Dalibor Kosek
- Laboratory of Molecular BiologyNational Institute of Diabetes and Digestive and Kidney DiseasesNational Institutes of HealthBethesdaMDUSA
| | - Alison B Hickman
- Laboratory of Molecular BiologyNational Institute of Diabetes and Digestive and Kidney DiseasesNational Institutes of HealthBethesdaMDUSA
| | - Rodolfo Ghirlando
- Laboratory of Molecular BiologyNational Institute of Diabetes and Digestive and Kidney DiseasesNational Institutes of HealthBethesdaMDUSA
| | - Susu He
- Laboratory of Molecular BiologyNational Institute of Diabetes and Digestive and Kidney DiseasesNational Institutes of HealthBethesdaMDUSA
- Present address:
State Key Laboratory of Pharmaceutical BiotechnologyMedical School of Nanjing UniversityNanjingJiangsuChina
| | - Fred Dyda
- Laboratory of Molecular BiologyNational Institute of Diabetes and Digestive and Kidney DiseasesNational Institutes of HealthBethesdaMDUSA
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2
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Martínez-Gómez J, Galimba KD, Coté EY, Sullivan AM, Di Stilio VS. Spontaneous homeotic mutants and genetic control of floral organ identity in a ranunculid. Evol Dev 2020; 23:197-214. [PMID: 33179410 DOI: 10.1111/ede.12357] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Revised: 09/11/2020] [Accepted: 09/14/2020] [Indexed: 12/25/2022]
Abstract
The regulation of floral organ identity was investigated using a forward genetic approach in five floral homeotic mutants of Thalictrum, a noncore eudicot. We hypothesized that these mutants carry defects in the floral patterning genes. Mutant characterization comprised comparative floral morphology and organ identity gene expression at early and late developmental stages, followed by sequence analysis of coding and intronic regions to identify transcription factor binding sites and protein-protein interaction (PPI) motifs. Mutants exhibited altered expression of floral MADS-box genes, which further informed the function of paralogs arising from gene duplications not found in reference model systems. The ensuing modified BCE models for the mutants supported instances of neofunctionalization (e.g., B-class genes expressed ectopically in sepals), partial redundancy (E-class), or subfunctionalization (C-class) of paralogs. A lack of deleterious mutations in the coding regions of candidate floral MADS-box genes suggested that cis-regulatory or trans-acting mutations are at play. Consistent with this hypothesis, double-flower mutants had transposon insertions or showed signs of transposon activity in the regulatory intron of AGAMOUS (AG) orthologs. Single amino acid substitutions were also found, yet they did not fall on any of the identified DNA binding or PPI motifs. In conclusion, we present evidence suggesting that transposon activity and regulatory mutations in floral homeotic genes likely underlie the striking phenotypes of these Thalictrum floral homeotic mutants.
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Affiliation(s)
| | - Kelsey D Galimba
- Department of Biology, University of Washington, Seattle, Washington, USA
| | - Erin Y Coté
- Department of Biology, University of Washington, Seattle, Washington, USA
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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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Feng JX, Riddle NC. Epigenetics and genome stability. Mamm Genome 2020; 31:181-195. [PMID: 32296924 DOI: 10.1007/s00335-020-09836-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2019] [Accepted: 04/07/2020] [Indexed: 12/19/2022]
Abstract
Maintaining genome stability is essential to an organism's health and survival. Breakdown of the mechanisms protecting the genome and the resulting genome instability are an important aspect of the aging process and have been linked to diseases such as cancer. Thus, a large network of interconnected pathways is responsible for ensuring genome integrity in the face of the continuous challenges that induce DNA damage. While these pathways are diverse, epigenetic mechanisms play a central role in many of them. DNA modifications, histone variants and modifications, chromatin structure, and non-coding RNAs all carry out a variety of functions to ensure that genome stability is maintained. Epigenetic mechanisms ensure the functions of centromeres and telomeres that are essential for genome stability. Epigenetic mechanisms also protect the genome from the invasion by transposable elements and contribute to various DNA repair pathways. In this review, we highlight the integral role of epigenetic mechanisms in the maintenance of genome stability and draw attention to issues in need of further study.
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Affiliation(s)
- Justina X Feng
- Department of Biology, The University of Alabama at Birmingham, Birmingham, AL, USA
| | - Nicole C Riddle
- Department of Biology, The University of Alabama at Birmingham, Birmingham, AL, USA.
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Zhang X, Zhao M, Lisch D. Cost-Effective Profiling of Mutator Transposon Insertions in Maize by Next-Generation Sequencing. Methods Mol Biol 2020; 2072:39-50. [PMID: 31541437 DOI: 10.1007/978-1-4939-9865-4_5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Transposable elements can be highly mutagenic because when they transpose they can insert into genes and disrupt their function, a propensity which has been exploited in many organisms to generate tagged mutant alleles. The Mutator (Mu) family transposon is a family of DNA-type transposons in maize with a particularly high duplication frequency, which results in large numbers of new mutations in lineages that carry active Mu elements. Here we describe a rapid and cost-effective Miseq-based Mu transposon profiling pipeline. This method can also be used for identifying flanking sequences of other types of long insertions such as T-DNAs.
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Affiliation(s)
- Xinyan Zhang
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN, USA
| | - Meixia Zhao
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN, USA
| | - Damon Lisch
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN, USA.
- Center for Plant Biology, Purdue University, West Lafayette, IN, USA.
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The first comprehensive phylogenetic and biochemical analysis of NADH diphosphatases reveals that the enzyme from Tuber melanosporum is highly active towards NAD .. Sci Rep 2019; 9:16753. [PMID: 31728067 PMCID: PMC6856373 DOI: 10.1038/s41598-019-53138-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Accepted: 10/29/2019] [Indexed: 11/23/2022] Open
Abstract
Nudix (for nucleoside diphosphatases linked to other moieties, X) hydrolases are a diverse family of proteins capable of cleaving an enormous variety of substrates, ranging from nucleotide sugars to NAD+-capped RNAs. Although all the members of this superfamily share a common conserved catalytic motif, the Nudix box, their substrate specificity lies in specific sequence traits, which give rise to different subfamilies. Among them, NADH pyrophosphatases or diphosphatases (NADDs) are poorly studied and nothing is known about their distribution. To address this, we designed a Prosite-compatible pattern to identify new NADDs sequences. In silico scanning of the UniProtKB database showed that 3% of Nudix proteins were NADDs and displayed 21 different domain architectures, the canonical architecture (NUDIX-like_zf-NADH-PPase_NUDIX) being the most abundant (53%). Interestingly, NADD fungal sequences were prominent among eukaryotes, and were distributed over several Classes, including Pezizomycetes. Unexpectedly, in this last fungal Class, NADDs were found to be present from the most common recent ancestor to Tuberaceae, following a molecular phylogeny distribution similar to that previously described using two thousand single concatenated genes. Finally, when truffle-forming ectomycorrhizal Tuber melanosporum NADD was biochemically characterized, it showed the highest NAD+/NADH catalytic efficiency ratio ever described.
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Hickman AB, Voth AR, Ewis H, Li X, Craig NL, Dyda F. Structural insights into the mechanism of double strand break formation by Hermes, a hAT family eukaryotic DNA transposase. Nucleic Acids Res 2019; 46:10286-10301. [PMID: 30239795 PMCID: PMC6212770 DOI: 10.1093/nar/gky838] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Accepted: 09/07/2018] [Indexed: 12/12/2022] Open
Abstract
Some DNA transposons relocate from one genomic location to another using a mechanism that involves generating double-strand breaks at their transposon ends by forming hairpins on flanking DNA. The same double-strand break mode is employed by the V(D)J recombinase at signal-end/coding-end junctions during the generation of antibody diversity. How flanking hairpins are formed during DNA transposition has remained elusive. Here, we describe several co-crystal structures of the Hermes transposase bound to DNA that mimics the reaction step immediately prior to hairpin formation. Our results reveal a large DNA conformational change between the initial cleavage step and subsequent hairpin formation that changes which strand is acted upon by a single active site. We observed that two factors affect the conformational change: the complement of divalent metal ions bound by the catalytically essential DDE residues, and the identity of the –2 flanking base pair. Our data also provides a mechanistic link between the efficiency of hairpin formation (an A:T basepair is favored at the –2 position) and Hermes' strong target site preference. Furthermore, we have established that the histidine residue within a conserved C/DxxH motif present in many transposase families interacts directly with the scissile phosphate, suggesting a crucial role in catalysis.
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Affiliation(s)
- Alison B Hickman
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Andrea Regier Voth
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Hosam Ewis
- Howard Hughes Medical Institute, Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Xianghong Li
- Howard Hughes Medical Institute, Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Nancy L Craig
- Howard Hughes Medical Institute, Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Fred Dyda
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
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Dupeyron M, Singh KS, Bass C, Hayward A. Evolution of Mutator transposable elements across eukaryotic diversity. Mob DNA 2019; 10:12. [PMID: 30988700 PMCID: PMC6446971 DOI: 10.1186/s13100-019-0153-8] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Accepted: 03/01/2019] [Indexed: 11/15/2022] Open
Abstract
Background Mutator-like elements (MULEs) are a significant superfamily of DNA transposons on account of their: (i) great transpositional activity and propensity for insertion in or near gene sequences, (ii) their consequent high mutagenic capacity, and, (iii) their tendency to acquire host gene fragments. Consequently, MULEs are important genetic tools and represent a key study system for research into host-transposon interactions. Yet, while several studies have focused on the impacts of MULEs on crop and fungus genomes, their evolution remains poorly explored. Results We perform comprehensive bioinformatic and phylogenetic analyses to address currently available MULE diversity and reconstruct evolution for the group. For this, we mine MULEs from online databases, and combine search results with available transposase sequences retrieved from previously published studies. Our analyses uncover two entirely new MULE clades that contain elements almost entirely restricted to arthropod hosts, considerably expanding the set of MULEs known from this group, suggesting that many additional MULEs may await discovery from further arthropod genomes. In several cases, close relationships occur between MULEs recovered from distantly related host organisms, suggesting that horizontal transfer events may have played an important role in the evolution of the group. However, it is apparent that MULEs from plants remain separate from MULEs identified from other host groups. MULE structure varies considerably across phylogeny, and TIR length is shown to vary greatly both within and between MULE groups. Our phylogeny suggests that MULE diversity is clustered in well-supported groups, typically according to host taxonomy. With reference to this, we make suggestions on how MULE diversity can be partitioned to provide a robust taxonomic framework. Conclusions Our study represents a considerable advance in the understanding of MULE diversity, host range and evolution, and provides a taxonomic framework for the classification of further MULE elements that await discovery. Our findings also raise a number of questions relating to MULE biology, suggesting that this group will provide a rich avenue for future study. Electronic supplementary material The online version of this article (10.1186/s13100-019-0153-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Mathilde Dupeyron
- Centre for Ecology and Conservation, University of Exeter, Penryn Campus, Penryn, Cornwall, TR10 9FE UK
| | - Kumar S Singh
- Centre for Ecology and Conservation, University of Exeter, Penryn Campus, Penryn, Cornwall, TR10 9FE UK
| | - Chris Bass
- Centre for Ecology and Conservation, University of Exeter, Penryn Campus, Penryn, Cornwall, TR10 9FE UK
| | - Alexander Hayward
- Centre for Ecology and Conservation, University of Exeter, Penryn Campus, Penryn, Cornwall, TR10 9FE UK
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Muszewska A, Steczkiewicz K, Stepniewska-Dziubinska M, Ginalski K. Cut-and-Paste Transposons in Fungi with Diverse Lifestyles. Genome Biol Evol 2017; 9:3463-3477. [PMID: 29228286 PMCID: PMC5751038 DOI: 10.1093/gbe/evx261] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/07/2017] [Indexed: 02/06/2023] Open
Abstract
Transposable elements (TEs) shape genomes via recombination and transposition, lead to chromosomal rearrangements, create new gene neighborhoods, and alter gene expression. They play key roles in adaptation either to symbiosis in Amanita genus or to pathogenicity in Pyrenophora tritici-repentis. Despite growing evidence of their importance, the abundance and distribution of mobile elements replicating in a "cut-and-paste" fashion is barely described so far. In order to improve our knowledge on this old and ubiquitous class of transposable elements, 1,730 fungal genomes were scanned using both de novo and homology-based approaches. DNA TEs have been identified across the whole data set and display uneven distribution from both DNA TE classification and fungal taxonomy perspectives. DNA TE content correlates with genome size, which confirms that many transposon families proliferate simultaneously. In contrast, it is independent from intron density, average gene distance and GC content. TE count is associated with species' lifestyle and tends to be elevated in plant symbionts and decreased in animal parasites. Lastly, we found that fungi with both RIP and RNAi systems have more total DNA TE sequences but less elements retaining a functional transposase, what reflects stringent control over transposition.
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Affiliation(s)
- Anna Muszewska
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Kamil Steczkiewicz
- Laboratory of Bioinformatics and Systems Biology, CeNT, University of Warsaw, Poland
| | | | - Krzysztof Ginalski
- Laboratory of Bioinformatics and Systems Biology, CeNT, University of Warsaw, Poland
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