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Zhang Y, Chen Z, Zhang W, Sarwar R, Wang Z, Tan X. Genome-wide analysis of the NYN domain gene family in Brassica napus and its function role in plant growth and development. Gene 2024; 930:148864. [PMID: 39151674 DOI: 10.1016/j.gene.2024.148864] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2024] [Revised: 07/21/2024] [Accepted: 08/13/2024] [Indexed: 08/19/2024]
Abstract
The NYN domain gene family consists of genes that encode ribonucleases that are characterized by a newly identified NYN domain. Members of the family were widely distributed in all life kingdoms and play a crucial role in various RNA regulation processes, although the wide genome overview of the NYN domain gene family is not yet available in any species. Rapeseed (Brassica napus L.), a polyploid model species, is an important oilseed crop. Here, the phylogenetic analysis of these BnaNYNs revealed five distinct groups strongly supported by gene structure, conserved domains, and conserved motifs. The survey of the expansion of the gene family showed that the birth of BnaNYNs is explained by various duplication events. Furthermore, tissue-specific expression analysis, protein-protein interaction prediction, and cis-element prediction suggested a role for BnaNYNs in plant growth and development. Interestingly, the data showed that three tandem duplicated BnaNYNs (TDBs) exhibited distinct expression patterns from those other BnaNYNs and had a high similarity in protein sequence level. Furthermore, the analysis of one of these TDBs, BnaNYN57, showed that overexpression of BnaNYN57 in Arabidopsis thaliana and B. napus accelerated plant growth and significantly increased silique length, while RNA interference resulted in the opposite growth pattern. It suggesting a key role for the TDBs in processes related to plant growth and development.
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Affiliation(s)
- Yijie Zhang
- Institute of Life Sciences, Jiangsu University, 301# Xuefu Road, Zhenjiang 212013, PR China.
| | - Zhuo Chen
- Institute of Life Sciences, Jiangsu University, 301# Xuefu Road, Zhenjiang 212013, PR China
| | - Wenhua Zhang
- Institute of Life Sciences, Jiangsu University, 301# Xuefu Road, Zhenjiang 212013, PR China
| | - Rehman Sarwar
- Institute of Life Sciences, Jiangsu University, 301# Xuefu Road, Zhenjiang 212013, PR China
| | - Zheng Wang
- Institute of Life Sciences, Jiangsu University, 301# Xuefu Road, Zhenjiang 212013, PR China.
| | - Xiaoli Tan
- Institute of Life Sciences, Jiangsu University, 301# Xuefu Road, Zhenjiang 212013, PR China.
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2
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Schmid LM, Manavski N, Chi W, Meurer J. Chloroplast Ribosome Biogenesis Factors. PLANT & CELL PHYSIOLOGY 2024; 65:516-536. [PMID: 37498958 DOI: 10.1093/pcp/pcad082] [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: 05/24/2023] [Revised: 07/13/2023] [Accepted: 07/25/2023] [Indexed: 07/29/2023]
Abstract
The formation of chloroplasts can be traced back to an ancient event in which a eukaryotic host cell containing mitochondria ingested a cyanobacterium. Since then, chloroplasts have retained many characteristics of their bacterial ancestor, including their transcription and translation machinery. In this review, recent research on the maturation of rRNA and ribosome assembly in chloroplasts is explored, along with their crucial role in plant survival and their implications for plant acclimation to changing environments. A comparison is made between the ribosome composition and auxiliary factors of ancient and modern chloroplasts, providing insights into the evolution of ribosome assembly factors. Although the chloroplast contains ancient proteins with conserved functions in ribosome assembly, newly evolved factors have also emerged to help plants acclimate to changes in their environment and internal signals. Overall, this review offers a comprehensive analysis of the molecular mechanisms underlying chloroplast ribosome assembly and highlights the importance of this process in plant survival, acclimation and adaptation.
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Affiliation(s)
- Lisa-Marie Schmid
- Plant Molecular Biology, Faculty of Biology, Ludwig-Maximilians-University Munich, Großhaderner Street 2-4, Planegg-Martinsried 82152, Germany
| | - Nikolay Manavski
- Plant Molecular Biology, Faculty of Biology, Ludwig-Maximilians-University Munich, Großhaderner Street 2-4, Planegg-Martinsried 82152, Germany
| | - Wei Chi
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Jörg Meurer
- Plant Molecular Biology, Faculty of Biology, Ludwig-Maximilians-University Munich, Großhaderner Street 2-4, Planegg-Martinsried 82152, Germany
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3
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Liehrmann A, Delannoy E, Launay-Avon A, Gilbault E, Loudet O, Castandet B, Rigaill G. DiffSegR: an RNA-seq data driven method for differential expression analysis using changepoint detection. NAR Genom Bioinform 2023; 5:lqad098. [PMID: 37954572 PMCID: PMC10632193 DOI: 10.1093/nargab/lqad098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Revised: 09/27/2023] [Accepted: 10/23/2023] [Indexed: 11/14/2023] Open
Abstract
To fully understand gene regulation, it is necessary to have a thorough understanding of both the transcriptome and the enzymatic and RNA-binding activities that shape it. While many RNA-Seq-based tools have been developed to analyze the transcriptome, most only consider the abundance of sequencing reads along annotated patterns (such as genes). These annotations are typically incomplete, leading to errors in the differential expression analysis. To address this issue, we present DiffSegR - an R package that enables the discovery of transcriptome-wide expression differences between two biological conditions using RNA-Seq data. DiffSegR does not require prior annotation and uses a multiple changepoints detection algorithm to identify the boundaries of differentially expressed regions in the per-base log2 fold change. In a few minutes of computation, DiffSegR could rightfully predict the role of chloroplast ribonuclease Mini-III in rRNA maturation and chloroplast ribonuclease PNPase in (3'/5')-degradation of rRNA, mRNA and tRNA precursors as well as intron accumulation. We believe DiffSegR will benefit biologists working on transcriptomics as it allows access to information from a layer of the transcriptome overlooked by the classical differential expression analysis pipelines widely used today. DiffSegR is available at https://aliehrmann.github.io/DiffSegR/index.html.
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Affiliation(s)
- Arnaud Liehrmann
- Institute of Plant Sciences Paris-Saclay (IPS2), Université Paris-Saclay, CNRS, INRAE, Université Evry, Gif sur Yvette, 91190, France
- Institute of Plant Sciences Paris-Saclay (IPS2), Université Paris Cité, CNRS, INRAE, Gif sur Yvette, 91190, France
- Laboratoire de Mathématiques et de Modélisation d’Evry (LaMME), Université d’Evry-Val-d’Essonne, UMR CNRS 8071, ENSIIE, USC INRAE, Evry,91037, France
| | - Etienne Delannoy
- Institute of Plant Sciences Paris-Saclay (IPS2), Université Paris-Saclay, CNRS, INRAE, Université Evry, Gif sur Yvette, 91190, France
- Institute of Plant Sciences Paris-Saclay (IPS2), Université Paris Cité, CNRS, INRAE, Gif sur Yvette, 91190, France
| | - Alexandra Launay-Avon
- Institute of Plant Sciences Paris-Saclay (IPS2), Université Paris-Saclay, CNRS, INRAE, Université Evry, Gif sur Yvette, 91190, France
- Institute of Plant Sciences Paris-Saclay (IPS2), Université Paris Cité, CNRS, INRAE, Gif sur Yvette, 91190, France
| | - Elodie Gilbault
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), 78000, Versailles, France
| | - Olivier Loudet
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), 78000, Versailles, France
| | - Benoît Castandet
- Institute of Plant Sciences Paris-Saclay (IPS2), Université Paris-Saclay, CNRS, INRAE, Université Evry, Gif sur Yvette, 91190, France
- Institute of Plant Sciences Paris-Saclay (IPS2), Université Paris Cité, CNRS, INRAE, Gif sur Yvette, 91190, France
| | - Guillem Rigaill
- Institute of Plant Sciences Paris-Saclay (IPS2), Université Paris-Saclay, CNRS, INRAE, Université Evry, Gif sur Yvette, 91190, France
- Institute of Plant Sciences Paris-Saclay (IPS2), Université Paris Cité, CNRS, INRAE, Gif sur Yvette, 91190, France
- Laboratoire de Mathématiques et de Modélisation d’Evry (LaMME), Université d’Evry-Val-d’Essonne, UMR CNRS 8071, ENSIIE, USC INRAE, Evry,91037, France
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4
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Robson JK, Ferguson JN, McAusland L, Atkinson JA, Tranchant-Dubreuil C, Cubry P, Sabot F, Wells DM, Price AH, Wilson ZA, Murchie EH. Chlorophyll fluorescence-based high-throughput phenotyping facilitates the genetic dissection of photosynthetic heat tolerance in African (Oryza glaberrima) and Asian (Oryza sativa) rice. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:5181-5197. [PMID: 37347829 PMCID: PMC10498015 DOI: 10.1093/jxb/erad239] [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: 12/05/2022] [Accepted: 06/20/2023] [Indexed: 06/24/2023]
Abstract
Rising temperatures and extreme heat events threaten rice production. Half of the global population relies on rice for basic nutrition, and therefore developing heat-tolerant rice is essential. During vegetative development, reduced photosynthetic rates can limit growth and the capacity to store soluble carbohydrates. The photosystem II (PSII) complex is a particularly heat-labile component of photosynthesis. We have developed a high-throughput chlorophyll fluorescence-based screen for photosynthetic heat tolerance capable of screening hundreds of plants daily. Through measuring the response of maximum PSII efficiency to increasing temperature, this platform generates data for modelling the PSII-temperature relationship in large populations in a small amount of time. Coefficients from these models (photosynthetic heat tolerance traits) demonstrated high heritabilities across African (Oryza glaberrima) and Asian (Oryza sativa, Bengal Assam Aus Panel) rice diversity sets, highlighting valuable genetic variation accessible for breeding. Genome-wide association studies were performed across both species for these traits, representing the first documented attempt to characterize the genetic basis of photosynthetic heat tolerance in any species to date. A total of 133 candidate genes were highlighted. These were significantly enriched with genes whose predicted roles suggested influence on PSII activity and the response to stress. We discuss the most promising candidates for improving photosynthetic heat tolerance in rice.
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Affiliation(s)
- Jordan K Robson
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, UK
| | - John N Ferguson
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, UK
- Department of Plant Sciences, University of Cambridge, Cambridge, UK
- School of Life Sciences, University of Essex, Colchester, UK
| | - Lorna McAusland
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, UK
| | - Jonathan A Atkinson
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, UK
| | | | - Phillipe Cubry
- Institut de Recherche pour le Developpement, 911 Av. Agropolis, 34394 Montpellier, France
| | - François Sabot
- Institut de Recherche pour le Developpement, 911 Av. Agropolis, 34394 Montpellier, France
| | - Darren M Wells
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, UK
| | - Adam H Price
- Institut de Recherche pour le Developpement, 911 Av. Agropolis, 34394 Montpellier, France
| | - Zoe A Wilson
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, UK
| | - Erik H Murchie
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, UK
- School of Biological Sciences, University of Aberdeen, Aberdeen, UK
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5
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Zhang Y, Tian L, Lu C. Chloroplast gene expression: Recent advances and perspectives. PLANT COMMUNICATIONS 2023; 4:100611. [PMID: 37147800 PMCID: PMC10504595 DOI: 10.1016/j.xplc.2023.100611] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 04/11/2023] [Accepted: 05/01/2023] [Indexed: 05/07/2023]
Abstract
Chloroplasts evolved from an ancient cyanobacterial endosymbiont more than 1.5 billion years ago. During subsequent coevolution with the nuclear genome, the chloroplast genome has remained independent, albeit strongly reduced, with its own transcriptional machinery and distinct features, such as chloroplast-specific innovations in gene expression and complicated post-transcriptional processing. Light activates the expression of chloroplast genes via mechanisms that optimize photosynthesis, minimize photodamage, and prioritize energy investments. Over the past few years, studies have moved from describing phases of chloroplast gene expression to exploring the underlying mechanisms. In this review, we focus on recent advances and emerging principles that govern chloroplast gene expression in land plants. We discuss engineering of pentatricopeptide repeat proteins and its biotechnological effects on chloroplast RNA research; new techniques for characterizing the molecular mechanisms of chloroplast gene expression; and important aspects of chloroplast gene expression for improving crop yield and stress tolerance. We also discuss biological and mechanistic questions that remain to be answered in the future.
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Affiliation(s)
- Yi Zhang
- National Key Laboratory of Wheat Improvement, College of Life Sciences, Shandong Agricultural University, Taian, Shandong 271018, China
| | - Lin Tian
- National Key Laboratory of Wheat Improvement, College of Life Sciences, Shandong Agricultural University, Taian, Shandong 271018, China
| | - Congming Lu
- National Key Laboratory of Wheat Improvement, College of Life Sciences, Shandong Agricultural University, Taian, Shandong 271018, China.
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6
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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.
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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
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7
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Liu K, Lee KP, Duan J, Kim EY, Singh RM, Di M, Meng Z, Kim C. Cooperative role of AtRsmD and AtRimM proteins in modification and maturation of 16S rRNA in plastids. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 114:310-324. [PMID: 36752655 DOI: 10.1111/tpj.16135] [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: 08/12/2022] [Accepted: 02/01/2023] [Indexed: 05/10/2023]
Abstract
Chloroplast pre-ribosomal RNA (rRNA) undergoes maturation, which is critical for ribosome assembly. While the central and auxiliary factors in rRNA maturation have been elucidated in bacteria, their mode of action remains largely unexplored in chloroplasts. We now reveal chloroplast-specific factors involved in 16S rRNA maturation, Arabidopsis thaliana orthologs of bacterial RsmD methyltransferase (AtRsmD) and ribosome maturation factor RimM (AtRimM). A forward genetic screen aimed to find suppressors of the Arabidopsis yellow variegated 2 (var2) mutant defective in photosystem II quality control found a causal nonsense mutation in AtRsmD. The substantially impaired 16S rRNA maturation and translation due to the mutation rescued the leaf variegation phenotype by lowering the levels of chloroplast-encoded proteins, including photosystem II core proteins, in var2. The subsequent co-immunoprecipitation coupled with mass spectrometry analyses and bimolecular fluorescence complementation assay found that AtRsmD interacts with AtRimM. Consistent with their interaction, loss of AtRimM also considerably impairs 16S rRNA maturation with decelerated m2 G915 modification in 16S rRNA catalyzed by AtRsmD. The atrimM mutation also rescued var2 mutant phenotypes, corroborating the functional interplay between AtRsmD and AtRimM towards modification and maturation of 16S rRNA and chloroplast proteostasis. The maturation and post-transcriptional modifications of rRNA are critical to assembling ribosomes responsible for protein translation. Here, we revealed that the cooperative regulation of 16S rRNA m2 G915 modifications by AtRsmD methyltransferase and ribosome assembly factor AtRimM contributes to 16S rRNA maturation, ribosome assembly, and proteostasis in chloroplasts.
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Affiliation(s)
- Kaiwei Liu
- Shanghai Center for Plant Stress Biology, Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
- University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Keun Pyo Lee
- Shanghai Center for Plant Stress Biology, Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Jianli Duan
- Shanghai Center for Plant Stress Biology, Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Eun Yu Kim
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences (CEMPS), Chinese Academy of Sciences, Shanghai, 200032, China
| | - Rahul Mohan Singh
- Shanghai Center for Plant Stress Biology, Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Minghui Di
- Shanghai Center for Plant Stress Biology, Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
- University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Zhuoling Meng
- Shanghai Center for Plant Stress Biology, Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
- University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Chanhong Kim
- Shanghai Center for Plant Stress Biology, Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
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8
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Thagun C, Horii Y, Mori M, Fujita S, Ohtani M, Tsuchiya K, Kodama Y, Odahara M, Numata K. Non-transgenic Gene Modulation via Spray Delivery of Nucleic Acid/Peptide Complexes into Plant Nuclei and Chloroplasts. ACS NANO 2022; 16:3506-3521. [PMID: 35195009 PMCID: PMC8945396 DOI: 10.1021/acsnano.1c07723] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
Genetic engineering of economically important traits in plants is an effective way to improve global welfare. However, introducing foreign DNA molecules into plant genomes to create genetically engineered plants not only requires a lengthy testing period and high developmental costs but also is not well-accepted by the public due to safety concerns about its effects on human and animal health and the environment. Here, we present a high-throughput nucleic acids delivery platform for plants using peptide nanocarriers applied to the leaf surface by spraying. The translocation of sub-micrometer-scale nucleic acid/peptide complexes upon spraying varied depending on the physicochemical characteristics of the peptides and was controlled by a stomata-dependent-uptake mechanism in plant cells. We observed efficient delivery of DNA molecules into plants using cell-penetrating peptide (CPP)-based foliar spraying. Moreover, using foliar spraying, we successfully performed gene silencing by introducing small interfering RNA molecules in plant nuclei via siRNA-CPP complexes and, more importantly, in chloroplasts via our CPP/chloroplast-targeting peptide-mediated delivery system. This technology enables effective nontransgenic engineering of economically important plant traits in agricultural systems.
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Affiliation(s)
- Chonprakun Thagun
- Department
of Material Chemistry, Graduate School of Engineering, Kyoto University, Kyoto-Daigaku-Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Yoko Horii
- Biomacromolecules
Research Team, RIKEN Center for Sustainable
Resource Science, 2-1 Hirosawa, Wako-shi, Saitama 351-0198, Japan
| | - Maai Mori
- Biomacromolecules
Research Team, RIKEN Center for Sustainable
Resource Science, 2-1 Hirosawa, Wako-shi, Saitama 351-0198, Japan
| | - Seiya Fujita
- Department
of Material Chemistry, Graduate School of Engineering, Kyoto University, Kyoto-Daigaku-Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Misato Ohtani
- Department
of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8562, Japan
| | - Kousuke Tsuchiya
- Department
of Material Chemistry, Graduate School of Engineering, Kyoto University, Kyoto-Daigaku-Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
- Biomacromolecules
Research Team, RIKEN Center for Sustainable
Resource Science, 2-1 Hirosawa, Wako-shi, Saitama 351-0198, Japan
| | - Yutaka Kodama
- Biomacromolecules
Research Team, RIKEN Center for Sustainable
Resource Science, 2-1 Hirosawa, Wako-shi, Saitama 351-0198, Japan
- Center
for Bioscience Research and Education, Utsunomiya
University, Tochigi 321-8505, Japan
| | - Masaki Odahara
- Biomacromolecules
Research Team, RIKEN Center for Sustainable
Resource Science, 2-1 Hirosawa, Wako-shi, Saitama 351-0198, Japan
- (Ma.O.)
| | - Keiji Numata
- Department
of Material Chemistry, Graduate School of Engineering, Kyoto University, Kyoto-Daigaku-Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
- Biomacromolecules
Research Team, RIKEN Center for Sustainable
Resource Science, 2-1 Hirosawa, Wako-shi, Saitama 351-0198, Japan
- (K.N.)
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9
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Zhang J, Hess WR, Zhang C. "Life is short, and art is long": RNA degradation in cyanobacteria and model bacteria. MLIFE 2022; 1:21-39. [PMID: 38818322 PMCID: PMC10989914 DOI: 10.1002/mlf2.12015] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Revised: 03/03/2022] [Accepted: 03/03/2022] [Indexed: 06/01/2024]
Abstract
RNA turnover plays critical roles in the regulation of gene expression and allows cells to respond rapidly to environmental changes. In bacteria, the mechanisms of RNA turnover have been extensively studied in the models Escherichia coli and Bacillus subtilis, but not much is known in other bacteria. Cyanobacteria are a diverse group of photosynthetic organisms that have great potential for the sustainable production of valuable products using CO2 and solar energy. A better understanding of the regulation of RNA decay is important for both basic and applied studies of cyanobacteria. Genomic analysis shows that cyanobacteria have more than 10 ribonucleases and related proteins in common with E. coli and B. subtilis, and only a limited number of them have been experimentally investigated. In this review, we summarize the current knowledge about these RNA-turnover-related proteins in cyanobacteria. Although many of them are biochemically similar to their counterparts in E. coli and B. subtilis, they appear to have distinct cellular functions, suggesting a different mechanism of RNA turnover regulation in cyanobacteria. The identification of new players involved in the regulation of RNA turnover and the elucidation of their biological functions are among the future challenges in this field.
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Affiliation(s)
- Ju‐Yuan Zhang
- State Key Laboratory of Freshwater Ecology and Biotechnology and Key Laboratory of Algal Biology, Institute of HydrobiologyChinese Academy of SciencesWuhanChina
| | - Wolfgang R. Hess
- Genetics and Experimental Bioinformatics, Faculty of BiologyUniversity of FreiburgFreiburgGermany
| | - Cheng‐Cai Zhang
- State Key Laboratory of Freshwater Ecology and Biotechnology and Key Laboratory of Algal Biology, Institute of HydrobiologyChinese Academy of SciencesWuhanChina
- Institut WUT‐AMUAix‐Marseille University and Wuhan University of TechnologyWuhanChina
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10
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RNase III, Ribosome Biogenesis and Beyond. Microorganisms 2021; 9:microorganisms9122608. [PMID: 34946208 PMCID: PMC8708148 DOI: 10.3390/microorganisms9122608] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Revised: 12/12/2021] [Accepted: 12/15/2021] [Indexed: 12/17/2022] Open
Abstract
The ribosome is the universal catalyst for protein synthesis. Despite extensive studies, the diversity of structures and functions of this ribonucleoprotein is yet to be fully understood. Deciphering the biogenesis of the ribosome in a step-by-step manner revealed that this complexity is achieved through a plethora of effectors involved in the maturation and assembly of ribosomal RNAs and proteins. Conserved from bacteria to eukaryotes, double-stranded specific RNase III enzymes play a large role in the regulation of gene expression and the processing of ribosomal RNAs. In this review, we describe the canonical role of RNase III in the biogenesis of the ribosome comparing conserved and unique features from bacteria to eukaryotes. Furthermore, we report additional roles in ribosome biogenesis re-enforcing the importance of RNase III.
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11
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CAF Proteins Help SOT1 Regulate the Stability of Chloroplast ndhA Transcripts. Int J Mol Sci 2021; 22:ijms222312639. [PMID: 34884441 PMCID: PMC8657633 DOI: 10.3390/ijms222312639] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Revised: 11/20/2021] [Accepted: 11/20/2021] [Indexed: 12/26/2022] Open
Abstract
Protein-mediated RNA stabilization plays profound roles in chloroplast gene expression. Genetic studies have indicated that chloroplast ndhA transcripts, encoding a key subunit of the NADH dehydrogenase-like complex that mediates photosystem I cyclic electron transport and facilitates chlororespiration, are stabilized by PPR53 and its orthologs, but the underlying mechanisms are unclear. Here, we report that CHLOROPLAST RNA SPLICING 2 (CRS2)-ASSOCIATED FACTOR (CAF) proteins activate SUPPRESSOR OF THYLAKOID FORMATION 1 (SOT1), an ortholog of PPR53 in Arabidopsis thaliana, enhancing their affinity for the 5' ends of ndhA transcripts to stabilize these molecules while inhibiting the RNA endonuclease activity of the SOT1 C-terminal SMR domain. In addition, we established that SOT1 improves the splicing efficiency of ndhA by facilitating the association of CAF2 with the ndhA intron, which may be due to the SOT1-mediated stability of the ndhA transcripts. Our findings shed light on the importance of PPR protein interaction partners in moderating RNA metabolism.
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12
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Guilcher M, Liehrmann A, Seyman C, Blein T, Rigaill G, Castandet B, Delannoy E. Full Length Transcriptome Highlights the Coordination of Plastid Transcript Processing. Int J Mol Sci 2021; 22:ijms222011297. [PMID: 34681956 PMCID: PMC8537030 DOI: 10.3390/ijms222011297] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2021] [Revised: 10/08/2021] [Accepted: 10/11/2021] [Indexed: 11/29/2022] Open
Abstract
Plastid gene expression involves many post-transcriptional maturation steps resulting in a complex transcriptome composed of multiple isoforms. Although short-read RNA-Seq has considerably improved our understanding of the molecular mechanisms controlling these processes, it is unable to sequence full-length transcripts. This information is crucial, however, when it comes to understanding the interplay between the various steps of plastid gene expression. Here, we describe a protocol to study the plastid transcriptome using nanopore sequencing. In the leaf of Arabidopsis thaliana, with about 1.5 million strand-specific reads mapped to the chloroplast genome, we could recapitulate most of the complexity of the plastid transcriptome (polygenic transcripts, multiple isoforms associated with post-transcriptional processing) using virtual Northern blots. Even if the transcripts longer than about 2500 nucleotides were missing, the study of the co-occurrence of editing and splicing events identified 42 pairs of events that were not occurring independently. This study also highlighted a preferential chronology of maturation events with splicing happening after most sites were edited.
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Affiliation(s)
- Marine Guilcher
- Institute of Plant Sciences Paris-Saclay (IPS2), Université Paris-Saclay, CNRS, INRAE, Université Evry, 91405 Orsay, France; (M.G.); (A.L.); (T.B.); (G.R.); (B.C.)
- Institute of Plant Sciences Paris-Saclay (IPS2), Université de Paris, CNRS, INRAE, 91405 Orsay, France
| | - Arnaud Liehrmann
- Institute of Plant Sciences Paris-Saclay (IPS2), Université Paris-Saclay, CNRS, INRAE, Université Evry, 91405 Orsay, France; (M.G.); (A.L.); (T.B.); (G.R.); (B.C.)
- Institute of Plant Sciences Paris-Saclay (IPS2), Université de Paris, CNRS, INRAE, 91405 Orsay, France
- Laboratoire de Mathématiques et de Modélisation d’Evry (LaMME), Université d’Evry-Val-d’Essonne, UMR CNRS 8071, ENSIIE, USC INRAE, 91000 Evry, France;
| | - Chloé Seyman
- Laboratoire de Mathématiques et de Modélisation d’Evry (LaMME), Université d’Evry-Val-d’Essonne, UMR CNRS 8071, ENSIIE, USC INRAE, 91000 Evry, France;
| | - Thomas Blein
- Institute of Plant Sciences Paris-Saclay (IPS2), Université Paris-Saclay, CNRS, INRAE, Université Evry, 91405 Orsay, France; (M.G.); (A.L.); (T.B.); (G.R.); (B.C.)
- Institute of Plant Sciences Paris-Saclay (IPS2), Université de Paris, CNRS, INRAE, 91405 Orsay, France
| | - Guillem Rigaill
- Institute of Plant Sciences Paris-Saclay (IPS2), Université Paris-Saclay, CNRS, INRAE, Université Evry, 91405 Orsay, France; (M.G.); (A.L.); (T.B.); (G.R.); (B.C.)
- Institute of Plant Sciences Paris-Saclay (IPS2), Université de Paris, CNRS, INRAE, 91405 Orsay, France
- Laboratoire de Mathématiques et de Modélisation d’Evry (LaMME), Université d’Evry-Val-d’Essonne, UMR CNRS 8071, ENSIIE, USC INRAE, 91000 Evry, France;
| | - Benoit Castandet
- Institute of Plant Sciences Paris-Saclay (IPS2), Université Paris-Saclay, CNRS, INRAE, Université Evry, 91405 Orsay, France; (M.G.); (A.L.); (T.B.); (G.R.); (B.C.)
- Institute of Plant Sciences Paris-Saclay (IPS2), Université de Paris, CNRS, INRAE, 91405 Orsay, France
| | - Etienne Delannoy
- Institute of Plant Sciences Paris-Saclay (IPS2), Université Paris-Saclay, CNRS, INRAE, Université Evry, 91405 Orsay, France; (M.G.); (A.L.); (T.B.); (G.R.); (B.C.)
- Institute of Plant Sciences Paris-Saclay (IPS2), Université de Paris, CNRS, INRAE, 91405 Orsay, France
- Correspondence:
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13
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Boher P, Soler M, Fernández-Piñán S, Torrent X, Müller SY, Kelly KA, Serra O, Figueras M. Silencing of StRIK in potato suggests a role in periderm related to RNA processing and stress. BMC PLANT BIOLOGY 2021; 21:409. [PMID: 34493224 PMCID: PMC8424952 DOI: 10.1186/s12870-021-03141-z] [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: 01/21/2021] [Accepted: 07/06/2021] [Indexed: 06/13/2023]
Abstract
BACKGROUND The periderm is a protective barrier crucial for land plant survival, but little is known about genetic factors involved in its development and regulation. Using a transcriptomic approach in the cork oak (Q. suber) periderm, we previously identified an RS2-INTERACTING KH PROTEIN (RIK) homologue of unknown function containing a K homology (KH)-domain RNA-binding protein, as a regulatory candidate gene in the periderm. RESULTS To gain insight into the function of RIK in the periderm, potato (S. tuberosum) tuber periderm was used as a model: the full-length coding sequence of RIK, hereafter referred to as StRIK, was isolated, the transcript profile analyzed and gene silencing in potato performed to analyze the silencing effects on periderm anatomy and transcriptome. The StRIK transcript accumulated in all vegetative tissues studied, including periderm and other suberized tissues such as root and also in wounded tissues. Downregulation of StRIK in potato by RNA interference (StRIK-RNAi) did not show any obvious effects on tuber periderm anatomy but, unlike Wild type, transgenic plants flowered. Global transcript profiling of the StRIK-RNAi periderm did show altered expression of genes associated with RNA metabolism, stress and signaling, mirroring the biological processes found enriched within the in silico co-expression network of the Arabidopsis orthologue. CONCLUSIONS The ubiquitous expression of StRIK transcript, the flower associated phenotype and the differential expression of StRIK-RNAi periderm point out to a general regulatory role of StRIK in diverse plant developmental processes. The transcriptome analysis suggests that StRIK might play roles in RNA maturation and stress response in the periderm.
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Affiliation(s)
- Pau Boher
- Laboratori del Suro, Biology Department, Universitat de Girona, Campus Montilivi, E-17071 Girona, Catalonia Spain
| | - Marçal Soler
- Laboratori del Suro, Biology Department, Universitat de Girona, Campus Montilivi, E-17071 Girona, Catalonia Spain
| | - Sandra Fernández-Piñán
- Laboratori del Suro, Biology Department, Universitat de Girona, Campus Montilivi, E-17071 Girona, Catalonia Spain
| | - Xènia Torrent
- Laboratori del Suro, Biology Department, Universitat de Girona, Campus Montilivi, E-17071 Girona, Catalonia Spain
| | - Sebastian Y. Müller
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge, CB2 3EA UK
| | - Krystyna A. Kelly
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge, CB2 3EA UK
| | - Olga Serra
- Laboratori del Suro, Biology Department, Universitat de Girona, Campus Montilivi, E-17071 Girona, Catalonia Spain
| | - Mercè Figueras
- Laboratori del Suro, Biology Department, Universitat de Girona, Campus Montilivi, E-17071 Girona, Catalonia Spain
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14
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Michel EJS, Ponnala L, van Wijk KJ. Tissue-type specific accumulation of the plastoglobular proteome, transcriptional networks, and plastoglobular functions. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:4663-4679. [PMID: 33884419 DOI: 10.1093/jxb/erab175] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Accepted: 04/16/2021] [Indexed: 05/28/2023]
Abstract
Plastoglobules are dynamic protein-lipid microcompartments in plastids enriched for isoprenoid-derived metabolites. Chloroplast plastoglobules support formation, remodeling, and controlled dismantling of thylakoids during developmental transitions and environmental responses. However, the specific molecular functions of most plastoglobule proteins are still poorly understood. This review harnesses recent co-mRNA expression data from combined microarray and RNA-seq information in ATTED-II on an updated inventory of 34 PG proteins, as well as proteomics data across 30 Arabidopsis tissue types from ATHENA. Hierarchical clustering based on relative abundance for the plastoglobule proteins across non-photosynthetic and photosynthetic tissue types showed their coordinated protein accumulation across Arabidopsis parts, tissue types, development, and senescence. Evaluation of mRNA-based forced networks at different coefficient thresholds identified a central hub with seven plastoglobule proteins and four peripheral modules. Enrichment of specific nuclear transcription factors (e.g. Golden2-like) and support for crosstalk between plastoglobules and the plastid gene expression was observed, and specific ABC1 kinases appear part of a light signaling network. Examples of other specific findings are that FBN7b is involved with upstream steps of tetrapyrrole biosynthesis and that ABC1K9 is involved in starch metabolism. This review provides new insights into the functions of plastoglobule proteins and an improved framework for experimental studies.
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Affiliation(s)
- Elena J S Michel
- School of Integrative Plant Sciences (SIPS), Section of Plant Biology, Cornell University, Ithaca, NY 14853, USA
| | | | - Klaas J van Wijk
- School of Integrative Plant Sciences (SIPS), Section of Plant Biology, Cornell University, Ithaca, NY 14853, USA
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15
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Wu S, Wang Y, Wang J, Li X, Li J, Ye K. Profiling of RNA ribose methylation in Arabidopsis thaliana. Nucleic Acids Res 2021; 49:4104-4119. [PMID: 33784398 PMCID: PMC8053127 DOI: 10.1093/nar/gkab196] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 02/20/2021] [Accepted: 03/10/2021] [Indexed: 11/30/2022] Open
Abstract
Eukaryotic rRNAs and snRNAs are decorated with abundant 2′-O-methylated nucleotides (Nm) that are predominantly synthesized by box C/D snoRNA-guided enzymes. In the model plant Arabidopsis thaliana, C/D snoRNAs have been well categorized, but there is a lack of systematic mapping of Nm. Here, we applied RiboMeth-seq to profile Nm in cytoplasmic, chloroplast and mitochondrial rRNAs and snRNAs. We identified 111 Nm in cytoplasmic rRNAs and 19 Nm in snRNAs and assigned guide for majority of the detected sites using an updated snoRNA list. At least four sites are directed by guides with multiple specificities as shown in yeast. We found that C/D snoRNAs frequently form extra pairs with nearby sequences of methylation sites, potentially facilitating the substrate binding. Chloroplast and mitochondrial rRNAs contain five almost identical methylation sites, including two novel sites mediating ribosomal subunit joining. Deletion of FIB1 or FIB2 gene reduced the accumulation of C/D snoRNA and rRNA methylation with FIB1 playing a bigger role in methylation. Our data reveal the comprehensive 2′-O-methylation maps for Arabidopsis rRNAs and snRNAs and would facilitate study of their function and biosynthesis.
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Affiliation(s)
- Songlin Wu
- Key Laboratory of RNA Biology, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yuqiu Wang
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences, Peking University, Beijing 100871, China
| | - Jiayin Wang
- Key Laboratory of RNA Biology, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xilong Li
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, 100101 Beijing, China
| | - Jiayang Li
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, 100101 Beijing, China
| | - Keqiong Ye
- Key Laboratory of RNA Biology, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing 100049, China
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16
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Méteignier LV, Ghandour R, Zimmerman A, Kuhn L, Meurer J, Zoschke R, Hammani K. Arabidopsis mTERF9 protein promotes chloroplast ribosomal assembly and translation by establishing ribonucleoprotein interactions in vivo. Nucleic Acids Res 2021; 49:1114-1132. [PMID: 33398331 PMCID: PMC7826268 DOI: 10.1093/nar/gkaa1244] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2020] [Revised: 12/07/2020] [Accepted: 12/13/2020] [Indexed: 12/13/2022] Open
Abstract
The mitochondrial transcription termination factor proteins are nuclear-encoded nucleic acid binders defined by degenerate tandem helical-repeats of ∼30 amino acids. They are found in metazoans and plants where they localize in organelles. In higher plants, the mTERF family comprises ∼30 members and several of these have been linked to plant development and response to abiotic stress. However, knowledge of the molecular basis underlying these physiological effects is scarce. We show that the Arabidopsis mTERF9 protein promotes the accumulation of the 16S and 23S rRNAs in chloroplasts, and interacts predominantly with the 16S rRNA in vivo and in vitro. Furthermore, mTERF9 is found in large complexes containing ribosomes and polysomes in chloroplasts. The comprehensive analysis of mTERF9 in vivo protein interactome identified many subunits of the 70S ribosome whose assembly is compromised in the null mterf9 mutant, putative ribosome biogenesis factors and CPN60 chaperonins. Protein interaction assays in yeast revealed that mTERF9 directly interact with these proteins. Our data demonstrate that mTERF9 integrates protein-protein and protein-RNA interactions to promote chloroplast ribosomal assembly and translation. Besides extending our knowledge of mTERF functional repertoire in plants, these findings provide an important insight into the chloroplast ribosome biogenesis.
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Affiliation(s)
- Louis-Valentin Méteignier
- Institut de Biologie Moléculaire des Plantes, Centre National de la Recherche Scientifique (CNRS), Université de Strasbourg, 12 rue du Général Zimmer, 67084 Strasbourg, France
| | - Rabea Ghandour
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
| | - Aude Zimmerman
- Institut de Biologie Moléculaire des Plantes, Centre National de la Recherche Scientifique (CNRS), Université de Strasbourg, 12 rue du Général Zimmer, 67084 Strasbourg, France
| | - Lauriane Kuhn
- Plateforme protéomique Strasbourg Esplanade FRC1589 du CNRS, Université de Strasbourg, 15 rue René Descartes, 67084 Strasbourg, France
| | - Jörg Meurer
- Plant Sciences, Faculty of Biology, Ludwig-Maximilians-University Munich, Großhaderner Street 2-4, 82152 Planegg-Martinsried, Germany
| | - Reimo Zoschke
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
| | - Kamel Hammani
- Institut de Biologie Moléculaire des Plantes, Centre National de la Recherche Scientifique (CNRS), Université de Strasbourg, 12 rue du Général Zimmer, 67084 Strasbourg, France
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17
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Wang X, Yang Z, Zhang Y, Zhou W, Zhang A, Lu C. Pentatricopeptide repeat protein PHOTOSYSTEM I BIOGENESIS FACTOR2 is required for splicing of ycf3. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2020; 62:1741-1761. [PMID: 32250043 DOI: 10.1111/jipb.12936] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2019] [Accepted: 03/27/2020] [Indexed: 05/04/2023]
Abstract
To gain a better understanding of the molecular mechanisms of photosystem I (PSI) biogenesis, we characterized the Arabidopsis thaliana photosystem I biogenesis factor 2 (pbf2) mutant, which lacks PSI complex. PBF2 encodes a P-class pentatricopeptide repeat (PPR) protein. In the pbf2 mutants, we observed a striking decrease in the transcript level of only one gene, the chloroplast gene ycf3, which is essential for PSI assembly. Further analysis of ycf3 transcripts showed that PBF2 is specifically required for the splicing of ycf3 intron 1. Computational prediction of binding sequences and electrophoretic mobility shift assays reveal that PBF2 specifically binds to a sequence in ycf3 intron 1. Moreover, we found that PBF2 interacted with two general factors for group II intron splicing CHLOROPLAST RNA SPLICING2-ASSOCIATED FACTOR1 (CAF1) and CAF2, and facilitated the association of these two factors with ycf3 intron 1. Our results suggest that PBF2 is specifically required for the splicing of ycf3 intron 1 through cooperating with CAF1 and CAF2. Our results also suggest that additional proteins are required to contribute to the specificity of CAF-dependent group II intron splicing.
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Affiliation(s)
- Xuemei Wang
- Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zhipan Yang
- Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yi Zhang
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, 271018, China
| | - Wen Zhou
- Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Aihong Zhang
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, 271018, China
| | - Congming Lu
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, 271018, China
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18
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MacIntosh GC, Castandet B. Organellar and Secretory Ribonucleases: Major Players in Plant RNA Homeostasis. PLANT PHYSIOLOGY 2020; 183:1438-1452. [PMID: 32513833 PMCID: PMC7401137 DOI: 10.1104/pp.20.00076] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Accepted: 05/31/2020] [Indexed: 05/05/2023]
Abstract
Organellar and secretory RNases, associated with different cellular compartments, are essential to maintain cellular homeostasis during development and in stress responses.
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Affiliation(s)
- Gustavo C MacIntosh
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, Iowa, 50011
| | - Benoît Castandet
- Université Paris-Saclay, Centre National de la Recherche Scientifique, Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement, Univ Evry, Institute of Plant Sciences Paris-Saclay (IPS2), 91405, Orsay, France
- Université de Paris, Centre National de la Recherche Scientifique, Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement, Institute of Plant Sciences Paris-Saclay (IPS2), 91405, Orsay, France
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19
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Castandet B, Germain A, Hotto AM, Stern DB. Systematic sequencing of chloroplast transcript termini from Arabidopsis thaliana reveals >200 transcription initiation sites and the extensive imprints of RNA-binding proteins and secondary structures. Nucleic Acids Res 2020; 47:11889-11905. [PMID: 31732725 PMCID: PMC7145512 DOI: 10.1093/nar/gkz1059] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Revised: 10/02/2019] [Accepted: 11/05/2019] [Indexed: 12/23/2022] Open
Abstract
Chloroplast transcription requires numerous quality control steps to generate the complex but selective mixture of accumulating RNAs. To gain insight into how this RNA diversity is achieved and regulated, we systematically mapped transcript ends by developing a protocol called Terminome-seq. Using Arabidopsis thaliana as a model, we catalogued >215 primary 5′ ends corresponding to transcription start sites (TSS), as well as 1628 processed 5′ ends and 1299 3′ ends. While most termini were found in intergenic regions, numerous abundant termini were also found within coding regions and introns, including several major TSS at unexpected locations. A consistent feature was the clustering of both 5′ and 3′ ends, contrasting with the prevailing description of discrete 5′ termini, suggesting an imprecision of the transcription and/or RNA processing machinery. Numerous termini correlated with the extremities of small RNA footprints or predicted stem-loop structures, in agreement with the model of passive RNA protection. Terminome-seq was also implemented for pnp1–1, a mutant lacking the processing enzyme polynucleotide phosphorylase. Nearly 2000 termini were altered in pnp1–1, revealing a dominant role in shaping the transcriptome. In summary, Terminome-seq permits precise delineation of the roles and regulation of the many factors involved in organellar transcriptome quality control.
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Affiliation(s)
- Benoît Castandet
- Boyce Thompson Institute, Ithaca, NY 14853, USA.,Institut des Sciences des Plantes de Paris Saclay (IPS2), UEVE, INRA, CNRS, Univ. Paris Sud, Université Paris-Saclay, F-91192 Gif sur Yvette, France.,Université de Paris, IPS2, F-91192 Gif sur Yvette, France
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20
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Plant Ribonuclease J: An Essential Player in Maintaining Chloroplast RNA Quality Control for Gene Expression. PLANTS 2020; 9:plants9030334. [PMID: 32151111 PMCID: PMC7154860 DOI: 10.3390/plants9030334] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Revised: 03/02/2020] [Accepted: 03/03/2020] [Indexed: 12/27/2022]
Abstract
RNA quality control is an indispensable but poorly understood process that enables organisms to distinguish functional RNAs from nonfunctional or inhibitory ones. In chloroplasts, whose gene expression activities are required for photosynthesis, retrograde signaling, and plant development, RNA quality control is of paramount importance, as transcription is relatively unregulated. The functional RNA population is distilled from this initial transcriptome by a combination of RNA-binding proteins and ribonucleases. One of the key enzymes is RNase J, a 5′→3′ exoribonuclease and an endoribonuclease that has been shown to trim 5′ RNA termini and eliminate deleterious antisense RNA. In the absence of RNase J, embryo development cannot be completed. Land plant RNase J contains a highly conserved C-terminal domain that is found in GT-1 DNA-binding transcription factors and is not present in its bacterial, archaeal, and algal counterparts. The GT-1 domain may confer specificity through DNA and/or RNA binding and/or protein–protein interactions and thus be an element in the mechanisms that identify target transcripts among diverse RNA populations. Further understanding of chloroplast RNA quality control relies on discovering how RNase J is regulated and how its specificity is imparted.
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21
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Iost I, Chabas S, Darfeuille F. Maturation of atypical ribosomal RNA precursors in Helicobacter pylori. Nucleic Acids Res 2019; 47:5906-5921. [PMID: 31006803 PMCID: PMC6582327 DOI: 10.1093/nar/gkz258] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Revised: 03/28/2019] [Accepted: 04/18/2019] [Indexed: 01/01/2023] Open
Abstract
In most bacteria, ribosomal RNA is transcribed as a single polycistronic precursor that is first processed by RNase III. This double-stranded specific RNase cleaves two large stems flanking the 23S and 16S rRNA mature sequences, liberating three 16S, 23S and 5S rRNA precursors, which are further processed by other ribonucleases. Here, we investigate the rRNA maturation pathway of the human gastric pathogen Helicobacter pylori. This bacterium has an unusual arrangement of its rRNA genes, the 16S rRNA gene being separated from a 23S-5S rRNA cluster. We show that RNase III also initiates processing in this organism, by cleaving two typical stem structures encompassing 16S and 23S rRNAs and an atypical stem–loop located upstream of the 5S rRNA. Deletion of RNase III leads to the accumulation of a large 23S-5S precursor that is found in polysomes, suggesting that it can function in translation. Finally, we characterize a cis-encoded antisense RNA overlapping the leader of the 23S-5S rRNA precursor. We present evidence that this antisense RNA interacts with this precursor, forming an intermolecular complex that is cleaved by RNase III. This pairing induces additional specific cleavages of the rRNA precursor coupled with a rapid degradation of the antisense RNA.
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Affiliation(s)
- Isabelle Iost
- ARNA Laboratory, Inserm U1212, CNRS UMR 5320, Université de Bordeaux, France
| | - Sandrine Chabas
- ARNA Laboratory, Inserm U1212, CNRS UMR 5320, Université de Bordeaux, France
| | - Fabien Darfeuille
- ARNA Laboratory, Inserm U1212, CNRS UMR 5320, Université de Bordeaux, France
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22
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Dorrell RG, Nisbet RER, Barbrook AC, Rowden SJL, Howe CJ. Integrated Genomic and Transcriptomic Analysis of the Peridinin Dinoflagellate Amphidinium carterae Plastid. Protist 2019; 170:358-373. [PMID: 31415953 DOI: 10.1016/j.protis.2019.06.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Revised: 06/10/2019] [Accepted: 06/14/2019] [Indexed: 01/17/2023]
Abstract
The plastid genomes of peridinin-containing dinoflagellates are highly unusual, possessing very few genes, which are located on small chromosomal elements termed "minicircles". These minicircles may contain genes, or no recognisable coding information. Transcripts produced from minicircles may undergo unusual processing events, such as the addition of a 3' poly(U) tail. To date, little is known about the genetic or transcriptional diversity of non-coding sequences in peridinin dinoflagellate plastids. These sequences include empty minicircles, and regions of non-coding DNA in coding minicircles. Here, we present an integrated plastid genome and transcriptome for the model peridinin dinoflagellate Amphidinium carterae, identifying a previously undescribed minicircle. We also profile transcripts covering non-coding regions of the psbA and petB/atpA minicircles. We present evidence that antisense transcripts are produced within the A. carterae plastid, but show that these transcripts undergo different end cleavage events from sense transcripts, and do not receive 3' poly(U) tails. The difference in processing events between sense and antisense transcripts may enable the removal of non-coding transcripts from peridinin dinoflagellate plastid transcript pools.
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Affiliation(s)
| | - R Ellen R Nisbet
- Department of Biochemistry, University of Cambridge, United Kingdom
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23
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Zhang Y, Lu C. The Enigmatic Roles of PPR-SMR Proteins in Plants. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2019; 6:1900361. [PMID: 31380188 PMCID: PMC6662315 DOI: 10.1002/advs.201900361] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Revised: 04/03/2019] [Indexed: 05/21/2023]
Abstract
The pentatricopeptide repeat (PPR) protein family, with more than 400 members, is one of the largest and most diverse protein families in land plants. A small subset of PPR proteins contain a C-terminal small MutS-related (SMR) domain. Although there are relatively few PPR-SMR proteins, they play essential roles in embryo development, chloroplast biogenesis and gene expression, and plastid-to-nucleus retrograde signaling. Here, recent advances in understanding the roles of PPR-SMR proteins and the SMR domain based on a combination of genetic, biochemical, and physiological analyses are described. In addition, the potential of the PPR-SMR protein SOT1 to serve as a tool for RNA manipulation is highlighted.
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Affiliation(s)
- Yi Zhang
- State Key Laboratory of Crop BiologyCollege of Life SciencesShandong Agricultural UniversityTaianShandong271018P. R. China
| | - Congming Lu
- State Key Laboratory of Crop BiologyCollege of Life SciencesShandong Agricultural UniversityTaianShandong271018P. R. China
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24
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Bechhofer DH, Deutscher MP. Bacterial ribonucleases and their roles in RNA metabolism. Crit Rev Biochem Mol Biol 2019; 54:242-300. [PMID: 31464530 PMCID: PMC6776250 DOI: 10.1080/10409238.2019.1651816] [Citation(s) in RCA: 109] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Revised: 07/22/2019] [Accepted: 07/31/2019] [Indexed: 12/16/2022]
Abstract
Ribonucleases (RNases) are mediators in most reactions of RNA metabolism. In recent years, there has been a surge of new information about RNases and the roles they play in cell physiology. In this review, a detailed description of bacterial RNases is presented, focusing primarily on those from Escherichia coli and Bacillus subtilis, the model Gram-negative and Gram-positive organisms, from which most of our current knowledge has been derived. Information from other organisms is also included, where relevant. In an extensive catalog of the known bacterial RNases, their structure, mechanism of action, physiological roles, genetics, and possible regulation are described. The RNase complement of E. coli and B. subtilis is compared, emphasizing the similarities, but especially the differences, between the two. Included are figures showing the three major RNA metabolic pathways in E. coli and B. subtilis and highlighting specific steps in each of the pathways catalyzed by the different RNases. This compilation of the currently available knowledge about bacterial RNases will be a useful tool for workers in the RNA field and for others interested in learning about this area.
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Affiliation(s)
- David H. Bechhofer
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Murray P. Deutscher
- Department of Biochemistry and Molecular Biology, University of Miami Miller School of Medicine, Miami, FL, USA
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25
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Abstract
RNases are key enzymes involved in RNA maturation and degradation. Although they play a crucial role in all domains of life, bacteria, archaea, and eukaryotes have evolved with their own sets of RNases and proteins modulating their activities. In bacteria, these enzymes allow modulation of gene expression to adapt to rapidly changing environments. Today, >20 RNases have been identified in both Escherichia coli and Bacillus subtilis, the paradigms of the Gram-negative and Gram-positive bacteria, respectively. However, only a handful of these enzymes are common to these two organisms and some of them are essential to only one. Moreover, although sets of RNases can be very similar in closely related bacteria such as the Firmicutes Staphylococcus aureus and B. subtilis, the relative importance of individual enzymes in posttranscriptional regulation in these organisms varies. In this review, we detail the role of the main RNases involved in RNA maturation and degradation in Gram-positive bacteria, with an emphasis on the roles of RNase J1, RNase III, and RNase Y. We also discuss how other proteins such as helicases can modulate the RNA-degradation activities of these enzymes.
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26
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RNA-stabilization factors in chloroplasts of vascular plants. Essays Biochem 2018; 62:51-64. [PMID: 29453323 PMCID: PMC5897788 DOI: 10.1042/ebc20170061] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Revised: 01/02/2018] [Accepted: 01/12/2018] [Indexed: 12/23/2022]
Abstract
In contrast to the cyanobacterial ancestor, chloroplast gene expression is predominantly governed on the post-transcriptional level such as modifications of the RNA sequence, decay rates, exo- and endonucleolytic processing as well as translational events. The concerted function of numerous chloroplast RNA-binding proteins plays a fundamental and often essential role in all these processes but our understanding of their impact in regulation of RNA degradation is only at the beginning. Moreover, metabolic processes and post-translational modifications are thought to affect the function of RNA protectors. These protectors contain a variety of different RNA-recognition motifs, which often appear as multiple repeats. They are required for normal plant growth and development as well as diverse stress responses and acclimation processes. Interestingly, most of the protectors are plant specific which reflects a fast-evolving RNA metabolism in chloroplasts congruent with the diverging RNA targets. Here, we mainly focused on the characteristics of known chloroplast RNA-binding proteins that protect exonuclease-sensitive sites in chloroplasts of vascular plants.
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27
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Gordon GC, Cameron JC, Pfleger BF. Distinct and redundant functions of three homologs of RNase III in the cyanobacterium Synechococcus sp. strain PCC 7002. Nucleic Acids Res 2018; 46:1984-1997. [PMID: 29373746 PMCID: PMC5829567 DOI: 10.1093/nar/gky041] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Revised: 01/11/2018] [Accepted: 01/16/2018] [Indexed: 12/19/2022] Open
Abstract
RNase III is a ribonuclease that recognizes and cleaves double-stranded RNA. Across bacteria, RNase III is involved in rRNA maturation, CRISPR RNA maturation, controlling gene expression, and turnover of messenger RNAs. Many organisms have only one RNase III while others have both a full-length RNase III and another version that lacks a double-stranded RNA binding domain (mini-III). The genome of the cyanobacterium Synechococcus sp. strain PCC 7002 (PCC 7002) encodes three homologs of RNase III, two full-length and one mini-III, that are not essential even when deleted in combination. To discern if each enzyme had distinct responsibilities, we collected and sequenced global RNA samples from the wild type strain, the single, double, and triple RNase III mutants. Approximately 20% of genes were differentially expressed in various mutants with some operons and regulons showing complex changes in expression levels between mutants. Two RNase III's had a role in 23S rRNA maturation and the third was involved in copy number regulation one of six native plasmids. In vitro, purified RNase III enzymes were capable of cleaving some of the known Escherichia coli RNase III target sequences, highlighting the remarkably conserved substrate specificity between organisms yet complex regulation of gene expression.
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Affiliation(s)
- Gina C Gordon
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, WI 53706, USA
- Microbiology Doctoral Training Program, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Jeffrey C Cameron
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Brian F Pfleger
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, WI 53706, USA
- Microbiology Doctoral Training Program, University of Wisconsin-Madison, Madison, WI 53706, USA
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28
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Abstract
Since its first use in plants in 2007, high-throughput RNA sequencing (RNA-Seq) has generated a vast amount of data for both model and nonmodel species. Organellar transcriptomes, however, are virtually always overlooked at the data analysis step. We therefore developed ChloroSeq, a bioinformatic pipeline aimed at facilitating the systematic analysis of chloroplast RNA metabolism, and we provide here a step-by-step user's manual. Following the alignment of quality-controlled data to the genome of interest, ChloroSeq measures genome expression level along with splicing and RNA editing efficiencies. When used in combination with the Tuxedo suite (TopHat and Cufflinks), ChloroSeq allows the simultaneous analysis of organellar and nuclear transcriptomes, opening the way to a better understanding of nucleus-organelle cross talk. We also describe the use of R commands to produce publication-quality figures based on ChloroSeq outputs. The effectiveness of the pipeline is illustrated through analysis of an RNA-Seq dataset covering the transition from growth to maturation to senescence of Arabidopsis thaliana leaves.
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29
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Cavaiuolo M, Kuras R, Wollman F, Choquet Y, Vallon O. Small RNA profiling in Chlamydomonas: insights into chloroplast RNA metabolism. Nucleic Acids Res 2017; 45:10783-10799. [PMID: 28985404 PMCID: PMC5737564 DOI: 10.1093/nar/gkx668] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2017] [Revised: 07/18/2017] [Accepted: 07/28/2017] [Indexed: 12/20/2022] Open
Abstract
In Chlamydomonas reinhardtii, regulation of chloroplast gene expression is mainly post-transcriptional. It requires nucleus-encoded trans-acting protein factors for maturation/stabilization (M factors) or translation (T factors) of specific target mRNAs. We used long- and small-RNA sequencing to generate a detailed map of the transcriptome. Clusters of sRNAs marked the 5' end of all mature mRNAs. Their absence in M-factor mutants reflects the protection of transcript 5' end by the cognate factor. Enzymatic removal of 5'-triphosphates allowed identifying those cosRNA that mark a transcription start site. We detected another class of sRNAs derived from low abundance transcripts, antisense to mRNAs. The formation of antisense sRNAs required the presence of the complementary mRNA and was stimulated when translation was inhibited by chloramphenicol or lincomycin. We propose that they derive from degradation of double-stranded RNAs generated by pairing of antisense and sense transcripts, a process normally hindered by the traveling of the ribosomes. In addition, chloramphenicol treatment, by freezing ribosomes on the mRNA, caused the accumulation of 32-34 nt ribosome-protected fragments. Using this 'in vivo ribosome footprinting', we identified the function and molecular target of two candidate trans-acting factors.
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Affiliation(s)
- Marina Cavaiuolo
- Unité Mixte de Recherche 7141, CNRS/UPMC, Institut de Biologie Physico-Chimique, F-75005 Paris, France
| | - Richard Kuras
- Unité Mixte de Recherche 7141, CNRS/UPMC, Institut de Biologie Physico-Chimique, F-75005 Paris, France
| | - Francis‐André Wollman
- Unité Mixte de Recherche 7141, CNRS/UPMC, Institut de Biologie Physico-Chimique, F-75005 Paris, France
| | - Yves Choquet
- Unité Mixte de Recherche 7141, CNRS/UPMC, Institut de Biologie Physico-Chimique, F-75005 Paris, France
| | - Olivier Vallon
- Unité Mixte de Recherche 7141, CNRS/UPMC, Institut de Biologie Physico-Chimique, F-75005 Paris, France
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Zhang YY, Hao YY, Wang YH, Wang CM, Wang YL, Long WH, Wang D, Liu X, Jiang L, Wan JM. Lethal albinic seedling, encoding a threonyl-tRNA synthetase, is involved in development of plastid protein synthesis system in rice. PLANT CELL REPORTS 2017; 36:1053-1064. [PMID: 28405745 DOI: 10.1007/s00299-017-2136-x] [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: 11/08/2016] [Accepted: 03/27/2017] [Indexed: 05/26/2023]
Abstract
An albinic rice is caused by mutation of threonyl-tRNA synthetase, which is essential for plant development by stabilizing of NEP and PEP gene expressions and chloroplast protein synthesis. Chloroplast biogenesis and development depend on complex genetic mechanisms. Apart from their function in translation, aminoacyl-tRNA synthetases (aaRSs) play additional role in gene expression regulation, RNA splicing, and cytokine activity. However, their detailed functions in plant development are still poorly understood. We isolated a lethal albinic seedling (las) mutant in rice. Physiological and ultrastructural analysis of las mutant plants revealed weak chlorophyll fluorescence, negligible chlorophyll accumulation, and defective thylakoid membrane development. By map based cloning we determined that the LAS allele gene encodes threonyl-tRNA synthetase (ThrRS). LAS was constitutively expressed with relatively high level in leaves. NEP-dependent gene transcripts accumulated in the developing chloroplasts, while PEP-dependent transcripts were reduced in the las mutant. This result indicated that PEP activity was impaired. Chloroplast-encoded protein levels were sharply reduced in the las mutant. Biogenesis of chloroplast rRNAs (16S and 23S rRNA) was arrested, leading to impaired translation and protein synthesis. Together, our findings indicated that LAS is essential not only for chloroplast development by stabilizing the NEP and PEP gene expression, but also for protein synthesis and construction of the ribosome system in rice chloroplasts.
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Affiliation(s)
- Yuan-Yan Zhang
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yuan-Yuan Hao
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yi-Hua Wang
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095, China
| | - Chun-Ming Wang
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yun-Long Wang
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095, China
| | - Wu-Hua Long
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095, China
| | - Di Wang
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095, China
| | - Xi Liu
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095, China
| | - Ling Jiang
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095, China
| | - Jian-Min Wan
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095, China.
- National Key Facility for Crop Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
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Abstract
Numerous attempts have been made to identify and engineer sequence-specific RNA endonucleases, as these would allow for efficient RNA manipulation. However, no natural RNA endonuclease that recognizes RNA in a sequence-specific manner has been described to date. Here, we report that SUPPRESSOR OF THYLAKOID FORMATION 1 (SOT1), an Arabidopsis pentatricopeptide repeat (PPR) protein with a small MutS-related (SMR) domain, has RNA endonuclease activity. We show that the SMR moiety of SOT1 performs the endonucleolytic maturation of 23S and 4.5S rRNA through the PPR domain, specifically recognizing a 13-nucleotide RNA sequence in the 5' end of the chloroplast 23S-4.5S rRNA precursor. In addition, we successfully engineered the SOT1 protein with altered PPR motifs to recognize and cleave a predicted RNA substrate. Our findings point to SOT1 as an exciting tool for RNA manipulation.
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32
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Identification of protein structural elements responsible for the diversity of sequence preferences among Mini-III RNases. Sci Rep 2016; 6:38612. [PMID: 27924926 PMCID: PMC5141509 DOI: 10.1038/srep38612] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2016] [Accepted: 11/10/2016] [Indexed: 01/21/2023] Open
Abstract
Many known endoribonucleases select their substrates based on the presence of one or a few specific nucleotides at or near the cleavage site. In some cases, selectivity is also determined by the structural features of the substrate. We recently described the sequence-specific cleavage of double-stranded RNA by Mini-III RNase from Bacillus subtilis in vitro. Here, we characterized the sequence specificity of eight other members of the Mini-III RNase family from different bacterial species. High-throughput analysis of the cleavage products of Φ6 bacteriophage dsRNA indicated subtle differences in sequence preference between these RNases, which were confirmed and characterized by systematic analysis of the cleavage kinetics of a set of short dsRNA substrates. We also showed that the sequence specificities of Mini-III RNases are not reflected by different binding affinities for cognate and non-cognate sequences, suggesting that target selection occurs predominantly at the cleavage step. We were able to identify two structural elements, the α4 helix and α5b-α6 loop that were involved in target selection. Characterization of the sequence specificity of the eight Mini-III RNases may provide a basis for better understanding RNA substrate recognition by Mini-III RNases and adopting these enzymes and their engineered derivatives as tools for RNA research.
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33
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Mermigka G, Helm JM, Vlatakis I, Schumacher HT, Vamvaka E, Kalantidis K. ERIL1, the plant homologue of ERI-1, is involved in the processing of chloroplastic rRNAs. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2016; 88:839-853. [PMID: 27531275 DOI: 10.1111/tpj.13304] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2015] [Revised: 08/05/2016] [Accepted: 08/09/2016] [Indexed: 06/06/2023]
Abstract
Proteins belonging to the enhancer of RNA interference-1 subfamily of 3'-5' exoribonucleases participate in divergent RNA pathways. They degrade small interfering RNAs (siRNAs), thus suppressing RNA interference, and are involved in the maturation of ribosomal RNAs and the degradation of histone messenger RNAs (mRNAs). Here, we report evidence for the role of the plant homologue of these proteins, which we termed ENHANCED RNA INTERFERENCE-1-LIKE-1 (ERIL1), in chloroplast function. In vitro assays with AtERIL1 proved that the conserved 3'-5' exonuclease activity is shared among all homologues studied. Confocal microscopy revealed that ERL1, a nucleus-encoded protein, is targeted to the chloroplast. To gain insight into its role in plants, we used Nicotiana benthamiana and Arabidopsis thaliana plants that constitutively overexpress or suppress ERIL1. In the mutant lines of both species we observed malfunctions in photosynthetic ability. Molecular analysis showed that ERIL1 participates in the processing of chloroplastic ribosomal RNAs (rRNAs). Lastly, our results suggest that the missexpression of ERIL1 may have an indirect effect on the microRNA (miRNA) pathway. Altogether our data point to an additional piece of the puzzle in the complex RNA metabolism of chloroplasts.
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Affiliation(s)
- Glykeria Mermigka
- Department of Biology, University of Crete, Vassilika Vouton, Heraklion/Crete, GR-71409, Greece
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology - Hellas, Heraklion/Crete, GR-71110, Greece
| | - Jutta Maria Helm
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology - Hellas, Heraklion/Crete, GR-71110, Greece
| | - Ioannis Vlatakis
- Department of Biology, University of Crete, Vassilika Vouton, Heraklion/Crete, GR-71409, Greece
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology - Hellas, Heraklion/Crete, GR-71110, Greece
| | - Heiko Tobias Schumacher
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology - Hellas, Heraklion/Crete, GR-71110, Greece
| | - Evgenia Vamvaka
- Department of Biology, University of Crete, Vassilika Vouton, Heraklion/Crete, GR-71409, Greece
| | - Kriton Kalantidis
- Department of Biology, University of Crete, Vassilika Vouton, Heraklion/Crete, GR-71409, Greece
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology - Hellas, Heraklion/Crete, GR-71110, Greece
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ChloroSeq, an Optimized Chloroplast RNA-Seq Bioinformatic Pipeline, Reveals Remodeling of the Organellar Transcriptome Under Heat Stress. G3-GENES GENOMES GENETICS 2016; 6:2817-27. [PMID: 27402360 PMCID: PMC5015939 DOI: 10.1534/g3.116.030783] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Abstract
Although RNA-Seq has revolutionized transcript analysis, organellar transcriptomes are rarely assessed even when present in published datasets. Here, we describe the development and application of a rapid and convenient method, ChloroSeq, to delineate qualitative and quantitative features of chloroplast RNA metabolism from strand-specific RNA-Seq datasets, including processing, editing, splicing, and relative transcript abundance. The use of a single experiment to analyze systematically chloroplast transcript maturation and abundance is of particular interest due to frequent pleiotropic effects observed in mutants that affect chloroplast gene expression and/or photosynthesis. To illustrate its utility, ChloroSeq was applied to published RNA-Seq datasets derived from Arabidopsis thaliana grown under control and abiotic stress conditions, where the organellar transcriptome had not been examined. The most appreciable effects were found for heat stress, which induces a global reduction in splicing and editing efficiency, and leads to increased abundance of chloroplast transcripts, including genic, intergenic, and antisense transcripts. Moreover, by concomitantly analyzing nuclear transcripts that encode chloroplast gene expression regulators from the same libraries, we demonstrate the possibility of achieving a holistic understanding of the nucleus-organelle system. ChloroSeq thus represents a unique method for streamlining RNA-Seq data interpretation of the chloroplast transcriptome and its regulators.
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Mao MY, Yang YM, Li KZ, Lei L, Li M, Yang Y, Tao X, Yin JX, Zhang R, Ma XR, Hu T. The rnc Gene Promotes Exopolysaccharide Synthesis and Represses the vicRKX Gene Expressions via MicroRNA-Size Small RNAs in Streptococcus mutans. Front Microbiol 2016; 7:687. [PMID: 27242713 PMCID: PMC4861726 DOI: 10.3389/fmicb.2016.00687] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2016] [Accepted: 04/26/2016] [Indexed: 02/05/2023] Open
Abstract
Dental caries is a biofilm-dependent disease that largely relies on the ability of Streptococcus mutans to synthesize exopolysaccharides. Although the rnc gene is suggested to be involved in virulence mechanisms in many other bacteria, the information regarding it in S. mutans is very limited. Here, using deletion or overexpression mutant assay, we demonstrated that rnc in S. mutans significantly positively regulated exopolysaccharide synthesis and further altered biofilm formation. Meanwhile, the cariogenecity of S. mutans was decreased by deletion of rnc in a specific pathogen-free (SPF) rat model. Interestingly, analyzing the expression at mRNA level, we found the downstream vic locus was repressed by rnc in S. mutans. Using deep sequencing and bioinformatics analysis, for the first time, three putative microRNA-size small RNAs (msRNAs) targeting vicRKX were predicted in S. mutans. The expression levels of these msRNAs were negatively correlated with vicRKX but positively correlated with rnc, indicating rnc probably repressed vicRKX expression through msRNAs at the post-transcriptional level. In all, the results present that rnc has a potential role in the regulation of exopolysaccharide synthesis and can affect vicRKX expressions via post-transcriptional repression in S. mutans. This study provides an alternative avenue for further research aimed at preventing caries.
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Affiliation(s)
- Meng-Ying Mao
- State Key Laboratory of Oral Diseases, West China Hospital of Stomatology, Sichuan University Chengdu, China
| | - Ying-Ming Yang
- State Key Laboratory of Oral Diseases, West China Hospital of Stomatology, Sichuan University Chengdu, China
| | - Ke-Zeng Li
- State Key Laboratory of Oral Diseases, West China Hospital of Stomatology, Sichuan UniversityChengdu, China; Department of Dentistry, Yan'an Hospital Affiliated to Kunming Medical UniversityKunming, China
| | - Lei Lei
- State Key Laboratory of Oral Diseases, West China Hospital of Stomatology, Sichuan University Chengdu, China
| | - Meng Li
- State Key Laboratory of Oral Diseases, West China Hospital of Stomatology, Sichuan University Chengdu, China
| | - Yan Yang
- State Key Laboratory of Oral Diseases, West China Hospital of Stomatology, Sichuan University Chengdu, China
| | - Xiang Tao
- Chengdu Institute of Biology, Chinese Academy of Sciences Chengdu, China
| | - Jia-Xin Yin
- State Key Laboratory of Oral Diseases, West China Hospital of Stomatology, Sichuan University Chengdu, China
| | - Ru Zhang
- State Key Laboratory of Oral Diseases, West China Hospital of Stomatology, Sichuan UniversityChengdu, China; Department of Endodontics and Operative Dentistry School of Stomatology, Capital Medical UniversityBeijing, China
| | - Xin-Rong Ma
- Chengdu Institute of Biology, Chinese Academy of Sciences Chengdu, China
| | - Tao Hu
- State Key Laboratory of Oral Diseases, West China Hospital of Stomatology, Sichuan University Chengdu, China
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36
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CORRECTION. THE PLANT CELL 2016; 28:984-989. [PMID: 27053425 PMCID: PMC4863388 DOI: 10.1105/tpc.16.00094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
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37
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Zoschke R, Watkins KP, Miranda RG, Barkan A. The PPR-SMR protein PPR53 enhances the stability and translation of specific chloroplast RNAs in maize. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2016; 85:594-606. [PMID: 26643268 PMCID: PMC4777676 DOI: 10.1111/tpj.13093] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2015] [Revised: 11/19/2015] [Accepted: 11/24/2015] [Indexed: 05/09/2023]
Abstract
Pentatricopeptide repeat (PPR) proteins are helical repeat proteins that bind RNA and influence gene expression in mitochondria and chloroplasts. Several PPR proteins in plants harbor a carboxy-terminal small-MutS-related (SMR) domain, but the functions of the SMR appendage are unknown. To address this issue, we studied a maize PPR-SMR protein denoted PPR53 (GRMZM2G438524), which is orthologous to the Arabidopsis protein SOT1 (AT5G46580). Null ppr53 alleles condition a chlorotic, seedling-lethal phenotype and a reduction in plastid ribosome content. Plastome-wide transcriptome and translatome analyses revealed strong defects in the expression of the ndhA and rrn23 genes, which were superimposed on secondary effects resulting from a decrease in plastid ribosome content. Transcripts with processed 5'-ends mapping approximately 70 nucleotides upstream of rrn23 and ndhA are absent in ppr53 mutants, and the translational efficiency of the residual ndhA mRNAs is reduced. Recombinant PPR53 binds with high affinity and specificity to the 5' proximal region of the PPR53-dependent 23S rRNA, suggesting that PPR53 protects this RNA via a barrier mechanism similar to that described for several PPR proteins lacking SMR motifs. However, recombinant PPR53 did not bind with high affinity to the ndhA 5' untranslated region, suggesting that PPR53's RNA-stabilization and translation-enhancing effects at the ndhA locus involve the participation of other factors.
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Affiliation(s)
- Reimo Zoschke
- Institute of Molecular Biology, University of Oregon, Eugene, OR 97403
| | | | - Rafael G. Miranda
- Institute of Molecular Biology, University of Oregon, Eugene, OR 97403
| | - Alice Barkan
- Institute of Molecular Biology, University of Oregon, Eugene, OR 97403
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38
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Wu W, Liu S, Ruwe H, Zhang D, Melonek J, Zhu Y, Hu X, Gusewski S, Yin P, Small ID, Howell KA, Huang J. SOT1, a pentatricopeptide repeat protein with a small MutS-related domain, is required for correct processing of plastid 23S-4.5S rRNA precursors in Arabidopsis thaliana. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2016; 85:607-21. [PMID: 26800847 DOI: 10.1111/tpj.13126] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2015] [Accepted: 01/12/2016] [Indexed: 05/22/2023]
Abstract
Ribosomal RNA processing is essential for plastid ribosome biogenesis, but is still poorly understood in higher plants. Here, we show that SUPPRESSOR OF THYLAKOID FORMATION1 (SOT1), a plastid-localized pentatricopeptide repeat (PPR) protein with a small MutS-related domain, is required for maturation of the 23S-4.5S rRNA dicistron. Loss of SOT1 function leads to slower chloroplast development, suppression of leaf variegation, and abnormal 23S and 4.5S processing. Predictions based on the PPR motif sequences identified the 5' end of the 23S-4.5S rRNA dicistronic precursor as a putative SOT1 binding site. This was confirmed by electrophoretic mobility shift assay, and by loss of the abundant small RNA 'footprint' associated with this site in sot1 mutants. We found that more than half of the 23S-4.5S rRNA dicistrons in sot1 mutants contain eroded and/or unprocessed 5' and 3' ends, and that the endonucleolytic cleavage product normally released from the 5' end of the precursor is absent in a sot1 null mutant. We postulate that SOT1 binding protects the 5' extremity of the 23S-4.5S rRNA dicistron from exonucleolytic attack, and favours formation of the RNA structure that allows endonucleolytic processing of its 5' and 3' ends.
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MESH Headings
- Arabidopsis/genetics
- Arabidopsis/metabolism
- Arabidopsis Proteins/genetics
- Arabidopsis Proteins/metabolism
- Base Sequence
- Binding Sites/genetics
- Blotting, Western
- Gene Expression Regulation, Plant
- Mutation
- Plants, Genetically Modified
- Plastids/genetics
- Plastids/metabolism
- Protein Binding
- RNA Precursors/genetics
- RNA Precursors/metabolism
- RNA Processing, Post-Transcriptional
- RNA, Ribosomal/genetics
- RNA, Ribosomal/metabolism
- RNA, Ribosomal, 23S/genetics
- RNA, Ribosomal, 23S/metabolism
- Reverse Transcriptase Polymerase Chain Reaction
- Sequence Homology, Nucleic Acid
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Affiliation(s)
- Wenjuan Wu
- National Key Laboratory of Plant Molecular Genetics, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Sheng Liu
- Australian Research Council Centre of Excellence in Plant Energy Biology, The University of Western Australia, Crawley, Western Australia, 6009, Australia
| | - Hannes Ruwe
- Australian Research Council Centre of Excellence in Plant Energy Biology, The University of Western Australia, Crawley, Western Australia, 6009, Australia
| | - Delin Zhang
- National Key Laboratory of Crop Genetic Improvement, National Centre of Plant Gene Research, Huazhong Agricultural University, Wuhan, 430070, China
| | - Joanna Melonek
- Australian Research Council Centre of Excellence in Plant Energy Biology, The University of Western Australia, Crawley, Western Australia, 6009, Australia
| | - Yajuan Zhu
- National Key Laboratory of Plant Molecular Genetics, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Xupeng Hu
- National Key Laboratory of Plant Molecular Genetics, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Sandra Gusewski
- Australian Research Council Centre of Excellence in Plant Energy Biology, The University of Western Australia, Crawley, Western Australia, 6009, Australia
| | - Ping Yin
- National Key Laboratory of Crop Genetic Improvement, National Centre of Plant Gene Research, Huazhong Agricultural University, Wuhan, 430070, China
| | - Ian D Small
- Australian Research Council Centre of Excellence in Plant Energy Biology, The University of Western Australia, Crawley, Western Australia, 6009, Australia
- Centre of Excellence in Computational Systems Biology, The University of Western Australia, Crawley, Western Australia, 6009, Australia
| | - Katharine A Howell
- Australian Research Council Centre of Excellence in Plant Energy Biology, The University of Western Australia, Crawley, Western Australia, 6009, Australia
| | - Jirong Huang
- National Key Laboratory of Plant Molecular Genetics, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
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39
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Dorrell RG, Hinksman GA, Howe CJ. Diversity of transcripts and transcript processing forms in plastids of the dinoflagellate alga Karenia mikimotoi. PLANT MOLECULAR BIOLOGY 2016; 90:233-47. [PMID: 26768263 PMCID: PMC4717168 DOI: 10.1007/s11103-015-0408-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2015] [Accepted: 11/12/2015] [Indexed: 05/05/2023]
Abstract
Plastids produce a vast diversity of transcripts. These include mature transcripts containing coding sequences, and their processing precursors, as well as transcripts that lack direct coding functions, such as antisense transcripts. Although plastid transcriptomes have been characterised for many plant species, less is known about the transcripts produced in other plastid lineages. We characterised the transcripts produced in the fucoxanthin-containing plastids of the dinoflagellate alga Karenia mikimotoi. This plastid lineage, acquired through tertiary endosymbiosis, utilises transcript processing pathways that are very different from those found in plants and green algae, including 3' poly(U) tail addition, and extensive substitutional editing of transcript sequences. We have sequenced the plastid transcriptome of K. mikimotoi, and have detected evidence for divergent evolution of fucoxanthin plastid genomes. We have additionally characterised polycistronic and monocistronic transcripts from two plastid loci, psbD-tRNA (Met)-ycf4 and rpl36-rps13-rps11. We find evidence for a range of transcripts produced from each locus that differ in terms of editing state, 5' end cleavage position, and poly(U) tail addition. Finally, we identify antisense transcripts in K. mikimotoi, which appear to undergo different processing events from the corresponding sense transcripts. Overall, our study provides insights into the diversity of transcripts and processing intermediates found in plastid lineages across the eukaryotes.
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Affiliation(s)
- Richard G Dorrell
- Department of Biochemistry, University of Cambridge, Cambridge, UK.
- School of Biology, École Normale Supérieure, Paris, France.
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40
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Yang L, Wang YL, Dai JC, Liu M, Li X, Tang H. Biochemical properties of Bacillus Calmette Guerin ribonuclease III. J Basic Microbiol 2015; 56:392-404. [PMID: 26632143 DOI: 10.1002/jobm.201500360] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2015] [Accepted: 10/18/2015] [Indexed: 11/11/2022]
Abstract
Double-stranded RNA (dsRNA) is discovered to participate in the regulation of gene expression in both bacterial and eukaryotic cells. Members of ribonuclease III (RNase III) family recognize RNA motifs and cleave substrates at specific sites in a divalent-metal-ion-dependent manner. In this study, we find the RNase III from Bacillus Calmette Guerin (BCG-RNase III) cleaves small hairpin RNA based on the conserved stem structure associated with Mycobacterium 16S ribosomal RNA precursor at specific sites which are not determined. To evaluate the influence of remnant endogenous ribonucleases from expression host on RNA cleavage assays for RNase III, we use E44A and D48A mutant of the enzyme to perform RNA cleavage assays and find that remnant ribonucleases have no effect on cleavage assays. The RNA cleavage activity of the enzyme can be supported by Mg(2+), Mn(2+), and Co(2+) and enhanced with the increasing salt concentration. The catalytic activity of the enzyme is exhibited when the temperature of the reaction buffer ranges from 30 to 55 °C and the pH of the buffer from 7.0 to 10.0. Two major cleavage sites in RNA substrate are identified using RNA Ligase Mediated Rapid Amplification of cDNA Ends (RLM-RACE).
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Affiliation(s)
- Lei Yang
- Tianjin Life Science Research Center and Basic Medical School, Tianjin Medical University, Tianjin, China.,Department of Clinical Laboratory, Tianjin First Center Hospital, Tianjin, China
| | - Yan-Li Wang
- Tianjin Life Science Research Center and Basic Medical School, Tianjin Medical University, Tianjin, China.,Department of Clinical Laboratory, Tianjin Hospital of ITCWM Nankai Hospital, Tianjin, China
| | - Jin-Chuan Dai
- Tianjin Life Science Research Center and Basic Medical School, Tianjin Medical University, Tianjin, China
| | - Min Liu
- Tianjin Life Science Research Center and Basic Medical School, Tianjin Medical University, Tianjin, China
| | - Xin Li
- Tianjin Life Science Research Center and Basic Medical School, Tianjin Medical University, Tianjin, China
| | - Hua Tang
- Tianjin Life Science Research Center and Basic Medical School, Tianjin Medical University, Tianjin, China
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41
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Chevalier F, Ghulam MM, Rondet D, Pfannschmidt T, Merendino L, Lerbs-Mache S. Characterization of the psbH precursor RNAs reveals a precise endoribonuclease cleavage site in the psbT/psbH intergenic region that is dependent on psbN gene expression. PLANT MOLECULAR BIOLOGY 2015; 88:357-67. [PMID: 26012647 DOI: 10.1007/s11103-015-0325-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2014] [Accepted: 04/23/2015] [Indexed: 05/15/2023]
Abstract
The plastid psbB operon harbours 5 genes, psbB, psbT, psbH, petB and petD. A sixth gene, the psbN gene, is located on the opposite DNA strand in the psbT/psbH intergenic region. Its transcription produces antisense RNA to a large part of the psbB pentacistronic mRNA. We have investigated whether transcription of the psbN gene, i.e. production of antisense RNA, influences psbT/psbH intergenic processing. Results reveal the existence of four different psbH precursor RNAs. Three of them result from processing and one is produced by transcription initiation. One of the processed RNAs is probably created by site-specific RNA cleavage. This RNA is absent in plants where the psbN gene is not transcribed suggesting that cleavage at this site is dependent on the formation of sense/antisense double-stranded RNA. In order to characterize the nuclease that might be responsible for double-stranded RNA cleavage, we analysed csp41a and csp41b knock-out mutants and the corresponding double mutant. Both CSP41 proteins are known to interact physically and CSP41a had been shown to cleave within 3'-untranslated region stem-loop structures, which contain double-stranded RNA, in vitro. We demonstrate that the psbH RNA, that is absent in plants where the psbN gene is not transcribed, is also strongly diminished in all csp41 plants. Altogether, results reveal a site-specific endoribonuclease cleavage event that seems to depend on antisense RNA and might implicate endoribonuclease activity of CSP41a.
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Affiliation(s)
- Fabien Chevalier
- Laboratoire Physiologie Cellulaire Végétale, UMR 5168, CNRS, Grenoble, France
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