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Causier B, McKay M, Hopes T, Lloyd J, Wang D, Harrison CJ, Davies B. The TOPLESS corepressor regulates developmental switches in the bryophyte Physcomitrium patens that were critical for plant terrestrialisation. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 115:1331-1344. [PMID: 37243383 PMCID: PMC10953049 DOI: 10.1111/tpj.16322] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 04/27/2023] [Accepted: 05/23/2023] [Indexed: 05/28/2023]
Abstract
The plant-specific TOPLESS (TPL) family of transcriptional corepressors is integral to multiple angiosperm developmental processes. Despite this, we know little about TPL function in other plants. To address this gap, we investigated the roles TPL plays in the bryophyte Physcomitrium patens, which diverged from angiosperms approximately 0.5 billion years ago. Although complete loss of PpTPL function is lethal, transgenic lines with reduced PpTPL activity revealed that PpTPLs are essential for two fundamental developmental switches in this plant: the transitions from basal photosynthetic filaments (chloronemata) to specialised foraging filaments (caulonemata) and from two-dimensional (2D) to three-dimensional (3D) growth. Using a transcriptomics approach, we integrated PpTPL into the regulatory network governing 3D growth and we propose that PpTPLs represent another important class of regulators that are essential for the 2D-to-3D developmental switch. Transcriptomics also revealed a previously unknown role for PpTPL in the regulation of flavonoids. Intriguingly, 3D growth and the formation of caulonemata were crucial innovations that facilitated the colonisation of land by plants, a major transformative event in the history of life on Earth. We conclude that TPL, which existed before the land plants, was co-opted into new developmental pathways, enabling phytoterrestrialisation and the evolution of land plants.
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Affiliation(s)
- Barry Causier
- Centre for Plant Sciences, Faculty of Biological SciencesUniversity of LeedsLeedsLS2 9JTUK
| | - Mary McKay
- Centre for Plant Sciences, Faculty of Biological SciencesUniversity of LeedsLeedsLS2 9JTUK
| | - Tayah Hopes
- Centre for Plant Sciences, Faculty of Biological SciencesUniversity of LeedsLeedsLS2 9JTUK
- School of Molecular and Cellular Biology, Faculty of Biological SciencesUniversity of LeedsLeedsLS2 9JTUK
| | - James Lloyd
- Centre for Plant Sciences, Faculty of Biological SciencesUniversity of LeedsLeedsLS2 9JTUK
- Australian Research Council Centre of Excellence in Plant Energy Biology, School of Molecular SciencesThe University of Western AustraliaPerthWA6009Australia
| | - Dapeng Wang
- LeedsOmicsUniversity of LeedsLeedsLS2 9JTUK
- National Heart and Lung Institute, Imperial College LondonLondonSW3 6LYUK
| | - C. Jill Harrison
- School of Biological SciencesUniversity of Bristol24 Tyndall AvenueBristolBS8 1TQUK
| | - Brendan Davies
- Centre for Plant Sciences, Faculty of Biological SciencesUniversity of LeedsLeedsLS2 9JTUK
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2
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Belshaw N, Grouneva I, Aram L, Gal A, Hopes A, Mock T. Efficient gene replacement by CRISPR/Cas-mediated homologous recombination in the model diatom Thalassiosira pseudonana. THE NEW PHYTOLOGIST 2023; 238:438-452. [PMID: 36307966 DOI: 10.1111/nph.18587] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Accepted: 10/18/2022] [Indexed: 06/16/2023]
Abstract
CRISPR/Cas enables targeted genome editing in many different plant and algal species including the model diatom Thalassiosira pseudonana. However, efficient gene targeting by homologous recombination (HR) to date is only reported for photosynthetic organisms in their haploid life-cycle phase. Here, a CRISPR/Cas construct, assembled using Golden Gate cloning, enabled highly efficient HR in a diploid photosynthetic organism. Homologous recombination was induced in T. pseudonana using sequence-specific CRISPR/Cas, paired with a dsDNA donor matrix, generating substitution of the silacidin, nitrate reductase and urease genes by a resistance cassette (FCP:NAT). Up to c. 85% of NAT-resistant T. pseudonana colonies screened positive for HR by nested PCR. Precise integration of FCP:NAT at each locus was confirmed using an inverse PCR approach. The knockout of the nitrate reductase and urease genes impacted growth on nitrate and urea, respectively, while the knockout of the silacidin gene in T. pseudonana caused a significant increase in cell size, confirming the role of this gene for cell-size regulation in centric diatoms. Highly efficient gene targeting by HR makes T. pseudonana as genetically tractable as Nannochloropsis and Physcomitrella, hence rapidly advancing functional diatom biology, bionanotechnology and biotechnological applications targeted on harnessing the metabolic potential of diatoms.
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Affiliation(s)
- Nigel Belshaw
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
| | - Irina Grouneva
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
| | - Lior Aram
- Department of Plant and Environmental Sciences, Faculty of Biochemistry, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Assaf Gal
- Department of Plant and Environmental Sciences, Faculty of Biochemistry, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Amanda Hopes
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
| | - Thomas Mock
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
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3
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Guan Y, Ma L, Wang Q, Zhao J, Wang S, Wu J, Liu Y, Sun H, Huang J. Horizontally acquired fungal killer protein genes affect cell development in mosses. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 113:665-676. [PMID: 36507655 DOI: 10.1111/tpj.16060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Revised: 11/25/2022] [Accepted: 12/08/2022] [Indexed: 06/17/2023]
Abstract
The moss Physcomitrium patens is crucial for studying plant development and evolution. Although the P. patens genome includes genes acquired from bacteria, fungi and viruses, the functions and evolutionary significance of these acquired genes remain largely unclear. Killer protein 4 (KP4) is a toxin secreted by the phytopathogenic fungus Ustilago maydis that inhibits the growth of sensitive target strains by blocking their calcium uptake. Here, we show that KP4 genes in mosses were acquired from fungi through at least three independent events of horizontal gene transfer. Two paralogous copies of KP4 (PpKP4-1 and PpKP4-2) exist in P. patens. Knockout mutants ppkp4-1 and ppkp4-2 showed cell death at the protonemal stage, and ppkp4-2 also exhibited defects in tip growth. We provide experimental evidence indicating that PpKP4-1/2 affects P. patens protonemal cell development by mediating cytoplasmic calcium and that KP4 genes are functionally conserved between P. patens and fungi. The present study provides additional insights into the role of horizontal gene transfer in land plant development and evolution.
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Affiliation(s)
- Yanlong Guan
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
| | - Lan Ma
- Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
| | - Qia Wang
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
| | - Jinjie Zhao
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
| | - Shuanghua Wang
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jinsong Wu
- Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
| | - Yang Liu
- Key Laboratory of Southern Subtropical Plant Diversity, Fairy Lake Botanical Garden, Shenzhen & Chinese Academy of Science, Shenzhen, 518004, China
| | - Hang Sun
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
| | - Jinling Huang
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
- Institute of Plant Stress Biology, State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, 475001, China
- Department of Biology, East Carolina University, Greenville, NC, 27858, USA
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4
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Nemec‐Venza Z, Madden C, Stewart A, Liu W, Novák O, Pěnčík A, Cuming AC, Kamisugi Y, Harrison CJ. CLAVATA modulates auxin homeostasis and transport to regulate stem cell identity and plant shape in a moss. THE NEW PHYTOLOGIST 2022; 234:149-163. [PMID: 35032334 PMCID: PMC9303531 DOI: 10.1111/nph.17969] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Accepted: 12/21/2021] [Indexed: 05/26/2023]
Abstract
The CLAVATA pathway is a key regulator of stem cell function in the multicellular shoot tips of Arabidopsis, where it acts via the WUSCHEL transcription factor to modulate hormone homeostasis. Broad-scale evolutionary comparisons have shown that CLAVATA is a conserved regulator of land plant stem cell function, but CLAVATA acts independently of WUSCHEL-like (WOX) proteins in bryophytes. The relationship between CLAVATA, hormone homeostasis and the evolution of land plant stem cell functions is unknown. Here we show that in the moss, Physcomitrella (Physcomitrium patens), CLAVATA affects stem cell activity by modulating hormone homeostasis. CLAVATA pathway genes are expressed in the tip cells of filamentous tissues, regulating cell identity, filament branching, plant spread and auxin synthesis. The receptor-like kinase PpRPK2 plays the major role, and Pprpk2 mutants have abnormal responses to cytokinin, auxin and auxin transport inhibition, and show reduced expression of PIN auxin transporters. We propose a model whereby PpRPK2 modulates auxin gradients in filaments to determine stem cell identity and overall plant form. Our data indicate that CLAVATA-mediated auxin homeostasis is a fundamental property of plant stem cell function, probably exhibited by the last shared common ancestor of land plants.
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Affiliation(s)
- Zoe Nemec‐Venza
- School of Biological SciencesUniversity of Bristol24 Tyndall AvenueBristolBS8 1TQUK
| | - Connor Madden
- School of Biological SciencesUniversity of Bristol24 Tyndall AvenueBristolBS8 1TQUK
- Division of Psychological Medicine & Clinical NeurosciencesMRC Centre for Neuropsychiatric Genetics & GenomicsCardiff University School of MedicineHeath ParkCardiffCF14 4XNUK
| | - Amy Stewart
- School of Biological SciencesUniversity of Bristol24 Tyndall AvenueBristolBS8 1TQUK
| | - Wei Liu
- School of Biological SciencesUniversity of Bristol24 Tyndall AvenueBristolBS8 1TQUK
| | - Ondřej Novák
- Laboratory of Growth RegulatorsFaculty of Science of Palacký University and Institute of Experimental Botany of the Czech Academy of SciencesŠlechtitelů 27Olomouc78371Czech Republic
| | - Aleš Pěnčík
- Laboratory of Growth RegulatorsFaculty of Science of Palacký University and Institute of Experimental Botany of the Czech Academy of SciencesŠlechtitelů 27Olomouc78371Czech Republic
| | - Andrew C. Cuming
- Centre for Plant SciencesFaculty of Biological SciencesUniversity of LeedsLeedsLS2 9JTUK
| | - Yasuko Kamisugi
- School of Biological SciencesUniversity of Bristol24 Tyndall AvenueBristolBS8 1TQUK
- Centre for Plant SciencesFaculty of Biological SciencesUniversity of LeedsLeedsLS2 9JTUK
| | - C. Jill Harrison
- School of Biological SciencesUniversity of Bristol24 Tyndall AvenueBristolBS8 1TQUK
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5
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Zhu L. Targeted Gene Knockouts by Protoplast Transformation in the Moss Physcomitrella patens. Front Genome Ed 2022; 3:719087. [PMID: 34977859 PMCID: PMC8718793 DOI: 10.3389/fgeed.2021.719087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Accepted: 11/30/2021] [Indexed: 11/15/2022] Open
Abstract
Targeted gene knockout is particularly useful for analyzing gene functions in plant growth, signaling, and development. By transforming knockout cassettes consisting of homologous sequences of the target gene into protoplasts, the classical gene targeting method aims to obtain targeted gene replacement, allowing for the characterization of gene functions in vivo. The moss Physcomitrella patens is a known model organism for a high frequency of homologous recombination and thus harbors a remarkable rate of gene targeting. Other moss features, including easy to culture, dominant haploidy phase, and sequenced genome, make gene targeting prevalent in Physcomitrella patens. However, even gene targeting was powerful to generate knockouts, researchers using this method still experienced technical challenges. For example, obtaining a good number of targeted knockouts after protoplast transformation and regeneration disturbed the users. Off-target mutations such as illegitimate random integration mediated by nonhomologous end joining and targeted insertion wherein one junction on-target but the other end off-target is commonly present in the knockouts. Protoplast fusion during transformation and regeneration was also a problem. This review will discuss the advantages and technical challenges of gene targeting. Recently, CRISPR-Cas9 is a revolutionary technology and becoming a hot topic in plant gene editing. In the second part of this review, CRISPR-Cas9 technology will be focused on and compared to gene targeting regarding the practical use in Physcomitrella patens. This review presents an updated perspective of the gene targeting and CRISPR-Cas9 techniques to plant biologists who may consider studying gene functions in the model organism Physcomitrella patens.
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Affiliation(s)
- Lei Zhu
- Department of Botany and Plant Sciences, University of California, Riverside, CA, United States
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6
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Rempfer C, Wiedemann G, Schween G, Kerres KL, Lucht JM, Horres R, Decker EL, Reski R. Autopolyploidization affects transcript patterns and gene targeting frequencies in Physcomitrella. PLANT CELL REPORTS 2022; 41:153-173. [PMID: 34636965 PMCID: PMC8803787 DOI: 10.1007/s00299-021-02794-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Accepted: 09/23/2021] [Indexed: 06/13/2023]
Abstract
In Physcomitrella, whole-genome duplications affected the expression of about 3.7% of the protein-encoding genes, some of them relevant for DNA repair, resulting in a massively reduced gene-targeting frequency. Qualitative changes in gene expression after an autopolyploidization event, a pure duplication of the whole genome (WGD), might be relevant for a different regulation of molecular mechanisms between angiosperms growing in a life cycle with a dominant diploid sporophytic stage and the haploid-dominant mosses. Whereas angiosperms repair DNA double-strand breaks (DSB) preferentially via non-homologous end joining (NHEJ), in the moss Physcomitrella homologous recombination (HR) is the main DNA-DSB repair pathway. HR facilitates the precise integration of foreign DNA into the genome via gene targeting (GT). Here, we studied the influence of ploidy on gene expression patterns and GT efficiency in Physcomitrella using haploid plants and autodiploid plants, generated via an artificial WGD. Single cells (protoplasts) were transfected with a GT construct and material from different time-points after transfection was analysed by microarrays and SuperSAGE sequencing. In the SuperSAGE data, we detected 3.7% of the Physcomitrella genes as differentially expressed in response to the WGD event. Among the differentially expressed genes involved in DNA-DSB repair was an upregulated gene encoding the X-ray repair cross-complementing protein 4 (XRCC4), a key player in NHEJ. Analysing the GT efficiency, we observed that autodiploid plants were significantly GT suppressed (p < 0.001) attaining only one third of the expected GT rates. Hence, an alteration of global transcript patterns, including genes related to DNA repair, in autodiploid Physcomitrella plants correlated with a drastic suppression of HR.
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Affiliation(s)
- Christine Rempfer
- Plant Biotechnology, Faculty of Biology, University of Freiburg, Schaenzlestr. 1, 79104, Freiburg, Germany
- Spemann Graduate School of Biology and Medicine (SGBM), University of Freiburg, 79104, Freiburg, Germany
| | - Gertrud Wiedemann
- Plant Biotechnology, Faculty of Biology, University of Freiburg, Schaenzlestr. 1, 79104, Freiburg, Germany
- Department of Hematology and Central Hematology Laboratory, Inselspital, Bern University Hospital, University of Bern, 3010, Bern, Switzerland
| | - Gabriele Schween
- Plant Biotechnology, Faculty of Biology, University of Freiburg, Schaenzlestr. 1, 79104, Freiburg, Germany
- Corteva Agriscience, Pioneer Hi-Bred Northern Europe, Münstertäler Strasse 26, 79427, Eschbach, Germany
| | - Klaus L Kerres
- Plant Biotechnology, Faculty of Biology, University of Freiburg, Schaenzlestr. 1, 79104, Freiburg, Germany
| | - Jan M Lucht
- Plant Biotechnology, Faculty of Biology, University of Freiburg, Schaenzlestr. 1, 79104, Freiburg, Germany
- Scienceindustries, Nordstrasse 15, 8006, Zurich, Switzerland
| | - Ralf Horres
- GenXPro GmbH, Altenhöferallee 3, 60438, Frankfurt am Main, Germany
| | - Eva L Decker
- Plant Biotechnology, Faculty of Biology, University of Freiburg, Schaenzlestr. 1, 79104, Freiburg, Germany
| | - Ralf Reski
- Plant Biotechnology, Faculty of Biology, University of Freiburg, Schaenzlestr. 1, 79104, Freiburg, Germany.
- Spemann Graduate School of Biology and Medicine (SGBM), University of Freiburg, 79104, Freiburg, Germany.
- Signalling Research Centres BIOSS and CIBSS, Schaenzlestr. 18, 79104, Freiburg, Germany.
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7
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Chong GL, Tu SL. RNA-seq analysis of alternative pre-mRNA splicing regulation mediated by photoreceptors in Physcomitrium patens. Methods Enzymol 2022; 683:227-241. [PMID: 37087189 DOI: 10.1016/bs.mie.2022.08.022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
Abstract
Plants require light for carbon fixation in photosynthesis and activate a suite of signal-transducing photoreceptors that regulate plant development, ranging from seed germination to flowering and fruiting. Light perception by these photoreceptors triggers massive alterations of gene expression patterns and alternative splicing (AS) of many genes in plants. RNA sequencing (RNA-seq) is a powerful tool to study the full-length transcriptomes and AS of many model organisms, including the moss Physcomitrium patens. RNA-Seq has been applied successfully in transcriptome profiling of plants' developmental processes and responses to various environmental perturbations. Studies using this method provide valuable insights into the genetic networks of plants. Here we describe the use of a high-throughput Illumina sequencing system together with bioinformatics analysis software for transcriptome and AS analysis of Physcomitrium patens in response to red light (RL).
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8
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Chen Z, Wang W, Dong X, Pu X, Gao B, Liu L. Functional redundancy and divergence of β-carbonic anhydrases in Physcomitrella patens. PLANTA 2020; 252:20. [PMID: 32671568 DOI: 10.1007/s00425-020-03429-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Accepted: 07/10/2020] [Indexed: 06/11/2023]
Abstract
β-carbonic anhydrases, which function in regulating plant growth, C/N status, and stomata number, showed functional redundancy and divergence in Physcomitrella patens. Carbonic anhydrases (CAs) catalyze the interconversion of CO2 and HCO3-. Plants have three evolutionarily unrelated CA families: α-, β-, and γ-CAs. βCAs are abundant in plants and are involved in CO2 assimilation, stress responses, and stomata formation. Recent studies of βCAs have mainly examined C3 or C4 plants, whereas their functions in non-vascular plants are mostly unknown. In this study, phylogenetic analysis revealed that the evolution of βCAs were conserved between subaerial green algae and bryophytes after terrestrialization event, and βCAs from some cyanobacteria might begin evolving for the adaptation of terrestrial environment/habitat. In addition, we investigated the physiological roles of βCAs in the basal land plant Physcomitrella patens. High PpβCA expression levels in different tissues suggest that PpβCAs play important roles in development in P. patens. Plants treated with 1-10 mM NaHCO3 had higher fresh and dry weight, PpβCA expression, total CA activity, and photosynthetic yield (Fv/Fm) compared with water-treated plants. However, treatment with 10 mM NaHCO3 influenced the C/N status. Further study of six Ppβca single-gene mutants revealed that PpβCAs have functional redundancy and divergence in regulating the C/N ratio of plants and stomatal formation. This study provides new insight into the physiological roles of βCAs in basal land plants.
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Affiliation(s)
- Zexi Chen
- Department of Economic Plants and Biotechnology, Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650204, China
- University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Wenbo Wang
- Department of Economic Plants and Biotechnology, Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650204, China
- University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiumei Dong
- Department of Economic Plants and Biotechnology, Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650204, China
| | - Xiaojun Pu
- Department of Economic Plants and Biotechnology, Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650204, China
| | - Bei Gao
- State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong, 999077, China
| | - Li Liu
- Department of Economic Plants and Biotechnology, Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650204, China.
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei University, Wuhan, 430062, China.
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9
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Campos ML, Prado GS, Dos Santos VO, Nascimento LC, Dohms SM, da Cunha NB, Ramada MHS, Grossi-de-Sa MF, Dias SC. Mosses: Versatile plants for biotechnological applications. Biotechnol Adv 2020; 41:107533. [PMID: 32151692 DOI: 10.1016/j.biotechadv.2020.107533] [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: 09/02/2019] [Revised: 02/11/2020] [Accepted: 02/12/2020] [Indexed: 02/03/2023]
Abstract
Mosses have long been recognized as powerful experimental tools for the elucidation of complex processes in plant biology. Recent increases in the availability of sequenced genomes and mutant collections, the establishment of novel technologies for targeted mutagenesis, and the development of viable protocols for large-scale production in bioreactors are now transforming mosses into one of the most versatile tools for biotechnological applications. In the present review, we highlight the astonishing biotechnological potential of mosses and how these plants are being exploited for industrial, pharmaceutical, and environmental applications. We focus on the biological features that support their use as model organisms for basic and applied research, and how these are being leveraged to explore the biotechnological potential in an increasing number of species. Finally, we also provide an overview of the available moss cultivation protocols from an industrial perspective, offering insights into batch operations that are not yet well established or do not even exist in the literature. Our goal is to bolster the use of mosses as factories for the biosynthesis of molecules of interest and to show how these species can be harnessed for the generation of novel and commercially useful bioproducts.
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Affiliation(s)
- Marcelo Lattarulo Campos
- Integrative Plant Research Laboratory, Departamento de Botânica e Ecologia, Instituto de Biociências, Universidade Federal de Mato Grosso, Cuiabá, MT, Brazil.
| | - Guilherme Souza Prado
- Laboratório de Interação Molecular Planta-Praga, Embrapa Recursos Genéticos e Biotecnologia, Brasília, DF, Brazil; Programa de Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília, DF, Brazil
| | - Vanessa Olinto Dos Santos
- Laboratório de Interação Molecular Planta-Praga, Embrapa Recursos Genéticos e Biotecnologia, Brasília, DF, Brazil
| | - Lara Camelo Nascimento
- Centro de Análises Bioquímicas e Proteômicas, Universidade Católica de Brasília, Brasilia, DF, Brazil
| | - Stephan Machado Dohms
- Programa de Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília, DF, Brazil.
| | - Nicolau Brito da Cunha
- Centro de Análises Bioquímicas e Proteômicas, Universidade Católica de Brasília, Brasilia, DF, Brazil; Programa de Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília, DF, Brazil
| | - Marcelo Henrique Soller Ramada
- Centro de Análises Bioquímicas e Proteômicas, Universidade Católica de Brasília, Brasilia, DF, Brazil; Programa de Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília, DF, Brazil.
| | - Maria Fatima Grossi-de-Sa
- Laboratório de Interação Molecular Planta-Praga, Embrapa Recursos Genéticos e Biotecnologia, Brasília, DF, Brazil; Programa de Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília, DF, Brazil.
| | - Simoni Campos Dias
- Centro de Análises Bioquímicas e Proteômicas, Universidade Católica de Brasília, Brasilia, DF, Brazil; Programa de Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília, DF, Brazil; Programa de Pós-Graduação em Biologia Animal, Universidade de Brasília, Campus Darcy Ribeiro, Brasília, DF, Brazil.
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10
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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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11
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Arif MA, Hiss M, Tomek M, Busch H, Meyberg R, Tintelnot S, Reski R, Rensing SA, Frank W. ABA-Induced Vegetative Diaspore Formation in Physcomitrella patens. FRONTIERS IN PLANT SCIENCE 2019; 10:315. [PMID: 30941155 PMCID: PMC6433873 DOI: 10.3389/fpls.2019.00315] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Accepted: 02/26/2019] [Indexed: 05/08/2023]
Abstract
The phytohormone abscisic acid (ABA) is a pivotal regulator of gene expression in response to various environmental stresses such as desiccation, salt and cold causing major changes in plant development and physiology. Here we show that in the moss Physcomitrella patens exogenous application of ABA triggers the formation of vegetative diaspores (brachycytes or brood cells) that enable plant survival in unfavorable environmental conditions. Such diaspores are round-shaped cells characterized by the loss of the central vacuole, due to an increased starch and lipid storage preparing these cells for growth upon suitable environmental conditions. To gain insights into the gene regulation underlying these developmental and physiological changes, we analyzed early transcriptome changes after 30, 60, and 180 min of ABA application and identified 1,030 differentially expressed genes. Among these, several groups can be linked to specific morphological and physiological changes during diaspore formation, such as genes involved in cell wall modifications. Furthermore, almost all members of ABA-dependent signaling and regulation were transcriptionally induced. Network analysis of transcription-associated genes revealed a large overlap of our study with ABA-dependent regulation in response to dehydration, cold stress, and UV-B light, indicating a fundamental function of ABA in diverse stress responses in moss. We also studied the evolutionary conservation of ABA-dependent regulation between moss and the seed plant Arabidopsis thaliana pointing to an early evolution of ABA-mediated stress adaptation during the conquest of the terrestrial habitat by plants.
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Affiliation(s)
- M. Asif Arif
- Plant Molecular Cell Biology, Department Biology I, Ludwig-Maximilians-Universität München, LMU Biocenter, Planegg-Martinsried, Germany
| | - Manuel Hiss
- Plant Cell Biology, Faculty of Biology, University of Marburg, Marburg, Germany
| | - Marta Tomek
- Plant Biotechnology, Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Hauke Busch
- Lübeck Institute of Experimental Dermatology, University of Lübeck, Lübeck, Germany
| | - Rabea Meyberg
- Plant Cell Biology, Faculty of Biology, University of Marburg, Marburg, Germany
| | - Stefanie Tintelnot
- Plant Biotechnology, Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Ralf Reski
- Plant Biotechnology, Faculty of Biology, University of Freiburg, Freiburg, Germany
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Freiburg, Germany
| | - Stefan A. Rensing
- Plant Cell Biology, Faculty of Biology, University of Marburg, Marburg, Germany
- BIOSS Centre for Biological Signalling Studies, University of Freiburg, Freiburg, Germany
- *Correspondence: Stefan A. Rensing, Wolfgang Frank,
| | - Wolfgang Frank
- Plant Molecular Cell Biology, Department Biology I, Ludwig-Maximilians-Universität München, LMU Biocenter, Planegg-Martinsried, Germany
- *Correspondence: Stefan A. Rensing, Wolfgang Frank,
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12
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Zhou D, Tan L, Li J, Liu T, Hu Y, Li Y, Kawamoto S, Liu C, Guo S, Wang A. Identification of Homologous Recombination Events in Mouse Embryonic Stem Cells Using Southern Blotting and Polymerase Chain Reaction. J Vis Exp 2018. [PMID: 30531726 DOI: 10.3791/58467] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Relative to the issues of off-target effects and the difficulty of inserting a long DNA fragment in the application of designer nucleases for genome editing, embryonic stem (ES) cell-based gene-targeting technology does not have these shortcomings and is widely used to modify animal/mouse genome ranging from large deletions/insertions to single nucleotide substitutions. Notably, identifying the relatively few homologous recombination (HR) events necessary to obtain desired ES clones is a key step, which demands accurate and reliable methods. Southern blotting and/or conventional PCR are often utilized for this purpose. Here, we describe the detailed procedures of using those two methods to identify HR events that occurred in mouse ES cells in which the endogenous Myh9 gene is intended to be disrupted and replaced by cDNAs encoding other nonmuscle myosin heavy chain IIs (NMHC IIs). The whole procedure of Southern blotting includes the construction of targeting vector(s), electroporation, drug selection, the expansion and storage of ES cells/clones, the preparation, digestion, and blotting of genomic DNA (gDNA), the hybridization and washing of probe(s), and a final step of autoradiography on the X-ray films. PCR can be performed directly with prepared and diluted gDNA. To obtain ideal results, the probes and restriction enzyme (RE) cutting sites for Southern blotting and the primers for PCR should be carefully planned. Though the execution of Southern blotting is time-consuming and labor-intensive and PCR results have false positives, the correct identification by Southern blotting and the rapid screening by PCR allow the sole or combined application of these methods described in this paper to be widely used and consulted by most labs in the identification of genotypes of ES cells and genetically modified animals.
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Affiliation(s)
- Dan Zhou
- Lab of Animal Models and Functional Genomics (LAMFG), The Key Laboratory of Animal Vaccine & Protein Engineering, College of Veterinary Medicine, Hunan Agricultural University (HUNAU); Department of Pathology, Georgetown University Medical School
| | - Lei Tan
- Lab of Animal Models and Functional Genomics (LAMFG), The Key Laboratory of Animal Vaccine & Protein Engineering, College of Veterinary Medicine, Hunan Agricultural University (HUNAU)
| | - Jian Li
- College of Food Science and Technology, Hunan Agricultural University (HUNAU)
| | - Tanbin Liu
- Lab of Animal Models and Functional Genomics (LAMFG), The Key Laboratory of Animal Vaccine & Protein Engineering, College of Veterinary Medicine, Hunan Agricultural University (HUNAU)
| | - Yi Hu
- Lab of Animal Models and Functional Genomics (LAMFG), The Key Laboratory of Animal Vaccine & Protein Engineering, College of Veterinary Medicine, Hunan Agricultural University (HUNAU)
| | - Yalan Li
- Lab of Animal Models and Functional Genomics (LAMFG), The Key Laboratory of Animal Vaccine & Protein Engineering, College of Veterinary Medicine, Hunan Agricultural University (HUNAU)
| | - Sachiyo Kawamoto
- Lab of Molecular Cardiology (LMC), National Heart, Lung, and Blood Institute (NHLBI)/National Institutes of Health (NIH)
| | - Chengyu Liu
- Transgenic Core, National Heart, Lung, and Blood Institute (NHLBI)/National Institutes of Health (NIH)
| | - Shiyin Guo
- College of Food Science and Technology, Hunan Agricultural University (HUNAU);
| | - Aibing Wang
- Lab of Animal Models and Functional Genomics (LAMFG), The Key Laboratory of Animal Vaccine & Protein Engineering, College of Veterinary Medicine, Hunan Agricultural University (HUNAU);
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13
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Ulfstedt M, Hu GZ, Johansson M, Ronne H. Testing of Auxotrophic Selection Markers for Use in the Moss Physcomitrella Provides New Insights into the Mechanisms of Targeted Recombination. FRONTIERS IN PLANT SCIENCE 2017; 8:1850. [PMID: 29163580 PMCID: PMC5675891 DOI: 10.3389/fpls.2017.01850] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2017] [Accepted: 10/11/2017] [Indexed: 05/30/2023]
Abstract
The moss Physcomitrella patens is unique among plants in that homologous recombination can be used to knock out genes, just like in yeast. Furthermore, transformed plasmids can be rescued from Physcomitrella back into Escherichia coli, similar to yeast. In the present study, we have tested if a third important tool from yeast molecular genetics, auxotrophic selection markers, can be used in Physcomitrella. Two auxotrophic moss strains were made by knocking out the PpHIS3 gene encoding imidazoleglycerol-phosphate dehydratase, and the PpTRP1 gene encoding phosphoribosylanthranilate isomerase, disrupting the biosynthesis of histidine and tryptophan, respectively. The resulting PpHIS3Δ and PpTRP1Δ knockout strains were unable to grow on medium lacking histidine or tryptophan. The PpHIS3Δ strain was used to test selection of transformants by complementation of an auxotrophic marker. We found that the PpHIS3Δ strain could be complemented by transformation with a plasmid expressing the PpHIS3 gene from the CaMV 35S promoter, allowing the strain to grow on medium lacking histidine. Both linearized plasmids and circular supercoiled plasmids could complement the auxotrophic marker, and plasmids from both types of transformants could be rescued back into E. coli. Plasmids rescued from circular transformants were identical to the original plasmid, whereas plasmids rescued from linearized transformants had deletions generated by recombination between micro-homologies in the plasmids. Our results show that cloning by complementation of an auxotrophic marker works in Physcomitrella, which opens the door for using auxotrophic selection markers in moss molecular genetics. This will facilitate the adaptation of shuttle plasmid dependent methods from yeast molecular genetics for use in Physcomitrella.
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Affiliation(s)
- Mikael Ulfstedt
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Guo-Zhen Hu
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Monika Johansson
- Department of Molecular Sciences, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Hans Ronne
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden
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14
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Rawat A, Brejšková L, Hála M, Cvrčková F, Žárský V. The Physcomitrella patens exocyst subunit EXO70.3d has distinct roles in growth and development, and is essential for completion of the moss life cycle. THE NEW PHYTOLOGIST 2017; 216:438-454. [PMID: 28397275 DOI: 10.1111/nph.14548] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2017] [Accepted: 02/24/2017] [Indexed: 05/28/2023]
Abstract
The exocyst, an evolutionarily conserved secretory vesicle-tethering complex, spatially controls exocytosis and membrane turnover in fungi, metazoans and plants. The exocyst subunit EXO70 exists in multiple paralogs in land plants, forming three conserved clades with assumed distinct roles. Here we report functional analysis of the first moss exocyst subunit to be studied, Physcomitrella patens PpEXO70.3d (Pp1s97_91V6), from the, as yet, poorly characterized EXO70.3 clade. Following phylogenetic analysis to confirm the presence of three ancestral land plant EXO70 clades outside angiosperms, we prepared and phenotypically characterized loss-of-function Ppexo70.3d mutants and localized PpEXO70.3d in vivo using green fluorescent protein-tagged protein expression. Disruption of PpEXO70.3d caused pleiotropic cell elongation and differentiation defects in protonemata, altered response towards exogenous auxin, increased endogenous IAA concentrations, along with defects in bud and gametophore development. During mid-archegonia development, an abnormal egg cell is formed and subsequently collapses, resulting in mutant sterility. Mutants exhibited altered cell wall and cuticle deposition, as well as compromised cytokinesis, consistent with the protein localization to the cell plate. Despite some functional redundancy allowing survival of moss lacking PpEXO70.3d, this subunit has an essential role in the moss life cycle, indicating sub-functionalization within the moss EXO70 family.
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Affiliation(s)
- Anamika Rawat
- Laboratory of Cell Morphogenesis, Department of Experimental Plant Biology, Faculty of Science, Charles University, Viničná 5, 128 44, Prague 2, Czech Republic
- Institute of Experimental Botany, Academy of Sciences of the Czech Republic, 165 02, Prague 6, Czech Republic
| | - Lucie Brejšková
- Laboratory of Cell Morphogenesis, Department of Experimental Plant Biology, Faculty of Science, Charles University, Viničná 5, 128 44, Prague 2, Czech Republic
- Institute of Experimental Botany, Academy of Sciences of the Czech Republic, 165 02, Prague 6, Czech Republic
| | - Michal Hála
- Laboratory of Cell Morphogenesis, Department of Experimental Plant Biology, Faculty of Science, Charles University, Viničná 5, 128 44, Prague 2, Czech Republic
- Institute of Experimental Botany, Academy of Sciences of the Czech Republic, 165 02, Prague 6, Czech Republic
| | - Fatima Cvrčková
- Laboratory of Cell Morphogenesis, Department of Experimental Plant Biology, Faculty of Science, Charles University, Viničná 5, 128 44, Prague 2, Czech Republic
| | - Viktor Žárský
- Laboratory of Cell Morphogenesis, Department of Experimental Plant Biology, Faculty of Science, Charles University, Viničná 5, 128 44, Prague 2, Czech Republic
- Institute of Experimental Botany, Academy of Sciences of the Czech Republic, 165 02, Prague 6, Czech Republic
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15
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Horst NA, Reski R. Microscopy of Physcomitrella patens sperm cells. PLANT METHODS 2017; 13:33. [PMID: 28491120 PMCID: PMC5424408 DOI: 10.1186/s13007-017-0186-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Accepted: 05/02/2017] [Indexed: 05/03/2023]
Abstract
BACKGROUND Archegoniates (bryophytes, ferns and gymnosperms), such as the moss Physcomitrella patens, possess freely motile sperm cells (spermatozoids) which reach the egg cell via surface water. Although these motile flagellated sperm cells are a traditional botanical subject, they have not been thoroughly analysed in the flagship non-seed plant model species P. patens. Protocols are required to determine the behaviour of wild type sperms as a prerequisite for future research such as the characterization of mutants or factors that influence sperm number, morphology, viability and motility. RESULTS Here, we present protocols for the observation of fixed, as well as live sperms utilizing a standard microscope at intermediate magnifications. Fixed samples can be used for the fast assessment of sperm number and morphology. To determine functionality, the observation of live sperms is required. Protocols for determining both sperm motility and viability are provided, allowing both parameters to be distinguished. CONCLUSIONS These step-by-step protocols are particularly useful for researchers so far not familiar with the analysis of motile gametes and are meant to aid the establishment and improvement of these analyses in order to stimulate research on spermatogenesis in the moss model species P. patens.
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Affiliation(s)
- Nelly A. Horst
- Plant Biotechnology, Faculty of Biology, University of Freiburg, Schaenzlestr. 1, 79104 Freiburg, Germany
| | - Ralf Reski
- Plant Biotechnology, Faculty of Biology, University of Freiburg, Schaenzlestr. 1, 79104 Freiburg, Germany
- BIOSS – Centre for Biological Signalling Studies, University of Freiburg, Schaenzlestr. 18, 79104 Freiburg, Germany
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16
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Chater CC, Caine RS, Tomek M, Wallace S, Kamisugi Y, Cuming AC, Lang D, MacAlister CA, Casson S, Bergmann DC, Decker EL, Frank W, Gray JE, Fleming A, Reski R, Beerling DJ. Origin and function of stomata in the moss Physcomitrella patens. NATURE PLANTS 2016; 2:16179. [PMID: 27892923 PMCID: PMC5131878 DOI: 10.1038/nplants.2016.179] [Citation(s) in RCA: 96] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2016] [Accepted: 10/20/2016] [Indexed: 05/02/2023]
Abstract
Stomata are microscopic valves on plant surfaces that originated over 400 million years (Myr) ago and facilitated the greening of Earth's continents by permitting efficient shoot-atmosphere gas exchange and plant hydration1. However, the core genetic machinery regulating stomatal development in non-vascular land plants is poorly understood2-4 and their function has remained a matter of debate for a century5. Here, we show that genes encoding the two basic helix-loop-helix proteins PpSMF1 (SPEECH, MUTE and FAMA-like) and PpSCREAM1 (SCRM1) in the moss Physcomitrella patens are orthologous to transcriptional regulators of stomatal development in the flowering plant Arabidopsis thaliana and essential for stomata formation in moss. Targeted P. patens knockout mutants lacking either PpSMF1 or PpSCRM1 develop gametophytes indistinguishable from wild-type plants but mutant sporophytes lack stomata. Protein-protein interaction assays reveal heterodimerization between PpSMF1 and PpSCRM1, which, together with moss-angiosperm gene complementations6, suggests deep functional conservation of the heterodimeric SMF1 and SCRM1 unit is required to activate transcription for moss stomatal development, as in A. thaliana7. Moreover, stomata-less sporophytes of ΔPpSMF1 and ΔPpSCRM1 mutants exhibited delayed dehiscence, implying stomata might have promoted dehiscence in the first complex land-plant sporophytes.
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Affiliation(s)
- Caspar C. Chater
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de Mexico, Cuernavaca, Mexico
| | - Robert S. Caine
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield S10 2TN, UK
| | - Marta Tomek
- Plant Biotechnology, Faculty of Biology, University of Freiburg, Schaenzlestr. 1, 79104 Freiburg, Germany
| | - Simon Wallace
- Royal College of Veterinary Surgeons, Belgravia House, 62-64 Horseferry Rd, London SW1P 2AF, UK
| | - Yasuko Kamisugi
- Centre for Plant Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - Andrew C. Cuming
- Centre for Plant Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - Daniel Lang
- Plant Biotechnology, Faculty of Biology, University of Freiburg, Schaenzlestr. 1, 79104 Freiburg, Germany
| | - Cora A. MacAlister
- Department of Molecular Cellular and Developmental Biology, University of Michigan, Ann Arbor, Michigan, 48109-1048, USA
| | - Stuart Casson
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield S10 2TN, UK
| | | | - Eva L. Decker
- Plant Biotechnology, Faculty of Biology, University of Freiburg, Schaenzlestr. 1, 79104 Freiburg, Germany
| | - Wolfgang Frank
- Plant Molecular Cell Biology, Faculty of Biology, Ludwig-Maximilians-Universität München, LMU Biocenter, Großhaderner Straße 2, 82152 Planegg-Martinsried, Germany
| | - Julie E. Gray
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield S10 2TN, UK
| | - Andrew Fleming
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield S10 2TN, UK
| | - Ralf Reski
- Plant Biotechnology, Faculty of Biology, University of Freiburg, Schaenzlestr. 1, 79104 Freiburg, Germany
- BIOSS – Centre for Biological Signalling Studies, 79104 Freiburg, Germany
| | - David J. Beerling
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield S10 2TN, UK
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17
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Caine RS, Chater CC, Kamisugi Y, Cuming AC, Beerling DJ, Gray JE, Fleming AJ. An ancestral stomatal patterning module revealed in the non-vascular land plant Physcomitrella patens. Development 2016; 143:3306-14. [PMID: 27407102 PMCID: PMC5047656 DOI: 10.1242/dev.135038] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2016] [Accepted: 05/26/2016] [Indexed: 11/20/2022]
Abstract
The patterning of stomata plays a vital role in plant development and has emerged as a paradigm for the role of peptide signals in the spatial control of cellular differentiation. Research in Arabidopsis has identified a series of epidermal patterning factors (EPFs), which interact with an array of membrane-localised receptors and associated proteins (encoded by ERECTA and TMM genes) to control stomatal density and distribution. However, although it is well-established that stomata arose very early in the evolution of land plants, until now it has been unclear whether the established angiosperm stomatal patterning system represented by the EPF/TMM/ERECTA module reflects a conserved, universal mechanism in the plant kingdom. Here, we use molecular genetics to show that the moss Physcomitrella patens has conserved homologues of angiosperm EPF, TMM and at least one ERECTA gene that function together to permit the correct patterning of stomata and that, moreover, elements of the module retain function when transferred to Arabidopsis Our data characterise the stomatal patterning system in an evolutionarily distinct branch of plants and support the hypothesis that the EPF/TMM/ERECTA module represents an ancient patterning system.
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Affiliation(s)
- Robert S Caine
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield S10 2TN, UK
| | - Caspar C Chater
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield S10 2TN, UK
| | - Yasuko Kamisugi
- Centre for Plant Science, University of Leeds, Leeds LS2 9JT, UK
| | - Andrew C Cuming
- Centre for Plant Science, University of Leeds, Leeds LS2 9JT, UK
| | - David J Beerling
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield S10 2TN, UK
| | - Julie E Gray
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield S10 2TN, UK
| | - Andrew J Fleming
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield S10 2TN, UK
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18
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The Transcriptional Response to DNA-Double-Strand Breaks in Physcomitrella patens. PLoS One 2016; 11:e0161204. [PMID: 27537368 PMCID: PMC4990234 DOI: 10.1371/journal.pone.0161204] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2016] [Accepted: 08/01/2016] [Indexed: 12/11/2022] Open
Abstract
The model bryophyte Physcomitrella patens is unique among plants in supporting the generation of mutant alleles by facile homologous recombination-mediated gene targeting (GT). Reasoning that targeted transgene integration occurs through the capture of transforming DNA by the homology-dependent pathway for DNA double-strand break (DNA-DSB) repair, we analysed the genome-wide transcriptomic response to bleomycin-induced DNA damage and generated mutants in candidate DNA repair genes. Massively parallel (Illumina) cDNA sequencing identified potential participants in gene targeting. Transcripts encoding DNA repair proteins active in multiple repair pathways were significantly up-regulated. These included Rad51, CtIP, DNA ligase 1, Replication protein A and ATR in homology-dependent repair, Xrcc4, DNA ligase 4, Ku70 and Ku80 in non-homologous end-joining and Rad1, Tebichi/polymerase theta, PARP in microhomology-mediated end-joining. Differentially regulated cell-cycle components included up-regulated Rad9 and Hus1 DNA-damage-related checkpoint proteins and down-regulated D-type cyclins and B-type CDKs, commensurate with the imposition of a checkpoint at G2 of the cell cycle characteristic of homology-dependent DNA-DSB repair. Candidate genes, including ATP-dependent chromatin remodelling helicases associated with repair and recombination, were knocked out and analysed for growth defects, hypersensitivity to DNA damage and reduced GT efficiency. Targeted knockout of PpCtIP, a cell-cycle activated mediator of homology-dependent DSB resection, resulted in bleomycin-hypersensitivity and greatly reduced GT efficiency.
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19
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Stevenson SR, Kamisugi Y, Trinh CH, Schmutz J, Jenkins JW, Grimwood J, Muchero W, Tuskan GA, Rensing SA, Lang D, Reski R, Melkonian M, Rothfels CJ, Li FW, Larsson A, Wong GKS, Edwards TA, Cuming AC. Genetic Analysis of Physcomitrella patens Identifies ABSCISIC ACID NON-RESPONSIVE, a Regulator of ABA Responses Unique to Basal Land Plants and Required for Desiccation Tolerance. THE PLANT CELL 2016; 28:1310-27. [PMID: 27194706 PMCID: PMC4944411 DOI: 10.1105/tpc.16.00091] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2016] [Revised: 04/18/2016] [Accepted: 05/13/2016] [Indexed: 05/19/2023]
Abstract
The anatomically simple plants that first colonized land must have acquired molecular and biochemical adaptations to drought stress. Abscisic acid (ABA) coordinates responses leading to desiccation tolerance in all land plants. We identified ABA nonresponsive mutants in the model bryophyte Physcomitrella patens and genotyped a segregating population to map and identify the ABA NON-RESPONSIVE (ANR) gene encoding a modular protein kinase comprising an N-terminal PAS domain, a central EDR domain, and a C-terminal MAPKKK-like domain. anr mutants fail to accumulate dehydration tolerance-associated gene products in response to drought, ABA, or osmotic stress and do not acquire ABA-dependent desiccation tolerance. The crystal structure of the PAS domain, determined to 1.7-Å resolution, shows a conserved PAS-fold that dimerizes through a weak dimerization interface. Targeted mutagenesis of a conserved tryptophan residue within the PAS domain generates plants with ABA nonresponsive growth and strongly attenuated ABA-responsive gene expression, whereas deleting this domain retains a fully ABA-responsive phenotype. ANR orthologs are found in early-diverging land plant lineages and aquatic algae but are absent from more recently diverged vascular plants. We propose that ANR genes represent an ancestral adaptation that enabled drought stress survival of the first terrestrial colonizers but were lost during land plant evolution.
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Affiliation(s)
- Sean R Stevenson
- Centre for Plant Sciences, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - Yasuko Kamisugi
- Centre for Plant Sciences, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - Chi H Trinh
- Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - Jeremy Schmutz
- Department of Energy Joint Genome Institute, Walnut Creek, California 94598 HudsonAlpha Institute for Biotechnology, Huntsville, Alabama 35806
| | - Jerry W Jenkins
- Department of Energy Joint Genome Institute, Walnut Creek, California 94598 HudsonAlpha Institute for Biotechnology, Huntsville, Alabama 35806
| | - Jane Grimwood
- Department of Energy Joint Genome Institute, Walnut Creek, California 94598 HudsonAlpha Institute for Biotechnology, Huntsville, Alabama 35806
| | - Wellington Muchero
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831
| | - Gerald A Tuskan
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831
| | - Stefan A Rensing
- University of Marburg, Plant Cell Biology, D-35043 Marburg, Germany BIOSS Centre for Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany
| | - Daniel Lang
- BIOSS Centre for Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany Plant Biotechnology, Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany
| | - Ralf Reski
- BIOSS Centre for Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany Plant Biotechnology, Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany
| | | | - Carl J Rothfels
- Department of Integrative Biology, University of California, Berkeley California 94720-3140
| | - Fay-Wei Li
- Department of Biology, Duke University, Durham, North Carolina 27708
| | - Anders Larsson
- Uppsala University, Systematic Biology, 752 36 Uppsala, Sweden
| | - Gane K-S Wong
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta T6G 2E9, Canada Department of Medicine, University of Alberta, Edmonton, Alberta T6G 2E1, Canada BGI-Shenzhen, Shenzhen 518083, China
| | - Thomas A Edwards
- Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - Andrew C Cuming
- Centre for Plant Sciences, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, United Kingdom
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20
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Generating Targeted Gene Knockout Lines in Physcomitrella patens to Study Evolution of Stress-Responsive Mechanisms. Methods Mol Biol 2016. [PMID: 26867627 DOI: 10.1007/978-1-4939-3356-3_18] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/30/2023]
Abstract
The moss Physcomitrella patens possesses highly efficient homologous recombination allowing targeted gene manipulations and displays many features of the early land plants including high tolerance to abiotic stresses. It is therefore an invaluable model organism for studies of gene functions and comparative studies of evolution of stress responses in plants. Here, we describe a method for generating targeted gene knockout lines in P. patens using a polyethylene glycol-mediated transformation of protoplasts including basic in vitro growth, propagation, and maintenance techniques.
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21
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Horst NA, Katz A, Pereman I, Decker EL, Ohad N, Reski R. A single homeobox gene triggers phase transition, embryogenesis and asexual reproduction. NATURE PLANTS 2016; 2:15209. [PMID: 27250874 DOI: 10.1038/nplants.2015.209] [Citation(s) in RCA: 88] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2015] [Accepted: 11/27/2015] [Indexed: 05/17/2023]
Abstract
Plants characteristically alternate between haploid gametophytic and diploid sporophytic stages. Meiosis and fertilization respectively initiate these two different ontogenies(1). Genes triggering ectopic embryo development on vegetative sporophytic tissues are well described(2,3); however, a genetic control of embryo development from gametophytic tissues remains elusive. Here, in the moss Physcomitrella patens we show that ectopic overexpression of the homeobox gene BELL1 induces embryo formation and subsequently reproductive diploid sporophytes from specific gametophytic cells without fertilization. In line with this, BELL1 loss-of-function mutants have a wild-type phenotype, except that their egg cells are bigger and unable to form embryos. Our results identify BELL1 as a master regulator for the gametophyte-to-sporophyte transition in P. patens and provide mechanistic insights into the evolution of embryos that can generate multicellular diploid sporophytes. This developmental innovation facilitated the colonization of land by plants about 500 million years ago(4) and thus shaped our current ecosystems.
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Affiliation(s)
- Nelly A Horst
- Plant Biotechnology, Faculty of Biology, University of Freiburg, Schaenzlestr. 1, 79104 Freiburg, Germany
| | - Aviva Katz
- Department of Molecular Biology and Ecology of Plants, Tel-Aviv University, Tel-Aviv 69978, Israel
| | - Idan Pereman
- Department of Molecular Biology and Ecology of Plants, Tel-Aviv University, Tel-Aviv 69978, Israel
| | - Eva L Decker
- Plant Biotechnology, Faculty of Biology, University of Freiburg, Schaenzlestr. 1, 79104 Freiburg, Germany
| | - Nir Ohad
- Department of Molecular Biology and Ecology of Plants, Tel-Aviv University, Tel-Aviv 69978, Israel
- The Manna Center Program for Food Safety &Security, Tel Aviv University, Tel-Aviv 69978, Israel
| | - Ralf Reski
- Plant Biotechnology, Faculty of Biology, University of Freiburg, Schaenzlestr. 1, 79104 Freiburg, Germany
- BIOSS - Centre for Biological Signalling Studies, 79104 Freiburg, Germany
- FRIAS - Freiburg Institute for Advanced Studies, 79104 Freiburg, Germany
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Kamisugi Y, Mitsuya S, El‐Shami M, Knight CD, Cuming AC, Baker A. Giant peroxisomes in a moss (Physcomitrella patens) peroxisomal biogenesis factor 11 mutant. THE NEW PHYTOLOGIST 2016; 209:576-89. [PMID: 26542980 PMCID: PMC4738463 DOI: 10.1111/nph.13739] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2015] [Accepted: 10/01/2015] [Indexed: 05/22/2023]
Abstract
Peroxisomal biogenesis factor 11 (PEX11) proteins are found in yeasts, mammals and plants, and play a role in peroxisome morphology and regulation of peroxisome division. The moss Physcomitrella patens has six PEX11 isoforms which fall into two subfamilies, similar to those found in monocots and dicots. We carried out targeted gene disruption of the Phypa_PEX11-1 gene and compared the morphological and cellular phenotypes of the wild-type and mutant strains. The mutant grew more slowly and the development of gametophores was retarded. Mutant chloronemal filaments contained large cellular structures which excluded all other cellular organelles. Expression of fluorescent reporter proteins revealed that the mutant strain had greatly enlarged peroxisomes up to 10 μm in diameter. Expression of a vacuolar membrane marker confirmed that the enlarged structures were not vacuoles, or peroxisomes sequestered within vacuoles as a result of pexophagy. Phypa_PEX11 targeted to peroxisome membranes could rescue the knock out phenotype and interacted with Fission1 on the peroxisome membrane. Moss PEX11 functions in peroxisome division similar to PEX11 in other organisms but the mutant phenotype is more extreme and environmentally determined, making P. patens a powerful system in which to address mechanisms of peroxisome proliferation and division.
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Affiliation(s)
- Yasuko Kamisugi
- Centre for Plant SciencesFaculty of Biological SciencesUniversity of LeedsLeedsLS2 9JTUK
| | - Shiro Mitsuya
- Centre for Plant SciencesFaculty of Biological SciencesUniversity of LeedsLeedsLS2 9JTUK
| | - Mahmoud El‐Shami
- Centre for Plant SciencesFaculty of Biological SciencesUniversity of LeedsLeedsLS2 9JTUK
| | - Celia D. Knight
- Centre for Plant SciencesFaculty of Biological SciencesUniversity of LeedsLeedsLS2 9JTUK
| | - Andrew C. Cuming
- Centre for Plant SciencesFaculty of Biological SciencesUniversity of LeedsLeedsLS2 9JTUK
| | - Alison Baker
- Centre for Plant SciencesFaculty of Biological SciencesUniversity of LeedsLeedsLS2 9JTUK
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Wendeler E, Zobell O, Chrost B, Reiss B. Recombination products suggest the frequent occurrence of aberrant gene replacement in the moss Physcomitrella patens. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2015; 81:548-558. [PMID: 25557140 DOI: 10.1111/tpj.12749] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2014] [Revised: 11/20/2014] [Accepted: 12/11/2014] [Indexed: 06/04/2023]
Abstract
In gene replacement, a variant of gene targeting, transformed DNA integrates into the genome by homologous recombination (HR) to replace resident sequences. Gene replacement in the moss Physcomitrella patens is extremely efficient, but often large amounts of additional DNA are integrated at the target locus. A detailed analysis of recombination junctions of PpCOL2 gene knockout mutants shows that the integrated DNA can be highly rearranged. Our data suggest that the replaced sequences were excised by HR and became integrated back into the genome by non-homologous end-joining (NHEJ). RAD51-mediated strand-invasion and subsequent strand-exchange is central to the two-end invasion pathway, the major gene replacement pathway in yeast. In this pathway, integration is initiated by the free ends of a single replacement vector-derived donor molecule which then integrates as an entity. Gene replacement in P. patens is entirely RAD51-dependent suggesting the existence of a pathway mechanistically similar to two-end invasion. However, invasion of the two ends does not seem to be stringently coordinated in P. patens. Actually, often only one fragment end became integrated by HR, or one-sided integration of two independent donor fragments occurred simultaneously leading to a double-strand break that is subsequently sealed by NHEJ and thus causes the observed rearrangements.
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Affiliation(s)
- Edelgard Wendeler
- Max-Planck-Institute for Plant Breeding Research, Carl-von-Linne-Weg 10, 50829, Cologne, Germany
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24
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Wallace S, Chater CC, Kamisugi Y, Cuming AC, Wellman CH, Beerling DJ, Fleming AJ. Conservation of Male Sterility 2 function during spore and pollen wall development supports an evolutionarily early recruitment of a core component in the sporopollenin biosynthetic pathway. THE NEW PHYTOLOGIST 2015; 205:390-401. [PMID: 25195943 DOI: 10.1111/nph.13012] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2014] [Accepted: 07/25/2014] [Indexed: 05/07/2023]
Abstract
The early evolution of plants required the acquisition of a number of key adaptations to overcome physiological difficulties associated with survival on land. One of these was a tough sporopollenin wall that enclosed reproductive propagules and provided protection from desiccation and UV-B radiation. All land plants possess such walled spores (or their derived homologue, pollen). We took a reverse genetics approach, consisting of knock-out and complementation experiments to test the functional conservation of the sporopollenin-associated gene MALE STERILTY 2 (which is essential for pollen wall development in Arabidopsis thaliana) in the bryophyte Physcomitrella patens. Knock-outs of a putative moss homologue of the A. thaliana MS2 gene, which is highly expressed in the moss sporophyte, led to spores with highly defective walls comparable to that observed in the A. thaliana ms2 mutant, and extremely compromised germination. Conversely, the moss MS2 gene could not rescue the A. thaliana ms2 phenotype. The results presented here suggest that a core component of the biochemical and developmental pathway required for angiosperm pollen wall development was recruited early in land plant evolution but the continued increase in pollen wall complexity observed in angiosperms has been accompanied by divergence in MS2 gene function.
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Affiliation(s)
- Simon Wallace
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, S10 2TN, UK
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25
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Decker EL, Wiedemann G, Reski R. Gene Targeting for Precision Glyco-Engineering: Production of Biopharmaceuticals Devoid of Plant-Typical Glycosylation in Moss Bioreactors. Methods Mol Biol 2015; 1321:213-24. [PMID: 26082225 DOI: 10.1007/978-1-4939-2760-9_15] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Abstract
One of the main challenges for the production of biopharmaceuticals in plant-based systems is the modulation of plant-specific glycosylation patterns towards a humanized form. Posttranslational modifications in plants are similar to those in humans, but several differences affect product quality and efficacy and can also cause immune responses in patients. In the moss Physcomitrella patens highly efficient gene targeting via homologous recombination enables glyco-engineering to obtain suitable platform lines for the production of recombinant proteins and biopharmaceuticals. Here we describe the methods which are effective for creating gene targeting constructs and transgenic moss lines as well as confirming successful homologous integration of the constructs and modification of target gene expression.
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Affiliation(s)
- Eva L Decker
- Plant Biotechnology, Faculty of Biology, University of Freiburg, Freiburg, Germany
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26
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Finiuk NS, Chaplya AY, Mitina NY, Boiko NM, Lobachevska OV, Miahkota OS, Yemets AI, Blume YB, Zaichenko OS, Stoika RS. Genetic transformation of moss Ceratodon purpureus by means of polycationic carriers of DNA. CYTOL GENET+ 2014. [DOI: 10.3103/s0095452714060048] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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27
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Systematic targeted gene deletion using the gene-synthesis method in fission yeast. J Microbiol Methods 2014; 106:72-77. [DOI: 10.1016/j.mimet.2014.08.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2014] [Revised: 08/04/2014] [Accepted: 08/11/2014] [Indexed: 11/24/2022]
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28
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Charlot F, Chelysheva L, Kamisugi Y, Vrielynck N, Guyon A, Epert A, Le Guin S, Schaefer DG, Cuming AC, Grelon M, Nogué F. RAD51B plays an essential role during somatic and meiotic recombination in Physcomitrella. Nucleic Acids Res 2014; 42:11965-78. [PMID: 25260587 PMCID: PMC4231755 DOI: 10.1093/nar/gku890] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The eukaryotic RecA homologue Rad51 is a key factor in homologous recombination and recombinational repair. Rad51-like proteins have been identified in yeast (Rad55, Rad57 and Dmc1), plants and vertebrates (RAD51B, RAD51C, RAD51D, XRCC2, XRCC3 and DMC1). RAD51 and DMC1 are the strand-exchange proteins forming a nucleofilament for strand invasion, however, the function of the paralogues in the process of homologous recombination is less clear. In yeast the two Rad51 paralogues, Rad55 and Rad57, have been shown to be involved in somatic and meiotic HR and they are essential to the formation of the Rad51/DNA nucleofilament counterbalancing the anti-recombinase activity of the SRS2 helicase. Here, we examined the role of RAD51B in the model bryophyte Physcomitrella patens. Mutant analysis shows that RAD51B is essential for the maintenance of genome integrity, for resistance to DNA damaging agents and for gene targeting. Furthermore, we set up methods to investigate meiosis in Physcomitrella and we demonstrate that the RAD51B protein is essential for meiotic homologous recombination. Finally, we show that all these functions are independent of the SRS2 anti-recombinase protein, which is in striking contrast to what is found in budding yeast where the RAD51 paralogues are fully dependent on the SRS2 anti-recombinase function.
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Affiliation(s)
- Florence Charlot
- INRA, Institut Jean-Pierre Bourgin UMR1318, Saclay Plant Sciences, Versailles, France AgroParisTech, Institut Jean-Pierre Bourgin UMR1318, Saclay Plant Sciences, Versailles, France
| | - Liudmila Chelysheva
- INRA, Institut Jean-Pierre Bourgin UMR1318, Saclay Plant Sciences, Versailles, France AgroParisTech, Institut Jean-Pierre Bourgin UMR1318, Saclay Plant Sciences, Versailles, France
| | - Yasuko Kamisugi
- Centre for Plant Sciences, Faculty of Biological Sciences, Leeds University, Leeds LS2 9JT, UK
| | - Nathalie Vrielynck
- INRA, Institut Jean-Pierre Bourgin UMR1318, Saclay Plant Sciences, Versailles, France AgroParisTech, Institut Jean-Pierre Bourgin UMR1318, Saclay Plant Sciences, Versailles, France
| | - Anouchka Guyon
- INRA, Institut Jean-Pierre Bourgin UMR1318, Saclay Plant Sciences, Versailles, France AgroParisTech, Institut Jean-Pierre Bourgin UMR1318, Saclay Plant Sciences, Versailles, France
| | - Aline Epert
- INRA, Institut Jean-Pierre Bourgin UMR1318, Saclay Plant Sciences, Versailles, France AgroParisTech, Institut Jean-Pierre Bourgin UMR1318, Saclay Plant Sciences, Versailles, France
| | - Sylvia Le Guin
- INRA, Institut Jean-Pierre Bourgin UMR1318, Saclay Plant Sciences, Versailles, France AgroParisTech, Institut Jean-Pierre Bourgin UMR1318, Saclay Plant Sciences, Versailles, France
| | - Didier G Schaefer
- Laboratoire de Biologie Moleculaire et Cellulaire, Institut de Biologie, Universite de Neuchatel, rue Emile-Argand 11, CH-2007 Neuchatel, Switzerland
| | - Andrew C Cuming
- Centre for Plant Sciences, Faculty of Biological Sciences, Leeds University, Leeds LS2 9JT, UK
| | - Mathilde Grelon
- INRA, Institut Jean-Pierre Bourgin UMR1318, Saclay Plant Sciences, Versailles, France AgroParisTech, Institut Jean-Pierre Bourgin UMR1318, Saclay Plant Sciences, Versailles, France
| | - Fabien Nogué
- INRA, Institut Jean-Pierre Bourgin UMR1318, Saclay Plant Sciences, Versailles, France AgroParisTech, Institut Jean-Pierre Bourgin UMR1318, Saclay Plant Sciences, Versailles, France
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29
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Štafa A, Miklenić M, Zunar B, Lisnić B, Symington LS, Svetec IK. Sgs1 and Exo1 suppress targeted chromosome duplication during ends-in and ends-out gene targeting. DNA Repair (Amst) 2014; 22:12-23. [PMID: 25089886 DOI: 10.1016/j.dnarep.2014.07.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2014] [Revised: 07/05/2014] [Accepted: 07/09/2014] [Indexed: 10/24/2022]
Abstract
Gene targeting is extremely efficient in the yeast Saccharomyces cerevisiae. It is performed by transformation with a linear, non-replicative DNA fragment carrying a selectable marker and containing ends homologous to the particular locus in a genome. However, even in S. cerevisiae, transformation can result in unwanted (aberrant) integration events, the frequency and spectra of which are quite different for ends-out and ends-in transformation assays. It has been observed that gene replacement (ends-out gene targeting) can result in illegitimate integration, integration of the transforming DNA fragment next to the target sequence and duplication of a targeted chromosome. By contrast, plasmid integration (ends-in gene targeting) is often associated with multiple targeted integration events but illegitimate integration is extremely rare and a targeted chromosome duplication has not been reported. Here we systematically investigated the influence of design of the ends-out assay on the success of targeted genetic modification. We have determined transformation efficiency, fidelity of gene targeting and spectra of all aberrant events in several ends-out gene targeting assays designed to insert, delete or replace a particular sequence in the targeted region of the yeast genome. Furthermore, we have demonstrated for the first time that targeted chromosome duplications occur even during ends-in gene targeting. Most importantly, the whole chromosome duplication is POL32 dependent pointing to break-induced replication (BIR) as the underlying mechanism. Moreover, the occurrence of duplication of the targeted chromosome was strikingly increased in the exo1Δ sgs1Δ double mutant but not in the respective single mutants demonstrating that the Exo1 and Sgs1 proteins independently suppress whole chromosome duplication during gene targeting.
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Affiliation(s)
- Anamarija Štafa
- Laboratory for Biology and Microbial Genetics, Department of Biochemical Engineering, Faculty of Food Technology and Biotechnology, University of Zagreb, Zagreb 10000, Croatia; Department of Microbiology and Immunology, Columbia University Medical Center, New York, NY 10032, USA.
| | - Marina Miklenić
- Laboratory for Biology and Microbial Genetics, Department of Biochemical Engineering, Faculty of Food Technology and Biotechnology, University of Zagreb, Zagreb 10000, Croatia
| | - Bojan Zunar
- Laboratory for Biology and Microbial Genetics, Department of Biochemical Engineering, Faculty of Food Technology and Biotechnology, University of Zagreb, Zagreb 10000, Croatia
| | - Berislav Lisnić
- Laboratory for Biology and Microbial Genetics, Department of Biochemical Engineering, Faculty of Food Technology and Biotechnology, University of Zagreb, Zagreb 10000, Croatia
| | - Lorraine S Symington
- Department of Microbiology and Immunology, Columbia University Medical Center, New York, NY 10032, USA
| | - Ivan-Krešimir Svetec
- Laboratory for Biology and Microbial Genetics, Department of Biochemical Engineering, Faculty of Food Technology and Biotechnology, University of Zagreb, Zagreb 10000, Croatia.
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30
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Dangwal M, Kapoor S, Kapoor M. The PpCMT chromomethylase affects cell growth and interacts with the homolog of LIKE HETEROCHROMATIN PROTEIN 1 in the moss Physcomitrella patens. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2014; 77:589-603. [PMID: 24329971 DOI: 10.1111/tpj.12406] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2013] [Revised: 11/30/2013] [Accepted: 12/03/2013] [Indexed: 05/06/2023]
Abstract
Chromomethylases (CMTs) are plant-specific cytosine DNA methyltransferases that are involved in maintenance of CpNpG methylation. In seed plants, histone methylation and interaction of CMT with LIKE HETEROCHROMATIN PROTEIN 1 (LHP1) is essential for recruitment of CMT to target sites. LHP1 has been characterized as a putative component of the POLYCOMB REPRESSIVE COMPLEX1 (PRC1) in plants, and functions downstream of PRC2 to maintain genes in repressed state for orchestrated development. In the present study, we show that targeted disruption of PpCMT results in an approximately 50% reduction in global cytosine methylation levels. This affects growth of apical cells, predominantly growth of side branch initials emerging from chloronema cells. In some places, these cells develop thick walls with plasmolyzed cellular contents. Transcript accumulation patterns of genes involved in apical cell extension and metabolism of hemicelluloses, such as xyloglucans, in the primary cell walls decreased many fold in ppcmt mutant lines, as determined by real-time PCR. Using yeast two-hybrid method and bimolecular fluorescence complementation assay, we show that PpCMT and PpLHP1 interact through their chromo domains, while PpLHP1 homodimerizes through its chromo shadow domain. The results presented in this study provide insight into the role of the single chromomethylase, PpCMT, in proliferation of protonema filaments, and shed light on the evolutionary conservation of proteins interacting with these methylases in the early land plant, Physcomitrella patens.
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Affiliation(s)
- Meenakshi Dangwal
- University School of Biotechnology, Guru Gobind Singh Indraprastha University, Sector 16C, Dwarka, New Delhi, 110078, India
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31
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Lloyd JPB, Davies B. SMG1 is an ancient nonsense-mediated mRNA decay effector. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2013; 76:800-10. [PMID: 24103012 DOI: 10.1111/tpj.12329] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2013] [Revised: 09/02/2013] [Accepted: 09/11/2013] [Indexed: 05/07/2023]
Abstract
Nonsense-mediated mRNA decay (NMD) is a eukaryotic process that targets selected mRNAs for destruction, for both quality control and gene regulatory purposes. SMG1, the core kinase of the NMD machinery in animals, phosphorylates the highly conserved UPF1 effector protein to activate NMD. However, SMG1 is missing from the genomes of fungi and the model flowering plant Arabidopsis thaliana, leading to the conclusion that SMG1 is animal-specific and questioning the mechanistic conservation of the pathway. Here we show that SMG1 is not animal-specific, by identifying SMG1 in a range of eukaryotes, including all examined green plants with the exception of A. thaliana. Knockout of SMG1 by homologous recombination in the basal land plant Physcomitrella patens reveals that SMG1 has a conserved role in the NMD pathway across kingdoms. SMG1 has been lost at various points during the evolution of eukaryotes from multiple lineages, including an early loss in the fungal lineage and a very recent observable gene loss in A. thaliana. These findings suggest that the SMG1 kinase functioned in the NMD pathway of the last common eukaryotic ancestor.
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Affiliation(s)
- James P B Lloyd
- Faculty of Biological Sciences, Centre for Plant Sciences, University of Leeds, Leeds, LS2 9JT, UK
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Kubo M, Imai A, Nishiyama T, Ishikawa M, Sato Y, Kurata T, Hiwatashi Y, Reski R, Hasebe M. System for stable β-estradiol-inducible gene expression in the moss Physcomitrella patens. PLoS One 2013; 8:e77356. [PMID: 24086772 PMCID: PMC3785464 DOI: 10.1371/journal.pone.0077356] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2013] [Accepted: 09/02/2013] [Indexed: 01/02/2023] Open
Abstract
Inducible transgene expression provides a useful tool to analyze gene function. The moss Physcomitrellapatens is a model basal land plant with well-developed research tools, including a high efficiency of gene targeting and substantial genomics resources. However, current systems for controlled transgene expression remain limited. Here we report the development of an estrogen receptor mediated inducible gene expression system, based on the system used in flowering plants. After identifying the appropriate promoters to drive the chimeric transducer, we succeeded in inducing transcription over 1,000-fold after 24 h incubation with β-estradiol. The P. patens system was also effective for high-level long-term induction of gene expression; transcript levels of the activated gene were maintained for at least seven days on medium containing β-estradiol. We also established two potentially neutral targeting sites and a set of vectors for reproducible expression of two transgenes. This β-estradiol-dependent system will be useful to test genes individually or in combination, allowing stable, inducible transgenic expression in P. patens.
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Affiliation(s)
- Minoru Kubo
- National Institute for Basic Biology, Okazaki, Japan
- ERATO, Japan Science and Technology Agency, Okazaki, Japan
- Plant Biotechnology, Faculty of Biology, University of Freiburg, Freiburg, Germany
- FRIAS – Freiburg Institute for Advanced Studies, Freiburg, Germany
- * E-mail: (MK); (MH)
| | - Akihiro Imai
- National Institute for Basic Biology, Okazaki, Japan
- ERATO, Japan Science and Technology Agency, Okazaki, Japan
- Department of Biology, Duke University, Durham, North Carolina, United States of America
| | - Tomoaki Nishiyama
- National Institute for Basic Biology, Okazaki, Japan
- ERATO, Japan Science and Technology Agency, Okazaki, Japan
- Advanced Science Research Center, Kanazawa University, Kanazawa, Japan
| | - Masaki Ishikawa
- National Institute for Basic Biology, Okazaki, Japan
- ERATO, Japan Science and Technology Agency, Okazaki, Japan
- School of Life Science, The Graduate University for Advanced Studies, Okazaki, Japan
| | | | - Tetsuya Kurata
- ERATO, Japan Science and Technology Agency, Okazaki, Japan
| | - Yuji Hiwatashi
- National Institute for Basic Biology, Okazaki, Japan
- School of Life Science, The Graduate University for Advanced Studies, Okazaki, Japan
| | - Ralf Reski
- Plant Biotechnology, Faculty of Biology, University of Freiburg, Freiburg, Germany
- FRIAS – Freiburg Institute for Advanced Studies, Freiburg, Germany
- BIOSS – Centre for Biological Signalling Studies, Freiburg, Germany
| | - Mitsuyasu Hasebe
- National Institute for Basic Biology, Okazaki, Japan
- ERATO, Japan Science and Technology Agency, Okazaki, Japan
- School of Life Science, The Graduate University for Advanced Studies, Okazaki, Japan
- * E-mail: (MK); (MH)
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Homologous recombination-mediated gene targeting in the liverwort Marchantia polymorpha L. Sci Rep 2013; 3:1532. [PMID: 23524944 PMCID: PMC3607118 DOI: 10.1038/srep01532] [Citation(s) in RCA: 102] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2013] [Accepted: 03/11/2013] [Indexed: 11/16/2022] Open
Abstract
The liverwort Marchantia polymorpha is an emerging model organism on account of its ideal characteristics for molecular genetics in addition to occupying a crucial position in the evolution of land plants. Here we describe a method for gene targeting by applying a positive/negative selection system for reduction of non-homologous random integration to an efficient Agrobacterium-mediated transformation system using M. polymorpha sporelings. The targeting efficiency was evaluated by knocking out the NOP1 gene, which impaired air-chamber formation. Homologous recombination was observed in about 2% of the thalli that passed the positive/negative selection. With the advantage of utilizing the haploid gametophytic generation, this strategy should facilitate further molecular genetic analysis of M. polymorpha, in which many of the mechanisms found in land plants are conserved, yet in a less complex form.
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Gerotto C, Alboresi A, Giacometti GM, Bassi R, Morosinotto T. Coexistence of plant and algal energy dissipation mechanisms in the moss Physcomitrella patens. THE NEW PHYTOLOGIST 2012; 196:763-773. [PMID: 23005032 DOI: 10.1111/j.1469-8137.2012.04345.x] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2012] [Accepted: 08/08/2012] [Indexed: 05/20/2023]
Abstract
Although light is the source of energy for photosynthetic organisms, it causes oxidative stress when in excess. Plants and algae prevent reactive oxygen species (ROS) formation by activation of nonphotochemical quenching (NPQ), which dissipates excess excitation energy as heat. Although NPQ is found in both algae and plants, these organisms rely on two different proteins for its activation, Light harvesting complex stress-related (LHCSR) and Photosystem II subunit S (PSBS). In the moss Physcomitrella patens, both proteins are present and active. Several P. patens lines depleted in or over-expressing PSBS and/or LHCSR at various levels were generated by exploiting the ability of Physcomitrella to undergo homologous recombination. The analysis of the transgenic lines showed that either protein is sufficient, alone, for NPQ activation independently of the other, supporting the idea that they rely on different activation mechanisms. Modulation of PSBS and/or LHCSR contents was found to be correlated with NPQ amplitude, indicating that plants and algae can directly modulate their ability to dissipate energy simply by altering the accumulation level of one or both of these proteins. The availability of a large range of P. patens genotypes differing in PSBS and LHCSR content allowed comparison of their activation mechanisms and discussion of implications for the evolution of photoprotection during land colonization.
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Affiliation(s)
- Caterina Gerotto
- Dipartimento di Biologia, Università di Padova, Via Ugo Bassi 58 B, 35121, Padova, Italy
| | - Alessandro Alboresi
- Dipartimento di Biotecnologie, Università di Verona, Strada le Grazie 15, 37134, Verona, Italy
| | - Giorgio M Giacometti
- Dipartimento di Biologia, Università di Padova, Via Ugo Bassi 58 B, 35121, Padova, Italy
| | - Roberto Bassi
- Dipartimento di Biotecnologie, Università di Verona, Strada le Grazie 15, 37134, Verona, Italy
| | - Tomas Morosinotto
- Dipartimento di Biologia, Università di Padova, Via Ugo Bassi 58 B, 35121, Padova, Italy
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Ruibal C, Salamó IP, Carballo V, Castro A, Bentancor M, Borsani O, Szabados L, Vidal S. Differential contribution of individual dehydrin genes from Physcomitrella patens to salt and osmotic stress tolerance. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2012; 190:89-102. [PMID: 22608523 DOI: 10.1016/j.plantsci.2012.03.009] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2011] [Revised: 03/16/2012] [Accepted: 03/28/2012] [Indexed: 05/02/2023]
Abstract
The moss Physcomitrella patens can withstand extreme environmental conditions including drought and salt stress. Tolerance to dehydration in mosses is thought to rely on efficient limitation of stress-induced cell damage and repair of cell injury upon stress relief. Dehydrin proteins (DHNs) are part of a conserved cell protecting mechanism in plants although their role in stress tolerance is not well understood. Four DHNs and two DHN-like proteins were identified in the predicted proteome of P. patens. Expression of PpDHNA and PpDHNB was induced by salt and osmotic stress and controlled by abscisic acid. Subcellular localization of the encoded proteins suggested that these dehydrins are localized in cytosol and accumulate near membranes during stress. Comparative analysis of dhnA and dhnB targeted knockout mutants of P. patens revealed that both genes play a role in cellular protection during salt and osmotic stress, although PpDHNA has a higher contribution to stress tolerance. Overexpression of PpDHNA and PpDHNB genes in transgenic Arabidopsis improved rosette and root growth in stress conditions, although PpDHNA was more efficient in this role. These results suggest that specific DHNs contribute considerably to the high stress tolerance of mosses and offer novel tools for genetic engineering stress tolerance of higher plants.
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Affiliation(s)
- Cecilia Ruibal
- Laboratorio de Biología Molecular Vegetal, Facultad de Ciencias, Universidad de la República, Iguá 4225, CP 11400 Montevideo, Uruguay.
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Goss CA, Brockmann DJ, Bushoven JT, Roberts AW. A CELLULOSE SYNTHASE (CESA) gene essential for gametophore morphogenesis in the moss Physcomitrella patens. PLANTA 2012; 235:1355-67. [PMID: 22215046 DOI: 10.1007/s00425-011-1579-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2011] [Accepted: 12/19/2011] [Indexed: 05/11/2023]
Abstract
In seed plants, different groups of orthologous genes encode the CELLULOSE SYNTHASE (CESA) proteins that are responsible for cellulose biosynthesis in primary and secondary cell walls. The seven CESA sequences of the moss Physcomitrella patens (Hedw.) B. S. G. form a monophyletic sister group to seed plant CESAs, consistent with independent CESA diversification and specialization in moss and seed plant lines. The role of PpCESA5 in the development of P. patens was investigated by targeted mutagenesis. The cesa5 knockout lines were tested for cellulose deficiency using carbohydrate-binding module affinity cytochemistry and the morphology of the leafy gametophores was analyzed by 3D reconstruction of confocal images. No defects were identified in the development of the filamentous protonema or in production of bud initials that normally give rise to the leafy gametophores. However, the gametophore buds were cellulose deficient and defects in subsequent cell expansion, cytokinesis, and leaf initiation resulted in the formation of irregular cell clumps instead of leafy shoots. Analysis of the cesa5 knockout phenotype indicates that a biophysical model of organogenesis can be extended to the moss gametophore shoot apical meristem.
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Affiliation(s)
- Chessa A Goss
- Department of Biological Sciences, CBLS, University of Rhode Island, Kingston, RI 02881, USA
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Kamisugi Y, Schaefer DG, Kozak J, Charlot F, Vrielynck N, Holá M, Angelis KJ, Cuming AC, Nogué F. MRE11 and RAD50, but not NBS1, are essential for gene targeting in the moss Physcomitrella patens. Nucleic Acids Res 2011; 40:3496-510. [PMID: 22210882 PMCID: PMC3333855 DOI: 10.1093/nar/gkr1272] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
The moss Physcomitrella patens is unique among plant models for the high frequency with which targeted transgene insertion occurs via homologous recombination. Transgene integration is believed to utilize existing machinery for the detection and repair of DNA double-strand breaks (DSBs). We undertook targeted knockout of the Physcomitrella genes encoding components of the principal sensor of DNA DSBs, the MRN complex. Loss of function of PpMRE11 or PpRAD50 strongly and specifically inhibited gene targeting, whilst rates of untargeted transgene integration were relatively unaffected. In contrast, disruption of the PpNBS1 gene retained the wild-type capacity to integrate transforming DNA efficiently at homologous loci. Analysis of the kinetics of DNA-DSB repair in wild-type and mutant plants by single-nucleus agarose gel electrophoresis revealed that bleomycin-induced fragmentation of genomic DNA was repaired at approximately equal rates in each genotype, although both the Ppmre11 and Pprad50 mutants exhibited severely restricted growth and development and enhanced sensitivity to UV-B and bleomycin-induced DNA damage, compared with wild-type and Ppnbs1 plants. This implies that while extensive DNA repair can occur in the absence of a functional MRN complex; this is unsupervised in nature and results in the accumulation of deleterious mutations incompatible with normal growth and development.
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Affiliation(s)
- Yasuko Kamisugi
- Centre for Plant Sciences, Faculty of Biological Sciences, Leeds University, Leeds LS2 9JT, UK
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38
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Liu YC, Vidali L. Efficient polyethylene glycol (PEG) mediated transformation of the moss Physcomitrella patens. J Vis Exp 2011:2560. [PMID: 21540817 PMCID: PMC3169274 DOI: 10.3791/2560] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022] Open
Abstract
A simple and efficient method to transform Physcomitrella pantens protoplasts is described. This method is adapted from protocols for Physocmitrella protonemal protoplast and Arabidopsis mesophyll protoplast transformation. Due to its capacity to undergo efficient mitotic homologous recombination, Physcomitrella patens has emerged as an important model system in recent years. This capacity allows high frequencies of gene targeting, which is not seen in other model plants such as Arabidopsis. To take full advantage of this system, we need an effective and easy method to deliver DNA into moss cells. The most common ways to transform this moss are particle bombardment and PEG-mediated DNA uptake. Although particle bombardment can produce a high transformation efficiency, gene guns are not readily available to many laboratories and the protocol is difficult to standardize. On the other hand, PEG mediated transformation does not require specialized equipments, and can be performed in any laboratory with a sterile hood. Here, we show a simple and highly efficient method for transformation of moss protoplasts. This method can generate more than 120 transient transformants per microgram of DNA, which is an improvement from the most efficient protocol previously reported. Because of its simplicity, efficiency, and reproducibility, this method can be applied to projects requiring large number of transformants as well as for routine transformation.
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Affiliation(s)
- Yen-Chun Liu
- Department of Biology and Biotechnology, Worcester Polytechnic Institute
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39
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Roberts AW, Dimos CS, Budziszek MJ, Goss CA, Lai V. Knocking out the wall: protocols for gene targeting in Physcomitrella patens. Methods Mol Biol 2011; 715:273-90. [PMID: 21222091 DOI: 10.1007/978-1-61779-008-9_19] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
The moss Physcomitrella patens has become established as a model for investigating plant gene function due to the feasibility of gene targeting. The chemical composition of the P. patens cell wall is similar to that of vascular plants and phylogenetic analyses of glycosyltransferase sequences from the P. patens genome have identified genes that putatively encode cell wall biosynthetic enzymes, providing a basis for investigating the evolution of cell wall polysaccharides and the enzymes that synthesize them. The protocols described in this chapter provide methods for targeted gene knockout in P. patens, from constructing vectors and maintaining cultures to transforming protoplasts and analyzing the genotypes and phenotypes of the resulting transformed lines.
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Affiliation(s)
- Alison W Roberts
- Department of Biological Sciences, Center for Biotechnology and Life Sciences, University of Rhode Island, Kingston, RI, USA
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40
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Franconi R, Demurtas OC, Massa S. Plant-derived vaccines and other therapeutics produced in contained systems. Expert Rev Vaccines 2010; 9:877-92. [PMID: 20673011 DOI: 10.1586/erv.10.91] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2023]
Abstract
The use of contained plant systems for the production of biopharmaceuticals represents a powerful alternative to current methods, combining the benefits of whole-plant systems and cell cultures. In vitro contained production systems include plant cell suspensions, hairy root cultures, novel plants grown in contained conditions and microalgae. These systems show intrinsic advantages, such as control over growth conditions, production in compliance with good manufacturing practice and avoidance of political resistance to the release of genetically modified field crops. At present, one of the two plant-produced vaccine-related products that have gone all the way through production and regulatory hurdles derives from tobacco cell suspensions, and the second is a human therapeutic enzyme, which is expected to reach commercial development soon and derives from carrot suspension cells. In the future, several other products from contained systems are expected to reach the clinical trial stage.
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Affiliation(s)
- Rosella Franconi
- Italian National Agency for New Technologies, UTBIORAD, CR Casaccia, Rome, Italy.
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Cove DJ, Perroud PF, Charron AJ, McDaniel SF, Khandelwal A, Quatrano RS. The moss Physcomitrella patens: a novel model system for plant development and genomic studies. Cold Spring Harb Protoc 2010; 2009:pdb.emo115. [PMID: 20147063 DOI: 10.1101/pdb.emo115] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Affiliation(s)
- David J Cove
- Department of Biology, Washington University, St. Louis, MO 63130, USA
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Koduri PKH, Gordon GS, Barker EI, Colpitts CC, Ashton NW, Suh DY. Genome-wide analysis of the chalcone synthase superfamily genes of Physcomitrella patens. PLANT MOLECULAR BIOLOGY 2010; 72:247-63. [PMID: 19876746 DOI: 10.1007/s11103-009-9565-z] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2009] [Accepted: 10/19/2009] [Indexed: 05/08/2023]
Abstract
Enzymes of the chalcone synthase (CHS) superfamily catalyze the production of a variety of secondary metabolites in bacteria, fungi and plants. Some of these metabolites have played important roles during the early evolution of land plants by providing protection from various environmental assaults including UV irradiation. The genome of the moss, Physcomitrella patens, contains at least 17 putative CHS superfamily genes. Three of these genes (PpCHS2b, PpCHS3 and PpCHS5) exist in multiple copies and all have corresponding ESTs. PpCHS11 and probably also PpCHS9 encode non-CHS enzymes, while PpCHS10 appears to be an ortholog of plant genes encoding anther-specific CHS-like enzymes. It was inferred from the genomic locations of genes comprising it that the moss CHS superfamily expanded through tandem and segmental duplication events. Inferred exon-intron architectures and results from phylogenetic analysis of representative CHS superfamily genes of P. patens and other plants showed that intron gain and loss occurred several times during evolution of this gene superfamily. A high proportion of P. patens CHS genes (7 of 14 genes for which the full sequence is known and probably 3 additional genes) are intronless, prompting speculation that CHS gene duplication via retrotransposition has occurred at least twice in the moss lineage. Analyses of sequence similarities, catalytic motifs and EST data indicated that a surprisingly large number (as many as 13) of the moss CHS superfamily genes probably encode active CHS. EST distribution data and different light responsiveness observed with selected genes provide evidence for their differential regulation. Observed diversity within the moss CHS superfamily and amenability to gene manipulation make Physcomitrella a highly suitable model system for studying expansion and functional diversification of the plant CHS superfamily of genes.
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Affiliation(s)
- P K Harshavardhan Koduri
- Department of Chemistry and Biochemistry, University of Regina, 3737 Wascana Parkway, Regina, SK, S4S 0A2, Canada
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Rescue and characterization of episomally replicating DNA from the moss Physcomitrella. Proc Natl Acad Sci U S A 2009; 106:19444-9. [PMID: 19892729 DOI: 10.1073/pnas.0908037106] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The moss Physcomitrella is unique among plants in that it permits efficient gene targeting by homologous recombination. Furthermore, transformed DNA can replicate episomally in Physcomitrella. Here we show that episomally replicating DNA can be rescued back into Escherichia coli, and we use such rescue to study the fate of the transformed DNA. Significantly, plasmids rescued from moss transformed with circular DNA are identical to the original plasmid, whereas plasmids rescued from moss transformed with linearized DNA frequently have deletions created by direct repeat recombination. These events are highly predictable in that they target the longest direct repeat on the plasmid if this repeat is at least 12 bp. Episomal transformants obtained with linearized DNA show a more than 1,000-fold amplification of the DNA whereas transformants obtained with circular DNA have much lower copy numbers. Most episomal transformants quickly lose the plasmid in the absence of selection, but a semistable type of transformant that loses the plasmid at a much lower frequency was also observed. The consistent rescue of the original plasmid, or of predictable derivatives thereof, suggests that molecular genetics methods which rely on shuttle plasmids are feasible in Physcomitrella.
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44
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Papdi C, Joseph MP, Salamó IP, Vidal S, Szabados L. Genetic technologies for the identification of plant genes controlling environmental stress responses. FUNCTIONAL PLANT BIOLOGY : FPB 2009; 36:696-720. [PMID: 32688681 DOI: 10.1071/fp09047] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2009] [Accepted: 06/11/2009] [Indexed: 06/11/2023]
Abstract
Abiotic conditions such as light, temperature, water availability and soil parameters determine plant growth and development. The adaptation of plants to extreme environments or to sudden changes in their growth conditions is controlled by a well balanced, genetically determined signalling system, which is still far from being understood. The identification and characterisation of plant genes which control responses to environmental stresses is an essential step to elucidate the complex regulatory network, which determines stress tolerance. Here, we review the genetic approaches, which have been used with success to identify plant genes which control responses to different abiotic stress factors. We describe strategies and concepts for forward and reverse genetic screens, conventional and insertion mutagenesis, TILLING, gene tagging, promoter trapping, activation mutagenesis and cDNA library transfer. The utility of the various genetic approaches in plant stress research we review is illustrated by several published examples.
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Affiliation(s)
- Csaba Papdi
- Institute of Plant Biology, Biological Research Centre, 6726-Szeged, Temesvári krt. 62, Hungary
| | - Mary Prathiba Joseph
- Institute of Plant Biology, Biological Research Centre, 6726-Szeged, Temesvári krt. 62, Hungary
| | - Imma Pérez Salamó
- Institute of Plant Biology, Biological Research Centre, 6726-Szeged, Temesvári krt. 62, Hungary
| | - Sabina Vidal
- Facultad de Ciencias, Universidad de la República, Iguá 4225, CP 11400, Montevideo, Uruguay
| | - László Szabados
- Institute of Plant Biology, Biological Research Centre, 6726-Szeged, Temesvári krt. 62, Hungary
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45
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Mittmann F, Dienstbach S, Weisert A, Forreiter C. Analysis of the phytochrome gene family in Ceratodon purpureus by gene targeting reveals the primary phytochrome responsible for photo- and polarotropism. PLANTA 2009; 230:27-37. [PMID: 19330350 DOI: 10.1007/s00425-009-0922-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2009] [Accepted: 03/06/2009] [Indexed: 05/13/2023]
Abstract
Using gene targeting by homologous recombination in Ceratodon purpureus, we were able to knock out four phytochrome photoreceptor genes independently and to analyze their function with respect to red light dependent phototropism, polarotropism, and chlorophyll content. The strongest phenotype was found in knock-out lines of a newly described phytochrome gene termed CpPHY4 lacking photo- and polarotropic responses at moderate fluence rates. Eliminating the atypical phytochrome gene CpPHY1, which is the only known phytochrome-like gene containing a putative C-terminal tyrosine kinase-like domain, affects red light-induced chlorophyll accumulation. This result was surprising, since no light dependent function was ever allocated to this unusual gene.
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Affiliation(s)
- Franz Mittmann
- Department of Plant Physiology, Justus Liebig University, Senckenbergstrasse 3, 35390 Giessen, Germany
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46
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Charron AJ, Quatrano RS. Between a rock and a dry place: the water-stressed moss. MOLECULAR PLANT 2009; 2:478-86. [PMID: 19825631 DOI: 10.1093/mp/ssp018] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
The earliest land plants faced a suite of abiotic stresses largely unknown to their aquatic algal ancestors. The descendants of these plants evolved two general mechanisms for survival in the relatively arid aerial environment. While the vascular plants or 'tracheophytes' developed tissue specializations to transport and retain water, the other main lineages of land plants, the bryophytes, retained a simple, nonvascular morphology. The bryophytes--mosses, hornworts, and liverworts--continually undergo a co-equilibration of their water content with the surrounding environment and rely to a great extent on intrinsic cellular mechanisms to mitigate damage due to water stress. This short review will focus on the cellular and molecular responses to dehydration and rehydration in mosses, and offer insights into general plant responses to water stress.
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Affiliation(s)
- Audra J Charron
- Department of Biology, Washington University in St Louis, 1 Brookings Dr., St Louis, MO 63130, USA
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47
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Kamisugi Y, von Stackelberg M, Lang D, Care M, Reski R, Rensing SA, Cuming AC. A sequence-anchored genetic linkage map for the moss, Physcomitrella patens. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2008; 56:855-66. [PMID: 18657236 PMCID: PMC2667646 DOI: 10.1111/j.1365-313x.2008.03637.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
The moss Physcomitrella patens is a model for the study of plant cell biology and, by virtue of its basal position in land plant phylogeny, for comparative analysis of the evolution of plant gene function and development. It is ideally suited for 'reverse genetic' analysis by virtue of its outstanding ability to undertake targeted transgene integration by homologous recombination. However, gene identification through mutagenesis and map-based cloning has hitherto not been possible, due to the lack of a genetic linkage map. Using molecular markers [amplified fragment length polymorphisms (AFLP) and simple sequence repeats (SSR)] we have generated genetic linkage maps for Physcomitrella. One hundred and seventy-nine gene-specific SSR markers were mapped in 46 linkage groups, and 1574 polymorphic AFLP markers were identified. Integrating the SSR- and AFLP-based maps generated 31 linkage groups comprising 1420 markers. Anchorage of the integrated linkage map with gene-specific SSR markers coupled with computational prediction of AFLP loci has enabled its correspondence with the newly sequenced Physcomitrella genome. The generation of a linkage map densely populated with molecular markers and anchored to the genome sequence now provides a resource for forward genetic interrogation of the organism and for the development of a pipeline for the map-based cloning of Physcomitrella genes. This will radically enhance the potential of Physcomitrella for determining how gene function has evolved for the acquisition of complex developmental strategies within the plant kingdom.
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Affiliation(s)
- Yasuko Kamisugi
- Centre for Plant Sciences, Faculty of Biological Sciences, Leeds UniversityLeeds LS2 9JT, UK
| | - Mark von Stackelberg
- Plant Biotechnology, Faculty of Biology, University of Freiburg, Schaenzlestrasse 1D-79104 Freiburg, Germany
| | - Daniel Lang
- Plant Biotechnology, Faculty of Biology, University of Freiburg, Schaenzlestrasse 1D-79104 Freiburg, Germany
| | - Matthew Care
- Centre for Plant Sciences, Faculty of Biological Sciences, Leeds UniversityLeeds LS2 9JT, UK
| | - Ralf Reski
- Plant Biotechnology, Faculty of Biology, University of Freiburg, Schaenzlestrasse 1D-79104 Freiburg, Germany
- Freiburg Initiative for Systems Biology (FRISYS), Faculty of Biology, Schaenzlestrasse 1D-79104 Freiburg, Germany
| | - Stefan A Rensing
- Freiburg Initiative for Systems Biology (FRISYS), Faculty of Biology, Schaenzlestrasse 1D-79104 Freiburg, Germany
- * For correspondence (fax +44 113 3433144; e-mail ; fax +49 761 203 6945; e-mail )
| | - Andrew C Cuming
- Centre for Plant Sciences, Faculty of Biological Sciences, Leeds UniversityLeeds LS2 9JT, UK
- * For correspondence (fax +44 113 3433144; e-mail ; fax +49 761 203 6945; e-mail )
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48
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Perroud PF, Quatrano RS. BRICK1 is required for apical cell growth in filaments of the moss Physcomitrella patens but not for gametophore morphology. THE PLANT CELL 2008; 20:411-22. [PMID: 18263777 PMCID: PMC2276446 DOI: 10.1105/tpc.107.053256] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2007] [Revised: 01/11/2008] [Accepted: 01/25/2008] [Indexed: 05/19/2023]
Abstract
When BRK1, a member of the Wave/SCAR complex, is deleted in Physcomitrella patens (Deltabrk1), we report a striking reduction of filament growth resulting in smaller and fewer cells with misplaced cross walls compared with the normal protonemal cells. Using an inducible green fluorescent protein-talin to detect actin in living tissue, a characteristic broad accumulation of actin is observed at the tip of wild-type apical cells, whereas in Deltabrk1, smaller, more distinct foci of actin are present. Insertion of brk1-yfp into Deltabrk1 rescues the mutant phenotype and results in BRK1 being localized only in the tip of apical cells, the exclusive site of cell extension and division in the filament. Like BRK1, ARPC4 and At RABA4d are normally localized at the tip of apical cells and their localization is correlated with rapid tip growth in filaments. However, neither marker accumulates in apical cells of Deltabrk1 filaments. Although the Deltabrk1 phenotypes in protonema are severe, the leafy shoots or gametophores are normally shaped but stunted. These and other results suggest that BRK1 functions directly or indirectly in the selective accumulation/stabilization of actin and other proteins required for polar cell growth of filaments but not for the basic structure of the gametophore.
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49
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Singer SD, Ashton NW. Revelation of ancestral roles of KNOX genes by a functional analysis of Physcomitrella homologues. PLANT CELL REPORTS 2007; 26:2039-54. [PMID: 17724598 DOI: 10.1007/s00299-007-0409-5] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2007] [Revised: 06/25/2007] [Accepted: 07/03/2007] [Indexed: 05/16/2023]
Abstract
KNOX genes are indispensable elements of indeterminate apical growth programmes of vascular plant sporophytes. Since little is known about the roles of such genes in non-vascular plants, functional analysis of moss KNOX homologues (MKN genes) was undertaken using the genetically amenable model plant, Physcomitrella patens. Three MKN genes were inactivated by targeted gene knockout to produce single, double and triple mutants. MKN2 (a class 1 KNOX gene) mutants were characterised by premature sporogenesis, abnormal sporophyte ontogeny and irregular spore development. MKN4 (a second class 1 gene) mutants were phenotypically normal. MKN1-3 (a class 2 KNOX gene) mutants exhibited defects in spore coat morphology. Analysis of double and triple mutants revealed that the abnormal sporophytic phenotype of MKN2 mutants was accentuated by mutating MKN4 and to a lesser degree by mutating MKN1-3. The aberrant spore phenotype of MKN1-3 and MKN2 mutants was exacerbated by mutating MKN4. This study provides the first instance in which an abnormal phenotype has been associated with the disruption of a class 2 KNOX gene as well as the first demonstrated case of functional redundancy between a class 1 and a class 2 KNOX gene. We conclude that KNOX genes play significant roles in programming sporophytic development in moss and we provide evidence that ancestral function(s) of this gene family were instrumental in the successful transition of plants to a terrestrial environment.
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Affiliation(s)
- S D Singer
- Department of Biology, University of Regina, Regina, SK, Canada
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50
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Markmann-Mulisch U, Wendeler E, Zobell O, Schween G, Steinbiss HH, Reiss B. Differential requirements for RAD51 in Physcomitrella patens and Arabidopsis thaliana development and DNA damage repair. THE PLANT CELL 2007; 19:3080-9. [PMID: 17921313 PMCID: PMC2174717 DOI: 10.1105/tpc.107.054049] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2007] [Revised: 09/10/2007] [Accepted: 09/14/2007] [Indexed: 05/19/2023]
Abstract
RAD51, the eukaryotic homolog of the bacterial RecA recombinase, plays a central role in homologous recombination (HR) in yeast and animals. Loss of RAD51 function causes lethality in vertebrates but not in other animals or in the flowering plant Arabidopsis thaliana, suggesting that RAD51 is vital for highly developed organisms but not for others. Here, we found that loss of RAD51 function in the moss Physcomitrella patens, a plant of less complexity, caused a significant vegetative phenotype, indicating an important function for RAD51 in this organism. Moreover, loss of RAD51 caused marked hypersensitivity to the double-strand break-inducing agent bleomycin in P. patens but not in Arabidopsis. Therefore, HR is used for somatic DNA damage repair in P. patens but not in Arabidopsis. These data imply fundamental differences in the use of recombination pathways between plants. Moreover, these data demonstrate that the importance of RAD51 for viability is independent of taxonomic position or complexity of an organism. The involvement of HR in DNA damage repair in the slowly evolving species P. patens but not in fast-evolving Arabidopsis suggests that the choice of the recombination pathway is related to the speed of evolution in plants.
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Affiliation(s)
- Ulrich Markmann-Mulisch
- Department of Plant Developmental Biology, Max-Planck-Institut für Züchtungsforschung, D-50829 Cologne, Germany
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