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Capilla-Pérez L, Solier V, Gilbault E, Lian Q, Goel M, Huettel B, Keurentjes JJB, Loudet O, Mercier R. Enhanced recombination empowers the detection and mapping of Quantitative Trait Loci. Commun Biol 2024; 7:829. [PMID: 38977904 PMCID: PMC11231358 DOI: 10.1038/s42003-024-06530-w] [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: 01/22/2024] [Accepted: 07/02/2024] [Indexed: 07/10/2024] Open
Abstract
Modern plant breeding, such as genomic selection and gene editing, is based on the knowledge of the genetic architecture of desired traits. Quantitative trait loci (QTL) analysis, which combines high throughput phenotyping and genotyping of segregating populations, is a powerful tool to identify these genetic determinants and to decipher the underlying mechanisms. However, meiotic recombination, which shuffles genetic information between generations, is limited: Typically only one to two exchange points, called crossovers, occur between a pair of homologous chromosomes. Here we test the effect on QTL analysis of boosting recombination, by mutating the anti-crossover factors RECQ4 and FIGL1 in Arabidopsis thaliana full hybrids and lines in which a single chromosome is hybrid. We show that increasing recombination ~6-fold empowers the detection and resolution of QTLs, reaching the gene scale with only a few hundred plants. Further, enhanced recombination unmasks some secondary QTLs undetected under normal recombination. These results show the benefits of enhanced recombination to decipher the genetic bases of traits.
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Affiliation(s)
- Laia Capilla-Pérez
- Max Planck Institute for Plant Breeding Research, MPIPZ, Department of Chromosome Biology, Carl-von-Linné Weg 10, 50829, Cologne, Germany
| | - Victor Solier
- Max Planck Institute for Plant Breeding Research, MPIPZ, Department of Chromosome Biology, Carl-von-Linné Weg 10, 50829, Cologne, Germany
| | - Elodie Gilbault
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), 78000, Versailles, France
| | - Qichao Lian
- Max Planck Institute for Plant Breeding Research, MPIPZ, Department of Chromosome Biology, Carl-von-Linné Weg 10, 50829, Cologne, Germany
| | - Manish Goel
- Max Planck Institute for Plant Breeding Research, MPIPZ, Department of Chromosome Biology, Carl-von-Linné Weg 10, 50829, Cologne, Germany
- Ludwig-Maximilians-Universität München, Fakultät für Biologie, Biozentrum Martinsried, 82152, Planegg-Martinsried, Germany
| | - Bruno Huettel
- Max Planck Institute for Plant Breeding Research, MPIPZ, Genome Center, Carl-von-Linné Weg 10, 50829, Cologne, Germany
| | - Joost J B Keurentjes
- Laboratory of Genetics, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
| | - Olivier Loudet
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), 78000, Versailles, France.
| | - Raphael Mercier
- Max Planck Institute for Plant Breeding Research, MPIPZ, Department of Chromosome Biology, Carl-von-Linné Weg 10, 50829, Cologne, Germany.
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2
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Arter M, Keeney S. Divergence and conservation of the meiotic recombination machinery. Nat Rev Genet 2024; 25:309-325. [PMID: 38036793 DOI: 10.1038/s41576-023-00669-8] [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] [Accepted: 10/03/2023] [Indexed: 12/02/2023]
Abstract
Sexually reproducing eukaryotes use recombination between homologous chromosomes to promote chromosome segregation during meiosis. Meiotic recombination is almost universally conserved in its broad strokes, but specific molecular details often differ considerably between taxa, and the proteins that constitute the recombination machinery show substantial sequence variability. The extent of this variation is becoming increasingly clear because of recent increases in genomic resources and advances in protein structure prediction. We discuss the tension between functional conservation and rapid evolutionary change with a focus on the proteins that are required for the formation and repair of meiotic DNA double-strand breaks. We highlight phylogenetic relationships on different time scales and propose that this remarkable evolutionary plasticity is a fundamental property of meiotic recombination that shapes our understanding of molecular mechanisms in reproductive biology.
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Affiliation(s)
- Meret Arter
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Scott Keeney
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
- Howard Hughes Medical Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
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3
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Bazile J, Nadaud I, Lasserre-Zuber P, Kitt J, De Oliveira R, Choulet F, Sourdille P. TaRECQ4 contributes to maintain both homologous and homoeologous recombination during wheat meiosis. FRONTIERS IN PLANT SCIENCE 2024; 14:1342976. [PMID: 38348162 PMCID: PMC10859459 DOI: 10.3389/fpls.2023.1342976] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Accepted: 12/29/2023] [Indexed: 02/15/2024]
Abstract
Introduction Meiotic recombination (or crossover, CO) is essential for gamete fertility as well as for alleles and genes reshuffling that is at the heart of plant breeding. However, CO remains a limited event, which strongly hampers the rapid production of original and improved cultivars. RecQ4 is a gene encoding a helicase protein that, when mutated, contributes to improve recombination rate in all species where it has been evaluated so far. Methods In this study, we developed wheat (Triticum aestivum L.) triple mutant (TM) for the three homoeologous copies of TaRecQ4 as well as mutants for two copies and heterozygous for the last one (Htz-A, Htz-B, Htz-D). Results Phenotypic observation revealed a significant reduction of fertility and pollen viability in TM and Htz-B plants compared to wild type plants suggesting major defects during meiosis. Cytogenetic analyses of these plants showed that complete absence of TaRecQ4 as observed in TM plants, leads to chromosome fragmentation during the pachytene stage, resulting in problems in the segregation of chromosomes during meiosis. Htz-A and Htz-D mutants had an almost normal meiotic progression indicating that both TaRecQ4-A and TaRecQ4-D copies are functional and that there is no dosage effect for TaRecQ4 in bread wheat. On the contrary, the TaRecQ4-B copy seems knocked-out, probably because of a SNP leading to a Threonine>Alanine change at position 539 (T539A) of the protein, that occurs in the crucial helicase ATP bind/DEAD/ResIII domain which unwinds nucleic acids. Occurrence of numerous multivalents in TM plants suggests that TaRecQ4 could also play a role in the control of homoeologous recombination. Discussion These findings provide a foundation for further molecular investigations into wheat meiosis regulation to fully understand the underlying mechanisms of how TaRecQ4 affects chiasma formation, as well as to identify ways to mitigate these defects and enhance both homologous and homoeologous recombination efficiency in wheat.
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Affiliation(s)
- Jeanne Bazile
- INRAE, UMR 1095 INRAE – UCA Genetics, Diversity & Ecophysiology of Cereals, Clermont-Ferrand, France
| | - Isabelle Nadaud
- INRAE, UMR 1095 INRAE – UCA Genetics, Diversity & Ecophysiology of Cereals, Clermont-Ferrand, France
| | - Pauline Lasserre-Zuber
- INRAE, UMR 1095 INRAE – UCA Genetics, Diversity & Ecophysiology of Cereals, Clermont-Ferrand, France
| | - Jonathan Kitt
- INRAE, UMR 1095 INRAE – UCA Genetics, Diversity & Ecophysiology of Cereals, Clermont-Ferrand, France
| | - Romain De Oliveira
- Biotech Research and Innovation Centre (BRIC), Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Frédéric Choulet
- INRAE, UMR 1095 INRAE – UCA Genetics, Diversity & Ecophysiology of Cereals, Clermont-Ferrand, France
| | - Pierre Sourdille
- INRAE, UMR 1095 INRAE – UCA Genetics, Diversity & Ecophysiology of Cereals, Clermont-Ferrand, France
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Dluzewska J, Dziegielewski W, Szymanska-Lejman M, Gazecka M, Henderson IR, Higgins JD, Ziolkowski PA. MSH2 stimulates interfering and inhibits non-interfering crossovers in response to genetic polymorphism. Nat Commun 2023; 14:6716. [PMID: 37872134 PMCID: PMC10593791 DOI: 10.1038/s41467-023-42511-z] [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: 04/17/2023] [Accepted: 10/13/2023] [Indexed: 10/25/2023] Open
Abstract
Meiotic crossovers can be formed through the interfering pathway, in which one crossover prevents another from forming nearby, or by an independent non-interfering pathway. In Arabidopsis, local sequence polymorphism between homologs can stimulate interfering crossovers in a MSH2-dependent manner. To understand how MSH2 regulates crossovers formed by the two pathways, we combined Arabidopsis mutants that elevate non-interfering crossovers with msh2 mutants. We demonstrate that MSH2 blocks non-interfering crossovers at polymorphic loci, which is the opposite effect to interfering crossovers. We also observe MSH2-independent crossover inhibition at highly polymorphic sites. We measure recombination along the chromosome arms in lines differing in patterns of heterozygosity and observe a MSH2-dependent crossover increase at the boundaries between heterozygous and homozygous regions. Here, we show that MSH2 is a master regulator of meiotic DSB repair in Arabidopsis, with antagonistic effects on interfering and non-interfering crossovers, which shapes the crossover landscape in relation to interhomolog polymorphism.
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Affiliation(s)
- Julia Dluzewska
- Laboratory of Genome Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Poznań, Poland
| | - Wojciech Dziegielewski
- Laboratory of Genome Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Poznań, Poland
| | - Maja Szymanska-Lejman
- Laboratory of Genome Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Poznań, Poland
| | - Monika Gazecka
- Laboratory of Genome Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Poznań, Poland
- Department of Molecular Virology, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznań, Poland
| | - Ian R Henderson
- Department of Plant Sciences, University of Cambridge, Cambridge, UK
| | - James D Higgins
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
| | - Piotr A Ziolkowski
- Laboratory of Genome Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Poznań, Poland.
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5
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Katche EI, Schierholt A, Schiessl SV, He F, Lv Z, Batley J, Becker HC, Mason AS. Genetic factors inherited from both diploid parents interact to affect genome stability and fertility in resynthesized allotetraploid Brassica napus. G3 (BETHESDA, MD.) 2023; 13:jkad136. [PMID: 37313757 PMCID: PMC10411605 DOI: 10.1093/g3journal/jkad136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 04/24/2023] [Accepted: 05/31/2023] [Indexed: 06/15/2023]
Abstract
Established allopolyploids are known to be genomically stable and fertile. However, in contrast, most newly resynthesized allopolyploids are infertile and meiotically unstable. Identifying the genetic factors responsible for genome stability in newly formed allopolyploid is key to understanding how 2 genomes come together to form a species. One hypothesis is that established allopolyploids may have inherited specific alleles from their diploid progenitors which conferred meiotic stability. Resynthesized Brassica napus lines are often unstable and infertile, unlike B. napus cultivars. We tested this hypothesis by characterizing 41 resynthesized B. napus lines produced by crosses between 8 Brassica rapa and 8 Brassica oleracea lines for copy number variation resulting from nonhomologous recombination events and fertility. We resequenced 8 B. rapa and 5 B. oleracea parent accessions and analyzed 19 resynthesized lines for allelic variation in a list of meiosis gene homologs. SNP genotyping was performed using the Illumina Infinium Brassica 60K array for 3 individuals per line. Self-pollinated seed set and genome stability (number of copy number variants) were significantly affected by the interaction between both B. rapa and B. oleracea parental genotypes. We identified 13 putative meiosis gene candidates which were significantly associated with frequency of copy number variants and which contained putatively harmful mutations in meiosis gene haplotypes for further investigation. Our results support the hypothesis that allelic variants inherited from parental genotypes affect genome stability and fertility in resynthesized rapeseed.
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Affiliation(s)
- Elizabeth Ihien Katche
- Plant Breeding Department, University of Bonn, Bonn 53115, Germany
- Department of Plant Breeding, Justus Liebig University, Giessen 35392, Germany
| | - Antje Schierholt
- Department of Crop Sciences, Division of Plant Breeding Methodology, Georg-August University Göttingen, Göttingen 37073, Germany
| | - Sarah-Veronica Schiessl
- Department of Plant Breeding, Justus Liebig University, Giessen 35392, Germany
- Department of Botany and Molecular Evolution, Senckenberg Research Institute and Natural History Museum Frankfurt, Frankfurt am Main D-60325, Germany
| | - Fei He
- Plant Breeding Department, University of Bonn, Bonn 53115, Germany
| | - Zhenling Lv
- Plant Breeding Department, University of Bonn, Bonn 53115, Germany
- Department of Plant Breeding, Justus Liebig University, Giessen 35392, Germany
| | - Jacqueline Batley
- School of Biological Sciences, University of Western Australia, Perth, WA 6009, Australia
| | - Heiko C Becker
- Department of Crop Sciences, Division of Plant Breeding Methodology, Georg-August University Göttingen, Göttingen 37073, Germany
| | - Annaliese S Mason
- Plant Breeding Department, University of Bonn, Bonn 53115, Germany
- Department of Plant Breeding, Justus Liebig University, Giessen 35392, Germany
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6
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Campos-Martin R, Schmickler S, Goel M, Schneeberger K, Tresch A. Reliable genotyping of recombinant genomes using a robust hidden Markov model. PLANT PHYSIOLOGY 2023; 192:821-836. [PMID: 36946207 PMCID: PMC10231367 DOI: 10.1093/plphys/kiad191] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Revised: 01/20/2023] [Accepted: 01/27/2023] [Indexed: 06/01/2023]
Abstract
Meiotic recombination is an essential mechanism during sexual reproduction and includes the exchange of chromosome segments between homologous chromosomes. New allelic combinations are transmitted to the new generation, introducing novel genetic variation in the offspring genomes. With the improvement of high-throughput whole-genome sequencing technologies, large numbers of recombinant individuals can now be sequenced with low sequencing depth at low costs, necessitating computational methods for reconstructing their haplotypes. The main challenge is the uncertainty in haplotype calling that arises from the low information content of a single genomic position. Straightforward sliding window-based approaches are difficult to tune and fail to place recombination breakpoints precisely. Hidden Markov model (HMM)-based approaches, on the other hand, tend to over-segment the genome. Here, we present RTIGER, an HMM-based model that exploits in a mathematically precise way the fact that true chromosome segments typically have a certain minimum length. We further separate the task of identifying the correct haplotype sequence from the accurate placement of haplotype borders, thereby maximizing the accuracy of border positions. By comparing segmentations based on simulated data with known underlying haplotypes, we highlight the reasons for RTIGER outperforming traditional segmentation approaches. We then analyze the meiotic recombination pattern of segregants of 2 Arabidopsis (Arabidopsis thaliana) accessions and a previously described hyper-recombining mutant. RTIGER is available as an R package with an efficient Julia implementation of the core algorithm.
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Affiliation(s)
- Rafael Campos-Martin
- Faculty of Medicine, University Hospital Cologne, Cologne 50937, Germany
- Department of Chromosome Biology, Max Planck Institute for Plant Breeding Research, Cologne 50829, Germany
- Division of Neurogenetics and Molecular Psychiatry, Department of Psychiatry and Psychotherapy, University of Cologne, Medical Faculty, Cologne 50937, Germany
| | - Sophia Schmickler
- Faculty of Medicine, University Hospital Cologne, Cologne 50937, Germany
| | - Manish Goel
- Department of Chromosome Biology, Max Planck Institute for Plant Breeding Research, Cologne 50829, Germany
- Faculty for Biology, LMU Munich, Planegg-Martinsried 82152, Germany
| | - Korbinian Schneeberger
- Department of Chromosome Biology, Max Planck Institute for Plant Breeding Research, Cologne 50829, Germany
- Faculty for Biology, LMU Munich, Planegg-Martinsried 82152, Germany
- Cluster of Excellence on Plant Sciences, Heinrich-Heine University, Düsseldorf 40225, Germany
| | - Achim Tresch
- Faculty of Medicine, University Hospital Cologne, Cologne 50937, Germany
- CECAD, University of Cologne, Cologne 50931, Germany
- Center for Data and Simulation Science, University of Cologne, Cologne 50931, Germany
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Rafiei N, Ronceret A. Crossover interference mechanism: New lessons from plants. Front Cell Dev Biol 2023; 11:1156766. [PMID: 37274744 PMCID: PMC10236007 DOI: 10.3389/fcell.2023.1156766] [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: 02/01/2023] [Accepted: 04/17/2023] [Indexed: 06/06/2023] Open
Abstract
Plants are the source of our understanding of several fundamental biological principles. It is well known that Gregor Mendel discovered the laws of Genetics in peas and that maize was used for the discovery of transposons by Barbara McClintock. Plant models are still useful for the understanding of general key biological concepts. In this article, we will focus on discussing the recent plant studies that have shed new light on the mysterious mechanisms of meiotic crossover (CO) interference, heterochiasmy, obligatory CO, and CO homeostasis. Obligatory CO is necessary for the equilibrated segregation of homologous chromosomes during meiosis. The tight control of the different male and female CO rates (heterochiasmy) enables both the maximization and minimization of genome shuffling. An integrative model can now predict these observed aspects of CO patterning in plants. The mechanism proposed considers the Synaptonemal Complex as a canalizing structure that allows the diffusion of a class I CO limiting factor linearly on synapsed bivalents. The coarsening of this limiting factor along the SC explains the interfering spacing between COs. The model explains the observed coordinated processes between synapsis, CO interference, CO insurance, and CO homeostasis. It also easily explains heterochiasmy just considering the different male and female SC lengths. This mechanism is expected to be conserved in other species.
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8
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Chen P, De Winne N, De Jaeger G, Ito M, Heese M, Schnittger A. KNO1‐mediated autophagic degradation of the Bloom syndrome complex component RMI1 promotes homologous recombination. EMBO J 2023; 42:e111980. [PMID: 36970874 PMCID: PMC10183828 DOI: 10.15252/embj.2022111980] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2022] [Revised: 01/30/2023] [Accepted: 03/12/2023] [Indexed: 03/29/2023] Open
Abstract
Homologous recombination (HR) is a key DNA damage repair pathway that is tightly adjusted to the state of a cell. A central regulator of homologous recombination is the conserved helicase-containing Bloom syndrome complex, renowned for its crucial role in maintaining genome integrity. Here, we show that in Arabidopsis thaliana, Bloom complex activity is controlled by selective autophagy. We find that the recently identified DNA damage regulator KNO1 facilitates K63-linked ubiquitination of RMI1, a structural component of the complex, thereby triggering RMI1 autophagic degradation and resulting in increased homologous recombination. Conversely, reduced autophagic activity makes plants hypersensitive to DNA damage. KNO1 itself is also controlled at the level of proteolysis, in this case mediated by the ubiquitin-proteasome system, becoming stabilized upon DNA damage via two redundantly acting deubiquitinases, UBP12 and UBP13. These findings uncover a regulatory cascade of selective and interconnected protein degradation steps resulting in a fine-tuned HR response upon DNA damage.
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9
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Wang Y, Jiang Z, Qin A, Wang F, Chang E, Liu Y, Nie W, Tan C, Yuan Y, Dong Y, Huang R, Jia Z, Wang J. Population Structure, Genetic Diversity and Candidate Genes for the Adaptation to Environmental Stress in Picea koraiensis. PLANTS (BASEL, SWITZERLAND) 2023; 12:1266. [PMID: 36986954 PMCID: PMC10055018 DOI: 10.3390/plants12061266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 03/07/2023] [Accepted: 03/08/2023] [Indexed: 06/19/2023]
Abstract
Picea koraiensis is major silvicultural and timber species in northeast China, and its distribution area is an important transition zone for genus spruce migration. The degree of intraspecific differentiation of P. koraiensis is high, but population structure and differentiation mechanisms are not clear. In this study, 523,761 single nucleotide polymorphisms (SNPs) were identified in 113 individuals from 9 populations of P. koraiensis by genotyping-by-sequencing (GBS). Population genomic analysis showed that P. koraiensis was divided into three geoclimatic regions: Great Khingan Mountains climatic region, Lesser Khingan Mountains climatic region, and Changbai Mountain climatic region. Mengkeshan (MKS) population on the northern edge of the distribution area and Wuyiling (WYL) population located in the mining area are two highly differentiated groups. Selective sweep analysis showed that MKS and WYL populations had 645 and 1126 selected genes, respectively. Genes selected in the MKS population were associated with flowering and photomorphogenesis, cellular response to water deficit, and glycerophospholipid metabolism; genes selected in the WYL population were associated with metal ion transport, biosynthesis of macromolecules, and DNA repair. Climatic factors and heavy metal stress drives divergence in MKS and WYL populations, respectively. Our findings provide insights into adaptive divergence mechanisms in Picea and will contribute to molecular breeding studies.
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Affiliation(s)
- Ya Wang
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China
| | - Zeping Jiang
- Key Laboratory of Forest Ecology and Environment of National Forestry and Grassland Administration, Ecology and Nature Conservation Institute, Chinese Academy of Forestry, Beijing 100091, China
| | - Aili Qin
- Key Laboratory of Forest Ecology and Environment of National Forestry and Grassland Administration, Ecology and Nature Conservation Institute, Chinese Academy of Forestry, Beijing 100091, China
| | - Fude Wang
- Forestry Research Institute in Heilongjiang Province, Harbin 150081, China
| | - Ermei Chang
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China
| | - Yifu Liu
- Key Laboratory of Forest Ecology and Environment of National Forestry and Grassland Administration, Ecology and Nature Conservation Institute, Chinese Academy of Forestry, Beijing 100091, China
| | - Wen Nie
- Key Laboratory of Forest Ecology and Environment of National Forestry and Grassland Administration, Ecology and Nature Conservation Institute, Chinese Academy of Forestry, Beijing 100091, China
| | - Cancan Tan
- Key Laboratory of Forest Ecology and Environment of National Forestry and Grassland Administration, Ecology and Nature Conservation Institute, Chinese Academy of Forestry, Beijing 100091, China
| | - Yanchao Yuan
- Key Laboratory of Forest Ecology and Environment of National Forestry and Grassland Administration, Ecology and Nature Conservation Institute, Chinese Academy of Forestry, Beijing 100091, China
| | - Yao Dong
- Key Laboratory of Forest Ecology and Environment of National Forestry and Grassland Administration, Ecology and Nature Conservation Institute, Chinese Academy of Forestry, Beijing 100091, China
| | - Ruizhi Huang
- Key Laboratory of Forest Ecology and Environment of National Forestry and Grassland Administration, Ecology and Nature Conservation Institute, Chinese Academy of Forestry, Beijing 100091, China
| | - Zirui Jia
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China
| | - Junhui Wang
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China
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10
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Emmenecker C, Mézard C, Kumar R. Repair of DNA double-strand breaks in plant meiosis: role of eukaryotic RecA recombinases and their modulators. PLANT REPRODUCTION 2023; 36:17-41. [PMID: 35641832 DOI: 10.1007/s00497-022-00443-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Accepted: 05/09/2022] [Indexed: 06/15/2023]
Abstract
Homologous recombination during meiosis is crucial for the DNA double-strand breaks (DSBs) repair that promotes the balanced segregation of homologous chromosomes and enhances genetic variation. In most eukaryotes, two recombinases RAD51 and DMC1 form nucleoprotein filaments on single-stranded DNA generated at DSB sites and play a central role in the meiotic DSB repair and genome stability. These nucleoprotein filaments perform homology search and DNA strand exchange to initiate repair using homologous template-directed sequences located elsewhere in the genome. Multiple factors can regulate the assembly, stability, and disassembly of RAD51 and DMC1 nucleoprotein filaments. In this review, we summarize the current understanding of the meiotic functions of RAD51 and DMC1 and the role of their positive and negative modulators. We discuss the current models and regulators of homology searches and strand exchange conserved during plant meiosis. Manipulation of these repair factors during plant meiosis also holds a great potential to accelerate plant breeding for crop improvements and productivity.
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Affiliation(s)
- Côme Emmenecker
- Institut Jean-Pierre Bourgin (IJPB), Université Paris-Saclay, INRAE, AgroParisTech, 78000, Versailles, France
- University of Paris-Sud, Université Paris-Saclay, 91405, Orsay, France
| | - Christine Mézard
- Institut Jean-Pierre Bourgin (IJPB), CNRS, Université Paris-Saclay, INRAE, AgroParisTech, 78000, Versailles, France.
| | - Rajeev Kumar
- Institut Jean-Pierre Bourgin (IJPB), Université Paris-Saclay, INRAE, AgroParisTech, 78000, Versailles, France.
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11
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Calvo‐Baltanás V, De Jaeger‐Braet J, Cher WY, Schönbeck N, Chae E, Schnittger A, Wijnker E. Knock-down of gene expression throughout meiosis and pollen formation by virus-induced gene silencing in Arabidopsis thaliana. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 111:19-37. [PMID: 35340073 PMCID: PMC9543169 DOI: 10.1111/tpj.15733] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Revised: 02/16/2022] [Accepted: 02/18/2022] [Indexed: 06/14/2023]
Abstract
Through the inactivation of genes that act during meiosis it is possible to direct the genetic make-up of plants in subsequent generations and optimize breeding schemes. Offspring may show higher recombination of parental alleles resulting from elevated crossover (CO) incidence, or by omission of meiotic divisions, offspring may become polyploid. However, stable mutations in genes essential for recombination, or for either one of the two meiotic divisions, can have pleiotropic effects on plant morphology and line stability, for instance by causing lower fertility. Therefore, it is often favorable to temporarily change gene expression during meiosis rather than relying on stable null mutants. It was previously shown that virus-induced gene silencing (VIGS) can be used to transiently reduce CO frequencies. We asked if VIGS could also be used to modify other processes throughout meiosis and during pollen formation in Arabidopsis thaliana. Here, we show that VIGS-mediated knock-down of FIGL1, RECQ4A/B, OSD1 and QRT2 can induce (i) an increase in chiasma numbers, (ii) unreduced gametes and (iii) pollen tetrads. We further show that VIGS can target both sexes and different genetic backgrounds and can simultaneously silence different gene copies. The successful knock-down of these genes in A. thaliana suggests that VIGS can be exploited to manipulate any process during or shortly after meiosis. Hence, the transient induction of changes in inheritance patterns can be used as a powerful tool for applied research and biotechnological applications.
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Affiliation(s)
- Vanesa Calvo‐Baltanás
- Laboratory of GeneticsWageningen University & ResearchDroevendaalsesteeg 1Wageningen6700 AAthe Netherlands
- Department of Developmental Biology, Institut für Pflanzenwissenschaften und MikrobiologieUniversity of HamburgOhnhorststrasse 18Hamburg22609Germany
- Department of Biological SciencesNational University of Singapore14 Science Drive 4Singapore117543Singapore
| | - Joke De Jaeger‐Braet
- Department of Developmental Biology, Institut für Pflanzenwissenschaften und MikrobiologieUniversity of HamburgOhnhorststrasse 18Hamburg22609Germany
| | - Wei Yuan Cher
- A*STAR, Institute of Molecular and Cell Biology (IMCB)61 Biopolis DriveProteos138673Singapore
| | - Nils Schönbeck
- Department of Developmental Biology, Institut für Pflanzenwissenschaften und MikrobiologieUniversity of HamburgOhnhorststrasse 18Hamburg22609Germany
- UKEMartinistrasse 5220251HamburgGermany
| | - Eunyoung Chae
- Department of Biological SciencesNational University of Singapore14 Science Drive 4Singapore117543Singapore
| | - Arp Schnittger
- Department of Developmental Biology, Institut für Pflanzenwissenschaften und MikrobiologieUniversity of HamburgOhnhorststrasse 18Hamburg22609Germany
| | - Erik Wijnker
- Laboratory of GeneticsWageningen University & ResearchDroevendaalsesteeg 1Wageningen6700 AAthe Netherlands
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12
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Transcriptome Profiling Identifies Candidate Genes Contributing to Male and Female Gamete Development in Synthetic Brassica Allohexaploids. PLANTS 2022; 11:plants11121556. [PMID: 35736707 PMCID: PMC9228180 DOI: 10.3390/plants11121556] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/29/2022] [Revised: 06/07/2022] [Accepted: 06/09/2022] [Indexed: 11/17/2022]
Abstract
Polyploidy plays a crucial role in plant evolution and speciation. The development of male and female gametes is essential to the reproductive capacity of polyploids, but their gene expression pattern has not been fully explored in newly established polyploids. The present study aimed to reveal a detailed atlas of gene expression for gamete development in newly synthetic Brassica allohexaploids that are not naturally existing species. Comparative transcriptome profiling between developing anthers (staged from meiosis to mature pollen) and ovules (staged from meiosis to mature embryo sac) was performed using RNA-Seq analysis. A total of 8676, 9775 and 4553 upregulated differentially expressed genes (DEGs) were identified for the development of both gametes, for male-only, and for female-only gamete development, respectively, in the synthetic Brassica allohexaploids. By combining gene ontology (GO) biological process analysis and data from the published literature, we identified 37 candidate genes for DNA double-strand break formation, synapsis and the crossover of homologous recombination during male and female meiosis and 51 candidate genes for tapetum development, sporopollenin biosynthesis and pollen wall development in male gamete development. Furthermore, 23 candidate genes for mitotic progression, nuclear positioning and cell specification and development were enriched in female gamete development. This study lays a good foundation for revealing the molecular regulation of genes related to male and female gamete development in Brassica allohexaploids and provides more resourceful genetic information on the reproductive biology of Brassica polyploid breeding.
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13
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Verma P, Kumari P, Negi S, Yadav G, Gaur V. Holliday junction resolution by At-HIGLE: an SLX1 lineage endonuclease from Arabidopsis thaliana with a novel in-built regulatory mechanism. Nucleic Acids Res 2022; 50:4630-4646. [PMID: 35412622 PMCID: PMC9071465 DOI: 10.1093/nar/gkac239] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Revised: 03/24/2022] [Accepted: 04/01/2022] [Indexed: 12/14/2022] Open
Abstract
Holliday junction is the key homologous recombination intermediate, resolved by structure-selective endonucleases (SSEs). SLX1 is the most promiscuous SSE of the GIY-YIG nuclease superfamily. In fungi and animals, SLX1 nuclease activity relies on a non-enzymatic partner, SLX4, but no SLX1-SLX4 like complex has ever been characterized in plants. Plants exhibit specialized DNA repair and recombination machinery. Based on sequence similarity with the GIY-YIG nuclease domain of SLX1 proteins from fungi and animals, At-HIGLE was identified to be a possible SLX1 like nuclease from plants. Here, we elucidated the crystal structure of the At-HIGLE nuclease domain from Arabidopsis thaliana, establishing it as a member of the SLX1-lineage of the GIY-YIG superfamily with structural changes in DNA interacting regions. We show that At-HIGLE can process branched-DNA molecules without an SLX4 like protein. Unlike fungal SLX1, At-HIGLE exists as a catalytically active homodimer capable of generating two coordinated nicks during HJ resolution. Truncating the extended C-terminal region of At-HIGLE increases its catalytic activity, changes the nicking pattern, and monomerizes At-HIGLE. Overall, we elucidated the first structure of a plant SLX1-lineage protein, showed its HJ resolving activity independent of any regulatory protein, and identified an in-built novel regulatory mechanism engaging its C-terminal region.
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Affiliation(s)
- Prabha Verma
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Poonam Kumari
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Shreya Negi
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Gitanjali Yadav
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Vineet Gaur
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India
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14
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Hacker L, Capdeville N, Feller L, Enderle-Kukla J, Dorn A, Puchta H. The DNA-dependent protease AtWSS1A suppresses persistent double strand break formation during replication. THE NEW PHYTOLOGIST 2022; 233:1172-1187. [PMID: 34761387 DOI: 10.1111/nph.17848] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Accepted: 11/01/2021] [Indexed: 06/13/2023]
Abstract
The protease WSS1A is an important factor in the repair of DNA-protein crosslinks in plants. Here we show that the loss of WSS1A leads to a reduction of 45S rDNA repeats and chromosomal fragmentation in Arabidopsis. Moreover, in the absence of any factor of the RTR (RECQ4A/TOP3α/RMI1/2) complex, which is involved in the dissolution of DNA replication intermediates, WSS1A becomes essential for viability. If WSS1A loss is combined with loss of the classical (c) or alternative (a) nonhomologous end joining (NHEJ) pathways of double-strand break (DSB) repair, the resulting mutants show proliferation defects and enhanced chromosome fragmentation, which is especially aggravated in the absence of aNHEJ. This indicates that WSS1A is involved either in the suppression of DSB formation or in DSB repair itself. To test the latter we induced DSB by CRISPR/Cas9 at different loci in wild-type and mutant cells and analyzed their repair by deep sequencing. However, no change in the quality of the repair events and only a slight increase in their quantity was found. Thus, by removing complex DNA-protein structures, WSS1A seems to be required for the repair of replication intermediates which would otherwise be resolved into persistent DSB leading to genome instability.
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Affiliation(s)
- Leonie Hacker
- Botanical Institute, Molecular Biology and Biochemistry, Karlsruhe Institute of Technology, Fritz-Haber-Weg 4, Karlsruhe, 76131, Germany
| | - Niklas Capdeville
- Botanical Institute, Molecular Biology and Biochemistry, Karlsruhe Institute of Technology, Fritz-Haber-Weg 4, Karlsruhe, 76131, Germany
| | - Laura Feller
- Botanical Institute, Molecular Biology and Biochemistry, Karlsruhe Institute of Technology, Fritz-Haber-Weg 4, Karlsruhe, 76131, Germany
| | - Janina Enderle-Kukla
- Botanical Institute, Molecular Biology and Biochemistry, Karlsruhe Institute of Technology, Fritz-Haber-Weg 4, Karlsruhe, 76131, Germany
| | - Annika Dorn
- Botanical Institute, Molecular Biology and Biochemistry, Karlsruhe Institute of Technology, Fritz-Haber-Weg 4, Karlsruhe, 76131, Germany
| | - Holger Puchta
- Botanical Institute, Molecular Biology and Biochemistry, Karlsruhe Institute of Technology, Fritz-Haber-Weg 4, Karlsruhe, 76131, Germany
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15
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Vu TV, Das S, Nguyen CC, Kim J, Kim JY. Single-strand annealing: Molecular mechanisms and potential applications in CRISPR-Cas-based precision genome editing. Biotechnol J 2021; 17:e2100413. [PMID: 34846104 DOI: 10.1002/biot.202100413] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Revised: 11/22/2021] [Accepted: 11/29/2021] [Indexed: 12/24/2022]
Abstract
BACKGROUND Spontaneous double-stranded DNA breaks (DSBs) frequently occur within the genome of all living organisms and must be well repaired for survival. Recently, more important roles of the DSB repair pathways that were previously thought to be minor pathways, such as single-strand annealing (SSA), have been shown. Nevertheless, the biochemical mechanisms and applications of the SSA pathway in genome editing have not been updated. PURPOSE AND SCOPE Understanding the molecular mechanism of SSA is important to design potential applications in gene editing. This review provides insights into the recent progress of SSA studies and establishes a model for their potential applications in precision genome editing. SUMMARY AND CONCLUSION The SSA mechanism involved in DNA DSB repair appears to be activated by a complex signaling cascade starting with broken end sensing and 5'-3' resection to reveal homologous repeats on the 3' ssDNA overhangs that flank the DSB. Annealing the repeats would help to amend the discontinuous ends and restore the intact genome, resulting in the missing of one repeat and the intervening sequence between the repeats. We proposed a model for CRISPR-Cas-based precision insertion or replacement of DNA fragments to take advantage of the characteristics. The proposed model can add a tool to extend the choice for precision gene editing. Nevertheless, the model needs to be experimentally validated and optimized with SSA-favorable conditions for practical applications.
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Affiliation(s)
- Tien Van Vu
- Division of Applied Life Science (BK21 Four Program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, Republic of Korea.,National Key Laboratory for Plant Cell Biotechnology, Agricultural Genetics Institute, Bac Tu Liem, Hanoi, Vietnam
| | - Swati Das
- Division of Applied Life Science (BK21 Four Program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, Republic of Korea
| | - Cam Chau Nguyen
- Division of Applied Life Science (BK21 Four Program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, Republic of Korea
| | - Jihae Kim
- Division of Applied Life Science (BK21 Four Program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, Republic of Korea
| | - Jae-Yean Kim
- Division of Applied Life Science (BK21 Four Program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, Republic of Korea.,Division of Life Science, Gyeongsang National University, Jinju, Republic of Korea
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16
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Wolter F, Schindele P, Beying N, Scheben A, Puchta H. Different DNA repair pathways are involved in single-strand break-induced genomic changes in plants. THE PLANT CELL 2021; 33:3454-3469. [PMID: 34375428 PMCID: PMC8566284 DOI: 10.1093/plcell/koab204] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Accepted: 08/04/2021] [Indexed: 05/03/2023]
Abstract
In nature, single-strand breaks (SSBs) in DNA occur more frequently (by orders of magnitude) than double-strand breaks (DSBs). SSBs induced by the CRISPR/Cas9 nickase at a distance of 50-100 bp on opposite strands are highly mutagenic, leading to insertions/deletions (InDels), with insertions mainly occurring as direct tandem duplications. As short tandem repeats are overrepresented in plant genomes, this mechanism seems to be important for genome evolution. We investigated the distance at which paired 5'-overhanging SSBs are mutagenic and which DNA repair pathways are essential for insertion formation in Arabidopsis thaliana. We were able to detect InDel formation up to a distance of 250 bp, although with much reduced efficiency. Surprisingly, the loss of the classical nonhomologous end joining (NHEJ) pathway factors KU70 or DNA ligase 4 completely abolished tandem repeat formation. The microhomology-mediated NHEJ factor POLQ was required only for patch-like insertions, which are well-known from DSB repair as templated insertions from ectopic sites. As SSBs can also be repaired using homology, we furthermore asked whether the classical homologous recombination (HR) pathway is involved in this process in plants. The fact that RAD54 is not required for homology-mediated SSB repair demonstrates that the mechanisms for DSB- and SSB-induced HR differ in plants.
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Affiliation(s)
- Felix Wolter
- Botanical Institute, Karlsruhe Institute of Technology, 76131 Karlsruhe, Germany
| | - Patrick Schindele
- Botanical Institute, Karlsruhe Institute of Technology, 76131 Karlsruhe, Germany
| | - Natalja Beying
- Botanical Institute, Karlsruhe Institute of Technology, 76131 Karlsruhe, Germany
| | - Armin Scheben
- Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Holger Puchta
- Botanical Institute, Karlsruhe Institute of Technology, 76131 Karlsruhe, Germany
- Author for correspondence:
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17
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Gutiérrez Pinzón Y, González Kise JK, Rueda P, Ronceret A. The Formation of Bivalents and the Control of Plant Meiotic Recombination. FRONTIERS IN PLANT SCIENCE 2021; 12:717423. [PMID: 34557215 PMCID: PMC8453087 DOI: 10.3389/fpls.2021.717423] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2021] [Accepted: 08/13/2021] [Indexed: 06/06/2023]
Abstract
During the first meiotic division, the segregation of homologous chromosomes depends on the physical association of the recombined homologous DNA molecules. The physical tension due to the sites of crossing-overs (COs) is essential for the meiotic spindle to segregate the connected homologous chromosomes to the opposite poles of the cell. This equilibrated partition of homologous chromosomes allows the first meiotic reductional division. Thus, the segregation of homologous chromosomes is dependent on their recombination. In this review, we will detail the recent advances in the knowledge of the mechanisms of recombination and bivalent formation in plants. In plants, the absence of meiotic checkpoints allows observation of subsequent meiotic events in absence of meiotic recombination or defective meiotic chromosomal axis formation such as univalent formation instead of bivalents. Recent discoveries, mainly made in Arabidopsis, rice, and maize, have highlighted the link between the machinery of double-strand break (DSB) formation and elements of the chromosomal axis. We will also discuss the implications of what we know about the mechanisms regulating the number and spacing of COs (obligate CO, CO homeostasis, and interference) in model and crop plants.
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18
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Sprink T, Hartung F. Heterologous Complementation of SPO11-1 and -2 Depends on the Splicing Pattern. Int J Mol Sci 2021; 22:ijms22179346. [PMID: 34502253 PMCID: PMC8430568 DOI: 10.3390/ijms22179346] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Revised: 08/20/2021] [Accepted: 08/23/2021] [Indexed: 11/16/2022] Open
Abstract
In the past, major findings in meiosis have been achieved, but questions towards the global understanding of meiosis remain concealed. In plants, one of these questions covers the need for two diverse meiotic active SPO11 proteins. In Arabidopsis and other plants, both meiotic SPO11 are indispensable in a functional form for double strand break induction during meiotic prophase I. This stands in contrast to mammals and fungi, where a single SPO11 is present and sufficient. We aimed to investigate the specific function and evolution of both meiotic SPO11 paralogs in land plants. By performing immunostaining of both SPO11-1 and -2, an investigation of the spatiotemporal localization of each SPO11 during meiosis was achieved. We further exchanged SPO11-1 and -2 in Arabidopsis and could show a species-specific function of the respective SPO11. By additional changes of regions between SPO11-1 and -2, a sequence-specific function for both the SPO11 proteins was revealed. Furthermore, the previous findings about the aberrant splicing of each SPO11 were refined by narrowing them down to a specific developmental phase. These findings let us suggest that the function of both SPO11 paralogs is highly sequence specific and that the orthologs are species specific.
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19
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Rönspies M, Dorn A, Schindele P, Puchta H. CRISPR-Cas-mediated chromosome engineering for crop improvement and synthetic biology. NATURE PLANTS 2021; 7:566-573. [PMID: 33958776 DOI: 10.1038/s41477-021-00910-4] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Accepted: 03/31/2021] [Indexed: 05/20/2023]
Abstract
Plant breeding relies on the presence of genetic variation, as well as on the ability to break or stabilize genetic linkages between traits. The development of the genome-editing tool clustered regularly interspaced short palindromic repeats (CRISPR)-CRISPR-associated protein (Cas) has allowed breeders to induce genetic variability in a controlled and site-specific manner, and to improve traits with high efficiency. However, the presence of genetic linkages is a major obstacle to the transfer of desirable traits from wild species to their cultivated relatives. One way to address this issue is to create mutants with deficiencies in the meiotic recombination machinery, thereby enhancing global crossover frequencies between homologous parental chromosomes. Although this seemed to be a promising approach at first, thus far, no crossover frequencies could be enhanced in recombination-cold regions of the genome. Additionally, this approach can lead to unintended genomic instabilities due to DNA repair defects. Therefore, efforts have been undertaken to obtain predefined crossovers between homologues by inducing site-specific double-strand breaks (DSBs) in meiotic, as well as in somatic plant cells using CRISPR-Cas tools. However, this strategy has not been able to produce a substantial number of heritable homologous recombination-based crossovers. Most recently, heritable chromosomal rearrangements, such as inversions and translocations, have been obtained in a controlled way using CRISPR-Cas in plants. This approach unlocks a completely new way of manipulating genetic linkages, one in which the DSBs are induced in somatic cells, enabling the formation of chromosomal rearrangements in the megabase range, by DSB repair via non-homologous end-joining. This technology might also enable the restructuring of genomes more globally, resulting in not only the obtainment of synthetic plant chromosome, but also of novel plant species.
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Affiliation(s)
- Michelle Rönspies
- Botanical Institute, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Annika Dorn
- Botanical Institute, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Patrick Schindele
- Botanical Institute, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Holger Puchta
- Botanical Institute, Karlsruhe Institute of Technology, Karlsruhe, Germany.
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20
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Whitbread AL, Dorn A, Röhrig S, Puchta H. Different functional roles of RTR complex factors in DNA repair and meiosis in Arabidopsis and tomato. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 106:965-977. [PMID: 33619799 DOI: 10.1111/tpj.15211] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Accepted: 02/19/2021] [Indexed: 06/12/2023]
Abstract
The RTR (RecQ/Top3/Rmi1) complex has been elucidated as essential for ensuring genome stability in eukaryotes. Fundamental for the dissolution of Holliday junction (HJ)-like recombination intermediates, the factors have been shown to play further, partly distinct roles in DNA repair and homologous recombination. Across all kingdoms, disruption of this complex results in characteristic phenotypes including hyper-recombination and sensitivity to genotoxins. The type IA topoisomerase TOP3α has been shown as essential for viability in various animals. In contrast, in the model plant species Arabidopsis, the top3α mutant is viable. rmi1 mutants are deficient in the repair of DNA damage. Moreover, as opposed to other eukaryotes, TOP3α and RMI1 were found to be indispensable for proper meiotic progression, with mutants showing severe meiotic defects and sterility. We now established mutants of both TOP3α and RMI1 in tomato using CRISPR/Cas technology. Surprisingly, we found phenotypes that differed dramatically from those of Arabidopsis: the top3α mutants proved to be embryo-lethal, implying an essential role of the topoisomerase in tomato. In contrast, no defect in somatic DNA repair or meiosis was detectable for rmi1 mutants in tomato. This points to a differentiation of function of RTR complex partners between plant species. Our results indicate that there are relevant differences in the roles of basic factors involved in DNA repair and meiosis within dicotyledons, and thus should be taken as a note of caution when generalizing knowledge regarding basic biological processes obtained in the model plant Arabidopsis for the entire plant kingdom.
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Affiliation(s)
- Amy Leanne Whitbread
- Karlsruhe Institute of Technology, Botanical Institute, Fritz-Haber-Weg 4, Karlsruhe, 76133, Germany
| | - Annika Dorn
- Karlsruhe Institute of Technology, Botanical Institute, Fritz-Haber-Weg 4, Karlsruhe, 76133, Germany
| | - Sarah Röhrig
- Karlsruhe Institute of Technology, Botanical Institute, Fritz-Haber-Weg 4, Karlsruhe, 76133, Germany
| | - Holger Puchta
- Karlsruhe Institute of Technology, Botanical Institute, Fritz-Haber-Weg 4, Karlsruhe, 76133, Germany
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21
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Abstract
Meiotic and somatic recombination share a common set of factors. Thus, the analysis of somatic DNA repair in meiotic mutant lines should be of special interest. Growth defects of mutant plants induced by specific genotoxins can thereby hint to DNA repair functions of the affected proteins. Here, we describe two kinds of approaches to characterize deficiencies in DNA repair in mutant lines of Arabidopsis thaliana, after genotoxin treatment.
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22
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The Dark Side of UV-Induced DNA Lesion Repair. Genes (Basel) 2020; 11:genes11121450. [PMID: 33276692 PMCID: PMC7761550 DOI: 10.3390/genes11121450] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 11/27/2020] [Accepted: 11/29/2020] [Indexed: 12/12/2022] Open
Abstract
In their life cycle, plants are exposed to various unfavorable environmental factors including ultraviolet (UV) radiation emitted by the Sun. UV-A and UV-B, which are partially absorbed by the ozone layer, reach the surface of the Earth causing harmful effects among the others on plant genetic material. The energy of UV light is sufficient to induce mutations in DNA. Some examples of DNA damage induced by UV are pyrimidine dimers, oxidized nucleotides as well as single and double-strand breaks. When exposed to light, plants can repair major UV-induced DNA lesions, i.e., pyrimidine dimers using photoreactivation. However, this highly efficient light-dependent DNA repair system is ineffective in dim light or at night. Moreover, it is helpless when it comes to the repair of DNA lesions other than pyrimidine dimers. In this review, we have focused on how plants cope with deleterious DNA damage that cannot be repaired by photoreactivation. The current understanding of light-independent mechanisms, classified as dark DNA repair, indispensable for the maintenance of plant genetic material integrity has been presented.
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23
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Dorn A, Puchta H. DNA repair meets climate change. NATURE PLANTS 2020; 6:1398-1399. [PMID: 33199894 DOI: 10.1038/s41477-020-00804-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Affiliation(s)
- Annika Dorn
- Botanical Institute-Molecular Biology and Biochemistry, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Holger Puchta
- Botanical Institute-Molecular Biology and Biochemistry, Karlsruhe Institute of Technology, Karlsruhe, Germany.
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24
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Verma P, Tandon R, Yadav G, Gaur V. Structural Aspects of DNA Repair and Recombination in Crop Improvement. Front Genet 2020; 11:574549. [PMID: 33024442 PMCID: PMC7516265 DOI: 10.3389/fgene.2020.574549] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2020] [Accepted: 08/25/2020] [Indexed: 12/18/2022] Open
Abstract
The adverse effects of global climate change combined with an exponentially increasing human population have put substantial constraints on agriculture, accelerating efforts towards ensuring food security for a sustainable future. Conventional plant breeding and modern technologies have led to the creation of plants with better traits and higher productivity. Most crop improvement approaches (conventional breeding, genome modification, and gene editing) primarily rely on DNA repair and recombination (DRR). Studying plant DRR can provide insights into designing new strategies or improvising the present techniques for crop improvement. Even though plants have evolved specialized DRR mechanisms compared to other eukaryotes, most of our insights about plant-DRRs remain rooted in studies conducted in animals. DRR mechanisms in plants include direct repair, nucleotide excision repair (NER), base excision repair (BER), mismatch repair (MMR), non-homologous end joining (NHEJ) and homologous recombination (HR). Although each DRR pathway acts on specific DNA damage, there is crosstalk between these. Considering the importance of DRR pathways as a tool in crop improvement, this review focuses on a general description of each DRR pathway, emphasizing on the structural aspects of key DRR proteins. The review highlights the gaps in our understanding and the importance of studying plant DRR in the context of crop improvement.
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Affiliation(s)
- Prabha Verma
- National Institute of Plant Genome Research, New Delhi, India
| | - Reetika Tandon
- National Institute of Plant Genome Research, New Delhi, India
| | - Gitanjali Yadav
- National Institute of Plant Genome Research, New Delhi, India
| | - Vineet Gaur
- National Institute of Plant Genome Research, New Delhi, India
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25
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Taagen E, Bogdanove AJ, Sorrells ME. Counting on Crossovers: Controlled Recombination for Plant Breeding. TRENDS IN PLANT SCIENCE 2020; 25:455-465. [PMID: 31959421 DOI: 10.1016/j.tplants.2019.12.017] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Revised: 12/03/2019] [Accepted: 12/11/2019] [Indexed: 05/02/2023]
Abstract
Crossovers (COs), that drive genetic exchange between homologous chromosomes, are strongly biased toward subtelomeric regions in plant species. Manipulating the rate and positions of COs to increase the genetic variation accessible to breeders is a longstanding goal. Use of genome editing reagents that induce double-stranded breaks (DSBs) or modify the epigenome at desired sites of recombination, and manipulation of CO factors, are increasingly applicable approaches for achieving this goal. These strategies for 'controlled recombination' have potential to reduce the time and expense associated with traditional breeding, reveal currently inaccessible genetic diversity, and increase control over the inheritance of preferred haplotypes. Considerable challenges to address include translating knowledge from models to crop species and determining the best stages of the breeding cycle at which to control recombination.
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Affiliation(s)
- Ella Taagen
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA.
| | - Adam J Bogdanove
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA
| | - Mark E Sorrells
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA
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26
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Nibau C, Lloyd A, Dadarou D, Betekhtin A, Tsilimigka F, Phillips DW, Doonan JH. CDKG1 Is Required for Meiotic and Somatic Recombination Intermediate Processing in Arabidopsis. THE PLANT CELL 2020; 32:1308-1322. [PMID: 32047050 PMCID: PMC7145484 DOI: 10.1105/tpc.19.00942] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Revised: 01/22/2020] [Accepted: 02/08/2020] [Indexed: 05/12/2023]
Abstract
The Arabidopsis (Arabidopsis thaliana) cyclin-dependent kinase G1 (CDKG1) is necessary for recombination and synapsis during male meiosis at high ambient temperature. In the cdkg1-1 mutant, synapsis is impaired and there is a dramatic reduction in the number of class I crossovers, resulting in univalents at metaphase I and pollen sterility. Here, we demonstrate that CDKG1 is necessary for the processing of recombination intermediates in the canonical ZMM recombination pathway and that loss of CDKG1 results in increased class II crossovers. While synapsis and events associated with class I crossovers are severely compromised in a cdkg1-1 mutant, they can be restored by increasing the number of recombination intermediates in the double cdkg1-1 fancm-1 mutant. Despite this, recombination intermediates are not correctly resolved, leading to the formation of chromosome aggregates at metaphase I. Our results show that CDKG1 acts early in the recombination process and is necessary to stabilize recombination intermediates. Finally, we show that the effect on recombination is not restricted to meiosis and that CDKG1 is also required for normal levels of DNA damage-induced homologous recombination in somatic tissues.
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Affiliation(s)
- Candida Nibau
- Institute of Biological, Rural and Environmental Sciences, Aberystwyth University, Gogerddan, Aberystwyth SY23 3EB, United Kingdom
| | - Andrew Lloyd
- Institute of Biological, Rural and Environmental Sciences, Aberystwyth University, Gogerddan, Aberystwyth SY23 3EB, United Kingdom
| | - Despoina Dadarou
- Institute of Biological, Rural and Environmental Sciences, Aberystwyth University, Gogerddan, Aberystwyth SY23 3EB, United Kingdom
| | - Alexander Betekhtin
- Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia in Katowice, Katowice 40-007, Poland
| | - Foteini Tsilimigka
- Institute of Biological, Rural and Environmental Sciences, Aberystwyth University, Gogerddan, Aberystwyth SY23 3EB, United Kingdom
| | - Dylan W Phillips
- Institute of Biological, Rural and Environmental Sciences, Aberystwyth University, Gogerddan, Aberystwyth SY23 3EB, United Kingdom
| | - John H Doonan
- Institute of Biological, Rural and Environmental Sciences, Aberystwyth University, Gogerddan, Aberystwyth SY23 3EB, United Kingdom
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Gonzalez V, Spampinato CP. The mismatch repair protein MSH6 regulates somatic recombination in Arabidopsis thaliana. DNA Repair (Amst) 2020; 87:102789. [PMID: 31945543 DOI: 10.1016/j.dnarep.2020.102789] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Revised: 11/29/2019] [Accepted: 01/08/2020] [Indexed: 11/28/2022]
Abstract
The mismatch repair (MMR) pathway promotes genome stability by controlling the fidelity of replication and recombination. The first step of the pathway involves recognition of the mismatch by heterodimers composed of MutS homologs (MSH). Although MSH6 has been well characterized in yeasts and humans, the role of the plant protein has not been extensively studied. We first analyzed gene expression in Arabidopsis thaliana. The use of transgenic plants expressing the β-glucuronidase (GUS) reporter gene under the control of approximately 1-kb region upstream of the start codon of the AtMSH6 gene demonstrated that MSH6 is preferentially expressed in undifferentiated cells with an intense cell division rate. We then examined protein function in meiotic and somatic recombination. Suppression of AtMSH6 did not affect the rate of meiotic recombination, but increased the frequency of recombination between two homeologous repeats of a marker gene by 3-fold relative to wild-type plants. Expression of the AtMSH6 gene under the control of its own promoter in msh6 homozygous mutant plants rescued the altered somatic recombination phenotype. We conclude that MSH6 shows a functional conservation across different biological kingdoms and a functional specificity in plants.
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Affiliation(s)
- Valentina Gonzalez
- Centro de Estudios Fotosintéticos y Bioquímicos (CEFOBI), Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, 2000, Rosario, Argentina
| | - Claudia P Spampinato
- Centro de Estudios Fotosintéticos y Bioquímicos (CEFOBI), Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, 2000, Rosario, Argentina.
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28
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Raz A, Dahan-Meir T, Melamed-Bessudo C, Leshkowitz D, Levy AA. Redistribution of Meiotic Crossovers Along Wheat Chromosomes by Virus-Induced Gene Silencing. FRONTIERS IN PLANT SCIENCE 2020; 11:635139. [PMID: 33613593 PMCID: PMC7890124 DOI: 10.3389/fpls.2020.635139] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2020] [Accepted: 12/31/2020] [Indexed: 05/08/2023]
Abstract
Meiotic recombination is the main driver of genetic diversity in wheat breeding. The rate and location of crossover (CO) events are regulated by genetic and epigenetic factors. In wheat, most COs occur in subtelomeric regions but are rare in centromeric and pericentric areas. The aim of this work was to increase COs in both "hot" and "cold" chromosomal locations. We used Virus-Induced gene Silencing (VIGS) to downregulate the expression of recombination-suppressing genes XRCC2 and FANCM and of epigenetic maintenance genes MET1 and DDM1 during meiosis. VIGS suppresses genes in a dominant, transient and non-transgenic manner, which is convenient in wheat, a hard-to-transform polyploid. F1 hybrids of a cross between two tetraploid lines whose genome was fully sequenced (wild emmer and durum wheat), were infected with a VIGS vector ∼ 2 weeks before meiosis. Recombination was measured in F2 seedlings derived from F1-infected plants and non-infected controls. We found significant up and down-regulation of CO rates along subtelomeric regions as a result of silencing either MET1, DDM1 or XRCC2 during meiosis. In addition, we found up to 93% increase in COs in XRCC2-VIGS treatment in the pericentric regions of some chromosomes. Silencing FANCM showed no effect on CO. Overall, we show that CO distribution was affected by VIGS treatments rather than the total number of COs which did not change. We conclude that transient silencing of specific genes during meiosis can be used as a simple, fast and non-transgenic strategy to improve breeding abilities in specific chromosomal regions.
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Affiliation(s)
- Amir Raz
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, Israel
- Department of Plant Science, MIGAL Galilee Research Institute, Kiryat Shmona, Israel
- Amir Raz,
| | - Tal Dahan-Meir
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Cathy Melamed-Bessudo
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Dena Leshkowitz
- Bioinformatics Unit, Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot, Israel
| | - Avraham A. Levy
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, Israel
- *Correspondence: Avraham A. Levy,
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29
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Cruz MV, Mori GM, Signori-Müller C, da Silva CC, Oh DH, Dassanayake M, Zucchi MI, Oliveira RS, de Souza AP. Local adaptation of a dominant coastal tree to freshwater availability and solar radiation suggested by genomic and ecophysiological approaches. Sci Rep 2019; 9:19936. [PMID: 31882752 PMCID: PMC6934818 DOI: 10.1038/s41598-019-56469-w] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Accepted: 12/07/2019] [Indexed: 12/21/2022] Open
Abstract
Local adaptation is often a product of environmental variations in geographical space and has implications for biodiversity conservation. We investigated the role of latitudinal heterogeneity in climate on the organization of genetic and phenotypic variation in the dominant coastal tree Avicennia schaueriana. In a common garden experiment, samples from an equatorial region, with pronounced seasonality in precipitation, accumulated less biomass, and showed lower stomatal conductance and transpiration, narrower xylem vessels, smaller leaves and higher reflectance of long wavelengths by the stem epidermis than samples from a subtropical region, with seasonality in temperature and no dry season. Transcriptomic differences identified between trees sampled under field conditions at equatorial and subtropical sites, were enriched in functional categories such as responses to temperature, solar radiation, water deficit, photosynthesis and cell wall biosynthesis. Remarkably, the diversity based on genome-wide SNPs revealed a north-south genetic structure and signatures of selection were identified for loci associated with photosynthesis, anthocyanin accumulation and the responses to osmotic and hypoxia stresses. Our results suggest the existence of divergence in key resource-use characteristics, likely driven by seasonality in water deficit and solar radiation. These findings provide a basis for conservation plans and for predicting coastal plants responses to climate change.
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Affiliation(s)
- Mariana Vargas Cruz
- Department of Plant Biology, Institute of Biology, University of Campinas (Unicamp), Campinas, SP, 13083-863, Brazil
- Center for Molecular Biology and Genetic Engineering, University of Campinas (Unicamp), Campinas, SP, 13083-875, Brazil
| | - Gustavo Maruyama Mori
- Institute of Biosciences, São Paulo State University (Unesp), São Vicente, SP, 11330-900, Brazil
| | - Caroline Signori-Müller
- Department of Plant Biology, Institute of Biology, University of Campinas (Unicamp), Campinas, SP, 13083-863, Brazil
| | - Carla Cristina da Silva
- Center for Molecular Biology and Genetic Engineering, University of Campinas (Unicamp), Campinas, SP, 13083-875, Brazil
| | - Dong-Ha Oh
- Department of Biological Sciences, Louisiana State University (LSU), Louisiana, LA, 70803, United States
| | - Maheshi Dassanayake
- Department of Biological Sciences, Louisiana State University (LSU), Louisiana, LA, 70803, United States
| | | | - Rafael Silva Oliveira
- Department of Plant Biology, Institute of Biology, University of Campinas (Unicamp), Campinas, SP, 13083-863, Brazil
| | - Anete Pereira de Souza
- Department of Plant Biology, Institute of Biology, University of Campinas (Unicamp), Campinas, SP, 13083-863, Brazil.
- Center for Molecular Biology and Genetic Engineering, University of Campinas (Unicamp), Campinas, SP, 13083-875, Brazil.
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30
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DNA Helicases as Safekeepers of Genome Stability in Plants. Genes (Basel) 2019; 10:genes10121028. [PMID: 31835565 PMCID: PMC6947026 DOI: 10.3390/genes10121028] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Revised: 12/05/2019] [Accepted: 12/07/2019] [Indexed: 02/07/2023] Open
Abstract
Genetic information of all organisms is coded in double-stranded DNA. DNA helicases are essential for unwinding this double strand when it comes to replication, repair or transcription of genetic information. In this review, we will focus on what is known about a variety of DNA helicases that are required to ensure genome stability in plants. Due to their sessile lifestyle, plants are especially exposed to harmful environmental factors. Moreover, many crop plants have large and highly repetitive genomes, making them absolutely dependent on the correct interplay of DNA helicases for safeguarding their stability. Although basic features of a number of these enzymes are conserved between plants and other eukaryotes, a more detailed analysis shows surprising peculiarities, partly also between different plant species. This is additionally of high relevance for plant breeding as a number of these helicases are also involved in crossover control during meiosis and influence the outcome of different approaches of CRISPR/Cas based plant genome engineering. Thus, gaining knowledge about plant helicases, their interplay, as well as the manipulation of their pathways, possesses the potential for improving agriculture. In the long run, this might even help us cope with the increasing obstacles of climate change threatening food security in completely new ways.
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31
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Wolter F, Puchta H. In planta gene targeting can be enhanced by the use of CRISPR/Cas12a. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2019; 100:1083-1094. [PMID: 31381206 DOI: 10.1111/tpj.14488] [Citation(s) in RCA: 57] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2019] [Revised: 07/08/2019] [Accepted: 07/29/2019] [Indexed: 05/20/2023]
Abstract
The controlled change of plant genomes by homologous recombination (HR) is still difficult to achieve. We previously developed the in planta gene targeting (ipGT) technology which depends on the simultaneous activation of the target locus by a double-strand break and the excision of the target vector. Whereas the use of SpCas9 resulted in low ipGT frequencies in Arabidopsis, we were recently able to improve the efficiency by using egg cell-specific expression of the potent but less broadly applicable SaCas9 nuclease. In this study, we now tested whether we could improve ipGT further, by either performing it in cells with enhanced intrachromosomal HR efficiencies or by the use of Cas12a, a different kind of CRISPR/Cas nuclease with an alternative cutting mechanism. We could show before that plants possess three kinds of DNA ATPase complexes, which all lead to instabilities of homologous genomic repeats if lost by mutation. As these proteins act in independent pathways, we tested ipGT in double mutants in which intrachromosomal HR is enhanced 20-80-fold. However, we were not able to obtain higher ipGT frequencies, indicating that mechanisms for gene targeting (GT) and chromosomal repeat-induced HR differ. However, using LbCas12a, the GT frequencies were higher than with SaCas9, despite a lower non-homologous end-joining (NHEJ) induction efficiency, demonstrating the particular suitability of Cas12a to induce HR. As SaCas9 has substantial restrictions due to its longer GC rich PAM sequence, the use of LbCas12a with its AT-rich PAM broadens the range of ipGT drastically, particularly when targeting in CG-deserts like promoters and introns.
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Affiliation(s)
- Felix Wolter
- Botanical Institute, Karlsruhe Institute of Technology, POB 6980, 76049, Karlsruhe, Germany
| | - Holger Puchta
- Botanical Institute, Karlsruhe Institute of Technology, POB 6980, 76049, Karlsruhe, Germany
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32
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DNA- and DNA-Protein-Crosslink Repair in Plants. Int J Mol Sci 2019; 20:ijms20174304. [PMID: 31484324 PMCID: PMC6747210 DOI: 10.3390/ijms20174304] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Revised: 08/30/2019] [Accepted: 09/01/2019] [Indexed: 12/12/2022] Open
Abstract
DNA-crosslinks are one of the most severe types of DNA lesions. Crosslinks (CLs) can be subdivided into DNA-intrastrand CLs, DNA-interstrand CLs (ICLs) and DNA-protein crosslinks (DPCs), and arise by various exogenous and endogenous sources. If left unrepaired before the cell enters S-phase, ICLs and DPCs pose a major threat to genomic integrity by blocking replication. In order to prevent the collapse of replication forks and impairment of cell division, complex repair pathways have emerged. In mammals, ICLs are repaired by the so-called Fanconi anemia (FA) pathway, which includes 22 different FANC genes, while in plants only a few of these genes are conserved. In this context, two pathways of ICL repair have been defined, each requiring the interaction of a helicase (FANCJB/RTEL1) and a nuclease (FAN1/MUS81). Moreover, homologous recombination (HR) as well as postreplicative repair factors are also involved. Although DPCs possess a comparable toxic potential to cells, it has only recently been shown that at least three parallel pathways for DPC repair exist in plants, defined by the protease WSS1A, the endonuclease MUS81 and tyrosyl-DNA phosphodiesterase 1 (TDP1). The importance of crosslink repair processes are highlighted by the fact that deficiencies in the respective pathways are associated with diverse hereditary disorders.
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33
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Dorn A, Feller L, Castri D, Röhrig S, Enderle J, Herrmann NJ, Block-Schmidt A, Trapp O, Köhler L, Puchta H. An Arabidopsis FANCJ helicase homologue is required for DNA crosslink repair and rDNA repeat stability. PLoS Genet 2019; 15:e1008174. [PMID: 31120885 PMCID: PMC6550410 DOI: 10.1371/journal.pgen.1008174] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Revised: 06/05/2019] [Accepted: 05/03/2019] [Indexed: 11/18/2022] Open
Abstract
Proteins of the Fanconi Anemia (FA) complementation group are required for crosslink (CL) repair in humans and their loss leads to severe pathological phenotypes. Here we characterize a homolog of the Fe-S cluster helicase FANCJ in the model plant Arabidopsis, AtFANCJB, and show that it is involved in interstrand CL repair. It acts at a presumably early step in concert with the nuclease FAN1 but independently of the nuclease AtMUS81, and is epistatic to both error-prone and error-free post-replicative repair in Arabidopsis. The simultaneous knock out of FANCJB and the Fe-S cluster helicase RTEL1 leads to induced cell death in root meristems, indicating an important role of the enzymes in replicative DNA repair. Surprisingly, we found that AtFANCJB is involved in safeguarding rDNA stability in plants. In the absence of AtRTEL1 and AtFANCJB, we detected a synergetic reduction to about one third of the original number of 45S rDNA copies. It is tempting to speculate that the detected rDNA instability might be due to deficiencies in G-quadruplex structure resolution and might thus contribute to pathological phenotypes of certain human genetic diseases.
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Affiliation(s)
- Annika Dorn
- Botanical Institute, Molecular Biology and Biochemistry, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Laura Feller
- Botanical Institute, Molecular Biology and Biochemistry, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Dominique Castri
- Botanical Institute, Molecular Biology and Biochemistry, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Sarah Röhrig
- Botanical Institute, Molecular Biology and Biochemistry, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Janina Enderle
- Botanical Institute, Molecular Biology and Biochemistry, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Natalie J. Herrmann
- Botanical Institute, Molecular Biology and Biochemistry, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Astrid Block-Schmidt
- Botanical Institute, Molecular Biology and Biochemistry, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Oliver Trapp
- Botanical Institute, Molecular Biology and Biochemistry, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Laura Köhler
- Botanical Institute, Molecular Biology and Biochemistry, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Holger Puchta
- Botanical Institute, Molecular Biology and Biochemistry, Karlsruhe Institute of Technology, Karlsruhe, Germany
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34
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Gardiner LJ, Wingen LU, Bailey P, Joynson R, Brabbs T, Wright J, Higgins JD, Hall N, Griffiths S, Clavijo BJ, Hall A. Analysis of the recombination landscape of hexaploid bread wheat reveals genes controlling recombination and gene conversion frequency. Genome Biol 2019; 20:69. [PMID: 30982471 PMCID: PMC6463664 DOI: 10.1186/s13059-019-1675-6] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Accepted: 03/13/2019] [Indexed: 12/01/2022] Open
Abstract
BACKGROUND Sequence exchange between homologous chromosomes through crossing over and gene conversion is highly conserved among eukaryotes, contributing to genome stability and genetic diversity. A lack of recombination limits breeding efforts in crops; therefore, increasing recombination rates can reduce linkage drag and generate new genetic combinations. RESULTS We use computational analysis of 13 recombinant inbred mapping populations to assess crossover and gene conversion frequency in the hexaploid genome of wheat (Triticum aestivum). We observe that high-frequency crossover sites are shared between populations and that closely related parents lead to populations with more similar crossover patterns. We demonstrate that gene conversion is more prevalent and covers more of the genome in wheat than in other plants, making it a critical process in the generation of new haplotypes, particularly in centromeric regions where crossovers are rare. We identify quantitative trait loci for altered gene conversion and crossover frequency and confirm functionality for a novel RecQ helicase gene that belongs to an ancient clade that is missing in some plant lineages including Arabidopsis. CONCLUSIONS This is the first gene to be demonstrated to be involved in gene conversion in wheat. Harnessing the RecQ helicase has the potential to break linkage drag utilizing widespread gene conversions.
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Affiliation(s)
| | | | | | | | | | | | - James D. Higgins
- Department of Genetics and Genome Biology, University of Leicester, Leicester, LE1 7RH UK
| | - Neil Hall
- Earlham Institute, Norwich, NR4 7UZ UK
- School of Biological Sciences, University of East Anglia, Norwich, NR4 7TJ UK
| | | | | | - Anthony Hall
- Earlham Institute, Norwich, NR4 7UZ UK
- School of Biological Sciences, University of East Anglia, Norwich, NR4 7TJ UK
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35
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Enderle J, Dorn A, Beying N, Trapp O, Puchta H. The Protease WSS1A, the Endonuclease MUS81, and the Phosphodiesterase TDP1 Are Involved in Independent Pathways of DNA-protein Crosslink Repair in Plants. THE PLANT CELL 2019; 31:775-790. [PMID: 30760561 PMCID: PMC6501609 DOI: 10.1105/tpc.18.00824] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Revised: 01/08/2019] [Accepted: 02/11/2019] [Indexed: 05/04/2023]
Abstract
DNA-protein crosslinks (DPCs) represent a severe threat to the genome integrity; however, the main mechanisms of DPC repair were only recently elucidated in humans and yeast. Here we define the pathways for DPC repair in plants. Using CRISPR/Cas9, we could show that only one of two homologs of the universal repair proteases SPARTAN/ weak suppressor of smt3 (Wss1), WSS1A, is essential for DPC repair in Arabidopsis (Arabidopsis thaliana). WSS1A defective lines exhibit developmental defects and are hypersensitive to camptothecin (CPT) and cis-platin. Interestingly, the CRISPR/Cas9 mutants of TYROSYL-DNA PHOSPHODIESTERASE 1 (TDP1) are insensitive to CPT, and only the wss1A tdp1 double mutant reveals a higher sensitivity than the wss1A single mutant. This indicates that TDP1 defines a minor backup pathway in the repair of DPCs. Moreover, we found that knock out of the endonuclease METHYL METHANESULFONATE AND UV SENSITIVE PROTEIN 81 (MUS81) results in a strong sensitivity to DPC-inducing agents. The fact that wss1A mus81 and tdp1 mus81 double mutants exhibit growth defects and an increase in dead cells in root meristems after CPT treatment demonstrates that there are three independent pathways for DPC repair in Arabidopsis. These pathways are defined by their different biochemical specificities, as main actors, the DNA endonuclease MUS81 and the protease WSS1A, and the phosphodiesterase TDP1 as backup.
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Affiliation(s)
- Janina Enderle
- Botanical Institute, Molecular Biology and Biochemistry, Karlsruhe Institute of Technology, Fritz-Haber-Weg 4, Karlsruhe 76131, Germany
| | - Annika Dorn
- Botanical Institute, Molecular Biology and Biochemistry, Karlsruhe Institute of Technology, Fritz-Haber-Weg 4, Karlsruhe 76131, Germany
| | - Natalja Beying
- Botanical Institute, Molecular Biology and Biochemistry, Karlsruhe Institute of Technology, Fritz-Haber-Weg 4, Karlsruhe 76131, Germany
| | - Oliver Trapp
- Botanical Institute, Molecular Biology and Biochemistry, Karlsruhe Institute of Technology, Fritz-Haber-Weg 4, Karlsruhe 76131, Germany
| | - Holger Puchta
- Botanical Institute, Molecular Biology and Biochemistry, Karlsruhe Institute of Technology, Fritz-Haber-Weg 4, Karlsruhe 76131, Germany
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36
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Interhomolog polymorphism shapes meiotic crossover within the Arabidopsis RAC1 and RPP13 disease resistance genes. PLoS Genet 2018; 14:e1007843. [PMID: 30543623 PMCID: PMC6307820 DOI: 10.1371/journal.pgen.1007843] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Revised: 12/27/2018] [Accepted: 11/20/2018] [Indexed: 12/11/2022] Open
Abstract
During meiosis, chromosomes undergo DNA double-strand breaks (DSBs), which can be repaired using a homologous chromosome to produce crossovers. Meiotic recombination frequency is variable along chromosomes and tends to concentrate in narrow hotspots. We mapped crossover hotspots located in the Arabidopsis thaliana RAC1 and RPP13 disease resistance genes, using varying haplotypic combinations. We observed a negative non-linear relationship between interhomolog divergence and crossover frequency within the hotspots, consistent with polymorphism locally suppressing crossover repair of DSBs. The fancm, recq4a recq4b, figl1 and msh2 mutants, or lines with increased HEI10 dosage, are known to show increased crossovers throughout the genome. Surprisingly, RAC1 crossovers were either unchanged or decreased in these genetic backgrounds, showing that chromosome location and local chromatin environment are important for regulation of crossover activity. We employed deep sequencing of crossovers to examine recombination topology within RAC1, in wild type, fancm, recq4a recq4b and fancm recq4a recq4b backgrounds. The RAC1 recombination landscape was broadly conserved in the anti-crossover mutants and showed a negative relationship with interhomolog divergence. However, crossovers at the RAC1 5'-end were relatively suppressed in recq4a recq4b backgrounds, further indicating that local context may influence recombination outcomes. Our results demonstrate the importance of interhomolog divergence in shaping recombination within plant disease resistance genes and crossover hotspots.
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37
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Mieulet D, Aubert G, Bres C, Klein A, Droc G, Vieille E, Rond-Coissieux C, Sanchez M, Dalmais M, Mauxion JP, Rothan C, Guiderdoni E, Mercier R. Unleashing meiotic crossovers in crops. NATURE PLANTS 2018. [PMID: 30478361 DOI: 10.1101/343509] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Improved plant varieties are important in our attempts to face the challenges of a growing human population and limited planet resources. Plant breeding relies on meiotic crossovers to combine favourable alleles into elite varieties1. However, meiotic crossovers are relatively rare, typically one to three per chromosome2, limiting the efficiency of the breeding process and related activities such as genetic mapping. Several genes that limit meiotic recombination were identified in the model species Arabidopsis thaliana2. Mutation of these genes in Arabidopsis induces a large increase in crossover frequency. However, it remained to be demonstrated whether crossovers could also be increased in crop species hybrids. We explored the effects of mutating the orthologues of FANCM3, RECQ44 or FIGL15 on recombination in three distant crop species, rice (Oryza sativa), pea (Pisum sativum) and tomato (Solanum lycopersicum). We found that the single recq4 mutation increases crossovers about three-fold in these crops, suggesting that manipulating RECQ4 may be a universal tool for increasing recombination in plants. Enhanced recombination could be used with other state-of-the-art technologies such as genomic selection, genome editing or speed breeding6 to enhance the pace and efficiency of plant improvement.
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Affiliation(s)
- Delphine Mieulet
- CIRAD, UMR AGAP, Montpellier, France
- Université Montpellier, CIRAD, INRA Montpellier SupAgro, Montpellier, France
| | - Gregoire Aubert
- Agroécologie, AgroSup Dijon, INRA, Université Bourgogne Franche-Comté, Dijon, France
| | - Cecile Bres
- UMR 1332 BFP, INRA, Université Bordeaux, Villenave d'Ornon, France
| | - Anthony Klein
- Agroécologie, AgroSup Dijon, INRA, Université Bourgogne Franche-Comté, Dijon, France
| | - Gaëtan Droc
- CIRAD, UMR AGAP, Montpellier, France
- Université Montpellier, CIRAD, INRA Montpellier SupAgro, Montpellier, France
| | - Emilie Vieille
- Agroécologie, AgroSup Dijon, INRA, Université Bourgogne Franche-Comté, Dijon, France
| | - Celine Rond-Coissieux
- Agroécologie, AgroSup Dijon, INRA, Université Bourgogne Franche-Comté, Dijon, France
| | - Myriam Sanchez
- Agroécologie, AgroSup Dijon, INRA, Université Bourgogne Franche-Comté, Dijon, France
| | - Marion Dalmais
- Institute of Plant Sciences, Paris-Saclay IPS2, CNRS, INRA, Université Paris-Sud, Université Evry, Université Paris-Saclay, Orsay, France
| | | | | | - Emmanuel Guiderdoni
- CIRAD, UMR AGAP, Montpellier, France
- Université Montpellier, CIRAD, INRA Montpellier SupAgro, Montpellier, France
| | - Raphael Mercier
- Institut Jean-Pierre Bourgin, UMR1318 INRA-AgroParisTech, Université Paris-Saclay, Versailles, France.
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38
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Mieulet D, Aubert G, Bres C, Klein A, Droc G, Vieille E, Rond-Coissieux C, Sanchez M, Dalmais M, Mauxion JP, Rothan C, Guiderdoni E, Mercier R. Unleashing meiotic crossovers in crops. NATURE PLANTS 2018; 4:1010-1016. [PMID: 30478361 DOI: 10.1038/s41477-018-0311-x] [Citation(s) in RCA: 73] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2018] [Accepted: 10/17/2018] [Indexed: 05/21/2023]
Abstract
Improved plant varieties are important in our attempts to face the challenges of a growing human population and limited planet resources. Plant breeding relies on meiotic crossovers to combine favourable alleles into elite varieties1. However, meiotic crossovers are relatively rare, typically one to three per chromosome2, limiting the efficiency of the breeding process and related activities such as genetic mapping. Several genes that limit meiotic recombination were identified in the model species Arabidopsis thaliana2. Mutation of these genes in Arabidopsis induces a large increase in crossover frequency. However, it remained to be demonstrated whether crossovers could also be increased in crop species hybrids. We explored the effects of mutating the orthologues of FANCM3, RECQ44 or FIGL15 on recombination in three distant crop species, rice (Oryza sativa), pea (Pisum sativum) and tomato (Solanum lycopersicum). We found that the single recq4 mutation increases crossovers about three-fold in these crops, suggesting that manipulating RECQ4 may be a universal tool for increasing recombination in plants. Enhanced recombination could be used with other state-of-the-art technologies such as genomic selection, genome editing or speed breeding6 to enhance the pace and efficiency of plant improvement.
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Affiliation(s)
- Delphine Mieulet
- CIRAD, UMR AGAP, Montpellier, France
- Université Montpellier, CIRAD, INRA Montpellier SupAgro, Montpellier, France
| | - Gregoire Aubert
- Agroécologie, AgroSup Dijon, INRA, Université Bourgogne Franche-Comté, Dijon, France
| | - Cecile Bres
- UMR 1332 BFP, INRA, Université Bordeaux, Villenave d'Ornon, France
| | - Anthony Klein
- Agroécologie, AgroSup Dijon, INRA, Université Bourgogne Franche-Comté, Dijon, France
| | - Gaëtan Droc
- CIRAD, UMR AGAP, Montpellier, France
- Université Montpellier, CIRAD, INRA Montpellier SupAgro, Montpellier, France
| | - Emilie Vieille
- Agroécologie, AgroSup Dijon, INRA, Université Bourgogne Franche-Comté, Dijon, France
| | - Celine Rond-Coissieux
- Agroécologie, AgroSup Dijon, INRA, Université Bourgogne Franche-Comté, Dijon, France
| | - Myriam Sanchez
- Agroécologie, AgroSup Dijon, INRA, Université Bourgogne Franche-Comté, Dijon, France
| | - Marion Dalmais
- Institute of Plant Sciences, Paris-Saclay IPS2, CNRS, INRA, Université Paris-Sud, Université Evry, Université Paris-Saclay, Orsay, France
| | | | | | - Emmanuel Guiderdoni
- CIRAD, UMR AGAP, Montpellier, France
- Université Montpellier, CIRAD, INRA Montpellier SupAgro, Montpellier, France
| | - Raphael Mercier
- Institut Jean-Pierre Bourgin, UMR1318 INRA-AgroParisTech, Université Paris-Saclay, Versailles, France.
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Dorn A, Röhrig S, Papp K, Schröpfer S, Hartung F, Knoll A, Puchta H. The topoisomerase 3α zinc-finger domain T1 of Arabidopsis thaliana is required for targeting the enzyme activity to Holliday junction-like DNA repair intermediates. PLoS Genet 2018; 14:e1007674. [PMID: 30222730 PMCID: PMC6160208 DOI: 10.1371/journal.pgen.1007674] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Revised: 09/27/2018] [Accepted: 08/31/2018] [Indexed: 12/18/2022] Open
Abstract
Topoisomerase 3α, a class I topoisomerase, consists of a TOPRIM domain, an active centre and a variable number of zinc-finger domains (ZFDs) at the C-terminus, in multicellular organisms. Whereas the functions of the TOPRIM domain and the active centre are known, the specific role of the ZFDs is still obscure. In contrast to mammals where a knockout of TOP3α leads to lethality, we found that CRISPR/Cas induced mutants in Arabidopsis are viable but show growth retardation and meiotic defects, which can be reversed by the expression of the complete protein. However, complementation with AtTOP3α missing either the TOPRIM-domain or carrying a mutation of the catalytic tyrosine of the active centre leads to embryo lethality. Surprisingly, this phenotype can be overcome by the simultaneous removal of the ZFDs from the protein. In combination with a mutation of the nuclease AtMUS81, the TOP3α knockout proved to be also embryo lethal. Here, expression of TOP3α without ZFDs, and in particular without the conserved ZFD T1, leads to only a partly complementation in root growth-in contrast to the complete protein, that restores root length to mus81-1 mutant level. Expressing the E. coli resolvase RusA in this background, which is able to process Holliday junction (HJ)-like recombination intermediates, we could rescue this root growth defect. Considering all these results, we conclude that the ZFD T1 is specifically required for targeting the topoisomerase activity to HJ like recombination intermediates to enable their processing. In the case of an inactivated enzyme, this leads to cell death due to the masking of these intermediates, hindering their resolution by MUS81.
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Affiliation(s)
- Annika Dorn
- Botanical Institute, Molecular Biology and Biochemistry, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Sarah Röhrig
- Botanical Institute, Molecular Biology and Biochemistry, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Kristin Papp
- Botanical Institute, Molecular Biology and Biochemistry, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Susan Schröpfer
- Botanical Institute, Molecular Biology and Biochemistry, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Frank Hartung
- Botanical Institute, Molecular Biology and Biochemistry, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Alexander Knoll
- Botanical Institute, Molecular Biology and Biochemistry, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Holger Puchta
- Botanical Institute, Molecular Biology and Biochemistry, Karlsruhe Institute of Technology, Karlsruhe, Germany
- * E-mail:
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40
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Röhrig S, Dorn A, Enderle J, Schindele A, Herrmann NJ, Knoll A, Puchta H. The RecQ-like helicase HRQ1 is involved in DNA crosslink repair in Arabidopsis in a common pathway with the Fanconi anemia-associated nuclease FAN1 and the postreplicative repair ATPase RAD5A. THE NEW PHYTOLOGIST 2018; 218:1478-1490. [PMID: 29577315 DOI: 10.1111/nph.15109] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Accepted: 02/12/2018] [Indexed: 05/24/2023]
Abstract
RecQ helicases are important caretakers of genome stability and occur in varying copy numbers in different eukaryotes. Subsets of RecQ paralogs are involved in DNA crosslink (CL) repair. The orthologs of AtRECQ2, AtRECQ3 and AtHRQ1, HsWRN, DmRECQ5 and ScHRQ1 participate in CL repair in their respective organisms, and we aimed to define the function of these helicases for plants. We obtained Arabidopsis mutants of the three RecQ helicases and determined their sensitivity against CL agents in single- and double-mutant analyses. Only Athrq1, but not Atrecq2 and Atrecq3, mutants proved to be sensitive to intra- and interstrand crosslinking agents. AtHRQ1 is specifically involved in the repair of replicative damage induced by CL agents. It shares pathways with the Fanconi anemia-related endonuclease FAN1 but not with the endonuclease MUS81. Most surprisingly, AtHRQ1 is epistatic to the ATPase RAD5A for intra- as well as interstrand CL repair. We conclude that, as in fungi, AtHRQ1 has a conserved function in DNA excision repair. Additionally, HRQ1 not only shares pathways with the Fanconi anemia repair factors, but in contrast to fungi also seems to act in a common pathway with postreplicative DNA repair.
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Affiliation(s)
- Sarah Röhrig
- Botanical Institute, Karlsruhe Institute of Technology, Karlsruhe, BW, 76131, Germany
| | - Annika Dorn
- Botanical Institute, Karlsruhe Institute of Technology, Karlsruhe, BW, 76131, Germany
| | - Janina Enderle
- Botanical Institute, Karlsruhe Institute of Technology, Karlsruhe, BW, 76131, Germany
| | - Angelina Schindele
- Botanical Institute, Karlsruhe Institute of Technology, Karlsruhe, BW, 76131, Germany
| | - Natalie J Herrmann
- Botanical Institute, Karlsruhe Institute of Technology, Karlsruhe, BW, 76131, Germany
| | - Alexander Knoll
- Botanical Institute, Karlsruhe Institute of Technology, Karlsruhe, BW, 76131, Germany
| | - Holger Puchta
- Botanical Institute, Karlsruhe Institute of Technology, Karlsruhe, BW, 76131, Germany
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Abstract
Meiosis halves diploid chromosome numbers to haploid levels that are essential for sexual reproduction in most eukaryotes. Meiotic recombination ensures the formation of bivalents between homologous chromosomes (homologs) and their subsequent proper segregation. It also results in genetic diversity among progeny that influences evolutionary responses to selection. Moreover, crop breeding depends upon the action of meiotic recombination to rearrange elite traits between parental chromosomes. An understanding of the molecular mechanisms that drive meiotic recombination is important for both fundamental research and practical applications. This review emphasizes advances made during the past 5 years, primarily in Arabidopsis and rice, by summarizing newly characterized genes and proteins and examining the regulatory mechanisms that modulate their action.
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Affiliation(s)
- Yingxiang Wang
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center of Genetics and Development, Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 200438, China;
| | - Gregory P Copenhaver
- Department of Biology and the Integrative Program for Biological and Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599-3280, USA;
- Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, North Carolina 27599-3280, USA
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Fernandes JB, Séguéla-Arnaud M, Larchevêque C, Lloyd AH, Mercier R. Unleashing meiotic crossovers in hybrid plants. Proc Natl Acad Sci U S A 2018; 115:2431-2436. [PMID: 29183972 DOI: 10.1101/159640] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/28/2023] Open
Abstract
Meiotic crossovers shuffle parental genetic information, providing novel combinations of alleles on which natural or artificial selection can act. However, crossover events are relatively rare, typically one to three exchange points per chromosome pair. Recent work has identified three pathways limiting meiotic crossovers in Arabidopsis thaliana that rely on the activity of FANCM [Crismani W, et al. (2012) Science 336:1588-1590], RECQ4 [Séguéla-Arnaud M, et al. (2015) Proc Natl Acad Sci USA 112:4713-4718], and FIGL1 [Girard C, et al. (2015) PLoS Genet 11:e1005369]. Here we analyzed recombination in plants in which one, two, or all three of these pathways were disrupted in both pure line and hybrid contexts. The greatest effect was observed when combining recq4 and figl1 mutations, which increased the hybrid genetic map length from 389 to 3,037 cM. This corresponds to an unprecedented 7.8-fold increase in crossover frequency. Disrupting the three pathways did not further increase recombination, suggesting that some upper limit had been reached. The increase in crossovers is not uniform along chromosomes and rises from centromere to telomere. Finally, although in wild type recombination is much higher in male meiosis than in female meiosis (490 cM vs. 290 cM), female recombination is higher than male recombination in recq4 figl1 (3,200 cM vs. 2,720 cM), suggesting that the factors that make wild-type female meiosis less recombinogenic than male wild-type meiosis do not apply in the mutant context. The massive increase in recombination observed in recq4 figl1 hybrids opens the possibility of manipulating recombination to enhance plant breeding efficiency.
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Affiliation(s)
- Joiselle Blanche Fernandes
- Institut Jean-Pierre Bourgin (IJPB), Institut National de la Recherche Agronomique, AgroParisTech, CNRS, Université Paris-Saclay, 78000 Versailles, France
- Université Paris-Sud, Université Paris-Saclay, 91405 Orsay, France
| | - Mathilde Séguéla-Arnaud
- Institut Jean-Pierre Bourgin (IJPB), Institut National de la Recherche Agronomique, AgroParisTech, CNRS, Université Paris-Saclay, 78000 Versailles, France
| | - Cécile Larchevêque
- Institut Jean-Pierre Bourgin (IJPB), Institut National de la Recherche Agronomique, AgroParisTech, CNRS, Université Paris-Saclay, 78000 Versailles, France
| | - Andrew H Lloyd
- Institut Jean-Pierre Bourgin (IJPB), Institut National de la Recherche Agronomique, AgroParisTech, CNRS, Université Paris-Saclay, 78000 Versailles, France
| | - Raphael Mercier
- Institut Jean-Pierre Bourgin (IJPB), Institut National de la Recherche Agronomique, AgroParisTech, CNRS, Université Paris-Saclay, 78000 Versailles, France;
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43
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Fernandes JB, Séguéla-Arnaud M, Larchevêque C, Lloyd AH, Mercier R. Unleashing meiotic crossovers in hybrid plants. Proc Natl Acad Sci U S A 2018; 115:2431-2436. [PMID: 29183972 PMCID: PMC5877974 DOI: 10.1073/pnas.1713078114] [Citation(s) in RCA: 102] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Meiotic crossovers shuffle parental genetic information, providing novel combinations of alleles on which natural or artificial selection can act. However, crossover events are relatively rare, typically one to three exchange points per chromosome pair. Recent work has identified three pathways limiting meiotic crossovers in Arabidopsis thaliana that rely on the activity of FANCM [Crismani W, et al. (2012) Science 336:1588-1590], RECQ4 [Séguéla-Arnaud M, et al. (2015) Proc Natl Acad Sci USA 112:4713-4718], and FIGL1 [Girard C, et al. (2015) PLoS Genet 11:e1005369]. Here we analyzed recombination in plants in which one, two, or all three of these pathways were disrupted in both pure line and hybrid contexts. The greatest effect was observed when combining recq4 and figl1 mutations, which increased the hybrid genetic map length from 389 to 3,037 cM. This corresponds to an unprecedented 7.8-fold increase in crossover frequency. Disrupting the three pathways did not further increase recombination, suggesting that some upper limit had been reached. The increase in crossovers is not uniform along chromosomes and rises from centromere to telomere. Finally, although in wild type recombination is much higher in male meiosis than in female meiosis (490 cM vs. 290 cM), female recombination is higher than male recombination in recq4 figl1 (3,200 cM vs. 2,720 cM), suggesting that the factors that make wild-type female meiosis less recombinogenic than male wild-type meiosis do not apply in the mutant context. The massive increase in recombination observed in recq4 figl1 hybrids opens the possibility of manipulating recombination to enhance plant breeding efficiency.
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Affiliation(s)
- Joiselle Blanche Fernandes
- Institut Jean-Pierre Bourgin (IJPB), Institut National de la Recherche Agronomique, AgroParisTech, CNRS, Université Paris-Saclay, 78000 Versailles, France
- Université Paris-Sud, Université Paris-Saclay, 91405 Orsay, France
| | - Mathilde Séguéla-Arnaud
- Institut Jean-Pierre Bourgin (IJPB), Institut National de la Recherche Agronomique, AgroParisTech, CNRS, Université Paris-Saclay, 78000 Versailles, France
| | - Cécile Larchevêque
- Institut Jean-Pierre Bourgin (IJPB), Institut National de la Recherche Agronomique, AgroParisTech, CNRS, Université Paris-Saclay, 78000 Versailles, France
| | - Andrew H Lloyd
- Institut Jean-Pierre Bourgin (IJPB), Institut National de la Recherche Agronomique, AgroParisTech, CNRS, Université Paris-Saclay, 78000 Versailles, France
| | - Raphael Mercier
- Institut Jean-Pierre Bourgin (IJPB), Institut National de la Recherche Agronomique, AgroParisTech, CNRS, Université Paris-Saclay, 78000 Versailles, France;
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Wiedemann G, van Gessel N, Köchl F, Hunn L, Schulze K, Maloukh L, Nogué F, Decker EL, Hartung F, Reski R. RecQ Helicases Function in Development, DNA Repair, and Gene Targeting in Physcomitrella patens. THE PLANT CELL 2018; 30:717-736. [PMID: 29514942 PMCID: PMC5894843 DOI: 10.1105/tpc.17.00632] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2017] [Revised: 02/16/2018] [Accepted: 03/06/2018] [Indexed: 05/18/2023]
Abstract
RecQ DNA helicases are genome surveillance proteins found in all kingdoms of life. They are characterized best in humans, as mutations in RecQ genes lead to developmental abnormalities and diseases. To better understand RecQ functions in plants we concentrated on Arabidopsis thaliana and Physcomitrella patens, the model species predominantly used for studies on DNA repair and gene targeting. Phylogenetic analysis of the six P. patens RecQ genes revealed their orthologs in humans and plants. Because Arabidopsis and P. patens differ in their RecQ4 and RecQ6 genes, reporter and deletion moss mutants were generated and gene functions studied in reciprocal cross-species and cross-kingdom approaches. Both proteins can be found in meristematic moss tissues, although at low levels and with distinct expression patterns. PpRecQ4 is involved in embryogenesis and in subsequent development as demonstrated by sterility of ΔPpRecQ4 mutants and by morphological aberrations. Additionally, ΔPpRecQ4 displays an increased sensitivity to DNA damages and an increased rate of gene targeting. Therefore, we conclude that PpRecQ4 acts as a repressor of recombination. In contrast, PpRecQ6 is not obviously important for moss development or DNA repair but does function as a potent enhancer of gene targeting.
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Affiliation(s)
- Gertrud Wiedemann
- Plant Biotechnology, Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany
| | - Nico van Gessel
- Plant Biotechnology, Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany
| | - Fabian Köchl
- Plant Biotechnology, Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany
| | - Lisa Hunn
- Plant Biotechnology, Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany
| | - Katrin Schulze
- Julius Kuehn Institute, Institute for Biosafety in Plant Biotechnology, 06484 Quedlinburg, Germany
| | - Lina Maloukh
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, 78000 Versailles, France
| | - Fabien Nogué
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, 78000 Versailles, France
| | - Eva L Decker
- Plant Biotechnology, Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany
| | - Frank Hartung
- Julius Kuehn Institute, Institute for Biosafety in Plant Biotechnology, 06484 Quedlinburg, Germany
| | - Ralf Reski
- Plant Biotechnology, Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany
- BIOSS Centre for Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany
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45
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Massive crossover elevation via combination of HEI10 and recq4a recq4b during Arabidopsis meiosis. Proc Natl Acad Sci U S A 2018; 115:2437-2442. [PMID: 29463699 DOI: 10.1073/pnas.1713071115] [Citation(s) in RCA: 78] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
During meiosis, homologous chromosomes undergo reciprocal crossovers, which generate genetic diversity and underpin classical crop improvement. Meiotic recombination initiates from DNA double-strand breaks (DSBs), which are processed into single-stranded DNA that can invade a homologous chromosome. The resulting joint molecules can ultimately be resolved as crossovers. In Arabidopsis, competing pathways balance the repair of ∼100-200 meiotic DSBs into ∼10 crossovers per meiosis, with the excess DSBs repaired as noncrossovers. To bias DSB repair toward crossovers, we simultaneously increased dosage of the procrossover E3 ligase gene HEI10 and introduced mutations in the anticrossovers helicase genes RECQ4A and RECQ4B As HEI10 and recq4a recq4b increase interfering and noninterfering crossover pathways, respectively, they combine additively to yield a massive meiotic recombination increase. Interestingly, we also show that increased HEI10 dosage increases crossover coincidence, which indicates an effect on interference. We also show that patterns of interhomolog polymorphism and heterochromatin drive recombination increases distally towards the subtelomeres in both HEI10 and recq4a recq4b backgrounds, while the centromeres remain crossover suppressed. These results provide a genetic framework for engineering meiotic recombination landscapes in plant genomes.
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46
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Kalinina NO, Makarova S, Makhotenko A, Love AJ, Taliansky M. The Multiple Functions of the Nucleolus in Plant Development, Disease and Stress Responses. FRONTIERS IN PLANT SCIENCE 2018; 9:132. [PMID: 29479362 PMCID: PMC5811523 DOI: 10.3389/fpls.2018.00132] [Citation(s) in RCA: 66] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2017] [Accepted: 01/23/2018] [Indexed: 05/18/2023]
Abstract
The nucleolus is the most conspicuous domain in the eukaryotic cell nucleus, whose main function is ribosomal RNA (rRNA) synthesis and ribosome biogenesis. However, there is growing evidence that the nucleolus is also implicated in many other aspects of cell biology, such as regulation of cell cycle, growth and development, senescence, telomerase activity, gene silencing, responses to biotic and abiotic stresses. In the first part of the review, we briefly assess the traditional roles of the plant nucleolus in rRNA synthesis and ribosome biogenesis as well as possible functions in other RNA regulatory pathways such as splicing, nonsense-mediated mRNA decay and RNA silencing. In the second part of the review we summarize recent progress and discuss already known and new hypothetical roles of the nucleolus in plant growth and development. In addition, this part will highlight studies showing new nucleolar functions involved in responses to pathogen attack and abiotic stress. Cross-talk between the nucleolus and Cajal bodies is also discussed in the context of their association with poly(ADP ribose)polymerase (PARP), which is known to play a crucial role in various physiological processes including growth, development and responses to biotic and abiotic stresses.
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Affiliation(s)
- Natalia O. Kalinina
- Branch of the Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, Russia
- Natalia O. Kalinina
| | - Svetlana Makarova
- Branch of the Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, Russia
| | - Antonida Makhotenko
- Branch of the Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, Russia
| | | | - Michael Taliansky
- Branch of the Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, Russia
- The James Hutton Institute, Dundee, United Kingdom
- *Correspondence: Michael Taliansky
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47
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Zhang M, Zhao J, Li L, Gao Y, Zhao L, Patil SB, Fang J, Zhang W, Yang Y, Li M, Li X. The Arabidopsis U-box E3 ubiquitin ligase PUB30 negatively regulates salt tolerance by facilitating BRI1 kinase inhibitor 1 (BKI1) degradation. PLANT, CELL & ENVIRONMENT 2017; 40:2831-2843. [PMID: 28865087 DOI: 10.1111/pce.13064] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2017] [Revised: 08/23/2017] [Accepted: 08/25/2017] [Indexed: 06/07/2023]
Abstract
The Arabidopsis U-box E3 ubiquitin ligases play an important role in the ubiquitin/26S proteasome-mediated protein degradation pathway. Recently, PUB30 has been reported to participate in the salt stress response during seed germination stage in abscisic acid (ABA)-independent manner, but the molecular mechanism remains to be elucidated. Here, we displayed that the pub30 mutant was more tolerant to salt stress during seed germination, whereas the mutant of its closest homologue PUB31 showed mild sensitivity to salt stress. PUB30 exhibited E3 ubiquitin ligase activity in vitro. PUB30 specifically interacted with BRI1 kinase inhibitor 1 (BKI1), a regulator playing dual roles in brassinosteroids signaling, in vitro and in vivo. We found that BKI1 protein was ubiquitinated and degraded by the 26S proteasome. The degradation of BKI1 was slowed down in the pub30-1 mutant compared with that in the wild type. The bki1 mutant was sensitive to salt, whereas the transgenic plants overexpressing BKI1 showed salt tolerant phenotype. All these results indicate that PUB30 negatively regulates salt tolerance probably through regulating the degradation of BKI1 and brassinosteroids signaling in Arabidopsis.
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Affiliation(s)
- Ming Zhang
- College of Agriculture, Northeast Agricultural University, Harbin, 150030, China
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
- Industrial Crop Institute, Heilongjiang Academy of Agricultural Sciences, Harbin, 150086, China
| | - Jinfeng Zhao
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Long Li
- College of Life Sciences, Shenyang Agricultural University, Shenyang, 110161, China
| | - Yanan Gao
- College of Life Sciences, Liaocheng University, Liaocheng, 252059, China
| | - Linlin Zhao
- College of Life Sciences, Liaocheng University, Liaocheng, 252059, China
| | - Suyash Bhimgonda Patil
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Jingjing Fang
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Wenhui Zhang
- College of Life Sciences, Liaocheng University, Liaocheng, 252059, China
| | - Yuhong Yang
- College of Life Sciences, Shenyang Agricultural University, Shenyang, 110161, China
| | - Ming Li
- College of Agriculture, Northeast Agricultural University, Harbin, 150030, China
| | - Xueyong Li
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
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Séguéla-Arnaud M, Choinard S, Larchevêque C, Girard C, Froger N, Crismani W, Mercier R. RMI1 and TOP3α limit meiotic CO formation through their C-terminal domains. Nucleic Acids Res 2017; 45:1860-1871. [PMID: 27965412 PMCID: PMC5389728 DOI: 10.1093/nar/gkw1210] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2016] [Accepted: 11/23/2016] [Indexed: 01/04/2023] Open
Abstract
At meiosis, hundreds of programmed DNA double-strand breaks (DSBs) form and are repaired by homologous recombination. From this large number of DSBs, only a subset yields crossovers (COs), with a minimum of one CO per chromosome pair. All DSBs must be repaired and every recombination intermediate must be resolved to avoid subsequent entanglement and chromosome breakage. The conserved BLM-TOP3α-RMI1 (BTR) complex acts on early and late meiotic recombination intermediates to both limit CO outcome and promote chromosome integrity. In Arabidopsis, the BLM homologues RECQ4A and RECQ4B act redundantly to prevent meiotic extra COs, but recombination intermediates are fully resolved in their absence. In contrast, TOP3α is needed for both processes. Here we show through the characterization of specific mutants that RMI1 is a major anti-CO factor, in addition to being essential to prevent chromosome breakage and entanglement. Further, our findings suggest a specific role of the C-terminal domains of RMI1 and TOP3α, that respectively contain an Oligo Binding domain (OB2) and ZINC finger motifs, in preventing extra-CO. We propose that these domains of TOP3α and RMI1 define a sub-domain of the BTR complex which is dispensable for the resolution of recombination intermediates but crucial to limit extra-COs.
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Affiliation(s)
- Mathilde Séguéla-Arnaud
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, RD10, 78000 Versailles, France
| | - Sandrine Choinard
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, RD10, 78000 Versailles, France
| | - Cécile Larchevêque
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, RD10, 78000 Versailles, France
| | - Chloé Girard
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, RD10, 78000 Versailles, France
| | - Nicole Froger
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, RD10, 78000 Versailles, France
| | - Wayne Crismani
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, RD10, 78000 Versailles, France
| | - Raphael Mercier
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, RD10, 78000 Versailles, France
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Hatkevich T, Sekelsky J. Bloom syndrome helicase in meiosis: Pro-crossover functions of an anti-crossover protein. Bioessays 2017; 39. [PMID: 28792069 DOI: 10.1002/bies.201700073] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The functions of the Bloom syndrome helicase (BLM) and its orthologs are well characterized in mitotic DNA damage repair, but their roles within the context of meiotic recombination are less clear. In meiotic recombination, multiple repair pathways are used to repair meiotic DSBs, and current studies suggest that BLM may regulate the use of these pathways. Based on literature from Saccharomyces cerevisiae, Arabidopsis thaliana, Mus musculus, Drosophila melanogaster, and Caenorhabditis elegans, we present a unified model for a critical meiotic role of BLM and its orthologs. In this model, BLM and its orthologs utilize helicase activity to regulate the use of various pathways in meiotic recombination by continuously disassembling recombination intermediates. This unwinding activity provides the meiotic program with a steady pool of early recombination substrates, increasing the probability for a DSB to be processed by the appropriate pathway. As a result of BLM activity, crossovers are properly placed throughout the genome, promoting proper chromosomal disjunction at the end of meiosis. This unified model can be used to further refine the complex role of BLM and its orthologs in meiotic recombination.
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Affiliation(s)
- Talia Hatkevich
- Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Jeff Sekelsky
- Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.,Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.,Integrative Program in Biological and Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
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Yadav V, Hemansi, Kim N, Tuteja N, Yadav P. G Quadruplex in Plants: A Ubiquitous Regulatory Element and Its Biological Relevance. FRONTIERS IN PLANT SCIENCE 2017; 8:1163. [PMID: 28725233 PMCID: PMC5495829 DOI: 10.3389/fpls.2017.01163] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Accepted: 06/16/2017] [Indexed: 10/31/2023]
Abstract
G quadruplexes (G4) are higher-order DNA and RNA secondary structures formed by G-rich sequences that are built around tetrads of hydrogen-bonded guanine bases. Potential G4 quadruplex sequences have been identified in G-rich eukaryotic non-telomeric and telomeric genomic regions. Upon function, G4 formation is known to involve in chromatin remodeling, gene regulation and has been associated with genomic instability, genetic diseases and cancer progression. The natural role and biological validation of G4 structures is starting to be explored, and is of particular interest for the therapeutic interventions for human diseases. However, the existence and physiological role of G4 DNA and G4 RNA in plants species have not been much investigated yet and therefore, is of great interest for the development of improved crop varieties for sustainable agriculture. In this context, several recent studies suggests that these highly diverse G4 structures in plants can be employed to regulate expression of genes involved in several pathophysiological conditions including stress response to biotic and abiotic stresses as well as DNA damage. In the current review, we summarize the recent findings regarding the emerging functional significance of G4 structures in plants and discuss their potential value in the development of improved crop varieties.
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Affiliation(s)
- Vikas Yadav
- Department of Biochemistry, Central University of HaryanaMahendergarh, India
| | - Hemansi
- Department of Microbiology, Central University of HaryanaMahendergarh, India
| | - Nayun Kim
- Department of Microbiology and Molecular Genetics, University of Texas Health Science Center at Houston, HoustonTX, United States
- The University of Texas Graduate School of Biomedical Sciences, HoustonTX, United States
| | - Narendra Tuteja
- Plant Molecular Biology Group, International Centre for Genetic Engineering and Biotechnology (ICGEB)New Delhi, India
| | - Puja Yadav
- Department of Microbiology, Central University of HaryanaMahendergarh, India
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