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Kwok van der Giezen F, Honkanen S, Colas des Francs-Small C, Bond C, Small I. Applications of Synthetic Pentatricopeptide Repeat Proteins. PLANT & CELL PHYSIOLOGY 2024; 65:503-515. [PMID: 38035801 PMCID: PMC11094755 DOI: 10.1093/pcp/pcad150] [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: 07/31/2023] [Revised: 11/20/2023] [Accepted: 11/29/2023] [Indexed: 12/02/2023]
Abstract
RNA-binding proteins play integral roles in the regulation of essential processes in cells and as such are attractive targets for engineering to manipulate gene expression at the RNA level. Expression of transcripts in chloroplasts and mitochondria is heavily regulated by pentatricopeptide repeat (PPR) proteins. The diverse roles of PPR proteins and their naturally modular architecture make them ideal candidates for engineering. Synthetic PPR proteins are showing great potential to become valuable tools for controlling the expression of plastid and mitochondrial transcripts. In this review, by 'synthetic', we mean both rationally modified natural PPR proteins and completely novel proteins designed using the principles learned from their natural counterparts. We focus on the many different applications of synthetic PPR proteins, covering both their use in basic research to learn more about protein-RNA interactions and their use to achieve specific outcomes in RNA processing and the control of gene expression. We describe the challenges associated with the design, construction and deployment of synthetic PPR proteins and provide perspectives on how they might be assembled and used in future biotechnology applications.
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Affiliation(s)
- Farley Kwok van der Giezen
- Australian Research Council Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, 35 Stirling Highway, Perth, WA 6009, Australia
| | - Suvi Honkanen
- Australian Research Council Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, 35 Stirling Highway, Perth, WA 6009, Australia
| | - Catherine Colas des Francs-Small
- Australian Research Council Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, 35 Stirling Highway, Perth, WA 6009, Australia
| | - Charles Bond
- School of Molecular Sciences, The University of Western Australia, 35 Stirling Highway, Perth, WA 6009, 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, Perth, WA 6009, Australia
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Lin Y, Yang H, Liu H, Lu X, Cao H, Li B, Chang Y, Guo Z, Ding D, Hu Y, Xue Y, Liu Z, Tang J. A P-type pentatricopeptide repeat protein ZmRF5 promotes 5' region partial cleavages of atp6c transcripts to restore the fertility of CMS-C maize by recruiting a splicing factor. PLANT BIOTECHNOLOGY JOURNAL 2024; 22:1269-1281. [PMID: 38073308 PMCID: PMC11022799 DOI: 10.1111/pbi.14263] [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: 07/29/2023] [Revised: 10/31/2023] [Accepted: 11/26/2023] [Indexed: 04/18/2024]
Abstract
A fast evolution within mitochondria genome(s) often generates discords between nuclear and mitochondria, which is manifested as cytoplasmic male sterility (CMS) and fertility restoration (Rf) system. The maize CMS-C trait is regulated by the chimeric mitochondrial gene, atp6c, and can be recovered by the restorer gene ZmRf5. Through positional cloning in this study, we identified the nuclear restorer gene, ZmRf5, which encodes a P-type pentatricopeptide repeat (PPR) family protein. The over-expression of ZmRf5 brought back the fertility to CMS-C plants, whereas its genomic editing by CRISPR/Cas9 induced abortive pollens in the restorer line. ZmRF5 is sorted to mitochondria, and recruited RS31A, a splicing factor, through MORF8 to form a cleaving/restoring complex, which promoted the cleaving of the CMS-associated transcripts atp6c by shifting the major cleavage site from 480th nt to 344 th nt for fast degradation, and preserved just right amount of atp6c RNA for protein translation, providing adequate ATP6C to assembly complex V, thus restoring male fertility. Interestingly, ATP6C in the sterile line CMo17A, with similar cytology and physiology changes to YU87-1A, was accumulated much less than it in NMo17B, exhibiting a contrary trend in the YU87-1 nuclear genome previously reported, and was restored to normal level in the presence of ZmRF5. Collectively these findings unveil a new molecular mechanism underlying fertility restoration by which ZmRF5 cooperates with MORF8 and RS31A to restore CMS-C fertility in maize, complemented and perfected the sterility mechanism, and enrich the perspectives on communications between nucleus and mitochondria.
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Affiliation(s)
- Yanan Lin
- State Key Laboratory of Wheat and Maize Crop Science, College of AgronomyHenan Agricultural UniversityZhengzhouChina
| | - Huili Yang
- State Key Laboratory of Wheat and Maize Crop Science, College of AgronomyHenan Agricultural UniversityZhengzhouChina
| | - Hongmei Liu
- State Key Laboratory of Wheat and Maize Crop Science, College of AgronomyHenan Agricultural UniversityZhengzhouChina
| | - Xiuyuan Lu
- State Key Laboratory of Wheat and Maize Crop Science, College of AgronomyHenan Agricultural UniversityZhengzhouChina
| | - Haofei Cao
- State Key Laboratory of Wheat and Maize Crop Science, College of AgronomyHenan Agricultural UniversityZhengzhouChina
| | - Bing Li
- State Key Laboratory of Wheat and Maize Crop Science, College of AgronomyHenan Agricultural UniversityZhengzhouChina
| | - Yongyuan Chang
- State Key Laboratory of Wheat and Maize Crop Science, College of AgronomyHenan Agricultural UniversityZhengzhouChina
| | - Zhanyong Guo
- State Key Laboratory of Wheat and Maize Crop Science, College of AgronomyHenan Agricultural UniversityZhengzhouChina
| | - Dong Ding
- State Key Laboratory of Wheat and Maize Crop Science, College of AgronomyHenan Agricultural UniversityZhengzhouChina
| | - Yanmin Hu
- State Key Laboratory of Wheat and Maize Crop Science, College of AgronomyHenan Agricultural UniversityZhengzhouChina
| | - Yadong Xue
- State Key Laboratory of Wheat and Maize Crop Science, College of AgronomyHenan Agricultural UniversityZhengzhouChina
| | - Zonghua Liu
- State Key Laboratory of Wheat and Maize Crop Science, College of AgronomyHenan Agricultural UniversityZhengzhouChina
| | - Jihua Tang
- State Key Laboratory of Wheat and Maize Crop Science, College of AgronomyHenan Agricultural UniversityZhengzhouChina
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Huynh SD, Melonek J, Colas des Francs-Small C, Bond CS, Small I. A unique C-terminal domain contributes to the molecular function of Restorer-of-fertility proteins in plant mitochondria. THE NEW PHYTOLOGIST 2023; 240:830-845. [PMID: 37551058 DOI: 10.1111/nph.19166] [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: 05/09/2023] [Accepted: 07/10/2023] [Indexed: 08/09/2023]
Abstract
Restorer-of-fertility (Rf) genes encode pentatricopeptide repeat (PPR) proteins that are targeted to mitochondria where they specifically bind to transcripts that induce cytoplasmic male sterility and repress their expression. In searching for a molecular signature unique to this class of proteins, we found that a majority of known Rf proteins have a distinct domain, which we called RfCTD (Restorer-of-fertility C-terminal domain), and its presence correlates with the ability to induce cleavage of the mitochondrial RNA target. A screen of 219 angiosperm genomes from 123 genera using a sequence profile that can quickly and accurately identify RfCTD sequences revealed considerable variation in RFL/RfCTD gene numbers across flowering plants. We observed that plant genera with bisexual flowers have significantly higher numbers of RFL genes compared to those with unisexual flowers, consistent with a role of these proteins in restoration of male fertility. We show that removing the RfCTD from the RFL protein RNA PROCESSING FACTOR 2-nad6 prevented cleavage of its RNA target, the nad6 transcript, in Arabidopsis thaliana mitochondria. We provide a simple way of identifying putative Rf candidates in genome sequences, new insights into the molecular mode of action of Rf proteins and the evolution of fertility restoration in flowering plants.
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Affiliation(s)
- Sang Dang Huynh
- School of Molecular Sciences, ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, Crawley, WA, 6009, Australia
| | - Joanna Melonek
- School of Molecular Sciences, ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, Crawley, WA, 6009, Australia
| | - Catherine Colas des Francs-Small
- School of Molecular Sciences, ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, Crawley, WA, 6009, Australia
| | - Charles S Bond
- School of Molecular Sciences, The University of Western Australia, Crawley, WA, 6009, Australia
| | - Ian Small
- School of Molecular Sciences, ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, Crawley, WA, 6009, Australia
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Park G, Shahwar D, Jang G, Shin J, Kwon G, Kim Y, Hong CO, Jin B, Kim H, Lee O, Park Y. Identification of a novel locus C2 controlling canary yellow flesh color in watermelons. Front Genet 2023; 14:1256627. [PMID: 37795242 PMCID: PMC10545963 DOI: 10.3389/fgene.2023.1256627] [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: 07/11/2023] [Accepted: 08/29/2023] [Indexed: 10/06/2023] Open
Abstract
The flesh color of watermelon is an important trait that is determined by carotenoid composition and affects consumers' fruit desirability. Although a complete dominant control by C locus (Cllcyb) for canary yellow flesh (CY) over red flesh has been reported, red and CY colors frequently appear as a mixed pattern in the same flesh (incomplete canary yellow, ICY) in F1 and inbred lines carrying dominant C alleles. Therefore, we examined the genetic control of the mixed color pattern in ICY using whole-genome resequencing of three ICY (ICY group) and three CY inbred lines (CY group), as well as genetic linkage mapping of an F2 population. The segregation pattern in 135 F2 plants indicated that CY is controlled by a single locus (named C 2) dominant over ICY. The whole-genome resequencing of ICY and CY inbred lines revealed an ICY/CY-specific region of approximately 27.60-27.88 Mb on Chr. 2 that was polymorphic between the ICY and CY groups. Our genetic map, using nine cleaved amplified polymorphic sequence markers developed based on the single-nucleotide polymorphisms from the ICY/CY-specific region, confirmed that C 2 is located on Chr. 2 and cosegregated with the marker (M7) derived from a non-synonymous single-nucleotide polymorphism of the pentatricopeptide repeat (PPR) gene (ClPPR, Cla97C02G039880). Additionally, 27 watermelon inbred lines of ICY, CY, and red flesh were evaluated using previously reported Cllcyb (C locus)-based markers and our C 2 locus-linked ClPPR-based marker (M7). As a result, dominant alleles at the C 2 locus were required to produce CY, in addition to dominant alleles at the C locus, while a recessive homozygous genotype at the C locus gave the red flesh irrespective of the genotype at the C 2 locus. Using a ClPPR-based cleaved amplified polymorphic sequence developed in this study and Cllcyb-based markers, watermelon cultivars with CY, ICY, and red flesh could be successfully discerned, implying that the combined use of these markers will be efficient for marker-assisted selection of flesh color in watermelon breeding.
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Affiliation(s)
- Girim Park
- Department of Horticultural Bioscience, Pusan National University, Miryang, Republic of Korea
| | - Durre Shahwar
- Department of Horticultural Bioscience, Pusan National University, Miryang, Republic of Korea
| | - Gaeun Jang
- Department of Horticultural Bioscience, Pusan National University, Miryang, Republic of Korea
| | - Jagyeong Shin
- Department of Horticultural Bioscience, Pusan National University, Miryang, Republic of Korea
| | - Gibeom Kwon
- Partner Seeds Co., Ltd., Gimje, Republic of Korea
| | - Younjae Kim
- Partner Seeds Co., Ltd., Gimje, Republic of Korea
| | - Chang Oh Hong
- Department of Life Science and Environmental Biochemistry, Pusan National University, Miryang, Republic of Korea
- Life and Industry Convergence Research Institute, Pusan National University, Miryang, Republic of Korea
| | - Bingkui Jin
- UNELL Biotechnology Co., Ltd., Weifang, China
| | - Hoytaek Kim
- Department of Horticulture, Sunchon National University, Sunchon, Republic of Korea
| | - Oakjin Lee
- National Institute of Horticultural and Herbal Science, Rural Development Administration, Wanju, Republic of Korea
| | - Younghoon Park
- Department of Horticultural Bioscience, Pusan National University, Miryang, Republic of Korea
- Life and Industry Convergence Research Institute, Pusan National University, Miryang, Republic of Korea
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Liu S, Liu M, Cao Y, Xu Y, Liu H, Zhu Q, Zhang X, Luan F. Identification of chromosome region and candidate genes for canary-yellow flesh (Cyf) locus in watermelon (Citrullus lanatus). PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2023; 329:111594. [PMID: 36642105 DOI: 10.1016/j.plantsci.2023.111594] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Revised: 01/06/2023] [Accepted: 01/09/2023] [Indexed: 06/17/2023]
Abstract
Genetic control of fruit flesh color in watermelon is complex, and significant knowledge gaps still exist. In the present study, we investigated the genetic basis of canary-yellow flesh color in watermelon inbred line PI 635597 using a segregating population derived from a cross between PI 635597 and another inbred line, Cream of Saskatchewan (pale yellow flesh color). We showed that a single dominant gene controls the canary-yellow flesh color for the Cyf (canary-yellow flesh) trait. Bulk segregant analysis (BSA) and fine genetic mapping narrowed down the Cyf locus to a 79.62-kb region on chromosome 6, which harbors 10 predicted genes. Sequence variation analysis in the promoter and coding regions and gene expression analysis in both parental lines and selected watermelon accessions with diverse fruit flesh colors support Cla97C06G122050 (unknown protein) and Cla97C06G122120 (pentatricopeptide repeat) as predicted candidate genes for the Cyf locus. Marker-assisted selection and sequence alignment showed that the Cyf locus could differentiate canary-yellow flesh and pale-yellow flesh. Our results indicate that the Cyf locus might be responsible for canary-yellow flesh color and carotenoid accumulation levels.
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Affiliation(s)
- Shi Liu
- Key Laboratory of Biology and Genetic Improvement of Horticulture Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Northeast Agricultural University, Harbin, Heilongjiang Province, China; College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, Heilongjiang Province, China.
| | - Mengqiu Liu
- Key Laboratory of Biology and Genetic Improvement of Horticulture Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Northeast Agricultural University, Harbin, Heilongjiang Province, China; College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, Heilongjiang Province, China.
| | - Yue Cao
- Key Laboratory of Biology and Genetic Improvement of Horticulture Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Northeast Agricultural University, Harbin, Heilongjiang Province, China; College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, Heilongjiang Province, China.
| | - Yan Xu
- Key Laboratory of Biology and Genetic Improvement of Horticulture Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Northeast Agricultural University, Harbin, Heilongjiang Province, China; College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, Heilongjiang Province, China.
| | - Hongyu Liu
- Key Laboratory of Biology and Genetic Improvement of Horticulture Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Northeast Agricultural University, Harbin, Heilongjiang Province, China; College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, Heilongjiang Province, China.
| | - Qianglong Zhu
- Agronomy College, Jiangxi Agricultural University, Nanchang, Jiangxi Province, China.
| | - Xian Zhang
- College of Horticulture, Northwest of A&F University, Yangling, Shaanxi Province, China.
| | - Feishi Luan
- Key Laboratory of Biology and Genetic Improvement of Horticulture Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Northeast Agricultural University, Harbin, Heilongjiang Province, China; College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, Heilongjiang Province, China.
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Schleicher S, Binder S. In Arabidopsis thaliana mitochondria 5' end polymorphisms of nad4L-atp4 and nad3-rps12 transcripts are linked to RNA PROCESSING FACTORs 1 and 8. PLANT MOLECULAR BIOLOGY 2021; 106:335-348. [PMID: 33909186 PMCID: PMC8270843 DOI: 10.1007/s11103-021-01153-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Accepted: 04/12/2021] [Indexed: 05/14/2023]
Abstract
RNA PROCESSING FACTORs 1 AND 8 (RPF1 and RPF8), both restorer of fertility like pentatricopeptide repeat proteins, are required for processing of dicistronic nad4L-atp4 and nad3-rps12 transcripts in Arabidopsis mitochondria. In mitochondria of Arabidopsis thaliana (Arabidopsis), the 5' termini of many RNAs are generated on the post-transcriptional level. This process is still poorly understood in terms of both the underlying mechanism as well as proteins required. Our studies now link the generation of polymorphic 5' extremities of the dicistronic nad3-rps12 and nad4L-atp4 transcripts to the function of the P-type pentatricopeptide repeat proteins RNA PROCESSING FACTORs 8 (RPF8) and 1 (RPF1). RPF8 is required to generate the nad3-rps12 -141 5' end in ecotype Van-0 whereas the RPF8 allele in Col has no function in the generation of any 5' terminus of this transcript. This observation strongly suggests the involvement of an additional factor in the generation of the -229 5' end of nad3-rps12 transcripts in Col. RPF1, previously found to be necessary for the generation of the -228 5' end of the major 1538 nucleotide-long nad4 mRNAs, is also important for the formation of nad4L-atp4 transcripts with a 5' end at position -318 in Col. Many Arabidopsis ecotypes contain inactive RPF1 alleles resulting in the accumulation of various low abundant nad4L-atp4 RNAs which might represent precursor and/or degradation products. Some of these ecotypes accumulate major, but slightly smaller RNA species. The introduction of RPF1 into these lines not only establishes the formation of the major nad4L-atp4 dicistronic mRNA with the -318 5' terminus, the presence of this gene also suppresses the accumulation of most alternative nad4L-atp4 RNAs. Beside RPF1, several other factors contribute to nad4L-atp4 transcript formation.
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Affiliation(s)
- Sarah Schleicher
- Institut Molekulare Botanik, Universität Ulm, Albert-Einstein-Allee 11, 89069, Ulm, Germany
| | - Stefan Binder
- Institut Molekulare Botanik, Universität Ulm, Albert-Einstein-Allee 11, 89069, Ulm, Germany.
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Durand S, Ricou A, Simon M, Dehaene N, Budar F, Camilleri C. A restorer-of-fertility-like pentatricopeptide repeat protein promotes cytoplasmic male sterility in Arabidopsis thaliana. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 105:124-135. [PMID: 33098690 DOI: 10.1111/tpj.15045] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Accepted: 10/15/2020] [Indexed: 06/11/2023]
Abstract
Pentatricopeptide repeat (PPR) proteins form a large family of proteins targeted to organelles, where they post-transcriptionally modulate gene expression through binding to specific RNA sequences. Among them, the mitochondria-targeted restorer-of-fertility (Rf) PPRs inhibit peculiar mitochondrial genes that are detrimental to male gametes and cause cytoplasmic male sterility (CMS). Here, we revealed three nuclear loci involved in CMS in a cross between two distant Arabidopsis thaliana strains, Sha and Cvi-0. We identified the causal gene at one of these loci as RFL24, a conserved gene encoding a PPR protein related to known Rf PPRs. By analysing fertile revertants obtained in a male sterile background, we demonstrate that RFL24 promotes pollen abortion, in contrast with the previously described Rf PPRs, which allow pollen to survive in the presence of a sterilizing cytoplasm. We show that the sterility caused by the RFL24 Cvi-0 allele results from higher expression of the gene during early pollen development. Finally, we predict a binding site for RFL24 upstream of two mitochondrial genes, the CMS gene and the important gene cob. These results suggest that the conservation of RFL24 is linked to a primary role of ensuring a proper functioning of mitochondria, and that it was subsequently diverted by the CMS gene to its benefit.
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Affiliation(s)
- Stéphanie Durand
- Institut Jean-Pierre Bourgin, INRAE, AgroParisTech, Université Paris-Saclay, Versailles, 78000, France
| | - Anthony Ricou
- Institut Jean-Pierre Bourgin, INRAE, AgroParisTech, Université Paris-Saclay, Versailles, 78000, France
| | - Matthieu Simon
- Institut Jean-Pierre Bourgin, INRAE, AgroParisTech, Université Paris-Saclay, Versailles, 78000, France
| | - Noémie Dehaene
- Institut Jean-Pierre Bourgin, INRAE, AgroParisTech, Université Paris-Saclay, Versailles, 78000, France
- Univ. Paris-Sud, Université Paris-Saclay, Orsay, 91405, France
| | - Françoise Budar
- Institut Jean-Pierre Bourgin, INRAE, AgroParisTech, Université Paris-Saclay, Versailles, 78000, France
| | - Christine Camilleri
- Institut Jean-Pierre Bourgin, INRAE, AgroParisTech, Université Paris-Saclay, Versailles, 78000, France
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Tiwari B, Habermann K, Arif MA, Weil HL, Garcia-Molina A, Kleine T, Mühlhaus T, Frank W. Identification of small RNAs during cold acclimation in Arabidopsis thaliana. BMC PLANT BIOLOGY 2020; 20:298. [PMID: 32600430 PMCID: PMC7325139 DOI: 10.1186/s12870-020-02511-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Accepted: 06/22/2020] [Indexed: 05/21/2023]
Abstract
BACKGROUND Cold stress causes dynamic changes in gene expression that are partially caused by small non-coding RNAs since they regulate protein coding transcripts and act in epigenetic gene silencing pathways. Thus, a detailed analysis of transcriptional changes of small RNAs (sRNAs) belonging to all known sRNA classes such as microRNAs (miRNA) and small interfering RNA (siRNAs) in response to cold contributes to an understanding of cold-related transcriptome changes. RESULT We subjected A. thaliana plants to cold acclimation conditions (4 °C) and analyzed the sRNA transcriptomes after 3 h, 6 h and 2 d. We found 93 cold responsive differentially expressed miRNAs and only 14 of these were previously shown to be cold responsive. We performed miRNA target prediction for all differentially expressed miRNAs and a GO analysis revealed the overrepresentation of miRNA-targeted transcripts that code for proteins acting in transcriptional regulation. We also identified a large number of differentially expressed cis- and trans-nat-siRNAs, as well as sRNAs that are derived from long non-coding RNAs. By combining the results of sRNA and mRNA profiling with miRNA target predictions and publicly available information on transcription factors, we reconstructed a cold-specific, miRNA and transcription factor dependent gene regulatory network. We verified the validity of links in the network by testing its ability to predict target gene expression under cold acclimation. CONCLUSION In A. thaliana, miRNAs and sRNAs derived from cis- and trans-NAT gene pairs and sRNAs derived from lncRNAs play an important role in regulating gene expression in cold acclimation conditions. This study provides a fundamental database to deepen our knowledge and understanding of regulatory networks in cold acclimation.
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Affiliation(s)
- Bhavika Tiwari
- Department of Biology I, Plant Molecular Cell Biology, Ludwig-Maximilians-Universität München, LMU Biocenter, Großhaderner Str. 2-4, 82152 Planegg-Martinsried, Germany
| | - Kristin Habermann
- Department of Biology I, Plant Molecular Cell Biology, Ludwig-Maximilians-Universität München, LMU Biocenter, Großhaderner Str. 2-4, 82152 Planegg-Martinsried, Germany
| | - M. Asif Arif
- Department of Biology I, Plant Molecular Cell Biology, Ludwig-Maximilians-Universität München, LMU Biocenter, Großhaderner Str. 2-4, 82152 Planegg-Martinsried, Germany
| | - Heinrich Lukas Weil
- Computational Systems Biology, Technische Universität Kaiserslautern, Paul-Ehrlich-Straße 23, 67663 Kaiserslautern, Germany
| | - Antoni Garcia-Molina
- Department of Biology I, Plant Molecular Biology, Ludwig-Maximilians-Universität München, LMU Biocenter, Großhaderner Str. 2-4, 82152 Planegg-Martinsried, Germany
| | - Tatjana Kleine
- Department of Biology I, Plant Molecular Biology, Ludwig-Maximilians-Universität München, LMU Biocenter, Großhaderner Str. 2-4, 82152 Planegg-Martinsried, Germany
| | - Timo Mühlhaus
- Computational Systems Biology, Technische Universität Kaiserslautern, Paul-Ehrlich-Straße 23, 67663 Kaiserslautern, Germany
| | - Wolfgang Frank
- Department of Biology I, Plant Molecular Cell Biology, Ludwig-Maximilians-Universität München, LMU Biocenter, Großhaderner Str. 2-4, 82152 Planegg-Martinsried, Germany
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Zhang Y, Huang X, Zou J, Liao X, Liu Y, Lian T, Nian H. Major contribution of transcription initiation to 5'-end formation of mitochondrial steady-state transcripts in maize. RNA Biol 2018; 16:104-117. [PMID: 30585757 DOI: 10.1080/15476286.2018.1561604] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
In plant mitochondria, some steady-state transcripts contain primary 5' ends derived from transcription initiation, while the others have processed 5' termini generated by post-transcriptional processing. Differentiation and mapping of the primary and processed transcripts are important for unraveling the molecular mechanism(s) underlying transcription and transcript end maturation. However, previous efforts to systematically differentiate these two types of transcripts in plant mitochondria failed. At present, it is considered that the majority of mature mRNAs may have processed 5' ends in Arabidopsis. Here, by combination of circular RT-PCR, quantitative RT-PCR, RNA 5'-polyphosphatase treatment and Northern blot, we successfully discriminated and mapped the primary and processed transcripts in maize mitochondria. Among the thirty-five mature and eight precursor RNAs analyzed in this study, about one half (21/43) were found to have multiple isoforms. In total, seventy-seven steady-state transcripts were determined, and forty-seven of them had primary 5' ends. Most transcription initiation sites (126/167) were downstream of a crTA-motif. These data suggested a major contribution of transcription initiation to 5'-end formation of steady-state transcripts in maize mitochondria. Moreover, the mapping results revealed that mature RNA termini had largely been formed before trans-splicing, and C→U RNA editing was accompanied with trans-splicing and transcript end formation in maize mitochondria.
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Affiliation(s)
- Yafeng Zhang
- a State Key Laboratory of Conservation and Utilization of Subtropical Agro-Bioresources , South China Agricultural University , Guangzhou , China.,b Guangdong Provincial Key Laboratory of Plant Molecular Breeding, College of Agriculture , South China Agricultural University , Guangzhou , China
| | - Xiaoyu Huang
- b Guangdong Provincial Key Laboratory of Plant Molecular Breeding, College of Agriculture , South China Agricultural University , Guangzhou , China
| | - Jingyun Zou
- b Guangdong Provincial Key Laboratory of Plant Molecular Breeding, College of Agriculture , South China Agricultural University , Guangzhou , China
| | - Xun Liao
- b Guangdong Provincial Key Laboratory of Plant Molecular Breeding, College of Agriculture , South China Agricultural University , Guangzhou , China
| | - Yujun Liu
- c Institute of Crop Science, College of Agriculture and Biotechnology , Zhejiang University , Hangzhou , China
| | - Tengxiang Lian
- a State Key Laboratory of Conservation and Utilization of Subtropical Agro-Bioresources , South China Agricultural University , Guangzhou , China.,b Guangdong Provincial Key Laboratory of Plant Molecular Breeding, College of Agriculture , South China Agricultural University , Guangzhou , China.,d Guangdong Subcenter of the National Center for Soybean Improvement, College of Agriculture , South China Agricultural University , Guangzhou , China
| | - Hai Nian
- a State Key Laboratory of Conservation and Utilization of Subtropical Agro-Bioresources , South China Agricultural University , Guangzhou , China.,b Guangdong Provincial Key Laboratory of Plant Molecular Breeding, College of Agriculture , South China Agricultural University , Guangzhou , China.,d Guangdong Subcenter of the National Center for Soybean Improvement, College of Agriculture , South China Agricultural University , Guangzhou , China
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Colas des Francs-Small C, Vincis Pereira Sanglard L, Small I. Targeted cleavage of nad6 mRNA induced by a modified pentatricopeptide repeat protein in plant mitochondria. Commun Biol 2018; 1:166. [PMID: 30320233 PMCID: PMC6181959 DOI: 10.1038/s42003-018-0166-8] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Accepted: 09/06/2018] [Indexed: 12/27/2022] Open
Abstract
Mitochondrial genes encode key components of the cellular energy machinery, but their genetic analysis is difficult or impossible in most organisms (including plants) because of the lack of viable transformation approaches. We report here a method to block the expression of the mitochondrial nad6 gene encoding a subunit of respiratory complex I in Arabidopsis thaliana, via the modification of the specificity of the RNA-binding protein RNA PROCESSING FACTOR 2 (RPF2). We show that the modified RPF2 binds and specifically induces cleavage of nad6 RNA, almost eliminating expression of the Nad6 protein and consequently complex I accumulation and activity. To our knowledge, this is the first example of a targeted block in expression of a specific mitochondrial transcript by a custom-designed RNA-binding protein. This opens the path to reverse genetics studies on mitochondrial gene functions and leads to potential applications in agriculture. Catherine Colas des Francs-Small et al. used an engineered pentatricopeptide repeat protein to induce cleavage of nad6 mRNA in the mitochondria of Arabidopsis thaliana, eliminating its expression. The approach has potential for use in functional characterization of mitochondrial genes and future agricultural applications.
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Affiliation(s)
- Catherine Colas des Francs-Small
- Australian Research Council Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Crawley, WA, 6009, Australia.
| | - Lilian Vincis Pereira Sanglard
- Australian Research Council Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Crawley, WA, 6009, Australia
| | - Ian Small
- Australian Research Council Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Crawley, WA, 6009, Australia.
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11
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Zhang YF, Suzuki M, Sun F, Tan BC. The Mitochondrion-Targeted PENTATRICOPEPTIDE REPEAT78 Protein Is Required for nad5 Mature mRNA Stability and Seed Development in Maize. MOLECULAR PLANT 2017; 10:1321-1333. [PMID: 28951060 DOI: 10.1016/j.molp.2017.09.009] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2017] [Revised: 08/27/2017] [Accepted: 09/10/2017] [Indexed: 05/06/2023]
Abstract
Pentatricopepetide repeat (PPR) proteins are a large family of RNA-binding proteins involved in RNA metabolism in plant organelles. Although many PPR proteins have been functionally studied, few of them are identified with a function in mitochondrial RNA stability. By using a reverse genetic approach, we characterized the role of the mitochondrion-targeted PPR78 protein in nad5 mature mRNA stability and maize (Zea mays) seed development. Loss of PPR78 function leads to a dramatic reduction in the steady-state level of mitochondrial nad5 mature mRNA, blocks the assembly of complex I in the electron transport chain, and causes an arrest in embryogenesis and endosperm development. Characterization of a second strong allele confirms the function of PPR78 in nad5 mRNA accumulation and maize seed development. The generation of mature nad5 requires the assembly of three distinct precursor RNAs via trans-splicing reactions, and the accumulation of nad5T1 precursor is reduced in the ppr78 mutants. However, it is the instability of mature nad5 rather than nad5T1 causing loss of the full-length nad5 transcript, and degradation of nad5 losing both translation start and stop codons is enriched in the mutant. Our data imply the assembly of mature nad5 mRNA precedes the protection of PPR78.
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Affiliation(s)
- Ya-Feng Zhang
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, College of Agriculture, South China Agricultural University, Guangzhou 510642, China
| | - Masaharu Suzuki
- Plant Molecular and Cellular Biology Program, University of Florida, Gainesville, Florida 32611, USA
| | - Feng Sun
- Key Laboratory of Plant Cell Engineering and Germplasm Innovation, Ministry of Education, School of Life Sciences, Shandong University, Jinan 250100, China
| | - Bao-Cai Tan
- Key Laboratory of Plant Cell Engineering and Germplasm Innovation, Ministry of Education, School of Life Sciences, Shandong University, Jinan 250100, China.
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12
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Stoll K, Jonietz C, Schleicher S, des Francs-Small CC, Small I, Binder S. In Arabidopsis thaliana distinct alleles encoding mitochondrial RNA PROCESSING FACTOR 4 support the generation of additional 5' termini of ccmB transcripts. PLANT MOLECULAR BIOLOGY 2017; 93:659-668. [PMID: 28229269 DOI: 10.1007/s11103-017-0591-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2016] [Accepted: 02/09/2017] [Indexed: 06/06/2023]
Abstract
In plant mitochondria, the 5' ends of many transcripts are generated post-transcriptionally. We show that the pentatricopeptide repeat (PPR) protein RNA PROCESSING FACTOR 4 (RPF4) supports the generation of extra 5' ends of ccmB transcripts in Landsberg erecta (Ler) and a number of other Arabidopsis thaliana ecotypes. RPF4 was identified in Ler applying a forward genetic approach supported by complementation studies of ecotype Columbia (Col), which generates the Ler-type extra ccmB 5' termini only after the introduction of the RPF4 allele from Ler. Studies with chimeric RPF4 proteins composed of various parts of the RPF4 proteins from Ler and Col identified differences in the N-terminal and central PPR motifs that explain ecotype-specific variations in ccmB processing. These results fit well with binding site predictions in ccmB transcripts based on the known determinants of nucleotide base recognition by PPR motifs.
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Affiliation(s)
- Katrin Stoll
- Institut Molekulare Botanik, Universität Ulm, Albert-Einstein-Allee 11, 89069, Ulm, Germany
| | - Christian Jonietz
- Institut Molekulare Botanik, Universität Ulm, Albert-Einstein-Allee 11, 89069, Ulm, Germany
| | - Sarah Schleicher
- Institut Molekulare Botanik, Universität Ulm, Albert-Einstein-Allee 11, 89069, Ulm, Germany
| | - Catherine Colas des Francs-Small
- Australian Research Council 40 Centre of Excellence in Plant Energy Biology, University of Western Australia, Crawley, WA, 6009, Australia
| | - Ian Small
- Australian Research Council 40 Centre of Excellence in Plant Energy Biology, University of Western Australia, Crawley, WA, 6009, Australia
| | - Stefan Binder
- Institut Molekulare Botanik, Universität Ulm, Albert-Einstein-Allee 11, 89069, Ulm, Germany.
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13
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Shokolenko IN, Alexeyev MF. Mitochondrial transcription in mammalian cells. Front Biosci (Landmark Ed) 2017; 22:835-853. [PMID: 27814650 DOI: 10.2741/4520] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
As a consequence of recent discoveries of intimate involvement of mitochondria with key cellular processes, there has been a resurgence of interest in all aspects of mitochondrial biology, including the intricate mechanisms of mitochondrial DNA maintenance and expression. Despite four decades of research, there remains a lot to be learned about the processes that enable transcription of genetic information from mitochondrial DNA to RNA, as well as their regulation. These processes are vitally important, as evidenced by the lethality of inactivating the central components of mitochondrial transcription machinery. Here, we review the current understanding of mitochondrial transcription and its regulation in mammalian cells. We also discuss key theories in the field and highlight controversial subjects and future directions as we see them.
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Affiliation(s)
- Inna N Shokolenko
- University of South Alabama, Patt Capps Covey College of Allied Health Professions, Biomedical Sciences Department, 5721 USA Drive N, HAHN 4021, Mobile, AL 36688-0002, USA
| | - Mikhail F Alexeyev
- Department of Physiology and Cell Biology, University of South Alabama, 5851 USA Dr. North, MSB3074, Mobile, AL 36688, USA,
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14
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Binder S, Stoll K, Stoll B. Maturation of 5' ends of plant mitochondrial RNAs. PHYSIOLOGIA PLANTARUM 2016; 157:280-8. [PMID: 26833432 DOI: 10.1111/ppl.12423] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2015] [Revised: 12/11/2015] [Accepted: 12/15/2015] [Indexed: 05/26/2023]
Abstract
The generation of mature RNAs, i.e. mRNAs, rRNAs or tRNAs, is a complex process in all genetic systems. RNA-internal processes such as splicing or RNA editing, but also posttranscriptional processes modulating 5' and 3' termini of transcripts, contribute to RNA maturation. In this article, we focus on the posttranscriptional formation of 5' termini of mitochondrial RNAs in seed plants, with particular emphasis on the model plant species Arabidopsis thaliana (Arabidopsis). We will summarize the progress made in recent studies of proteins involved in this process. In addition, we will evaluate whether 5' processing proceeds endo- or exo-nucleolytically. Despite the considerable progress made, many details of this process remain unsolved. In particular, it is still unclear why there is frequent 5' processing of many mRNAs although impaired processing does not interfere with mitochondrial function and plant fitness. Thus, the importance of 5' processing for plant mitochondria is still puzzling.
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Affiliation(s)
- Stefan Binder
- Institut Molekulare Botanik, Universität Ulm, Ulm, D-89069, Germany
| | - Katrin Stoll
- Institut Molekulare Botanik, Universität Ulm, Ulm, D-89069, Germany
| | - Birgit Stoll
- Institut Molekulare Botanik, Universität Ulm, Ulm, D-89069, Germany
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15
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Goto S, Kawaguchi Y, Sugita C, Ichinose M, Sugita M. P-class pentatricopeptide repeat protein PTSF1 is required for splicing of the plastid pre-tRNA(I) (le) in Physcomitrella patens. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2016; 86:493-503. [PMID: 27117879 DOI: 10.1111/tpj.13184] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2016] [Revised: 03/31/2016] [Accepted: 04/05/2016] [Indexed: 06/05/2023]
Abstract
Pentatricopeptide repeat (PPR) proteins are widely distributed in eukaryotes and are mostly localized in mitochondria or plastids. PPR proteins play essential roles in various RNA processing steps in organelles; however, the function of the majority of PPR proteins remains unknown. To examine the function of plastid PPR proteins, PpPPR_4 gene knock-out mutants were characterized in Physcomitrella patens. The knock-out mosses displayed severe growth retardation and reduced effective quantum yield of photosystem II. Immunoblot analysis showed that knock-out of PpPPR_4 resulted in a strongly reduced level of plastid-encoded proteins, such as photosystem II reaction center protein D1, the β subunit of ATP synthase, and the stromal enzyme, Rubisco. To further investigate whether knock-out of the PpPPR_4 gene affects plastid gene expression, we analyzed steady-state transcript levels of protein- and rRNA-coding genes by quantitative RT-PCR. This analysis showed that the level of many protein-coding transcripts increased in the mutants. In contrast, splicing of a spacer tRNA(I) (le) precursor encoded by the rrn operon was specifically impaired in the mutants, whereas the accumulation of other plastid tRNAs and rRNAs was not largely affected. Thus, the defect in tRNA(I) (le) splicing leads to a considerable reduction of mature tRNA(I) (le) , which may be accountable for the reduced protein level. An RNA mobility shift assay showed that the recombinant PpPPR_4 bound preferentially to domain III of the tRNA(I) (le) group-II intron. These results provide evidence that PpPPR_4 functions in RNA splicing of the tRNA(I) (le) intron, and hence PpPPR_4 was named plastid tRNA splicing factor 1 (PTSF1).
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Affiliation(s)
- Seiya Goto
- Center for Gene Research, Nagoya University, Nagoya, 464-8602, Japan
| | | | - Chieko Sugita
- Center for Gene Research, Nagoya University, Nagoya, 464-8602, Japan
| | - Mizuho Ichinose
- Center for Gene Research, Nagoya University, Nagoya, 464-8602, Japan
- Institute of Transformative Bio-Molecules (ITbM), Nagoya University, Nagoya, 464-8602, Japan
| | - Mamoru Sugita
- Center for Gene Research, Nagoya University, Nagoya, 464-8602, Japan
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16
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Fujii S, Suzuki T, Giegé P, Higashiyama T, Koizuka N, Shikanai T. The Restorer-of-fertility-like 2 pentatricopeptide repeat protein and RNase P are required for the processing of mitochondrial orf291 RNA in Arabidopsis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2016; 86:504-13. [PMID: 27122350 DOI: 10.1111/tpj.13185] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2016] [Accepted: 04/14/2016] [Indexed: 05/27/2023]
Abstract
Eukaryotes harbor mitochondria obtained via ancient symbiosis events. The successful evolution of energy production in mitochondria has been dependent on the control of mitochondrial gene expression by the nucleus. In flowering plants, the nuclear-encoded pentatricopeptide repeat (PPR) superfamily proteins are widely involved in mitochondrial RNA metabolism. Here, we show that an Arabidopsis nuclear-encoded RNA-binding protein, Restorer-of-fertility-like PPR protein 2 (RFL2), is required for RNA degradation of the mitochondrial orf291 transcript via endonucleolytic cleavage of the transcript in the middle of its reading frame. Both in vivo and in vitro, this RNA cleavage requires the activity of mitochondrial proteinaceous RNase P, which is possibly recruited to the site by RFL2. The site of RNase P cleavage likely forms a tRNA-like structure in the orf291 transcript. This study presents an example of functional collaboration between a PPR protein and an endonuclease in RNA cleavage. Furthermore, we show that the RFL2-binding region within the orf291 gene is hypervariable in the family Brassicaceae, possibly correlated with the rapid evolution of the RNA-recognition interfaces of the RFL proteins.
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Affiliation(s)
- Sota Fujii
- Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara, 630-0192, Japan
| | - Takamasa Suzuki
- Division of Biological Science, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, 464-8602, Japan
- Japan Science and Technology Agency, ERATO, Higashiyama Live-Holonics Project, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, 464-8602, Japan
| | - Philippe Giegé
- Institut de Biologie Moléculaire des Plantes, 12 Rue du Général Zimmer, Strasbourg, 67084, France
| | - Tetsuya Higashiyama
- Division of Biological Science, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, 464-8602, Japan
- Japan Science and Technology Agency, ERATO, Higashiyama Live-Holonics Project, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, 464-8602, Japan
- WPI-ITbM, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, 464-8602, Japan
| | - Nobuya Koizuka
- Faculty of Agriculture, Tamagawa University, 6-1-1 Tamagawa-Gakuen, Machida, Tokyo, 194-8610, Japan
| | - Toshiharu Shikanai
- Department of Botany, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto, 606-8502, Japan
- CREST, Japan Science and Technology Agency, Chiyoda-ku, Tokyo, 102-0076, Japan
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17
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Leu KC, Hsieh MH, Wang HJ, Hsieh HL, Jauh GY. Distinct role of Arabidopsis mitochondrial P-type pentatricopeptide repeat protein-modulating editing protein, PPME, in nad1 RNA editing. RNA Biol 2016; 13:593-604. [PMID: 27149614 PMCID: PMC4962808 DOI: 10.1080/15476286.2016.1184384] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
The mitochondrion is an important power generator in most eukaryotic cells. To preserve its function, many essential nuclear-encoded factors play specific roles in mitochondrial RNA metabolic processes, including RNA editing. RNA editing consists of post-transcriptional deamination, which alters specific nucleotides in transcripts to mediate gene expression. In plant cells, many pentatricopeptide repeat proteins (PPRs) participate in diverse organellar RNA metabolic processes, but only PLS-type PPRs are involved in RNA editing. Here, we report a P-type PPR protein from Arabidopsis thaliana, P-type PPR-Modulating Editing (PPME), which has a distinct role in mitochondrial nad1 RNA editing via RNA binding activity. In the homozygous ppme mutant, cytosine (C)-to-uracil (U) conversions at both the nad1-898 and 937 sites were abolished, disrupting Arg300-to-Trp300 and Pro313-to-Ser313 amino acid changes in the mitochondrial NAD1 protein. NAD1 is a critical component of mitochondrial respiration complex I; its activity is severely reduced in the homozygous ppme mutant, resulting in significantly altered growth and development. Both abolished RNA editing and defective complex I activity were completely rescued by CaMV 35S promoter- and PPME native promoter-driven PPME genomic fragments tagged with GFP in a homozygous ppme background. Our experimental results demonstrate a distinct role of a P-type PPR protein, PPME, in RNA editing in plant organelles.
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Affiliation(s)
- Kuan-Chieh Leu
- a Institute of Plant Biology, National Taiwan University , Taipei , Taiwan.,b Institute of Plant and Microbial Biology, Academia Sinica, Nankang , Taipei , Taiwan
| | - Ming-Hsiun Hsieh
- b Institute of Plant and Microbial Biology, Academia Sinica, Nankang , Taipei , Taiwan
| | - Huei-Jing Wang
- b Institute of Plant and Microbial Biology, Academia Sinica, Nankang , Taipei , Taiwan
| | - Hsu-Liang Hsieh
- a Institute of Plant Biology, National Taiwan University , Taipei , Taiwan
| | - Guang-Yuh Jauh
- b Institute of Plant and Microbial Biology, Academia Sinica, Nankang , Taipei , Taiwan.,c Biotechnology Center, National Chung-Hsing University , Taichung , Taiwan
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18
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Stoll B, Binder S. Two NYN domain containing putative nucleases are involved in transcript maturation in Arabidopsis mitochondria. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2016; 85:278-288. [PMID: 26711866 DOI: 10.1111/tpj.13111] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2015] [Revised: 12/11/2015] [Accepted: 12/14/2015] [Indexed: 06/05/2023]
Abstract
Plant mitochondrial transcripts frequently undergo maturation processes at their 5' ends. This almost completely enigmatic process requires the function of several proteins such as RNA processing factors, which are selectively involved in distinct 5' processing events. As RNA processing factors represent pentatricopeptide repeat proteins without apparent enzymatic function, it is hypothesized that a ribonuclease, most likely with endonucleolytic activity is involved in the 5' end maturation. We have now applied a reverse genetic approach to analyze the role of two potential mitochondrial nucleases, MNU1 and MNU2, in Arabidopsis thaliana. Both proteins contain several RNA-binding domains and NYN domains found in other endonucleases. A thorough analysis of various mitochondrial transcripts in MNU1 and MNU2 mutants revealed aberrant transcript pattern characterized by a decrease in mature RNA species often accompanied by an accumulation of larger, 5' extended precursor molecules. In addition, severely reduced amounts of nad9 mRNAs in the rpf2-1/mnu2-1 double mutant indicate a corporate function of RNA processing factor 2 and MNU2 in the maturation of these transcripts. However, the dramatic reduction of the nad9 mRNA is not reflected by the level of the corresponding Nad9 protein, which is found to be only moderately lowered. Collectively, our analysis strongly suggests a function of MNU1 and MNU2 in 5' processing of plant mitochondrial transcripts.
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Affiliation(s)
- Birgit Stoll
- Institut Molekulare Botanik, Universität Ulm, Ulm, D-89069, Germany
| | - Stefan Binder
- Institut Molekulare Botanik, Universität Ulm, Ulm, D-89069, Germany
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19
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Binder S, Kühn K. Determining mitochondrial transcript termini for the study of transcription start sites and transcript 5' end maturation. Methods Mol Biol 2015; 1305:13-30. [PMID: 25910724 DOI: 10.1007/978-1-4939-2639-8_2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/22/2023]
Abstract
Mitochondrial gene expression in plants is considerably more complex than in animals or fungi. In plants, mitochondrial transcripts are generated from transcription initiation at numerous, poorly conserved promoters located throughout the mitochondrial genome. Most genes have more than one transcription start site. Posttranscriptional RNA 5' end maturation contributes to the diversity of transcripts produced from each mitochondrial gene. Understanding transcriptional mechanisms and transcript maturation requires knowledge on transcription start sites and processing sites. This chapter describes two different, complementary experimental approaches for determining these sites in mitochondrial genomes through mapping of transcript 5' ends. In order to distinguish 5' ends deriving from transcription initiation, both strategies exploit the presence of triphosphates at these specific 5' termini.
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Affiliation(s)
- Stefan Binder
- Molekulare Botanik, Universität Ulm, Albert-Einstein-Allee 11, Ulm, 89069, Germany
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20
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Stoll K, Jonietz C, Binder S. In Arabidopsis thaliana two co-adapted cyto-nuclear systems correlate with distinct ccmC transcript sizes. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2015; 81:247-257. [PMID: 25399870 DOI: 10.1111/tpj.12724] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2014] [Revised: 10/29/2014] [Accepted: 11/04/2014] [Indexed: 06/04/2023]
Abstract
Plant mitochondrial transcripts undergo maturation processes at both termini. Although frequently observed, the post-transcriptional formation of mature 5' ends is still poorly understood. We now analyzed the processing of transcripts derived from the mitochondrial ccmC gene, coding for a component of the cytochrome c maturation system. In Arabidopsis thaliana (Arabidopsis) there are two mitochondrial ccmC configurations, discriminated by a 66-bp sequence segment located approximately 500 bp upstream of the ccmC gene. In Arabidopsis accessions these divergent mitochondrial genotypes correlate with the generation of two different 5' termini that map to positions around -484 in accession Columbia (Col ccmC genotype) or -390 in accession C24 relative to the translation start codon (C24 ccmC genotype). Previously we identified RNA PROCESSING FACTOR 3 (RPF3), a pentatricopeptide repeat (PPR) protein required for the maturation of ccmCmRNAs with -484 5' ends transcribed from the Col ccmC genotype. Now we identified several accessions defective in maturation of ccmC transcripts. Taking advantage of this natural genetic variation we identified RNA PROCESSING FACTOR 6 (RPF6), a PPR protein necessary for the generation of ccmCmRNAs with -390 5' ends transcribed from the C24 ccmC genotype. Both Col-type and C24-type accessions encode RPF3 and RPF6 so that they can process ccmC transcripts derived from the two different mitochondrial genotypes. These factors and their cognate RNA recognition sites in the different ccmC genotypes are an intriguing example for the evolution of two co-adapted cyto-nuclear systems required for the same process i.e. 5' maturation of ccmC transcripts.
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Affiliation(s)
- Katrin Stoll
- Institut Molekulare Botanik, Universität Ulm, D-89069, Ulm, Germany
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21
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Stoll B, Zendler D, Binder S. RNA processing factor 7 and polynucleotide phosphorylase are necessary for processing and stability of nad2 mRNA in Arabidopsis mitochondria. RNA Biol 2014; 11:968-76. [PMID: 25181358 DOI: 10.4161/rna.29781] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Post-transcriptional maturation of plant mitochondrial transcripts requires several steps. Among these, the generation of mature 5' ends is still one of the most enigmatic processes. Toward a characterization of proteins involved in 5' processing of mitochondrial transcripts in Arabidopsis (Arabidopsis thaliana), we now analyzed 5' maturation of nad2 transcripts. Based on natural genetic variation affecting 5' ends of nad2 transcripts in ecotype Can-0 and complementation studies we now identified RNA processing factor 7, which takes part in the generation of the 5' terminus of the mature nad2 mRNA. RPF7 is a relatively short regular P-class pentatricopeptide repeat protein comprising seven canonical P repeats and a single short S repeat. The corresponding allele in Can-0 encodes a truncated version of this protein lacking two C-terminal repeats, which are essential for the function of RPF7. Furthermore we established transgenic plants expressing artifical microRNAs targeting the mitochondrial polynucleotide phosphorylase (PNPase), which results in substantial reduction of the PNPase mRNA levels and strong knockdown of this gene. Detailed quantitative studies of 5' and 3' extended nad2 precursor RNAs in these knockdown plants as well as in the rpf7-1 knockout mutant suggest that 5' processing contributes to the stability of mitochondrial transcripts in plants.
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Affiliation(s)
- Birgit Stoll
- Institut Molekulare Botanik, Universität Ulm, Germany
| | | | - Stefan Binder
- Institut Molekulare Botanik, Universität Ulm, Germany
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