1
|
Xu M, Zhang X, Cao J, Liu J, He Y, Guan Q, Tian X, Tang J, Li X, Ren D, Bu Q, Wang Z. OsPGL3A encodes a DYW-type pentatricopeptide repeat protein involved in chloroplast RNA processing and regulated chloroplast development. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2024; 44:29. [PMID: 38549701 PMCID: PMC10965880 DOI: 10.1007/s11032-024-01468-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/25/2023] [Accepted: 03/19/2024] [Indexed: 04/24/2024]
Abstract
The chloroplast serves as the primary site of photosynthesis, and its development plays a crucial role in regulating plant growth and morphogenesis. The Pentatricopeptide Repeat Sequence (PPR) proteins constitute a vast protein family that function in the post-transcriptional modification of RNA within plant organelles. In this study, we characterized mutant of rice with pale green leaves (pgl3a). The chlorophyll content of pgl3a at the seedling stage was significantly reduced compared to the wild type (WT). Transmission electron microscopy (TEM) and quantitative PCR analysis revealed that pgl3a exhibited aberrant chloroplast development compared to the wild type (WT), accompanied by significant alterations in gene expression levels associated with chloroplast development and photosynthesis. The Mutmap analysis revealed that a single base deletionin the coding region of Os03g0136700 in pgl3a. By employing CRISPR/Cas9 mediated gene editing, two homozygous cr-pgl3a mutants were generated and exhibited a similar phenotype to pgl3a, thereby confirming that Os03g0136700 was responsible for pgl3a. Consequently, it was designated as OsPGL3A. OsPGL3A belongs to the DYW-type PPR protein family and is localized in chloroplasts. Furthermore, we demonstrated that the RNA editing efficiency of rps8-182 and rpoC2-4106, and the splicing efficiency of ycf3-1 were significantly decreased in pgl3a mutants compared to WT. Collectively, these results indicate that OsPGL3A plays a crucial role in chloroplast development by regulating the editing and splicing of chloroplast genes in rice. Supplementary Information The online version contains supplementary material available at 10.1007/s11032-024-01468-7.
Collapse
Affiliation(s)
- Min Xu
- Key Laboratory of Soybean Molecular Design Breeding, State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, 150081 Heilongjiang China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Xinying Zhang
- College of Life Science, Northeast Agricultural University, Harbin, 150030 Heilongjiang China
| | - Jinzhe Cao
- Key Laboratory of the Ministry of Education for Ecological Restoration of Saline Vegetation, College of Life Sciences, Northeast Forestry University, Harbin, 150040 Heilongjiang China
| | - Jiali Liu
- Key Laboratory of the Ministry of Education for Ecological Restoration of Saline Vegetation, College of Life Sciences, Northeast Forestry University, Harbin, 150040 Heilongjiang China
| | - Yiyuan He
- Key Laboratory of Soybean Molecular Design Breeding, State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, 150081 Heilongjiang China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Qingjie Guan
- Key Laboratory of the Ministry of Education for Ecological Restoration of Saline Vegetation, College of Life Sciences, Northeast Forestry University, Harbin, 150040 Heilongjiang China
| | - Xiaojie Tian
- Key Laboratory of Soybean Molecular Design Breeding, State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, 150081 Heilongjiang China
| | - Jiaqi Tang
- Key Laboratory of Soybean Molecular Design Breeding, State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, 150081 Heilongjiang China
| | - Xiufeng Li
- Key Laboratory of Soybean Molecular Design Breeding, State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, 150081 Heilongjiang China
| | - Deyong Ren
- State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Hangzhou, 310006 People’s Republic of China
| | - Qingyun Bu
- Key Laboratory of Soybean Molecular Design Breeding, State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, 150081 Heilongjiang China
| | - Zhenyu Wang
- Key Laboratory of Soybean Molecular Design Breeding, State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, 150081 Heilongjiang China
| |
Collapse
|
2
|
McCray TN, Azim MF, Burch-Smith TM. The dicot homolog of maize PPR103 carries a C-terminal DYW domain and may have a role in C-to-U editing of some chloroplast RNA transcripts. PLANT MOLECULAR BIOLOGY 2024; 114:28. [PMID: 38485794 PMCID: PMC10940495 DOI: 10.1007/s11103-024-01424-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Accepted: 01/30/2024] [Indexed: 03/18/2024]
Abstract
In plants, cytidine-to-uridine (C-to-U) editing is a crucial step in processing mitochondria- and chloroplast-encoded transcripts. This editing requires nuclear-encoded proteins including members of the pentatricopeptide (PPR) family, especially PLS-type proteins carrying the DYW domain. IPI1/emb175/PPR103 is a nuclear gene encoding a PLS-type PPR protein essential for survival in Arabidopsis thaliana and maize. Arabidopsis IPI1 was identified as likely interacting with ISE2, a chloroplast-localized RNA helicase associated with C-to-U RNA editing in Arabidopsis and maize. Notably, while the Arabidopsis and Nicotiana IPI1 orthologs possess complete DYW motifs at their C-termini, the maize homolog, ZmPPR103, lacks this triplet of residues which are essential for editing. In this study we examined the function of IPI1 in chloroplast RNA processing in N. benthamiana to gain insight into the importance of the DYW domain to the function of the EMB175/PPR103/ IPI1 proteins. Structural predictions suggest that evolutionary loss of residues identified as critical for catalyzing C-to-U editing in other members of this class of proteins, were likely to lead to reduced or absent editing activity in the Nicotiana and Arabidopsis IPI1 orthologs. Virus-induced gene silencing of NbIPI1 led to defects in chloroplast ribosomal RNA processing and changes to stability of rpl16 transcripts, revealing conserved function with its maize ortholog. NbIPI1-silenced plants also had defective C-to-U RNA editing in several chloroplast transcripts, a contrast from the finding that maize PPR103 had no role in editing. The results indicate that in addition to its role in transcript stability, NbIPI1 may contribute to C-to-U editing in N. benthamiana chloroplasts.
Collapse
Affiliation(s)
- Tyra N McCray
- School of Genome Science and Technology, University of Tennessee, Knoxville, TN, 37996, USA
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, TN, 37996, USA
| | - Mohammad F Azim
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, TN, 37996, USA
- Donald Danforth Plant Science Center, St. Louis, MO, 63132, USA
| | - Tessa M Burch-Smith
- School of Genome Science and Technology, University of Tennessee, Knoxville, TN, 37996, USA.
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, TN, 37996, USA.
- Donald Danforth Plant Science Center, St. Louis, MO, 63132, USA.
| |
Collapse
|
3
|
Peng Y, Wang Z, Li M, Wang T, Su Y. Characterization and analysis of multi-organ full-length transcriptomes in Sphaeropteris brunoniana and Alsophila latebrosa highlight secondary metabolism and chloroplast RNA editing pattern of tree ferns. BMC PLANT BIOLOGY 2024; 24:73. [PMID: 38273309 PMCID: PMC10811885 DOI: 10.1186/s12870-024-04746-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Accepted: 01/11/2024] [Indexed: 01/27/2024]
Abstract
BACKGROUND Sphaeropteris brunoniana and Alsophila latebrosa are both old relict and rare tree ferns, which have experienced the constant changes of climate and environment. However, little is known about their high-quality genetic information and related research on environmental adaptation mechanisms of them. In this study, combined with PacBio and Illumina platforms, transcriptomic analysis was conducted on the roots, rachis, and pinna of S. brunoniana and A. latebrosa to identify genes and pathways involved in environmental adaptation. Additionally, based on the transcriptomic data of tree ferns, chloroplast genes were mined to analyze their gene expression levels and RNA editing events. RESULTS In the study, we obtained 11,625, 14,391 and 10,099 unigenes of S. brunoniana root, rachis, and pinna, respectively. Similarly, a total of 13,028, 11,431 and 12,144 unigenes were obtained of A. latebrosa root, rachis, and pinna, respectively. According to the enrichment results of differentially expressed genes, a large number of differentially expressed genes were enriched in photosynthesis and secondary metabolic pathways of S. brunoniana and A. latebrosa. Based on gene annotation results and phenylpropanoid synthesis pathways, two lignin synthesis pathways (H-lignin and G-lignin) were characterized of S. brunoniana. Among secondary metabolic pathways of A. latebrosa, three types of WRKY transcription factors were identified. Additionally, based on transcriptome data obtained in this study, reported transcriptome data, and laboratory available transcriptome data, positive selection sites were identified from 18 chloroplast protein-coding genes of four tree ferns. Among them, RNA editing was found in positive selection sites of four tree ferns. RNA editing affected the protein secondary structure of the rbcL gene. Furthermore, the expression level of chloroplast genes indicated high expression of genes related to the chloroplast photosynthetic system in all four species. CONCLUSIONS Overall, this work provides a comprehensive transcriptome resource of S. brunoniana and A. latebrosa, laying the foundation for future tree fern research.
Collapse
Affiliation(s)
- Yang Peng
- School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, China
| | - Zhen Wang
- School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, China
| | - Minghui Li
- School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, China
| | - Ting Wang
- Research Institute of Sun Yat-Sen University in Shenzhen, Shenzhen, 518057, China.
- College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China.
| | - Yingjuan Su
- School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, China.
- Research Institute of Sun Yat-Sen University in Shenzhen, Shenzhen, 518057, China.
| |
Collapse
|
4
|
Yang Y, Oldenkott B, Ramanathan S, Lesch E, Takenaka M, Schallenberg-Rüdinger M, Knoop V. DYW cytidine deaminase domains have a long-range impact on RNA recognition by the PPR array of chimeric plant C-to-U RNA editing factors and strongly affect target selection. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 116:840-854. [PMID: 37565789 DOI: 10.1111/tpj.16412] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 07/20/2023] [Accepted: 07/23/2023] [Indexed: 08/12/2023]
Abstract
The protein factors for the specific C-to-U RNA editing events in plant mitochondria and chloroplasts possess unique arrays of RNA-binding pentatricopeptide repeats (PPRs) linked to carboxy-terminal cytidine deaminase DYW domains via the extension motifs E1 and E2. The E1 and E2 motifs have distant similarities to tetratricopeptide repeats known to mediate protein-protein interactions but their precise function is unclear. Here, we investigate the tolerance of PPR56 and PPR65, two functionally characterized RNA editing factors of the moss Physcomitrium patens, for the creation of chimeras by variably replacing their C-terminal protein regions. Making use of a heterologous RNA editing assay system in Escherichia coli we find that heterologous DYW domains can strongly restrict or widen the spectrum of off-targets in the bacterial transcriptome for PPR56. Surprisingly, our data suggest that these changes are not only caused by the preference of a given heterologous DYW domain for the immediate sequence environment of the cytidine to be edited but also by a long-range impact on the nucleotide selectivity of the upstream PPRs.
Collapse
Affiliation(s)
- Yingying Yang
- IZMB - Institut für Zelluläre und Molekulare Botanik, Abteilung Molekulare Evolution, Universität Bonn, Kirschallee 1, D-53115, Bonn, Germany
| | - Bastian Oldenkott
- IZMB - Institut für Zelluläre und Molekulare Botanik, Abteilung Molekulare Evolution, Universität Bonn, Kirschallee 1, D-53115, Bonn, Germany
| | - Shyam Ramanathan
- IZMB - Institut für Zelluläre und Molekulare Botanik, Abteilung Molekulare Evolution, Universität Bonn, Kirschallee 1, D-53115, Bonn, Germany
| | - Elena Lesch
- IZMB - Institut für Zelluläre und Molekulare Botanik, Abteilung Molekulare Evolution, Universität Bonn, Kirschallee 1, D-53115, Bonn, Germany
| | - Mizuki Takenaka
- Department of Botany Graduate School of Science, Kyoto University, Oiwake-cho, Sakyo-ku, Kyoto, 606-8502, Japan
| | - Mareike Schallenberg-Rüdinger
- IZMB - Institut für Zelluläre und Molekulare Botanik, Abteilung Molekulare Evolution, Universität Bonn, Kirschallee 1, D-53115, Bonn, Germany
| | - Volker Knoop
- IZMB - Institut für Zelluläre und Molekulare Botanik, Abteilung Molekulare Evolution, Universität Bonn, Kirschallee 1, D-53115, Bonn, Germany
| |
Collapse
|
5
|
Dhingra Y, Gupta S, Gupta V, Agarwal M, Katiyar-Agarwal S. The emerging role of epitranscriptome in shaping stress responses in plants. PLANT CELL REPORTS 2023; 42:1531-1555. [PMID: 37481775 DOI: 10.1007/s00299-023-03046-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Accepted: 07/03/2023] [Indexed: 07/25/2023]
Abstract
KEY MESSAGE RNA modifications and editing changes constitute 'epitranscriptome' and are crucial in regulating the development and stress response in plants. Exploration of the epitranscriptome and associated machinery would facilitate the engineering of stress tolerance in crops. RNA editing and modifications post-transcriptionally decorate almost all classes of cellular RNAs, including tRNAs, rRNAs, snRNAs, lncRNAs and mRNAs, with more than 170 known modifications, among which m6A, Ψ, m5C, 8-OHG and C-to-U editing are the most abundant. Together, these modifications constitute the "epitranscriptome", and contribute to changes in several RNA attributes, thus providing an additional structural and functional diversification to the "cellular messages" and adding another layer of gene regulation in organisms, including plants. Numerous evidences suggest that RNA modifications have a widespread impact on plant development as well as in regulating the response of plants to abiotic and biotic stresses. High-throughput sequencing studies demonstrate that the landscapes of m6A, m5C, Am, Cm, C-to-U, U-to-G, and A-to-I editing are remarkably dynamic during stress conditions in plants. GO analysis of transcripts enriched in Ψ, m6A and m5C modifications have identified bonafide components of stress regulatory pathways. Furthermore, significant alterations in the expression pattern of genes encoding writers, readers, and erasers of certain modifications have been documented when plants are grown in challenging environments. Notably, manipulating the expression levels of a few components of RNA editing machinery markedly influenced the stress tolerance in plants. We provide updated information on the current understanding on the contribution of RNA modifications in shaping the stress responses in plants. Unraveling of the epitranscriptome has opened new avenues for designing crops with enhanced productivity and stress resilience in view of global climate change.
Collapse
Affiliation(s)
- Yashika Dhingra
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, 110021, India
| | - Shitij Gupta
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, 110021, India
- Institute of Plant Sciences, University of Bern, Altenbergrain 21, Bern, Switzerland
| | - Vaishali Gupta
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, 110021, India
| | - Manu Agarwal
- Department of Botany, University of Delhi North Campus, Delhi, 110007, India
| | - Surekha Katiyar-Agarwal
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, 110021, India.
| |
Collapse
|
6
|
Boyd RD, Hayes ML. A ribonuclease activity linked to DYW1 in vitro is inhibited by RIP/MORF proteins. Sci Rep 2023; 13:10723. [PMID: 37400527 PMCID: PMC10318007 DOI: 10.1038/s41598-023-36969-6] [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: 12/06/2022] [Accepted: 06/13/2023] [Indexed: 07/05/2023] Open
Abstract
Organellar C-to-U RNA editing in plants occurs in complexes composed of various classes of nuclear-encoded proteins. DYW-deaminases are zinc metalloenzymes that catalyze hydrolytic deamination required for C-to-U modification editing. Solved crystal structures for DYW-deaminase domains display all structural features consistent with a canonical cytidine deamination mechanism. However, some recombinant DYW-deaminases from plants have been associated with ribonuclease activity in vitro. Direct ribonuclease activity by an editing factor is confounding since it is not required for deamination of cytosine, theoretically would be inimical for mRNA editing, and does not have a clear physiological function in vivo. His-tagged recombinant DYW1 from Arabidopsis thaliana (rAtDYW1) was expressed and purified using immobilized metal affinity chromatography (IMAC). Fluorescently labeled RNA oligonucleotides were incubated with recombinant AtDYW1 under different conditions. Percent relative cleavage of RNA probes was recorded at multiple time points from triplicate reactions. The effects of treatment with zinc chelators EDTA and 1, 10-phenanthroline were examined for rAtDYW1. Recombinant His-tagged RNA editing factors AtRIP2, ZmRIP9, AtRIP9, AtOZ1, AtCRR4, and AtORRM1 were expressed in E. coli and purified. Ribonuclease activity was assayed for rAtDYW1 in the presence of different editing factors. Lastly, the effects on nuclease activity in the presence of nucleotides and modified nucleosides were investigated. RNA cleavage observed in this study was linked to the recombinant editing factor rAtDYW1 in vitro. The cleavage reaction is sensitive to high concentrations of zinc chelators, indicating a role for zinc ions for activity. The addition of equal molar concentrations of recombinant RIP/MORF proteins reduced cleavage activity associated with rAtDYW1. However, addition of equal molar concentrations of purified recombinant editing complex proteins AtCRR4, AtORRM1, and AtOZ1 did not strongly inhibit ribonuclease activity on RNAs lacking an AtCRR4 cis-element. Though AtCRR4 inhibited AtDYW1 activity for oligonucleotides with a cognate cis-element. The observation that editing factors limit ribonuclease activity of rAtDYW1 in vitro, suggests that nuclease activities are limited to RNAs in absence of native editing complex partners. Purified rAtDYW1 was associated with the hydrolysis of RNA in vitro, and activity was specifically inhibited by RNA editing factors.
Collapse
Affiliation(s)
- Robert D Boyd
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Michael L Hayes
- Department of Chemistry and Biochemistry, California State University Los Angeles, Los Angeles, CA, 90032, USA.
| |
Collapse
|
7
|
Small I, Melonek J, Bohne AV, Nickelsen J, Schmitz-Linneweber C. Plant organellar RNA maturation. THE PLANT CELL 2023; 35:1727-1751. [PMID: 36807982 PMCID: PMC10226603 DOI: 10.1093/plcell/koad049] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Revised: 01/05/2023] [Accepted: 01/17/2023] [Indexed: 05/30/2023]
Abstract
Plant organellar RNA metabolism is run by a multitude of nucleus-encoded RNA-binding proteins (RBPs) that control RNA stability, processing, and degradation. In chloroplasts and mitochondria, these post-transcriptional processes are vital for the production of a small number of essential components of the photosynthetic and respiratory machinery-and consequently for organellar biogenesis and plant survival. Many organellar RBPs have been functionally assigned to individual steps in RNA maturation, often specific to selected transcripts. While the catalog of factors identified is ever-growing, our knowledge of how they achieve their functions mechanistically is far from complete. This review summarizes the current knowledge of plant organellar RNA metabolism taking an RBP-centric approach and focusing on mechanistic aspects of RBP functions and the kinetics of the processes they are involved in.
Collapse
Affiliation(s)
- Ian Small
- Australian Research Council Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Crawley 6009, Australia
| | - Joanna Melonek
- Australian Research Council Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Crawley 6009, Australia
| | | | - Jörg Nickelsen
- Department of Molecular Plant Sciences, LMU Munich, 82152 Martinsried, Germany
| | | |
Collapse
|
8
|
Ni J, Song W, Ali NA, Zhang Y, Xing J, Su K, Sun X, Zhao X. The ATP Synthase γ Subunit ATPC1 Regulates RNA Editing in Chloroplasts. Int J Mol Sci 2023; 24:ijms24119203. [PMID: 37298153 DOI: 10.3390/ijms24119203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 05/22/2023] [Accepted: 05/23/2023] [Indexed: 06/12/2023] Open
Abstract
RNA editing is the process of modifying RNA molecules by inserting, deleting, or substituting nucleotides. In flowering plants, RNA editing occurs predominantly in RNAs encoded by the organellar genomes of mitochondria and chloroplasts, and the main type of editing involves the substitution of cytidine with uridine at specific sites. Abnormal RNA editing in plants can affect gene expression, organelle function, plant growth, and reproduction. In this study, we report that ATPC1, the gamma subunit of ATP synthase in Arabidopsis chloroplasts, has an unexpected role in the regulation of editing at multiple sites of plastid RNAs. The loss of function of ATPC1 severely arrests chloroplast development, causing a pale-green phenotype and early seedling lethality. Disruption of ATPC1 increases the editing of matK-640, rps12-i-58, atpH-3'UTR-13210, and ycf2-as-91535 sites while decreasing the editing of rpl23-89, rpoA-200, rpoC1-488, and ndhD-2 sites. We further show that ATPC1 participates in RNA editing by interacting with known multiple-site chloroplast RNA editing factors, including MORFs, ORRM1, and OZ1. The transcriptome in the atpc1 mutant is profoundly affected, with a pattern of defective expression of chloroplast development-related genes. These results reveal that the ATP synthase γ subunit ATPC1 is involved in multiple-site RNA editing in Arabidopsis chloroplasts.
Collapse
Affiliation(s)
- Jia Ni
- Key Laboratory of Nuclear Agricultural Sciences of Ministry of Agriculture and Rural Affairs, Key Laboratory of Nuclear Agricultural Sciences of Zhejiang Province, Institute of Nuclear Agricultural Sciences, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Wenjian Song
- Key Laboratory of Nuclear Agricultural Sciences of Ministry of Agriculture and Rural Affairs, Key Laboratory of Nuclear Agricultural Sciences of Zhejiang Province, Institute of Nuclear Agricultural Sciences, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Nadia Ahmed Ali
- Key Laboratory of Nuclear Agricultural Sciences of Ministry of Agriculture and Rural Affairs, Key Laboratory of Nuclear Agricultural Sciences of Zhejiang Province, Institute of Nuclear Agricultural Sciences, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Yayi Zhang
- Key Laboratory of Nuclear Agricultural Sciences of Ministry of Agriculture and Rural Affairs, Key Laboratory of Nuclear Agricultural Sciences of Zhejiang Province, Institute of Nuclear Agricultural Sciences, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Jiani Xing
- Key Laboratory of Nuclear Agricultural Sciences of Ministry of Agriculture and Rural Affairs, Key Laboratory of Nuclear Agricultural Sciences of Zhejiang Province, Institute of Nuclear Agricultural Sciences, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Kexing Su
- Key Laboratory of Nuclear Agricultural Sciences of Ministry of Agriculture and Rural Affairs, Key Laboratory of Nuclear Agricultural Sciences of Zhejiang Province, Institute of Nuclear Agricultural Sciences, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Xingxing Sun
- Key Laboratory of Nuclear Agricultural Sciences of Ministry of Agriculture and Rural Affairs, Key Laboratory of Nuclear Agricultural Sciences of Zhejiang Province, Institute of Nuclear Agricultural Sciences, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Xiaobo Zhao
- Key Laboratory of Nuclear Agricultural Sciences of Ministry of Agriculture and Rural Affairs, Key Laboratory of Nuclear Agricultural Sciences of Zhejiang Province, Institute of Nuclear Agricultural Sciences, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| |
Collapse
|
9
|
Lan J, Lin Q, Zhou C, Liu X, Miao R, Ma T, Chen Y, Mou C, Jing R, Feng M, Nguyen T, Ren Y, Cheng Z, Zhang X, Liu S, Jiang L, Wan J. Young Leaf White Stripe encodes a P-type PPR protein required for chloroplast development. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2023. [PMID: 36897026 DOI: 10.1111/jipb.13477] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2022] [Accepted: 03/07/2023] [Indexed: 05/09/2023]
Abstract
Pentatricopeptide repeat (PPR) proteins function in post-transcriptional regulation of organellar gene expression. Although several PPR proteins are known to function in chloroplast development in rice (Oryza sativa), the detailed molecular functions of many PPR proteins remain unclear. Here, we characterized a rice young leaf white stripe (ylws) mutant, which has defective chloroplast development during early seedling growth. Map-based cloning revealed that YLWS encodes a novel P-type chloroplast-targeted PPR protein with 11 PPR motifs. Further expression analyses showed that many nuclear- and plastid-encoded genes in the ylws mutant were significantly changed at the RNA and protein levels. The ylws mutant was impaired in chloroplast ribosome biogenesis and chloroplast development under low-temperature conditions. The ylws mutation causes defects in the splicing of atpF, ndhA, rpl2, and rps12, and editing of ndhA, ndhB, and rps14 transcripts. YLWS directly binds to specific sites in the atpF, ndhA, and rpl2 pre-mRNAs. Our results suggest that YLWS participates in chloroplast RNA group II intron splicing and plays an important role in chloroplast development during early leaf development.
Collapse
Affiliation(s)
- Jie Lan
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095, China
| | - Qibing Lin
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Chunlei Zhou
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095, China
| | - Xi Liu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095, China
| | - Rong Miao
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095, China
| | - Tengfei Ma
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yaping Chen
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095, China
| | - Changling Mou
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095, China
| | - Ruonan Jing
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095, China
| | - Miao Feng
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Thanhliem Nguyen
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yulong Ren
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Zhijun Cheng
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Xin Zhang
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Shijia Liu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095, China
| | - Ling Jiang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095, China
| | - Jianmin Wan
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095, China
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| |
Collapse
|
10
|
McCray TN, Azim MF, Burch-Smith TM. The dicot homolog of maize PPR103 carries a C-terminal DYW domain and is required for C-to-U editing of chloroplast RNA transcripts. RESEARCH SQUARE 2023:rs.3.rs-2574001. [PMID: 36865278 PMCID: PMC9980218 DOI: 10.21203/rs.3.rs-2574001/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
In plants, cytidine-to-uridine (C-to-U) editing is a crucial step in processing mitochondria and chloroplast-encoded transcripts. This editing requires nuclear-encoded proteins including members of the pentatricopeptide (PPR) family, especially PLS-type proteins carrying the DYW domain. IPI1/emb175/PPR103 is a nuclear gene encoding a PLS-type PPR protein essential for survival in Arabidopsis thaliana and maize. Arabidopsis IPI1 was identified as likely interacting with ISE2, a chloroplast-localized RNA helicase associated with C-to-U RNA editing in Arabidopsis and maize. Notably, while the Arabidopsis and Nicotiana IPI1 homologs possess complete DYW motifs at their C-termini, the maize homolog, ZmPPR103, lacks this triplet of residues which are essential for editing. We examined the function of ISE2 and IPI1 in chloroplast RNA processing in N. benthamiana. A combination of deep sequencing and Sanger sequencing revealed C-to-U editing at 41 sites in 18 transcripts, with 34 sites conserved in the closely related N. tabacum. Virus induced gene silencing of NbISE2 or NbIPI1 led to defective C-to-U revealed that they have overlapping roles at editing a site in the rpoB transcript but have distinct roles in editing other transcripts. This finding contrasts with maize ppr103 mutants that showed no defects in editing. The results indicate that NbISE2 and NbIPI1 are important for C-to-U editing in N. benthamiana chloroplasts, and they may function in a complex to edit specific sites while having antagonistic effects on editing others. That NbIPI1, carrying a DYW domain, is involved in organelle C-to-U RNA editing supports previous work showing that this domain catalyzes RNA editing.
Collapse
Affiliation(s)
- Tyra N. McCray
- School of Genome Science and Technology, University of Tennessee, Knoxville, TN 37996
- Department of Biochemistry and Cellular & Molecular Biology, University of Tennessee, Knoxville, TN 37996
| | - Mohammad F. Azim
- Department of Biochemistry and Cellular & Molecular Biology, University of Tennessee, Knoxville, TN 37996
- Donald Danforth Plant Science Center, St. Louis, MO 63132
| | - Tessa M. Burch-Smith
- School of Genome Science and Technology, University of Tennessee, Knoxville, TN 37996
- Department of Biochemistry and Cellular & Molecular Biology, University of Tennessee, Knoxville, TN 37996
- Donald Danforth Plant Science Center, St. Louis, MO 63132
| |
Collapse
|
11
|
McDowell R, Small I, Bond CS. Synthetic PPR proteins as tools for sequence-specific targeting of RNA. Methods 2022; 208:19-26. [DOI: 10.1016/j.ymeth.2022.10.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Revised: 09/29/2022] [Accepted: 10/11/2022] [Indexed: 11/06/2022] Open
|
12
|
Loiacono FV, Walther D, Seeger S, Thiele W, Gerlach I, Karcher D, Schöttler MA, Zoschke R, Bock R. Emergence of Novel RNA-Editing Sites by Changes in the Binding Affinity of a Conserved PPR Protein. Mol Biol Evol 2022; 39:6760358. [PMID: 36227729 PMCID: PMC9750133 DOI: 10.1093/molbev/msac222] [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: 07/29/2022] [Revised: 09/23/2022] [Accepted: 10/07/2022] [Indexed: 01/07/2023] Open
Abstract
RNA editing converts cytidines to uridines in plant organellar transcripts. Editing typically restores codons for conserved amino acids. During evolution, specific C-to-U editing sites can be lost from some plant lineages by genomic C-to-T mutations. By contrast, the emergence of novel editing sites is less well documented. Editing sites are recognized by pentatricopeptide repeat (PPR) proteins with high specificity. RNA recognition by PPR proteins is partially predictable, but prediction is often inadequate for PPRs involved in RNA editing. Here we have characterized evolution and recognition of a recently gained editing site. We demonstrate that changes in the RNA recognition motifs that are not explainable with the current PPR code allow an ancient PPR protein, QED1, to uniquely target the ndhB-291 site in Brassicaceae. When expressed in tobacco, the Arabidopsis QED1 edits 33 high-confident off-target sites in chloroplasts and mitochondria causing a spectrum of mutant phenotypes. By manipulating the relative expression levels of QED1 and ndhB-291, we show that the target specificity of the PPR protein depends on the RNA:protein ratio. Finally, our data suggest that the low expression levels of PPR proteins are necessary to ensure the specificity of editing site selection and prevent deleterious off-target editing.
Collapse
Affiliation(s)
- F Vanessa Loiacono
- Department of Organelle Biology, Biotechnology and Molecular Ecophysiology, Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, D-14476 Potsdam-Golm, Germany
| | - Dirk Walther
- Department of Organelle Biology, Biotechnology and Molecular Ecophysiology, Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, D-14476 Potsdam-Golm, Germany
| | - Stefanie Seeger
- Department of Organelle Biology, Biotechnology and Molecular Ecophysiology, Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, D-14476 Potsdam-Golm, Germany
| | - Wolfram Thiele
- Department of Organelle Biology, Biotechnology and Molecular Ecophysiology, Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, D-14476 Potsdam-Golm, Germany
| | - Ines Gerlach
- Department of Organelle Biology, Biotechnology and Molecular Ecophysiology, Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, D-14476 Potsdam-Golm, Germany
| | - Daniel Karcher
- Department of Organelle Biology, Biotechnology and Molecular Ecophysiology, Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, D-14476 Potsdam-Golm, Germany
| | - Mark Aurel Schöttler
- Department of Organelle Biology, Biotechnology and Molecular Ecophysiology, Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, D-14476 Potsdam-Golm, Germany
| | - Reimo Zoschke
- Department of Organelle Biology, Biotechnology and Molecular Ecophysiology, Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, D-14476 Potsdam-Golm, Germany
| | | |
Collapse
|
13
|
U-to-C RNA editing by synthetic PPR-DYW proteins in bacteria and human culture cells. Commun Biol 2022; 5:968. [PMID: 36109586 PMCID: PMC9478123 DOI: 10.1038/s42003-022-03927-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Accepted: 08/31/2022] [Indexed: 11/22/2022] Open
Abstract
Programmable RNA editing offers significant therapeutic potential for a wide range of genetic diseases. Currently, several deaminase enzymes, including ADAR and APOBEC, can perform programmable adenosine-to-inosine or cytidine-to-uridine RNA correction. However, enzymes to perform guanosine-to-adenosine and uridine-to-cytidine (U-to-C) editing are still lacking to complete the set of transition reactions. It is believed that the DYW:KP proteins, specific to seedless plants, catalyze the U-to-C reactions in mitochondria and chloroplasts. In this study, we designed seven DYW:KP domains based on consensus sequences and fused them to a designer RNA-binding pentatricopeptide repeat (PPR) domain. We show that three of these PPR-DYW:KP proteins edit targeted uridine to cytidine in bacteria and human cells. In addition, we show that these proteins have a 5′ but not apparent 3′ preference for neighboring nucleotides. Our results establish the DYW:KP aminase domain as a potential candidate for the development of a U-to-C editing tool in human cells. DYW:KP domains, designed on proteins found in the mitochondria and chloroplasts of seedless plants, are fused to a designer RNA-binding pentatricopeptide repeat (PPR) domain to edit targeted uridine to cytidine in bacteria and human cells.
Collapse
|
14
|
Li Y, Yu C, Mo R, Zhu Z, Dong Z, Hu X, Deng W, Zhuang C. Screening and Verification of Photosynthesis and Chloroplast-Related Genes in Mulberry by Comparative RNA-Seq and Virus-Induced Gene Silencing. Int J Mol Sci 2022; 23:ijms23158620. [PMID: 35955752 PMCID: PMC9368790 DOI: 10.3390/ijms23158620] [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: 05/12/2022] [Revised: 07/20/2022] [Accepted: 07/29/2022] [Indexed: 12/05/2022] Open
Abstract
Photosynthesis is one of the most important factors in mulberry growth and production. To study the photosynthetic regulatory network of mulberry we sequenced the transcriptomes of two high-yielding (E1 and E2) and one low-yielding (H32) mulberry genotypes at two-time points (10:00 and 12:00). Re-annotation of the mulberry genome based on the transcriptome sequencing data identified 22,664 high-quality protein-coding genes with a BUSCO-assessed completeness of 93.4%. A total of 6587 differentially expressed genes (DEGs) were obtained in the transcriptome analysis. Functional annotation and enrichment revealed 142 out of 6587 genes involved in the photosynthetic pathway and chloroplast development. Moreover, 3 out of 142 genes were further examined using the VIGS technique; the leaves of MaCLA1- and MaTHIC-silenced plants were markedly yellowed or even white, and the leaves of MaPKP2-silenced plants showed a wrinkled appearance. The expression levels of the ensiled plants were reduced, and the levels of chlorophyll b and total chlorophyll were lower than those of the control plants. Co-expression analysis showed that MaCLA1 was co-expressed with CHUP1 and YSL3; MaTHIC was co-expressed with MaHSP70, MaFLN1, and MaEMB2794; MaPKP2 was mainly co-expressed with GH9B7, GH3.1, and EDA9. Protein interaction network prediction revealed that MaCLA1 was associated with RPE, TRA2, GPS1, and DXR proteins; MaTHIC was associated with TH1, PUR5, BIO2, and THI1; MaPKP2 was associated with ENOC, LOS2, and PGI1. This study offers a useful resource for further investigation of the molecular mechanisms involved in mulberry photosynthesis and preliminary insight into the regulatory network of photosynthesis.
Collapse
Affiliation(s)
- Yong Li
- College of Life Sciences, South China Agricultural University, Guangzhou 510642, China;
- Cash Crops Research Institute, Hubei Academy of Agricultural Sciences, Wuhan 430064, China; (C.Y.); (R.M.); (Z.Z.); (Z.D.); (X.H.)
| | - Cui Yu
- Cash Crops Research Institute, Hubei Academy of Agricultural Sciences, Wuhan 430064, China; (C.Y.); (R.M.); (Z.Z.); (Z.D.); (X.H.)
| | - Rongli Mo
- Cash Crops Research Institute, Hubei Academy of Agricultural Sciences, Wuhan 430064, China; (C.Y.); (R.M.); (Z.Z.); (Z.D.); (X.H.)
| | - Zhixian Zhu
- Cash Crops Research Institute, Hubei Academy of Agricultural Sciences, Wuhan 430064, China; (C.Y.); (R.M.); (Z.Z.); (Z.D.); (X.H.)
| | - Zhaoxia Dong
- Cash Crops Research Institute, Hubei Academy of Agricultural Sciences, Wuhan 430064, China; (C.Y.); (R.M.); (Z.Z.); (Z.D.); (X.H.)
| | - Xingming Hu
- Cash Crops Research Institute, Hubei Academy of Agricultural Sciences, Wuhan 430064, China; (C.Y.); (R.M.); (Z.Z.); (Z.D.); (X.H.)
| | - Wen Deng
- Cash Crops Research Institute, Hubei Academy of Agricultural Sciences, Wuhan 430064, China; (C.Y.); (R.M.); (Z.Z.); (Z.D.); (X.H.)
- Correspondence: (W.D.); (C.Z.); Tel.: +86-27-87106001 (W.D.); +86-20-85288399 (C.Z.)
| | - Chuxiong Zhuang
- College of Life Sciences, South China Agricultural University, Guangzhou 510642, China;
- Correspondence: (W.D.); (C.Z.); Tel.: +86-27-87106001 (W.D.); +86-20-85288399 (C.Z.)
| |
Collapse
|
15
|
Andrade-Marcial M, Pacheco-Arjona R, Góngora-Castillo E, De-la-Peña C. Chloroplastic pentatricopeptide repeat proteins (PPR) in albino plantlets of Agave angustifolia Haw. reveal unexpected behavior. BMC PLANT BIOLOGY 2022; 22:352. [PMID: 35850575 PMCID: PMC9295523 DOI: 10.1186/s12870-022-03742-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Accepted: 07/04/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND Pentatricopeptide repeat (PPR) proteins play an essential role in the post-transcriptional regulation of genes in plastid genomes. Although important advances have been made in understanding the functions of these genes, there is little information available on chloroplastic PPR genes in non-model plants and less in plants without chloroplasts. In the present study, a comprehensive and multifactorial bioinformatic strategy was applied to search for putative PPR genes in the foliar and meristematic tissues of green and albino plantlets of the non-model plant Agave angustifolia Haw. RESULTS A total of 1581 PPR transcripts were identified, of which 282 were chloroplastic. Leaf tissue in the albino plantlets showed the highest levels of expression of chloroplastic PPRs. The search for hypothetical targets of 12 PPR sequences in the chloroplast genes of A. angustifolia revealed their action on transcripts related to ribosomes and translation, photosystems, ATP synthase, plastid-encoded RNA polymerase and RuBisCO. CONCLUSIONS Our results suggest that the expression of PPR genes depends on the state of cell differentiation and plastid development. In the case of the albino leaf tissue, which lacks functional chloroplasts, it is possible that anterograde and retrograde signaling networks are severely compromised, leading to a compensatory anterograde response characterized by an increase in the expression of PPR genes.
Collapse
Affiliation(s)
- M Andrade-Marcial
- Unidad de Biotecnología, Centro de Investigación Científica de Yucatán, Calle 43 No. 130 x 32 y 34. Col. Chuburná de Hidalgo, 97205, Mérida, Yucatán, Mexico
| | - R Pacheco-Arjona
- Facultad de Medicina Veterinaria y Zootecnia, Consejo Nacional de Ciencia y Tecnología- Universidad Autónoma de Yucatán, Mérida, Mexico
| | - E Góngora-Castillo
- Consejo Nacional de Ciencia y Tecnología-Unidad De Biotecnología, Centro de Investigación Científica de Yucatán, Calle 43 No. 130 x 32 y 34. Col. Chuburná de Hidalgo, 97205, Mérida, Yucatán, Mexico
| | - C De-la-Peña
- Unidad de Biotecnología, Centro de Investigación Científica de Yucatán, Calle 43 No. 130 x 32 y 34. Col. Chuburná de Hidalgo, 97205, Mérida, Yucatán, Mexico.
| |
Collapse
|
16
|
OTP970 Is Required for RNA Editing of Chloroplast ndhB Transcripts in Arabidopsis thaliana. Genes (Basel) 2022; 13:genes13010139. [PMID: 35052479 PMCID: PMC8774829 DOI: 10.3390/genes13010139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 01/09/2022] [Accepted: 01/10/2022] [Indexed: 11/19/2022] Open
Abstract
RNA editing is essential for compensating for defects or mutations in haploid organelle genomes and is regulated by numerous trans-factors. Pentatricopeptide repeat (PPR) proteins are the prime factors that are involved in RNA editing; however, many have not yet been identified. Here, we screened the plastid-targeted PLS-DYW subfamily of PPR proteins belonging to Arabidopsis thaliana and identified ORGANELLE TRANSCRIPT PROCESSING 970 (OTP970) as a key player in RNA editing in plastids. A loss-of-function otp970 mutant was impaired in RNA editing of ndhB transcripts at site 149 (ndhB-C149). RNA-immunoprecipitation analysis indicated that OTP970 was associated with the ndhB-C149 site. The complementation of the otp970 mutant with OTP970 lacking the DYW domain (OTP970∆DYW) failed to restore the RNA editing of ndhB-C149. ndhB gene encodes the B subunit of the NADH dehydrogenase-like (NDH) complex; however, neither NDH activity and stability nor NDH-PSI supercomplex formation were affected in otp970 mutant compared to the wild type, indicating that alteration in amino acid sequence is not necessary for NdhB function. Together, these results suggest that OTP970 is involved in the RNA editing of ndhB-C149 and that the DYW domain is essential for its function.
Collapse
|
17
|
Gipson AB, Hanson MR, Bentolila S. The RanBP2 zinc finger domains of chloroplast RNA editing factor OZ1 are required for protein-protein interactions and conversion of C to U. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 109:215-226. [PMID: 34743362 DOI: 10.1111/tpj.15569] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Revised: 10/26/2021] [Accepted: 11/05/2021] [Indexed: 06/13/2023]
Abstract
In the chloroplast, organelle zinc finger 1 (OZ1) is a RanBP2-type zinc finger (Znf) protein required for many RNA editing events, a process by which specific cytosines are enzymatically converted to uracils as a correction mechanism for missense mutations in the organelle genomes. RNA editing is carried out by a large multi-protein complex called the 'editosome' that contains members of the pentatricopeptide repeat (PPR) protein family, the RNA editing factor interacting protein (also known as MORF) family and the organelle RNA-recognition motif (ORRM) family, in addition to OZ1. OZ1 is an 82-kDa protein with distinct domains, including a pair of Znf domains and a unique C-terminal region. To elucidate the functions of these domains, we have generated truncations of OZ1 for use in protein-protein interaction assays that identified the C-terminal region of OZ1, as well as the Znf domains as the primary interactors with PPR proteins, which are factors required for site-specificity and enzymatic editing. Expression of these OZ1 truncations in vivo showed that the Znf domains were required to restore chloroplast RNA editing in oz1 knockout plants. Mutation of key structural residues in the Znf domains showed that they are necessary for editing and required for interaction with ORRM1, a general editing factor with an RNA-binding domain. These functional characterizations of the Znfs and novel C-terminal domain contribute to our understanding of the model for the chloroplast plant editosome.
Collapse
Affiliation(s)
- Andrew B Gipson
- Department of Molecular Biology and Genetics, Biotechnology Building, Cornell University, Ithaca, NY, 14853, USA
| | - Maureen R Hanson
- Department of Molecular Biology and Genetics, Biotechnology Building, Cornell University, Ithaca, NY, 14853, USA
| | - Stéphane Bentolila
- Department of Molecular Biology and Genetics, Biotechnology Building, Cornell University, Ithaca, NY, 14853, USA
| |
Collapse
|
18
|
Takenaka M, Takenaka S, Barthel T, Frink B, Haag S, Verbitskiy D, Oldenkott B, Schallenberg-Rüdinger M, Feiler CG, Weiss MS, Palm GJ, Weber G. DYW domain structures imply an unusual regulation principle in plant organellar RNA editing catalysis. Nat Catal 2021; 4:510-522. [PMID: 34712911 PMCID: PMC7611903 DOI: 10.1038/s41929-021-00633-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
RNA editosomes selectively deaminate cytidines to uridines in plant organellar transcripts–mostly to restore protein functionality and consequently facilitate mitochondrial and chloroplast function. The RNA editosomal pentatricopeptide repeat proteins serve target RNA recognition, whereas the intensively studied DYW domain elicits catalysis. Here we present structures and functional data of a DYW domain in an inactive ground state and activated. DYW domains harbour a cytidine deaminase fold and a C-terminal DYW motif, with catalytic and structural zinc atoms, respectively. A conserved gating domain within the deaminase fold regulates the active site sterically and mechanistically in a process that we termed gated zinc shutter. Based on the structures, an autoinhibited ground state and its activation are cross-validated by RNA editing assays and differential scanning fluorimetry. We anticipate that, in vivo, the framework of an active plant RNA editosome triggers the release of DYW autoinhibition to ensure a controlled and coordinated cytidine deamination playing a key role in mitochondrial and chloroplast homeostasis.
Collapse
Affiliation(s)
- Mizuki Takenaka
- Department of Botany, Graduate School of Science, Kyoto University, Kyoto, Japan
| | - Sachi Takenaka
- Department of Botany, Graduate School of Science, Kyoto University, Kyoto, Japan.,These authors contributed equally: Sachi Takenaka, Tatjana Barthel
| | - Tatjana Barthel
- University of Greifswald, Molecular Structural Biology, Greifswald, Germany.,Present address: Helmholtz-Zentrum Berlin für Materialien und Energie, Macromolecular Crystallography, Berlin, Germany.,These authors contributed equally: Sachi Takenaka, Tatjana Barthel
| | - Brody Frink
- Department of Botany, Graduate School of Science, Kyoto University, Kyoto, Japan
| | - Sascha Haag
- Molekulare Botanik, Universität Ulm, Ulm, Germany
| | | | - Bastian Oldenkott
- Institut für Zelluläre und Molekulare Botanik, Abteilung Molekulare Evolution, University of Bonn, Bonn, Germany
| | | | - Christian G Feiler
- Helmholtz-Zentrum Berlin für Materialien und Energie, Macromolecular Crystallography, Berlin, Germany
| | - Manfred S Weiss
- Helmholtz-Zentrum Berlin für Materialien und Energie, Macromolecular Crystallography, Berlin, Germany
| | - Gottfried J Palm
- University of Greifswald, Molecular Structural Biology, Greifswald, Germany
| | - Gert Weber
- Helmholtz-Zentrum Berlin für Materialien und Energie, Macromolecular Crystallography, Berlin, Germany
| |
Collapse
|
19
|
Liu XY, Jiang RC, Wang Y, Tang JJ, Sun F, Yang YZ, Tan BC. ZmPPR26, a DYW-type pentatricopeptide repeat protein, is required for C-to-U RNA editing at atpA-1148 in maize chloroplasts. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:4809-4821. [PMID: 33929512 DOI: 10.1093/jxb/erab185] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Accepted: 04/29/2021] [Indexed: 06/12/2023]
Abstract
Pentatricopeptide repeat (PPR) proteins are involved in the C-to-U RNA editing of organellar transcripts. The maize genome contains over 600 PPR proteins and few have been found to function in the C-to-U RNA editing in chloroplasts. Here, we report the function of ZmPPR26 in the C-to-U RNA editing and chloroplast biogenesis in maize. ZmPPR26 encodes a DYW-type PPR protein targeted to chloroplasts. The zmppr26 mutant exhibits albino seedling-lethal phenotype. Loss of function of ZmPPR26 abolishes the editing at atpA-1148 site, and decreases the editing at ndhF-62, rpl20-308, rpl2-2, rpoC2-2774, petB-668, rps8-182, and ndhA-50 sites. Overexpression of ZmPPR26 in zmppr26 restores the editing efficiency and rescues the albino seedling-lethal phenotype. Abolished editing at atpA-1148 causes a Leu to Ser change at AtpA-383 that leads to a reduction in the abundance of chloroplast ATP synthase in zmppr26. The accumulation of photosynthetic complexes are also markedly reduced in zmppr26, providing an explanation for the albino seedling-lethal phenotype. These results indicate that ZmPPR26 is required for the editing at atpA-1148 and is important for editing at the other seven sites in maize chloroplasts. The editing at atpA-1148 is critical for AtpA function, assembly of ATP synthase complex, and chloroplast biogenesis in maize.
Collapse
Affiliation(s)
- Xin-Yuan Liu
- Key Lab of Plant Development and Environment Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, China
| | - Rui-Cheng Jiang
- Key Lab of Plant Development and Environment Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, China
| | - Yong Wang
- Key Lab of Plant Development and Environment Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, China
| | - Jiao-Jiao Tang
- Key Lab of Plant Development and Environment Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, China
| | - Feng Sun
- Key Lab of Plant Development and Environment Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, China
| | - Yan-Zhuo Yang
- Key Lab of Plant Development and Environment Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, China
| | - Bao-Cai Tan
- Key Lab of Plant Development and Environment Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, China
| |
Collapse
|
20
|
Feiz L, Strickler SR, van Eck J, Mao L, Movahed N, Taylor C, Gourabathini P, Fei Z, Stern DB. Setaria viridis chlorotic and seedling-lethal mutants define critical functions for chloroplast gene expression. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 104:917-931. [PMID: 32812296 DOI: 10.1111/tpj.14968] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Accepted: 06/24/2020] [Indexed: 06/11/2023]
Abstract
Deep insights into chloroplast biogenesis have been obtained by mutant analysis; however, in C4 plants a relevant mutant collection has only been developed and exploited for maize. Here, we report the initial characterization of an ethyl methyl sulfonate-induced mutant population for the C4 model Setaria viridis. Approximately 1000 M2 families were screened for the segregation of pale-green seedlings in the M3 generation, and a subset of these was identified to be deficient in post-transcriptional steps of chloroplast gene expression. Causative mutations were identified for three lines using deep sequencing-based bulked segregant analysis, and in one case confirmed by transgenic complementation. Using chloroplast RNA-sequencing and other molecular assays, we describe phenotypes of mutants deficient in PSRP7, a plastid-specific ribosomal protein, OTP86, an RNA editing factor, and cpPNP, the chloroplast isozyme of polynucleotide phosphorylase. The psrp mutant is globally defective in chloroplast translation, and has varying deficiencies in the accumulation of chloroplast-encoded proteins. The otp86 mutant, like its Arabidopsis counterpart, is specifically defective in editing of the rps14 mRNA; however, the conditional pale-green mutant phenotype contrasts with the normal growth of the Arabidopsis mutant. The pnp mutant exhibited multiple defects in 3' end maturation as well as other qualitative changes in the chloroplast RNA population. Overall, our collection opens the door to global analysis of photosynthesis and early seedling development in an emerging C4 model.
Collapse
Affiliation(s)
- Leila Feiz
- Boyce Thompson Institute, Ithaca, New York, 14853, USA
| | | | - Joyce van Eck
- Boyce Thompson Institute, Ithaca, New York, 14853, USA
| | - Linyong Mao
- Boyce Thompson Institute, Ithaca, New York, 14853, USA
- Department of Biochemistry and Molecular Biology, Howard University, Washington, DC, 20059, USA
| | - Navid Movahed
- Boyce Thompson Institute, Ithaca, New York, 14853, USA
- Q² Solutions, Ithaca, New York, 14850, USA
| | - Caroline Taylor
- Boyce Thompson Institute, Ithaca, New York, 14853, USA
- Lansing High School, Lansing, New York, 14882, USA
- Cornell University, Ithaca, New York, New York, 14850, USA
| | | | - Zhangjun Fei
- Boyce Thompson Institute, Ithaca, New York, 14853, USA
| | - David B Stern
- Boyce Thompson Institute, Ithaca, New York, 14853, USA
| |
Collapse
|
21
|
Karaca N, Ates D, Nemli S, Ozkuru E, Yilmaz H, Yagmur B, Kartal C, Tosun M, Ozdestan O, Otles S, Kahriman A, Chang P, Tanyolac MB. Identification of SNP Markers Associated with Iron and Zinc Concentrations in Cicer Seeds. Curr Genomics 2020; 21:212-223. [PMID: 33071615 PMCID: PMC7521033 DOI: 10.2174/1389202921666200413150951] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Revised: 03/18/2020] [Accepted: 03/27/2020] [Indexed: 12/30/2022] Open
Abstract
Background Cicer reticulatum L. is the wild progenitor of chickpea Cicer arietinum L., the fourth most important pulse crop in the world. Iron (Fe) and zinc (Zn) are vital micronutrients that play crucial roles in sustaining life by acting as co-factors for various proteins. Aims and Objectives
In order to improve micronutrient-dense chickpea lines, this study aimed to investigate variability and detect DNA markers associated with Fe and Zn concentrations in the seeds of 73 cultivated (C. arietinum L.) and 107 C. reticulatum genotypes. Methods
A set of 180 accessions was genotyped using 20,868 single nucleotide polymorphism (SNP) markers obtained from genotyping by sequencing analysis. Results
The results revealed substantial variation in the seed Fe and Zn concentration of the surveyed population. Using STRUCTURE software, the population structure was divided into two groups according to the principal component analysis and neighbor-joining tree analysis. A total of 23 and 16 associated SNP markers related to Fe and Zn concentrations, respectively were identified in TASSEL software by the mixed linear model method. Significant SNP markers found in more than two environments were accepted as more reliable than those that only existed in a single environment. Conclusion
The identified markers can be used in marker-assisted selection in chickpea breeding programs for the improvement of seed Fe and Zn concentrations in the chickpea.
Collapse
Affiliation(s)
- Nur Karaca
- 1Ege University, Department of Bioengineering, Bornova, Izmir35100, Turkey; 2Ege University, Faculty of Fisheries, Bornova, Izmir35100, Turkey; 3Ege University, Department of Soil Science and Plant Nutrition, Bornova, Izmir35100, Turkey; 4Ege University, Department of Food Engineering, Bornova, Izmir35100, Turkey; 5Department of Field Crops, Ege University, Bornova, Izmir35100, Turkey; 6Harran University, Department of Field Crops, 63000 Sanliurfa, Turkey; 7University of Southern California, Los Angeles, CA90007, USA
| | - Duygu Ates
- 1Ege University, Department of Bioengineering, Bornova, Izmir35100, Turkey; 2Ege University, Faculty of Fisheries, Bornova, Izmir35100, Turkey; 3Ege University, Department of Soil Science and Plant Nutrition, Bornova, Izmir35100, Turkey; 4Ege University, Department of Food Engineering, Bornova, Izmir35100, Turkey; 5Department of Field Crops, Ege University, Bornova, Izmir35100, Turkey; 6Harran University, Department of Field Crops, 63000 Sanliurfa, Turkey; 7University of Southern California, Los Angeles, CA90007, USA
| | - Seda Nemli
- 1Ege University, Department of Bioengineering, Bornova, Izmir35100, Turkey; 2Ege University, Faculty of Fisheries, Bornova, Izmir35100, Turkey; 3Ege University, Department of Soil Science and Plant Nutrition, Bornova, Izmir35100, Turkey; 4Ege University, Department of Food Engineering, Bornova, Izmir35100, Turkey; 5Department of Field Crops, Ege University, Bornova, Izmir35100, Turkey; 6Harran University, Department of Field Crops, 63000 Sanliurfa, Turkey; 7University of Southern California, Los Angeles, CA90007, USA
| | - Esin Ozkuru
- 1Ege University, Department of Bioengineering, Bornova, Izmir35100, Turkey; 2Ege University, Faculty of Fisheries, Bornova, Izmir35100, Turkey; 3Ege University, Department of Soil Science and Plant Nutrition, Bornova, Izmir35100, Turkey; 4Ege University, Department of Food Engineering, Bornova, Izmir35100, Turkey; 5Department of Field Crops, Ege University, Bornova, Izmir35100, Turkey; 6Harran University, Department of Field Crops, 63000 Sanliurfa, Turkey; 7University of Southern California, Los Angeles, CA90007, USA
| | - Hasan Yilmaz
- 1Ege University, Department of Bioengineering, Bornova, Izmir35100, Turkey; 2Ege University, Faculty of Fisheries, Bornova, Izmir35100, Turkey; 3Ege University, Department of Soil Science and Plant Nutrition, Bornova, Izmir35100, Turkey; 4Ege University, Department of Food Engineering, Bornova, Izmir35100, Turkey; 5Department of Field Crops, Ege University, Bornova, Izmir35100, Turkey; 6Harran University, Department of Field Crops, 63000 Sanliurfa, Turkey; 7University of Southern California, Los Angeles, CA90007, USA
| | - Bulent Yagmur
- 1Ege University, Department of Bioengineering, Bornova, Izmir35100, Turkey; 2Ege University, Faculty of Fisheries, Bornova, Izmir35100, Turkey; 3Ege University, Department of Soil Science and Plant Nutrition, Bornova, Izmir35100, Turkey; 4Ege University, Department of Food Engineering, Bornova, Izmir35100, Turkey; 5Department of Field Crops, Ege University, Bornova, Izmir35100, Turkey; 6Harran University, Department of Field Crops, 63000 Sanliurfa, Turkey; 7University of Southern California, Los Angeles, CA90007, USA
| | - Canan Kartal
- 1Ege University, Department of Bioengineering, Bornova, Izmir35100, Turkey; 2Ege University, Faculty of Fisheries, Bornova, Izmir35100, Turkey; 3Ege University, Department of Soil Science and Plant Nutrition, Bornova, Izmir35100, Turkey; 4Ege University, Department of Food Engineering, Bornova, Izmir35100, Turkey; 5Department of Field Crops, Ege University, Bornova, Izmir35100, Turkey; 6Harran University, Department of Field Crops, 63000 Sanliurfa, Turkey; 7University of Southern California, Los Angeles, CA90007, USA
| | - Muzaffer Tosun
- 1Ege University, Department of Bioengineering, Bornova, Izmir35100, Turkey; 2Ege University, Faculty of Fisheries, Bornova, Izmir35100, Turkey; 3Ege University, Department of Soil Science and Plant Nutrition, Bornova, Izmir35100, Turkey; 4Ege University, Department of Food Engineering, Bornova, Izmir35100, Turkey; 5Department of Field Crops, Ege University, Bornova, Izmir35100, Turkey; 6Harran University, Department of Field Crops, 63000 Sanliurfa, Turkey; 7University of Southern California, Los Angeles, CA90007, USA
| | - Ozgul Ozdestan
- 1Ege University, Department of Bioengineering, Bornova, Izmir35100, Turkey; 2Ege University, Faculty of Fisheries, Bornova, Izmir35100, Turkey; 3Ege University, Department of Soil Science and Plant Nutrition, Bornova, Izmir35100, Turkey; 4Ege University, Department of Food Engineering, Bornova, Izmir35100, Turkey; 5Department of Field Crops, Ege University, Bornova, Izmir35100, Turkey; 6Harran University, Department of Field Crops, 63000 Sanliurfa, Turkey; 7University of Southern California, Los Angeles, CA90007, USA
| | - Semih Otles
- 1Ege University, Department of Bioengineering, Bornova, Izmir35100, Turkey; 2Ege University, Faculty of Fisheries, Bornova, Izmir35100, Turkey; 3Ege University, Department of Soil Science and Plant Nutrition, Bornova, Izmir35100, Turkey; 4Ege University, Department of Food Engineering, Bornova, Izmir35100, Turkey; 5Department of Field Crops, Ege University, Bornova, Izmir35100, Turkey; 6Harran University, Department of Field Crops, 63000 Sanliurfa, Turkey; 7University of Southern California, Los Angeles, CA90007, USA
| | - Abdullah Kahriman
- 1Ege University, Department of Bioengineering, Bornova, Izmir35100, Turkey; 2Ege University, Faculty of Fisheries, Bornova, Izmir35100, Turkey; 3Ege University, Department of Soil Science and Plant Nutrition, Bornova, Izmir35100, Turkey; 4Ege University, Department of Food Engineering, Bornova, Izmir35100, Turkey; 5Department of Field Crops, Ege University, Bornova, Izmir35100, Turkey; 6Harran University, Department of Field Crops, 63000 Sanliurfa, Turkey; 7University of Southern California, Los Angeles, CA90007, USA
| | - Peter Chang
- 1Ege University, Department of Bioengineering, Bornova, Izmir35100, Turkey; 2Ege University, Faculty of Fisheries, Bornova, Izmir35100, Turkey; 3Ege University, Department of Soil Science and Plant Nutrition, Bornova, Izmir35100, Turkey; 4Ege University, Department of Food Engineering, Bornova, Izmir35100, Turkey; 5Department of Field Crops, Ege University, Bornova, Izmir35100, Turkey; 6Harran University, Department of Field Crops, 63000 Sanliurfa, Turkey; 7University of Southern California, Los Angeles, CA90007, USA
| | - Muhammed Bahattin Tanyolac
- 1Ege University, Department of Bioengineering, Bornova, Izmir35100, Turkey; 2Ege University, Faculty of Fisheries, Bornova, Izmir35100, Turkey; 3Ege University, Department of Soil Science and Plant Nutrition, Bornova, Izmir35100, Turkey; 4Ege University, Department of Food Engineering, Bornova, Izmir35100, Turkey; 5Department of Field Crops, Ege University, Bornova, Izmir35100, Turkey; 6Harran University, Department of Field Crops, 63000 Sanliurfa, Turkey; 7University of Southern California, Los Angeles, CA90007, USA
| |
Collapse
|
22
|
Oldenkott B, Burger M, Hein AC, Jörg A, Senkler J, Braun HP, Knoop V, Takenaka M, Schallenberg-Rüdinger M. One C-to-U RNA Editing Site and Two Independently Evolved Editing Factors: Testing Reciprocal Complementation with DYW-Type PPR Proteins from the Moss Physcomitrium ( Physcomitrella) patens and the Flowering Plants Macadamia integrifolia and Arabidopsis. THE PLANT CELL 2020; 32:2997-3018. [PMID: 32616665 PMCID: PMC7474288 DOI: 10.1105/tpc.20.00311] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Revised: 06/09/2020] [Accepted: 06/30/2020] [Indexed: 05/15/2023]
Abstract
Cytidine-to-uridine RNA editing is a posttranscriptional process in plant organelles, mediated by specific pentatricopeptide repeat (PPR) proteins. In angiosperms, hundreds of sites undergo RNA editing. By contrast, only 13 sites are edited in the moss Physcomitrium (Physcomitrella) patens Some are conserved between the two species, like the mitochondrial editing site nad5eU598RC. The PPR proteins assigned to this editing site are known in both species: the DYW-type PPR protein PPR79 in P. patens and the E+-type PPR protein CWM1 in Arabidopsis (Arabidopsis thaliana). CWM1 also edits sites ccmCeU463RC, ccmBeU428SL, and nad5eU609VV. Here, we reciprocally expressed the P. patens and Arabidopsis editing factors in the respective other genetic environment. Surprisingly, the P. patens editing factor edited all target sites when expressed in the Arabidopsis cwm1 mutant background, even when carboxy-terminally truncated. Conversely, neither Arabidopsis CWM1 nor CWM1-PPR79 chimeras restored editing in P. patens ppr79 knockout plants. A CWM1-like PPR protein from the early diverging angiosperm macadamia (Macadamia integrifolia) features a complete DYW domain and fully rescued editing of nad5eU598RC when expressed in P. patens. We conclude that (1) the independently evolved P. patens editing factor PPR79 faithfully operates in the more complex Arabidopsis editing system, (2) truncated PPR79 recruits catalytic DYW domains in trans when expressed in Arabidopsis, and (3) the macadamia CWM1-like protein retains the capacity to work in the less complex P. patens editing environment.
Collapse
Affiliation(s)
- Bastian Oldenkott
- Institut für Zelluläre und Molekulare Botanik, Abt. Molekulare Evolution, University of Bonn, 53115 Bonn, Germany
| | | | - Anke-Christiane Hein
- Institut für Zelluläre und Molekulare Botanik, Abt. Molekulare Evolution, University of Bonn, 53115 Bonn, Germany
| | - Anja Jörg
- Molekulare Botanik, Universität Ulm, 89069 Ulm, Germany
| | - Jennifer Senkler
- Department of Plant Proteomics, Institute of Plant Genetics, Leibniz Universität Hannover, 30419 Hannover, Germany
| | - Hans-Peter Braun
- Department of Plant Proteomics, Institute of Plant Genetics, Leibniz Universität Hannover, 30419 Hannover, Germany
| | - Volker Knoop
- Institut für Zelluläre und Molekulare Botanik, Abt. Molekulare Evolution, University of Bonn, 53115 Bonn, Germany
| | - Mizuki Takenaka
- Molekulare Botanik, Universität Ulm, 89069 Ulm, Germany
- Department of Botany, Graduate School of Science, Kyoto University, Oiwake-cho, Sakyo-ku, Kyoto 606-8502, Japan
| | | |
Collapse
|
23
|
Huang J, Lu G, Liu L, Raihan MS, Xu J, Jian L, Zhao L, Tran TM, Zhang Q, Liu J, Li W, Wei C, Braun DM, Li Q, Fernie AR, Jackson D, Yan J. The Kernel Size-Related Quantitative Trait Locus qKW9 Encodes a Pentatricopeptide Repeat Protein That Aaffects Photosynthesis and Grain Filling. PLANT PHYSIOLOGY 2020; 183:1696-1709. [PMID: 32482908 PMCID: PMC7401109 DOI: 10.1104/pp.20.00374] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Accepted: 05/19/2020] [Indexed: 05/10/2023]
Abstract
In maize (Zea mays), kernel weight is an important component of yield that has been selected during domestication. Many genes associated with kernel weight have been identified through mutant analysis. Most are involved in the biogenesis and functional maintenance of organelles or other fundamental cellular activities. However, few quantitative trait loci (QTLs) underlying quantitative variation in kernel weight have been cloned. Here, we characterize a QTL, qKW9, associated with maize kernel weight. This QTL encodes a DYW motif pentatricopeptide repeat protein involved in C-to-U editing of ndhB, a subunit of the chloroplast NADH dehydrogenase-like complex. In a null qkw9 background, C-to-U editing of ndhB was abolished, and photosynthesis was reduced, resulting in less maternal photosynthate available for grain filling. Characterization of qKW9 highlights the importance of optimizing photosynthesis for maize grain yield production.
Collapse
Affiliation(s)
- Juan Huang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Gang Lu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Lei Liu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724
| | - Mohammad Sharif Raihan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Jieting Xu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
- Wimi Biotechnology Company, Xinbei District, Changzhou City, Jiangsu 213000, China
| | - Liumei Jian
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Lingxiao Zhao
- Jiangsu Key Laboratory of Crop Genetics and Physiology, Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou 225009, China
- Jiangsu Xuzhou Sweetpotato Research Center, Xuzhou, Jiangsu 221000, China
| | - Thu M Tran
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724
- Division of Biological Sciences, Interdisciplinary Plant Group, Missouri Maize Center, University of Missouri, Columbia, Missouri 65211
| | - Qinghua Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Jie Liu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Wenqiang Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Cunxu Wei
- Jiangsu Key Laboratory of Crop Genetics and Physiology, Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou 225009, China
| | - David M Braun
- Division of Biological Sciences, Interdisciplinary Plant Group, Missouri Maize Center, University of Missouri, Columbia, Missouri 65211
| | - Qing Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Alisdair R Fernie
- Department of Molecular Physiology, Max-Planck-Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
| | - David Jackson
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724
| | - Jianbing Yan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| |
Collapse
|
24
|
Rodrigues NF, Nogueira FCS, Domont GB, Margis R. Identification of soybean trans-factors associated with plastid RNA editing sites. Genet Mol Biol 2020; 43:e20190067. [PMID: 32459826 PMCID: PMC7231544 DOI: 10.1590/1678-4685-gmb-2019-0067] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Accepted: 08/09/2019] [Indexed: 12/05/2022] Open
Abstract
RNA editing is a posttranscriptional process that changes nucleotide sequences, among which cytosine-to-uracil by a deamination reaction can revert non-neutral codon mutations. Pentatricopeptide repeat (PPR) proteins comprise a family of RNA-binding proteins, with members acting as editing trans-factors that recognize specific RNA cis-elements and perform the deamination reaction. PPR proteins are classified into P and PLS subfamilies. In this work, we have designed RNA biotinylated probes based in soybean plastid RNA editing sites to perform trans-factor specific protein isolation. Soybean cis-elements from these three different RNA probes show differences in respect to other species. Pulldown samples were submitted to mass spectrometry for protein identification. Among detected proteins, five corresponded to PPR proteins. More than one PPR protein, with distinct functional domains, was pulled down with each one of the RNA probes. Comparison of the soybean PPR proteins to Arabidopsis allowed identification of the closest homologous. Differential gene expression analysis demonstrated that the PPR locus Glyma.02G174500 doubled its expression under salt stress, which correlates with the increase of its potential rps14 editing. The present study represents the first identification of RNA editing trans-factors in soybean. Data also indicated that potential multiple trans-factors should interact with RNA cis-elements to perform the RNA editing.
Collapse
Affiliation(s)
- Nureyev F. Rodrigues
- Universidade Federal do Rio Grande do Sul (UFRGS), Centro de Biotecnologia,
Programa de Pós-Graduação em Biologia Celular e Molecular (PPGBCM), Porto Alegre,
RS, Brazil
| | - Fábio C. S. Nogueira
- Universidade Federal do Rio de Janeiro (UFRJ), Instituto de Química,
Departamento de Bioquímica, Programa de Pós-Graduação em Bioquímica (PPGBq), Unidade
Proteômica, Rio de Janeiro, RJ, Brazil
- Universidade Federal do Rio de Janeiro (UFRJ), Instituto de Química,
Laboratório de Apoio ao Desenvolvimento Tecnológico (LADETEC), Rio de Janeiro, RJ,
Brazil
| | - Gilberto B. Domont
- Universidade Federal do Rio de Janeiro (UFRJ), Instituto de Química,
Departamento de Bioquímica, Programa de Pós-Graduação em Bioquímica (PPGBq), Unidade
Proteômica, Rio de Janeiro, RJ, Brazil
| | - Rogerio Margis
- Universidade Federal do Rio Grande do Sul (UFRGS), Centro de Biotecnologia,
Programa de Pós-Graduação em Biologia Celular e Molecular (PPGBCM), Porto Alegre,
RS, Brazil
- Universidade Federal do Rio Grande do Sul (UFRGS), Departamento de
Biofísica, Porto Alegre, RS, Brazil
| |
Collapse
|
25
|
Zhao X, Huang J, Chory J. Unraveling the Linkage between Retrograde Signaling and RNA Metabolism in Plants. TRENDS IN PLANT SCIENCE 2020; 25:141-147. [PMID: 31791654 DOI: 10.1016/j.tplants.2019.10.009] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Revised: 10/09/2019] [Accepted: 10/23/2019] [Indexed: 05/25/2023]
Abstract
Retrograde signals are signals that originate in organelles to regulate nuclear gene expression. In plant cells, retrograde signaling from both chloroplasts and mitochondria is essential for plant development and growth. Over the past few years, substantial progress has been made in unraveling the linkages between chloroplast retrograde signaling and nuclear RNA metabolism processes or plastidial RNA editing. These findings add to the complexity of the regulation of organelle-to-nucleus communication. Chloroplast development and function rely on the coordinated regulation of chloroplast and nuclear gene expression, especially under stress conditions. A better understanding of retrograde signaling and RNA metabolism, as well as their connection, is essential for breeding stress-tolerant plants to cope with the dynamic and rapidly changing environment.
Collapse
Affiliation(s)
- Xiaobo Zhao
- Institute of Nuclear Agricultural Sciences, Key Laboratory of Nuclear Agricultural Sciences of Ministry of Agriculture and Zhejiang Province, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China; Howard Hughes Medical Institute, Salk Institute for Biological Studies, La Jolla, CA 92037, USA; Plant Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA.
| | - Jianyan Huang
- Howard Hughes Medical Institute, Salk Institute for Biological Studies, La Jolla, CA 92037, USA; Plant Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Joanne Chory
- Howard Hughes Medical Institute, Salk Institute for Biological Studies, La Jolla, CA 92037, USA; Plant Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA.
| |
Collapse
|
26
|
Hayes ML, Santibanez PI. A plant pentatricopeptide repeat protein with a DYW-deaminase domain is sufficient for catalyzing C-to-U RNA editing in vitro. J Biol Chem 2020; 295:3497-3505. [PMID: 31996373 DOI: 10.1074/jbc.ra119.011790] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Revised: 01/23/2020] [Indexed: 12/27/2022] Open
Abstract
Pentatricopeptide repeat (PPR) proteins with C-terminal DYW domains are present in organisms that undergo C-to-U editing of organelle RNA transcripts. PPR domains act as specificity factors through electrostatic interactions between a pair of polar residues and the nitrogenous bases of an RNA target. DYW-deaminase domains act as the editing enzyme. Two moss (Physcomitrella patens) PPR proteins containing DYW-deaminase domains, PPR65 and PPR56, can convert Cs to Us in cognate, exogenous RNA targets co-expressed in Escherichia coli We show here that purified, recombinant PPR65 exhibits robust editase activity on synthetic RNAs containing cognate, mitochondrial PpccmFC sequences in vitro, indicating that a PPR protein with a DYW domain is solely sufficient for catalyzing C-to-U RNA editing in vitro Monomeric fractions possessed the highest conversion efficiency, and oligomeric fractions had reduced activity. Inductively coupled plasma (ICP)-MS analysis indicated a stoichiometry of two zinc ions per highly active PPR65 monomer. Editing activity was sensitive to addition of zinc acetate or the zinc chelators 1,10-o-phenanthroline and EDTA. Addition of ATP or nonhydrolyzable nucleotide analogs stimulated PPR65-catalyzed RNA-editing activity on PpccmFC substrates, indicating potential allosteric regulation of PPR65 by ATP. Unlike for bacterial cytidine deaminase, addition of two putative transition-state analogs, zebularine and tetrahydrouridine, failed to disrupt RNA-editing activity. RNA oligonucleotides with a single incorporated zebularine also did not disrupt editing in vitro, suggesting that PPR65 cannot bind modified bases due to differences in the structure of the active site compared with other zinc-dependent nucleotide deaminases.
Collapse
Affiliation(s)
- Michael L Hayes
- Department of Chemistry and Biochemistry, California State University Los Angeles, Los Angeles, California 90032.
| | - Paola I Santibanez
- Department of Chemistry and Biochemistry, California State University Los Angeles, Los Angeles, California 90032
| |
Collapse
|
27
|
Ishibashi K, Small I, Shikanai T. Evolutionary Model of Plastidial RNA Editing in Angiosperms Presumed from Genome-Wide Analysis of Amborella trichopoda. PLANT & CELL PHYSIOLOGY 2019; 60:2141-2151. [PMID: 31150097 DOI: 10.1093/pcp/pcz111] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Accepted: 05/21/2019] [Indexed: 05/08/2023]
Abstract
Amborella trichopoda is placed close to the base of the angiosperm lineage (basal angiosperm). By genome-wide RNA sequencing, we identified 184C-to-U RNA editing sites in the plastid genome of Amborella. This number is much higher than that observed in other angiosperms including maize (44 sites), rice (39 sites) and grape (115 sites). Despite the high frequency of RNA editing, the biased distribution of RNA editing sites in the genome, target codon preference and nucleotide preference adjacent to the edited cytidine are similar to that in other angiosperms, suggesting a common editing machinery. Consistent with this idea, the Amborella nuclear genome encodes 2-3 times more of the E- and DYW-subclass members of pentatricopeptide repeat proteins responsible for RNA editing site recognition in plant organelles. Among 165 editing sites in plastid protein coding sequences in Amborella, 100 sites were conserved at least in one out of 38 species selected to represent key branching points of the angiosperm phylogenetic tree. We assume these 100 sites represent at least a subset of the sites in the plastid editotype of ancestral angiosperms. We then mapped the loss and gain of editing sites on the phylogenetic tree of angiosperms. Our results support the idea that the evolution of angiosperms has led to the loss of RNA editing sites in plastids.
Collapse
Affiliation(s)
- Kota Ishibashi
- Department of Botany, Graduate School of Science, Kyoto University, Oiwake-cho, Kitashirakawa, Sakyo-ku, Kyoto, Japan
| | - Ian Small
- Australian Research Council Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Crawley, WA, Australia
| | - Toshiharu Shikanai
- Department of Botany, Graduate School of Science, Kyoto University, Oiwake-cho, Kitashirakawa, Sakyo-ku, Kyoto, Japan
| |
Collapse
|
28
|
MORF9 Functions in Plastid RNA Editing with Tissue Specificity. Int J Mol Sci 2019; 20:ijms20184635. [PMID: 31546885 PMCID: PMC6769653 DOI: 10.3390/ijms20184635] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Revised: 09/11/2019] [Accepted: 09/13/2019] [Indexed: 11/17/2022] Open
Abstract
RNA editing in plant mitochondria and plastids converts specific nucleotides from cytidine (C) to uridine (U). These editing events differ among plant species and are relevant to developmental stages or are impacted by environmental conditions. Proteins of the MORF family are essential components of plant editosomes. One of the members, MORF9, is considered the core protein of the editing complex and is involved in the editing of most sites in chloroplasts. In this study, the phenotypes of a T-DNA insertion line with loss of MORF9 and of the genetic complementation line of Arabidopsis were analyzed, and the editing efficiencies of plastid RNAs in roots, rosette leaves, and flowers from the morf9 mutant and the wild-type (WT) control were compared by bulk-cDNA sequencing. The results showed that most of the known MORF9-associated plastid RNA editing events in rosette leaves and flowers were similarly reduced by morf9 mutation, with the exception that the editing rate of the sites ndhB-872 and psbF-65 declined in the leaves and that of ndhB-586 decreased only in the flowers. In the roots, however, the loss of MORF9 had a much lower effect on overall plastid RNA editing, with nine sites showing no significant editing efficiency change, including accD-794, ndhD-383, psbZ-50, ndhF-290, ndhD-878, matK-706, clpP1-559, rpoA-200, and ndhD-674, which were reduced in the other tissues. Furthermore, we found that during plant aging, MORF9 mRNA level, but not the protein level, was downregulated in senescent leaves. On the basis of these observations, we suggest that MORF9-mediated RNA editing is tissue-dependent and the resultant organelle proteomes are pertinent to the specific tissue functions.
Collapse
|
29
|
Dedow LK, Bailey-Serres J. Searching for a Match: Structure, Function and Application of Sequence-Specific RNA-Binding Proteins. PLANT & CELL PHYSIOLOGY 2019; 60:1927-1938. [PMID: 31329953 DOI: 10.1093/pcp/pcz072] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Accepted: 04/11/2019] [Indexed: 05/21/2023]
Abstract
Plants encode over 1800 RNA-binding proteins (RBPs) that modulate a myriad of steps in gene regulation from chromatin organization to translation, yet only a small number of these proteins and their target transcripts have been functionally characterized. Two classes of eukaryotic RBPs, pentatricopeptide repeat (PPR) and pumilio/fem-3 binding factors (PUF), recognize and bind to specific sequential RNA sequences through protein-RNA interactions. These modular proteins possess helical structural units containing key residues with high affinity for specific nucleotides, whose sequential order determines binding to a specific target RNA sequence. PPR proteins are nucleus-encoded, but largely regulate post-transcriptional gene regulation within plastids and mitochondria, including splicing, translation and RNA editing. Plant PUFs are involved in gene regulatory processes within the cell nucleus and cytoplasm. The modular structures of PPRs and PUFs that determine sequence specificity has facilitated identification of their RNA targets and biological functions. The protein-based RNA-targeting of PPRs and PUFs contrasts to the prokaryotic cluster regularly interspaced short palindromic repeats (CRISPR)-associated proteins (Cas) that target RNAs in prokaryotes. Together the PPR, PUF and CRISPR-Cas systems provide varied opportunities for RNA-targeted engineering applications.
Collapse
|
30
|
Sandoval R, Boyd RD, Kiszter AN, Mirzakhanyan Y, Santibańez P, Gershon PD, Hayes ML. Stable native RIP9 complexes associate with C-to-U RNA editing activity, PPRs, RIPs, OZ1, ORRM1 and ISE2. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2019; 99:1116-1126. [PMID: 31077462 PMCID: PMC6744336 DOI: 10.1111/tpj.14384] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Revised: 04/23/2019] [Accepted: 04/30/2019] [Indexed: 05/02/2023]
Abstract
The mitochondrial and chloroplast mRNAs of the majority of land plants are modified through cytidine to uridine (C-to-U) RNA editing. Previously, forward and reverse genetic screens demonstrated a requirement for pentatricopeptide repeat (PPR) proteins for RNA editing. Moreover, chloroplast editing factors OZ1, RIP2, RIP9 and ORRM1 were identified in co-immunoprecipitation (co-IP) experiments, albeit the minimal complex sufficient for editing activity was never deduced. The current study focuses on isolated, intact complexes that are capable of editing distinct sites. Peak editing activity for four sites was discovered in size-exclusion chromatography (SEC) fractions ≥ 670 kDa, while fractions estimated to be approximately 413 kDa exhibited the greatest ability to convert a substrate containing the editing site rps14 C80. RNA content peaked in the ≥ 670 kDa fraction. Treatment of active chloroplast extracts with RNase A abolished the relationship of editing activity with high-MW fractions, suggesting a structural RNA component in native complexes. By immunoblotting, RIP9, OTP86, OZ1 and ORRM1 were shown to be present in active gel filtration fractions, though OZ1 and ORRM1 were mainly found in low-MW inactive fractions. Active editing factor complexes were affinity-purified using anti-RIP9 antibodies, and orthologs to putative Arabidopsis thaliana RNA editing factor PPR proteins, RIP2, RIP9, RIP1, OZ1, ORRM1 and ISE2 were identified via mass spectrometry. Western blots from co-IP studies revealed the mutual association of OTP86 and OZ1 with native RIP9 complexes. Thus, RIP9 complexes were discovered to be highly associated with C-to-U RNA editing activity and other editing factors indicative of their critical role in vascular plant editosomes.
Collapse
Affiliation(s)
- Rafael Sandoval
- Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - Robert D. Boyd
- Department of Chemistry and Biochemistry, California State University Los Angeles, Los Angeles, California, 90032, USA
| | - Alena N. Kiszter
- Department of Chemistry, Graz University of Technology, Graz, Austria
| | - Yeva Mirzakhanyan
- Department of Molecular Biology and Biochemistry, University of California Irvine, Irvine, California 92697, USA
| | - Paola Santibańez
- Department of Chemistry and Biochemistry, California State University Los Angeles, Los Angeles, California, 90032, USA
| | - Paul D. Gershon
- Department of Molecular Biology and Biochemistry, University of California Irvine, Irvine, California 92697, USA
| | - Michael L. Hayes
- Department of Chemistry and Biochemistry, California State University Los Angeles, Los Angeles, California, 90032, USA
- To whom correspondence should be addressed. Michael L. Hayes: Department of Chemistry and Biochemistry, California State University Los Angeles, Los Angeles, CA 90032; ; Tel.(323) 343-2144
| |
Collapse
|
31
|
GUN1 interacts with MORF2 to regulate plastid RNA editing during retrograde signaling. Proc Natl Acad Sci U S A 2019; 116:10162-10167. [PMID: 30988197 PMCID: PMC6525534 DOI: 10.1073/pnas.1820426116] [Citation(s) in RCA: 79] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
During development or under stress, chloroplasts generate signals that regulate the expression of a large number of nuclear genes, a process called retrograde signaling. GENOMES UNCOUPLED 1 (GUN1) is an important regulator of this pathway. In this study, we have discovered an unexpected role for GUN1 in plastid RNA editing, as gun1 mutations affect RNA-editing efficiency at multiple sites in plastids during retrograde signaling. GUN1 plays a direct role in RNA editing by physically interacting with MULTIPLE ORGANELLAR RNA EDITING FACTOR 2 (MORF2). MORF2 overexpression causes widespread RNA-editing changes and a strong genomes uncoupled (gun) molecular phenotype similar to gun1 MORF2 further interacts with RNA-editing site-specificity factors: ORGANELLE TRANSCRIPT PROCESSING 81 (OTP81), ORGANELLE TRANSCRIPT PROCESSING 84 (OTP84), and YELLOW SEEDLINGS 1 (YS1). We further show that otp81, otp84, and ys1 single mutants each exhibit a very weak gun phenotype, but combining the three mutations enhances the phenotype. Our study uncovers a role for GUN1 in the regulation of RNA-editing efficiency in damaged chloroplasts and suggests that MORF2 is involved in retrograde signaling.
Collapse
|
32
|
Ruwe H, Gutmann B, Schmitz-Linneweber C, Small I, Kindgren P. The E domain of CRR2 participates in sequence-specific recognition of RNA in plastids. THE NEW PHYTOLOGIST 2019; 222:218-229. [PMID: 30393849 DOI: 10.1111/nph.15578] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2018] [Accepted: 10/28/2018] [Indexed: 06/08/2023]
Abstract
Pentatricopeptide repeat (PPR) proteins are modular RNA-binding proteins involved in different aspects of RNA metabolism in organelles. PPR proteins of the PLS subclass often contain C-terminal domains that are important for their function, but the role of one of these domains, the E domain, is far from resolved. Here, we elucidate the role of the E domain in CRR2 in plastids. We identified a surprisingly large number of small RNAs that represent in vivo footprints of the Arabidopsis PLS-class PPR protein CRR2. An unexpectedly strong base conservation was found in the nucleotides aligned to the E domain. We used both in vitro and in vivo experiments to reveal the role of the E domain of CRR2. The E domain of CRR2 can be predictably altered to prefer different nucleotides in its RNA ligand, and position 5 of the E1-motif is biologically important for the PPR-RNA interaction. The 'code' of the E domain PPR motifs is different from that of P- and S-motifs. The findings presented here show that the E domain of CRR2 is involved in sequence-specific interaction with its RNA ligand and have implications for our ability to predict RNA targets for PLS-PPRs and their use as biotechnological tools to manipulate specific RNAs in vivo.
Collapse
Affiliation(s)
- Hannes Ruwe
- Institut für Biologie, Humboldt-Universität zu Berlin, Philippstr. 13, 10115, Berlin, Germany
| | - Bernard Gutmann
- Australian Research Council Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, 35 Stirling Highway, Crawley, 6009, WA, Australia
| | | | - Ian Small
- Australian Research Council Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, 35 Stirling Highway, Crawley, 6009, WA, Australia
| | - Peter Kindgren
- Australian Research Council Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, 35 Stirling Highway, Crawley, 6009, WA, Australia
| |
Collapse
|
33
|
Brenner WG, Mader M, Müller NA, Hoenicka H, Schroeder H, Zorn I, Fladung M, Kersten B. High Level of Conservation of Mitochondrial RNA Editing Sites Among Four Populus Species. G3 (BETHESDA, MD.) 2019; 9:709-717. [PMID: 30617214 PMCID: PMC6404595 DOI: 10.1534/g3.118.200763] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Accepted: 12/01/2019] [Indexed: 01/29/2023]
Abstract
RNA editing occurs in the endosymbiont organelles of higher plants as C-to-U conversions of defined nucleotides. The availability of large quantities of RNA sequencing data makes it possible to identify RNA editing sites and to quantify their editing extent. We have investigated RNA editing in 34 protein-coding mitochondrial transcripts of four Populus species, a genus noteworthy for its remarkably small number of RNA editing sites compared to other angiosperms. 27 of these transcripts were subject to RNA editing in at least one species. In total, 355 RNA editing sites were identified with high confidence, their editing extents ranging from 10 to 100%. The most heavily edited transcripts were ccmB with the highest density of RNA editing sites (53.7 sites / kb) and ccmFn with the highest number of sites (39 sites). Most of the editing events are at position 1 or 2 of the codons, usually altering the encoded amino acid, and are highly conserved among the species, also with regard to their editing extent. However, one SNP was found in the newly sequenced and annotated mitochondrial genome of P. alba resulting in the loss of an RNA editing site compared to P. tremula and P. davidiana This SNP causes a C-to-T transition and an amino acid exchange from Ser to Phe, highlighting the widely discussed role of RNA editing in compensating mutations.
Collapse
Affiliation(s)
| | - Malte Mader
- Thünen Institute of Forest Genetics, 22927 Grosshansdorf, Germany
| | | | - Hans Hoenicka
- Thünen Institute of Forest Genetics, 22927 Grosshansdorf, Germany
| | - Hilke Schroeder
- Thünen Institute of Forest Genetics, 22927 Grosshansdorf, Germany
| | - Ingo Zorn
- Thünen Institute of Forest Genetics, 22927 Grosshansdorf, Germany
| | - Matthias Fladung
- Thünen Institute of Forest Genetics, 22927 Grosshansdorf, Germany
| | - Birgit Kersten
- Thünen Institute of Forest Genetics, 22927 Grosshansdorf, Germany
| |
Collapse
|
34
|
Toyoshima M, Sakata M, Ohnishi K, Tokumaru Y, Kato Y, Tokutsu R, Sakamoto W, Minagawa J, Matsuda F, Shimizu H. Targeted proteome analysis of microalgae under high-light conditions by optimized protein extraction of photosynthetic organisms. J Biosci Bioeng 2019; 127:394-402. [DOI: 10.1016/j.jbiosc.2018.09.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Revised: 08/23/2018] [Accepted: 09/02/2018] [Indexed: 12/14/2022]
|
35
|
Kawabe A, Furihata HY, Tsujino Y, Kawanabe T, Fujii S, Yoshida T. Divergence of RNA editing among Arabidopsis species. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2019; 280:241-247. [PMID: 30824002 DOI: 10.1016/j.plantsci.2018.12.009] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Revised: 12/05/2018] [Accepted: 12/12/2018] [Indexed: 05/25/2023]
Abstract
RNA editing altered the RNA sequence by replacing the C nucleotide to U in the organellar genomes of plants. RNA editing status sometimes differed among distant species. The pattern of conservation and variation of RNA editing status made it possible to evaluate evolutionary mechanisms impacting functional aspects of RNA editing. In this study, divergence of RNA editing in the chloroplast genome among Arabidopsis species was analyzed to determine 9 losses and 1 gain in RNA editing. All changes in A. thaliana lineage resulted from changes to the chloroplast genome sequence, whereas changes in the A. lyrata / halleri lineage were possibly due to exclusive changes in the nuclear editing factors. One loss of RNA editing in A. lyrata was caused by a deficiency in the PPR gene OTP80. The changes in RNA editing occurred approximately every two million years and were not observed at functionally important sites. These results highlight the conserved nature of RNA editing status suggesting the importance of RNA editing during evolution.
Collapse
Affiliation(s)
- Akira Kawabe
- Faculty of Life Sciences, Kyoto Sangyo University, Kyoto, 603-8555, Japan.
| | - Hazuka Y Furihata
- Faculty of Life Sciences, Kyoto Sangyo University, Kyoto, 603-8555, Japan
| | - Yudai Tsujino
- Faculty of Life Sciences, Kyoto Sangyo University, Kyoto, 603-8555, Japan
| | - Takahiro Kawanabe
- Faculty of Life Sciences, Kyoto Sangyo University, Kyoto, 603-8555, Japan
| | - Sota Fujii
- Graduate School of Agriculture and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Takanori Yoshida
- Faculty of Life Sciences, Kyoto Sangyo University, Kyoto, 603-8555, Japan
| |
Collapse
|
36
|
Takenaka M, Jörg A, Burger M, Haag S. RNA editing mutants as surrogates for mitochondrial SNP mutants. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2019; 135:310-321. [PMID: 30599308 DOI: 10.1016/j.plaphy.2018.12.014] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Revised: 12/13/2018] [Accepted: 12/16/2018] [Indexed: 06/09/2023]
Abstract
In terrestrial plants, RNA editing converts specific cytidines to uridines in mitochondrial and plastidic transcripts. Most of these events appear to be important for proper function of organellar encoded genes, since translated proteins from edited mRNAs show higher similarity with evolutionary conserved polypeptide sequences. So far about 100 nuclear encoded proteins have been characterized as RNA editing factors in plant organelles. Respective RNA editing mutants reduce or lose editing activity at different sites and display various macroscopic phenotypes from pale or albino in the case of chloroplasts to growth retardation or even embryonic lethality. Therefore, RNA editing mutants can be a useful resource of surrogate mutants for organellar encoded genes, especially for mitochondrially encoded genes that it is so far unfeasible to manipulate. However, connections between RNA editing defects and observed phenotypes in the mutants are often hard to elucidate, since RNA editing factors often target multiple RNA sites in different genes simultaneously. In this review article, we summarize the physiological aspects of respective RNA editing mutants and discuss them as surrogate mutants for functional analysis of mitochondrially encoded genes.
Collapse
Affiliation(s)
- Mizuki Takenaka
- Department of Botany, Graduate School of Science, Kyoto University, Oiwake-cho, Sakyo-ku, Kyoto, 606-8502, Japan.
| | - Anja Jörg
- Molekulare Botanik, Universität Ulm, Albert-Einstein-Allee 11, 89069, Ulm, Germany
| | - Matthias Burger
- Molekulare Botanik, Universität Ulm, Albert-Einstein-Allee 11, 89069, Ulm, Germany
| | - Sascha Haag
- Molekulare Botanik, Universität Ulm, Albert-Einstein-Allee 11, 89069, Ulm, Germany
| |
Collapse
|
37
|
Jiang T, Zhang J, Rong L, Feng Y, Wang Q, Song Q, Zhang L, Ouyang M. ECD1 functions as an RNA-editing trans-factor of rps14-149 in plastids and is required for early chloroplast development in seedlings. JOURNAL OF EXPERIMENTAL BOTANY 2018; 69:3037-3051. [PMID: 29648606 PMCID: PMC5972661 DOI: 10.1093/jxb/ery139] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Accepted: 03/29/2018] [Indexed: 05/18/2023]
Abstract
Chloroplast development is a highly complex process and the regulatory mechanisms have not yet been fully characterized. In this study, we identified Early Chloroplast Development 1 (ECD1), a chloroplast-localized pentatricopeptide repeat protein (PPR) belonging to the PLS subfamily. Inactivation of ECD1 in Arabidopsis led to embryo lethality, and abnormal embryogenesis occurred in ecd1/+ heterozygous plants. A decrease in ECD1 expression induced by RNAi resulted in seedlings with albino cotyledons but normal true leaves. The aberrant morphology and under-developed thylakoid membrane system in cotyledons of RNAi seedlings suggests a role of ECD1 specifically in chloroplast development in seedlings. In cotyledons of ECD1-RNAi plants, RNA-editing of rps14-149 (encoding ribosomal protein S14) was seriously impaired. In addition, dramatically decreased plastid-encoded RNA polymerase-dependent gene expression and abnormal chloroplast rRNA processing were also observed. Taken together, our results indicate that ECD1 is indispensable for chloroplast development at the seedling stage in Arabidopsis.
Collapse
Affiliation(s)
- Tian Jiang
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Jing Zhang
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Liwei Rong
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yanjiang Feng
- Cultivation and Crop Tillage Institute of Heilongjiang Academy of Agricultural Sciences, Harbin, China
| | - Qi Wang
- Cultivation and Crop Tillage Institute of Heilongjiang Academy of Agricultural Sciences, Harbin, China
| | - Qiulai Song
- Cultivation and Crop Tillage Institute of Heilongjiang Academy of Agricultural Sciences, Harbin, China
| | - Lixin Zhang
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Min Ouyang
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- Correspondence:
| |
Collapse
|
38
|
Sun YK, Gutmann B, Yap A, Kindgren P, Small I. Editing of Chloroplast rps14 by PPR Editing Factor EMB2261 Is Essential for Arabidopsis Development. FRONTIERS IN PLANT SCIENCE 2018; 9:841. [PMID: 29973946 PMCID: PMC6019781 DOI: 10.3389/fpls.2018.00841] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Accepted: 05/30/2018] [Indexed: 05/04/2023]
Abstract
RNA editing in plastids is known to be required for embryogenesis, but no single editing event had been shown to be essential. We show that the emb2261-2 mutation is lethal through a failure to express an editing factor that specifically recognizes the rps14-2 site. EMB2261 was predicted to bind the cis-element upstream of the rps14-2 site and genetic complementation with promoters of different strength followed by RNA-seq analysis was conducted to test the correlation between rps14-2 editing and EMB2261 expression. Rps14-2 is the only editing event in Arabidopsis chloroplasts that correlates with EMB2261 expression. Sequence divergence between the cis-element and the EMB2261 protein sequence in plants where rps14-2 editing is not required adds support to the association between them. We conclude that EMB2261 is the specificity factor for rps14-2 editing. This editing event converts P51 in Rps14 to L51, which is conserved among species lacking RNA editing, implying the importance of the editing event to Rps14 function. Rps14 is an essential ribosomal subunit for plastid translation, which, in turn, is essential for Arabidopsis embryogenesis.
Collapse
|
39
|
Ma F, Hu Y, Ju Y, Jiang Q, Cheng Z, Zhang Q. A novel tetratricopeptide repeat protein, WHITE TO GREEN1, is required for early chloroplast development and affects RNA editing in chloroplasts. JOURNAL OF EXPERIMENTAL BOTANY 2017; 68:5829-5843. [PMID: 29140512 PMCID: PMC5854136 DOI: 10.1093/jxb/erx383] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2017] [Accepted: 10/05/2017] [Indexed: 05/24/2023]
Abstract
The chloroplast is essential for plant photosynthesis and production, but the regulatory mechanism of chloroplast development is still elusive. Here, a novel gene, WHITE TO GREEN1 (WTG1), was identified to have a function in chloroplast development and plastid gene expression by screening Arabidopsis leaf coloration mutants. WTG1 encodes a chloroplast-localized tetratricopeptide repeat protein that is expressed widely in Arabidopsis cells. Disruption of WTG1 suppresses plant growth, retards leaf greening and chloroplast development, and represses photosynthetic gene expression, but complemented expression of WTG1 restored a normal phenotype. Moreover, WTG1 protein is associated with the organelle RNA editing factors MORF8 and MORF9, and RNA editing of the plastid petL-5 and ndhG-50 transcripts was affected in wtg1 mutants. These results indicate that WTG1 affects both transcriptional and posttranscriptional regulation of plastid gene expression, and provide evidence for the involvement of a tetratricopeptide repeat protein in chloroplast RNA editing in Arabidopsis.
Collapse
Affiliation(s)
- Fei Ma
- Key Laboratory of Ministry of Education for Cell Proliferation and Differentiation, College of Life Sciences, Peking University, China
| | - Yingchun Hu
- Key Laboratory of Ministry of Education for Cell Proliferation and Differentiation, College of Life Sciences, Peking University, China
| | - Yan Ju
- Key Laboratory of Ministry of Education for Cell Proliferation and Differentiation, College of Life Sciences, Peking University, China
| | - Qianru Jiang
- Key Laboratory of Ministry of Education for Cell Proliferation and Differentiation, College of Life Sciences, Peking University, China
| | - Zhijun Cheng
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, China
| | - Quan Zhang
- Key Laboratory of Ministry of Education for Cell Proliferation and Differentiation, College of Life Sciences, Peking University, China
| |
Collapse
|
40
|
Hassani D, Khalid M, Bilal M, Zhang YD, Huang D. Pentatricopeptide Repeat-directed RNA Editing and Their Biomedical Applications. INT J PHARMACOL 2017. [DOI: 10.3923/ijp.2017.762.772] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
|
41
|
Bayer-Császár E, Haag S, Jörg A, Glass F, Härtel B, Obata T, Meyer EH, Brennicke A, Takenaka M. The conserved domain in MORF proteins has distinct affinities to the PPR and E elements in PPR RNA editing factors. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2017; 1860:813-828. [PMID: 28549935 DOI: 10.1016/j.bbagrm.2017.05.004] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 03/03/2017] [Revised: 05/11/2017] [Accepted: 05/14/2017] [Indexed: 11/15/2022]
Abstract
In plant organelles specific nucleotide motifs at C to U RNA editing sites are recognized by the PLS-class of pentatricopeptide repeat (PPR) proteins, which are additionally characterized by a C-terminal E domain. The PPR elements bind the nucleotides in the target RNA, while the function of the E domain has remained unknown. At most sites RNA editing also requires multiple organellar RNA editing factor (MORF) proteins. To understand how these two types of proteins are involved in RNA editing complexes, we systematically analyzed their protein-protein interactions. In vivo pull-down and yeast two-hybrid assays show that MORF proteins connect with selected PPR proteins. In a loss of function mutant of MORF1, a single amino acid alteration in the conserved MORF domain abrogates interactions with many PLS-class PPR proteins, implying the requirement of direct interaction to PPR proteins for the RNA editing function of MORF1. Subfragment analyses show that predominantly the N-terminal/central regions of the MORF domain in MORF1 and MORF3 bind the PPR proteins. Within the PPR proteins, the E domains in addition to PPR elements contact MORF proteins. In chimeric PPR proteins, different E domains alter the specificity of the interaction with MORF proteins. The selective interactions between E domain containing PPR and MORF proteins suggest that the E domains and MORF proteins play a key role for specific protein complexes to assemble at different RNA editing sites.
Collapse
Affiliation(s)
| | - Sascha Haag
- Molekulare Botanik, Universität Ulm, 89069 Ulm, Germany
| | - Anja Jörg
- Molekulare Botanik, Universität Ulm, 89069 Ulm, Germany
| | | | | | - Toshihiro Obata
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, 14476 Potsdam, Golm, Germany
| | - Etienne H Meyer
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, 14476 Potsdam, Golm, Germany
| | | | | |
Collapse
|
42
|
Hajrah NH, Obaid AY, Atef A, Ramadan AM, Arasappan D, Nelson CA, Edris S, Mutwakil MZ, Alhebshi A, Gadalla NO, Makki RM, Al-Kordy MA, El-Domyati FM, Sabir JSM, Khiyami MA, Hall N, Bahieldin A, Jansen RK. Transcriptomic analysis of salt stress responsive genes in Rhazya stricta. PLoS One 2017; 12:e0177589. [PMID: 28520766 PMCID: PMC5433744 DOI: 10.1371/journal.pone.0177589] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2017] [Accepted: 04/29/2017] [Indexed: 11/24/2022] Open
Abstract
Rhazya stricta is an evergreen shrub that is widely distributed across Western and South Asia, and like many other members of the Apocynaceae produces monoterpene indole alkaloids that have anti-cancer properties. This species is adapted to very harsh desert conditions making it an excellent system for studying tolerance to high temperatures and salinity. RNA-Seq analysis was performed on R. stricta exposed to severe salt stress (500 mM NaCl) across four time intervals (0, 2, 12 and 24 h) to examine mechanisms of salt tolerance. A large number of transcripts including genes encoding tetrapyrroles and pentatricopeptide repeat (PPR) proteins were regulated only after 12 h of stress of seedlings grown in controlled greenhouse conditions. Mechanisms of salt tolerance in R. stricta may involve the upregulation of genes encoding chaperone protein Dnaj6, UDP-glucosyl transferase 85a2, protein transparent testa 12 and respiratory burst oxidase homolog protein b. Many of the highly-expressed genes act on protecting protein folding during salt stress and the production of flavonoids, key secondary metabolites in stress tolerance. Other regulated genes encode enzymes in the porphyrin and chlorophyll metabolic pathway with important roles during plant growth, photosynthesis, hormone signaling and abiotic responses. Heme biosynthesis in R. stricta leaves might add to the level of salt stress tolerance by maintaining appropriate levels of photosynthesis and normal plant growth as well as by the participation in reactive oxygen species (ROS) production under stress. We speculate that the high expression levels of PPR genes may be dependent on expression levels of their targeted editing genes. Although the results of PPR gene family indicated regulation of a large number of transcripts under salt stress, PPR actions were independent of the salt stress because their RNA editing patterns were unchanged.
Collapse
Affiliation(s)
- Nahid H. Hajrah
- Biotechnology Research Group, Department of Biological Sciences, Faculty of Science, King Abdulaziz University (KAU), Jeddah, Saudi Arabia
| | - Abdullah Y. Obaid
- Department of Chemistry, Faculty of Science, King Abdulaziz University (KAU), Jeddah, Saudi Arabia
| | - Ahmed Atef
- Biotechnology Research Group, Department of Biological Sciences, Faculty of Science, King Abdulaziz University (KAU), Jeddah, Saudi Arabia
| | - Ahmed M. Ramadan
- Biotechnology Research Group, Department of Biological Sciences, Faculty of Science, King Abdulaziz University (KAU), Jeddah, Saudi Arabia
- Agricultural Genetic Engineering Research Institute (AGERI), Agriculture Research Center (ARC), Giza, Egypt
| | - Dhivya Arasappan
- Department of Integrative Biology, University of Texas at Austin, Austin, Texas, United States of America
| | - Charllotte A. Nelson
- Centre of Genomic Research, Institute for Integrative Biology, Crown Street, Liverpool, United Kingdom
| | - Sherif Edris
- Biotechnology Research Group, Department of Biological Sciences, Faculty of Science, King Abdulaziz University (KAU), Jeddah, Saudi Arabia
- Department of Genetics, Faculty of Agriculture, Ain Shams University, Cairo, Egypt
- Princess Al-Jawhara Al-Brahim Centre of Excellence in Research of Hereditary Disorders (PACER-HD), Faculty of Medicine, King Abdulaziz University (KAU), Jeddah, Saudi Arabia
| | - Mohammed Z. Mutwakil
- Biotechnology Research Group, Department of Biological Sciences, Faculty of Science, King Abdulaziz University (KAU), Jeddah, Saudi Arabia
| | - Alawia Alhebshi
- Biotechnology Research Group, Department of Biological Sciences, Faculty of Science, King Abdulaziz University (KAU), Jeddah, Saudi Arabia
| | - Nour O. Gadalla
- Department of Arid Land Agriculture, Faculty of Meteorology, Environment and Arid Land Agriculture, King Abdulaziz University, Jeddah, Saudi Arabia
- Genetics and Cytology Department, Genetic Engineering and Biotechnology Division, National Research Center, Dokki, Egypt
| | - Rania M. Makki
- Biotechnology Research Group, Department of Biological Sciences, Faculty of Science, King Abdulaziz University (KAU), Jeddah, Saudi Arabia
| | - Madgy A. Al-Kordy
- Genetics and Cytology Department, Genetic Engineering and Biotechnology Division, National Research Center, Dokki, Egypt
| | - Fotouh M. El-Domyati
- Department of Genetics, Faculty of Agriculture, Ain Shams University, Cairo, Egypt
| | - Jamal S. M. Sabir
- Biotechnology Research Group, Department of Biological Sciences, Faculty of Science, King Abdulaziz University (KAU), Jeddah, Saudi Arabia
| | - Mohammad A. Khiyami
- King Abdulaziz City for Science and Technology (KACST), Riyadh, Saudi Arabia
| | - Neil Hall
- Biotechnology Research Group, Department of Biological Sciences, Faculty of Science, King Abdulaziz University (KAU), Jeddah, Saudi Arabia
- The Earlham Institute, Norwich Research Park, Norwich, United Kingdom
| | - Ahmed Bahieldin
- Biotechnology Research Group, Department of Biological Sciences, Faculty of Science, King Abdulaziz University (KAU), Jeddah, Saudi Arabia
- Department of Genetics, Faculty of Agriculture, Ain Shams University, Cairo, Egypt
| | - Robert K. Jansen
- Biotechnology Research Group, Department of Biological Sciences, Faculty of Science, King Abdulaziz University (KAU), Jeddah, Saudi Arabia
- Department of Integrative Biology, University of Texas at Austin, Austin, Texas, United States of America
- * E-mail:
| |
Collapse
|
43
|
Du L, Zhang J, Qu S, Zhao Y, Su B, Lv X, Li R, Wan Y, Xiao J. The Pentratricopeptide Repeat Protein Pigment-Defective Mutant2 is Involved in the Regulation of Chloroplast Development and Chloroplast Gene Expression in Arabidopsis. PLANT & CELL PHYSIOLOGY 2017; 58:747-759. [PMID: 28158776 DOI: 10.1093/pcp/pcx004] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2016] [Accepted: 01/08/2017] [Indexed: 05/10/2023]
Abstract
The development of functional chloroplasts, which is assisted by a series of nuclear-encoded auxiliary protein factors, is essential for plant autotrophic growth and development. To understand the molecular mechanisms underlying chloroplast development, we isolated and characterized a pigment-defective mutant, pdm2, and its corresponding variegated RNA interference (RNAi) lines in Arabidopsis. Sequence analysis revealed that PDM2 encodes a pentatricopeptide repeat protein that belongs to the P subgroup. Confocal microscopic analysis and immunoblotting of the chloroplast protein fraction showed that PDM2 was located in the stroma. In RNAi plants, protein-related photosynthesis was severely compromised. Furthermore, analysis of the transcript profile of chloroplast genes revealed that plastid-encoded polymerase-dependent transcript levels were markedly reduced, while nuclear-encoded polymerase-dependent transcript levels were increased, in RNAi plants. In addition, PDM2 affects plastid RNA editing efficiency in most editing sites, apparently by directly interacting with multiple organellar RNA editing factor 2 (MORF2) and MORF9. Thus, our results demonstrate that PDM2 is probably involved in the regulation of plastid gene expression required for normal chloroplast development.
Collapse
Affiliation(s)
- Liang Du
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, China
| | - Jian Zhang
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, China
| | - Shaofeng Qu
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, China
| | - Yuanyuan Zhao
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, China
| | - Bodan Su
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, China
| | - Xueqin Lv
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, China
| | - Ruili Li
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, China
| | - Yinglang Wan
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, China
| | - Jianwei Xiao
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, China
| |
Collapse
|
44
|
Sykes T, Yates S, Nagy I, Asp T, Small I, Studer B. In Silico Identification of Candidate Genes for Fertility Restoration in Cytoplasmic Male Sterile Perennial Ryegrass (Lolium perenne L.). Genome Biol Evol 2017; 9:351-362. [PMID: 26951780 PMCID: PMC5499803 DOI: 10.1093/gbe/evw047] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/27/2016] [Indexed: 12/24/2022] Open
Abstract
Perennial ryegrass (Lolium perenne L.) is widely used for forage production in both permanent and temporary grassland systems. To increase yields in perennial ryegrass, recent breeding efforts have been focused on strategies to more efficiently exploit heterosis by hybrid breeding. Cytoplasmic male sterility (CMS) is a widely applied mechanism to control pollination for commercial hybrid seed production and although CMS systems have been identified in perennial ryegrass, they are yet to be fully characterized. Here, we present a bioinformatics pipeline for efficient identification of candidate restorer of fertility (Rf) genes for CMS. From a high-quality draft of the perennial ryegrass genome, 373 pentatricopeptide repeat (PPR) genes were identified and classified, further identifying 25 restorer of fertility-like PPR (RFL) genes through a combination of DNA sequence clustering and comparison to known Rf genes. This extensive gene family was targeted as the majority of Rf genes in higher plants are RFL genes. These RFL genes were further investigated by phylogenetic analyses, identifying three groups of perennial ryegrass RFLs. These three groups likely represent genomic regions of active RFL generation and identify the probable location of perennial ryegrass PPR-Rf genes. This pipeline allows for the identification of candidate PPR-Rf genes from genomic sequence data and can be used in any plant species. Functional markers for PPR-Rf genes will facilitate map-based cloning of Rf genes and enable the use of CMS as an efficient tool to control pollination for hybrid crop production.
Collapse
Affiliation(s)
- Timothy Sykes
- Institute of Agricultural Sciences, Forage Crop Genetics, ETH Zurich, Zurich, Switzerland
| | - Steven Yates
- Institute of Agricultural Sciences, Forage Crop Genetics, ETH Zurich, Zurich, Switzerland
| | - Istvan Nagy
- Department of Molecular Biology and Genetics, Research Centre Flakkebjerg, Aarhus University, Slagelse, Denmark
| | - Torben Asp
- Department of Molecular Biology and Genetics, Research Centre Flakkebjerg, Aarhus University, Slagelse, Denmark
| | - Ian Small
- Plant Energy Biology, ARC Centre of Excellence, the University of Western Australia, Crawley, Western Australia, Australia
| | - Bruno Studer
- Institute of Agricultural Sciences, Forage Crop Genetics, ETH Zurich, Zurich, Switzerland
| |
Collapse
|
45
|
Zhang Z, Cui X, Wang Y, Wu J, Gu X, Lu T. The RNA Editing Factor WSP1 Is Essential for Chloroplast Development in Rice. MOLECULAR PLANT 2017; 10:86-98. [PMID: 27622591 DOI: 10.1016/j.molp.2016.08.009] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2016] [Revised: 08/31/2016] [Accepted: 08/31/2016] [Indexed: 05/10/2023]
Abstract
Although the multiple organellar RNA editing factors (MORFs) in the plastids of Arabidopsis thaliana have been extensively studied, molecular details underlying how MORFs affect plant development in other species, particularly in rice, remain largely unknown. Here we describe the characterization of wsp1, a rice mutant with white-stripe leaves and panicles. Notably, wsp1 exhibited nearly white immature panicles at the heading stage. Transmission electron microscopy analysis and chlorophyll content measurement revealed a chloroplast developmental defect and reduced chlorophyll accumulation in wsp1. Positional cloning of WSP1 found a point mutation in Os04g51280, whose putative product shares high sequence similarity with MORF proteins. Complementation experiments demonstrated that WSP1 was responsible for the variegated phenotypes of wsp1. WSP1 is localized to chloroplasts and the point mutation in wsp1 affected the editing of multiple organellar RNA sites. Owing to the defect in plastid RNA editing, chloroplast ribosome biogenesis and ndhA splicing were also impaired in wsp1, which may affect normal chloroplast development in the leaves and panicles at the heading stage. Together, our results demonstrate the importance of rice WSP1 protein in chloroplast development and broaden our knowledge about MORF family members in rice.
Collapse
Affiliation(s)
- Zhiguo Zhang
- Biotechnology Research Institute/National Key Facility for Genetic Resources and Gene Improvement, The Chinese Academy of Agricultural Sciences, Beijing 100081, P. R. China
| | - Xuean Cui
- Biotechnology Research Institute/National Key Facility for Genetic Resources and Gene Improvement, The Chinese Academy of Agricultural Sciences, Beijing 100081, P. R. China
| | - Yanwei Wang
- Biotechnology Research Institute/National Key Facility for Genetic Resources and Gene Improvement, The Chinese Academy of Agricultural Sciences, Beijing 100081, P. R. China
| | - Jinxia Wu
- Biotechnology Research Institute/National Key Facility for Genetic Resources and Gene Improvement, The Chinese Academy of Agricultural Sciences, Beijing 100081, P. R. China
| | - Xiaofeng Gu
- Biotechnology Research Institute/National Key Facility for Genetic Resources and Gene Improvement, The Chinese Academy of Agricultural Sciences, Beijing 100081, P. R. China.
| | - Tiegang Lu
- Biotechnology Research Institute/National Key Facility for Genetic Resources and Gene Improvement, The Chinese Academy of Agricultural Sciences, Beijing 100081, P. R. China.
| |
Collapse
|
46
|
Wang Y, Ren Y, Zhou K, Liu L, Wang J, Xu Y, Zhang H, Zhang L, Feng Z, Wang L, Ma W, Wang Y, Guo X, Zhang X, Lei C, Cheng Z, Wan J. WHITE STRIPE LEAF4 Encodes a Novel P-Type PPR Protein Required for Chloroplast Biogenesis during Early Leaf Development. FRONTIERS IN PLANT SCIENCE 2017; 8:1116. [PMID: 28694820 PMCID: PMC5483476 DOI: 10.3389/fpls.2017.01116] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2017] [Accepted: 06/09/2017] [Indexed: 05/18/2023]
Abstract
Pentatricopeptide repeat (PPR) proteins comprise a large family in higher plants and perform diverse functions in organellar RNA metabolism. Despite the rice genome encodes 477 PRR proteins, the regulatory effects of PRR proteins on chloroplast development remains unknown. In this study, we report the functional characterization of the rice white stripe leaf4 (wsl4) mutant. The wsl4 mutant develops white-striped leaves during early leaf development, characterized by decreased chlorophyll content and malformed chloroplasts. Positional cloning of the WSL4 gene, together with complementation and RNA-interference tests, reveal that it encodes a novel P-family PPR protein with 12 PPR motifs, and is localized to chloroplast nucleoids. Quantitative RT-PCR analyses demonstrate that WSL4 is a low temperature response gene abundantly expressed in young leaves. Further expression analyses show that many nuclear- and plastid-encoded genes in the wsl4 mutant are significantly affected at the RNA and protein levels. Notably, the wsl4 mutant causes defects in the splicing of atpF, ndhA, rpl2, and rps12. Our findings identify WSL4 as a novel P-family PPR protein essential for chloroplast RNA group II intron splicing during early leaf development in rice.
Collapse
Affiliation(s)
- Ying Wang
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural SciencesBeijing, China
| | - Yulong Ren
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural SciencesBeijing, China
| | - Kunneng Zhou
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural SciencesBeijing, China
| | - Linglong Liu
- National Key Laboratory for Crop Genetics and Germplasm Enhancement, Nanjing Agricultural UniversityNanjing, China
| | - Jiulin Wang
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural SciencesBeijing, China
| | - Yang Xu
- National Key Laboratory for Crop Genetics and Germplasm Enhancement, Nanjing Agricultural UniversityNanjing, China
| | - Huan Zhang
- National Key Laboratory for Crop Genetics and Germplasm Enhancement, Nanjing Agricultural UniversityNanjing, China
| | - Long Zhang
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural SciencesBeijing, China
| | - Zhiming Feng
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural SciencesBeijing, China
| | - Liwei Wang
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural SciencesBeijing, China
| | - Weiwei Ma
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural SciencesBeijing, China
| | - Yunlong Wang
- National Key Laboratory for Crop Genetics and Germplasm Enhancement, Nanjing Agricultural UniversityNanjing, China
| | - Xiuping Guo
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural SciencesBeijing, China
| | - Xin Zhang
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural SciencesBeijing, China
| | - Cailin Lei
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural SciencesBeijing, China
| | - Zhijun Cheng
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural SciencesBeijing, China
| | - Jianmin Wan
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural SciencesBeijing, China
- National Key Laboratory for Crop Genetics and Germplasm Enhancement, Nanjing Agricultural UniversityNanjing, China
- *Correspondence: Jianmin Wan, ;,
| |
Collapse
|
47
|
Shi X, Bentolila S, Hanson MR. Organelle RNA recognition motif-containing (ORRM) proteins are plastid and mitochondrial editing factors in Arabidopsis. PLANT SIGNALING & BEHAVIOR 2016; 11:e1167299. [PMID: 27082488 PMCID: PMC4977459 DOI: 10.1080/15592324.2016.1167299] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Post-transcriptional C-to-U RNA editing occurs at specific sites in plastid and plant mitochondrial transcripts. Members of the Arabidopsis pentatricopeptide repeat (PPR) motif-containing protein family and RNA-editing factor Interacting Protein (RIP, also known as MORF) family have been characterized as essential components of the RNA editing apparatus. Recent studies reveal that several organelle-targeted RNA recognition motif (RRM)-containing proteins are involved in either plastid or mitochondrial RNA editing. ORRM1 (Organelle RRM protein 1) is essential for plastid editing, whereas ORRM2, ORRM3 and ORRM4 are involved in mitochondrial RNA editing. The RRM domain of ORRM1, ORRM3 and ORRM4 is required for editing activity, whereas the auxiliary RIP and Glycine-Rich (GR) domains mediate the ORRM proteins' interactions with other editing factors. The identification of the ORRM proteins as RNA editing factors further expands our knowledge of the composition of the editosome.
Collapse
Affiliation(s)
- Xiaowen Shi
- Department of Molecular Biology and Genetics, Cornell University, Biotechnology Building, Ithaca, NY, USA
| | - Stephane Bentolila
- Department of Molecular Biology and Genetics, Cornell University, Biotechnology Building, Ithaca, NY, USA
| | - Maureen R. Hanson
- Department of Molecular Biology and Genetics, Cornell University, Biotechnology Building, Ithaca, NY, USA
- Maureen R Hanson
| |
Collapse
|
48
|
Hammani K, Takenaka M, Miranda R, Barkan A. A PPR protein in the PLS subfamily stabilizes the 5'-end of processed rpl16 mRNAs in maize chloroplasts. Nucleic Acids Res 2016; 44:4278-88. [PMID: 27095196 PMCID: PMC4872118 DOI: 10.1093/nar/gkw270] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
Pentatricopeptide repeat (PPR) proteins are a large family of helical-repeat proteins that bind RNA in mitochondria and chloroplasts. Precise RNA targets and functions have been assigned to only a small fraction of the >400 members of the PPR family in plants. We used the amino acid code governing the specificity of RNA binding by PPR repeats to infer candidate-binding sites for the maize protein PPR103 and its ortholog Arabidopsis EMB175. Genetic and biochemical data confirmed a predicted binding site in the chloroplast rpl16 5′UTR to be a site of PPR103 action. This site maps to the 5′ end of transcripts that fail to accumulate in ppr103 mutants. A small RNA corresponding to the predicted PPR103 binding site accumulates in a PPR103-dependent fashion, as expected of PPR103's in vivo footprint. Recombinant PPR103 bound specifically to this sequence in vitro. These observations imply that PPR103 stabilizes rpl16 mRNA by impeding 5′→3′ RNA degradation. Previously described PPR proteins with this type of function consist of canonical PPR motifs. By contrast, PPR103 is a PLS-type protein, an architecture typically associated with proteins that specify sites of RNA editing. However, PPR103 is not required to specify editing sites in chloroplasts.
Collapse
Affiliation(s)
- Kamel Hammani
- Centre National de la Recherche Scientifique (CNRS), Institut de Biologie Moléculaire des Plantes, 12 rue du Général Zimmer, 67084 Strasbourg, France
| | | | - Rafael Miranda
- Institute of Molecular Biology, University of Oregon, Eugene, OR 97403, USA
| | - Alice Barkan
- Institute of Molecular Biology, University of Oregon, Eugene, OR 97403, USA
| |
Collapse
|
49
|
Williams BP, Burgess SJ, Reyna-Llorens I, Knerova J, Aubry S, Stanley S, Hibberd JM. An Untranslated cis-Element Regulates the Accumulation of Multiple C4 Enzymes in Gynandropsis gynandra Mesophyll Cells. THE PLANT CELL 2016; 28:454-65. [PMID: 26772995 PMCID: PMC4790868 DOI: 10.1105/tpc.15.00570] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2015] [Accepted: 01/13/2016] [Indexed: 05/04/2023]
Abstract
C4 photosynthesis is a complex phenotype that allows more efficient carbon capture than the ancestral C3 pathway. In leaves of C4 species, hundreds of transcripts increase in abundance compared with C3 relatives and become restricted to mesophyll (M) or bundle sheath (BS) cells. However, no mechanism has been reported that regulates the compartmentation of multiple enzymes in M or BS cells. We examined mechanisms regulating CARBONIC ANHYDRASE4 (CA4) in C4 Gynandropsis gynandra. Increased abundance is directed by both the promoter region and introns of the G. gynandra gene. A nine-nucleotide motif located in the 5' untranslated region (UTR) is required for preferential accumulation of GUS in M cells. This element is present and functional in three additional 5' UTRs and six 3' UTRs where it determines accumulation of two isoforms of CA and pyruvate,orthophosphate dikinase in M cells. Although the GgCA4 5' UTR is sufficient to direct GUS accumulation in M cells, transcripts encoding GUS are abundant in both M and BS. Mutating the GgCA4 5' UTR abolishes enrichment of protein in M cells without affecting transcript abundance. The work identifies a mechanism that directs cell-preferential accumulation of multiple enzymes required for C4 photosynthesis.
Collapse
Affiliation(s)
- Ben P Williams
- Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, United Kingdom
| | - Steven J Burgess
- Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, United Kingdom
| | - Ivan Reyna-Llorens
- Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, United Kingdom
| | - Jana Knerova
- Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, United Kingdom
| | - Sylvain Aubry
- Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, United Kingdom
| | - Susan Stanley
- Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, United Kingdom
| | - Julian M Hibberd
- Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, United Kingdom
| |
Collapse
|
50
|
Glass F, Härtel B, Zehrmann A, Verbitskiy D, Takenaka M. MEF13 Requires MORF3 and MORF8 for RNA Editing at Eight Targets in Mitochondrial mRNAs in Arabidopsis thaliana. MOLECULAR PLANT 2015; 8:1466-77. [PMID: 26048647 DOI: 10.1016/j.molp.2015.05.008] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2015] [Revised: 05/07/2015] [Accepted: 05/17/2015] [Indexed: 05/02/2023]
Abstract
RNA editing sites in plant mitochondria and plastids are addressed by pentatricopeptide repeat (PPR) proteins with E or E and DYW domains, which recognize a specific nucleotide motif upstream of the edited nucleotide. In addition, some sites require MORF proteins for efficient RNA editing. Here, we assign the novel E domain-containing PPR protein, MEF13, as being required for editing at eight sites in Arabidopsis thaliana. A SNP in ecotype C24 altering the editing level at only one of the eight target sites was located by genomic mapping. An EMS mutant allele of the gene for MEF13 was identified in a SNaPshot screen of a mutated plant population. At all eight target sites of MEF13, editing levels are reduced in both morf3 and morf8 mutants, but at only one site in morf1 mutants, suggesting that specific MEF13-MORF interactions are required. Yeast two-hybrid analyses detect solid connections of MEF13 with MORF1 and weak contact with MORF3 proteins. Yeast three-hybrid (Y3H) analysis shows that the presence of MORF8 enhances the connection between MEF13 and MORF3, suggesting that a MORF3-MORF8 heteromer may form stably or transiently to establish interaction with MEF13.
Collapse
Affiliation(s)
| | | | - Anja Zehrmann
- Molekulare Botanik, Universität Ulm, 89069 Ulm, Germany
| | | | | |
Collapse
|