51
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Pu X, Liu L, Li P, Huo H, Dong X, Xie K, Yang H, Liu L. A CRISPR/LbCas12a-based method for highly efficient multiplex gene editing in Physcomitrella patens. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2019; 100:863-872. [PMID: 31350780 DOI: 10.1111/tpj.14478] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Revised: 07/02/2019] [Accepted: 07/16/2019] [Indexed: 06/10/2023]
Abstract
Due to their high efficiency, specificity, and flexibility, programmable nucleases, such as those of the clustered regularly interspaced short palindromic repeats (CRISPR)/Cas12a (Cpf1) system, have greatly expanded the applicability of editing the genomes of various organisms. Genes from different gene families or genes with redundant functions in the same gene family can be examined by assembling multiple CRISPR RNAs (crRNAs) in a single vector. However, the activity and efficiency of CRISPR/Cas12a in the non-vascular plant Physcomitrella patens are largely unknown. Here, we demonstrate that LbCas12a together with its mature crRNA can target multiple loci simultaneously in P. patens with high efficiency via co-delivery of LbCas12a and a crRNA expression cassette in vivo. The mutation frequencies induced by CRISPR/LbCas12a at a single locus ranged from 26.5 to 100%, with diverse deletions being the most common type of mutation. Our method expands the repertoire of genome editing tools available for P. patens and facilitates the creation of loss-of-function mutants of multiple genes from different gene families.
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Affiliation(s)
- Xiaojun Pu
- Key Laboratory for Economic Plants and Biotechnology, Kunming Institute of Botany, Chinese Academy of Sciences, and Yunnan Key Laboratory for Wild Plant Resources, Kunming, 650201, China
| | - Lina Liu
- Key Laboratory for Economic Plants and Biotechnology, Kunming Institute of Botany, Chinese Academy of Sciences, and Yunnan Key Laboratory for Wild Plant Resources, Kunming, 650201, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Ping Li
- Key Laboratory for Economic Plants and Biotechnology, Kunming Institute of Botany, Chinese Academy of Sciences, and Yunnan Key Laboratory for Wild Plant Resources, Kunming, 650201, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Heqiang Huo
- Department of Environmental Horticulture, Mid-Florida Research and Education Center, University of Florida, Gainesville, FL, 32703, USA
| | - Xiumei Dong
- Key Laboratory for Economic Plants and Biotechnology, Kunming Institute of Botany, Chinese Academy of Sciences, and Yunnan Key Laboratory for Wild Plant Resources, Kunming, 650201, China
| | - Kabin Xie
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Hong Yang
- Key Laboratory for Economic Plants and Biotechnology, Kunming Institute of Botany, Chinese Academy of Sciences, and Yunnan Key Laboratory for Wild Plant Resources, Kunming, 650201, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Li Liu
- Key Laboratory for Economic Plants and Biotechnology, Kunming Institute of Botany, Chinese Academy of Sciences, and Yunnan Key Laboratory for Wild Plant Resources, Kunming, 650201, China
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52
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Shih CJ, Chen HW, Hsieh HY, Lai YH, Chiu FY, Chen YR, Tu SL. Heterogeneous Nuclear Ribonucleoprotein H1 Coordinates with Phytochrome and the U1 snRNP Complex to Regulate Alternative Splicing in Physcomitrella patens. THE PLANT CELL 2019; 31:2510-2524. [PMID: 31409629 PMCID: PMC6790087 DOI: 10.1105/tpc.19.00314] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Revised: 07/15/2019] [Accepted: 08/06/2019] [Indexed: 05/03/2023]
Abstract
Plant photoreceptors tightly regulate gene expression to control photomorphogenic responses. Although gene expression is modulated by photoreceptors at various levels, the regulatory mechanism at the pre-mRNA splicing step remains unclear. Alternative splicing, a widespread mechanism in eukaryotes that generates two or more mRNAs from the same pre-mRNA, is largely controlled by splicing regulators, which recruit spliceosomal components to initiate pre-mRNA splicing. The red/far-red light photoreceptor phytochrome participates in light-mediated splicing regulation, but the detailed mechanism remains unclear. Here, using protein-protein interaction analysis, we demonstrate that in the moss Physcomitrella patens, phytochrome4 physically interacts with the splicing regulator heterogeneous nuclear ribonucleoprotein H1 (PphnRNP-H1) in the nucleus, a process dependent on red light. We show that PphnRNP-H1 is involved in red light-mediated phototropic responses in P. patens and that it binds with higher affinity to the splicing factor pre-mRNA-processing factor39-1 (PpPRP39-1) in the presence of red light-activated phytochromes. Furthermore, PpPRP39-1 associates with the core component of U1 small nuclear RNP in P. patens Genome-wide analyses demonstrated the involvement of both PphnRNP-H1 and PpPRP39-1 in light-mediated splicing regulation. Our results suggest that phytochromes target the early step of spliceosome assembly via a cascade of protein-protein interactions to control pre-mRNA splicing and photomorphogenic responses.
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Affiliation(s)
- Chueh-Ju Shih
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei 11529, Taiwan
- Molecular and Biological Agricultural Sciences Program, Taiwan International Graduate Program, Chung-Hsing University and Academia Sinica, Taipei 11529, Taiwan
- Graduate Institute of Biotechnology, National Chung-Hsing University, Taichung 402, Taiwan
| | - Hsiang-Wen Chen
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei 11529, Taiwan
| | - Hsin-Yu Hsieh
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei 11529, Taiwan
| | - Yung-Hua Lai
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei 11529, Taiwan
| | - Fang-Yi Chiu
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei 11529, Taiwan
| | - Yu-Rong Chen
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei 11529, Taiwan
| | - Shih-Long Tu
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei 11529, Taiwan
- Molecular and Biological Agricultural Sciences Program, Taiwan International Graduate Program, Chung-Hsing University and Academia Sinica, Taipei 11529, Taiwan
- Biotechnology Center, National Chung-Hsing University, Taichung 402, Taiwan
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53
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Mallett DR, Chang M, Cheng X, Bezanilla M. Efficient and modular CRISPR-Cas9 vector system for Physcomitrella patens. PLANT DIRECT 2019; 3:e00168. [PMID: 31523744 PMCID: PMC6739617 DOI: 10.1002/pld3.168] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Revised: 07/29/2019] [Accepted: 08/20/2019] [Indexed: 05/20/2023]
Abstract
CRISPR-Cas9 has been shown to be a valuable tool in recent years, allowing researchers to precisely edit the genome using an RNA-guided nuclease to initiate double-strand breaks. Until recently, classical RAD51-mediated homologous recombination has been a powerful tool for gene targeting in the moss Physcomitrella patens. However, CRISPR-Cas9-mediated genome editing in P. patens was shown to be more efficient than traditional homologous recombination (Plant Biotechnology Journal, 15, 2017, 122). CRISPR-Cas9 provides the opportunity to efficiently edit the genome at multiple loci as well as integrate sequences at precise locations in the genome using a simple transient transformation. To fully take advantage of CRISPR-Cas9 genome editing in P. patens, here we describe the generation and use of a flexible and modular CRISPR-Cas9 vector system. Without the need for gene synthesis, this vector system enables editing of up to 12 loci simultaneously. Using this system, we generated multiple lines that had null alleles at four distant loci. We also found that targeting multiple sites within a single locus can produce larger deletions, but the success of this depends on individual protospacers. To take advantage of homology-directed repair, we developed modular vectors to rapidly generate DNA donor plasmids to efficiently introduce DNA sequences encoding for fluorescent proteins at the 5' and 3' ends of gene coding regions. With regard to homology-directed repair experiments, we found that if the protospacer sequence remains on the DNA donor plasmid, then Cas9 cleaves the plasmid target as well as the genomic target. This can reduce the efficiency of introducing sequences into the genome. Furthermore, to ensure the generation of a null allele near the Cas9 cleavage site, we generated a homology plasmid harboring a "stop codon cassette" with downstream near-effortless genotyping.
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Affiliation(s)
- Darren R. Mallett
- Department of Biological SciencesDartmouth CollegeHanoverNew Hampshire
| | - Mingqin Chang
- Department of Biological SciencesDartmouth CollegeHanoverNew Hampshire
- Plant Biology Graduate ProgramUniversity of MassachusettsAmherstMassachusetts
| | - Xiaohang Cheng
- Department of Biological SciencesDartmouth CollegeHanoverNew Hampshire
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54
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Fesenko I, Kirov I, Kniazev A, Khazigaleeva R, Lazarev V, Kharlampieva D, Grafskaia E, Zgoda V, Butenko I, Arapidi G, Mamaeva A, Ivanov V, Govorun V. Distinct types of short open reading frames are translated in plant cells. Genome Res 2019; 29:1464-1477. [PMID: 31387879 PMCID: PMC6724668 DOI: 10.1101/gr.253302.119] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Accepted: 08/01/2019] [Indexed: 02/07/2023]
Abstract
Genomes contain millions of short (<100 codons) open reading frames (sORFs), which are usually dismissed during gene annotation. Nevertheless, peptides encoded by such sORFs can play important biological roles, and their impact on cellular processes has long been underestimated. Here, we analyzed approximately 70,000 transcribed sORFs in the model plant Physcomitrella patens (moss). Several distinct classes of sORFs that differ in terms of their position on transcripts and the level of evolutionary conservation are present in the moss genome. Over 5000 sORFs were conserved in at least one of 10 plant species examined. Mass spectrometry analysis of proteomic and peptidomic data sets suggested that tens of sORFs located on distinct parts of mRNAs and long noncoding RNAs (lncRNAs) are translated, including conserved sORFs. Translational analysis of the sORFs and main ORFs at a single locus suggested the existence of genes that code for multiple proteins and peptides with tissue-specific expression. Functional analysis of four lncRNA-encoded peptides showed that sORFs-encoded peptides are involved in regulation of growth and differentiation in moss. Knocking out lncRNA-encoded peptides resulted in a decrease of moss growth. In contrast, the overexpression of these peptides resulted in a diverse range of phenotypic effects. Our results thus open new avenues for discovering novel, biologically active peptides in the plant kingdom.
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Affiliation(s)
- Igor Fesenko
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, 117997 Moscow, Russian Federation
| | - Ilya Kirov
- Laboratory of marker-assisted and genomic selection of plants, All-Russian Research Institute of Agricultural Biotechnology, 127550 Moscow, Russian Federation
| | - Andrey Kniazev
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, 117997 Moscow, Russian Federation
| | - Regina Khazigaleeva
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, 117997 Moscow, Russian Federation
| | - Vassili Lazarev
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, 119435 Moscow, Russian Federation.,Moscow Institute of Physics and Technology (National Research University), 141701 Dolgoprudny, Moscow Region, Russian Federation
| | - Daria Kharlampieva
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, 119435 Moscow, Russian Federation
| | - Ekaterina Grafskaia
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, 119435 Moscow, Russian Federation.,Moscow Institute of Physics and Technology (National Research University), 141701 Dolgoprudny, Moscow Region, Russian Federation
| | - Viktor Zgoda
- Laboratory of System Biology, Institute of Biomedical Chemistry, 119121 Moscow, Russian Federation
| | - Ivan Butenko
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, 119435 Moscow, Russian Federation
| | - Georgy Arapidi
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, 117997 Moscow, Russian Federation.,Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, 119435 Moscow, Russian Federation
| | - Anna Mamaeva
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, 117997 Moscow, Russian Federation
| | - Vadim Ivanov
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, 117997 Moscow, Russian Federation
| | - Vadim Govorun
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, 119435 Moscow, Russian Federation
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55
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Guyon-Debast A, Rossetti P, Charlot F, Epert A, Neuhaus JM, Schaefer DG, Nogué F. The XPF-ERCC1 Complex Is Essential for Genome Stability and Is Involved in the Mechanism of Gene Targeting in Physcomitrella patens. FRONTIERS IN PLANT SCIENCE 2019; 10:588. [PMID: 31143199 PMCID: PMC6521618 DOI: 10.3389/fpls.2019.00588] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Accepted: 04/18/2019] [Indexed: 06/09/2023]
Abstract
The XPF-ERCC1 complex, a highly conserved structure-specific endonuclease, functions in multiple DNA repair pathways that are pivotal for maintaining genome stability, including nucleotide excision repair, interstrand crosslink repair, and homologous recombination. XPF-ERCC1 incises double-stranded DNA at double-strand/single-strand junctions, making it an ideal enzyme for processing DNA structures that contain partially unwound strands. Here, we have examined the role of the XPF-ERCC1 complex in the model bryophyte Physcomitrella patens which exhibits uniquely high gene targeting frequencies. We undertook targeted knockout of the Physcomitrella ERCC1 and XPF genes. Mutant analysis shows that the endonuclease complex is essential for resistance to UV-B and to the alkylating agent MMS, and contributes to the maintenance of genome integrity but is also involved in gene targeting in this model plant. Using different constructs we determine whether the function of the XPF-ERCC1 endonuclease complex in gene targeting was removal of 3' non-homologous termini, similar to SSA, or processing of looped-out heteroduplex intermediates. Interestingly, our data suggest a role of the endonuclease in both pathways and have implications for the mechanism of targeted gene replacement in plants and its specificities compared to yeast and mammalian cells.
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Affiliation(s)
- Anouchka Guyon-Debast
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, Versailles, France
| | - Patricia Rossetti
- Laboratoire de Biologie Moléculaire et Cellulaire, Institut de Biologie, Université de Neuchâtel, Neuchâtel, Switzerland
| | - Florence Charlot
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, Versailles, France
| | - Aline Epert
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, Versailles, France
| | - Jean-Marc Neuhaus
- Laboratoire de Biologie Moléculaire et Cellulaire, Institut de Biologie, Université de Neuchâtel, Neuchâtel, Switzerland
| | - Didier G. Schaefer
- Laboratoire de Biologie Moléculaire et Cellulaire, Institut de Biologie, Université de Neuchâtel, Neuchâtel, Switzerland
| | - Fabien Nogué
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, Versailles, France
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56
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Mara K, Charlot F, Guyon-Debast A, Schaefer DG, Collonnier C, Grelon M, Nogué F. POLQ plays a key role in the repair of CRISPR/Cas9-induced double-stranded breaks in the moss Physcomitrella patens. THE NEW PHYTOLOGIST 2019; 222:1380-1391. [PMID: 30636294 DOI: 10.1111/nph.15680] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Accepted: 01/05/2019] [Indexed: 05/19/2023]
Abstract
Double-stranded breaks can be repaired by different mechanisms such as homologous recombination (HR), classical nonhomologous end joining (C-NHEJ) and alternative end joining (Alt-EJ). Polymerase Q (POLQ) has been proposed to be the main factor involved in Alt-EJ-mediated DNA repair. Here we describe the role of POLQ in DNA repair and gene targeting in Physcomitrella patens. The disruption of the POLQ gene does not influence the genetic stability of P. patens nor its development. The polq mutant shows the same sensitivity as wild-type towards most of the genotoxic agents tested (ultraviolet (UV), methyl methanesulfonate (MMS) and cisplatin) with the notable exception of bleomycin for which it shows less sensitivity than the wild-type. Furthermore, we show that POLQ is involved in the repair of CRISPR-Cas9-induced double-stranded breaks in P. patens. We also demonstrate that POLQ is a potential competitor and/or inhibitor of the HR repair pathway. This finding has a consequence in terms of genetic engineering, as in the absence of POLQ the frequency of gene targeting is significantly increased and the number of clean two-sided HR-mediated insertions is enhanced. Therefore, the control of POLQ activity in plants could be a useful strategy to optimize the tools of genome engineering for plant breeding.
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Affiliation(s)
- Kostlend Mara
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, Versailles, 78000, France
| | - Florence Charlot
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, Versailles, 78000, France
| | - Anouchka Guyon-Debast
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, Versailles, 78000, France
| | - Didier G Schaefer
- Laboratory of Cell and Molecular Biology, Institute of Biology, University of Neuchâtel, Rue Emile-Argand 11, CH-2009 Neuchâtel, Switzerland
| | - Cécile Collonnier
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, Versailles, 78000, France
| | - Mathilde Grelon
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, Versailles, 78000, France
| | - Fabien Nogué
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, Versailles, 78000, France
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57
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Guzmán-Zapata D, Sandoval-Vargas JM, Macedo-Osorio KS, Salgado-Manjarrez E, Castrejón-Flores JL, Oliver-Salvador MDC, Durán-Figueroa NV, Nogué F, Badillo-Corona JA. Efficient Editing of the Nuclear APT Reporter Gene in Chlamydomonas reinhardtii via Expression of a CRISPR-Cas9 Module. Int J Mol Sci 2019; 20:E1247. [PMID: 30871076 PMCID: PMC6429146 DOI: 10.3390/ijms20051247] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2019] [Revised: 03/04/2019] [Accepted: 03/07/2019] [Indexed: 12/20/2022] Open
Abstract
The clustered regularly interspaced short palindromic repeat/CRISPR-associated protein 9 (CRISPR/Cas9) technology is a versatile and useful tool to perform genome editing in different organisms ranging from bacteria and yeast to plants and mammalian cells. For a couple of years, it was believed that the system was inefficient and toxic in the alga Chlamydomonas reinhardtii. However, recently the system has been successfully implemented in this model organism, albeit relying mostly on the electroporation of ribonucleoproteins (RNPs) into cell wall deficient strains. This requires a constant source of RNPs and limits the application of the technology to strains that are not necessarily the most relevant from a biotechnological point of view. Here, we show that transient expression of the Streptococcus pyogenes Cas9 gene and sgRNAs, targeted to the single-copy nuclear apt9 gene, encoding an adenine phosphoribosyl transferase (APT), results in efficient disruption at the expected locus. Introduction of indels to the apt9 locus results in cell insensitivity to the otherwise toxic compound 2-fluoroadenine (2-FA). We have used agitation with glass beads and particle bombardment to introduce the plasmids carrying the coding sequences for Cas9 and the sgRNAs in a cell-walled strain of C. reinhardtii (CC-125). Using sgRNAs targeting exons 1 and 3 of apt9, we obtained disruption efficiencies of 3 and 30% on preselected 2-FA resistant colonies, respectively. Our results show that transient expression of Cas9 and a sgRNA can be used for editing of the nuclear genome inexpensively and at high efficiency. Targeting of the APT gene could potentially be used as a pre-selection marker for multiplexed editing or disruption of genes of interest.
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Affiliation(s)
- Daniel Guzmán-Zapata
- Instituto Politécnico Nacional, Unidad Profesional Interdisciplinaria de Biotecnología. Av. Acueducto S/N., Col. Barrio La Laguna Ticomán, 07340 Mexico City, Mexico.
| | - José M Sandoval-Vargas
- Instituto Politécnico Nacional, Unidad Profesional Interdisciplinaria de Biotecnología. Av. Acueducto S/N., Col. Barrio La Laguna Ticomán, 07340 Mexico City, Mexico.
| | - Karla S Macedo-Osorio
- Instituto Politécnico Nacional, Unidad Profesional Interdisciplinaria de Biotecnología. Av. Acueducto S/N., Col. Barrio La Laguna Ticomán, 07340 Mexico City, Mexico.
| | - Edgar Salgado-Manjarrez
- Instituto Politécnico Nacional, Unidad Profesional Interdisciplinaria de Biotecnología. Av. Acueducto S/N., Col. Barrio La Laguna Ticomán, 07340 Mexico City, Mexico.
| | - José L Castrejón-Flores
- Instituto Politécnico Nacional, Unidad Profesional Interdisciplinaria de Biotecnología. Av. Acueducto S/N., Col. Barrio La Laguna Ticomán, 07340 Mexico City, Mexico.
| | - María Del Carmen Oliver-Salvador
- Instituto Politécnico Nacional, Unidad Profesional Interdisciplinaria de Biotecnología. Av. Acueducto S/N., Col. Barrio La Laguna Ticomán, 07340 Mexico City, Mexico.
| | - Noé V Durán-Figueroa
- Instituto Politécnico Nacional, Unidad Profesional Interdisciplinaria de Biotecnología. Av. Acueducto S/N., Col. Barrio La Laguna Ticomán, 07340 Mexico City, Mexico.
| | - Fabien Nogué
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, 78000 Versailles, France.
| | - Jesús A Badillo-Corona
- Instituto Politécnico Nacional, Unidad Profesional Interdisciplinaria de Biotecnología. Av. Acueducto S/N., Col. Barrio La Laguna Ticomán, 07340 Mexico City, Mexico.
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58
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Ermert AL, Nogué F, Stahl F, Gans T, Hughes J. CRISPR/Cas9-Mediated Knockout of Physcomitrella patens Phytochromes. Methods Mol Biol 2019; 2026:237-263. [PMID: 31317418 DOI: 10.1007/978-1-4939-9612-4_20] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/12/2023]
Abstract
Here we describe procedures for gene disruption and excision in Physcomitrella using CRISPR/Cas9 (clustered regularly interspaced short palindromic repeat/CRISPR-associated 9) methods, exemplarily targeting phytochrome (PHY) gene loci. Thereby double-strand breaks (DSBs) are induced using a single guide RNA (sgRNA) with the Cas9 nuclease, leading to insertions or deletions (indels) due to incorrect repair by the nonhomologous-end joining (NHEJ) mechanism. We also include protocols for excision of smaller genomic fragments or whole genes either with or without homologous recombination-assisted repair. The protocol can be adapted to target several loci simultaneously, thereby allowing the physiological analysis of phenotypes that would be masked by functional redundancy. In our particular case, multiple PHY gene knockouts would likely be valuable in understanding phytochrome functions in mosses and, perhaps, higher plants too. Target sites for site-directed induction of DSBs are predicted with the CRISPOR online-tool and are inserted in silico into sequence matrices for the design of sgRNA expression cassettes. The resulting DNAs are cloned into Gateway DONOR vectors and the respective expression plasmids used for moss cotransformation with a Cas9 expression plasmid and a selectable marker (either on a separate plasmid or on one of the other plasmids). After the selection process, genomic DNA is extracted and transformants are analyzed by PCR fingerprinting.
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Affiliation(s)
- Anna Lena Ermert
- Institute for Plant Physiology, Justus Liebig University, Giessen, Germany
| | - Fabien Nogué
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, Versailles, France.
| | - Fabian Stahl
- Institute for Plant Physiology, Justus Liebig University, Giessen, Germany
| | - Tanja Gans
- Institute for Plant Physiology, Justus Liebig University, Giessen, Germany
| | - Jon Hughes
- Institute for Plant Physiology, Justus Liebig University, Giessen, Germany.
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59
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Wu SZ, Yamada M, Mallett DR, Bezanilla M. Cytoskeletal discoveries in the plant lineage using the moss Physcomitrella patens. Biophys Rev 2018; 10:1683-1693. [PMID: 30382556 DOI: 10.1007/s12551-018-0470-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Accepted: 10/21/2018] [Indexed: 12/16/2022] Open
Abstract
Advances in cell biology have been largely driven by pioneering work in model systems, the majority of which are from one major eukaryotic lineage, the opisthokonts. However, with the explosion of genomic information in many lineages, it has become clear that eukaryotes have incredible diversity in many cellular systems, including the cytoskeleton. By identifying model systems in diverse lineages, it may be possible to begin to understand the evolutionary origins of the eukaryotic cytoskeleton. Within the plant lineage, cell biological studies in the model moss, Physcomitrella patens, have over the past decade provided key insights into how the cytoskeleton drives cell and tissue morphology. Here, we review P. patens attributes that make it such a rich resource for cytoskeletal cell biological inquiry and highlight recent key findings with regard to intracellular transport, microtubule-actin interactions, and gene discovery that promises for many years to provide new cytoskeletal players.
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Affiliation(s)
- Shu-Zon Wu
- Department of Biological Sciences, Dartmouth College, 78 College Street, Hanover, NH, 03755, USA
| | - Moe Yamada
- Department of Biological Sciences, Dartmouth College, 78 College Street, Hanover, NH, 03755, USA
- Division of Biological Science, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8602, Japan
| | - Darren R Mallett
- Department of Biological Sciences, Dartmouth College, 78 College Street, Hanover, NH, 03755, USA
| | - Magdalena Bezanilla
- Department of Biological Sciences, Dartmouth College, 78 College Street, Hanover, NH, 03755, USA.
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60
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Serif M, Dubois G, Finoux AL, Teste MA, Jallet D, Daboussi F. One-step generation of multiple gene knock-outs in the diatom Phaeodactylum tricornutum by DNA-free genome editing. Nat Commun 2018; 9:3924. [PMID: 30254261 PMCID: PMC6156588 DOI: 10.1038/s41467-018-06378-9] [Citation(s) in RCA: 72] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Accepted: 08/31/2018] [Indexed: 01/24/2023] Open
Abstract
Recently developed transgenic techniques to explore and exploit the metabolic potential of microalgae present several drawbacks associated with the delivery of exogenous DNA into the cells and its subsequent integration at random sites within the genome. Here, we report a highly efficient multiplex genome-editing method in the diatom Phaeodactylum tricornutum, relying on the biolistic delivery of CRISPR-Cas9 ribonucleoproteins coupled with the identification of two endogenous counter-selectable markers, PtUMPS and PtAPT. First, we demonstrate the functionality of RNP delivery by positively selecting the disruption of each of these genes. Then, we illustrate the potential of the approach for multiplexing by generating double-gene knock-out strains, with 65% to 100% efficiency, using RNPs targeting one of these markers and PtAureo1a, a photoreceptor-encoding gene. Finally, we created triple knock-out strains in one step by delivering six RNP complexes into Phaeodactylum cells. This approach could readily be applied to other hard-to-transfect organisms of biotechnological interest. The manipulation of diatom genomes is essential for industrial applications based on their metabolic abilities. Here the authors present an efficient multiplex DNA-free gene editing method using CRISPR-Cas9 and counter-selectable markers.
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Affiliation(s)
- Manuel Serif
- INSA, UPS, INP, LISBP, Université de Toulouse, 135 Avenue de Rangueil, F-31077, Toulouse, France.,INRA, LISBP, UMR792, 135 Avenue de Rangueil, F-31077, Toulouse, France.,CNRS, LISBP, UMR5504, 135 Avenue de Rangueil, F-31077, Toulouse, France
| | - Gwendoline Dubois
- INSA, UPS, INP, LISBP, Université de Toulouse, 135 Avenue de Rangueil, F-31077, Toulouse, France.,INRA, LISBP, UMR792, 135 Avenue de Rangueil, F-31077, Toulouse, France.,CNRS, LISBP, UMR5504, 135 Avenue de Rangueil, F-31077, Toulouse, France
| | - Anne-Laure Finoux
- INSA, UPS, INP, LISBP, Université de Toulouse, 135 Avenue de Rangueil, F-31077, Toulouse, France.,INRA, LISBP, UMR792, 135 Avenue de Rangueil, F-31077, Toulouse, France.,CNRS, LISBP, UMR5504, 135 Avenue de Rangueil, F-31077, Toulouse, France
| | - Marie-Ange Teste
- INSA, UPS, INP, LISBP, Université de Toulouse, 135 Avenue de Rangueil, F-31077, Toulouse, France.,INRA, LISBP, UMR792, 135 Avenue de Rangueil, F-31077, Toulouse, France.,CNRS, LISBP, UMR5504, 135 Avenue de Rangueil, F-31077, Toulouse, France
| | - Denis Jallet
- INSA, UPS, INP, LISBP, Université de Toulouse, 135 Avenue de Rangueil, F-31077, Toulouse, France.,INRA, LISBP, UMR792, 135 Avenue de Rangueil, F-31077, Toulouse, France.,CNRS, LISBP, UMR5504, 135 Avenue de Rangueil, F-31077, Toulouse, France
| | - Fayza Daboussi
- INSA, UPS, INP, LISBP, Université de Toulouse, 135 Avenue de Rangueil, F-31077, Toulouse, France. .,INRA, LISBP, UMR792, 135 Avenue de Rangueil, F-31077, Toulouse, France. .,CNRS, LISBP, UMR5504, 135 Avenue de Rangueil, F-31077, Toulouse, France.
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Li P, Yang H, Liu G, Ma W, Li C, Huo H, He J, Liu L. PpSARK Regulates Moss Senescence and Salt Tolerance through ABA Related Pathway. Int J Mol Sci 2018; 19:E2609. [PMID: 30177627 PMCID: PMC6163601 DOI: 10.3390/ijms19092609] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Revised: 08/30/2018] [Accepted: 08/30/2018] [Indexed: 11/18/2022] Open
Abstract
Senescence-associated receptor-like kinase (SARK) family members in Arabidopsis, soybean, and rice are known to be positive regulators of leaf senescence. In the meantime, SARKs are extensively involved in stress response. However, their function and underlying molecular mechanism in stress responses in moss are not well known. Here, we investigated functional roles of SARK isolated from Physcomitrella patens (PpSARK) in salt stress response and senescence. PpSARK transcripts significantly accumulated under NaCl and abscisic acid (ABA) treatments, with higher expression in the moss gametophyte stage. Insertional gain-of-function mutants of PpSARK (PpSARKg) were more tolerant to salt stress and ABA than wild type (WT), whereas senescence of mutants was delayed during the protonema stage. Expression of stress-responsive genes in the ABA related pathway, such as PpABI3, PpABI5, PpPP2C, and PpLEA were significantly higher in PpSARKg and WT under salt stress conditions, suggesting that PpSARK might positively regulate salt tolerance via an ABA-related pathway. Endogenous ABA contents also increased 3-fold under salt stress conditions. These results indicate that PpSARK functions as a positive regulator in salt stress responses, while possibly functioning as a negative regulator in senescence in moss.
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Affiliation(s)
- Ping Li
- Key Laboratory of Economic Plants and Biotechnology, Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Yunnan Key Laboratory for Wild Plant Resources, Kunming 650201, China.
- University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Hong Yang
- Key Laboratory of Economic Plants and Biotechnology, Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Yunnan Key Laboratory for Wild Plant Resources, Kunming 650201, China.
- University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Gaojing Liu
- Key Laboratory of Economic Plants and Biotechnology, Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Yunnan Key Laboratory for Wild Plant Resources, Kunming 650201, China.
| | - Wenzhang Ma
- Key Laboratory of Economic Plants and Biotechnology, Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Yunnan Key Laboratory for Wild Plant Resources, Kunming 650201, China.
| | - Chuanhong Li
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research, Huazhong Agricultural University, Wuhan 430070, China.
| | - Heqiang Huo
- Mid-Florida Research and Education Center, Department of Environmental Horticulture, University of Florida, Apopka, FL 32703, USA.
| | - Jianfang He
- Key Laboratory of Economic Plants and Biotechnology, Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Yunnan Key Laboratory for Wild Plant Resources, Kunming 650201, China.
- University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Li Liu
- Key Laboratory of Economic Plants and Biotechnology, Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Yunnan Key Laboratory for Wild Plant Resources, Kunming 650201, China.
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62
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Wang X, Tu M, Wang D, Liu J, Li Y, Li Z, Wang Y, Wang X. CRISPR/Cas9-mediated efficient targeted mutagenesis in grape in the first generation. PLANT BIOTECHNOLOGY JOURNAL 2018; 16:844-855. [PMID: 28905515 PMCID: PMC5866948 DOI: 10.1111/pbi.12832] [Citation(s) in RCA: 153] [Impact Index Per Article: 25.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2017] [Revised: 08/25/2017] [Accepted: 09/01/2017] [Indexed: 05/19/2023]
Abstract
The clustered regularly interspaced short palindromic repeats-associated protein 9 (CRISPR/Cas9) system is a powerful tool for editing plant genomes. Efficient genome editing of grape (Vitis vinifera) suspension cells using the type II CRISPR/Cas9 system has been demonstrated; however, it has not been established whether this system can be applied to get biallelic mutations in the first generation of grape. In this current study, we designed four guide RNAs for the VvWRKY52 transcription factor gene for using with the CRISPR/Cas9 system, and obtained transgenic plants via Agrobacterium-mediated transformation, using somatic embryos of the Thompson Seedless cultivar. Analysis of the first-generation transgenic plants verified 22 mutant plants of the 72 T-DNA-inserted plants. Of these, 15 lines carried biallelic mutations and seven were heterozygous. A range of RNA-guided editing events, including large deletions, were found in the mutant plants, while smaller deletions comprised the majority of the detected mutations. Sequencing of potential off-target sites for all four targets revealed no off-target events. In addition, knockout of VvWRKY52 in grape increased the resistance to Botrytis cinerea. We conclude that the CRISPR/Cas9 system allows precise genome editing in the first generation of grape and represents a useful tool for gene functional analysis and grape molecular breeding.
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Affiliation(s)
- Xianhang Wang
- State Key Laboratory of Crop Stress Biology in Arid AreasCollege of HorticultureNorthwest A&F UniversityYanglingShaanxiChina
- Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest ChinaMinistry of AgricultureNorthwest A&F UniversityYanglingShaanxiChina
| | - Mingxing Tu
- State Key Laboratory of Crop Stress Biology in Arid AreasCollege of HorticultureNorthwest A&F UniversityYanglingShaanxiChina
- Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest ChinaMinistry of AgricultureNorthwest A&F UniversityYanglingShaanxiChina
| | - Dejun Wang
- State Key Laboratory of Crop Stress Biology in Arid AreasCollege of HorticultureNorthwest A&F UniversityYanglingShaanxiChina
- Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest ChinaMinistry of AgricultureNorthwest A&F UniversityYanglingShaanxiChina
| | - Jianwei Liu
- State Key Laboratory of Crop Stress Biology in Arid AreasCollege of HorticultureNorthwest A&F UniversityYanglingShaanxiChina
- Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest ChinaMinistry of AgricultureNorthwest A&F UniversityYanglingShaanxiChina
| | - Yajuan Li
- State Key Laboratory of Crop Stress Biology in Arid AreasCollege of HorticultureNorthwest A&F UniversityYanglingShaanxiChina
- Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest ChinaMinistry of AgricultureNorthwest A&F UniversityYanglingShaanxiChina
| | - Zhi Li
- State Key Laboratory of Crop Stress Biology in Arid AreasCollege of HorticultureNorthwest A&F UniversityYanglingShaanxiChina
- Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest ChinaMinistry of AgricultureNorthwest A&F UniversityYanglingShaanxiChina
| | - Yuejin Wang
- State Key Laboratory of Crop Stress Biology in Arid AreasCollege of HorticultureNorthwest A&F UniversityYanglingShaanxiChina
- Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest ChinaMinistry of AgricultureNorthwest A&F UniversityYanglingShaanxiChina
| | - Xiping Wang
- State Key Laboratory of Crop Stress Biology in Arid AreasCollege of HorticultureNorthwest A&F UniversityYanglingShaanxiChina
- Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest ChinaMinistry of AgricultureNorthwest A&F UniversityYanglingShaanxiChina
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63
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Li Z, Woo HR, Guo H. Genetic redundancy of senescence-associated transcription factors in Arabidopsis. JOURNAL OF EXPERIMENTAL BOTANY 2018; 69:811-823. [PMID: 29309664 DOI: 10.1093/jxb/erx345] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2017] [Accepted: 09/29/2017] [Indexed: 05/25/2023]
Abstract
Leaf senescence is a genetically programmed process that constitutes the last stage of leaf development, and involves massive changes in gene expression. As a result of the intensive efforts that have been made to elucidate the molecular genetic mechanisms underlying leaf senescence, 184 genes that alter leaf senescence phenotypes when mutated or overexpressed have been identified in Arabidopsis thaliana over the past two decades. Concurrently, experimental evidence on functional redundancy within senescence-associated genes (SAGs) has increased. In this review, we focus on transcription factors that play regulatory roles in Arabidopsis leaf senescence, and describe the relationships among gene duplication, gene expression level, and senescence phenotypes. Previous findings and our re-analysis demonstrate the widespread existence of duplicate SAG pairs and a correlation between gene expression levels in duplicate genes and senescence-related phenotypic severity of the corresponding mutants. We also highlight effective and powerful tools that are available for functional analyses of redundant SAGs. We propose that the study of duplicate SAG pairs offers a unique opportunity to understand the regulation of leaf senescence and can guide the investigation of the functions of redundant SAGs via reverse genetic approaches.
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Affiliation(s)
- Zhonghai Li
- Center for Plant Aging Research, Institute for Basic Science (IBS), Daegu, Republic of Korea
| | - Hye Ryun Woo
- Department of New Biology, Daegu Gyeongbuk Institute of Science and Technology (DGIST), Daegu, Republic of Korea
| | - Hongwei Guo
- Department of Biology, South University of Science and Technology of China, Shenzhen, Guangdong, China
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64
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Deciphering the Evolution and Development of the Cuticle by Studying Lipid Transfer Proteins in Mosses and Liverworts. PLANTS 2018; 7:plants7010006. [PMID: 29342939 PMCID: PMC5874595 DOI: 10.3390/plants7010006] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Revised: 12/10/2017] [Accepted: 01/11/2018] [Indexed: 12/26/2022]
Abstract
When plants conquered land, they developed specialized organs, tissues, and cells in order to survive in this new and harsh terrestrial environment. New cell polymers such as the hydrophobic lipid-based polyesters cutin, suberin, and sporopollenin were also developed for protection against water loss, radiation, and other potentially harmful abiotic factors. Cutin and waxes are the main components of the cuticle, which is the waterproof layer covering the epidermis of many aerial organs of land plants. Although the in vivo functions of the group of lipid binding proteins known as lipid transfer proteins (LTPs) are still rather unclear, there is accumulating evidence suggesting a role for LTPs in the transfer and deposition of monomers required for cuticle assembly. In this review, we first present an overview of the data connecting LTPs with cuticle synthesis. Furthermore, we propose liverworts and mosses as attractive model systems for revealing the specific function and activity of LTPs in the biosynthesis and evolution of the plant cuticle.
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65
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Barbieri EM, Muir P, Akhuetie-Oni BO, Yellman CM, Isaacs FJ. Precise Editing at DNA Replication Forks Enables Multiplex Genome Engineering in Eukaryotes. Cell 2017; 171:1453-1467.e13. [PMID: 29153834 DOI: 10.1016/j.cell.2017.10.034] [Citation(s) in RCA: 81] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2016] [Revised: 08/29/2017] [Accepted: 10/19/2017] [Indexed: 02/08/2023]
Abstract
We describe a multiplex genome engineering technology in Saccharomyces cerevisiae based on annealing synthetic oligonucleotides at the lagging strand of DNA replication. The mechanism is independent of Rad51-directed homologous recombination and avoids the creation of double-strand DNA breaks, enabling precise chromosome modifications at single base-pair resolution with an efficiency of >40%, without unintended mutagenic changes at the targeted genetic loci. We observed the simultaneous incorporation of up to 12 oligonucleotides with as many as 60 targeted mutations in one transformation. Iterative transformations of a complex pool of oligonucleotides rapidly produced large combinatorial genomic diversity >105. This method was used to diversify a heterologous β-carotene biosynthetic pathway that produced genetic variants with precise mutations in promoters, genes, and terminators, leading to altered carotenoid levels. Our approach of engineering the conserved processes of DNA replication, repair, and recombination could be automated and establishes a general strategy for multiplex combinatorial genome engineering in eukaryotes.
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Affiliation(s)
- Edward M Barbieri
- Department of Molecular, Cellular, & Developmental Biology, Yale University, New Haven, CT 06520, USA; Systems Biology Institute, Yale University, West Haven, CT 06516, USA
| | - Paul Muir
- Department of Molecular, Cellular, & Developmental Biology, Yale University, New Haven, CT 06520, USA; Systems Biology Institute, Yale University, West Haven, CT 06516, USA
| | - Benjamin O Akhuetie-Oni
- Department of Molecular, Cellular, & Developmental Biology, Yale University, New Haven, CT 06520, USA; Systems Biology Institute, Yale University, West Haven, CT 06516, USA
| | - Christopher M Yellman
- Department of Molecular, Cellular, & Developmental Biology, Yale University, New Haven, CT 06520, USA; Systems Biology Institute, Yale University, West Haven, CT 06516, USA
| | - Farren J Isaacs
- Department of Molecular, Cellular, & Developmental Biology, Yale University, New Haven, CT 06520, USA; Systems Biology Institute, Yale University, West Haven, CT 06516, USA.
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66
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Ako AE, Perroud PF, Innocent J, Demko V, Olsen OA, Johansen W. An intragenic mutagenesis strategy in Physcomitrella patens to preserve intron splicing. Sci Rep 2017; 7:5111. [PMID: 28698618 PMCID: PMC5505980 DOI: 10.1038/s41598-017-05309-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2017] [Accepted: 05/26/2017] [Indexed: 12/27/2022] Open
Abstract
Gene targeting is a powerful reverse genetics technique for site-specific genome modification. Intrinsic homologous recombination in the moss Physcomitrella patens permits highly effective gene targeting, a characteristic that makes this organism a valuable model for functional genetics. Functional characterization of domains located within a multi-domain protein depends on the ability to generate mutants harboring genetic modifications at internal gene positions while maintaining the reading-frames of the flanking exons. In this study, we designed and evaluated different gene targeting constructs for targeted gene manipulation of sequences corresponding to internal domains of the DEFECTIVE KERNEL1 protein in Physcomitrella patens. Our results show that gene targeting-associated mutagenesis of introns can have adverse effects on splicing, corrupting the normal reading frame of the transcript. We show that successful genetic modification of internal sequences of multi-exon genes depends on gene-targeting strategies which insert the selection marker cassette into the 5' end of the intron and preserve the nucleotide sequence of the targeted intron.
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Affiliation(s)
- Ako Eugene Ako
- Inland Norway University of Applied Sciences, Holsetgata 31, N-2318, Hamar, Norway
| | - Pierre-François Perroud
- Philipps University Marburg, Plant Cell Biology II, Karl-von-Frisch-Str. 8, 35043, Marburg, Germany
| | - Joseph Innocent
- Inland Norway University of Applied Sciences, Holsetgata 31, N-2318, Hamar, Norway
| | - Viktor Demko
- Norwegian University of Life Sciences, P.O. Box 5003, N-1432, As, Norway
| | - Odd-Arne Olsen
- Norwegian University of Life Sciences, P.O. Box 5003, N-1432, As, Norway.
| | - Wenche Johansen
- Inland Norway University of Applied Sciences, Holsetgata 31, N-2318, Hamar, Norway.
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67
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Russell JJ, Theriot JA, Sood P, Marshall WF, Landweber LF, Fritz-Laylin L, Polka JK, Oliferenko S, Gerbich T, Gladfelter A, Umen J, Bezanilla M, Lancaster MA, He S, Gibson MC, Goldstein B, Tanaka EM, Hu CK, Brunet A. Non-model model organisms. BMC Biol 2017; 15:55. [PMID: 28662661 PMCID: PMC5492503 DOI: 10.1186/s12915-017-0391-5] [Citation(s) in RCA: 128] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Model organisms are widely used in research as accessible and convenient systems to study a particular area or question in biology. Traditionally only a handful of organisms have been widely studied, but modern research tools are enabling researchers to extend the set of model organisms to include less-studied and more unusual systems. This Forum highlights a range of 'non-model model organisms' as emerging systems for tackling questions across the whole spectrum of biology (and beyond), the opportunities and challenges, and the outlook for the future.
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Affiliation(s)
- James J Russell
- Department of Biology, Howard Hughes Medical Institute Stanford University, Stanford, CA, 94305, USA
| | - Julie A Theriot
- Departments of Biochemistry and of Microbiology & Immunology, Howard Hughes Medical Institute Stanford University, Stanford, CA, 94305, USA.
| | - Pranidhi Sood
- Department of Biochemistry & Biophysics, University of California San Francisco, 600 16th St, San Francisco, CA, 94158, USA
| | - Wallace F Marshall
- Department of Biochemistry & Biophysics, University of California San Francisco, 600 16th St, San Francisco, CA, 94158, USA.
| | - Laura F Landweber
- Departments of Biochemistry & Molecular Biophysics and Biological Sciences, Columbia University, New York, NY, 10032, USA
| | | | - Jessica K Polka
- Visiting Scholar, Whitehead Institute, 9 Cambridge Center, Cambridge, MA, 02142, USA
| | - Snezhana Oliferenko
- The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
- Randall Division of Cell and Molecular Biophysics, New Hunt's House, Guy's Campus, King's College London, London, SE1 1UL, UK
| | - Therese Gerbich
- 516 Fordham Hall, University of North Carolina Chapel Hill, Chapel Hill, NC, 27514, USA
| | - Amy Gladfelter
- 516 Fordham Hall, University of North Carolina Chapel Hill, Chapel Hill, NC, 27514, USA
| | - James Umen
- Donald Danforth Plant Science Center, 975 N. Warson Rd, St. Louis, MO, 63132, USA
| | | | - Madeline A Lancaster
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Francis Crick Avenue, CB2 0QH, Cambridge, UK
| | - Shuonan He
- Stowers Institute for Medical Research, Kansas City, MO, 64110, USA
| | - Matthew C Gibson
- Stowers Institute for Medical Research, Kansas City, MO, 64110, USA
- Department of Anatomy and Cell Biology, The University of Kansas School of Medicine, Kansas City, KS, 66160, USA
| | - Bob Goldstein
- Biology Department, The University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Elly M Tanaka
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Campus Vienna Biocenter 1, 1030, Vienna, Austria
| | - Chi-Kuo Hu
- Department of Genetics, Stanford University, Stanford, CA, 94305, USA
| | - Anne Brunet
- Department of Genetics, Stanford University, Stanford, CA, 94305, USA
- Glenn Laboratories for the Biology of Aging at Stanford, Stanford, CA, 94305, USA
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68
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Morineau C, Bellec Y, Tellier F, Gissot L, Kelemen Z, Nogué F, Faure J. Selective gene dosage by CRISPR-Cas9 genome editing in hexaploid Camelina sativa. PLANT BIOTECHNOLOGY JOURNAL 2017; 15:729-739. [PMID: 27885771 PMCID: PMC5425392 DOI: 10.1111/pbi.12671] [Citation(s) in RCA: 145] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2016] [Revised: 11/20/2016] [Accepted: 11/21/2016] [Indexed: 05/03/2023]
Abstract
In many plant species, gene dosage is an important cause of phenotype variation. Engineering gene dosage, particularly in polyploid genomes, would provide an efficient tool for plant breeding. The hexaploid oilseed crop Camelina sativa, which has three closely related expressed subgenomes, is an ideal species for investigation of the possibility of creating a large collection of combinatorial mutants. Selective, targeted mutagenesis of the three delta-12-desaturase (FAD2) genes was achieved by CRISPR-Cas9 gene editing, leading to reduced levels of polyunsaturated fatty acids and increased accumulation of oleic acid in the oil. Analysis of mutations over four generations demonstrated the presence of a large variety of heritable mutations in the three isologous CsFAD2 genes. The different combinations of single, double and triple mutants in the T3 generation were isolated, and the complete loss-of-function mutants revealed the importance of delta-12-desaturation for Camelina development. Combinatorial association of different alleles for the three FAD2 loci provided a large diversity of Camelina lines with various lipid profiles, ranging from 10% to 62% oleic acid accumulation in the oil. The different allelic combinations allowed an unbiased analysis of gene dosage and function in this hexaploid species, but also provided a unique source of genetic variability for plant breeding.
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Affiliation(s)
- Céline Morineau
- Institut Jean‐Pierre Bourgin (IJPB)INRAAgroParisTechCNRSSaclay Plant Sciences (SPS)Université Paris‐SaclayVersaillesFrance
| | - Yannick Bellec
- Institut Jean‐Pierre Bourgin (IJPB)INRAAgroParisTechCNRSSaclay Plant Sciences (SPS)Université Paris‐SaclayVersaillesFrance
| | - Frédérique Tellier
- Institut Jean‐Pierre Bourgin (IJPB)INRAAgroParisTechCNRSSaclay Plant Sciences (SPS)Université Paris‐SaclayVersaillesFrance
| | - Lionel Gissot
- Institut Jean‐Pierre Bourgin (IJPB)INRAAgroParisTechCNRSSaclay Plant Sciences (SPS)Université Paris‐SaclayVersaillesFrance
| | - Zsolt Kelemen
- Institut Jean‐Pierre Bourgin (IJPB)INRAAgroParisTechCNRSSaclay Plant Sciences (SPS)Université Paris‐SaclayVersaillesFrance
| | - Fabien Nogué
- Institut Jean‐Pierre Bourgin (IJPB)INRAAgroParisTechCNRSSaclay Plant Sciences (SPS)Université Paris‐SaclayVersaillesFrance
| | - Jean‐Denis Faure
- Institut Jean‐Pierre Bourgin (IJPB)INRAAgroParisTechCNRSSaclay Plant Sciences (SPS)Université Paris‐SaclayVersaillesFrance
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69
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Malzahn A, Lowder L, Qi Y. Plant genome editing with TALEN and CRISPR. Cell Biosci 2017; 7:21. [PMID: 28451378 PMCID: PMC5404292 DOI: 10.1186/s13578-017-0148-4] [Citation(s) in RCA: 110] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2017] [Accepted: 04/19/2017] [Indexed: 11/10/2022] Open
Abstract
Genome editing promises giant leaps forward in advancing biotechnology, agriculture, and basic research. The process relies on the use of sequence specific nucleases (SSNs) to make DNA double stranded breaks at user defined genomic loci, which are subsequently repaired by two main DNA repair pathways: non-homologous end joining (NHEJ) and homology directed repair (HDR). NHEJ can result in frameshift mutations that often create genetic knockouts. These knockout lines are useful for functional and reverse genetic studies but also have applications in agriculture. HDR has a variety of applications as it can be used for gene replacement, gene stacking, and for creating various fusion proteins. In recent years, transcription activator-like effector nucleases and clustered regularly interspaced palindromic repeats (CRISPR) and CRISPR associated protein 9 or CRISPR from Prevotella and Francisella 1 have emerged as the preferred SSNs for research purposes. Here, we review their applications in plant research, discuss current limitations, and predict future research directions in plant genome editing.
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Affiliation(s)
- Aimee Malzahn
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD 20742 USA
| | - Levi Lowder
- Department of Biology, East Carolina University, Greenville, NC 27858 USA
| | - Yiping Qi
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD 20742 USA
- Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, MD 20850 USA
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70
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Li FW, Villarreal JC, Szövényi P. Hornworts: An Overlooked Window into Carbon-Concentrating Mechanisms. TRENDS IN PLANT SCIENCE 2017; 22:275-277. [PMID: 28283353 DOI: 10.1016/j.tplants.2017.02.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2016] [Revised: 02/09/2017] [Accepted: 02/10/2017] [Indexed: 05/12/2023]
Abstract
Hornworts are the only land plant lineage harboring a biophysical carbon-concentrating mechanism (CCM). Here, we argue that hornworts are a promising, yet currently overlooked, model system to study the evolution and genetic basis of CCMs. The results of such studies could have translational values toward engineering a CCM in crop plants.
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Affiliation(s)
- Fay-Wei Li
- Boyce Thompson Institute, Ithaca, NY, USA; Department of Systematic and Evolutionary Botany, University of Zurich, Zurich, Switzerland.
| | | | - Péter Szövényi
- Department of Systematic and Evolutionary Botany, University of Zurich, Zurich, Switzerland
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71
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Yamada M, Goshima G. Mitotic Spindle Assembly in Land Plants: Molecules and Mechanisms. BIOLOGY 2017; 6:biology6010006. [PMID: 28125061 PMCID: PMC5371999 DOI: 10.3390/biology6010006] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/01/2016] [Revised: 11/29/2016] [Accepted: 01/08/2017] [Indexed: 11/16/2022]
Abstract
In textbooks, the mitotic spindles of plants are often described separately from those of animals. How do they differ at the molecular and mechanistic levels? In this chapter, we first outline the process of mitotic spindle assembly in animals and land plants. We next discuss the conservation of spindle assembly factors based on database searches. Searches of >100 animal spindle assembly factors showed that the genes involved in this process are well conserved in plants, with the exception of two major missing elements: centrosomal components and subunits/regulators of the cytoplasmic dynein complex. We then describe the spindle and phragmoplast assembly mechanisms based on the data obtained from robust gene loss-of-function analyses using RNA interference (RNAi) or mutant plants. Finally, we discuss future research prospects of plant spindles.
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Affiliation(s)
- Moé Yamada
- Graduate School of Science, Division of Biological Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan.
| | - Gohta Goshima
- Graduate School of Science, Division of Biological Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan.
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Nomura T, Sakurai T, Osakabe Y, Osakabe K, Sakakibara H. Efficient and Heritable Targeted Mutagenesis in Mosses Using the CRISPR/Cas9 System. PLANT & CELL PHYSIOLOGY 2016; 57:2600-2610. [PMID: 27986915 DOI: 10.1093/pcp/pcw173] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2016] [Accepted: 10/05/2016] [Indexed: 05/20/2023]
Abstract
Targeted genome modification by RNA-guided nucleases derived from the clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR-associated nuclease 9 (Cas9) system has seen rapid development in many organisms, including several plant species. In the present study, we succeeded in introducing the CRISPR/Cas9 system into the non-model organism Scopelophila cataractae, a moss that exhibits heavy metal tolerance, and the model organism Physcomitrella patens Utilizing the process by which moss plants regenerate from protoplasts, we conducted targeted mutagenesis by expression of single-chain guide RNA (sgRNA) and Cas9 in protoplasts. Using this method, the acquisition rate of strains exhibiting phenotypic changes associated with the target genes was approximately 45-69%, and strains with phenotypic changes exhibited various insertion and deletion mutations. In addition, we report that our method is capable of multiplex targeted mutagenesis (two independent genes) and also permits the efficient introduction of large deletions (∼3 kbp). These results demonstrate that the CRISPR/Cas9 system can be used to accelerate investigations of bryology and land plant evolution.
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Affiliation(s)
- Toshihisa Nomura
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro, Tsurumi, Yokohama, 230-0045 Japan
| | - Tetsuya Sakurai
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro, Tsurumi, Yokohama, 230-0045 Japan
- Research and Education Faculty, Multidisciplinary Science Cluster, Interdisciplinary Science Unit, Kochi University, 200 Otsu, Monobe, Nankoku, Kochi, 783-8502 Japan
| | - Yuriko Osakabe
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro, Tsurumi, Yokohama, 230-0045 Japan
- Faculty of Bioscience and Bioindustry, Tokushima University, 2-1 Josanjima, Tokushima, 770-8513 Japan
| | - Keishi Osakabe
- Faculty of Bioscience and Bioindustry, Tokushima University, 2-1 Josanjima, Tokushima, 770-8513 Japan
| | - Hitoshi Sakakibara
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro, Tsurumi, Yokohama, 230-0045 Japan
- Graduate School of Bioagricultural Sciences, Nagoya University, Chikusa, Nagoya, 464-8601 Japan
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Simple and Efficient Targeting of Multiple Genes Through CRISPR-Cas9 in Physcomitrella patens. G3-GENES GENOMES GENETICS 2016; 6:3647-3653. [PMID: 27613750 PMCID: PMC5100863 DOI: 10.1534/g3.116.033266] [Citation(s) in RCA: 70] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Powerful genome editing technologies are needed for efficient gene function analysis. The CRISPR-Cas9 system has been adapted as an efficient gene-knock-out technology in a variety of species. However, in a number of situations, knocking out or modifying a single gene is not sufficient; this is particularly true for genes belonging to a common family, or for genes showing redundant functions. Like many plants, the model organism Physcomitrella patens has experienced multiple events of polyploidization during evolution that has resulted in a number of families of duplicated genes. Here, we report a robust CRISPR-Cas9 system, based on the codelivery of a CAS9 expressing cassette, multiple sgRNA vectors, and a cassette for transient transformation selection, for gene knock-out in multiple gene families. We demonstrate that CRISPR-Cas9-mediated targeting of five different genes allows the selection of a quintuple mutant, and all possible subcombinations of mutants, in one experiment, with no mutations detected in potential off-target sequences. Furthermore, we confirmed the observation that the presence of repeats in the vicinity of the cutting region favors deletion due to the alternative end joining pathway, for which induced frameshift mutations can be potentially predicted. Because the number of multiple gene families in Physcomitrella is substantial, this tool opens new perspectives to study the role of expanded gene families in the colonization of land by plants.
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