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Liu Y, Jiao B, Champer J, Qian W. Overriding Mendelian inheritance in Arabidopsis with a CRISPR toxin-antidote gene drive that impairs pollen germination. NATURE PLANTS 2024; 10:910-922. [PMID: 38886523 DOI: 10.1038/s41477-024-01692-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Accepted: 04/09/2024] [Indexed: 06/20/2024]
Abstract
Synthetic gene drives, inspired by natural selfish genetic elements and transmitted to progeny at super-Mendelian (>50%) frequencies, present transformative potential for disseminating traits that benefit humans throughout wild populations, even facing potential fitness costs. Here we constructed a gene drive system in plants called CRISPR-Assisted Inheritance utilizing NPG1 (CAIN), which uses a toxin-antidote mechanism in the male germline to override Mendelian inheritance. Specifically, a guide RNA-Cas9 cassette targets the essential No Pollen Germination 1 (NPG1) gene, serving as the toxin to block pollen germination. A recoded, CRISPR-resistant copy of NPG1 serves as the antidote, providing rescue only in pollen cells that carry the drive. To limit potential consequences of inadvertent release, we used self-pollinating Arabidopsis thaliana as a model. The drive demonstrated a robust 88-99% transmission rate over two successive generations, producing minimal resistance alleles that are unlikely to inhibit drive spread. Our study provides a strong basis for rapid genetic modification or suppression of outcrossing plant populations.
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Affiliation(s)
- Yang Liu
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, China
| | - Bingke Jiao
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Jackson Champer
- Center for Bioinformatics, School of Life Sciences, Center for Life Sciences, Peking University, Beijing, China
| | - Wenfeng Qian
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, China.
- University of Chinese Academy of Sciences, Beijing, China.
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Yu Q, Li H, Zhang B, Song Y, Sun Y, Ding Z. ATP Hydrolases Superfamily Protein 1 (ASP1) Maintains Root Stem Cell Niche Identity through Regulating Reactive Oxygen Species Signaling in Arabidopsis. PLANTS (BASEL, SWITZERLAND) 2024; 13:1469. [PMID: 38891278 PMCID: PMC11174532 DOI: 10.3390/plants13111469] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2024] [Revised: 05/16/2024] [Accepted: 05/24/2024] [Indexed: 06/21/2024]
Abstract
The maintenance of the root stem cell niche identity in Arabidopsis relies on the delicate balance of reactive oxygen species (ROS) levels in root tips; however, the intricate molecular mechanisms governing ROS homeostasis within the root stem cell niche remain unclear. In this study, we unveil the role of ATP hydrolase superfamily protein 1 (ASP1) in orchestrating root stem cell niche maintenance through its interaction with the redox regulator cystathionine β-synthase domain-containing protein 3 (CBSX3). ASP1 is exclusively expressed in the quiescent center (QC) cells and governs the integrity of the root stem cell niche. Loss of ASP1 function leads to enhanced QC cell division and distal stem cell differentiation, attributable to reduced ROS levels and diminished expression of SCARECROW and SHORT ROOT in root tips. Our findings illuminate the pivotal role of ASP1 in regulating ROS signaling to maintain root stem cell niche homeostasis, achieved through direct interaction with CBSX3.
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Affiliation(s)
- Qianqian Yu
- School of Life Sciences, Liaocheng University, Liaocheng 252000, China; (H.L.); (B.Z.); (Y.S.); (Y.S.)
| | - Hongyu Li
- School of Life Sciences, Liaocheng University, Liaocheng 252000, China; (H.L.); (B.Z.); (Y.S.); (Y.S.)
| | - Bing Zhang
- School of Life Sciences, Liaocheng University, Liaocheng 252000, China; (H.L.); (B.Z.); (Y.S.); (Y.S.)
| | - Yun Song
- School of Life Sciences, Liaocheng University, Liaocheng 252000, China; (H.L.); (B.Z.); (Y.S.); (Y.S.)
| | - Yueying Sun
- School of Life Sciences, Liaocheng University, Liaocheng 252000, China; (H.L.); (B.Z.); (Y.S.); (Y.S.)
| | - Zhaojun Ding
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, College of Life Sciences, Shandong University, Qingdao 266237, China;
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3
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Zhao S, Rong J. Single-cell RNA-seq reveals a link of ovule abortion and sugar transport in Camellia oleifera. FRONTIERS IN PLANT SCIENCE 2024; 15:1274013. [PMID: 38371413 PMCID: PMC10869455 DOI: 10.3389/fpls.2024.1274013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Accepted: 01/15/2024] [Indexed: 02/20/2024]
Abstract
Camellia oleifera is the most important woody oil crop in China. Seed number per fruit is an important yield trait in C. oleifera. Ovule abortion is generally observed in C. oleifera and significantly decreases the seed number per fruit. However, the mechanisms of ovule abortion remain poorly understood at present. Single-cell RNA sequencing (scRNA-seq) was performed using mature ovaries of two C. oleifera varieties with different ovule abortion rates (OARs). In total, 20,526 high-quality cells were obtained, and 18 putative cell clusters were identified. Six cell types including female gametophyte, protoxylem, protophloem, procambium, epidermis, and parenchyma cells were identified from three main tissue types of ovule, placenta, and pericarp inner layer. A comparative analysis on scRNA-seq data between high- and low-OAR varieties demonstrated that the overall expression of CoSWEET and CoCWINV in procambium cells, and CoSTP in the integument was significantly upregulated in the low-OAR variety. Both the infertile ovule before pollination and the abortion ovule producing after compatible pollination might be attributed to selective abortion caused by low sugar levels in the apoplast around procambium cells and a low capability of hexose uptake in the integument. Here, the first single-cell transcriptional landscape is reported in woody crop ovaries. Our investigation demonstrates that ovule abortion may be related to sugar transport in placenta and ovules and sheds light on further deciphering the mechanism of regulating sugar transport and the improvement of seed yield in C. oleifera.
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Affiliation(s)
- Songzi Zhao
- Jiangxi Province Key Laboratory of Camellia Germplasm Conservation and Utilization, Jiangxi Academy of Forestry, Nanchang, China
| | - Jun Rong
- Jiangxi Province Key Laboratory of Watershed Ecosystem Change and Biodiversity, Center for Watershed Ecology, Institute of Life Science and School of Life Sciences, Nanchang University, Nanchang, China
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Collins PP, Broad RC, Yogeeswaran K, Varsani A, Poole AM, Collings DA. Characterisation of the trans-membrane nucleoporins GP210 and NDC1 in Arabidopsis thaliana. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2023; 332:111719. [PMID: 37116717 DOI: 10.1016/j.plantsci.2023.111719] [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: 12/02/2022] [Revised: 03/28/2023] [Accepted: 04/23/2023] [Indexed: 05/05/2023]
Abstract
The nuclear pore is structurally conserved across eukaryotes as are many of the pore's constituent proteins. The transmembrane nuclear pore proteins GP210 and NDC1 span the nuclear envelope holding the nuclear pore in place. Orthologues of GP210 and NDC1 in Arabidopsis were investigated through characterisation of T-DNA insertional mutants. While the T-DNA insert into GP210 reduced expression of the gene, the insert in the NDC1 gene resulted in increased expression in both the ndc1 mutant as well as the ndc1/gp210 double mutant. The ndc1 and gp210 individual mutants showed little phenotypic difference from wild-type plants, but the ndc1/gp210 mutant showed a range of phenotypic effects. As with many plant nuclear pore protein mutants, these effects included non-nuclear phenotypes such as reduced pollen viability, reduced growth and glabrous leaves in mature plants. Importantly, however, ndc1/gp210 exhibited nuclear-specific effects including modifications to nuclear shape in different cell types. We also observed functional changes to nuclear transport in ndc1/gp210 plants, with low levels of cytoplasmic fluorescence observed in cells expressing nuclear-targeted GFP. The lack of phenotypes in individual insertional lines, and the relatively mild phenotype suggests that additional transmembrane nucleoporins, such as the recently-discovered CPR5, likely compensate for their loss.
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Affiliation(s)
- Patrick P Collins
- Biomolecular Interaction Centre, School of Biological Sciences, University of Canterbury, Private Bag 4800, Christchurch 8140, New Zealand
| | - Ronan C Broad
- Biomolecular Interaction Centre, School of Biological Sciences, University of Canterbury, Private Bag 4800, Christchurch 8140, New Zealand
| | - Krithika Yogeeswaran
- Biomolecular Interaction Centre, School of Biological Sciences, University of Canterbury, Private Bag 4800, Christchurch 8140, New Zealand
| | - Arvind Varsani
- Biomolecular Interaction Centre, School of Biological Sciences, University of Canterbury, Private Bag 4800, Christchurch 8140, New Zealand; The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, School of Life Sciences, Arizona State University, Tempe, AZ, USA
| | - Anthony M Poole
- Biomolecular Interaction Centre, School of Biological Sciences, University of Canterbury, Private Bag 4800, Christchurch 8140, New Zealand; School of Biological Sciences, University of Auckland, Auckland 1010, New Zealand
| | - David A Collings
- Biomolecular Interaction Centre, School of Biological Sciences, University of Canterbury, Private Bag 4800, Christchurch 8140, New Zealand; School of Environmental and Life Sciences, The University of Newcastle, Callaghan, NSW 2308, Australia; Research School of Biology, Australian National University, Canberra, ACT 2601, Australia.
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5
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Wen YJ, Wu X, Wang S, Han L, Shen B, Wang Y, Zhang J. Identification of QTN-by-environment interactions for yield related traits in maize under multiple abiotic stresses. FRONTIERS IN PLANT SCIENCE 2023; 14:1050313. [PMID: 36875585 PMCID: PMC9975332 DOI: 10.3389/fpls.2023.1050313] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Accepted: 02/01/2023] [Indexed: 06/18/2023]
Abstract
INTRODUCTION Quantitative trait nucleotide (QTN)-by-environment interactions (QEIs) play an increasingly essential role in the genetic dissection of complex traits in crops as global climate change accelerates. The abiotic stresses, such as drought and heat, are the major constraints on maize yields. Multi-environment joint analysis can improve statistical power in QTN and QEI detection, and further help us to understand the genetic basis and provide implications for maize improvement. METHODS In this study, 3VmrMLM was applied to identify QTNs and QEIs for three yield-related traits (grain yield, anthesis date, and anthesis-silking interval) of 300 tropical and subtropical maize inbred lines with 332,641 SNPs under well-watered and drought and heat stresses. RESULTS Among the total 321 genes around 76 QTNs and 73 QEIs identified in this study, 34 known genes were reported in previous maize studies to be truly associated with these traits, such as ereb53 (GRMZM2G141638) and thx12 (GRMZM2G016649) associated with drought stress tolerance, and hsftf27 (GRMZM2G025685) and myb60 (GRMZM2G312419) associated with heat stress. In addition, among 127 homologs in Arabidopsis out of 287 unreported genes, 46 and 47 were found to be significantly and differentially expressed under drought vs well-watered treatments, and high vs. normal temperature treatments, respectively. Using functional enrichment analysis, 37 of these differentially expressed genes were involved in various biological processes. Tissue-specific expression and haplotype difference analysis further revealed 24 candidate genes with significantly phenotypic differences across gene haplotypes under different environments, of which the candidate genes GRMZM2G064159, GRMZM2G146192, and GRMZM2G114789 around QEIs may have gene-by-environment interactions for maize yield. DISCUSSION All these findings may provide new insights for breeding in maize for yield-related traits adapted to abiotic stresses.
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Affiliation(s)
- Yang-Jun Wen
- College of Science, Nanjing Agricultural University, Nanjing, China
- Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
| | - Xinyi Wu
- College of Science, Nanjing Agricultural University, Nanjing, China
| | - Shengmeng Wang
- College of Science, Nanjing Agricultural University, Nanjing, China
| | - Le Han
- College of Science, Nanjing Agricultural University, Nanjing, China
| | - Bolin Shen
- College of Science, Nanjing Agricultural University, Nanjing, China
| | - Yuan Wang
- College of Science, Nanjing Agricultural University, Nanjing, China
| | - Jin Zhang
- College of Science, Nanjing Agricultural University, Nanjing, China
- Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
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6
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Viñegra de la Torre N, Vayssières A, Obeng-Hinneh E, Neumann U, Zhou Y, Lázaro A, Roggen A, Sun H, Stolze SC, Nakagami H, Schneeberger K, Timmers T, Albani MC. FLOWERING REPRESSOR AAA + ATPase 1 is a novel regulator of perennial flowering in Arabis alpina. THE NEW PHYTOLOGIST 2022; 236:729-744. [PMID: 35832005 DOI: 10.1111/nph.18374] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Accepted: 07/04/2022] [Indexed: 06/15/2023]
Abstract
Arabis alpina is a polycarpic perennial, in which PERPETUAL FLOWERING1 (PEP1) regulates flowering and perennial traits in a vernalization-dependent manner. Mutagenesis screens of the pep1 mutant established the role of other flowering time regulators in PEP1-parallel pathways. Here we characterized three allelic enhancers of pep1 (eop002, 085 and 091) which flower early. We mapped the causal mutations and complemented mutants with the identified gene. Using quantitative reverse transcriptase PCR and reporter lines, we determined the protein spatiotemporal expression patterns and localization within the cell. We also characterized its role in Arabidopsis thaliana using CRISPR and in A. alpina by introgressing mutant alleles into a wild-type background. These mutants carried lesions in an AAA+ ATPase of unknown function, FLOWERING REPRESSOR AAA+ ATPase 1 (AaFRAT1). AaFRAT1 was detected in the vasculature of young leaf primordia and the rib zone of flowering shoot apical meristems. At the subcellular level, AaFRAT1 was localized at the interphase between the endoplasmic reticulum and peroxisomes. Introgression lines carrying Aafrat1 alleles required less vernalization to flower and reduced number of vegetative axillary branches. By contrast, A. thaliana CRISPR lines showed weak flowering phenotypes. AaFRAT1 contributes to flowering time regulation and the perennial growth habit of A. alpina.
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Affiliation(s)
- Natanael Viñegra de la Torre
- Institute for Plant Sciences, University of Cologne, Zülpicher Str. 47b, 50674, Cologne, Germany
- Max Planck Institute for Plant Breeding Research, Carl-von-Linné Weg 10, 50829, Cologne, Germany
- Cluster of Excellence on Plant Sciences "From Complex Traits towards Synthetic Modules", 40225, Düsseldorf, Germany
| | - Alice Vayssières
- Institute for Plant Sciences, University of Cologne, Zülpicher Str. 47b, 50674, Cologne, Germany
- Max Planck Institute for Plant Breeding Research, Carl-von-Linné Weg 10, 50829, Cologne, Germany
- Cluster of Excellence on Plant Sciences "From Complex Traits towards Synthetic Modules", 40225, Düsseldorf, Germany
| | - Evelyn Obeng-Hinneh
- Institute for Plant Sciences, University of Cologne, Zülpicher Str. 47b, 50674, Cologne, Germany
- Max Planck Institute for Plant Breeding Research, Carl-von-Linné Weg 10, 50829, Cologne, Germany
- Cluster of Excellence on Plant Sciences "From Complex Traits towards Synthetic Modules", 40225, Düsseldorf, Germany
| | - Ulla Neumann
- Max Planck Institute for Plant Breeding Research, Carl-von-Linné Weg 10, 50829, Cologne, Germany
| | - Yanhao Zhou
- Institute for Plant Sciences, University of Cologne, Zülpicher Str. 47b, 50674, Cologne, Germany
- Max Planck Institute for Plant Breeding Research, Carl-von-Linné Weg 10, 50829, Cologne, Germany
- Cluster of Excellence on Plant Sciences "From Complex Traits towards Synthetic Modules", 40225, Düsseldorf, Germany
| | - Ana Lázaro
- Institute for Plant Sciences, University of Cologne, Zülpicher Str. 47b, 50674, Cologne, Germany
- Max Planck Institute for Plant Breeding Research, Carl-von-Linné Weg 10, 50829, Cologne, Germany
- Cluster of Excellence on Plant Sciences "From Complex Traits towards Synthetic Modules", 40225, Düsseldorf, Germany
| | - Adrian Roggen
- Institute for Plant Sciences, University of Cologne, Zülpicher Str. 47b, 50674, Cologne, Germany
- Max Planck Institute for Plant Breeding Research, Carl-von-Linné Weg 10, 50829, Cologne, Germany
| | - Hequan Sun
- Max Planck Institute for Plant Breeding Research, Carl-von-Linné Weg 10, 50829, Cologne, Germany
| | - Sara C Stolze
- Max Planck Institute for Plant Breeding Research, Carl-von-Linné Weg 10, 50829, Cologne, Germany
| | - Hirofumi Nakagami
- Max Planck Institute for Plant Breeding Research, Carl-von-Linné Weg 10, 50829, Cologne, Germany
| | - Korbinian Schneeberger
- Max Planck Institute for Plant Breeding Research, Carl-von-Linné Weg 10, 50829, Cologne, Germany
| | - Ton Timmers
- Max Planck Institute for Plant Breeding Research, Carl-von-Linné Weg 10, 50829, Cologne, Germany
| | - Maria C Albani
- Institute for Plant Sciences, University of Cologne, Zülpicher Str. 47b, 50674, Cologne, Germany
- Max Planck Institute for Plant Breeding Research, Carl-von-Linné Weg 10, 50829, Cologne, Germany
- Cluster of Excellence on Plant Sciences "From Complex Traits towards Synthetic Modules", 40225, Düsseldorf, Germany
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Dupouy G, McDermott E, Cashell R, Scian A, McHale M, Ryder P, de Groot J, Lucca N, Brychkova G, McKeown PC, Spillane C. Plastid ribosome protein L5 is essential for post-globular embryo development in Arabidopsis thaliana. PLANT REPRODUCTION 2022; 35:189-204. [PMID: 35247095 PMCID: PMC9352626 DOI: 10.1007/s00497-022-00440-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/17/2021] [Accepted: 02/14/2022] [Indexed: 06/14/2023]
Abstract
Plastid ribosomal proteins (PRPs) can play essential roles in plastid ribosome functioning that affect plant function and development. However, the roles of many PRPs remain unknown, including elucidation of which PRPs are essential or display redundancy. Here, we report that the nuclear-encoded PLASTID RIBOSOMAL PROTEIN L5 (PRPL5) is essential for early embryo development in A. thaliana, as homozygous loss-of-function mutations in the PRPL5 gene impairs chloroplast development and leads to embryo failure to develop past the globular stage. We confirmed the prpl5 embryo-lethal phenotype by generating a mutant CRISPR/Cas9 line and by genetic complementation. As PRPL5 underwent transfer to the nuclear genome early in the evolution of Embryophyta, PRPL5 can be expected to have acquired a chloroplast transit peptide. We identify and validate the presence of an N-terminal chloroplast transit peptide, but unexpectedly also confirm the presence of a conserved and functional Nuclear Localization Signal on the protein C-terminal end. This study highlights the fundamental role of the plastid translation machinery during the early stages of embryo development in plants and raises the possibility of additional roles of plastid ribosomal proteins in the nucleus.
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Affiliation(s)
- Gilles Dupouy
- Genetics and Biotechnology Lab, Plant and AgriBiosciences Research Centre (PABC), Ryan Institute, Aras de Brun, National University of Ireland Galway, University Road, Galway, H91 REW4, Ireland
| | - Emma McDermott
- Genetics and Biotechnology Lab, Plant and AgriBiosciences Research Centre (PABC), Ryan Institute, Aras de Brun, National University of Ireland Galway, University Road, Galway, H91 REW4, Ireland
| | - Ronan Cashell
- Genetics and Biotechnology Lab, Plant and AgriBiosciences Research Centre (PABC), Ryan Institute, Aras de Brun, National University of Ireland Galway, University Road, Galway, H91 REW4, Ireland
| | - Anna Scian
- Genetics and Biotechnology Lab, Plant and AgriBiosciences Research Centre (PABC), Ryan Institute, Aras de Brun, National University of Ireland Galway, University Road, Galway, H91 REW4, Ireland
| | - Marcus McHale
- Genetics and Biotechnology Lab, Plant and AgriBiosciences Research Centre (PABC), Ryan Institute, Aras de Brun, National University of Ireland Galway, University Road, Galway, H91 REW4, Ireland
| | - Peter Ryder
- Genetics and Biotechnology Lab, Plant and AgriBiosciences Research Centre (PABC), Ryan Institute, Aras de Brun, National University of Ireland Galway, University Road, Galway, H91 REW4, Ireland
| | - Joelle de Groot
- Genetics and Biotechnology Lab, Plant and AgriBiosciences Research Centre (PABC), Ryan Institute, Aras de Brun, National University of Ireland Galway, University Road, Galway, H91 REW4, Ireland
| | - Noel Lucca
- Genetics and Biotechnology Lab, Plant and AgriBiosciences Research Centre (PABC), Ryan Institute, Aras de Brun, National University of Ireland Galway, University Road, Galway, H91 REW4, Ireland
| | - Galina Brychkova
- Genetics and Biotechnology Lab, Plant and AgriBiosciences Research Centre (PABC), Ryan Institute, Aras de Brun, National University of Ireland Galway, University Road, Galway, H91 REW4, Ireland
| | - Peter C McKeown
- Genetics and Biotechnology Lab, Plant and AgriBiosciences Research Centre (PABC), Ryan Institute, Aras de Brun, National University of Ireland Galway, University Road, Galway, H91 REW4, Ireland
| | - Charles Spillane
- Genetics and Biotechnology Lab, Plant and AgriBiosciences Research Centre (PABC), Ryan Institute, Aras de Brun, National University of Ireland Galway, University Road, Galway, H91 REW4, Ireland.
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8
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Wang C, Blondel L, Quadrado M, Dargel-Graffin C, Mireau H. Pentatricopeptide repeat protein MITOCHONDRIAL STABILITY FACTOR 3 ensures mitochondrial RNA stability and embryogenesis. PLANT PHYSIOLOGY 2022; 190:669-681. [PMID: 35751603 PMCID: PMC9434245 DOI: 10.1093/plphys/kiac309] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Accepted: 06/09/2022] [Indexed: 05/29/2023]
Abstract
Gene expression in plant mitochondria is predominantly governed at the post-transcriptional level and relies mostly on nuclear-encoded proteins. However, the protein factors involved and the underlying molecular mechanisms are still not well understood. Here, we report on the function of the MITOCHONDRIAL STABILITY FACTOR 3 (MTSF3) protein, previously named EMBRYO DEFECTIVE 2794 (EMB2794), and show that it is essential for accumulation of the mitochondrial NADH dehydrogenase subunit 2 (nad2) transcript in Arabidopsis (Arabidopsis thaliana) but not for splicing of nad2 intron 2 as previously proposed. The MTSF3 gene encodes a pentatricopeptide repeat protein that localizes in the mitochondrion. An MTSF3 null mutation induces embryonic lethality, but viable mtsf3 mutant plants can be generated through partial complementation with the developmentally regulated ABSCISIC ACID INSENSITIVE3 promoter. Genetic analyses revealed growth retardation in rescued mtsf3 plants owing to the specific destabilization of mature nad2 mRNA and a nad2 precursor transcript bearing exons 3 to 5. Biochemical data demonstrate that MTSF3 protein specifically binds to the 3' terminus of nad2. Destabilization of nad2 mRNA induces a substantial decrease in complex I assembly and activity and overexpression of the alternative respiratory pathway. Our results support a role for MTSF3 protein in protecting two nad2 transcripts from degradation by mitochondrial exoribonucleases by binding to their 3' extremities.
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Affiliation(s)
- Chuande Wang
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), 78000, Versailles, France
| | - Lisa Blondel
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), 78000, Versailles, France
| | - Martine Quadrado
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), 78000, Versailles, France
| | - Céline Dargel-Graffin
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), 78000, Versailles, France
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9
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Kulichová K, Pieters J, Kumar V, Honys D, Hafidh S. A Plastid-Bound Ankyrin Repeat Protein Controls Gametophyte and Early Embryo Development in Arabidopsis thaliana. FRONTIERS IN PLANT SCIENCE 2022; 13:767339. [PMID: 35350296 PMCID: PMC8958021 DOI: 10.3389/fpls.2022.767339] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Accepted: 01/10/2022] [Indexed: 06/14/2023]
Abstract
Proplastids are essential precursors for multi-fate plastid biogenesis, including chloroplast differentiation, a powerhouse for photosynthesis in plants. Arabidopsis ankyrin repeat protein (AKRP, AT5G66055) is a plastid-localized protein with a putative function in plastid differentiation and morphogenesis. Loss of function of akrp leads to embryo developmental arrest. Whether AKRP is critical pre-fertilization has remained unresolved. Here, using reverse genetics, we report a new allele, akrp-3, that exhibited a reduced frequency of mutant embryos (<13%) compared to previously reported alleles. akrp-3 affected both male and female gametophytes resulting in reduced viability, incompetence in pollen tube attraction, altered gametic cell fate, and embryo arrest that were depleted of chlorophyll. AKRP is widely expressed, and the AKRP-GFP fusion localized to plastids of both gametophytes, in isolated chloroplast and co-localized with a plastid marker in pollen and pollen tubes. Cell-type-specific complementation of akrp-3 hinted at the developmental timing at which AKRP might play an essential role. Our findings provide a plausible insight into the crucial role of AKRP in the differentiation of both gametophytes and coupling embryo development with chlorophyll synthesis.
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Affiliation(s)
- Katarína Kulichová
- Laboratory of Pollen Biology, Institute of Experimental Botany of the Czech Academy of Sciences, Prague, Czechia
| | - Janto Pieters
- Laboratory of Pollen Biology, Institute of Experimental Botany of the Czech Academy of Sciences, Prague, Czechia
| | - Vinod Kumar
- Laboratory of Pollen Biology, Institute of Experimental Botany of the Czech Academy of Sciences, Prague, Czechia
| | - David Honys
- Laboratory of Pollen Biology, Institute of Experimental Botany of the Czech Academy of Sciences, Prague, Czechia
- Department of Plant Experimental Biology, Faculty of Science, Charles University, Prague, Czechia
| | - Said Hafidh
- Laboratory of Pollen Biology, Institute of Experimental Botany of the Czech Academy of Sciences, Prague, Czechia
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10
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Plant development: Suspensors as a battlefield for parental tug-of-war? Curr Biol 2021; 31:R1424-R1426. [PMID: 34752766 DOI: 10.1016/j.cub.2021.09.081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Parental contributions to zygotes can influence early embryogenesis and may regulate the distribution of maternal resources to progeny. A new study in Arabidopsis thaliana has demonstrated that signaling components from maternal sporophytic tissues and paternal gametes converge in zygotes to promote elongation of the extraembryonic suspensor, which supports the developing embryo proper.
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11
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Independent parental contributions initiate zygote polarization in Arabidopsis thaliana. Curr Biol 2021; 31:4810-4816.e5. [PMID: 34496220 DOI: 10.1016/j.cub.2021.08.033] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 07/09/2021] [Accepted: 08/11/2021] [Indexed: 12/24/2022]
Abstract
Embryogenesis of flowering plants is initiated by polarization of the zygote, a prerequisite for correct axis formation in the embryo. The daughter cells of the asymmetric zygote division form the pro-embryo and the mostly extra-embryonic suspensor.1 The suspensor plays a pivotal role in nutrient and hormone transport and rapid growth of the embryo.2,3 Zygote polarization is controlled by a MITOGEN-ACTIVATING PROTEIN (MAP) kinase signaling pathway including the MAPKK kinase (MAP3K) YODA (YDA)4 and the upstream membrane-associated proteins BRASINOSTEROID SIGNALING KINASE 1 (BSK1) and BSK2.5,6 Furthermore, suspensor development is controlled by cysteine-rich peptides of the EMBRYO SURROUNDING FACTOR 1 (ESF1) family.7 While they act genetically upstream of YDA, the corresponding receptor to perceive these potential ligands is unknown. In other developmental processes, such as stomata development, YDA activity is controlled by receptor kinases of the ERECTA family (ERf).8-12 While the receptor kinases upstream of BSK1/2 in the embryo have so far not been identified,1 YDA is in part activated by the sperm cell-derived BSK family member SHORT SUSPENSOR (SSP) that represents a naturally occurring, constitutively active variant of BSK1.5,13 It has been speculated that SSP might be a paternal component of a parental tug-of-war controlling resource allocation toward the embryo.2,13 Here, we show that in addition to SSP, the receptor kinase ERECTA plays a crucial role in zygote polarization as a maternally contributed part of the embryonic YDA pathway. We conclude that two independent parental contributions initiate zygote polarization and control embryo development.
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12
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Kao P, Schon MA, Mosiolek M, Enugutti B, Nodine MD. Gene expression variation in Arabidopsis embryos at single-nucleus resolution. Development 2021; 148:dev199589. [PMID: 34142712 PMCID: PMC8276985 DOI: 10.1242/dev.199589] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Accepted: 05/24/2021] [Indexed: 12/17/2022]
Abstract
Soon after fertilization of egg and sperm, plant genomes become transcriptionally activated and drive a series of coordinated cell divisions to form the basic body plan during embryogenesis. Early embryonic cells rapidly diversify from each other, and investigation of the corresponding gene expression dynamics can help elucidate underlying cellular differentiation programs. However, current plant embryonic transcriptome datasets either lack cell-specific information or have RNA contamination from surrounding non-embryonic tissues. We have coupled fluorescence-activated nuclei sorting together with single-nucleus mRNA-sequencing to construct a gene expression atlas of Arabidopsis thaliana early embryos at single-cell resolution. In addition to characterizing cell-specific transcriptomes, we found evidence that distinct epigenetic and transcriptional regulatory mechanisms operate across emerging embryonic cell types. These datasets and analyses, as well as the approach we devised, are expected to facilitate the discovery of molecular mechanisms underlying pattern formation in plant embryos. This article has an associated 'The people behind the papers' interview.
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Affiliation(s)
- Ping Kao
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna Bio Center (VBC), Dr Bohr-Gasse 3, 1030 Vienna, Austria
| | - Michael A. Schon
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna Bio Center (VBC), Dr Bohr-Gasse 3, 1030 Vienna, Austria
| | - Magdalena Mosiolek
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna Bio Center (VBC), Dr Bohr-Gasse 3, 1030 Vienna, Austria
| | - Balaji Enugutti
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna Bio Center (VBC), Dr Bohr-Gasse 3, 1030 Vienna, Austria
| | - Michael D. Nodine
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna Bio Center (VBC), Dr Bohr-Gasse 3, 1030 Vienna, Austria
- Laboratory of Molecular Biology, Wageningen University, Wageningen 6708 PB, The Netherlands
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13
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Jones SI, Hunt MR, Vodkin LO. An embryo lethal transgenic line manifests global expression changes and elevated protein/oil ratios in heterozygous soybean plants. PLoS One 2020; 15:e0233721. [PMID: 32516314 PMCID: PMC7282645 DOI: 10.1371/journal.pone.0233721] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Accepted: 05/11/2020] [Indexed: 11/18/2022] Open
Abstract
Understanding the molecular processes of seed development is important especially in agronomic crops that produce large amounts of nutrient reserves. Because soybean is a vital source of vegetable protein worldwide, producers are concerned about increasing the total amount of protein in the seed without substantially lowering the amount of oil, another economically important product. Here we describe a transgenic soybean line with increased protein and protein/oil ratio, containing an average of 42.2% protein vs. 38.5% in controls and with a protein/oil ratio of 2.02 vs. 1.76 in controls over several generations of greenhouse growth. Other phenotypic data show that the seeds are heavier, although there are overall lower yields per plant. We postulate these effects result from insertion site mutagenesis by the transgenic construct. As this line never achieves homozygosity and appears to be embryo lethal when homozygous, one functional copy of the gene is most likely essential for normal seed development. Global transcript analyses using RNA-Seq for 88,000 gene models over two stages of cotyledon development revealed that more genes are over-expressed in the transgenic line including ribosomal protein related genes and those in the membrane protein and transporters families. Localization of the insertion site should reveal the genes and developmental program that has been perturbed by the transgenic construct, resulting in this economically interesting increase in protein and the protein/oil ratio.
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Affiliation(s)
- Sarah I. Jones
- Department of Crop Sciences, University of Illinois, Urbana, Illinois, United States of America
| | - Matt R. Hunt
- Department of Crop Sciences, University of Illinois, Urbana, Illinois, United States of America
| | - Lila O. Vodkin
- Department of Crop Sciences, University of Illinois, Urbana, Illinois, United States of America
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14
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OsCpn60β1 is Essential for Chloroplast Development in Rice ( Oryza sativa L.). Int J Mol Sci 2020; 21:ijms21114023. [PMID: 32512821 PMCID: PMC7313468 DOI: 10.3390/ijms21114023] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Revised: 06/01/2020] [Accepted: 06/02/2020] [Indexed: 01/03/2023] Open
Abstract
The chaperonin 60 (Cpn60) protein is of great importance to plants due to its involvement in modulating the folding of numerous chloroplast protein polypeptides. In chloroplasts, Cpn60 is differentiated into two subunit types—Cpn60α and Cpn60β and the rice genome encodes three α and three β plastid chaperonin subunits. However, the functions of Cpn60 family members in rice were poorly understood. In order to investigate the molecular mechanism of OsCpn60β1, we attempted to disrupt the OsCpn60β1 gene by CRISPR/Cas9-mediated targeted mutagenesis in this study. We succeeded in the production of homozygous OsCpn60β1 knockout rice plants. The OsCpn60β1 mutant displayed a striking albino leaf phenotype and was seedling lethal. Electron microscopy observation demonstrated that chloroplasts were severely disrupted in the OsCpn60β1 mutant. In addition, OsCpn60β1 was located in the chloroplast and OsCpn60β1 is constitutively expressed in various tissues particularly in the green tissues. The label-free qualitative proteomics showed that photosynthesis-related pathways and ribosomal pathways were significantly inhibited in OsCpn60β1 mutants. These results indicate that OsCpn60β1 is essential for chloroplast development in rice.
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15
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Meinke DW. Genome-wide identification of EMBRYO-DEFECTIVE (EMB) genes required for growth and development in Arabidopsis. THE NEW PHYTOLOGIST 2020; 226:306-325. [PMID: 31334862 DOI: 10.1111/nph.16071] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2019] [Accepted: 07/10/2019] [Indexed: 05/20/2023]
Abstract
With the emergence of high-throughput methods in plant biology, the importance of long-term projects characterized by incremental advances involving multiple laboratories can sometimes be overlooked. Here, I highlight my 40-year effort to isolate and characterize the most common class of mutants encountered in Arabidopsis (Arabidopsis thaliana): those defective in embryo development. I present an updated dataset of 510 EMBRYO-DEFECTIVE (EMB) genes identified throughout the Arabidopsis community; include important details on 2200 emb mutants and 241 pigment-defective embryo (pde) mutants analyzed in my laboratory; provide curated datasets with key features and publication links for each EMB gene identified; revisit past estimates of 500-1000 total EMB genes in Arabidopsis; document 83 double mutant combinations reported to disrupt embryo development; emphasize the importance of following established nomenclature guidelines and acknowledging allele history in research publications; and consider how best to extend community-based curation and screening efforts to approach saturation for this diverse class of mutants in the future. Continued advances in identifying EMB genes and characterizing their loss-of-function mutant alleles are needed to understand genotype-to-phenotype relationships in Arabidopsis on a broad scale, and to document the contributions of large numbers of essential genes to plant growth and development.
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Affiliation(s)
- David W Meinke
- Department of Plant Biology, Ecology, and Evolution, Oklahoma State University, Stillwater, OK, 74078, USA
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16
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Cell lineage-specific transcriptome analysis for interpreting cell fate specification of proembryos. Nat Commun 2020; 11:1366. [PMID: 32170064 PMCID: PMC7070050 DOI: 10.1038/s41467-020-15189-w] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Accepted: 02/24/2020] [Indexed: 12/17/2022] Open
Abstract
In Arabidopsis, a zygote undergoes asymmetrical cell division that establishes the first two distinct cell types of early proembryos, apical and basal cells. However, the genome-wide transcriptional activities that guide divergence of apical and basal cell development remain unknown. Here, we present a comprehensive transcriptome analysis of apical and basal cell lineages, uncovering distinct molecular pathways during cell lineage specification. Selective deletion of inherited transcripts and specific de novo transcription contribute to the establishment of cell lineage-specific pathways for cell fate specification. Embryo-related pathways have been specifically activated in apical cell lineage since 1-cell embryo stage, but quick transcriptome remodeling toward suspensor-specific pathways are found in basal cell lineage. Furthermore, long noncoding RNAs and alternative splicing isoforms may be involved in cell lineage specification. This work also provides a valuable lineage-specific transcriptome resource to elucidate the molecular pathways for divergence of apical and basal cell lineages at genome-wide scale. Asymmetric division of the Arabidopsis zygote produces apical and basal cells that mainly develop into embryo and suspensor, respectively. Here, Zhou et al. show that de novo transcription and selective RNA turnover establish distinct apical and basal transcriptomes as early as the 1-cell stage of embryo development.
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Plotnikova A, Kellner MJ, Schon MA, Mosiolek M, Nodine MD. MicroRNA Dynamics and Functions During Arabidopsis Embryogenesis. THE PLANT CELL 2019; 31:2929-2946. [PMID: 31562217 PMCID: PMC6925019 DOI: 10.1105/tpc.19.00395] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Revised: 08/16/2019] [Accepted: 09/25/2019] [Indexed: 05/19/2023]
Abstract
MicroRNAs (miRNAs) are short noncoding RNAs that mediate the repression of target transcripts in plants and animals. Although miRNAs are required throughout plant development, relatively little is known regarding their embryonic functions. To systematically characterize embryonic miRNAs in Arabidopsis (Arabidopsis thaliana), we developed or applied high-throughput sequencing-based methods to profile hundreds of miRNAs and associated targets throughout embryogenesis. We discovered dozens of miRNAs that dynamically cleave and repress target transcripts, including 30 that encode transcription factors. Transcriptome analyses indicated that these miRNA:target interactions have profound effects on embryonic gene expression programs. Moreover, we demonstrated that the miRNA-mediated repression of six transcription factors are individually required for proper division patterns of various embryonic cell lineages. These data indicate that the miRNA-directed repression of multiple transcription factors is critically important for the establishment of the plant body plan, and they provide a foundation to further investigate how miRNAs contribute to these initial cellular differentiation events.
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Affiliation(s)
- Alexandra Plotnikova
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna Biocenter, 1030 Vienna, Austria
| | - Max J Kellner
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna Biocenter, 1030 Vienna, Austria
| | - Michael A Schon
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna Biocenter, 1030 Vienna, Austria
| | - Magdalena Mosiolek
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna Biocenter, 1030 Vienna, Austria
| | - Michael D Nodine
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna Biocenter, 1030 Vienna, Austria
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18
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Barrett LG, Legros M, Kumaran N, Glassop D, Raghu S, Gardiner DM. Gene drives in plants: opportunities and challenges for weed control and engineered resilience. Proc Biol Sci 2019; 286:20191515. [PMID: 31551052 PMCID: PMC6784734 DOI: 10.1098/rspb.2019.1515] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Accepted: 09/06/2019] [Indexed: 02/07/2023] Open
Abstract
Plant species, populations and communities are under threat from climate change, invasive pathogens, weeds and habitat fragmentation. Despite considerable research effort invested in genome engineering for crop improvement, the development of genetic tools for the management of wild plant populations has rarely been given detailed consideration. Gene drive systems that allow direct genetic management of plant populations via the spread of fitness-altering genetic modifications could be of great utility. However, despite the rapid development of synthetic tools and their enormous promise, little explicit consideration has been given to their application in plants and, to date, they remain untested. This article considers the potential utility of gene drives for the management of wild plant populations, and examines the factors that might influence the design, spread and efficacy of synthetic drives. To gain insight into optimal ways to design and deploy synthetic drive systems, we investigate the diversity of mechanisms underlying natural gene drives and their dynamics within plant populations and species. We also review potential approaches for engineering gene drives and discuss their potential application to plant genomes. We highlight the importance of considering the impact of plant life-history and genetic architecture on the dynamics of drive, investigate the potential for different types of resistance evolution, and touch on the ethical, regulatory and social challenges ahead.
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Affiliation(s)
- Luke G. Barrett
- CSIRO Agriculture and Food, Canberra, Australian Capital Territory, Australia
- CSIRO Synthetic Biology Future Science Platform, Canberra, Australian Capital Territory, Australia
| | - Mathieu Legros
- CSIRO Agriculture and Food, Canberra, Australian Capital Territory, Australia
- CSIRO Synthetic Biology Future Science Platform, Canberra, Australian Capital Territory, Australia
| | | | - Donna Glassop
- CSIRO Agriculture and Food, Canberra, Australian Capital Territory, Australia
| | - S. Raghu
- CSIRO Health and Biosecurity, Brisbane, Queensland, Australia
| | - Donald M. Gardiner
- CSIRO Agriculture and Food, Canberra, Australian Capital Territory, Australia
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19
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Tiwari LD, Grover A. Cpn60β4 protein regulates growth and developmental cycling and has bearing on flowering time in Arabidopsis thaliana plants. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2019; 286:78-88. [PMID: 31300145 DOI: 10.1016/j.plantsci.2019.05.022] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Revised: 05/25/2019] [Accepted: 05/28/2019] [Indexed: 06/10/2023]
Abstract
Chloroplastic Cpn60 proteins are type I chaperonins comprising of Cpn60α and Cpn60β subunits. Arabidopsis genome contains six entries in Cpn60 family, out of which two are for Cpn60α subunit and four for Cpn60β subunit. We noted that the cpn60β4 knockout mutant plants (T-DNA insertion salk_064887 line) differed from the wild type Col-0 plants in the developmental programming. cpn60β4 mutant plants showed early seed germination. Radical emergence, hypocotyl emergence and cotyledons opening were faster in cpn60β4 mutant plants than WT. Importantly, cpn60β4 mutant plants showed early-flowering phenotype. The number of flowers and siliques as well as weight of the seeds were higher in cpn60β4 mutant plants as compared to Col-0 plants. These effects were reverted to wild type like growth and developmental patterns when genomic fragment of Arabidopsis encompassing Cpn60β4 gene was complemented in the mutant background. The overexpression of Cpn60β4 gene using CaMV35 promoter in wild type background (OE-Cpn60β4) delayed the floral transition as against wild type plants. The plastid division were affected in cpn60β4 mutant plants compared to Col-0. The results of this study suggest that Cpn60β4 plays important role(s) in chloroplast development and is a key factor in plant growth, development and flowering in Arabidopsis.
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Affiliation(s)
- Lalit Dev Tiwari
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, 110021, India
| | - Anil Grover
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, 110021, India.
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20
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The plastidial pentose phosphate pathway is essential for postglobular embryo development in Arabidopsis. Proc Natl Acad Sci U S A 2019; 116:15297-15306. [PMID: 31296566 PMCID: PMC6660741 DOI: 10.1073/pnas.1908556116] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Many mutations that affect plastidial metabolism are embryo-lethal, as expected if the disrupted genes encode enzymes with essential housekeeping functions. However, some mutations that disrupt the plastidial oxidative pentose phosphate pathway (OPPP) cause developmental defects, as well as embryo arrest at the globular stage of development. We show that the OPPP provides the substrate for the pathway of purine synthesis, ribose-5-phosphate, and is thus essential for the generation of nucleic acids during the very early stages of embryo development. Inadequate purine synthesis leads to abnormal patterns of cell division in the embryo and blocks development beyond the globular stage. Therefore, defects in primary metabolic pathways can have profound consequences for development as well as simply reducing growth. Large numbers of genes essential for embryogenesis in Arabidopsis encode enzymes of plastidial metabolism. Disruption of many of these genes results in embryo arrest at the globular stage of development. However, the cause of lethality is obscure. We examined the role of the plastidial oxidative pentose phosphate pathway (OPPP) in embryo development. In nonphotosynthetic plastids the OPPP produces reductant and metabolic intermediates for central biosynthetic processes. Embryos with defects in various steps in the oxidative part of the OPPP had cell division defects and arrested at the globular stage, revealing an absolute requirement for the production via these steps of ribulose-5-phosphate. In the nonoxidative part of the OPPP, ribulose-5-phosphate is converted to ribose-5-phosphate (R5P)—required for purine nucleotide and histidine synthesis—and subsequently to erythrose-4-phosphate, which is required for synthesis of aromatic amino acids. We show that embryo development through the globular stage specifically requires synthesis of R5P rather than erythrose-4-phosphate. Either a failure to convert ribulose-5-phosphate to R5P or a block in purine nucleotide biosynthesis beyond R5P perturbs normal patterning of the embryo, disrupts endosperm development, and causes early developmental arrest. We suggest that seed abortion in mutants unable to synthesize R5P via the oxidative part of the OPPP stems from a lack of substrate for synthesis of purine nucleotides, and hence nucleic acids. Our results show that the plastidial OPPP is essential for normal developmental progression as well as for growth in the embryo.
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21
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Zhang Y, Lu C. The Enigmatic Roles of PPR-SMR Proteins in Plants. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2019; 6:1900361. [PMID: 31380188 PMCID: PMC6662315 DOI: 10.1002/advs.201900361] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Revised: 04/03/2019] [Indexed: 05/21/2023]
Abstract
The pentatricopeptide repeat (PPR) protein family, with more than 400 members, is one of the largest and most diverse protein families in land plants. A small subset of PPR proteins contain a C-terminal small MutS-related (SMR) domain. Although there are relatively few PPR-SMR proteins, they play essential roles in embryo development, chloroplast biogenesis and gene expression, and plastid-to-nucleus retrograde signaling. Here, recent advances in understanding the roles of PPR-SMR proteins and the SMR domain based on a combination of genetic, biochemical, and physiological analyses are described. In addition, the potential of the PPR-SMR protein SOT1 to serve as a tool for RNA manipulation is highlighted.
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Affiliation(s)
- Yi Zhang
- State Key Laboratory of Crop BiologyCollege of Life SciencesShandong Agricultural UniversityTaianShandong271018P. R. China
| | - Congming Lu
- State Key Laboratory of Crop BiologyCollege of Life SciencesShandong Agricultural UniversityTaianShandong271018P. R. China
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22
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Mach J. Fear Not the Unknown: OPENER as a Study in Shedding Light on Genes with Unknown Function. THE PLANT CELL 2019; 31:1420. [PMID: 31142580 PMCID: PMC6635872 DOI: 10.1105/tpc.19.00420] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
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23
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Wang W, Zhang X, Niittylä T. OPENER Is a Nuclear Envelope and Mitochondria Localized Protein Required for Cell Cycle Progression in Arabidopsis. THE PLANT CELL 2019; 31:1446-1465. [PMID: 31023726 PMCID: PMC6635878 DOI: 10.1105/tpc.19.00033] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Revised: 04/01/2019] [Accepted: 04/23/2019] [Indexed: 05/19/2023]
Abstract
Currently one-third of the proteins encoded by the Arabidopsis (Arabidopsis thaliana) genome are of unknown function. Some of these unknown proteins are likely to be involved in uncharacterized vital biological processes. Evolutionarily conserved single copy genes in flowering plants have been shown to be enriched in essential housekeeping functions. This together with publicly available gene expression data allows for a focused search for uncharacterized essential genes. Here we identify an essential single copy gene called OPENER (OPNR) in Arabidopsis. We show that OPNR is predominantly expressed in actively dividing cells and performs essential functions in seed development and root meristem maintenance. Cell cycle tracking using 5-ethynyl-2'-deoxyuridine staining and fluorescent cell cycle markers together with the increased size of nucleolus and nucleus in opnr mutants indicate that OPNR is required for cell cycle progression through the S or G2 phases. Intriguingly, OPNR localizes to the nuclear envelope and mitochondria. Furthermore, the nuclear envelope localization of OPNR is dependent on its interaction with nuclear inner membrane Sad1/UNC-84 (SUN) domain proteins SUN1 and SUN2. Taken together our results open a line of investigation into an evolutionarily conserved essential cellular process occurring in both the nuclear envelopes and mitochondria of dividing cells.
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Affiliation(s)
- Wei Wang
- Umea Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, 90183 Umea, Sweden
| | - Xueyang Zhang
- Umea Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, 90183 Umea, Sweden
| | - Totte Niittylä
- Umea Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, 90183 Umea, Sweden
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24
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Zuo Z, Weraduwage SM, Lantz AT, Sanchez LM, Weise SE, Wang J, Childs KL, Sharkey TD. Isoprene Acts as a Signaling Molecule in Gene Networks Important for Stress Responses and Plant Growth. PLANT PHYSIOLOGY 2019; 180:124-152. [PMID: 30760638 PMCID: PMC6501071 DOI: 10.1104/pp.18.01391] [Citation(s) in RCA: 57] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Accepted: 02/04/2019] [Indexed: 05/05/2023]
Abstract
Isoprene synthase converts dimethylallyl diphosphate to isoprene and appears to be necessary and sufficient to allow plants to emit isoprene at significant rates. Isoprene can protect plants from abiotic stress but is not produced naturally by all plants; for example, Arabidopsis (Arabidopsis thaliana) and tobacco (Nicotiana tabacum) do not produce isoprene. It is typically present at very low concentrations, suggesting a role as a signaling molecule; however, its exact physiological role and mechanism of action are not fully understood. We transformed Arabidopsis with a Eucalyptus globulus isoprene synthase The regulatory mechanisms of photosynthesis and isoprene emission were similar to those of native emitters, indicating that regulation of isoprene emission is not specific to isoprene-emitting species. Leaf chlorophyll and carotenoid contents were enhanced by isoprene, which also had a marked positive effect on hypocotyl, cotyledon, leaf, and inflorescence growth in Arabidopsis. By contrast, leaf and stem growth was reduced in tobacco engineered to emit isoprene. Expression of genes belonging to signaling networks or associated with specific growth regulators (e.g. gibberellic acid that promotes growth and jasmonic acid that promotes defense) and genes that lead to stress tolerance was altered by isoprene emission. Isoprene likely executes its effects on growth and stress tolerance through direct regulation of gene expression. Enhancement of jasmonic acid-mediated defense signaling by isoprene may trigger a growth-defense tradeoff leading to variations in the growth response. Our data support a role for isoprene as a signaling molecule.
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Affiliation(s)
- Zhaojiang Zuo
- School of Forestry and Biotechnology, Zhejiang Agriculture and Forestry University, Lin'an 311300, China
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824
| | - Sarathi M Weraduwage
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, Michigan 48824
- Plant Resilience Institute, Michigan State University, East Lansing, Michigan 48824
| | - Alexandra T Lantz
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824
| | - Lydia M Sanchez
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824
| | - Sean E Weise
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, Michigan 48824
| | - Jie Wang
- Department of Plant Biology, Michigan State University, East Lansing, Michigan 48824
| | - Kevin L Childs
- Department of Plant Biology, Michigan State University, East Lansing, Michigan 48824
| | - Thomas D Sharkey
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, Michigan 48824
- Plant Resilience Institute, Michigan State University, East Lansing, Michigan 48824
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25
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Armenta-Medina A, Gillmor CS. Genetic, molecular and parent-of-origin regulation of early embryogenesis in flowering plants. Curr Top Dev Biol 2019; 131:497-543. [DOI: 10.1016/bs.ctdb.2018.11.008] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
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26
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Caselli F, Beretta VM, Mantegazza O, Petrella R, Leo G, Guazzotti A, Herrera-Ubaldo H, de Folter S, Mendes MA, Kater MM, Gregis V. REM34 and REM35 Control Female and Male Gametophyte Development in Arabidopsis thaliana. FRONTIERS IN PLANT SCIENCE 2019; 10:1351. [PMID: 31708954 PMCID: PMC6821719 DOI: 10.3389/fpls.2019.01351] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Accepted: 10/01/2019] [Indexed: 05/13/2023]
Abstract
The REproductive Meristem (REM) gene family encodes for transcription factors belonging to the B3 DNA binding domain superfamily. In Arabidopsis thaliana, the REM gene family is composed of 45 members, preferentially expressed during flower, ovule, and seed developments. Only a few members of this family have been functionally characterized: VERNALIZATION1 (VRN1) and, most recently, TARGET OF FLC AND SVP1 (TFS1) regulate flowering time and VERDANDI (VDD), together with VALKYRIE (VAL) that control the death of the receptive synergid cell in the female gametophyte. We investigated the role of REM34, REM35, and REM36, three closely related and linked genes similarly expressed in both female and male gametophytes. Simultaneous silencing by RNA interference (RNAi) caused about 50% of the ovules to remain unfertilized. Careful evaluation of both ovule and pollen developments showed that this partial sterility of the transgenic RNAi lines was due to a postmeiotic block in both female and male gametophytes. Furthermore, protein interaction assays revealed that REM34 and REM35 interact, which suggests that they work together during the first stages of gametogenesis.
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Affiliation(s)
- Francesca Caselli
- Dipartimento di Bioscienze, Università degli Studi di Milano, Milan, Italy
| | | | - Otho Mantegazza
- Dipartimento di Bioscienze, Università degli Studi di Milano, Milan, Italy
| | - Rosanna Petrella
- Dipartimento di Bioscienze, Università degli Studi di Milano, Milan, Italy
| | - Giulia Leo
- Dipartimento di Bioscienze, Università degli Studi di Milano, Milan, Italy
| | - Andrea Guazzotti
- Dipartimento di Bioscienze, Università degli Studi di Milano, Milan, Italy
| | - Humberto Herrera-Ubaldo
- Laboratorio Nacional de Genómica para la Biodiversidad, Unidad de Genómica Avanzada, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Irapuato, Mexico
| | - Stefan de Folter
- Laboratorio Nacional de Genómica para la Biodiversidad, Unidad de Genómica Avanzada, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Irapuato, Mexico
| | | | - Martin M. Kater
- Dipartimento di Bioscienze, Università degli Studi di Milano, Milan, Italy
| | - Veronica Gregis
- Dipartimento di Bioscienze, Università degli Studi di Milano, Milan, Italy
- *Correspondence: Veronica Gregis,
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Forsthoefel NR, Klag KA, McNichol SR, Arnold CE, Vernon CR, Wood WW, Vernon DM. Arabidopsis PIRL6 Is Essential for Male and Female Gametogenesis and Is Regulated by Alternative Splicing. PLANT PHYSIOLOGY 2018; 178:1154-1169. [PMID: 30206104 PMCID: PMC6236607 DOI: 10.1104/pp.18.00329] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Accepted: 08/29/2018] [Indexed: 05/07/2023]
Abstract
Plant intracellular Ras-group leucine-rich repeat (LRR) proteins (PIRLs) are related to Ras-interacting animal LRR proteins that participate in developmental cell signaling. Systematic knockout analysis has implicated some members of the Arabidopsis (Arabidopsis thaliana) PIRL family in pollen development. However, for PIRL6, no bona fide knockout alleles have been recovered, suggesting that it may have an essential function in both male and female gametophytes. To test this hypothesis, we investigated PIRL6 expression and induced knockdown by RNA interference. Knockdown triggered defects in gametogenesis, resulting in abnormal pollen and early developmental arrest in the embryo sac. Consistent with this, PIRL6 was expressed in gametophytes: functional transcripts were detected in wild-type flowers but not in sporocyteless (spl) mutant flowers, which do not produce gametophytes. A genomic PIRL6-GFP fusion construct confirmed expression in both pollen and the embryo sac. Interestingly, PIRL6 is part of a convergent overlapping gene pair, a scenario associated with an increased likelihood of alternative splicing. We detected multiple alternative PIRL6 mRNAs in vegetative organs and spl mutant flowers, tissues that lacked the functionally spliced transcript. cDNA sequencing revealed that all contained intron sequences and premature termination codons. These alternative mRNAs accumulated in the nonsense-mediated decay mutant upf3, indicating that they are normally subjected to degradation. Together, these results demonstrate that PIRL6 is required in both male and female gametogenesis and suggest that sporophytic expression is negatively regulated by unproductive alternative splicing. This posttranscriptional mechanism may function to minimize PIRL6 protein expression in sporophyte tissues while allowing the overlapping adjacent gene to remain widely transcribed.
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Affiliation(s)
- Nancy R Forsthoefel
- Program in Biochemistry, Biophysics, and Molecular Biology, Whitman College, Walla Walla, Washington 99362
| | - Kendra A Klag
- Program in Biochemistry, Biophysics, and Molecular Biology, Whitman College, Walla Walla, Washington 99362
| | - Savannah R McNichol
- Program in Biochemistry, Biophysics, and Molecular Biology, Whitman College, Walla Walla, Washington 99362
| | - Claire E Arnold
- Program in Biochemistry, Biophysics, and Molecular Biology, Whitman College, Walla Walla, Washington 99362
| | - Corina R Vernon
- Program in Biochemistry, Biophysics, and Molecular Biology, Whitman College, Walla Walla, Washington 99362
| | - Whitney W Wood
- Program in Biochemistry, Biophysics, and Molecular Biology, Whitman College, Walla Walla, Washington 99362
| | - Daniel M Vernon
- Program in Biochemistry, Biophysics, and Molecular Biology, Whitman College, Walla Walla, Washington 99362
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A pex1 missense mutation improves peroxisome function in a subset of Arabidopsis pex6 mutants without restoring PEX5 recycling. Proc Natl Acad Sci U S A 2018; 115:E3163-E3172. [PMID: 29555730 DOI: 10.1073/pnas.1721279115] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
Peroxisomes are eukaryotic organelles critical for plant and human development because they house essential metabolic functions, such as fatty acid β-oxidation. The interacting ATPases PEX1 and PEX6 contribute to peroxisome function by recycling PEX5, a cytosolic receptor needed to import proteins targeted to the peroxisomal matrix. Arabidopsis pex6 mutants exhibit low PEX5 levels and defects in peroxisomal matrix protein import, oil body utilization, peroxisomal metabolism, and seedling growth. These defects are hypothesized to stem from impaired PEX5 retrotranslocation leading to PEX5 polyubiquitination and consequent degradation of PEX5 via the proteasome or of the entire organelle via autophagy. We recovered a pex1 missense mutation in a screen for second-site suppressors that restore growth to the pex6-1 mutant. Surprisingly, this pex1-1 mutation ameliorated the metabolic and physiological defects of pex6-1 without restoring PEX5 levels. Similarly, preventing autophagy by introducing an atg7-null allele partially rescued pex6-1 physiological defects without restoring PEX5 levels. atg7 synergistically improved matrix protein import in pex1-1 pex6-1, implying that pex1-1 improves peroxisome function in pex6-1 without impeding autophagy of peroxisomes (i.e., pexophagy). pex1-1 differentially improved peroxisome function in various pex6 alleles but worsened the physiological and molecular defects of a pex26 mutant, which is defective in the tether anchoring the PEX1-PEX6 hexamer to the peroxisome. Our results support the hypothesis that, beyond PEX5 recycling, PEX1 and PEX6 have additional functions in peroxisome homeostasis and perhaps in oil body utilization.
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29
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Wu R, Wang T, Warren BAW, Thomson SJ, Allan AC, Macknight RC, Varkonyi-Gasic E. Kiwifruit SVP2 controls developmental and drought-stress pathways. PLANT MOLECULAR BIOLOGY 2018; 96:233-244. [PMID: 29222611 DOI: 10.1007/s11103-017-0688-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Accepted: 11/30/2017] [Indexed: 05/20/2023]
Abstract
Genome-wide targets of Actinidia chinensis SVP2 confirm roles in ABA- and dehydration-mediated growth repression and reveal a conservation in mechanism of action between SVP genes of taxonomically distant Arabidopsis and a woody perennial kiwifruit. The molecular mechanisms underlying growth and dormancy in woody perennials are largely unknown. In Arabidopsis, the MADS-box transcription factor SHORT VEGETATIVE PHASE (SVP) plays a key role in the progression from vegetative to floral development, and in woody perennials SVP-like genes are also proposed to be involved in controlling dormancy. During kiwifruit development SVP2 has a role in growth inhibition, with high-chill kiwifruit Actinidia deliciosa transgenic lines overexpressing SVP2 showing suppressed bud outgrowth. Transcriptomic analyses of these plants suggests that SVP2 mimics the well-documented abscisic acid (ABA) effect on the plant dehydration response. To corroborate the growth inhibition role of SVP2 in kiwifruit development at the molecular level, we analysed the genome-wide direct targets of SVP2 using chromatin immunoprecipitation followed by high-throughput sequencing in kiwifruit A. chinensis. SVP2 was found to bind to at least 297 target sites in the kiwifruit genome, and potentially modulates 252 genes that function in a range of biological processes, especially those involved in repressing meristem activity and ABA-mediated dehydration pathways. In addition, our ChIP-seq analysis reveals remarkable conservation in mechanism of action between SVP genes of taxonomically distant plant species.
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Affiliation(s)
- Rongmei Wu
- The New Zealand Institute for Plant and Food Research Limited (PFR) Mt Albert, Auckland Mail Centre, Private Bag 92169, Auckland, 1142, New Zealand
| | - Tianchi Wang
- The New Zealand Institute for Plant and Food Research Limited (PFR) Mt Albert, Auckland Mail Centre, Private Bag 92169, Auckland, 1142, New Zealand
| | - Ben A W Warren
- The New Zealand Institute for Plant and Food Research Limited (PFR) Mt Albert, Auckland Mail Centre, Private Bag 92169, Auckland, 1142, New Zealand
| | - Susan J Thomson
- The New Zealand Institute for Plant and Food Research Limited (PFR) Lincoln, Christchurch Mail Centre, Private Bag 4704, Christchurch, 8140, New Zealand
| | - Andrew C Allan
- The New Zealand Institute for Plant and Food Research Limited (PFR) Mt Albert, Auckland Mail Centre, Private Bag 92169, Auckland, 1142, New Zealand
- School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland, New Zealand
| | - Richard C Macknight
- Department of Biochemistry, The New Zealand Institute for Plant and Food Research Limited, University of Otago, PO Box 56, Dunedin, 9054, New Zealand
| | - Erika Varkonyi-Gasic
- The New Zealand Institute for Plant and Food Research Limited (PFR) Mt Albert, Auckland Mail Centre, Private Bag 92169, Auckland, 1142, New Zealand.
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Robles P, Quesada V. Emerging Roles of Mitochondrial Ribosomal Proteins in Plant Development. Int J Mol Sci 2017; 18:ijms18122595. [PMID: 29207474 PMCID: PMC5751198 DOI: 10.3390/ijms18122595] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2017] [Revised: 11/28/2017] [Accepted: 12/01/2017] [Indexed: 11/26/2022] Open
Abstract
Mitochondria are the powerhouse of eukaryotic cells because they are responsible for energy production through the aerobic respiration required for growth and development. These organelles harbour their own genomes and translational apparatus: mitochondrial ribosomes or mitoribosomes. Deficient mitochondrial translation would impair the activity of this organelle, and is expected to severely perturb different biological processes of eukaryotic organisms. In plants, mitoribosomes consist of three rRNA molecules, encoded by the mitochondrial genome, and an undefined set of ribosomal proteins (mitoRPs), encoded by nuclear and organelle genomes. A detailed functional and structural characterisation of the mitochondrial translation apparatus in plants is currently lacking. In some plant species, presence of small gene families of mitoRPs whose members have functionally diverged has led to the proposal of the heterogeneity of the mitoribosomes. This hypothesis supports a dynamic composition of the mitoribosomes. Information on the effects of the impaired function of mitoRPs on plant development is extremely scarce. Nonetheless, several works have recently reported the phenotypic and molecular characterisation of plant mutants affected in mitoRPs that exhibit alterations in specific development aspects, such as embryogenesis, leaf morphogenesis or the formation of reproductive tissues. Some of these results would be in line with the ribosomal filter hypothesis, which proposes that ribosomes, besides being the machinery responsible for performing translation, are also able to regulate gene expression. This review describes the phenotypic effects on plant development displayed by the mutants characterised to date that are defective in genes which encode mitoRPs. The elucidation of plant mitoRPs functions will provide a better understanding of the mechanisms that control organelle gene expression and their contribution to plant growth and morphogenesis.
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Affiliation(s)
- Pedro Robles
- Instituto de Bioingeniería, Universidad Miguel Hernández, Campus de Elche, 03202 Elche, Spain.
| | - Víctor Quesada
- Instituto de Bioingeniería, Universidad Miguel Hernández, Campus de Elche, 03202 Elche, Spain.
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31
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Haploid Selection Favors Suppressed Recombination Between Sex Chromosomes Despite Causing Biased Sex Ratios. Genetics 2017; 207:1631-1649. [PMID: 29051194 DOI: 10.1534/genetics.117.300062] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Accepted: 10/11/2017] [Indexed: 11/18/2022] Open
Abstract
To date, research on the evolution of sex chromosomes has focused on sexually antagonistic selection among diploids, which has been shown to be a potent driver of the strata and reduced recombination that characterize many sex chromosomes. However, significant selection can also occur on haploid genotypes during less conspicuous life cycle stages, e.g., competition among sperm/pollen or meiotic drive during gamete/spore production. These haploid selective processes are typically sex-specific, e.g., gametic/gametophytic competition typically occurs among sperm/pollen, and meiotic drive typically occurs during either spermatogenesis or oogenesis. We use models to investigate whether sex-specific selection on haploids could drive the evolution of recombination suppression on the sex chromosomes, as has been demonstrated for sex-specific selection among diploids. A potential complication is that zygotic sex-ratios become biased when haploid selected loci become linked to the sex-determining region because the zygotic sex ratio is determined by the relative number and fitness of X- vs. Y-bearing sperm. Despite causing biased zygotic sex-ratios, we find that a period of sex-specific haploid selection generally favors recombination suppression on the sex chromosomes. Suppressed recombination is favored because it allows associations to build up between haploid-beneficial alleles and the sex that experiences haploid selection most often (e.g., pollen beneficial alleles become strongly associated with the male determining region, Y or Z). Haploid selected loci can favor recombination suppression even in the absence of selective differences between male and female diploids. Overall, we expand our view of the sex-specific life cycle stages that can drive sex chromosome evolution to include gametic competition and meiotic drive. Based on our models, sex chromosomes should become enriched for genes that experience haploid selection, as is expected for genes that experience sexually antagonistic selection. Thus, we generate a number of predictions that can be evaluated in emerging sex chromosome systems.
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32
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Ke X, Zou W, Ren Y, Wang Z, Li J, Wu X, Zhao J. Functional divergence of chloroplast Cpn60α subunits during Arabidopsis embryo development. PLoS Genet 2017; 13:e1007036. [PMID: 28961247 PMCID: PMC5636168 DOI: 10.1371/journal.pgen.1007036] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Revised: 10/11/2017] [Accepted: 09/20/2017] [Indexed: 02/03/2023] Open
Abstract
Chaperonins are a class of molecular chaperones that assist in the folding and assembly of a wide range of substrates. In plants, chloroplast chaperonins are composed of two different types of subunits, Cpn60α and Cpn60β, and duplication of Cpn60α and Cpn60β genes occurs in a high proportion of plants. However, the importance of multiple Cpn60α and Cpn60β genes in plants is poorly understood. In this study, we found that loss-of-function of CPNA2 (AtCpn60α2), a gene encoding the minor Cpn60α subunit in Arabidopsis thaliana, resulted in arrested embryo development at the globular stage, whereas the other AtCpn60α gene encoding the dominant Cpn60α subunit, CPNA1 (AtCpn60α1), mainly affected embryonic cotyledon development at the torpedo stage and thereafter. Further studies demonstrated that CPNA2 can form a functional chaperonin with CPNB2 (AtCpn60β2) and CPNB3 (AtCpn60β3), while the functional partners of CPNA1 are CPNB1 (AtCpn60β1) and CPNB2. We also revealed that the functional chaperonin containing CPNA2 could assist the folding of a specific substrate, KASI (β-ketoacyl-[acyl carrier protein] synthase I), and that the KASI protein level was remarkably reduced due to loss-of-function of CPNA2. Furthermore, the reduction in the KASI protein level was shown to be the possible cause for the arrest of cpna2 embryos. Our findings indicate that the two Cpn60α subunits in Arabidopsis play different roles during embryo development through forming distinct chaperonins with specific AtCpn60β to assist the folding of particular substrates, thus providing novel insights into functional divergence of Cpn60α subunits in plants. Chaperonins are large oligomeric complexes that are involved in the folding and assembly of numerous proteins in various species. In contrast to other types of chaperonins, chloroplast chaperonins are characterized by the hetero-oligomeric structure composed of two unique types of subunits, Cpn60α and Cpn60β, each of which is present in two or more paralogous forms in most of higher plants. However, the functional significance underlying the wide array of subunit types and complex oligomeric arrangement remains largely unknown. Here, we investigated the role of the minor Cpn60α subunit AtCpn60α2 in Arabidopsis embryo development, and found that AtCpn60α2 is important for the transition of globular embryos to heart-shaped embryos, whereas loss of the dominant Cpn60α subunit AtCpn60α1 affects embryonic cotyledon development. Further studies demonstrated that AtCpn60α2 could form functional chaperonins with AtCpn60β2 and AtCpn60β3 to specifically assist in folding of the substrate KASI, which is important for the formation of heart-shaped embryos. Our results suggest that duplication of Cpn60α genes in higher plants can increase the potential number of chloroplast chaperonin substrates and provide chloroplast chaperonins with more roles in plant growth and development, thus revealing the relationship between duplication and functional specialization of chaperonin genes.
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Affiliation(s)
- Xiaolong Ke
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China
| | - Wenxuan Zou
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China
| | - Yafang Ren
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China
| | - Zhiqin Wang
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China
| | - Jin Li
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China
| | - Xuan Wu
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China
| | - Jie Zhao
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China
- * E-mail:
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Rinaldi MA, Fleming WA, Gonzalez KL, Park J, Ventura MJ, Patel AB, Bartel B. The PEX1 ATPase Stabilizes PEX6 and Plays Essential Roles in Peroxisome Biology. PLANT PHYSIOLOGY 2017; 174:2231-2247. [PMID: 28600347 PMCID: PMC5543962 DOI: 10.1104/pp.17.00548] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2017] [Accepted: 06/07/2017] [Indexed: 05/29/2023]
Abstract
A variety of metabolic pathways are sequestered in peroxisomes, conserved organelles that are essential for human and plant survival. Peroxin (PEX) proteins generate and maintain peroxisomes. The PEX1 ATPase facilitates recycling of the peroxisome matrix protein receptor PEX5 and is the most commonly affected peroxin in human peroxisome biogenesis disorders. Here, we describe the isolation and characterization of, to our knowledge, the first Arabidopsis (Arabidopsis thaliana) pex1 missense alleles: pex1-2 and pex1-3pex1-2 displayed peroxisome-related defects accompanied by reduced PEX1 and PEX6 levels. These pex1-2 defects were exacerbated by growth at high temperature and ameliorated by growth at low temperature or by PEX6 overexpression, suggesting that PEX1 enhances PEX6 stability and vice versa. pex1-3 conferred embryo lethality when homozygous, confirming that PEX1, like several other Arabidopsis peroxins, is essential for embryogenesis. pex1-3 displayed symptoms of peroxisome dysfunction when heterozygous; this semidominance is consistent with PEX1 forming a heterooligomer with PEX6 that is poisoned by pex1-3 subunits. Blocking autophagy partially rescued PEX1/pex1-3 defects, including the restoration of normal peroxisome size, suggesting that increasing peroxisome abundance can compensate for the deficiencies caused by pex1-3 and that the enlarged peroxisomes visible in PEX1/pex1-3 may represent autophagy intermediates. Overexpressing PEX1 in wild-type plants impaired growth, suggesting that excessive PEX1 can be detrimental. Our genetic, molecular, and physiological data support the heterohexamer model of PEX1-PEX6 function in plants.
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Affiliation(s)
- Mauro A Rinaldi
- Department of BioSciences, Rice University, Houston, Texas 77005
| | | | - Kim L Gonzalez
- Department of BioSciences, Rice University, Houston, Texas 77005
| | - Jaeseok Park
- Department of BioSciences, Rice University, Houston, Texas 77005
| | | | - Ashish B Patel
- Department of BioSciences, Rice University, Houston, Texas 77005
| | - Bonnie Bartel
- Department of BioSciences, Rice University, Houston, Texas 77005
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Wang G, Zhong M, Shuai B, Song J, Zhang J, Han L, Ling H, Tang Y, Wang G, Song R. E+ subgroup PPR protein defective kernel 36 is required for multiple mitochondrial transcripts editing and seed development in maize and Arabidopsis. THE NEW PHYTOLOGIST 2017; 214:1563-1578. [PMID: 28277611 DOI: 10.1111/nph.14507] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2016] [Accepted: 01/30/2017] [Indexed: 05/02/2023]
Abstract
Mitochondria are semi-autonomous organelles that are the powerhouse of the cells. Plant mitochondrial RNA editing guided by pentatricopeptide repeat (PPR) proteins is essential for energy production. We identify a maize defective kernel mutant dek36, which produces small and collapsed kernels, leading to embryos and/or seedlings lethality. Seed filling in dek36 is drastically impaired, in line with the defects observed in the organization of endosperm transfer tissue. Positional cloning reveals that DEK36, encoding a mitochondria-targeted E+ subgroup PPR protein, is required for mitochondrial RNA editing at atp4-59, nad7-383 and ccmFN -302, thus resulting in decreased activities of mitochondrial complex I, complex III and complex IV in dek36. Loss-of-function of its Arabidopsis ortholog At DEK36 causes arrested embryo and endosperm development, leading to embryo lethality. At_dek36 also has RNA editing defects in atp4, nad7, ccmFN1 and ccmFN2 , but at the nonconserved sites. Importantly, efficiency of all editing sites in ccmFN1 , ccmFN2 and rps12 is severely decreased in At_dek36, probably caused by the impairment of their RNA stabilization. These results suggest that the DEK36 orthologue pair are essential for embryo and endosperm development in both maize and Arabidopsis, but through divergent function in regulating RNA metabolism of their mitochondrial targets.
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Affiliation(s)
- Gang Wang
- Shanghai Key Laboratory of Bio-Energy Crops, School of Life Sciences, Shanghai University, Shanghai, 200444, China
| | - Mingyu Zhong
- Shanghai Key Laboratory of Bio-Energy Crops, School of Life Sciences, Shanghai University, Shanghai, 200444, China
| | - Bilian Shuai
- Shanghai Key Laboratory of Bio-Energy Crops, School of Life Sciences, Shanghai University, Shanghai, 200444, China
| | - Jiandong Song
- Shanghai Key Laboratory of Bio-Energy Crops, School of Life Sciences, Shanghai University, Shanghai, 200444, China
| | - Jie Zhang
- Shanghai Key Laboratory of Bio-Energy Crops, School of Life Sciences, Shanghai University, Shanghai, 200444, China
| | - Liang Han
- Shanghai Key Laboratory of Bio-Energy Crops, School of Life Sciences, Shanghai University, Shanghai, 200444, China
| | - Huiling Ling
- Shanghai Key Laboratory of Bio-Energy Crops, School of Life Sciences, Shanghai University, Shanghai, 200444, China
| | - Yuanping Tang
- Shanghai Key Laboratory of Bio-Energy Crops, School of Life Sciences, Shanghai University, Shanghai, 200444, China
| | - Guifeng Wang
- Shanghai Key Laboratory of Bio-Energy Crops, School of Life Sciences, Shanghai University, Shanghai, 200444, China
| | - Rentao Song
- Shanghai Key Laboratory of Bio-Energy Crops, School of Life Sciences, Shanghai University, Shanghai, 200444, China
- National Maize Improvement Center of China, China Agricultural University, Beijing, 100193, China
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Wang WJ, Zheng KL, Gong XD, Xu JL, Huang JR, Lin DZ, Dong YJ. The rice TCD11 encoding plastid ribosomal protein S6 is essential for chloroplast development at low temperature. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2017; 259:1-11. [PMID: 28483049 DOI: 10.1016/j.plantsci.2017.02.007] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2016] [Revised: 02/18/2017] [Accepted: 02/20/2017] [Indexed: 05/20/2023]
Abstract
Plastid ribosome proteins (PRPs) are important components for chloroplast biogenesis and early chloroplast development. Although it has been known that chloroplast ribosomes are similar to bacterial ones, the precise molecular function of ribosomal proteins remains to be elucidated in rice. Here, we identified a novel rice mutant, designated tcd11 (thermo-sensitive chlorophyll-deficient mutant 11), characterized by the albino phenotype until it died at 20°C, while displaying normal phenotype at 32°C. The alteration of leaf color in tcd11 mutants was aligned with chlorophyll (Chl) content and chloroplast development. The map-based cloning and molecular complementation showed that TCD11 encodes the ribosomal small subunit protein S6 in chloroplasts (RPS6). TCD11 was abundantly expressed in leaves, suggesting its different expressions in tissues. In addition, the disruption of TCD11 greatly reduced the transcript levels of certain chloroplasts-associated genes and prevented the assembly of ribosome in chloroplasts at low temperature (20°C), whereas they recovered to nearly normal levels at high temperature (32°C). Thus, our data indicate that TCD11 plays an important role in chloroplast development at low temperature. Upon our knowledge, the observations from this study provide a first glimpse into the importance of RPS6 function in rice chloroplast development.
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Affiliation(s)
- Wen-Juan Wang
- Development Center of Plant Germplasm Resources, College of Life and Environment Sciences, Shanghai Normal University, Shanghai 200234, China
| | - Kai-Lun Zheng
- Development Center of Plant Germplasm Resources, College of Life and Environment Sciences, Shanghai Normal University, Shanghai 200234, China
| | - Xiao-Di Gong
- Development Center of Plant Germplasm Resources, College of Life and Environment Sciences, Shanghai Normal University, Shanghai 200234, China; Institute of Genetics and Developmental Biology Chinese Academy of Sciences, No.1 West Beichen Road, Chaoyang District, Beijing, 10010, China
| | - Jian-Long Xu
- The Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, 12 South Zhong-Guan Cun Street, Beijing 100081, China; Agricultural Genome Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Ji-Rong Huang
- Institute of Plant Physiology and Ecology, Shanghai Institute for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Dong-Zhi Lin
- Development Center of Plant Germplasm Resources, College of Life and Environment Sciences, Shanghai Normal University, Shanghai 200234, China.
| | - Yan-Jun Dong
- Development Center of Plant Germplasm Resources, College of Life and Environment Sciences, Shanghai Normal University, Shanghai 200234, China.
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Du L, Zhang J, Qu S, Zhao Y, Su B, Lv X, Li R, Wan Y, Xiao J. The Pentratricopeptide Repeat Protein Pigment-Defective Mutant2 is Involved in the Regulation of Chloroplast Development and Chloroplast Gene Expression in Arabidopsis. PLANT & CELL PHYSIOLOGY 2017; 58:747-759. [PMID: 28158776 DOI: 10.1093/pcp/pcx004] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2016] [Accepted: 01/08/2017] [Indexed: 05/10/2023]
Abstract
The development of functional chloroplasts, which is assisted by a series of nuclear-encoded auxiliary protein factors, is essential for plant autotrophic growth and development. To understand the molecular mechanisms underlying chloroplast development, we isolated and characterized a pigment-defective mutant, pdm2, and its corresponding variegated RNA interference (RNAi) lines in Arabidopsis. Sequence analysis revealed that PDM2 encodes a pentatricopeptide repeat protein that belongs to the P subgroup. Confocal microscopic analysis and immunoblotting of the chloroplast protein fraction showed that PDM2 was located in the stroma. In RNAi plants, protein-related photosynthesis was severely compromised. Furthermore, analysis of the transcript profile of chloroplast genes revealed that plastid-encoded polymerase-dependent transcript levels were markedly reduced, while nuclear-encoded polymerase-dependent transcript levels were increased, in RNAi plants. In addition, PDM2 affects plastid RNA editing efficiency in most editing sites, apparently by directly interacting with multiple organellar RNA editing factor 2 (MORF2) and MORF9. Thus, our results demonstrate that PDM2 is probably involved in the regulation of plastid gene expression required for normal chloroplast development.
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Affiliation(s)
- Liang Du
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, China
| | - Jian Zhang
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, China
| | - Shaofeng Qu
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, China
| | - Yuanyuan Zhao
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, China
| | - Bodan Su
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, China
| | - Xueqin Lv
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, China
| | - Ruili Li
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, China
| | - Yinglang Wan
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, China
| | - Jianwei Xiao
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, China
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Di Fino LM, D'Ambrosio JM, Tejos R, van Wijk R, Lamattina L, Munnik T, Pagnussat GC, Laxalt AM. Arabidopsis phosphatidylinositol-phospholipase C2 (PLC2) is required for female gametogenesis and embryo development. PLANTA 2017; 245:717-728. [PMID: 27999988 DOI: 10.1007/s00425-016-2634-z] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2016] [Accepted: 12/02/2016] [Indexed: 05/20/2023]
Abstract
AtPLC2 is an essential gene in Arabidopsis, since it is required for female gametogenesis and embryo development. AtPLC2 might play a role in cell division during embryo-sac development and early embryogenesis. Phosphoinositide-specific phospholipase C (PI-PLC) plays an important role in signal transduction during plant development and in the response to various biotic- and abiotic stresses. The Arabidopsis PI-PLC gene family is composed of nine members, named PLC1 to PLC9. Here, we report that PLC2 is involved in female gametophyte development and early embryogenesis. Using two Arabidopsis allelic T-DNA insertion lines with different phenotypic penetrations, we observed both female gametophytic defects and aberrant embryos. For the plc2-1 mutant (Ws background), no homozygous plants could be recovered in the offspring from self-pollinated plants. Nonetheless, plc2-1 hemizygous mutants are affected in female gametogenesis, showing embryo sacs arrested at early developmental stages. Allelic hemizygous plc2-2 mutant plants (Col-0 background) present reduced seed set and embryos arrested at the pre-globular stage with abnormal patterns of cell division. A low proportion (0.8%) of plc2-2 homozygous mutants was found to escape lethality and showed morphological defects and disrupted megagametogenesis. PLC2-promoter activity was observed during early megagametogenesis, and after fertilization in the embryo proper. Immunolocalization studies in early stage embryos revealed that PLC2 is restricted to the plasma membrane. Altogether, these results establish a role for PLC2 in both reproductive- and embryo development, presumably by controlling mitosis and/or the formation of cell-division planes.
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Affiliation(s)
- Luciano M Di Fino
- Instituto de Investigaciones Biológicas IIB-Consejo Nacional de Investigaciones Científicas y Técnicas, Universidad Nacional de Mar del Plata, 7600, Mar del Plata, Argentina
| | - Juan Martín D'Ambrosio
- Instituto de Investigaciones Biológicas IIB-Consejo Nacional de Investigaciones Científicas y Técnicas, Universidad Nacional de Mar del Plata, 7600, Mar del Plata, Argentina
| | - Ricardo Tejos
- Facultad de Recursos Naturales Renovables, Universidad Arturo Prat, 111093, Iquique, Chile
- Centro de Biología Molecular Vegetal, Departamento de Biología, Facultad de Ciencias, Universidad de Chile, 7800003, Santiago, Chile
| | - Ringo van Wijk
- Swammerdam Institute for Life Sciences, Section Plant Cell Biology, University of Amsterdam, 1098 XH, Amsterdam, The Netherlands
| | - Lorenzo Lamattina
- Instituto de Investigaciones Biológicas IIB-Consejo Nacional de Investigaciones Científicas y Técnicas, Universidad Nacional de Mar del Plata, 7600, Mar del Plata, Argentina
| | - Teun Munnik
- Swammerdam Institute for Life Sciences, Section Plant Cell Biology, University of Amsterdam, 1098 XH, Amsterdam, The Netherlands
| | - Gabriela C Pagnussat
- Instituto de Investigaciones Biológicas IIB-Consejo Nacional de Investigaciones Científicas y Técnicas, Universidad Nacional de Mar del Plata, 7600, Mar del Plata, Argentina.
| | - Ana M Laxalt
- Instituto de Investigaciones Biológicas IIB-Consejo Nacional de Investigaciones Científicas y Técnicas, Universidad Nacional de Mar del Plata, 7600, Mar del Plata, Argentina.
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An Arabidopsis Natural Epiallele Maintained by a Feed-Forward Silencing Loop between Histone and DNA. PLoS Genet 2017; 13:e1006551. [PMID: 28060933 PMCID: PMC5257005 DOI: 10.1371/journal.pgen.1006551] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2016] [Revised: 01/23/2017] [Accepted: 12/24/2016] [Indexed: 12/26/2022] Open
Abstract
The extent of epigenetic variation is currently well documented, but the number of natural epialleles described so far remains very limited. Determining the relevance of epigenetic changes for natural variation is an important question of research that we investigate by isolating natural epialleles segregating in Arabidopsis recombinant populations. We previously described a genetic incompatibility among Arabidopsis strains based on the silencing of a gene involved in fitness. Here, we isolated a new epiallele resulting from the silencing of a transfer-RNA editing gene in an Arabidopsis accession from the Netherlands (Nok-1). Crosses with the reference accession Col-0 show a complete incompatibility between this epiallele and another locus localized on a different chromosome. We demonstrate that conversion of an unmethylated version of this allele occurs in hybrids, associated with modifications of small RNA populations. These epialleles can also spontaneously revert within the population. Furthermore, we bring evidence that neither METHYLTRANSFERASE 1, maintaining methylation at CGs, nor components of RNA-directed DNA methylation, are key factors for the transmission of the epiallele over generations. This depends only on the self-reinforcing loop between CHROMOMETHYLASE 3 and KRYPTONITE, involving DNA methylated in the CHG context and histone H3 lysine 9 methylation. Our findings reveal a predominant role of this loop in maintaining a natural epiallele. Epialleles are gene variants based on epigenetic marks stably transmitted between generations. Most of the known epialleles existing in the wild were described in plant populations but very few are associated with phenotypes or agronomical traits. In this study, we isolated a new natural epiallele resulting from the silencing of a RNA editing gene essential for plants. We demonstrated that an incompatibility between two Arabidopsis strains depending on this epiallele, is based on DNA methylation of cytosines, an epigenetic mark influencing gene function. In F1 hybrids, obtained by crossing the incompatible parental lines, unmethylated versions of the allele can be converted to methylated ones. The epiallele can also spontaneously revert in very rare cases, within the population. The methylation status of this epiallele can therefore potentially change within the population and is maintained in a metastable state. Indeed, two enzymes promoting histone or DNA methylation, respectively, and acting in loop, are involved in maintaining the epiallele in natural populations, over generations.
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Parker N, Wang Y, Meinke D. Analysis of Arabidopsis Accessions Hypersensitive to a Loss of Chloroplast Translation. PLANT PHYSIOLOGY 2016; 172:1862-1875. [PMID: 27707889 PMCID: PMC5100756 DOI: 10.1104/pp.16.01291] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2016] [Accepted: 10/03/2016] [Indexed: 05/04/2023]
Abstract
Natural accessions of Arabidopsis (Arabidopsis thaliana) differ in their ability to tolerate a loss of chloroplast translation. These differences can be attributed in part to variation in a duplicated nuclear gene (ACC2) that targets homomeric acetyl-coenzyme A carboxylase (ACCase) to plastids. This functional redundancy allows limited fatty acid biosynthesis to occur in the absence of heteromeric ACCase, which is encoded in part by the plastid genome. In the presence of functional ACC2, tolerant alleles of several nuclear genes, not yet identified, enhance the growth of seedlings and embryos disrupted in chloroplast translation. ACC2 knockout mutants, by contrast, are hypersensitive. Here we describe an expanded search for hypersensitive accessions of Arabidopsis, evaluate whether all of these accessions are defective in ACC2, and characterize genotype-to-phenotype relationships for homomeric ACCase variants identified among 855 accessions with sequenced genomes. Null alleles with ACC2 nonsense mutations, frameshift mutations, small deletions, genomic rearrangements, and defects in RNA splicing are included among the most sensitive accessions examined. By contrast, most missense mutations affecting highly conserved residues failed to eliminate ACC2 function. Several accessions were identified where sensitivity could not be attributed to a defect in either ACC2 or Tic20-IV, the chloroplast membrane channel required for ACC2 uptake. Overall, these results underscore the central role of ACC2 in mediating Arabidopsis response to a loss of chloroplast translation, highlight future applications of this system to analyzing chloroplast protein import, and provide valuable insights into the mutational landscape of an important metabolic enzyme that is highly conserved throughout eukaryotes.
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Affiliation(s)
- Nicole Parker
- Department of Plant Biology, Ecology, and Evolution, Oklahoma State University, Stillwater, Oklahoma 74078
| | - Yixing Wang
- Department of Plant Biology, Ecology, and Evolution, Oklahoma State University, Stillwater, Oklahoma 74078
| | - David Meinke
- Department of Plant Biology, Ecology, and Evolution, Oklahoma State University, Stillwater, Oklahoma 74078
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Córdoba JP, Marchetti F, Soto D, Martin MV, Pagnussat GC, Zabaleta E. The CA domain of the respiratory complex I is required for normal embryogenesis in Arabidopsis thaliana. JOURNAL OF EXPERIMENTAL BOTANY 2016; 67:1589-603. [PMID: 26721503 PMCID: PMC5854192 DOI: 10.1093/jxb/erv556] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2015] [Accepted: 12/10/2015] [Indexed: 05/04/2023]
Abstract
The NADH-ubiquinone oxidoreductase [complex I (CI), EC 1.6.5.3] of the mitochondrial respiratory chain is the principal entry point of electrons, and vital in maintaining metabolism and the redox balance. In a variety of eukaryotic organisms, except animal and fungi (Opisthokonta), it contains an extra domain composed of putative gamma carbonic anhydrases subunits, named the CA domain, which was proposed to be essential for complex I assembly. There are two kinds of carbonic anhydrase subunits: CAs (of which there are three) and carbonic anhydrase-like proteins (CALs) (of which there are two). In plants, the CA domain has been linked to photorespiration. In this work, we report that Arabidopsis mutant plants affected in two specific CA subunits show a lethal phenotype. Double homozygous knockouts ca1ca2 embryos show a significant developmental delay compared to the non-homozygous embryos, which show a wild-type (WT) phenotype in the same silique. Mutant embryos show impaired mitochondrial membrane potential and mitochondrial reactive oxygen species (ROS) accumulation. The characteristic embryo greening does not take place and fewer but larger oil bodies are present. Although seeds look dark brown and wrinkled, they are able to germinate 12 d later than WT seeds. However, they die immediately, most likely due to oxidative stress.Since the CA domain is required for complex I biogenesis, it is predicted that in ca1ca2 mutants no complex I could be formed, triggering the lethal phenotype. The in vivo composition of a functional CA domain is proposed.
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Affiliation(s)
- Juan Pablo Córdoba
- Instituto de Investigaciones Biológicas IIB-CONICET-UNMdP, Funes 3250 3er nivel 7600 Mar del Plata, Argentina Received 6 October 2015; Revised 24 November 2015; Accepted 10 December 2015
| | - Fernanda Marchetti
- Instituto de Investigaciones Biológicas IIB-CONICET-UNMdP, Funes 3250 3er nivel 7600 Mar del Plata, Argentina Received 6 October 2015; Revised 24 November 2015; Accepted 10 December 2015
| | - Débora Soto
- Instituto de Investigaciones Biológicas IIB-CONICET-UNMdP, Funes 3250 3er nivel 7600 Mar del Plata, Argentina Received 6 October 2015; Revised 24 November 2015; Accepted 10 December 2015
| | - María Victoria Martin
- Instituto de Investigaciones Biológicas IIB-CONICET-UNMdP, Funes 3250 3er nivel 7600 Mar del Plata, Argentina Received 6 October 2015; Revised 24 November 2015; Accepted 10 December 2015
| | - Gabriela Carolina Pagnussat
- Instituto de Investigaciones Biológicas IIB-CONICET-UNMdP, Funes 3250 3er nivel 7600 Mar del Plata, Argentina Received 6 October 2015; Revised 24 November 2015; Accepted 10 December 2015
| | - Eduardo Zabaleta
- Instituto de Investigaciones Biológicas IIB-CONICET-UNMdP, Funes 3250 3er nivel 7600 Mar del Plata, Argentina Received 6 October 2015; Revised 24 November 2015; Accepted 10 December 2015
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Shockey J, Regmi A, Cotton K, Adhikari N, Browse J, Bates PD. Identification of Arabidopsis GPAT9 (At5g60620) as an Essential Gene Involved in Triacylglycerol Biosynthesis. PLANT PHYSIOLOGY 2016; 170:163-79. [PMID: 26586834 PMCID: PMC4704598 DOI: 10.1104/pp.15.01563] [Citation(s) in RCA: 109] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2015] [Accepted: 11/19/2015] [Indexed: 05/20/2023]
Abstract
The first step in the biosynthesis of nearly all plant membrane phospholipids and storage triacylglycerols is catalyzed by a glycerol-3-phosphate acyltransferase (GPAT). The requirement for an endoplasmic reticulum (ER)-localized GPAT for both of these critical metabolic pathways was recognized more than 60 years ago. However, identification of the gene(s) encoding this GPAT activity has remained elusive. Here, we present the results of a series of in vivo, in vitro, and in silico experiments in Arabidopsis (Arabidopsis thaliana) designed to assign this essential function to AtGPAT9. This gene has been highly conserved throughout evolution and is largely present as a single copy in most plants, features consistent with essential housekeeping functions. A knockout mutant of AtGPAT9 demonstrates both male and female gametophytic lethality phenotypes, consistent with the role in essential membrane lipid synthesis. Significant expression of developing seed AtGPAT9 is required for wild-type levels of triacylglycerol accumulation, and the transcript level is directly correlated to the level of microsomal GPAT enzymatic activity in seeds. Finally, the AtGPAT9 protein interacts with other enzymes involved in ER glycerolipid biosynthesis, suggesting the possibility of ER-localized lipid biosynthetic complexes. Together, these results suggest that GPAT9 is the ER-localized GPAT enzyme responsible for plant membrane lipid and oil biosynthesis.
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Affiliation(s)
- Jay Shockey
- U.S. Department of Agriculture-Agricultural Research Service, Southern Regional Research Center, New Orleans, Louisiana 70124 (J.S.);Department of Chemistry and Biochemistry, University of Southern Mississippi, Hattiesburg, Mississippi 39406 (A.R., P.D.B.); andInstitute of Biological Chemistry, Washington State University, Pullman, Washington 99163 (K.C., N.A., J.B.)
| | - Anushobha Regmi
- U.S. Department of Agriculture-Agricultural Research Service, Southern Regional Research Center, New Orleans, Louisiana 70124 (J.S.);Department of Chemistry and Biochemistry, University of Southern Mississippi, Hattiesburg, Mississippi 39406 (A.R., P.D.B.); andInstitute of Biological Chemistry, Washington State University, Pullman, Washington 99163 (K.C., N.A., J.B.)
| | - Kimberly Cotton
- U.S. Department of Agriculture-Agricultural Research Service, Southern Regional Research Center, New Orleans, Louisiana 70124 (J.S.);Department of Chemistry and Biochemistry, University of Southern Mississippi, Hattiesburg, Mississippi 39406 (A.R., P.D.B.); andInstitute of Biological Chemistry, Washington State University, Pullman, Washington 99163 (K.C., N.A., J.B.)
| | - Neil Adhikari
- U.S. Department of Agriculture-Agricultural Research Service, Southern Regional Research Center, New Orleans, Louisiana 70124 (J.S.);Department of Chemistry and Biochemistry, University of Southern Mississippi, Hattiesburg, Mississippi 39406 (A.R., P.D.B.); andInstitute of Biological Chemistry, Washington State University, Pullman, Washington 99163 (K.C., N.A., J.B.)
| | - John Browse
- U.S. Department of Agriculture-Agricultural Research Service, Southern Regional Research Center, New Orleans, Louisiana 70124 (J.S.);Department of Chemistry and Biochemistry, University of Southern Mississippi, Hattiesburg, Mississippi 39406 (A.R., P.D.B.); andInstitute of Biological Chemistry, Washington State University, Pullman, Washington 99163 (K.C., N.A., J.B.)
| | - Philip D Bates
- U.S. Department of Agriculture-Agricultural Research Service, Southern Regional Research Center, New Orleans, Louisiana 70124 (J.S.);Department of Chemistry and Biochemistry, University of Southern Mississippi, Hattiesburg, Mississippi 39406 (A.R., P.D.B.); andInstitute of Biological Chemistry, Washington State University, Pullman, Washington 99163 (K.C., N.A., J.B.)
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Kang Y, Li M, Sinharoy S, Verdier J. A Snapshot of Functional Genetic Studies in Medicago truncatula. FRONTIERS IN PLANT SCIENCE 2016; 7:1175. [PMID: 27555857 PMCID: PMC4977297 DOI: 10.3389/fpls.2016.01175] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2016] [Accepted: 07/21/2016] [Indexed: 05/21/2023]
Abstract
In the current context of food security, increase of plant protein production in a sustainable manner represents one of the major challenges of agronomic research, which could be partially resolved by increased cultivation of legume crops. Medicago truncatula is now a well-established model for legume genomic and genetic studies. With the establishment of genomics tools and mutant populations in M. truncatula, it has become an important resource to answer some of the basic biological questions related to plant development and stress tolerance. This review has an objective to overview a decade of genetic studies in this model plant from generation of mutant populations to nowadays. To date, the three biological fields, which have been extensively studied in M. truncatula, are the symbiotic nitrogen fixation, the seed development, and the abiotic stress tolerance, due to their significant agronomic impacts. In this review, we summarize functional genetic studies related to these three major biological fields. We integrated analyses of a nearly exhaustive list of genes into their biological contexts in order to provide an overview of the forefront research advances in this important legume model plant.
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Affiliation(s)
- Yun Kang
- Plant Biology Division, The Samuel Roberts Noble FoundationArdmore, OK, USA
| | - Minguye Li
- University of Chinese Academy of SciencesBeijing, China
- Shanghai Plant Stress Center, Shanghai Institutes of Biological Sciences, Chinese Academy of SciencesShanghai, China
| | - Senjuti Sinharoy
- Department of Biotechnology, University of CalcuttaCalcutta, India
| | - Jerome Verdier
- Shanghai Plant Stress Center, Shanghai Institutes of Biological Sciences, Chinese Academy of SciencesShanghai, China
- *Correspondence: Jerome Verdier
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Abstract
Diploid organisms manipulate the extent to which their haploid gametes experience selection. Animals typically produce sperm with a diploid complement of most proteins and RNA, limiting selection on the haploid genotype. Plants, however, exhibit extensive expression in pollen, with actively transcribed haploid genomes. Here we analyze models that track the evolution of genes that modify the strength of haploid selection to predict when evolution intensifies and when it dampens the "selective arena" within which male gametes compete for fertilization. Considering deleterious mutations, evolution leads diploid mothers to strengthen selection among haploid sperm/pollen, because this reduces the mutation load inherited by their diploid offspring. If, however, selection acts in opposite directions in haploids and diploids ("ploidally antagonistic selection"), mothers evolve to reduce haploid selection to avoid selectively amplifying alleles harmful to their offspring. Consequently, with maternal control, selection in the haploid phase either is maximized or reaches an intermediate state, depending on the deleterious mutation rate relative to the extent of ploidally antagonistic selection. By contrast, evolution generally leads diploid fathers to mask mutations in their gametes to the maximum extent possible, whenever masking (e.g., through transcript sharing) increases the average fitness of a father's gametes. We discuss the implications of this maternal-paternal conflict over the extent of haploid selection and describe empirical studies needed to refine our understanding of haploid selection among seemingly diploid organisms.
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Xu TT, Ren SC, Song XF, Liu CM. CLE19 expressed in the embryo regulates both cotyledon establishment and endosperm development in Arabidopsis. JOURNAL OF EXPERIMENTAL BOTANY 2015; 66:5217-27. [PMID: 26071532 PMCID: PMC4526921 DOI: 10.1093/jxb/erv293] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Embryo and endosperm development are two well co-ordinated developmental processes in seed formation; however, signals involved in embryo and endosperm interactions remain poorly understood. It has been shown before that CLAVATA3/ESR-RELATED 19 (CLE19) peptide is able to trigger root meristem consumption in a CLV2-dependent manner. In this study, the role of CLE19 in Arabidopsis seed development was explored using antagonistic peptide technology. CLE19 is expressed in the epidermal layers of the cotyledon primordia, hypocotyl, and root cap in the embryo. Transgenic plants carrying an antagonistic CLE19 G6T construct expressed under the control of CLE19 regulatory elements exhibited a dominant seed abortion phenotype, with defective cotyledon establishment in embryos and delayed nuclear proliferation and cellularization in endosperms. Ectopic expression of CLE19 G6T in Arabidopsis under the control of an endosperm-specific ALE1 promoter led to a similar defect in cotyledon establishment in embryos but without an evident effect on endosperm development. We therefore propose that CLE19 may act as a mobile peptide co-ordinating embryo and endosperm development.
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Affiliation(s)
- Ting-Ting Xu
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Nanxincun 20, Fragrant Hill, Beijing 100093, China University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shi-Chao Ren
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Nanxincun 20, Fragrant Hill, Beijing 100093, China University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiu-Fen Song
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Nanxincun 20, Fragrant Hill, Beijing 100093, China
| | - Chun-Ming Liu
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Nanxincun 20, Fragrant Hill, Beijing 100093, China
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Zhao P, Sun MX. The Maternal-to-Zygotic Transition in Higher Plants: Available Approaches, Critical Limitations, and Technical Requirements. Curr Top Dev Biol 2015; 113:373-98. [PMID: 26358879 DOI: 10.1016/bs.ctdb.2015.06.006] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Fertilization marks the turnover from the gametophyte to sporophyte generation in higher plants. After fertilization, sporophytic development undergoes genetic turnover from maternal to zygotic control: the maternal-to-zygotic transition (MZT). The MZT is thought to be critical for early embryogenesis; however, little is known about the time course or developmental impact of the MZT in higher plants. Here, we discuss what is known in the field and focus on techniques used in relevant studies and their limitations. Some significant questions and technical requirements for further investigations are also discussed.
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Affiliation(s)
- Peng Zhao
- Department of Cell and Developmental Biology, College of Life Sciences, State Key Laboratory of Hybrid Rice, Wuhan University, Wuhan, China
| | - Meng-Xiang Sun
- Department of Cell and Developmental Biology, College of Life Sciences, State Key Laboratory of Hybrid Rice, Wuhan University, Wuhan, China.
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Lin D, Jiang Q, Zheng K, Chen S, Zhou H, Gong X, Xu J, Teng S, Dong Y. Mutation of the rice ASL2 gene encoding plastid ribosomal protein L21 causes chloroplast developmental defects and seedling death. PLANT BIOLOGY (STUTTGART, GERMANY) 2015; 17:599-607. [PMID: 25280352 DOI: 10.1111/plb.12271] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2014] [Accepted: 09/22/2014] [Indexed: 05/19/2023]
Abstract
The plastid ribosome proteins (PRPs) play important roles in plastid protein biosynthesis, chloroplast differentiation and early chloroplast development. However, the specialised functions of individual protein components of the chloroplast ribosome in rice (Oryza sativa) remain unresolved. In this paper, we identified a novel rice PRP mutant named asl2 (Albino seedling lethality 2) exhibiting an albino, seedling death phenotype. In asl2 mutants, the alteration of leaf colour was associated with chlorophyll (Chl) content and abnormal chloroplast development. Through map-based cloning and complementation, the mutated ASL2 gene was isolated and found to encode the chloroplast 50S ribosome protein L21 (RPL21c), a component of the chloroplast ribosome large subunit, which was localised in chloroplasts. ASL2 was expressed at a higher level in the plumule and leaves, implying its tissue-specific expression. Additionally, the expression of ASL2 was regulated by light. The transcript levels of the majority of genes for Chl biosynthesis, photosynthesis and chloroplast development were strongly affected in asl2 mutants. Collectively, the absence of functional ASL2 caused chloroplast developmental defects and seedling death. This report establishes the important role of RPL21c in chloroplast development in rice.
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Affiliation(s)
- D Lin
- Development Center of Plant Germplasm Resources, College of Life and Environment Sciences, Shanghai Normal University, Shanghai, China
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Lafleur E, Kapfer C, Joly V, Liu Y, Tebbji F, Daigle C, Gray-Mitsumune M, Cappadocia M, Nantel A, Matton DP. The FRK1 mitogen-activated protein kinase kinase kinase (MAPKKK) from Solanum chacoense is involved in embryo sac and pollen development. JOURNAL OF EXPERIMENTAL BOTANY 2015; 66:1833-43. [PMID: 25576576 PMCID: PMC4378624 DOI: 10.1093/jxb/eru524] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
The fertilization-related kinase 1 (ScFRK1), a nuclear-localized mitogen-activated protein kinase kinase kinase (MAPKKK) from the wild potato species Solanum chacoense, belongs to a small group of pMEKKs that do not possess an extended N- or C-terminal regulatory domain. Initially selected based on its highly specific expression profile following fertilization, in situ expression analyses revealed that the ScFRK1 gene is also expressed early on during female gametophyte development in the integument and megaspore mother cell and, later, in the synergid and egg cells of the embryo sac. ScFRK1 mRNAs are also detected in pollen mother cells. Transgenic plants with lower or barely detectable levels of ScFRK1 mRNAs lead to the production of small fruits with severely reduced seed set, resulting from a concomitant decline in the number of normal embryo sacs produced. Megagametogenesis and microgametogenesis were affected, as megaspores did not progress beyond the functional megaspore (FG1) stage and the microspore collapsed around the first pollen mitosis. As for other mutants that affect embryo sac development, pollen tube guidance was severely affected in the ScFRK1 transgenic lines. Gametophyte to sporophyte communication was also affected, as observed from a marked change in the transcriptomic profiles of the sporophytic tissues of the ovule. The ScFRK1 MAPKKK is thus involved in a signalling cascade that regulates both male and female gamete development.
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Affiliation(s)
- Edith Lafleur
- Institut de recherche en biologie végétale, Département de sciences biologiques, Université de Montréal, 4101 rue Sherbrooke est, Montréal, QC H1X 2B2, Canada
| | - Christelle Kapfer
- Institut de recherche en biologie végétale, Département de sciences biologiques, Université de Montréal, 4101 rue Sherbrooke est, Montréal, QC H1X 2B2, Canada
| | - Valentin Joly
- Institut de recherche en biologie végétale, Département de sciences biologiques, Université de Montréal, 4101 rue Sherbrooke est, Montréal, QC H1X 2B2, Canada
| | - Yang Liu
- Institut de recherche en biologie végétale, Département de sciences biologiques, Université de Montréal, 4101 rue Sherbrooke est, Montréal, QC H1X 2B2, Canada
| | - Faiza Tebbji
- Institut de recherche en biologie végétale, Département de sciences biologiques, Université de Montréal, 4101 rue Sherbrooke est, Montréal, QC H1X 2B2, Canada Institut de recherche en biotechnologie, Conseil national de recherches du Canada, 6100 Avenue Royalmount, Montréal, QC H4P 2R2, Canada
| | - Caroline Daigle
- Institut de recherche en biologie végétale, Département de sciences biologiques, Université de Montréal, 4101 rue Sherbrooke est, Montréal, QC H1X 2B2, Canada
| | - Madoka Gray-Mitsumune
- Institut de recherche en biologie végétale, Département de sciences biologiques, Université de Montréal, 4101 rue Sherbrooke est, Montréal, QC H1X 2B2, Canada
| | - Mario Cappadocia
- Institut de recherche en biologie végétale, Département de sciences biologiques, Université de Montréal, 4101 rue Sherbrooke est, Montréal, QC H1X 2B2, Canada
| | - André Nantel
- Institut de recherche en biotechnologie, Conseil national de recherches du Canada, 6100 Avenue Royalmount, Montréal, QC H4P 2R2, Canada
| | - Daniel P Matton
- Institut de recherche en biologie végétale, Département de sciences biologiques, Université de Montréal, 4101 rue Sherbrooke est, Montréal, QC H1X 2B2, Canada
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Oellrich A, Walls RL, Cannon EKS, Cannon SB, Cooper L, Gardiner J, Gkoutos GV, Harper L, He M, Hoehndorf R, Jaiswal P, Kalberer SR, Lloyd JP, Meinke D, Menda N, Moore L, Nelson RT, Pujar A, Lawrence CJ, Huala E. An ontology approach to comparative phenomics in plants. PLANT METHODS 2015; 11:10. [PMID: 25774204 PMCID: PMC4359497 DOI: 10.1186/s13007-015-0053-y] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2014] [Accepted: 02/05/2015] [Indexed: 05/29/2023]
Abstract
BACKGROUND Plant phenotype datasets include many different types of data, formats, and terms from specialized vocabularies. Because these datasets were designed for different audiences, they frequently contain language and details tailored to investigators with different research objectives and backgrounds. Although phenotype comparisons across datasets have long been possible on a small scale, comprehensive queries and analyses that span a broad set of reference species, research disciplines, and knowledge domains continue to be severely limited by the absence of a common semantic framework. RESULTS We developed a workflow to curate and standardize existing phenotype datasets for six plant species, encompassing both model species and crop plants with established genetic resources. Our effort focused on mutant phenotypes associated with genes of known sequence in Arabidopsis thaliana (L.) Heynh. (Arabidopsis), Zea mays L. subsp. mays (maize), Medicago truncatula Gaertn. (barrel medic or Medicago), Oryza sativa L. (rice), Glycine max (L.) Merr. (soybean), and Solanum lycopersicum L. (tomato). We applied the same ontologies, annotation standards, formats, and best practices across all six species, thereby ensuring that the shared dataset could be used for cross-species querying and semantic similarity analyses. Curated phenotypes were first converted into a common format using taxonomically broad ontologies such as the Plant Ontology, Gene Ontology, and Phenotype and Trait Ontology. We then compared ontology-based phenotypic descriptions with an existing classification system for plant phenotypes and evaluated our semantic similarity dataset for its ability to enhance predictions of gene families, protein functions, and shared metabolic pathways that underlie informative plant phenotypes. CONCLUSIONS The use of ontologies, annotation standards, shared formats, and best practices for cross-taxon phenotype data analyses represents a novel approach to plant phenomics that enhances the utility of model genetic organisms and can be readily applied to species with fewer genetic resources and less well-characterized genomes. In addition, these tools should enhance future efforts to explore the relationships among phenotypic similarity, gene function, and sequence similarity in plants, and to make genotype-to-phenotype predictions relevant to plant biology, crop improvement, and potentially even human health.
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Affiliation(s)
- Anika Oellrich
- />Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, CB10 1SA UK
| | - Ramona L Walls
- />iPlant Collaborative, University of Arizona, 1657 E. Helen St., Tucson, Arizona 85721 USA
| | - Ethalinda KS Cannon
- />Department of Electrical and Computer Engineering Iowa State University, 1018 Crop Informatics Lab, Ames, Iowa 50011 USA
| | - Steven B Cannon
- />USDA-ARS Corn Insects and Crop Genetics Research Unit, Iowa State University, Crop Genome Informatics Lab, Iowa State University, Ames, IA 50011 USA
- />Department of Agronomy, Agronomy Hall, Iowa State University, Ames, IA 50010 USA
| | - Laurel Cooper
- />Department of Botany and Plant Pathology, 2082 Cordley Hall, Oregon State University, Corvallis, OR 97331 USA
| | - Jack Gardiner
- />Department of Genetics, Development and Cell Biology, Roy J Carver Co-Laboratory, Iowa State University, Ames, IA 50010 USA
| | - Georgios V Gkoutos
- />Department of Computer Science, Aberystwyth University, Llandinam Building, Aberystwyth, SY23 3DB UK
| | - Lisa Harper
- />USDA-ARS Corn Insects and Crop Genetics Research Unit, Iowa State University, Crop Genome Informatics Lab, Iowa State University, Ames, IA 50011 USA
| | - Mingze He
- />Department of Genetics, Development and Cell Biology, Roy J Carver Co-Laboratory, Iowa State University, Ames, IA 50010 USA
| | - Robert Hoehndorf
- />Computer, Electrical and Mathematical Sciences & Engineering Division and Computational Bioscience Research Center, King Abdullah University of Science and Technology, 4700 King Abdullah University of Science and Technology, P.O. Box 2882, Thuwal, 23955-6900 Kingdom of Saudi Arabia
| | - Pankaj Jaiswal
- />Department of Botany and Plant Pathology, 2082 Cordley Hall, Oregon State University, Corvallis, OR 97331 USA
| | - Scott R Kalberer
- />USDA-ARS Corn Insects and Crop Genetics Research Unit, Iowa State University, Crop Genome Informatics Lab, Iowa State University, Ames, IA 50011 USA
| | - John P Lloyd
- />Department of Plant Biology, Michigan State University, 220 Trowbridge Rd, East Lansing, MI 48824 USA
| | - David Meinke
- />Department of Botany, Oklahoma State University, 301 Physical Sciences, Stillwater, OK 74078 USA
| | - Naama Menda
- />Boyce Thompson Institute for Plant Research, 533 Tower Road, Ithaca, NY 14853 USA
| | - Laura Moore
- />Department of Botany and Plant Pathology, 2082 Cordley Hall, Oregon State University, Corvallis, OR 97331 USA
| | - Rex T Nelson
- />USDA-ARS Corn Insects and Crop Genetics Research Unit, Iowa State University, Crop Genome Informatics Lab, Iowa State University, Ames, IA 50011 USA
| | - Anuradha Pujar
- />Boyce Thompson Institute for Plant Research, 533 Tower Road, Ithaca, NY 14853 USA
| | - Carolyn J Lawrence
- />Department of Agronomy, Agronomy Hall, Iowa State University, Ames, IA 50010 USA
- />Department of Genetics, Development and Cell Biology, Roy J Carver Co-Laboratory, Iowa State University, Ames, IA 50010 USA
| | - Eva Huala
- />Phoenix Bioinformatics, 643 Bair Island Rd Suite 403, Redwood City, CA 94063 USA
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Tsugeki R, Tanaka-Sato N, Maruyama N, Terada S, Kojima M, Sakakibara H, Okada K. CLUMSY VEIN, the Arabidopsis DEAH-box Prp16 ortholog, is required for auxin-mediated development. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2015; 81:183-97. [PMID: 25384462 DOI: 10.1111/tpj.12721] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2014] [Revised: 10/29/2014] [Accepted: 10/31/2014] [Indexed: 05/25/2023]
Abstract
Pre-messenger RNA (pre-mRNA) splicing is essential in eukaryotic cells. In animals and yeasts, the DEAH-box RNA-dependent ATPase Prp16 mediates conformational change of the spliceosome, thereby facilitating pre-mRNA splicing. In yeasts, Prp16 also plays an important role in splicing fidelity. Conversely, PRP16 orthologs in Chlamydomonas reinhardtii and nematode do not have an important role in general pre-mRNA splicing, but are required for gene silencing and sex determination, respectively. Functions of PRP16 orthologs in higher plants have not been described until now. Here we show that the CLUMSY VEIN (CUV) gene encoding the unique Prp16 ortholog in Arabidopsis thaliana facilitates auxin-mediated development including male-gametophyte transmission, apical-basal patterning of embryonic and gynoecium development, stamen development, phyllotactic flower positioning, and vascular development. cuv-1 mutation differentially affects splicing and expression of genes involved in auxin biosynthesis, polar auxin transport, auxin perception and auxin signaling. The cuv-1 mutation does not have an equal influence on pre-mRNA substrates. We propose that Arabidopsis PRP16/CUV differentially facilitates expression of genes, which include genes involved in auxin biosynthesis, transport, perception and signaling, thereby collectively influencing auxin-mediated development.
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Affiliation(s)
- Ryuji Tsugeki
- Department of Botany, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto, 606-8502, Japan
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50
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Parker N, Wang Y, Meinke D. Natural variation in sensitivity to a loss of chloroplast translation in Arabidopsis. PLANT PHYSIOLOGY 2014; 166:2013-27. [PMID: 25336520 PMCID: PMC4256881 DOI: 10.1104/pp.114.249052] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Mutations that eliminate chloroplast translation in Arabidopsis (Arabidopsis thaliana) result in embryo lethality. The stage of embryo arrest, however, can be influenced by genetic background. To identify genes responsible for improved growth in the absence of chloroplast translation, we examined seedling responses of different Arabidopsis accessions on spectinomycin, an inhibitor of chloroplast translation, and crossed the most tolerant accessions with embryo-defective mutants disrupted in chloroplast ribosomal proteins generated in a sensitive background. The results indicate that tolerance is mediated by ACC2, a duplicated nuclear gene that targets homomeric acetyl-coenzyme A carboxylase to plastids, where the multidomain protein can participate in fatty acid biosynthesis. In the presence of functional ACC2, tolerance is enhanced by a second locus that maps to chromosome 5 and heightened by additional genetic modifiers present in the most tolerant accessions. Notably, some of the most sensitive accessions contain nonsense mutations in ACC2, including the "Nossen" line used to generate several of the mutants studied here. Functional ACC2 protein is therefore not required for survival in natural environments, where heteromeric acetyl-coenzyme A carboxylase encoded in part by the chloroplast genome can function instead. This work highlights an interesting example of a tandem gene duplication in Arabidopsis, helps to explain the range of embryo phenotypes found in Arabidopsis mutants disrupted in essential chloroplast functions, addresses the nature of essential proteins encoded by the chloroplast genome, and underscores the value of using natural variation to study the relationship between chloroplast translation, plant metabolism, protein import, and plant development.
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Affiliation(s)
- Nicole Parker
- Department of Botany, Oklahoma State University, Stillwater, Oklahoma 74078
| | - Yixing Wang
- Department of Botany, Oklahoma State University, Stillwater, Oklahoma 74078
| | - David Meinke
- Department of Botany, Oklahoma State University, Stillwater, Oklahoma 74078
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