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Yang S, Poretska O, Poppenberger B, Sieberer T. ALTERED MERISTEM PROGRAM1 sustains cellular differentiation by limiting HD-ZIP III transcription factor gene expression. PLANT PHYSIOLOGY 2024; 196:291-308. [PMID: 38781290 PMCID: PMC11376390 DOI: 10.1093/plphys/kiae300] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2024] [Revised: 04/29/2024] [Accepted: 05/01/2024] [Indexed: 05/25/2024]
Abstract
Plants show remarkable developmental and regenerative plasticity through the sustained activity of stem cells in meristems. Under certain conditions, pluripotency can even be reestablished in cells that have already entered differentiation. Mutation of the putative carboxypeptidase ALTERED MERISTEM PROGRAM1 (AMP1) in Arabidopsis (Arabidopsis thaliana) causes a set of hypertrophic phenotypes, indicating a defect in the suppression of pluripotency. A role of AMP1 in the miRNA-mediated inhibition of translation has previously been reported; however, how this activity is related to its developmental functions is unclear. Here, we examined the functional interaction between AMP1 and the Class III homeodomain-leucine zipper (HD-ZIP III) transcription factors, which are miRNA-controlled determinants of shoot meristem specification. We found that the HD-ZIP III transcriptional output is enhanced in the amp1 mutant and that plant lines with increased HD-ZIP III activity not only developed amp1 mutant-like phenotypes but also showed a synergistic genetic interaction with the mutant. Conversely, the reduction of HD-ZIP III function suppressed the shoot hypertrophy defects of the amp1 mutant. We further provide evidence that the expression domains of HD-ZIP III family members are expanded in the amp1 mutant and that this misexpression occurs at the transcriptional level and does not involve the function of miRNA165/166. Finally, amp1 mutant-specific phenotypes cannot be mimicked by a general inhibition of miRNA function in the AMP1 expression domain. These findings lead us to a model in which AMP1 restricts cellular pluripotency upstream of HD-ZIP III proteins, and this control appears to be not directly mediated by the canonical miRNA pathway.
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Affiliation(s)
- Saiqi Yang
- Research Unit Plant Growth Regulation, TUM School of Life Sciences, Technical University of Munich, DE-85354 Freising, Germany
| | - Olena Poretska
- Research Unit Plant Growth Regulation, TUM School of Life Sciences, Technical University of Munich, DE-85354 Freising, Germany
| | - Brigitte Poppenberger
- Professorship Biotechnology of Horticultural Crops, TUM School of Life Sciences, Technical University of Munich, DE-85354 Freising, Germany
| | - Tobias Sieberer
- Research Unit Plant Growth Regulation, TUM School of Life Sciences, Technical University of Munich, DE-85354 Freising, Germany
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2
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Feng L, Yan W, Tang X, Wu H, Pan Y, Lu D, Ling-Hu Q, Liu Y, Liu Y, Song X, Ali M, Fang L, Guo H, Li B. Multiple factors and features dictate the selective production of ct-siRNA in Arabidopsis. Commun Biol 2024; 7:474. [PMID: 38637717 PMCID: PMC11026412 DOI: 10.1038/s42003-024-06142-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Accepted: 04/03/2024] [Indexed: 04/20/2024] Open
Abstract
Coding transcript-derived siRNAs (ct-siRNAs) produced from specific endogenous loci can suppress the translation of their source genes to balance plant growth and stress response. In this study, we generated Arabidopsis mutants with deficiencies in RNA decay and/or post-transcriptional gene silencing (PTGS) pathways and performed comparative sRNA-seq analysis, revealing that multiple RNA decay and PTGS factors impede the ct-siRNA selective production. Genes that produce ct-siRNAs often show increased or unchanged expression and typically have higher GC content in sequence composition. The growth and development of plants can perturb the dynamic accumulation of ct-siRNAs from different gene loci. Two nitrate reductase genes, NIA1 and NIA2, produce massive amounts of 22-nt ct-siRNAs and are highly expressed in a subtype of mesophyll cells where DCL2 exhibits higher expression relative to DCL4, suggesting a potential role of cell-specific expression of ct-siRNAs. Overall, our findings unveil the multifaceted factors and features involved in the selective production and regulation of ct-siRNAs and enrich our understanding of gene silencing process in plants.
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Affiliation(s)
- Li Feng
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agriculture Sciences in Weifang, Weifang, Shandong, 261325, China
| | - Wei Yan
- Institute of Plant and Food Science, Department of Biology, Southern University of Science and Technology, Shenzhen, Guangdong, 518055, China
| | - Xianli Tang
- Institute of Plant and Food Science, Department of Biology, Southern University of Science and Technology, Shenzhen, Guangdong, 518055, China
| | - Huihui Wu
- Institute of Plant and Food Science, Department of Biology, Southern University of Science and Technology, Shenzhen, Guangdong, 518055, China
| | - Yajie Pan
- Institute of Plant and Food Science, Department of Biology, Southern University of Science and Technology, Shenzhen, Guangdong, 518055, China
| | - Dongdong Lu
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agriculture Sciences in Weifang, Weifang, Shandong, 261325, China
| | - Qianyan Ling-Hu
- Institute of Plant and Food Science, Department of Biology, Southern University of Science and Technology, Shenzhen, Guangdong, 518055, China
| | - Yuelin Liu
- Institute of Plant and Food Science, Department of Biology, Southern University of Science and Technology, Shenzhen, Guangdong, 518055, China
| | - Yongqi Liu
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agriculture Sciences in Weifang, Weifang, Shandong, 261325, China
| | - Xiehai Song
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agriculture Sciences in Weifang, Weifang, Shandong, 261325, China
| | - Muhammad Ali
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agriculture Sciences in Weifang, Weifang, Shandong, 261325, China
| | - Liang Fang
- Institute of Plant and Food Science, Department of Biology, Southern University of Science and Technology, Shenzhen, Guangdong, 518055, China
| | - Hongwei Guo
- Institute of Plant and Food Science, Department of Biology, Southern University of Science and Technology, Shenzhen, Guangdong, 518055, China.
| | - Bosheng Li
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agriculture Sciences in Weifang, Weifang, Shandong, 261325, China.
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3
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Zhou B, Yu H, Xue Y, Li M, Zhang C, Yu B. The spliceosome-associated protein CWC15 promotes miRNA biogenesis in Arabidopsis. Nat Commun 2024; 15:2399. [PMID: 38493158 PMCID: PMC10944506 DOI: 10.1038/s41467-024-46676-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Accepted: 02/26/2024] [Indexed: 03/18/2024] Open
Abstract
MicroRNAs (miRNAs) play a key role in regulating gene expression and their biogenesis is precisely controlled through modulating the activity of microprocessor. Here, we report that CWC15, a spliceosome-associated protein, acts as a positive regulator of miRNA biogenesis. CWC15 binds the promoters of genes encoding miRNAs (MIRs), promotes their activity, and increases the occupancy of DNA-dependent RNA polymerases at MIR promoters, suggesting that CWC15 positively regulates the transcription of primary miRNA transcripts (pri-miRNAs). In addition, CWC15 interacts with Serrate (SE) and HYL1, two key components of microprocessor, and is required for efficient pri-miRNA processing and the HYL1-pri-miRNA interaction. Moreover, CWC15 interacts with the 20 S proteasome and PRP4KA, facilitating SE phosphorylation by PRP4KA, and subsequent non-functional SE degradation by the 20 S proteasome. These data reveal that CWC15 ensures optimal miRNA biogenesis by maintaining proper SE levels and by modulating pri-miRNA levels. Taken together, this study uncovers the role of a conserved splicing-related protein in miRNA biogenesis.
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Affiliation(s)
- Bangjun Zhou
- Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE, 68588-0666, USA
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, NE, 68588-0118, USA
| | - Huihui Yu
- Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE, 68588-0666, USA
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, NE, 68588-0118, USA
| | - Yong Xue
- Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE, 68588-0666, USA
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, NE, 68588-0118, USA
| | - Mu Li
- Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE, 68588-0666, USA
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, NE, 68588-0118, USA
| | - Chi Zhang
- Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE, 68588-0666, USA
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, NE, 68588-0118, USA
| | - Bin Yu
- Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE, 68588-0666, USA.
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, NE, 68588-0118, USA.
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4
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Li M, Yu H, Zhou B, Gan L, Li S, Zhang C, Yu B. JANUS, a spliceosome-associated protein, promotes miRNA biogenesis in Arabidopsis. Nucleic Acids Res 2024; 52:420-430. [PMID: 37994727 PMCID: PMC10783502 DOI: 10.1093/nar/gkad1105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 10/27/2023] [Accepted: 11/06/2023] [Indexed: 11/24/2023] Open
Abstract
MicroRNAs (miRNAs) are important regulators of genes expression. Their levels are precisely controlled through modulating the activity of the microprocesser complex (MC). Here, we report that JANUS, a homology of the conserved U2 snRNP assembly factor in yeast and human, is required for miRNA accumulation. JANUS associates with MC components Dicer-like 1 (DCL1) and SERRATE (SE) and directly binds the stem-loop of pri-miRNAs. In a hypomorphic janus mutant, the activity of DCL1, the numbers of MC, and the interaction of primary miRNA transcript (pri-miRNAs) with MC are reduced. These data suggest that JANUS promotes the assembly and activity of MC through its interaction with MC and/or pri-miRNAs. In addition, JANUS modulates the transcription of some pri-miRNAs as it binds the promoter of pri-miRNAs and facilitates Pol II occupancy of at their promoters. Moreover, global splicing defects are detected in janus. Taken together, our study reveals a novel role of a conserved splicing factor in miRNA biogenesis.
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Affiliation(s)
- Mu Li
- Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE 68588–0666, USA
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, NE 68588–0118, USA
| | - Huihui Yu
- Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE 68588–0666, USA
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, NE 68588–0118, USA
| | - Bangjun Zhou
- Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE 68588–0666, USA
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, NE 68588–0118, USA
| | - Lu Gan
- Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE 68588–0666, USA
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, NE 68588–0118, USA
| | - Shengjun Li
- Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Energy Genetics, Shandong Energy Institute, Qingdao New Energy Shangdong Laboratory, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
| | - Chi Zhang
- Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE 68588–0666, USA
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, NE 68588–0118, USA
| | - Bin Yu
- Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE 68588–0666, USA
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, NE 68588–0118, USA
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5
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Singh M, Singh H, Kaur K, Shubhankar S, Singh S, Kaur A, Singh P. Characterization and regulation of salt upregulated cyclophilin from a halotolerant strain of Penicillium oxalicum. Sci Rep 2023; 13:17433. [PMID: 37833355 PMCID: PMC10575979 DOI: 10.1038/s41598-023-44606-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Accepted: 10/10/2023] [Indexed: 10/15/2023] Open
Abstract
Penicillium species are an industrially important group of fungi. Cyclophilins are ubiquitous proteins and several members of this family exhibit peptidyl-prolyl cis-trans isomerase (PPIase) activity. We had earlier demonstrated that the salt-induced PPIase activity in a halotolerant strain of P. oxalicum was associated with enhanced expression of a cyclophilin gene, PoxCYP18. Cloning and characterization of PoxCYP18 revealed that its cDNA consists of 522 bp encoding a protein of 173 amino acid residues, with predicted molecular mass and pI values of 18.91 kDa and 8.87, respectively. The recombinant PoxCYP18 can catalyze cis-trans isomerization of peptidyl-prolyl bond with a catalytic efficiency of 1.46 × 107 M-1 s-1 and is inhibited specifically only by cyclosporin A, with an inhibition constant of 5.04 ± 1.13 nM. PoxCYP18 consists of two cysteine residues at positions - 45 and - 170, and loses its activity under oxidizing conditions. Substitution of these residues alone or together by site-directed mutagenesis revealed that the PPIase activity of PoxCYP18 is regulated through a redox mechanism involving the formation of disulfide linkages. Heterologous expression of PoxCYP18 conferred enhanced tolerance to salt stress in transgenic E. coli cells, implying that this protein imparts protection to cellular processes against salt-induced damage.
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Affiliation(s)
- Mangaljeet Singh
- Department of Biotechnology, Guru Nanak Dev University, Amritsar, Punjab, 143005, India
| | - Harpreet Singh
- Department of Bioinformatics, Hans Raj Mahila Maha Vidyalaya, Jalandhar, Punjab, 144008, India
| | - Kirandeep Kaur
- Department of Biotechnology, Guru Nanak Dev University, Amritsar, Punjab, 143005, India
| | - Shubhankar Shubhankar
- Department of Biotechnology, Guru Nanak Dev University, Amritsar, Punjab, 143005, India
| | - Supreet Singh
- Department of Biotechnology, Guru Nanak Dev University, Amritsar, Punjab, 143005, India
| | - Amarjeet Kaur
- Department of Microbiology, Guru Nanak Dev University, Amritsar, Punjab, 143005, India
| | - Prabhjeet Singh
- Department of Biotechnology, Guru Nanak Dev University, Amritsar, Punjab, 143005, India.
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6
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Jha BK, Varikuti S, Verma C, Shivahare R, Bishop N, Dos Santos GP, McDonald J, Sur A, Myler PJ, Schenkman S, Satoskar AR, McGwire BS. Immunization with a Trypanosoma cruzi cyclophilin-19 deletion mutant protects against acute Chagas disease in mice. NPJ Vaccines 2023; 8:63. [PMID: 37185599 PMCID: PMC10130101 DOI: 10.1038/s41541-023-00647-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Accepted: 03/23/2023] [Indexed: 05/17/2023] Open
Abstract
Human infection with the protozoan parasite Trypanosoma cruzi causes Chagas disease for which there are no prophylactic vaccines. Cyclophilin 19 is a secreted cis-trans peptidyl isomerase expressed in all life stages of Trypanosoma cruzi. This protein in the insect stage leads to the inactivation of insect anti-parasitic peptides and parasite transformation whereas in the intracellular amastigotes it participates in generating ROS promoting the growth of parasites. We have generated a parasite mutant with depleted expression of Cyp19 by removal of 2 of 3 genes encoding this protein using double allelic homologous recombination. The mutant parasite line failed to replicate when inoculated into host cells in vitro or in mice indicating that Cyp19 is critical for infectivity. The mutant parasite line also fails to replicate in or cause clinical disease in immuno-deficient mice further validating their lack of virulence. Repeated inoculation of mutant parasites into immuno-competent mice elicits parasite-specific trypanolytic antibodies and a Th-1 biased immune response and challenge of mutant immunized mice with virulent wild-type parasites is 100% effective at preventing death from acute disease. These results suggest that parasite Cyp19 may be candidate for small molecule drug targeting and that the mutant parasite line may warrant further immunization studies for prevention of Chagas disease.
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Affiliation(s)
- Bijay Kumar Jha
- Division of Infectious Diseases, Department of Medicine, Wexner Medical Center, The Ohio State University, Columbus, OH, USA
| | - Sanjay Varikuti
- Departments of Pathology and Microbiology, Wexner Medical Center, The Ohio State University, Columbus, OH, USA
| | - Chaitenya Verma
- Departments of Pathology and Microbiology, Wexner Medical Center, The Ohio State University, Columbus, OH, USA
| | - Rahul Shivahare
- Division of Infectious Diseases, Department of Medicine, Wexner Medical Center, The Ohio State University, Columbus, OH, USA
| | - Nicholas Bishop
- Division of Infectious Diseases, Department of Medicine, Wexner Medical Center, The Ohio State University, Columbus, OH, USA
| | - Gregory P Dos Santos
- Department of Microbiology, Immunology and Parasitology, Federal University of Sao Paulo, Sao Paulo, Brazil
| | - Jacquelyn McDonald
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, WA, USA
| | - Aakash Sur
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, WA, USA
- Department of Biomedical Informatics and Medical Education, University of Washington, Seattle, WA, USA
| | - Peter J Myler
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, WA, USA
- Department of Biomedical Informatics and Medical Education, University of Washington, Seattle, WA, USA
- Department of Pediatrics, University of Washington, Seattle, WA, USA
- Department of Global Health, University of Washington, Seattle, WA, USA
| | - Sergio Schenkman
- Department of Microbiology, Immunology and Parasitology, Federal University of Sao Paulo, Sao Paulo, Brazil
| | - Abhay R Satoskar
- Departments of Pathology and Microbiology, Wexner Medical Center, The Ohio State University, Columbus, OH, USA.
| | - Bradford S McGwire
- Division of Infectious Diseases, Department of Medicine, Wexner Medical Center, The Ohio State University, Columbus, OH, USA.
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7
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Lemus T, Mason GA, Bubb KL, Alexandre CM, Queitsch C, Cuperus JT. AGO1 and HSP90 buffer different genetic variants in Arabidopsis thaliana. Genetics 2023; 223:iyac163. [PMID: 36303325 PMCID: PMC9910400 DOI: 10.1093/genetics/iyac163] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Accepted: 10/18/2022] [Indexed: 11/14/2022] Open
Abstract
Argonaute 1 (AGO1), the principal protein component of microRNA-mediated regulation, plays a key role in plant growth and development. AGO1 physically interacts with the chaperone HSP90, which buffers cryptic genetic variation in plants and animals. We sought to determine whether genetic perturbation of AGO1 in Arabidopsis thaliana would also reveal cryptic genetic variation, and if so, whether AGO1-dependent loci overlap with those dependent on HSP90. To address these questions, we introgressed a hypomorphic mutant allele of AGO1 into a set of mapping lines derived from the commonly used Arabidopsis strains Col-0 and Ler. Although we identified several cases in which AGO1 buffered genetic variation, none of the AGO1-dependent loci overlapped with those buffered by HSP90 for the traits assayed. We focused on 1 buffered locus where AGO1 perturbation uncoupled the traits days to flowering and rosette leaf number, which are otherwise closely correlated. Using a bulk segregant approach, we identified a nonfunctional Ler hua2 mutant allele as the causal AGO1-buffered polymorphism. Introduction of a nonfunctional hua2 allele into a Col-0 ago1 mutant background recapitulated the Ler-dependent ago1 phenotype, implying that coupling of these traits involves different molecular players in these closely related strains. Taken together, our findings demonstrate that even though AGO1 and HSP90 buffer genetic variation in the same traits, these robustness regulators interact epistatically with different genetic loci, suggesting that higher-order epistasis is uncommon. Plain Language Summary Argonaute 1 (AGO1), a key player in plant development, interacts with the chaperone HSP90, which buffers environmental and genetic variation. We found that AGO1 buffers environmental and genetic variation in the same traits; however, AGO1-dependent and HSP90-dependent loci do not overlap. Detailed analysis of a buffered locus found that a nonfunctional HUA2 allele decouples days to flowering and rosette leaf number in an AGO1-dependent manner, suggesting that the AGO1-dependent buffering acts at the network level.
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Affiliation(s)
- Tzitziki Lemus
- Department of Genome Sciences, University of Washington, Seattle, WA 98105, USA
| | - Grace Alex Mason
- Department of Genome Sciences, University of Washington, Seattle, WA 98105, USA
| | - Kerry L Bubb
- Department of Genome Sciences, University of Washington, Seattle, WA 98105, USA
| | | | - Christine Queitsch
- Department of Genome Sciences, University of Washington, Seattle, WA 98105, USA
| | - Josh T Cuperus
- Department of Genome Sciences, University of Washington, Seattle, WA 98105, USA
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8
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Zacharaki V, Meena SK, Kindgren P. The non-coding RNA SVALKA locus produces a cis-natural antisense transcript that negatively regulates the expression of CBF1 and biomass production at normal temperatures. PLANT COMMUNICATIONS 2023:100551. [PMID: 36681861 PMCID: PMC10363475 DOI: 10.1016/j.xplc.2023.100551] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Revised: 01/17/2023] [Accepted: 01/18/2023] [Indexed: 06/17/2023]
Abstract
Non-coding transcription is present in all eukaryotic genomes, but we lack fundamental knowledge about its importance for an organism's ability to develop properly. In plants, emerging evidence highlights the essential biological role of non-coding transcription in the regulation of coding transcription. However, we have few molecular insights into this regulation. Here, we show that a long isoform of the long non-coding RNA SVALKA-L (SVK-L) forms a natural antisense transcript to the host gene CBF1 and negatively regulates CBF1 mRNA levels at normal temperatures in the model plant Arabidopsis thaliana. Furthermore, we show detailed evidence for the specific mode of action of SVK-L. This pathway includes the formation of double-stranded RNA that is recognized by the DICER proteins and subsequent downregulation of CBF1 mRNA levels. Thus, the CBF1-SVK regulatory circuit is not only important for its previously known role in cold temperature acclimation but also for biomass production at normal temperatures. Our study characterizes the developmental role of SVK-L and offers mechanistic insight into how biologically important overlapping natural antisense transcripts can act on and fine-tune the steady-state levels of their host gene's mRNA.
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Affiliation(s)
- Vasiliki Zacharaki
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, 90187 Umeå, Sweden
| | - Shiv Kumar Meena
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, 90187 Umeå, Sweden
| | - Peter Kindgren
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, 90187 Umeå, Sweden.
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9
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Wilkinson SW, Hannan Parker A, Muench A, Wilson RS, Hooshmand K, Henderson MA, Moffat EK, Rocha PSCF, Hipperson H, Stassen JHM, López Sánchez A, Fomsgaard IS, Krokene P, Mageroy MH, Ton J. Long-lasting memory of jasmonic acid-dependent immunity requires DNA demethylation and ARGONAUTE1. NATURE PLANTS 2023; 9:81-95. [PMID: 36604579 DOI: 10.1038/s41477-022-01313-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Accepted: 11/10/2022] [Indexed: 06/17/2023]
Abstract
Stress can have long-lasting impacts on plants. Here we report the long-term effects of the stress hormone jasmonic acid (JA) on the defence phenotype, transcriptome and DNA methylome of Arabidopsis. Three weeks after transient JA signalling, 5-week-old plants retained induced resistance (IR) against herbivory but showed increased susceptibility to pathogens. Transcriptome analysis revealed long-term priming and/or upregulation of JA-dependent defence genes but repression of ethylene- and salicylic acid-dependent genes. Long-term JA-IR was associated with shifts in glucosinolate composition and required MYC2/3/4 transcription factors, RNA-directed DNA methylation, the DNA demethylase ROS1 and the small RNA (sRNA)-binding protein AGO1. Although methylome analysis did not reveal consistent changes in DNA methylation near MYC2/3/4-controlled genes, JA-treated plants were specifically enriched with hypomethylated ATREP2 transposable elements (TEs). Epigenomic characterization of mutants and transgenic lines revealed that ATREP2 TEs are regulated by RdDM and ROS1 and produce 21 nt sRNAs that bind to nuclear AGO1. Since ATREP2 TEs are enriched with sequences from IR-related defence genes, our results suggest that AGO1-associated sRNAs from hypomethylated ATREP2 TEs trans-regulate long-lasting memory of JA-dependent immunity.
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Affiliation(s)
- S W Wilkinson
- Plants, Photosynthesis and Soil, School of Biosciences, Institute for Sustainable Food, The University of Sheffield, Sheffield, UK.
| | - A Hannan Parker
- Plants, Photosynthesis and Soil, School of Biosciences, Institute for Sustainable Food, The University of Sheffield, Sheffield, UK
| | - A Muench
- Plants, Photosynthesis and Soil, School of Biosciences, Institute for Sustainable Food, The University of Sheffield, Sheffield, UK
| | - R S Wilson
- Plants, Photosynthesis and Soil, School of Biosciences, Institute for Sustainable Food, The University of Sheffield, Sheffield, UK
| | - K Hooshmand
- Department of Agroecology, Aarhus University, Slagelse, Denmark
| | - M A Henderson
- Plants, Photosynthesis and Soil, School of Biosciences, Institute for Sustainable Food, The University of Sheffield, Sheffield, UK
| | - E K Moffat
- Plants, Photosynthesis and Soil, School of Biosciences, Institute for Sustainable Food, The University of Sheffield, Sheffield, UK
| | - P S C F Rocha
- Plants, Photosynthesis and Soil, School of Biosciences, Institute for Sustainable Food, The University of Sheffield, Sheffield, UK
| | - H Hipperson
- Plants, Photosynthesis and Soil, School of Biosciences, Institute for Sustainable Food, The University of Sheffield, Sheffield, UK
| | - J H M Stassen
- Plants, Photosynthesis and Soil, School of Biosciences, Institute for Sustainable Food, The University of Sheffield, Sheffield, UK
| | - A López Sánchez
- Plants, Photosynthesis and Soil, School of Biosciences, Institute for Sustainable Food, The University of Sheffield, Sheffield, UK
| | - I S Fomsgaard
- Department of Agroecology, Aarhus University, Slagelse, Denmark
| | - P Krokene
- Division for Biotechnology and Plant Health, Norwegian Institute of Bioeconomy Research (NIBIO), Ås, Norway
| | - M H Mageroy
- Division for Biotechnology and Plant Health, Norwegian Institute of Bioeconomy Research (NIBIO), Ås, Norway
| | - J Ton
- Plants, Photosynthesis and Soil, School of Biosciences, Institute for Sustainable Food, The University of Sheffield, Sheffield, UK.
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10
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Qiao ZW, Wang DR, Wang X, You CX, Wang XF. Genome-wide identification and stress response analysis of cyclophilin gene family in apple (Malus × domestica). BMC Genomics 2022; 23:806. [PMID: 36474166 PMCID: PMC9727951 DOI: 10.1186/s12864-022-08976-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 10/29/2022] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Cyclophilin (CYP) belongs to the immunophilin family and has peptidyl-prolyl cis-trans isomerase (PPIase) activity, which catalyzes the cis-trans isomerization process of proline residues. CYPs widely exist in eukaryotes and prokaryotes, and contain a conserved cyclophilin-like domain (CLD). Plant cyclophilins are widely involved in a range of biological processes including stress response, metabolic regulation, and growth and development. RESULT In this study, 30 cyclophilin genes on 15 chromosomes were identified from the 'Golden Delicious' apple (M. domestica) genome. Phylogenetic analysis showed that the cyclophilin family genes can be divided into three clades in Malus. Collinear analysis showed that ten gene pairs were the result of segmental duplication. Analysis of gene and protein structure further supported the phylogenetic tree and collinearity analysis. The expression of MdCYPs in different organs was higher in leaves, flowers, and fruits. Ten and eight CYPs responded to drought and salt stress, respectively. MdCYP16, a nuclear-localized MD CYP, was screened from the intersection of the two expression profiling datasets and was highly sensitive to drought and salt stress. GUS staining of transgenic Arabidopsis indicated that MdCYP16 may be involved in the regulation of abiotic stress. CONCLUSION This study systematically analyzed members of the apple cyclophilin family and confirmed the involvement of MdCYP16 as a nuclear-localized MD cyclophilin that acts in response to salt and drought stress in apple. Our work identifies members of the apple cyclophilin gene family, and provides an important theoretical basis for in-depth study of cyclophilin function. Additionally, the analysis provides candidate genes that may be involved in stress response in apple.
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Affiliation(s)
- Zhi-Wen Qiao
- State Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, 271018, Shandong, China
| | - Da-Ru Wang
- State Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, 271018, Shandong, China
| | - Xun Wang
- State Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, 271018, Shandong, China
| | - Chun-Xiang You
- State Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, 271018, Shandong, China.
| | - Xiao-Fei Wang
- State Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, 271018, Shandong, China.
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11
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Sun T, Zhou Q, Zhou Z, Song Y, Li Y, Wang HB, Liu B. SQUINT Positively Regulates Resistance to the Pathogen Botrytis cinerea via miR156-SPL9 Module in Arabidopsis. PLANT & CELL PHYSIOLOGY 2022; 63:1414-1432. [PMID: 35445272 DOI: 10.1093/pcp/pcac042] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 03/23/2022] [Accepted: 04/20/2022] [Indexed: 06/14/2023]
Abstract
SQUINT (SQN) regulates plant maturation by promoting the activity of miR156, which functions primarily in the miR156-SQUAMOSA PROMOTER BINDING PROTEIN-LIKE9 (SPL9) module regulating plant growth and development. Here, we show that SQN acts in the jasmonate (JA) pathway, a major signaling pathway regulating plant responses to insect herbivory and pathogen infection. Arabidopsis thaliana sqn mutants showed elevated sensitivity to the necrotrophic fungus Botrytis cinerea compared with wild type. However, SQN is not involved in the early pattern-triggered immunity response often triggered by fungal attack. Rather, SQN positively regulates the JA pathway, as sqn loss-of-function mutants treated with B. cinerea showed reduced JA accumulation, JA response and sensitivity to JA. Furthermore, the miR156-SPL9 module regulates plant resistance to B. cinerea: mir156 mutant, and SPL9 overexpression plants displayed elevated sensitivity to B. cinerea. Moreover, constitutively expressing miR156a or reducing SPL9 expression in the sqn-1 mutant restored the sensitivity of Arabidopsis to B. cinerea and JA responses. These results suggest that SQN positively modulates plant resistance to B. cinerea through the JA pathway, and the miR156-SPL9 module functions as a bridge between SQN and JA to mediate plant resistance to this pathogen.
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Affiliation(s)
- Ting Sun
- Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, People's Republic of China
| | - Qi Zhou
- Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, People's Republic of China
| | - Zhou Zhou
- Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, People's Republic of China
| | - Yuxiao Song
- Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, People's Republic of China
| | - You Li
- Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, People's Republic of China
| | - Hong-Bin Wang
- Institute of Medical Plant Physiology and Ecology, School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou 510006, People's Republic of China
| | - Bing Liu
- Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, People's Republic of China
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12
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Abiri N, Sinjushin A, Tekdal D, Cetiner S. Evaluation of the Possible Contribution of Various Regulatory Genes to Determination of Carpel Number as a Potential Mechanism for Optimal Agricultural Yield. Int J Mol Sci 2022; 23:ijms23179723. [PMID: 36077121 PMCID: PMC9456115 DOI: 10.3390/ijms23179723] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Revised: 08/22/2022] [Accepted: 08/22/2022] [Indexed: 11/16/2022] Open
Abstract
Various regulatory genes encoding transcription factors and miRNAs regulate carpel number. Multicarpelly is normally associated with increased size of the floral meristem, and several genetic factors have been discovered that influence this characteristic. A fundamental understanding of the regulatory genes affecting carpel number can facilitate strategies for agricultural yield improvement, which is crucial, given that the global population is growing rapidly. A multicarpellate plant may provide a significantly higher yield than a plant bearing fewer carpels. Higher yields can be achieved via various means; in this review, we provide an overview of the current knowledge of the various regulatory factors that contribute to multicarpelly and the potential of increasing carpel number to achieve an increased yield.
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Affiliation(s)
- Naghmeh Abiri
- Faculty of Engineering and Natural Sciences, Sabanci University, 34956 Istanbul, Turkey
- Correspondence: ; Tel.: +90-5457874622
| | - Andrey Sinjushin
- Department of Genetics, Biological Faculty, Lomonosov Moscow State University, Leninskie Gory, 1-12, 119234 Moscow, Russia
| | - Dilek Tekdal
- Faculty of Science and Letters, Department of Biotechnology, Mersin University, 33343 Mersin, Turkey
| | - Selim Cetiner
- Faculty of Engineering and Natural Sciences, Sabanci University, 34956 Istanbul, Turkey
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13
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Hacquard T, Clavel M, Baldrich P, Lechner E, Pérez-Salamó I, Schepetilnikov M, Derrien B, Dubois M, Hammann P, Kuhn L, Brun D, Bouteiller N, Baumberger N, Vaucheret H, Meyers BC, Genschik P. The Arabidopsis F-box protein FBW2 targets AGO1 for degradation to prevent spurious loading of illegitimate small RNA. Cell Rep 2022; 39:110671. [PMID: 35417704 PMCID: PMC9035678 DOI: 10.1016/j.celrep.2022.110671] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 12/14/2021] [Accepted: 03/22/2022] [Indexed: 11/03/2022] Open
Abstract
RNA silencing is a conserved mechanism in eukaryotes involved in development and defense against viruses. In plants, ARGONAUTE1 (AGO1) protein plays a central role in both microRNA- and small interfering RNA-directed silencing, and its expression is regulated at multiple levels. Here, we report that the F-box protein FBW2 assembles an SCF complex that selectively targets for proteolysis AGO1 when it is unloaded and mutated. Although FBW2 loss of function does not lead to strong growth or developmental defects, it significantly increases RNA-silencing activity. Interestingly, under conditions in which small-RNA accumulation is affected, the failure to degrade AGO1 in fbw2 mutants becomes more deleterious for the plant. Accordingly, the non-degradable AGO1 protein assembles high-molecular-weight complexes and binds illegitimate small RNA, leading to off-target cleavage. Therefore, control of AGO1 homeostasis by FBW2 plays an important role in quality control of RNA silencing.
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Affiliation(s)
- Thibaut Hacquard
- Institut de biologie moléculaire des plantes, CNRS, Université de Strasbourg, 12, rue du Général Zimmer, 67084 Strasbourg, France
| | - Marion Clavel
- Institut de biologie moléculaire des plantes, CNRS, Université de Strasbourg, 12, rue du Général Zimmer, 67084 Strasbourg, France
| | | | - Esther Lechner
- Institut de biologie moléculaire des plantes, CNRS, Université de Strasbourg, 12, rue du Général Zimmer, 67084 Strasbourg, France
| | - Imma Pérez-Salamó
- Institut de biologie moléculaire des plantes, CNRS, Université de Strasbourg, 12, rue du Général Zimmer, 67084 Strasbourg, France
| | - Mikhail Schepetilnikov
- Institut de biologie moléculaire des plantes, CNRS, Université de Strasbourg, 12, rue du Général Zimmer, 67084 Strasbourg, France
| | - Benoît Derrien
- Institut de biologie moléculaire des plantes, CNRS, Université de Strasbourg, 12, rue du Général Zimmer, 67084 Strasbourg, France
| | - Marieke Dubois
- Institut de biologie moléculaire des plantes, CNRS, Université de Strasbourg, 12, rue du Général Zimmer, 67084 Strasbourg, France
| | - Philippe Hammann
- Plateforme Protéomique Strasbourg Esplanade du CNRS, Université de Strasbourg, 67084 Strasbourg, France
| | - Lauriane Kuhn
- Plateforme Protéomique Strasbourg Esplanade du CNRS, Université de Strasbourg, 67084 Strasbourg, France
| | - Danaé Brun
- Institut de biologie moléculaire des plantes, CNRS, Université de Strasbourg, 12, rue du Général Zimmer, 67084 Strasbourg, France
| | - Nathalie Bouteiller
- Institut Jean-Pierre Bourgin, INRAE, AgroParisTech, Université Paris-Saclay, 78000 Versailles, France
| | - Nicolas Baumberger
- Institut de biologie moléculaire des plantes, CNRS, Université de Strasbourg, 12, rue du Général Zimmer, 67084 Strasbourg, France
| | - Hervé Vaucheret
- Institut Jean-Pierre Bourgin, INRAE, AgroParisTech, Université Paris-Saclay, 78000 Versailles, France
| | - Blake C Meyers
- Donald Danforth Plant Science Center, Saint Louis 63132, MO, USA; Division of Plant Science and Technology, University of Missouri, Columbia, MO 65211, USA
| | - Pascal Genschik
- Institut de biologie moléculaire des plantes, CNRS, Université de Strasbourg, 12, rue du Général Zimmer, 67084 Strasbourg, France.
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Arabidopsis RBV is a conserved WD40 repeat protein that promotes microRNA biogenesis and ARGONAUTE1 loading. Nat Commun 2022; 13:1217. [PMID: 35260568 PMCID: PMC8904849 DOI: 10.1038/s41467-022-28872-x] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Accepted: 02/08/2022] [Indexed: 12/14/2022] Open
Abstract
MicroRNAs (miRNAs) play crucial roles in gene expression regulation through RNA cleavage or translation repression. Here, we report the identification of an evolutionarily conserved WD40 domain protein as a player in miRNA biogenesis in Arabidopsis thaliana. A mutation in the REDUCTION IN BLEACHED VEIN AREA (RBV) gene encoding a WD40 domain protein led to the suppression of leaf bleaching caused by an artificial miRNA; the mutation also led to a global reduction in the accumulation of endogenous miRNAs. The nuclear protein RBV promotes the transcription of MIR genes into pri-miRNAs by enhancing the occupancy of RNA polymerase II (Pol II) at MIR gene promoters. RBV also promotes the loading of miRNAs into AGO1. In addition, RNA-seq revealed a global splicing defect in the mutant. Thus, this evolutionarily conserved, nuclear WD40 domain protein acts in miRNA biogenesis and RNA splicing. MicroRNAs regulate gene expression through RNA cleavage or translation repression. Here the authors show that RBV, an evolutionarily conserved WD40 domain protein, acts to promote MIR transcription, pri-miRNA processing and miRNA loading into AGO1.
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15
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Li M, Yu H, Liu K, Yang W, Zhou B, Gan L, Li S, Zhang C, Yu B. Serrate-Associated Protein 1, a splicing-related protein, promotes miRNA biogenesis in Arabidopsis. THE NEW PHYTOLOGIST 2021; 232:1959-1973. [PMID: 34449907 PMCID: PMC8568667 DOI: 10.1111/nph.17691] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Accepted: 08/20/2021] [Indexed: 06/02/2023]
Abstract
MicroRNAs (miRNAs) are essential regulators of gene expression in metazoans and plants. In plants, most miRNAs are generated from primary miRNA transcripts (pri-miRNAs), which are processed by the Dicer-like 1 (DCL1) complex along with accessory proteins. Serrate-Associated Protein 1 (SEAP1), a conserved splicing-related protein, has been studied in human and yeast. However, the functions of SEAP1 in plants remain elusive. Lack of SEAP1 results in embryo lethality and knockdown of SEAP1 by an artificial miRNA (amiRSEAP1 ) causes pleiotropic developmental defects and reduction in miRNA accumulation. SEAP1 associates with the DCL1 complex, and may promote the interaction of the DCL1 complexes with pri-miRNAs. SEAP1 also enhances pri-miRNA accumulation, but does not affect pri-miRNA transcription, suggesting it may indirectly or directly stabilize pri-miRNAs. In addition, SEAP1 affects the splicing of some pri-miRNAs and intron retention of messenger RNAs at global levels. Our findings uncover both conserved and novel functions of SEAP1 in plants. Besides the role as a splicing factor, SEPA1 may promote miRNA biogenesis by positively modulating pri-miRNA splicing, processing and/or stability.
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Affiliation(s)
- Mu Li
- School of Biological Sciences & Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, Nebraska 68588–0666, USA
| | - Huihui Yu
- School of Biological Sciences & Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, Nebraska 68588–0666, USA
| | - Kan Liu
- School of Biological Sciences & Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, Nebraska 68588–0666, USA
| | - Weilong Yang
- School of Biological Sciences & Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, Nebraska 68588–0666, USA
| | - Bangjun Zhou
- School of Biological Sciences & Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, Nebraska 68588–0666, USA
| | - Lu Gan
- School of Biological Sciences & Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, Nebraska 68588–0666, USA
| | - Shengjun Li
- School of Biological Sciences & Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, Nebraska 68588–0666, USA
- Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Energy Genetics, Shandong Institute of Energy Technology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
| | - Chi Zhang
- School of Biological Sciences & Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, Nebraska 68588–0666, USA
| | - Bin Yu
- School of Biological Sciences & Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, Nebraska 68588–0666, USA
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16
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Cyclophilins and Their Functions in Abiotic Stress and Plant-Microbe Interactions. Biomolecules 2021; 11:biom11091390. [PMID: 34572603 PMCID: PMC8464771 DOI: 10.3390/biom11091390] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Revised: 09/15/2021] [Accepted: 09/17/2021] [Indexed: 01/12/2023] Open
Abstract
Plants have developed a variety of mechanisms and regulatory pathways to change their gene expression profiles in response to abiotic stress conditions and plant–microbe interactions. The plant–microbe interaction can be pathogenic or beneficial. Stress conditions, both abiotic and pathogenic, negatively affect the growth, development, yield and quality of plants, which is very important for crops. In contrast, the plant–microbe interaction could be growth-promoting. One of the proteins involved in plant response to stress conditions and plant–microbe interactions is cyclophilin. Cyclophilins (CyPs), together with FK506-binding proteins (FKBPs) and parvulins, belong to a big family of proteins with peptidyl-prolyl cis-trans isomerase activity (Enzyme Commission (EC) number 5.2.1.8). Genes coding for proteins with the CyP domain are widely expressed in all organisms examined, including bacteria, fungi, animals, and plants. Their different forms can be found in the cytoplasm, endoplasmic reticulum, nucleus, chloroplast, mitochondrion and in the phloem space. They are involved in numerous processes, such as protein folding, cellular signaling, mRNA processing, protein degradation and apoptosis. In the past few years, many new functions, and molecular mechanisms for cyclophilins have been discovered. In this review, we aim to summarize recent advances in cyclophilin research to improve our understanding of their biological functions in plant defense and symbiotic plant–microbe interactions.
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17
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Kumar V, Donev EN, Barbut FR, Kushwah S, Mannapperuma C, Urbancsok J, Mellerowicz EJ. Genome-Wide Identification of Populus Malectin/Malectin-Like Domain-Containing Proteins and Expression Analyses Reveal Novel Candidates for Signaling and Regulation of Wood Development. FRONTIERS IN PLANT SCIENCE 2020; 11:588846. [PMID: 33414796 PMCID: PMC7783096 DOI: 10.3389/fpls.2020.588846] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Accepted: 11/18/2020] [Indexed: 05/21/2023]
Abstract
Malectin domain (MD) is a ligand-binding protein motif of pro- and eukaryotes. It is particularly abundant in Viridiplantae, where it occurs as either a single (MD, PF11721) or tandemly duplicated domain (PF12819) called malectin-like domain (MLD). In herbaceous plants, MD- or MLD-containing proteins (MD proteins) are known to regulate development, reproduction, and resistance to various stresses. However, their functions in woody plants have not yet been studied. To unravel their potential role in wood development, we carried out genome-wide identification of MD proteins in the model tree species black cottonwood (Populus trichocarpa), and analyzed their expression and co-expression networks. P. trichocarpa had 146 MD genes assigned to 14 different clades, two of which were specific to the genus Populus. 87% of these genes were located on chromosomes, the rest being associated with scaffolds. Based on their protein domain organization, and in agreement with the exon-intron structures, the MD genes identified here could be classified into five superclades having the following domains: leucine-rich repeat (LRR)-MD-protein kinase (PK), MLD-LRR-PK, MLD-PK (CrRLK1L), MLD-LRR, and MD-Kinesin. Whereas the majority of MD genes were highly expressed in leaves, particularly under stress conditions, eighteen showed a peak of expression during secondary wall formation in the xylem and their co-expression networks suggested signaling functions in cell wall integrity, pathogen-associated molecular patterns, calcium, ROS, and hormone pathways. Thus, P. trichocarpa MD genes having different domain organizations comprise many genes with putative foliar defense functions, some of which could be specific to Populus and related species, as well as genes with potential involvement in signaling pathways in other tissues including developing wood.
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Affiliation(s)
- Vikash Kumar
- Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University of Agricultural Sciences, Umeå, Sweden
| | - Evgeniy N. Donev
- Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University of Agricultural Sciences, Umeå, Sweden
| | - Félix R. Barbut
- Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University of Agricultural Sciences, Umeå, Sweden
| | - Sunita Kushwah
- Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University of Agricultural Sciences, Umeå, Sweden
| | - Chanaka Mannapperuma
- Department of Plant Physiology, Umeå Plant Science Centre, Umeå University, Umeå, Sweden
| | - János Urbancsok
- Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University of Agricultural Sciences, Umeå, Sweden
| | - Ewa J. Mellerowicz
- Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University of Agricultural Sciences, Umeå, Sweden
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18
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Juvenile Leaves or Adult Leaves: Determinants for Vegetative Phase Change in Flowering Plants. Int J Mol Sci 2020; 21:ijms21249753. [PMID: 33371265 PMCID: PMC7766579 DOI: 10.3390/ijms21249753] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Revised: 12/15/2020] [Accepted: 12/17/2020] [Indexed: 12/14/2022] Open
Abstract
Vegetative leaves in Arabidopsis are classified as either juvenile leaves or adult leaves based on their specific traits, such as leaf shape and the presence of abaxial trichomes. The timing of the juvenile-to-adult phase transition during vegetative development, called the vegetative phase change, is a critical decision for plants, as this transition is associated with crop yield, stress responses, and immune responses. Juvenile leaves are characterized by high levels of miR156/157, and adult leaves are characterized by high levels of miR156/157 targets, SQUAMOSA PROMOTER BINDING PROTEIN-LIKE (SPL) transcription factors. The discovery of this miR156/157-SPL module provided a critical tool for elucidating the complex regulation of the juvenile-to-adult phase transition in plants. In this review, we discuss how the traits of juvenile leaves and adult leaves are determined by the miR156/157-SPL module and how different factors, including embryonic regulators, sugar, meristem regulators, hormones, and epigenetic proteins are involved in controlling the juvenile-to-adult phase transition, focusing on recent insights into vegetative phase change. We also highlight outstanding questions in the field that need further investigation. Understanding how vegetative phase change is regulated would provide a basis for manipulating agricultural traits under various conditions.
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Iki T, Takami M, Kai T. Modulation of Ago2 Loading by Cyclophilin 40 Endows a Unique Repertoire of Functional miRNAs during Sperm Maturation in Drosophila. Cell Rep 2020; 33:108380. [PMID: 33176138 DOI: 10.1016/j.celrep.2020.108380] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Revised: 09/25/2020] [Accepted: 10/21/2020] [Indexed: 12/14/2022] Open
Abstract
In gene silencing, Hsp90 chaperone machinery assists Argonaute (Ago) binding and unwinding of silencing small RNA (sRNA) duplexes. This enables the formation of effector RNA-induced silencing complex (RISC) that often displays cargo preferences. Hence, in Drosophila, microRNAs (miRNAs) and small-interfering RNAs (siRNAs) are differentially sorted into Ago1-RISC and Ago2-RISC, respectively. Here, we identify fly Cyclophilin 40 (Cyp40) as a testis-specialized Hsp90 co-chaperone essential for spermatogenesis and for modulating Ago2-RISC formation. We show that testis-distinctive Ago-sorting and strand-selection mechanisms accumulate a unique set of miRNAs on Ago2. Cyp40 interacts with duplex-incorporating Ago2 through Hsp90 in vitro and selectively promotes the build-up of Ago2-bound miRNAs, but not endogenous siRNAs, in vivo. Moreover, one of Cyp40-dependent Ago2-sorted miRNAs is required for late spermatogenesis, unraveling the physiological relevance of the unconventional yet conserved Drosophila miRNA-Ago2 sorting pathway. Collectively, these results identify RISC-regulatory roles for Hsp90 machinery and, more generally, highlight the tissue-specific adaptation of sRNA pathways through chaperone diversification.
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Affiliation(s)
- Taichiro Iki
- Laboratory of Germline Biology, Graduate School of Frontier Biosciences, Osaka University, Yamadaoka1-3, Suita, Osaka 565-0871, Japan.
| | - Moe Takami
- Laboratory of Germline Biology, Graduate School of Frontier Biosciences, Osaka University, Yamadaoka1-3, Suita, Osaka 565-0871, Japan
| | - Toshie Kai
- Laboratory of Germline Biology, Graduate School of Frontier Biosciences, Osaka University, Yamadaoka1-3, Suita, Osaka 565-0871, Japan.
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Singh H, Kaur K, Singh M, Kaur G, Singh P. Plant Cyclophilins: Multifaceted Proteins With Versatile Roles. FRONTIERS IN PLANT SCIENCE 2020; 11:585212. [PMID: 33193535 PMCID: PMC7641896 DOI: 10.3389/fpls.2020.585212] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Accepted: 09/22/2020] [Indexed: 05/03/2023]
Abstract
Cyclophilins constitute a family of ubiquitous proteins that bind cyclosporin A (CsA), an immunosuppressant drug. Several of these proteins possess peptidyl-prolyl cis-trans isomerase (PPIase) activity that catalyzes the cis-trans isomerization of the peptide bond preceding a proline residue, essential for correct folding of the proteins. Compared to prokaryotes and other eukaryotes studied until now, the cyclophilin gene families in plants exhibit considerable expansion. With few exceptions, the role of the majority of these proteins in plants is still a matter of conjecture. However, recent studies suggest that cyclophilins are highly versatile proteins with multiple functionalities, and regulate a plethora of growth and development processes in plants, ranging from hormone signaling to the stress response. The present review discusses the implications of cyclophilins in different facets of cellular processes, particularly in the context of plants, and provides a glimpse into the molecular mechanisms by which these proteins fine-tune the diverse physiological pathways.
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Affiliation(s)
- Harpreet Singh
- Department of Biotechnology, Guru Nanak Dev University, Amritsar, India
- Department of Bioinformatics, Hans Raj Mahila Maha Vidyalaya, Jalandhar, India
| | - Kirandeep Kaur
- Department of Biotechnology, Guru Nanak Dev University, Amritsar, India
| | - Mangaljeet Singh
- Department of Biotechnology, Guru Nanak Dev University, Amritsar, India
| | - Gundeep Kaur
- Department of Biotechnology, Guru Nanak Dev University, Amritsar, India
- William Harvey Heart Centre, Queen Mary University of London, London, United Kingdom
| | - Prabhjeet Singh
- Department of Biotechnology, Guru Nanak Dev University, Amritsar, India
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MAC5, an RNA-binding protein, protects pri-miRNAs from SERRATE-dependent exoribonuclease activities. Proc Natl Acad Sci U S A 2020; 117:23982-23990. [PMID: 32887800 DOI: 10.1073/pnas.2008283117] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
MAC5 is a component of the conserved MOS4-associated complex. It plays critical roles in development and immunity. Here we report that MAC5 is required for microRNA (miRNA) biogenesis. MAC5 interacts with Serrate (SE), which is a core component of the microprocessor that processes primary miRNA transcripts (pri-miRNAs) into miRNAs and binds the stem-loop region of pri-miRNAs. MAC5 is essential for both the efficient processing and the stability of pri-miRNAs. Interestingly, the reduction of pri-miRNA levels in mac5 is partially caused by XRN2/XRN3, the nuclear-localized 5'-to-3' exoribonucleases, and depends on SE. These results reveal that MAC5 plays a dual role in promoting pri-miRNA processing and stability through its interaction with SE and/or pri-miRNAs. This study also uncovers that pri-miRNAs need to be protected from nuclear RNA decay machinery, which is connected to the microprocessor.
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Tichá T, Samakovli D, Kuchařová A, Vavrdová T, Šamaj J. Multifaceted roles of HEAT SHOCK PROTEIN 90 molecular chaperones in plant development. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:3966-3985. [PMID: 32293686 DOI: 10.1093/jxb/eraa177] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Accepted: 04/06/2020] [Indexed: 05/20/2023]
Abstract
HEAT SHOCK PROTEINS 90 (HSP90s) are molecular chaperones that mediate correct folding and stability of many client proteins. These chaperones act as master molecular hubs involved in multiple aspects of cellular and developmental signalling in diverse organisms. Moreover, environmental and genetic perturbations affect both HSP90s and their clients, leading to alterations of molecular networks determining respectively plant phenotypes and genotypes and contributing to a broad phenotypic plasticity. Although HSP90 interaction networks affecting the genetic basis of phenotypic variation and diversity have been thoroughly studied in animals, such studies are just starting to emerge in plants. Here, we summarize current knowledge and discuss HSP90 network functions in plant development and cellular homeostasis.
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Affiliation(s)
- Tereza Tichá
- Department of Cell Biology, Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University Olomouc, Olomouc, Czech Republic
| | - Despina Samakovli
- Department of Cell Biology, Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University Olomouc, Olomouc, Czech Republic
| | - Anna Kuchařová
- Department of Cell Biology, Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University Olomouc, Olomouc, Czech Republic
| | - Tereza Vavrdová
- Department of Cell Biology, Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University Olomouc, Olomouc, Czech Republic
| | - Jozef Šamaj
- Department of Cell Biology, Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University Olomouc, Olomouc, Czech Republic
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23
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Dunker F, Trutzenberg A, Rothenpieler JS, Kuhn S, Pröls R, Schreiber T, Tissier A, Kemen A, Kemen E, Hückelhoven R, Weiberg A. Oomycete small RNAs bind to the plant RNA-induced silencing complex for virulence. eLife 2020; 9:56096. [PMID: 32441255 PMCID: PMC7297541 DOI: 10.7554/elife.56096] [Citation(s) in RCA: 70] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Accepted: 05/21/2020] [Indexed: 12/21/2022] Open
Abstract
The exchange of small RNAs (sRNAs) between hosts and pathogens can lead to gene silencing in the recipient organism, a mechanism termed cross-kingdom RNAi (ck-RNAi). While fungal sRNAs promoting virulence are established, the significance of ck-RNAi in distinct plant pathogens is not clear. Here, we describe that sRNAs of the pathogen Hyaloperonospora arabidopsidis, which represents the kingdom of oomycetes and is phylogenetically distant from fungi, employ the host plant’s Argonaute (AGO)/RNA-induced silencing complex for virulence. To demonstrate H. arabidopsidis sRNA (HpasRNA) functionality in ck-RNAi, we designed a novel CRISPR endoribonuclease Csy4/GUS reporter that enabled in situ visualization of HpasRNA-induced target suppression in Arabidopsis. The significant role of HpasRNAs together with AtAGO1 in virulence was revealed in plant atago1 mutants and by transgenic Arabidopsis expressing a short-tandem-target-mimic to block HpasRNAs, that both exhibited enhanced resistance. HpasRNA-targeted plant genes contributed to host immunity, as Arabidopsis gene knockout mutants displayed quantitatively enhanced susceptibility.
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Affiliation(s)
- Florian Dunker
- Faculty of Biology, Genetics, Biocenter Martinsried, LMU Munich, Martinsried, Germany
| | - Adriana Trutzenberg
- Faculty of Biology, Genetics, Biocenter Martinsried, LMU Munich, Martinsried, Germany
| | - Jan S Rothenpieler
- Faculty of Biology, Genetics, Biocenter Martinsried, LMU Munich, Martinsried, Germany
| | - Sarah Kuhn
- Faculty of Biology, Genetics, Biocenter Martinsried, LMU Munich, Martinsried, Germany
| | - Reinhard Pröls
- Phytopathology, School of Life Sciences Weihenstephan, Technical University of Munich, Freising, Germany
| | - Tom Schreiber
- Department of Cell and Metabolic Biology, Leibniz Institute of Plant Biochemistry, Halle, Germany
| | - Alain Tissier
- Department of Cell and Metabolic Biology, Leibniz Institute of Plant Biochemistry, Halle, Germany
| | - Ariane Kemen
- Center for Plant Molecular Biology, Interfaculty Institute of Microbiology and Infection Medicine Tübingen, University of Tübingen, Tübingen, Germany
| | - Eric Kemen
- Center for Plant Molecular Biology, Interfaculty Institute of Microbiology and Infection Medicine Tübingen, University of Tübingen, Tübingen, Germany
| | - Ralph Hückelhoven
- Phytopathology, School of Life Sciences Weihenstephan, Technical University of Munich, Freising, Germany
| | - Arne Weiberg
- Faculty of Biology, Genetics, Biocenter Martinsried, LMU Munich, Martinsried, Germany
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24
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Plant 22-nt siRNAs mediate translational repression and stress adaptation. Nature 2020; 581:89-93. [PMID: 32376953 DOI: 10.1038/s41586-020-2231-y] [Citation(s) in RCA: 85] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Accepted: 02/25/2020] [Indexed: 11/08/2022]
Abstract
Small interfering RNAs (siRNAs) are essential for proper development and immunity in eukaryotes1. Plants produce siRNAs with lengths of 21, 22 or 24 nucleotides. The 21- and 24-nucleotide species mediate cleavage of messenger RNAs and DNA methylation2,3, respectively, but the biological functions of the 22-nucleotide siRNAs remain unknown. Here we report the identification and characterization of a group of endogenous 22-nucleotide siRNAs that are generated by the DICER-LIKE 2 (DCL2) protein in plants. When cytoplasmic RNA decay and DCL4 are deficient, the resulting massive accumulation of 22-nucleotide siRNAs causes pleiotropic growth disorders, including severe dwarfism, meristem defects and pigmentation. Notably, two genes that encode nitrate reductases-NIA1 and NIA2-produce nearly half of the 22-nucleotide siRNAs. Production of 22-nucleotide siRNAs triggers the amplification of gene silencing and induces translational repression both gene specifically and globally. Moreover, these 22-nucleotide siRNAs preferentially accumulate upon environmental stress, especially those siRNAs derived from NIA1/2, which act to restrain translation, inhibit plant growth and enhance stress responses. Thus, our research uncovers the unique properties of 22-nucleotide siRNAs, and reveals their importance in plant adaptation to environmental stresses.
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25
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Du F, Gong W, Boscá S, Tucker M, Vaucheret H, Laux T. Dose-Dependent AGO1-Mediated Inhibition of the miRNA165/166 Pathway Modulates Stem Cell Maintenance in Arabidopsis Shoot Apical Meristem. PLANT COMMUNICATIONS 2020; 1:100002. [PMID: 33404539 PMCID: PMC7747967 DOI: 10.1016/j.xplc.2019.100002] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Revised: 08/04/2019] [Accepted: 08/09/2019] [Indexed: 05/28/2023]
Abstract
Pluripotent stem cells localized in proliferating growth centers, the meristems, are the origin of life-long organ formation and growth in higher plants. In the shoot apical meristem of Arabidopsis thaliana, the closely related ARGONAUTE proteins AGO1 and ZLL/AGO10 bind miR165/166 species to regulate mRNAs of HD-ZIP III transcription factors that are essential to maintaining stem cells. Several genetic studies showed that AGO1 and ZLL/AGO10 act redundantly to maintain stem cells. By contrast, the reported biochemical data suggested antagonistic functions: AGO1 utilizes miR165/166 to slice HD-ZIP III mRNAs, whereas ZLL/AGO10 promotes degradation of miR165/166 and thus stabilizes HD-ZIP III mRNAs. How these different functions are balanced in stem cell regulation has remained enigmatic. Here, we show that autorepression of AGO1 through miR168-mediated slicing of its own RNA is required to maintain the ability of AGO1 to suppress HD-ZIP III mRNAs. Increased AGO1 expression, either in the miR168a-2 mutant or by transgenic expression, inhibits this ability despite the presence of high levels of miR165/166, effectively uncoupling HD-ZIP III and miR165/166 expression. AGO1 activity can be restored, however, by increasing the levels of chaperones SQN and HSP90, which promote assembly of RNA-induced silencing complex (RISC). This suggests that cellular abundance of SQN and HSP chaperones limits AGO1-mediated RNA interference in shoot meristem stem cell regulation. Localized misexpression of AGO1 indicates that the cells surrounding the shoot meristem primordium play a crucial role in stem cell development. Taken together, our study provides a framework that reconciles biochemical and genetic data, showing that restriction of AGO1 levels by miR168-mediated autorepression is key to RISC homeostasis and the function of AGO1 in stem cell regulation.
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Affiliation(s)
- Fei Du
- Signalling Research Centres BIOSS and CIBSS, Faculty of Biology, University of Freiburg, Schänzlestrasse 1, 79104 Freiburg, Germany
| | - Wen Gong
- Signalling Research Centres BIOSS and CIBSS, Faculty of Biology, University of Freiburg, Schänzlestrasse 1, 79104 Freiburg, Germany
| | - Sonia Boscá
- Signalling Research Centres BIOSS and CIBSS, Faculty of Biology, University of Freiburg, Schänzlestrasse 1, 79104 Freiburg, Germany
| | - Matthew Tucker
- Signalling Research Centres BIOSS and CIBSS, Faculty of Biology, University of Freiburg, Schänzlestrasse 1, 79104 Freiburg, Germany
| | - Hervé Vaucheret
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, 78000 Versailles, France
| | - Thomas Laux
- Signalling Research Centres BIOSS and CIBSS, Faculty of Biology, University of Freiburg, Schänzlestrasse 1, 79104 Freiburg, Germany
- Sino-German Joint Research Center on Agricultural Biology, Shandong Agricultural University, Tai'an, Shandong, China
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26
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Hirata R, Mishiba KI, Koizumi N, Iwata Y. Deficiency in the double-stranded RNA binding protein HYPONASTIC LEAVES1 increases sensitivity to the endoplasmic reticulum stress inducer tunicamycin in Arabidopsis. BMC Res Notes 2019; 12:580. [PMID: 31521187 PMCID: PMC6744651 DOI: 10.1186/s13104-019-4623-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Accepted: 09/09/2019] [Indexed: 12/03/2022] Open
Abstract
Objective microRNA (miRNA) is a small non-coding RNA that regulates gene expression by sequence-dependent binding to protein-coding mRNA in eukaryotic cells. In plants, miRNA plays important roles in a plethora of physiological processes, including abiotic and biotic stress responses. The present study was conducted to investigate whether miRNA-mediated regulation is important for the endoplasmic reticulum (ER) stress response in Arabidopsis. Results We found that hyl1 mutant plants are more sensitive to tunicamycin, an inhibitor of N-linked glycosylation that causes ER stress than wild-type plants. Other miRNA-related mutants, se and ago1, exhibited similar sensitivity to the wild-type, indicating that the hypersensitive phenotype is attributable to the loss-of-function of HYL1, rather than deficiency in general miRNA biogenesis and function. However, the transcriptional response of select ER stress-responsive genes in hyl1 mutant plants was indistinguishable from that of wild-type plants, suggesting that the loss-of-function of HYL1 does not affect the ER stress signaling pathways.
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Affiliation(s)
- Rikako Hirata
- Graduate School of Life and Environmental Sciences, Osaka Prefecture University, 1-1 Gakuen-cho, Naka-ku, Sakai, 599-8531, Osaka, Japan
| | - Kei-Ichiro Mishiba
- Graduate School of Life and Environmental Sciences, Osaka Prefecture University, 1-1 Gakuen-cho, Naka-ku, Sakai, 599-8531, Osaka, Japan
| | - Nozomu Koizumi
- Graduate School of Life and Environmental Sciences, Osaka Prefecture University, 1-1 Gakuen-cho, Naka-ku, Sakai, 599-8531, Osaka, Japan
| | - Yuji Iwata
- Graduate School of Life and Environmental Sciences, Osaka Prefecture University, 1-1 Gakuen-cho, Naka-ku, Sakai, 599-8531, Osaka, Japan.
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27
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Kozeko LY. The Role of HSP90 Chaperones in Stability and Plasticity of Ontogenesis of Plants under Normal and Stressful Conditions (Arabidopsis thaliana). CYTOL GENET+ 2019. [DOI: 10.3103/s0095452719020063] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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28
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Wang J, Mei J, Ren G. Plant microRNAs: Biogenesis, Homeostasis, and Degradation. FRONTIERS IN PLANT SCIENCE 2019; 10:360. [PMID: 30972093 PMCID: PMC6445950 DOI: 10.3389/fpls.2019.00360] [Citation(s) in RCA: 131] [Impact Index Per Article: 26.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2018] [Accepted: 03/07/2019] [Indexed: 05/18/2023]
Abstract
MicroRNAs (miRNAs), a class of endogenous, tiny, non-coding RNAs, are master regulators of gene expression among most eukaryotes. Intracellular miRNA abundance is regulated under multiple levels of control including transcription, processing, RNA modification, RNA-induced silencing complex (RISC) assembly, miRNA-target interaction, and turnover. In this review, we summarize our current understanding of the molecular components and mechanisms that influence miRNA biogenesis, homeostasis, and degradation in plants. We also make comparisons with findings from other organisms where necessary.
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Affiliation(s)
| | | | - Guodong Ren
- State Key Laboratory of Genetic Engineering and Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, China
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29
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Chen Q, Chen QJ, Sun GQ, Zheng K, Yao ZP, Han YH, Wang LP, Duan YJ, Yu DQ, Qu YY. Genome-Wide Identification of Cyclophilin Gene Family in Cotton and Expression Analysis of the Fibre Development in Gossypium barbadense. Int J Mol Sci 2019; 20:E349. [PMID: 30654456 PMCID: PMC6359516 DOI: 10.3390/ijms20020349] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2018] [Revised: 01/10/2019] [Accepted: 01/12/2019] [Indexed: 11/17/2022] Open
Abstract
Cyclophilins (CYPs) are a member of the immunophilin superfamily (in addition to FKBPs and parvulins) and play a significant role in peptidyl-prolyl cis-trans isomerase (PPIase) activity. Previous studies have shown that CYPs have important functions in plants, but no genome-wide analysis of the cotton CYP gene family has been reported, and the specific biological function of this gene is still elusive. Based on the release of the cotton genome sequence, we identified 75, 78, 40 and 38 CYP gene sequences from G. barbadense, G. hirsutum, G. arboreum, and G. raimondii, respectively; 221 CYP genes were unequally located on chromosomes. Phylogenetic analysis showed that 231 CYP genes clustered into three major groups and eight subgroups. Collinearity analysis showed that segmental duplications played a significant role in the expansion of CYP members in cotton. There were light-responsiveness, abiotic-stress and hormone-response elements upstream of most of the CYPs. In addition, the motif composition analysis revealed that 49 cyclophilin proteins had extra domains, including TPR (tetratricopeptide repeat), coiled coil, U-box, RRM (RNA recognition motif), WD40 (RNA recognition motif) and zinc finger domains, along with the cyclophilin-like domain (CLD). The expression patterns based on qRT-PCR showed that six CYP expression levels showed greater differences between Xinhai21 (long fibres, G. barbadense) and Ashmon (short fibres, G. barbadense) at 10 and 20 days postanthesis (DPA). These results signified that CYP genes are involved in the elongation stage of cotton fibre development. This study provides a valuable resource for further investigations of CYP gene functions and molecular mechanisms in cotton.
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Affiliation(s)
- Qin Chen
- College of Agronomy, Xinjiang Agricultural University, Urumqi 830052, China.
| | - Quan-Jia Chen
- College of Agronomy, Xinjiang Agricultural University, Urumqi 830052, China.
| | - Guo-Qing Sun
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
| | - Kai Zheng
- College of Agronomy, Xinjiang Agricultural University, Urumqi 830052, China.
| | - Zheng-Pei Yao
- College of Agronomy, Xinjiang Agricultural University, Urumqi 830052, China.
| | - Yu-Hui Han
- College of Agronomy, Xinjiang Agricultural University, Urumqi 830052, China.
| | - Li-Ping Wang
- College of Agronomy, Xinjiang Agricultural University, Urumqi 830052, China.
| | - Ya-Jie Duan
- College of Agronomy, Xinjiang Agricultural University, Urumqi 830052, China.
| | - Dao-Qian Yu
- College of Agronomy, Xinjiang Agricultural University, Urumqi 830052, China.
- Cotton Research Institute, Chinese Academy of Agricultural Sciences, Anyang 455000, China.
| | - Yan-Ying Qu
- College of Agronomy, Xinjiang Agricultural University, Urumqi 830052, China.
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30
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Barbosa Dos Santos I, Park SW. Versatility of Cyclophilins in Plant Growth and Survival: A Case Study in Arabidopsis. Biomolecules 2019; 9:biom9010020. [PMID: 30634678 PMCID: PMC6358970 DOI: 10.3390/biom9010020] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Revised: 12/22/2018] [Accepted: 01/02/2019] [Indexed: 11/16/2022] Open
Abstract
Cyclophilins (CYPs) belong to a peptidyl-prolyl cis-trans isomerase family, and were first characterized in mammals as a target of an immunosuppressive drug, cyclosporin A, preventing proinflammatory cytokine production. In Arabidopsis, 29 CYPs and CYP-like proteins are found across all subcellular compartments, involved in various physiological processes including transcriptional regulation, organogenesis, photosynthetic and hormone signaling pathways, stress adaptation and defense responses. These important but diverse activities of CYPs must be reflected by their versatility as cellular and molecular modulators. However, our current knowledge regarding their mode of actions is still far from complete. This review will briefly revisit recent progresses on the roles and mechanisms of CYPs in Arabidopsis studies, and information gaps within, which help understanding the phenotypic and environmental plasticity of plants.
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Affiliation(s)
| | - Sang-Wook Park
- Department of Entomology and Plant Pathology Auburn University, Auburn, AL 36849, USA.
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31
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Pegler JL, Grof CPL, Eamens AL. The Plant microRNA Pathway: The Production and Action Stages. Methods Mol Biol 2019; 1932:15-39. [PMID: 30701489 DOI: 10.1007/978-1-4939-9042-9_2] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Plant microRNAs are an endogenous class of small regulatory RNA central to the posttranscriptional regulation of gene expression in plant development and environmental stress adaptation or in response to pathogen challenge. The plant microRNA pathway is readily separated into two distinct stages: (1) the production stage, which is localized to the plant cell nucleus and where the microRNA small RNA is processed from a double-stranded RNA precursor transcript, and (2) the action stage, which is localized to the plant cell cytoplasm and where the mature microRNA small RNA is loaded into an effector complex and is used by the complex as a sequence specificity guide to direct expression repression of target genes harboring highly complementary microRNA target sequences. Historical research indicated that the plant microRNA pathway was a highly structured, almost linear pathway requiring a small set of core machinery proteins. However, contemporary research has demonstrated that the plant microRNA pathway is highly dynamic, and to allow for this flexibility, a large and highly functionally diverse set of machinery proteins is now known to be required. For example, recent research has shown that plant microRNAs can regulate target gene expression via a translational repression mechanism of RNA silencing in addition to the standard messenger RNA cleavage-based mechanism of RNA silencing: a mode of RNA silencing originally assigned to all plant microRNAs. Using Arabidopsis thaliana as our model system, here we report on both the core and auxiliary sets of machinery proteins now known to be required for both microRNA production and microRNA action in plants.
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Affiliation(s)
- Joseph L Pegler
- Faculty of Science, Centre for Plant Science, School of Environmental and Life Sciences, University of Newcastle, Callaghan, NSW, Australia
| | - Christopher P L Grof
- Faculty of Science, Centre for Plant Science, School of Environmental and Life Sciences, University of Newcastle, Callaghan, NSW, Australia
| | - Andrew L Eamens
- Faculty of Science, Centre for Plant Science, School of Environmental and Life Sciences, University of Newcastle, Callaghan, NSW, Australia.
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32
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Correa JPDO, Silva EM, Nogueira FTS. Molecular Control by Non-coding RNAs During Fruit Development: From Gynoecium Patterning to Fruit Ripening. FRONTIERS IN PLANT SCIENCE 2018; 9:1760. [PMID: 30555499 PMCID: PMC6283909 DOI: 10.3389/fpls.2018.01760] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Accepted: 11/13/2018] [Indexed: 05/02/2023]
Abstract
Fruits are originated from the transition of a quiescent ovary to a fast-growing young fruit. The evolution of reproductive structures such as ovary and fruit has made seed dispersal easier, which is a key process for reproductive success in flowering plants. The complete fruit development and ripening are characterized by a remarkable phenotypic plasticity which is orchestrated by a myriad of genetic factors. In this context, transcriptional regulation by non-coding small (i.e., microRNAs) and long (lncRNAs) RNAs underlies important mechanisms controlling reproductive organ development. These mechanisms may act together and interact with other pathways (i.e., phytohormones) to regulate cell fate and coordinate reproductive organ development. Functional genomics has shown that non-coding RNAs regulate a diversity of developmental reproductive stages, from carpel formation and ovary development to the softening of the ripe/ripened fruit. This layer of transcriptional control has been associated with ovule, seed, and fruit development as well as fruit ripening, which are crucial developmental processes in breeding programs because of their relevance for crop production. The final ripe fruit is the result of a process under multiple levels of regulation, including mechanisms orchestrated by microRNAs and lncRNAs. Most of the studies we discuss involve work on tomato and Arabidopsis. In this review, we summarize non-coding RNA-controlled mechanisms described in the current literature that act coordinating the main steps of gynoecium development/patterning and fruit ripening.
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Affiliation(s)
| | | | - Fabio T. S. Nogueira
- Laboratory of Molecular Genetics of Plant Development, Department of Biological Sciences (LCB), Escola Superior de Agricultura “Luiz de Queiroz” (ESALQ), University of São Paulo, São Paulo, Brazil
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33
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Cardoso TCDS, Alves TC, Caneschi CM, Santana DDRG, Fernandes-Brum CN, Reis GLD, Daude MM, Ribeiro THC, Gómez MMD, Lima AA, Gomes LAA, Gomes MDS, Gandolfi PE, Amaral LRD, Chalfun-Júnior A, Maluf WR, de Souza Gomes M. New insights into tomato microRNAs. Sci Rep 2018; 8:16069. [PMID: 30375421 PMCID: PMC6207730 DOI: 10.1038/s41598-018-34202-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Accepted: 10/12/2018] [Indexed: 12/21/2022] Open
Abstract
Cultivated tomato, Solanum lycopersicum, is one of the most common fruits in the global food industry. Together with the wild tomato Solanum pennellii, it is widely used for developing better cultivars. MicroRNAs affect mRNA regulation, inhibiting its translation and/or promoting its degradation. Important proteins involved in these processes are ARGONAUTE and DICER. This study aimed to identify and characterize the genes involved in the miRNA processing pathway, miRNA molecules and target genes in both species. We validated the presence of pathway genes and miRNA in different NGS libraries and 6 miRNA families using quantitative RT-PCR. We identified 71 putative proteins in S. lycopersicum and 108 in S. pennellii likely involved in small RNAs processing. Of these, 29 and 32 participate in miRNA processing pathways, respectively. We identified 343 mature miRNAs, 226 pre-miRNAs in 87 families, including 192 miRNAs, which were not previously identified, belonging to 38 new families in S. lycopersicum. In S. pennellii, we found 388 mature miRNAs and 234 pre-miRNAs contained in 85 families. All miRNAs found in S. pennellii were unpublished, being identified for the first time in our study. Furthermore, we identified 2471 and 3462 different miRNA target in S. lycopersicum and S. pennellii, respectively.
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Affiliation(s)
- Thaís Cunha de Sousa Cardoso
- Laboratory of Bioinformatics and Molecular Analysis, Federal University of Uberlandia (UFU), Campus Patos de Minas, 38700-128, Patos de Minas, Brazil
| | - Tamires Caixeta Alves
- Laboratory of Bioinformatics and Molecular Analysis, Federal University of Uberlandia (UFU), Campus Patos de Minas, 38700-128, Patos de Minas, Brazil
| | - Carolina Milagres Caneschi
- Laboratory of Bioinformatics and Molecular Analysis, Federal University of Uberlandia (UFU), Campus Patos de Minas, 38700-128, Patos de Minas, Brazil
| | - Douglas Dos Reis Gomes Santana
- Laboratory of Bioinformatics and Molecular Analysis, Federal University of Uberlandia (UFU), Campus Patos de Minas, 38700-128, Patos de Minas, Brazil
| | | | - Gabriel Lasmar Dos Reis
- Department of Agriculture, Federal University of Lavras (UFLA), Lavras, 37 - 37200-000, Brazil
| | - Matheus Martins Daude
- Laboratory of Molecular Analysis, Federal University of Tocantins (UFT), Gurupi, 77402-970, Brazil
| | | | - Miguel Maurício Díaz Gómez
- Laboratory of Bioinformatics and Molecular Analysis, Federal University of Uberlandia (UFU), Campus Patos de Minas, 38700-128, Patos de Minas, Brazil
| | - André Almeida Lima
- Laboratory of Plant Molecular Physiology, Federal University of Lavras (UFLA), Lavras, 3037 - 37200-000, Brazil
| | | | - Marcos de Souza Gomes
- Laboratory of Bioinformatics and Molecular Analysis, Federal University of Uberlandia (UFU), Campus Patos de Minas, 38700-128, Patos de Minas, Brazil
| | - Peterson Elizandro Gandolfi
- Laboratory of Bioinformatics and Molecular Analysis, Federal University of Uberlandia (UFU), Campus Patos de Minas, 38700-128, Patos de Minas, Brazil
| | - Laurence Rodrigues do Amaral
- Laboratory of Bioinformatics and Molecular Analysis, Federal University of Uberlandia (UFU), Campus Patos de Minas, 38700-128, Patos de Minas, Brazil
| | - Antonio Chalfun-Júnior
- Laboratory of Plant Molecular Physiology, Federal University of Lavras (UFLA), Lavras, 3037 - 37200-000, Brazil
| | - Wilson Roberto Maluf
- Department of Agriculture, Federal University of Lavras (UFLA), Lavras, 37 - 37200-000, Brazil
| | - Matheus de Souza Gomes
- Laboratory of Bioinformatics and Molecular Analysis, Federal University of Uberlandia (UFU), Campus Patos de Minas, 38700-128, Patos de Minas, Brazil.
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Ma Z, Zhang X. Actions of plant Argonautes: predictable or unpredictable? CURRENT OPINION IN PLANT BIOLOGY 2018; 45:59-67. [PMID: 29857309 DOI: 10.1016/j.pbi.2018.05.007] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Revised: 04/25/2018] [Accepted: 05/12/2018] [Indexed: 06/08/2023]
Abstract
Argonaute (AGO) proteins are the key effector of RNA-induced silencing complex (RISC). Land plants typically encode numerous AGO proteins, and they can be typically divided into two major functional groups based on the species of their housed small RNAs (sRNAs). One group of AGOs, guided by 24-nucleotide (nt) sRNAs, canonically function in nuclei to implement transcriptional gene silencing (TGS), whereas the other group of AGOs, guided by 21-nt sRNAs, act in the cytoplasm to fulfill posttranscriptional gene silencing (PTGS). Many new discoveries have been recently made on functions and mechanisms of AGO proteins in plants, and some of the findings change our views on the conventional classification and roles of AGO proteins. In this review, we summarize our current knowledge of AGO proteins in plants.
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Affiliation(s)
- Zeyang Ma
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA; Institute for Plant Genomics and Biotechnology, Texas A&M University, College Station, TX 77843, USA
| | - Xiuren Zhang
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA; Institute for Plant Genomics and Biotechnology, Texas A&M University, College Station, TX 77843, USA.
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Sjögren L, Floris M, Barghetti A, Völlmy F, Linding R, Brodersen P. Farnesylated heat shock protein 40 is a component of membrane-bound RISC in Arabidopsis. J Biol Chem 2018; 293:16608-16622. [PMID: 30194279 PMCID: PMC6204899 DOI: 10.1074/jbc.ra118.003887] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Revised: 07/15/2018] [Indexed: 11/24/2022] Open
Abstract
ARGONAUTE1 (AGO1) binds directly to small regulatory RNA and is a key effector protein of post-transcriptional gene silencing mediated by microRNA (miRNA) and small interfering RNA (siRNA) in Arabidopsis. The formation of an RNA-induced silencing complex (RISC) of AGO1 and small RNA requires the function of the heat shock protein 70/90 chaperone system. Some functions of AGO1 occur in association with endomembranes, in particular the rough endoplasmic reticulum (RER), but proteins interacting with AGO1 in membrane fractions remain unidentified. In this study, we show that the farnesylated heat shock protein 40 homologs, J2 and J3, associate with AGO1 in membrane fractions in a manner that involves protein farnesylation. We also show that three changes in AGO1 function are detectable in mutants in protein farnesylation and J2/J3. First, perturbations of the HSP40/70/90 pathway by mutation of J3, HSP90, and farnesyl transferase affect the amounts of AGO1 associated with membranes. Second, miRNA association with membrane-bound polysomes is increased in farnesyl transferase and farnesylation-deficient J2/J3 mutants. Third, silencing by noncell autonomously acting short interfering RNAs is impaired. These observations highlight the involvement of farnesylated J2/J3 in small RNA-mediated gene regulation, and suggest that the importance of chaperone-AGO1 interaction is not limited to the RISC assembly process.
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Affiliation(s)
- Lars Sjögren
- From the Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, DK-2200 Copenhagen N and
| | - Maïna Floris
- From the Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, DK-2200 Copenhagen N and
| | - Andrea Barghetti
- From the Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, DK-2200 Copenhagen N and
| | - Franziska Völlmy
- the Biotech Research and Innovation Centre, Ole Maaløes Vej 5, DK-2200 Copenhagen N, Denmark
| | - Rune Linding
- the Biotech Research and Innovation Centre, Ole Maaløes Vej 5, DK-2200 Copenhagen N, Denmark
| | - Peter Brodersen
- From the Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, DK-2200 Copenhagen N and
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Bologna NG, Iselin R, Abriata LA, Sarazin A, Pumplin N, Jay F, Grentzinger T, Dal Peraro M, Voinnet O. Nucleo-cytosolic Shuttling of ARGONAUTE1 Prompts a Revised Model of the Plant MicroRNA Pathway. Mol Cell 2018; 69:709-719.e5. [PMID: 29398448 DOI: 10.1016/j.molcel.2018.01.007] [Citation(s) in RCA: 143] [Impact Index Per Article: 23.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2017] [Revised: 11/09/2017] [Accepted: 01/04/2018] [Indexed: 10/18/2022]
Abstract
Unlike in metazoans, plant microRNAs (miRNAs) undergo stepwise nuclear maturation before engaging cytosolic, sequence-complementary transcripts in association with the silencing effector protein ARGONAUTE1 (AGO1). Since their discovery, how and under which form plant miRNAs translocate to the cytosol has remained unclear, as has their sub-cellular AGO1 loading site(s). Here, we show that the N termini of all plant AGO1s contain a nuclear-localization (NLS) and nuclear-export signal (NES) that, in Arabidopsis thaliana (At), enables AtAGO1 nucleo-cytosolic shuttling in a Leptomycin-B-inhibited manner, diagnostic of CRM1(EXPO1)/NES-dependent nuclear export. Nuclear-only AtAGO1 contains the same 2'O-methylated miRNA cohorts as its nucleo-cytosolic counterpart, but it preferentially interacts with the miRNA loading chaperone HSP90. Furthermore, mature miRNA translocation and miRNA-mediated silencing both require AtAGO1 nucleo-cytosolic shuttling. These findings lead us to propose a substantially revised view of the plant miRNA pathway in which miRNAs are matured, methylated, loaded into AGO1 in the nucleus, and exported to the cytosol as AGO1:miRNA complexes in a CRM1(EXPO1)/NES-dependent manner.
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Affiliation(s)
- Nicolas G Bologna
- Department of Biology, Swiss Federal Institute of Technology (ETH), Universitätstrasse 2, Zürich 8092, Switzerland
| | - Raphael Iselin
- Department of Biology, Swiss Federal Institute of Technology (ETH), Universitätstrasse 2, Zürich 8092, Switzerland
| | - Luciano A Abriata
- Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne 1015, Switzerland; Swiss Institute of Bioinformatics, Lausanne 1015, Switzerland
| | - Alexis Sarazin
- Department of Biology, Swiss Federal Institute of Technology (ETH), Universitätstrasse 2, Zürich 8092, Switzerland
| | - Nathan Pumplin
- Department of Biology, Swiss Federal Institute of Technology (ETH), Universitätstrasse 2, Zürich 8092, Switzerland; Department of Plant Sciences, University of California, Davis, California 95616, USA
| | - Florence Jay
- Department of Biology, Swiss Federal Institute of Technology (ETH), Universitätstrasse 2, Zürich 8092, Switzerland
| | - Thomas Grentzinger
- Department of Biology, Swiss Federal Institute of Technology (ETH), Universitätstrasse 2, Zürich 8092, Switzerland
| | - Matteo Dal Peraro
- Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne 1015, Switzerland; Swiss Institute of Bioinformatics, Lausanne 1015, Switzerland
| | - Olivier Voinnet
- Department of Biology, Swiss Federal Institute of Technology (ETH), Universitätstrasse 2, Zürich 8092, Switzerland.
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Döll S, Kuhlmann M, Rutten T, Mette MF, Scharfenberg S, Petridis A, Berreth DC, Mock HP. Accumulation of the coumarin scopolin under abiotic stress conditions is mediated by the Arabidopsis thaliana THO/TREX complex. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2018; 93:431-444. [PMID: 29222952 DOI: 10.1111/tpj.13797] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2015] [Revised: 11/15/2017] [Accepted: 11/23/2017] [Indexed: 05/20/2023]
Abstract
Secondary metabolites are involved in the plant stress response. Among these are scopolin and its active form scopoletin, which are coumarin derivatives associated with reactive oxygen species scavenging and pathogen defence. Here we show that scopolin accumulation can be induced in the root by osmotic stress and in the leaf by low-temperature stress in Arabidopsis thaliana. A genetic screen for altered scopolin levels in A. thaliana revealed a mutant compromised in scopolin accumulation in response to stress; the lesion was present in a homologue of THO1 coding for a subunit of the THO/TREX complex. The THO/TREX complex contributes to RNA silencing, supposedly by trafficking precursors of small RNAs. Mutants defective in THO, AGO1, SDS3 and RDR6 were impaired with respect to scopolin accumulation in response to stress, suggesting a mechanism based on RNA silencing such as the trans-acting small interfering RNA pathway, which requires THO/TREX function.
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Affiliation(s)
- Stefanie Döll
- Department of Physiology and Cell Biology, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstraße 3, 06466, Seeland, OT Gatersleben, Germany
| | - Markus Kuhlmann
- Department of Molecular Genetics, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstraße 3, 06466, Seeland, OT Gatersleben, Germany
| | - Twan Rutten
- Department of Physiology and Cell Biology, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstraße 3, 06466, Seeland, OT Gatersleben, Germany
| | - Michael F Mette
- Department of Breeding Research, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstraße 3, 06466, Seeland, OT Gatersleben, Germany
| | - Sarah Scharfenberg
- Stress and Developmental Biology, Leibniz Institute of Plant Biochemistry (IPB), Weinberg 3, 06120, Halle (Saale), Germany
| | - Antonios Petridis
- Department of Physiology and Cell Biology, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstraße 3, 06466, Seeland, OT Gatersleben, Germany
| | - Dorothee-Carina Berreth
- Department of Physiology and Cell Biology, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstraße 3, 06466, Seeland, OT Gatersleben, Germany
| | - Hans-Peter Mock
- Department of Physiology and Cell Biology, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstraße 3, 06466, Seeland, OT Gatersleben, Germany
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Li S, Liu K, Zhou B, Li M, Zhang S, Zeng L, Zhang C, Yu B. MAC3A and MAC3B, Two Core Subunits of the MOS4-Associated Complex, Positively Influence miRNA Biogenesis. THE PLANT CELL 2018; 30:481-494. [PMID: 29437988 PMCID: PMC5868694 DOI: 10.1105/tpc.17.00953] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Revised: 01/16/2018] [Accepted: 01/31/2018] [Indexed: 05/18/2023]
Abstract
MAC3A and MAC3B are conserved U-box-containing proteins in eukaryotes. They are subunits of the MOS4-associated complex (MAC) that plays essential roles in plant immunity and development in Arabidopsis thaliana However, their functional mechanisms remain elusive. Here, we show that Arabidopsis MAC3A and MAC3B act redundantly in microRNA (miRNA) biogenesis. Lack of both MAC3A and MAC3B in the mac3b mac3b double mutant reduces the accumulation of miRNAs, causing elevated transcript levels of miRNA targets. mac3a mac3b also decreases the levels of primary miRNA transcripts (pri-miRNAs). However, MAC3A and MAC3B do not affect the promoter activity of genes encoding miRNAs (MIR genes), suggesting that they may not affect MIR transcription. This result, together with the fact that MAC3A associates with pri-miRNAs in vivo, indicates that MAC3A and MAC3B may stabilize pri-miRNAs. Furthermore, we find that MAC3A and MAC3B interact with the DCL1 complex that catalyzes miRNA maturation, promote DCL1 activity, and are required for the localization of HYL1, a component of the DCL1 complex. Besides MAC3A and MAC3B, two other MAC subunits, CDC5 and PRL1, also function in miRNA biogenesis. Based on these results, we propose that MAC functions as a complex to control miRNA levels through modulating pri-miRNA transcription, processing, and stability.
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Affiliation(s)
- Shengjun Li
- Qingdao Engineering Research Center of Biomass Resources and Environment, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
- Center for Plant Science Innovation University of Nebraska-Lincoln, Lincoln, Nebraska 68588-0666
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, Nebraska 68588-0118
| | - Kan Liu
- Center for Plant Science Innovation University of Nebraska-Lincoln, Lincoln, Nebraska 68588-0666
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, Nebraska 68588-0118
| | - Bangjun Zhou
- Center for Plant Science Innovation University of Nebraska-Lincoln, Lincoln, Nebraska 68588-0666
- Department of Plant Pathology, University of Nebraska, Lincoln, Nebraska 68583-0722
| | - Mu Li
- Center for Plant Science Innovation University of Nebraska-Lincoln, Lincoln, Nebraska 68588-0666
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, Nebraska 68588-0118
| | - Shuxin Zhang
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian 271018, China
| | - Lirong Zeng
- Center for Plant Science Innovation University of Nebraska-Lincoln, Lincoln, Nebraska 68588-0666
- Department of Plant Pathology, University of Nebraska, Lincoln, Nebraska 68583-0722
| | - Chi Zhang
- Center for Plant Science Innovation University of Nebraska-Lincoln, Lincoln, Nebraska 68588-0666
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, Nebraska 68588-0118
| | - Bin Yu
- Center for Plant Science Innovation University of Nebraska-Lincoln, Lincoln, Nebraska 68588-0666
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, Nebraska 68588-0118
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Hawasli AH, Rutlin J, Roland JL, Murphy RKJ, Song SK, Leuthardt EC, Shimony JS, Ray WZ. Spinal Cord Injury Disrupts Resting-State Networks in the Human Brain. J Neurotrauma 2018; 35:864-873. [PMID: 29179629 DOI: 10.1089/neu.2017.5212] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Despite 253,000 spinal cord injury (SCI) patients in the United States, little is known about how SCI affects brain networks. Spinal MRI provides only structural information with no insight into functional connectivity. Resting-state functional MRI (RS-fMRI) quantifies network connectivity through the identification of resting-state networks (RSNs) and allows detection of functionally relevant changes during disease. Given the robust network of spinal cord afferents to the brain, we hypothesized that SCI produces meaningful changes in brain RSNs. RS-fMRIs and functional assessments were performed on 10 SCI subjects. Blood oxygen-dependent RS-fMRI sequences were acquired. Seed-based correlation mapping was performed using five RSNs: default-mode (DMN), dorsal-attention (DAN), salience (SAL), control (CON), and somatomotor (SMN). RSNs were compared with normal control subjects using false-discovery rate-corrected two way t tests. SCI reduced brain network connectivity within the SAL, SMN, and DMN and disrupted anti-correlated connectivity between CON and SMN. When divided into separate cohorts, complete but not incomplete SCI disrupted connectivity within SAL, DAN, SMN and DMN and between CON and SMN. Finally, connectivity changed over time after SCI: the primary motor cortex decreased connectivity with the primary somatosensory cortex, the visual cortex decreased connectivity with the primary motor cortex, and the visual cortex decreased connectivity with the sensory parietal cortex. These unique findings demonstrate the functional network plasticity that occurs in the brain as a result of injury to the spinal cord. Connectivity changes after SCI may serve as biomarkers to predict functional recovery following an SCI and guide future therapy.
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Affiliation(s)
- Ammar H Hawasli
- 1 Department of Neurological Surgery, Washington University School of Medicine , Saint Louis, Missouri.,2 Department of Biomedical Engineering, Washington University School of Medicine , Saint Louis, Missouri.,3 Department of Orthopedic Surgery, Washington University School of Medicine , Saint Louis, Missouri
| | - Jerrel Rutlin
- 4 Department of Mallinckrodt Institute of Radiology, Washington University School of Medicine , Saint Louis, Missouri
| | - Jarod L Roland
- 1 Department of Neurological Surgery, Washington University School of Medicine , Saint Louis, Missouri
| | - Rory K J Murphy
- 5 Department of Neurosurgery, University of California San Francisco , California
| | - Sheng-Kwei Song
- 4 Department of Mallinckrodt Institute of Radiology, Washington University School of Medicine , Saint Louis, Missouri
| | - Eric C Leuthardt
- 1 Department of Neurological Surgery, Washington University School of Medicine , Saint Louis, Missouri.,2 Department of Biomedical Engineering, Washington University School of Medicine , Saint Louis, Missouri
| | - Joshua S Shimony
- 4 Department of Mallinckrodt Institute of Radiology, Washington University School of Medicine , Saint Louis, Missouri
| | - Wilson Z Ray
- 1 Department of Neurological Surgery, Washington University School of Medicine , Saint Louis, Missouri.,2 Department of Biomedical Engineering, Washington University School of Medicine , Saint Louis, Missouri
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40
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Paces J, Nic M, Novotny T, Svoboda P. Literature review of baseline information to support the risk assessment of RNAi‐based GM plants. ACTA ACUST UNITED AC 2017. [PMCID: PMC7163844 DOI: 10.2903/sp.efsa.2017.en-1246] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Jan Paces
- Institute of Molecular Genetics of the Academy of Sciences of the Czech Republic (IMG)
| | | | | | - Petr Svoboda
- Institute of Molecular Genetics of the Academy of Sciences of the Czech Republic (IMG)
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41
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Hanhart P, Thieß M, Amari K, Bajdzienko K, Giavalisco P, Heinlein M, Kehr J. Bioinformatic and expression analysis of the Brassica napus L. cyclophilins. Sci Rep 2017; 7:1514. [PMID: 28473712 PMCID: PMC5431436 DOI: 10.1038/s41598-017-01596-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2016] [Accepted: 03/29/2017] [Indexed: 12/15/2022] Open
Abstract
Cyclophilins (CYPs) are a group of ubiquitous proteins characterized by their ability to bind to the immunosuppressive drug cyclosporin A. The CYP family occurs in a wide range of organisms and contains a conserved peptidyl-prolyl cis/trans isomerase domain. In addition to fulfilling a basic role in protein folding, CYPs may also play diverse important roles, e.g. in protein degradation, mRNA processing, development, and stress responses. We performed a genome-wide database survey and identified a total of 94 CYP genes encoding 91 distinct proteins. Sequence alignment analysis of the putative BnCYP cyclophilin-like domains revealed highly conserved motifs. By using RNA-Seq, we could verify the presence of 77 BnCYP genes under control conditions. To identify phloem-specific BnCYP proteins in a complementary approach, we used LC-MS/MS to determine protein abundances in leaf and phloem extracts. We detected 26 BnCYPs in total with 12 being unique to phloem sap. Our analysis provides the basis for future studies concentrating on the functional characterization of individual members of this gene family in a plant of dual importance: as a crop and a model system for polyploidization and long-distance signalling.
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Affiliation(s)
- Patrizia Hanhart
- Molecular Plant Genetics, Universität Hamburg, Biozentrum Klein Flottbek, Ohnhorststraße 18, 22609, Hamburg, Germany
| | - Melanie Thieß
- Molecular Plant Genetics, Universität Hamburg, Biozentrum Klein Flottbek, Ohnhorststraße 18, 22609, Hamburg, Germany
| | - Khalid Amari
- Université de Strasbourg, CNRS, IBMP UPR 2357, 12 rue du Général Zimmer, F-67000, Strasbourg, France
| | - Krzysztof Bajdzienko
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Wissenschaftspark Potsdam-Golm, Am Mühlenberg 1, 14476, Potsdam, Germany
| | - Patrick Giavalisco
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Wissenschaftspark Potsdam-Golm, Am Mühlenberg 1, 14476, Potsdam, Germany
| | - Manfred Heinlein
- Université de Strasbourg, CNRS, IBMP UPR 2357, 12 rue du Général Zimmer, F-67000, Strasbourg, France
| | - Julia Kehr
- Molecular Plant Genetics, Universität Hamburg, Biozentrum Klein Flottbek, Ohnhorststraße 18, 22609, Hamburg, Germany.
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42
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Nguyen STT, Greaves T, McCurdy DW. Heteroblastic Development of Transfer Cells Is Controlled by the microRNA miR156/SPL Module. PLANT PHYSIOLOGY 2017; 173:1676-1691. [PMID: 28082719 PMCID: PMC5338675 DOI: 10.1104/pp.16.01741] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2016] [Accepted: 01/10/2017] [Indexed: 05/08/2023]
Abstract
We report that wall ingrowth deposition in phloem parenchyma (PP) transfer cells (TCs) in leaf veins of Arabidopsis (Arabidopsis thaliana) represents a novel trait of heteroblasty. Development of PP TCs involves extensive deposition of wall ingrowths adjacent to cells of the sieve element/companion cell complex. These PP TCs potentially facilitate phloem loading by enhancing efflux of symplasmic Suc for subsequent active uptake into cells of the sieve element/companion cell complex. PP TCs with extensive wall ingrowths are ubiquitous in mature cotyledons and juvenile leaves, but dramatically less so in mature adult leaves, an observation consistent with PP TC development reflecting vegetative phase change (VPC) in Arabidopsis. Consistent with this conclusion, the abundance of PP TCs with extensive wall ingrowths varied across rosette development in three ecotypes displaying differing durations of juvenile phase, and extensive deposition of wall ingrowths was observed in rejuvenated leaves following prolonged defoliation. PP TC development across juvenile, transition, and adult leaves correlated positively with levels of miR156, a major regulator of VPC in plants, and corresponding changes in wall ingrowth deposition were observed when miR156 was overexpressed or its activity suppressed by target mimicry. Analysis of plants carrying miR156-resistant forms of SQUAMOSA PROMOTER BINDING PROTEIN LIKE (SPL) genes showed that wall ingrowth deposition was increased in SPL9-group but not SPL3-group genes, indicating that SPL9-group genes may function as negative regulators of wall ingrowth deposition in PP TCs. Collectively, our results point to wall ingrowth deposition in PP TCs being under control of the genetic program regulating VPC.
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Affiliation(s)
- Suong T T Nguyen
- Centre for Plant Science, School of Environmental and Life Sciences, The University of Newcastle, Callaghan, NSW 2308, Australia
| | - Teighan Greaves
- Centre for Plant Science, School of Environmental and Life Sciences, The University of Newcastle, Callaghan, NSW 2308, Australia
| | - David W McCurdy
- Centre for Plant Science, School of Environmental and Life Sciences, The University of Newcastle, Callaghan, NSW 2308, Australia
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STV1, a ribosomal protein, binds primary microRNA transcripts to promote their interaction with the processing complex in Arabidopsis. Proc Natl Acad Sci U S A 2017; 114:1424-1429. [PMID: 28115696 DOI: 10.1073/pnas.1613069114] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
MicroRNAs (miRNAs) are key regulators of gene expression. They are processed from primary miRNA transcripts (pri-miRNAs), most of which are transcribed by DNA-dependent polymerase II (Pol II). miRNA levels are precisely controlled to maintain various biological processes. Here, we report that SHORT VALVE 1 (STV1), a conserved ribosomal protein, acts in miRNA biogenesis in Arabidopsis A portion of STV1 localizes in the nucleus and binds pri-miRNAs. Using pri-miR172b as a reporter, we show that STV1 binds the stem-loop flanked by a short 5' arm within pri-miRNAs. Lack of STV1 reduces the association of pri-miRNAs with their processing complex. These data suggest that STV1 promotes miRNA biogenesis through facilitating the recruitment of pri-miRNAs to their processing complex. Furthermore, we show that STV1 indirectly involves in the occupancy of Pol II at the promoters of miRNA coding genes (MIR) and influences MIR promoter activities. Based on these results, we propose that STV1 refines the accumulation of miRNAs through its combined effects on pri-miRNA processing and transcription. This study uncovers an extraribosomal function of STV1.
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Iki T, Ishikawa M, Yoshikawa M. In Vitro Formation of Plant RNA-Induced Silencing Complexes Using an Extract of Evacuolated Tobacco Protoplasts. Methods Mol Biol 2017; 1640:39-53. [PMID: 28608333 DOI: 10.1007/978-1-4939-7165-7_3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2023]
Abstract
Small RNA-mediated gene silencing is involved in a variety of biological processes among many eukaryotic organisms. The silencing effector, generally referred to as RNA-induced silencing complex (RISC), comprises an ARGONAUTE (AGO) protein and a small single-stranded guide RNA in its core. RISCs recognize target genes containing sequences complementary to the guide RNA and repress their expression transcriptionally or posttranscriptionally. In vitro systems that recapitulate RISC assembly are useful not only to decipher the molecular mechanisms underlying the assembly process itself but also to dissect the downstream silencing pathways mediated by RISCs. Here, we describe a method for in vitro plant RISC assembly, which relies on an extract of evacuolated protoplasts derived from Nicotiana tabacum BY-2 suspension-cultured cells. In this extract, synthetic duplexes of small RNAs are incorporated into AGO proteins that are synthesized by in vitro translation, and then duplex unwinding and selective strand elimination result in formation of mature RISCs.
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Affiliation(s)
- Taichiro Iki
- Graduate School of Frontier Biosciences, Osaka University, 1-3 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Masayuki Ishikawa
- Division of Plant and Microbial Sciences, Institute of Agrobiological Sciences, National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, ITsukuba, 305-8602, Ibaraki, Japan
| | - Manabu Yoshikawa
- Division of Plant and Microbial Sciences, Institute of Agrobiological Sciences, National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, ITsukuba, 305-8602, Ibaraki, Japan.
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45
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Iki T. Messages on small RNA duplexes in plants. JOURNAL OF PLANT RESEARCH 2017; 130:7-16. [PMID: 27878651 DOI: 10.1007/s10265-016-0876-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2016] [Accepted: 10/12/2016] [Indexed: 06/06/2023]
Abstract
Small RNA-mediated gene silencing encompasses diverse developmental events, stress responses, defense against pathogens, and maintenance of genome integrity. Extensive studies in model organisms have unveiled the molecular mechanisms underpinning the RNA silencing phenomena, and the accumulating knowledge have characterized the intricate pathways and the repertoire of proteins responsible for the actions of small RNAs characterized as microRNAs (miRNAs) or small interfering RNAs (siRNAs). Although the single-stranded, matured guide small RNAs direct the effector ribonucleoprotein complexes to induce gene silencing in sequence-specific manner, the double-stranded intermediate, the small RNA duplexes, which are processed as nascent products of the RNase III enzyme activities, act as key to determine the downstream molecular pathways and the fate of small RNAs. Based at the small RNA duplex-centered view, this review describes the recent advances in understanding the small RNA pathways in plants.
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Affiliation(s)
- Taichiro Iki
- Graduate School of Frontier Biosciences, Osaka University, Yamadaoka 1-3, Suita, Osaka, 565-0871, Japan.
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Cui Y, Fang X, Qi Y. TRANSPORTIN1 Promotes the Association of MicroRNA with ARGONAUTE1 in Arabidopsis. THE PLANT CELL 2016; 28:2576-2585. [PMID: 27662897 PMCID: PMC5134980 DOI: 10.1105/tpc.16.00384] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Revised: 08/29/2016] [Accepted: 09/23/2016] [Indexed: 05/19/2023]
Abstract
In Arabidopsis thaliana, microRNAs (miRNAs) are mainly loaded into ARGONAUTE1 (AGO1) to posttranscriptionally regulate gene expression. We previously found that ENHANCED MiRNA ACTIVITY1 (EMA1), an importin β family protein, negatively regulates miRNA loading into AGO1. In this study, through a suppressor screening of ema1, we identified another importin β protein, TRANSPORTIN1 (TRN1), as a regulatory component in the miRNA pathway. Mutation of TRN1 did not reduce miRNA accumulation, but it impaired miRNA activity. We found that TRN1 interacted with AGO1. Mutation of the three conserved residues required for cargo recognition of TRN1 reduced its interaction with AGO1 and compromised its function in regulating miRNA activity. Intriguingly, TRN1 dysfunction did not change the cytoplasmic-nuclear distribution of miRNAs and AGO1 but reduced the amount of miRNAs associated with AGO1. These results indicate that TRN1 positively regulates miRNA activity by promoting the association of miRNAs with AGO1, and they reveal opposing roles of two importin β family proteins in miRNA loading.
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Affiliation(s)
- Yuwei Cui
- Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
- Tsinghua-Peking Center for Life Sciences, Beijing 100084, China
| | - Xiaofeng Fang
- Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
- Tsinghua-Peking Center for Life Sciences, Beijing 100084, China
| | - Yijun Qi
- Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
- Tsinghua-Peking Center for Life Sciences, Beijing 100084, China
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Hibara KI, Isono M, Mimura M, Sentoku N, Kojima M, Sakakibara H, Kitomi Y, Yoshikawa T, Itoh JI, Nagato Y. Jasmonate regulates juvenile-to-adult phase transition in rice. Development 2016; 143:3407-16. [PMID: 27578792 DOI: 10.1242/dev.138602] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2016] [Accepted: 08/04/2016] [Indexed: 12/15/2022]
Abstract
Juvenile-to-adult phase transition is an important shift for the acquisition of adult vegetative characteristics and subsequent reproductive competence. We identified a recessive precocious (pre) mutant exhibiting a long leaf phenotype in rice. The long leaf phenotype is conspicuous in the second to the fourth leaves, which are juvenile and juvenile-to-adult transition leaves. We found that morphological and physiological traits, such as midrib formation, shoot meristem size, photosynthetic rate and plastochron, in juvenile and juvenile-to-adult transition stages of the pre mutant have precociously acquired adult characteristics. In agreement with these results, expression patterns of miR156 and miR172, which are microRNAs regulating phase change, support the accelerated juvenile-to-adult phase change in the pre mutant. The mutated gene encodes an allene oxide synthase (OsAOS1), which is a key enzyme for the biosynthesis of jasmonic acid (JA). The pre mutant showed a low level of JA and enhanced sensitivity to gibberellic acid, which promotes the phase change in some plant species. We also show that prolonged plastochron in the pre mutant is caused by accelerated PLASTOCHRON1 (PLA1) function. The present study reveals a substantial role of JA as a negative regulator of vegetative phase change.
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Affiliation(s)
- Ken-Ichiro Hibara
- Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, University of Tokyo, Tokyo 113-8657, Japan
| | - Miyako Isono
- Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, University of Tokyo, Tokyo 113-8657, Japan
| | - Manaki Mimura
- Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, University of Tokyo, Tokyo 113-8657, Japan
| | - Naoki Sentoku
- Institute of Agrobiological Sciences, National Agriculture and Food Research Organization, Ibaraki 305-8602, Japan
| | - Mikiko Kojima
- RIKEN Center for Sustainable Resource Science, Yokohama 230-0045, Japan
| | - Hitoshi Sakakibara
- RIKEN Center for Sustainable Resource Science, Yokohama 230-0045, Japan Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya 464-8601, Japan
| | - Yuka Kitomi
- Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, University of Tokyo, Tokyo 113-8657, Japan
| | - Takanori Yoshikawa
- Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, University of Tokyo, Tokyo 113-8657, Japan
| | - Jun-Ichi Itoh
- Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, University of Tokyo, Tokyo 113-8657, Japan
| | - Yasuo Nagato
- Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, University of Tokyo, Tokyo 113-8657, Japan
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Xu M, Hu T, Zhao J, Park MY, Earley KW, Wu G, Yang L, Poethig RS. Developmental Functions of miR156-Regulated SQUAMOSA PROMOTER BINDING PROTEIN-LIKE (SPL) Genes in Arabidopsis thaliana. PLoS Genet 2016; 12:e1006263. [PMID: 27541584 PMCID: PMC4991793 DOI: 10.1371/journal.pgen.1006263] [Citation(s) in RCA: 332] [Impact Index Per Article: 41.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2016] [Accepted: 07/27/2016] [Indexed: 01/18/2023] Open
Abstract
Correct developmental timing is essential for plant fitness and reproductive success. Two important transitions in shoot development-the juvenile-to-adult vegetative transition and the vegetative-to-reproductive transition-are mediated by a group of genes targeted by miR156, SQUAMOSA PROMOTER BINDING PROTEIN (SBP) genes. To determine the developmental functions of these genes in Arabidopsis thaliana, we characterized their expression patterns, and their gain-of-function and loss-of-function phenotypes. Our results reveal that SBP-LIKE (SPL) genes in Arabidopsis can be divided into three functionally distinct groups: 1) SPL2, SPL9, SPL10, SPL11, SPL13 and SPL15 contribute to both the juvenile-to-adult vegetative transition and the vegetative-to-reproductive transition, with SPL9, SP13 and SPL15 being more important for these processes than SPL2, SPL10 and SPL11; 2) SPL3, SPL4 and SPL5 do not play a major role in vegetative phase change or floral induction, but promote the floral meristem identity transition; 3) SPL6 does not have a major function in shoot morphogenesis, but may be important for certain physiological processes. We also found that miR156-regulated SPL genes repress adventitious root development, providing an explanation for the observation that the capacity for adventitious root production declines as the shoot ages. miR156 is expressed at very high levels in young seedlings, and declines in abundance as the shoot develops. It completely blocks the expression of its SPL targets in the first two leaves of the rosette, and represses these genes to different degrees at later stages of development, primarily by promoting their translational repression. These results provide a framework for future studies of this multifunctional family of transcription factors, and offer new insights into the role of miR156 in Arabidopsis development.
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Affiliation(s)
- Mingli Xu
- Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Tieqiang Hu
- Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Jianfei Zhao
- Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Mee-Yeon Park
- Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Keith W. Earley
- Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Gang Wu
- Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Li Yang
- Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - R. Scott Poethig
- Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- * E-mail:
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Gene-regulatory networks controlling inflorescence and flower development in Arabidopsis thaliana. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2016; 1860:95-105. [PMID: 27487457 DOI: 10.1016/j.bbagrm.2016.07.014] [Citation(s) in RCA: 65] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2016] [Revised: 07/21/2016] [Accepted: 07/22/2016] [Indexed: 11/23/2022]
Abstract
Reproductive development in plants is controlled by complex and intricate gene-regulatory networks of transcription factors. These networks integrate the information from endogenous, hormonal and environmental regulatory pathways. Many of the key players have been identified in Arabidopsis and other flowering plant species, and their interactions and molecular modes of action are being elucidated. An emerging theme is that there is extensive crosstalk between different pathways, which can be accomplished at the molecular level by modulation of transcription factor activity or of their downstream targets. In this review, we aim to summarize current knowledge on transcription factors and epigenetic regulators that control basic developmental programs during inflorescence and flower morphogenesis in the model plant Arabidopsis thaliana. This article is part of a Special Issue entitled: Plant Gene Regulatory Mechanisms and Networks, edited by Dr. Erich Grotewold and Dr. Nathan Springer.
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Effector-Triggered Immune Response in Arabidopsis thaliana Is a Quantitative Trait. Genetics 2016; 204:337-53. [PMID: 27412712 PMCID: PMC5012398 DOI: 10.1534/genetics.116.190678] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2016] [Accepted: 07/05/2016] [Indexed: 12/28/2022] Open
Abstract
We identified loci responsible for natural variation in Arabidopsis thaliana (Arabidopsis) responses to a bacterial pathogen virulence factor, HopAM1. HopAM1 is a type III effector protein secreted by the virulent Pseudomonas syringae strain Pto DC3000. Delivery of HopAM1 from disarmed Pseudomonas strains leads to local cell death, meristem chlorosis, or both, with varying intensities in different Arabidopsis accessions. These phenotypes are not associated with differences in bacterial growth restriction. We treated the two phenotypes as quantitative traits to identify host loci controlling responses to HopAM1. Genome-wide association (GWA) of 64 Arabidopsis accessions identified independent variants highly correlated with response to each phenotype. Quantitative trait locus (QTL) mapping in a recombinant inbred population between Bur-0 and Col-0 accessions revealed genetic linkage to regions distinct from the top GWA hits. Two major QTL associated with HopAM1-induced cell death were also associated with HopAM1-induced chlorosis. HopAM1-induced changes in Arabidopsis gene expression showed that rapid HopAM1-dependent cell death in Bur-0 is correlated with effector-triggered immune responses. Studies of the effect of mutations in known plant immune system genes showed, surprisingly, that both cell death and chlorosis phenotypes are enhanced by loss of EDS1, a regulatory hub in the plant immune-signaling network. Our results reveal complex genetic architecture for response to this particular type III virulence effector, in contrast to the typical monogenic control of cell death and disease resistance triggered by most type III effectors.
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