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Firouzabadi ED, Allami M, Mohammed EJ, Barzegar H, Dastpak M, Alemohammad R, Moghimi V, Mahmoudian RA, Nasrabadi F, Arghiani N, Kitamura Y, Hosseini SA, Ghasemi A, Farshchian M. Detection of novel PPP1R1B::STARD3 fusion transcript in acute myeloid leukemia: a case report. J Med Case Rep 2024; 18:269. [PMID: 38835078 PMCID: PMC11151611 DOI: 10.1186/s13256-024-04536-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Accepted: 03/22/2024] [Indexed: 06/06/2024] Open
Abstract
BACKGROUND Acute myeloid leukemia (AML) is the second most common type of leukemia in children. Although prognostic and diagnostic tests of AML patients have improved, there is still a great demand for new reliable clinical biomarkers for AML. Read-through fusion transcripts (RTFTs) are complex transcripts of adjacent genes whose molecular mechanisms are poorly understood. This is the first report of the presence of the PPP1R1B::STARD3 fusion transcript in an AML patient. Here, we investigated the presence of PPP1R1B::STARD3 RTFT in a case of AML using paired-end RNA sequencing (RNA-seq). CASE PRESENTATION A Persian 12-year-old male was admitted to Dr. Sheikh Hospital of Mashhad, Iran, in September 2019 with the following symptoms, including fever, convulsions, hemorrhage, and bone pain. The patient was diagnosed with AML (non-M3-FAB subtype) based on cell morphologies and immunophenotypical features. Chromosomal analysis using the G-banding technique revealed t (9;22) (q34;q13). CONCLUSIONS Single-cell RNA sequencing (scRNA-seq) analysis suggested that the PPP1R1B promoter may be responsible for the PPP1R1B::STARD3 expression. Alterations in the level of lipid metabolites implicate cancer development, and this fusion can play a crucial role in the cholesterol movement in cancer cells. PPP1R1B::STARD3 may be considered a candidate for targeted therapies of the cholesterol metabolic and the PI3K/AKT signaling pathways involved in cancer development and progression.
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Affiliation(s)
- Elahe Dehghani Firouzabadi
- Stem Cell and Regenerative Medicine Research Group, Academic Center for Education, Culture, and Research (ACECR), Mashhad, Razavi Khorasan, Iran
- Department of Biology, Faculty of Science, Hakim Sabzevar University, Sabzevar, Iran
| | - Mohammed Allami
- Department of Dentistry, Al-Manara College for Medical Sciences, Maysan, Iraq
- Department of Biology, Faculty of Science, Ferdowsi University of Mashhad, Mashhad, Iran
| | - Eman Jassim Mohammed
- Department of Biology, College of Science, Mustansiriyah University, Baghdad, Iraq
| | - Hossein Barzegar
- Stem Cell and Regenerative Medicine Research Group, Academic Center for Education, Culture, and Research (ACECR), Mashhad, Razavi Khorasan, Iran
| | - Mahtab Dastpak
- Department of Cell Biology, Harvard Medical School, 240 Longwood Ave, Boston, MA, 02115, USA
| | - Reza Alemohammad
- Stem Cell and Regenerative Medicine Research Group, Academic Center for Education, Culture, and Research (ACECR), Mashhad, Razavi Khorasan, Iran
| | - Vahid Moghimi
- Stem Cell and Regenerative Medicine Research Group, Academic Center for Education, Culture, and Research (ACECR), Mashhad, Razavi Khorasan, Iran
- Department of Biology, Faculty of Science, Hakim Sabzevar University, Sabzevar, Iran
| | - Reihaneh Alsadat Mahmoudian
- Basic Sciences Research Institute, Mashhad University of Medical Sciences, Mashhad, Iran
- Cancer Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Fatemeh Nasrabadi
- Stem Cell and Regenerative Medicine Research Group, Academic Center for Education, Culture, and Research (ACECR), Mashhad, Razavi Khorasan, Iran
| | - Nahid Arghiani
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
- Department of Biochemistry and Biomedicine, School of Life Sciences, University of Sussex, Brighton, UK
| | - Yohei Kitamura
- Department of Neurosurgery, Keio University School of Medicine, Tokyo, Japan
| | | | - Ali Ghasemi
- Department of Pediatrics Hematology and Oncology, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran.
| | - Moein Farshchian
- Stem Cell and Regenerative Medicine Research Group, Academic Center for Education, Culture, and Research (ACECR), Mashhad, Razavi Khorasan, Iran.
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2
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Smith AB, Ganguly DR, Moore M, Bowerman AF, Janapala Y, Shirokikh NE, Pogson BJ, Crisp PA. Dynamics of mRNA fate during light stress and recovery: from transcription to stability and translation. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 117:818-839. [PMID: 37947266 PMCID: PMC10952913 DOI: 10.1111/tpj.16531] [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: 03/22/2023] [Revised: 09/20/2023] [Accepted: 10/23/2023] [Indexed: 11/12/2023]
Abstract
Transcript stability is an important determinant of its abundance and, consequently, translational output. Transcript destabilisation can be rapid and is well suited for modulating the cellular response. However, it is unclear the extent to which RNA stability is altered under changing environmental conditions in plants. We previously hypothesised that recovery-induced transcript destabilisation facilitated a phenomenon of rapid recovery gene downregulation (RRGD) in Arabidopsis thaliana (Arabidopsis) following light stress, based on mathematical calculations to account for ongoing transcription. Here, we test this hypothesis and investigate processes regulating transcript abundance and fate by quantifying changes in transcription, stability and translation before, during and after light stress. We adapt syringe infiltration to apply a transcriptional inhibitor to soil-grown plants in combination with stress treatments. Compared with measurements in juvenile plants and cell culture, we find reduced stability across a range of transcripts encoding proteins involved in RNA binding and processing. We also observe light-induced destabilisation of transcripts, followed by their stabilisation during recovery. We propose that this destabilisation facilitates RRGD, possibly in combination with transcriptional shut-off that was confirmed for HSP101, ROF1 and GOLS1. We also show that translation remains highly dynamic over the course of light stress and recovery, with a bias towards transcript-specific increases in ribosome association, independent of changes in total transcript abundance, after 30 min of light stress. Taken together, we provide evidence for the combinatorial regulation of transcription and stability that occurs to coordinate translation during light stress and recovery in Arabidopsis.
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Affiliation(s)
- Aaron B. Smith
- Research School of BiologyThe Australian National UniversityCanberraAustralian Capital Territory2601Australia
| | - Diep R. Ganguly
- CSIRO Synthetic Biology Future Science PlatformCanberraAustralian Capital Territory2601Australia
- Department of BiologyUniversity of PennsylvaniaPhiladelphiaPennsylvania19104USA
| | - Marten Moore
- Research School of BiologyThe Australian National UniversityCanberraAustralian Capital Territory2601Australia
| | - Andrew F. Bowerman
- Research School of BiologyThe Australian National UniversityCanberraAustralian Capital Territory2601Australia
| | - Yoshika Janapala
- Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery InstituteMonash UniversityClaytonVictoria3800Australia
| | - Nikolay E. Shirokikh
- The John Curtin School of Medical Research, The Shine‐Dalgarno Centre for RNA InnovationThe Australian National UniversityCanberraAustralian Capital Territory2601Australia
| | - Barry J. Pogson
- Research School of BiologyThe Australian National UniversityCanberraAustralian Capital Territory2601Australia
| | - Peter A. Crisp
- School of Agriculture and Food SciencesThe University of QueenslandBrisbaneQueensland4072Australia
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3
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Prasetyaningrum P, Litthauer S, Vegliani F, Battle MW, Wood MW, Liu X, Dickson C, Jones MA. Inhibition of RNA degradation integrates the metabolic signals induced by osmotic stress into the Arabidopsis circadian system. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:5805-5819. [PMID: 37453132 PMCID: PMC10540740 DOI: 10.1093/jxb/erad274] [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: 02/05/2023] [Accepted: 07/12/2023] [Indexed: 07/18/2023]
Abstract
The circadian clock system acts as an endogenous timing reference that coordinates many metabolic and physiological processes in plants. Previous studies have shown that the application of osmotic stress delays circadian rhythms via 3'-phospho-adenosine 5'-phosphate (PAP), a retrograde signalling metabolite that is produced in response to redox stress within organelles. PAP accumulation leads to the inhibition of exoribonucleases (XRNs), which are responsible for RNA degradation. Interestingly, we are now able to demonstrate that post-transcriptional processing is crucial for the circadian response to osmotic stress. Our data show that osmotic stress increases the stability of specific circadian RNAs, suggesting that RNA metabolism plays a vital role in circadian clock coordination during drought. Inactivation of XRN4 is sufficient to extend circadian rhythms as part of this response, with PRR7 and LWD1 identified as transcripts that are post-transcriptionally regulated to delay circadian progression.
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Affiliation(s)
| | | | - Franco Vegliani
- School of Molecular Biosciences, University of Glasgow, Glasgow G12 8QQ, UK
| | | | | | - Xinmeng Liu
- School of Molecular Biosciences, University of Glasgow, Glasgow G12 8QQ, UK
| | - Cathryn Dickson
- School of Molecular Biosciences, University of Glasgow, Glasgow G12 8QQ, UK
| | - Matthew Alan Jones
- School of Molecular Biosciences, University of Glasgow, Glasgow G12 8QQ, UK
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4
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Zhou S, Zhao F, Zhu D, Zhang Q, Dai Z, Wu Z. Coupling of co-transcriptional splicing and 3' end Pol II pausing during termination in Arabidopsis. Genome Biol 2023; 24:206. [PMID: 37697420 PMCID: PMC10496290 DOI: 10.1186/s13059-023-03050-4] [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: 09/07/2022] [Accepted: 09/04/2023] [Indexed: 09/13/2023] Open
Abstract
BACKGROUND In Arabidopsis, RNA Polymerase II (Pol II) often pauses within a few hundred base pairs downstream of the polyadenylation site, reflecting efficient transcriptional termination, but how such pausing is regulated remains largely elusive. RESULT Here, we analyze Pol II dynamics at 3' ends by combining comprehensive experiments with mathematical modelling. We generate high-resolution serine 2 phosphorylated (Ser2P) Pol II positioning data specifically enriched at 3' ends and define a 3' end pause index (3'PI). The position but not the extent of the 3' end pause correlates with the termination window size. The 3'PI is not decreased but even mildly increased in the termination deficient mutant xrn3, indicating 3' end pause is a regulatory step early during the termination and before XRN3-mediated RNA decay that releases Pol II. Unexpectedly, 3'PI is closely associated with gene exon numbers and co-transcriptional splicing efficiency. Multiple exons genes often display stronger 3' end pauses and more efficient on-chromatin splicing than genes with fewer exons. Chemical inhibition of splicing strongly reduces the 3'PI and disrupts its correlation with exon numbers but does not globally impact 3' end readthrough levels. These results are further confirmed by fitting Pol II positioning data with a mathematical model, which enables the estimation of parameters that define Pol II dynamics. CONCLUSION Our work highlights that the number of exons via co-transcriptional splicing is a major determinant of Pol II pausing levels at the 3' end of genes in plants.
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Affiliation(s)
- Sixian Zhou
- Harbin Institute of Technology, Harbin, 150001, China
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Institute of Plant and Food Science, Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Fengli Zhao
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Institute of Plant and Food Science, Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Danling Zhu
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Institute of Plant and Food Science, Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Qiqi Zhang
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Institute of Plant and Food Science, Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Ziwei Dai
- Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, 518055, China.
| | - Zhe Wu
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Institute of Plant and Food Science, Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, 518055, China.
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5
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Han WY, Hou BH, Lee WC, Chan TC, Lin TH, Chen HM. Arabidopsis mRNA decay landscape shaped by XRN 5'-3' exoribonucleases. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 114:895-913. [PMID: 36987558 DOI: 10.1111/tpj.16181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Revised: 02/18/2023] [Accepted: 03/03/2023] [Indexed: 05/27/2023]
Abstract
5'-3' exoribonucleases (XRNs) play crucial roles in the control of RNA processing, quality, and quantity in eukaryotes. Although genome-wide profiling of RNA decay fragments is now feasible, how XRNs shape the plant mRNA degradome remains elusive. Here, we profiled and analyzed the RNA degradomes of Arabidopsis wild-type and mutant plants with defects in XRN activity. Deficiency of nuclear XRN3 or cytoplasmic XRN4 activity but not nuclear XRN2 activity greatly altered Arabidopsis mRNA decay profiles. Short excised linear introns and cleaved pre-mRNA fragments downstream of polyadenylation sites were polyadenylated and stabilized in the xrn3 mutant, demonstrating the unique function of XRN3 in the removal of cleavage remnants from pre-mRNA processing. Further analysis of stabilized XRN3 substrates confirmed that pre-mRNA 3' end cleavage frequently occurs after adenosine. The most abundant decay intermediates in wild-type plants include not only the primary substrates of XRN4 but also the products of XRN4-mediated cytoplasmic decay. An increase in decay intermediates with 5' ends upstream of a consensus motif in the xrn4 mutant suggests that there is an endonucleolytic cleavage mechanism targeting the 3' untranslated regions of many Arabidopsis mRNAs. However, analysis of decay fragments in the xrn4 mutant indicated that, except for microRNA-directed slicing, endonucleolytic cleavage events in the coding sequence rarely result in major decay intermediates. Together, these findings reveal the major substrates and products of nuclear and cytoplasmic XRNs along Arabidopsis transcripts and provide a basis for precise interpretation of RNA degradome data.
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Affiliation(s)
- Wan-Yin Han
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, 11529, Taiwan
- Molecular and Biological Agricultural Sciences Program, Taiwan International Graduate Program, National Chung-Hsing University, Taichung 40227, Taiwan, and Academia Sinica, Taipei, 11529, Taiwan
- Graduate Institute of Biotechnology, National Chung-Hsing University, Taichung, 40227, Taiwan
| | - Bo-Han Hou
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, 11529, Taiwan
| | - Wen-Chi Lee
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, 11529, Taiwan
| | - Tze-Ching Chan
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, 11529, Taiwan
| | - Tzu-Hsiang Lin
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, 11529, Taiwan
| | - Ho-Ming Chen
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, 11529, Taiwan
- Molecular and Biological Agricultural Sciences Program, Taiwan International Graduate Program, National Chung-Hsing University, Taichung 40227, Taiwan, and Academia Sinica, Taipei, 11529, Taiwan
- Biotechnology Center, National Chung-Hsing University, Taichung, 40227, Taiwan
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6
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Montez M, Majchrowska M, Krzyszton M, Bokota G, Sacharowski S, Wrona M, Yatusevich R, Massana F, Plewczynski D, Swiezewski S. Promoter-pervasive transcription causes RNA polymerase II pausing to boost DOG1 expression in response to salt. EMBO J 2023; 42:e112443. [PMID: 36705062 PMCID: PMC9975946 DOI: 10.15252/embj.2022112443] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Revised: 01/02/2023] [Accepted: 01/09/2023] [Indexed: 01/28/2023] Open
Abstract
Eukaryotic genomes are pervasively transcribed by RNA polymerase II. Yet, the molecular and biological implications of such a phenomenon are still largely puzzling. Here, we describe noncoding RNA transcription upstream of the Arabidopsis thaliana DOG1 gene, which governs salt stress responses and is a key regulator of seed dormancy. We find that expression of the DOG1 gene is induced by salt stress, thereby causing a delay in seed germination. We uncover extensive transcriptional activity on the promoter of the DOG1 gene, which produces a variety of lncRNAs. These lncRNAs, named PUPPIES, are co-directionally transcribed and extend into the DOG1 coding region. We show that PUPPIES RNAs respond to salt stress and boost DOG1 expression, resulting in delayed germination. This positive role of pervasive PUPPIES transcription on DOG1 gene expression is associated with augmented pausing of RNA polymerase II, slower transcription and higher transcriptional burst size. These findings highlight the positive role of upstream co-directional transcription in controlling transcriptional dynamics of downstream genes.
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Affiliation(s)
- Miguel Montez
- Laboratory of Seeds Molecular Biology, Institute of Biochemistry and BiophysicsPolish Academy of SciencesWarsawPoland
| | - Maria Majchrowska
- Laboratory of Seeds Molecular Biology, Institute of Biochemistry and BiophysicsPolish Academy of SciencesWarsawPoland
| | - Michal Krzyszton
- Laboratory of Seeds Molecular Biology, Institute of Biochemistry and BiophysicsPolish Academy of SciencesWarsawPoland
| | - Grzegorz Bokota
- Laboratory of Functional and Structural Genomics, Centre of New TechnologiesUniversity of WarsawWarsawPoland
| | - Sebastian Sacharowski
- Laboratory of Seeds Molecular Biology, Institute of Biochemistry and BiophysicsPolish Academy of SciencesWarsawPoland
| | - Magdalena Wrona
- Laboratory of Seeds Molecular Biology, Institute of Biochemistry and BiophysicsPolish Academy of SciencesWarsawPoland
| | - Ruslan Yatusevich
- Laboratory of Seeds Molecular Biology, Institute of Biochemistry and BiophysicsPolish Academy of SciencesWarsawPoland
| | - Ferran Massana
- Laboratory of Seeds Molecular Biology, Institute of Biochemistry and BiophysicsPolish Academy of SciencesWarsawPoland
| | - Dariusz Plewczynski
- Laboratory of Functional and Structural Genomics, Centre of New TechnologiesUniversity of WarsawWarsawPoland
- Laboratory of Bioinformatics and Computational Genomics, Faculty of Mathematics and Information ScienceWarsaw University of TechnologyWarsawPoland
| | - Szymon Swiezewski
- Laboratory of Seeds Molecular Biology, Institute of Biochemistry and BiophysicsPolish Academy of SciencesWarsawPoland
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7
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Kurihara Y, Makita Y, Kawauchi M, Kageyama A, Kuriyama T, Matsui M. Intergenic splicing-stimulated transcriptional readthrough is suppressed by nonsense-mediated mRNA decay in Arabidopsis. Commun Biol 2022; 5:1390. [PMID: 36539571 PMCID: PMC9768141 DOI: 10.1038/s42003-022-04348-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Accepted: 12/05/2022] [Indexed: 12/24/2022] Open
Abstract
Recent emerging evidence has shown that readthrough transcripts (RTs), including polycistronic mRNAs, are also transcribed in eukaryotes. However, the post-transcriptional regulation for these remains to be elucidated. Here, we identify 271 polycistronic RT-producing loci in Arabidopsis. Increased accumulation of RTs is detected in the nonsense-mediated mRNA decay (NMD)-deficient mutants compared with wild type, and the second open reading frames (ORFs) of bicistronic mRNAs are rarely translated in contrast to the first ORFs. Intergenic splicing (IS) events which occur between first and second genes are seen in 158 RTs. Splicing inhibition assays suggest that IS eliminates the chance of transcription termination at the polyadenylation sites of the first gene and promotes accumulation of RTs. These results indicate that RTs arise from genes whose transcription termination is relatively weak or attenuated by IS, but NMD selectively degrades them. Ultimately, this report presents a eukaryotic strategy for RNA metabolism.
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Affiliation(s)
- Yukio Kurihara
- grid.509461.f0000 0004 1757 8255Synthetic Genomics Research Group, RIKEN Center for Sustainable Resource Science, Suehiro-cho 1-7-22, Tsurumi-ku, Yokohama, Kanagawa 230-0045 Japan ,grid.26999.3d0000 0001 2151 536XDepartment of Life Sciences, Graduate School of Arts and Sciences, University of Tokyo, Komaba 3-8-1, Meguro-ku, Tokyo 153-8902 Japan
| | - Yuko Makita
- grid.509461.f0000 0004 1757 8255Synthetic Genomics Research Group, RIKEN Center for Sustainable Resource Science, Suehiro-cho 1-7-22, Tsurumi-ku, Yokohama, Kanagawa 230-0045 Japan ,grid.444244.60000 0004 0628 9167Faculty of Engineering, Maebashi Institute of Technology, Kamisadori 460-1, Maebashi, Gunma 371-0816 Japan
| | - Masaharu Kawauchi
- grid.509461.f0000 0004 1757 8255Synthetic Genomics Research Group, RIKEN Center for Sustainable Resource Science, Suehiro-cho 1-7-22, Tsurumi-ku, Yokohama, Kanagawa 230-0045 Japan
| | - Ami Kageyama
- grid.509461.f0000 0004 1757 8255Synthetic Genomics Research Group, RIKEN Center for Sustainable Resource Science, Suehiro-cho 1-7-22, Tsurumi-ku, Yokohama, Kanagawa 230-0045 Japan ,grid.268441.d0000 0001 1033 6139Graduate School of Nanobioscience, Department of Life and Environmental System Science, Yokohama City University, Yokohama, Kanagawa 236-0027 Japan
| | - Tomoko Kuriyama
- grid.509461.f0000 0004 1757 8255Synthetic Genomics Research Group, RIKEN Center for Sustainable Resource Science, Suehiro-cho 1-7-22, Tsurumi-ku, Yokohama, Kanagawa 230-0045 Japan
| | - Minami Matsui
- grid.509461.f0000 0004 1757 8255Synthetic Genomics Research Group, RIKEN Center for Sustainable Resource Science, Suehiro-cho 1-7-22, Tsurumi-ku, Yokohama, Kanagawa 230-0045 Japan ,grid.268441.d0000 0001 1033 6139Graduate School of Nanobioscience, Department of Life and Environmental System Science, Yokohama City University, Yokohama, Kanagawa 236-0027 Japan
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8
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Qin Y, Long Y, Zhai J. Genome-wide characterization of nascent RNA processing in plants. CURRENT OPINION IN PLANT BIOLOGY 2022; 69:102294. [PMID: 36063636 DOI: 10.1016/j.pbi.2022.102294] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2022] [Revised: 07/29/2022] [Accepted: 07/29/2022] [Indexed: 06/15/2023]
Abstract
Following transcription initiation, RNA polymerase II (Pol II) elongates through the genic region and terminates after the polyadenylation signal. This process is accompanied by splicing, 3' cleavage, and polyadenylation, to eventually form a mature mRNA. Recent advances in short-read and long-read high-throughput sequencing methods have shed light on the global landscape of these co-transcriptional events at nucleotide resolution. In this mini review, we summarize recent developments in genome-wide approaches that broadened our understanding of nascent RNA processing in plants.
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Affiliation(s)
- Yuwei Qin
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Institute of Plant and Food Science, Department of Biology, Southern University of Science and Technology (SUSTech), Shenzhen, Guangdong 518055, China
| | - Yanping Long
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Institute of Plant and Food Science, Department of Biology, Southern University of Science and Technology (SUSTech), Shenzhen, Guangdong 518055, China
| | - Jixian Zhai
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Institute of Plant and Food Science, Department of Biology, Southern University of Science and Technology (SUSTech), Shenzhen, Guangdong 518055, China.
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9
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Pagano A, Zannino L, Pagano P, Doria E, Dondi D, Macovei A, Biggiogera M, Araújo SDS, Balestrazzi A. Changes in genotoxic stress response, ribogenesis and PAP (3'-phosphoadenosine 5'-phosphate) levels are associated with loss of desiccation tolerance in overprimed Medicago truncatula seeds. PLANT, CELL & ENVIRONMENT 2022; 45:1457-1473. [PMID: 35188276 PMCID: PMC9311706 DOI: 10.1111/pce.14295] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Revised: 02/04/2022] [Accepted: 02/05/2022] [Indexed: 05/06/2023]
Abstract
Re-establishment of desiccation tolerance is essential for the survival of germinated seeds facing water deficit in the soil. The molecular and ultrastructural features of desiccation tolerance maintenance and loss within the nuclear compartment are not fully resolved. In the present study, the impact of desiccation-induced genotoxic stress on nucleolar ultrastructure and ribogenesis was explored along the rehydration-dehydration cycle applied in standard seed vigorization protocols. Primed and overprimed Medicago truncatula seeds, obtained through hydropriming followed by desiccation (dry-back), were analysed. In contrast to desiccation-tolerant primed seeds, overprimed seeds enter irreversible germination and do not survive dry-back. Reactive oxygen species, DNA damage and expression profiles of antioxidant/DNA Damage Response genes were measured, as main hallmarks of the seed response to desiccation stress. Nuclear ultrastructural features were also investigated. Overprimed seeds subjected to dry-back revealed altered rRNA accumulation profiles and up-regulation of genes involved in ribogenesis control. The signal molecule PAP (3'-phosphoadenosine 5'-phosphate) accumulated during dry-back only in primed seeds, as a distinctive feature of desiccation tolerance. The presented results show the molecular and ultrastructural landscapes of the seed desiccation response, including substantial changes in nuclear organization.
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Affiliation(s)
- Andrea Pagano
- Department of Biology and Biotechnology ‘L. Spallanzani'University of PaviaPaviaItaly
| | - Lorena Zannino
- Department of Biology and Biotechnology ‘L. Spallanzani'University of PaviaPaviaItaly
| | - Paola Pagano
- Department of Biology and Biotechnology ‘L. Spallanzani'University of PaviaPaviaItaly
| | - Enrico Doria
- Department of Biology and Biotechnology ‘L. Spallanzani'University of PaviaPaviaItaly
| | - Daniele Dondi
- Department of ChemistryUniversity of PaviaPaviaItaly
| | - Anca Macovei
- Department of Biology and Biotechnology ‘L. Spallanzani'University of PaviaPaviaItaly
| | - Marco Biggiogera
- Department of Biology and Biotechnology ‘L. Spallanzani'University of PaviaPaviaItaly
| | - Susana de Sousa Araújo
- Association BLC3‐Technology and Innovation CampusCentre Bio R&D UnitMacedo de CavaleirosPortugal
| | - Alma Balestrazzi
- Department of Biology and Biotechnology ‘L. Spallanzani'University of PaviaPaviaItaly
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10
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Krzyszton M, Kufel J. Analysis of mRNA-derived siRNAs in mutants of mRNA maturation and surveillance pathways in Arabidopsis thaliana. Sci Rep 2022; 12:1474. [PMID: 35087200 PMCID: PMC8795450 DOI: 10.1038/s41598-022-05574-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Accepted: 01/14/2022] [Indexed: 02/05/2023] Open
Abstract
Defects in RNA maturation and RNA decay factors may generate substrates for the RNA interference machinery. This phenomenon was observed in plants where mutations in some RNA-related factors lead to the production of RNA-quality control small interfering RNAs and several mutants show enhanced silencing of reporter transgenes. To assess the potential of RNAi activation on endogenous transcripts, we sequenced small RNAs from a set of Arabidopsis thaliana mutants with defects in various RNA metabolism pathways. We observed a global production of siRNAs caused by inefficient pre-mRNA cleavage and polyadenylation leading to read-through transcription into downstream antisense genes. In addition, in the lsm1a lsm1b double mutant, we identified NIA1, SMXL5, and several miRNA-targeted mRNAs as producing siRNAs, a group of transcripts suggested being especially sensitive to deficiencies in RNA metabolism. However, in most cases, RNA metabolism perturbations do not lead to the widespread production of siRNA derived from mRNA molecules. This observation is contrary to multiple studies based on reporter transgenes and suggests that only a very high accumulation of defective mRNA species caused by specific mutations or substantial RNA processing defects trigger RNAi pathways.
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Affiliation(s)
- Michal Krzyszton
- Laboratory of Seeds Molecular Biology, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106, Warsaw, Poland.
| | - Joanna Kufel
- Faculty of Biology, Institute of Genetics and Biotechnology, University of Warsaw, Pawinskiego 5a, 02-106, Warsaw, Poland.
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11
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Mo W, Liu B, Zhang H, Jin X, Lu D, Yu Y, Liu Y, Jia J, Long Y, Deng X, Cao X, Guo H, Zhai J. Landscape of transcription termination in Arabidopsis revealed by single-molecule nascent RNA sequencing. Genome Biol 2021; 22:322. [PMID: 34823554 PMCID: PMC8613925 DOI: 10.1186/s13059-021-02543-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2021] [Accepted: 11/01/2021] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND The dynamic process of transcription termination produces transient RNA intermediates that are difficult to distinguish from each other via short-read sequencing methods. RESULTS Here, we use single-molecule nascent RNA sequencing to characterize the various forms of transient RNAs during termination at genome-wide scale in wildtype Arabidopsis and in atxrn3, fpa, and met1 mutants. Our data reveal a wide range of termination windows among genes, ranging from ~ 50 nt to over 1000 nt. We also observe efficient termination before downstream tRNA genes, suggesting that chromatin structure around the promoter region of tRNA genes may block pol II elongation. 5' Cleaved readthrough transcription in atxrn3 with delayed termination can run into downstream genes to produce normally spliced and polyadenylated mRNAs in the absence of their own transcription initiation. Consistent with previous reports, we also observe long chimeric transcripts with cryptic splicing in fpa mutant; but loss of CG DNA methylation has no obvious impact on termination in the met1 mutant. CONCLUSIONS Our method is applicable to establish a comprehensive termination landscape in a broad range of species.
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Affiliation(s)
- Weipeng Mo
- Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, 518055, China
- Institute of Plant and Food Science, Southern University of Science and Technology, Shenzhen, 518055, China
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Bo Liu
- Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, 518055, China
- Institute of Plant and Food Science, Southern University of Science and Technology, Shenzhen, 518055, China
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Hong Zhang
- Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, 518055, China
- Institute of Plant and Food Science, Southern University of Science and Technology, Shenzhen, 518055, China
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Xianhao Jin
- Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, 518055, China
- Institute of Plant and Food Science, Southern University of Science and Technology, Shenzhen, 518055, China
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Dongdong Lu
- Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, 518055, China
- Institute of Plant and Food Science, Southern University of Science and Technology, Shenzhen, 518055, China
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Yiming Yu
- Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, 518055, China
- Institute of Plant and Food Science, Southern University of Science and Technology, Shenzhen, 518055, China
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Yuelin Liu
- Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, 518055, China
- Institute of Plant and Food Science, Southern University of Science and Technology, Shenzhen, 518055, China
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Jinbu Jia
- Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, 518055, China
- Institute of Plant and Food Science, Southern University of Science and Technology, Shenzhen, 518055, China
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Yanping Long
- Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, 518055, China
- Institute of Plant and Food Science, Southern University of Science and Technology, Shenzhen, 518055, China
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Xian Deng
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Xiaofeng Cao
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Hongwei Guo
- Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, 518055, China
- Institute of Plant and Food Science, Southern University of Science and Technology, Shenzhen, 518055, China
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Jixian Zhai
- Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, 518055, China.
- Institute of Plant and Food Science, Southern University of Science and Technology, Shenzhen, 518055, China.
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Southern University of Science and Technology, Shenzhen, 518055, China.
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12
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Liu H, Moore CL. On the Cutting Edge: Regulation and Therapeutic Potential of the mRNA 3' End Nuclease. Trends Biochem Sci 2021; 46:772-784. [PMID: 33941430 PMCID: PMC8364479 DOI: 10.1016/j.tibs.2021.04.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Revised: 03/18/2021] [Accepted: 04/02/2021] [Indexed: 12/24/2022]
Abstract
Cleavage of nascent transcripts is a fundamental process for eukaryotic mRNA maturation and for the production of different mRNA isoforms. In eukaryotes, cleavage of mRNA precursors by the highly conserved endonuclease CPSF73 is critical for mRNA stability, export from the nucleus, and translation. As an essential enzyme in the cell, CPSF73 surprisingly shows promise as a drug target for specific cancers and for protozoan parasites. In this review, we cover our current understanding of CPSF73 in cleavage and polyadenylation, histone pre-mRNA processing, and transcription termination. We discuss the potential of CPSF73 as a target for novel therapeutics and highlight further research into the regulation of CPSF73 that will be critical to understanding its role in cancer and other diseases.
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Affiliation(s)
- Huiyun Liu
- Department of Developmental, Molecular, and Chemical Biology, Tufts University School of Medicine, Boston, MA 02111, USA
| | - Claire L Moore
- Department of Developmental, Molecular, and Chemical Biology, Tufts University School of Medicine, Boston, MA 02111, USA.
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13
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Phua SY, De Smet B, Remacle C, Chan KX, Van Breusegem F. Reactive oxygen species and organellar signaling. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:5807-5824. [PMID: 34009340 DOI: 10.1093/jxb/erab218] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Accepted: 05/14/2021] [Indexed: 05/07/2023]
Abstract
The evolution of photosynthesis and its associated metabolic pathways has been crucial to the successful establishment of plants, but has also challenged plant cells in the form of production of reactive oxygen species (ROS). Intriguingly, multiple forms of ROS are generated in virtually every plant cell compartment through diverse pathways. As a result, a sophisticated network of ROS detoxification and signaling that is simultaneously tailored to individual organelles and safeguards the entire cell is necessary. Here we take an organelle-centric view on the principal sources and sinks of ROS across the plant cell and provide insights into the ROS-induced organelle to nucleus retrograde signaling pathways needed for operational readjustments during environmental stresses.
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Affiliation(s)
- Su Yin Phua
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent,Belgium
- Center for Plant Systems Biology, VIB, Ghent,Belgium
| | - Barbara De Smet
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent,Belgium
- Center for Plant Systems Biology, VIB, Ghent,Belgium
| | - Claire Remacle
- Genetics and Physiology of Microalgae, InBios/Phytosystems, Université de Liège, Liège,Belgium
| | - Kai Xun Chan
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent,Belgium
- Center for Plant Systems Biology, VIB, Ghent,Belgium
| | - Frank Van Breusegem
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent,Belgium
- Center for Plant Systems Biology, VIB, Ghent,Belgium
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14
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Kleine T, Nägele T, Neuhaus HE, Schmitz-Linneweber C, Fernie AR, Geigenberger P, Grimm B, Kaufmann K, Klipp E, Meurer J, Möhlmann T, Mühlhaus T, Naranjo B, Nickelsen J, Richter A, Ruwe H, Schroda M, Schwenkert S, Trentmann O, Willmund F, Zoschke R, Leister D. Acclimation in plants - the Green Hub consortium. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 106:23-40. [PMID: 33368770 DOI: 10.1111/tpj.15144] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Revised: 12/08/2020] [Accepted: 12/14/2020] [Indexed: 05/04/2023]
Abstract
Acclimation is the capacity to adapt to environmental changes within the lifetime of an individual. This ability allows plants to cope with the continuous variation in ambient conditions to which they are exposed as sessile organisms. Because environmental changes and extremes are becoming even more pronounced due to the current period of climate change, enhancing the efficacy of plant acclimation is a promising strategy for mitigating the consequences of global warming on crop yields. At the cellular level, the chloroplast plays a central role in many acclimation responses, acting both as a sensor of environmental change and as a target of cellular acclimation responses. In this Perspective article, we outline the activities of the Green Hub consortium funded by the German Science Foundation. The main aim of this research collaboration is to understand and strategically modify the cellular networks that mediate plant acclimation to adverse environments, employing Arabidopsis, tobacco (Nicotiana tabacum) and Chlamydomonas as model organisms. These efforts will contribute to 'smart breeding' methods designed to create crop plants with improved acclimation properties. To this end, the model oilseed crop Camelina sativa is being used to test modulators of acclimation for their potential to enhance crop yield under adverse environmental conditions. Here we highlight the current state of research on the role of gene expression, metabolism and signalling in acclimation, with a focus on chloroplast-related processes. In addition, further approaches to uncovering acclimation mechanisms derived from systems and computational biology, as well as adaptive laboratory evolution with photosynthetic microbes, are highlighted.
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Affiliation(s)
- Tatjana Kleine
- Plant Molecular Biology, Faculty of Biology, Ludwig-Maximilians-Universität München, Planegg-Martinsried, 82152, Germany
| | - Thomas Nägele
- Plant Evolutionary Cell Biology, Faculty of Biology, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Munich, 82152, Germany
| | - H Ekkehard Neuhaus
- Plant Physiology, Department of Biology, Technische Universität Kaiserslautern, Kaiserslautern, 67663, Germany
| | | | - Alisdair R Fernie
- Central Metabolism, Max-Planck-Institut für Molekulare Pflanzenphysiologie, Potsdam-Golm, 14476, Germany
| | - Peter Geigenberger
- Plant Metabolism, Faculty of Biology, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Munich, 82152, Germany
| | - Bernhard Grimm
- Plant Physiology, Institute of Biology, Humboldt-Universität zu Berlin, Berlin, 10115, Germany
| | - Kerstin Kaufmann
- Plant Cell and Molecular Biology, Institute of Biology, Humboldt-Universität zu Berlin, Berlin, 10115, Germany
| | - Edda Klipp
- Theoretical Biophysics, Institute of Biology, Humboldt-Universität zu Berlin, Berlin, 10115, Germany
| | - Jörg Meurer
- Plant Molecular Biology, Faculty of Biology, Ludwig-Maximilians-Universität München, Planegg-Martinsried, 82152, Germany
| | - Torsten Möhlmann
- Plant Physiology, Department of Biology, Technische Universität Kaiserslautern, Kaiserslautern, 67663, Germany
| | - Timo Mühlhaus
- Computational Systems Biology, Department of Biology, Technische Universität Kaiserslautern, Kaiserslautern, 67663, Germany
| | - Belen Naranjo
- Plant Molecular Biology, Faculty of Biology, Ludwig-Maximilians-Universität München, Planegg-Martinsried, 82152, Germany
| | - Jörg Nickelsen
- Molecular Plant Science, Faculty of Biology, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Munich, 82152, Germany
| | - Andreas Richter
- Physiology of Plant Organelles, Institute of Biology, Humboldt-Universität zu Berlin, Berlin, 10115, Germany
| | - Hannes Ruwe
- Molecular Genetics, Institute of Biology, Humboldt-Universität zu Berlin, Berlin, 10115, Germany
| | - Michael Schroda
- Molecular Biotechnology & Systems Biology, Department of Biology, Technische Universität Kaiserslautern, Kaiserslautern, 67663, Germany
| | - Serena Schwenkert
- Plant Biochemistry and Physiology, Faculty of Biology, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Munich, 82152, Germany
| | - Oliver Trentmann
- Plant Physiology, Department of Biology, Technische Universität Kaiserslautern, Kaiserslautern, 67663, Germany
| | - Felix Willmund
- Molecular Genetics of Eukaryotes, Department of Biology, Technische Universität Kaiserslautern, Kaiserslautern, 67663, Germany
| | - Reimo Zoschke
- Translational Regulation in Plants, Max-Planck-Institut für Molekulare Pflanzenphysiologie, Potsdam-Golm, 14476, Germany
| | - Dario Leister
- Plant Molecular Biology, Faculty of Biology, Ludwig-Maximilians-Universität München, Planegg-Martinsried, 82152, Germany
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15
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Liu M, Zhu J, Dong Z. Immediate transcriptional responses of Arabidopsis leaves to heat shock. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2021; 63:468-483. [PMID: 32644278 DOI: 10.1111/jipb.12990] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Accepted: 07/08/2020] [Indexed: 05/26/2023]
Abstract
Plants have evolved efficient mechanisms for adapting to temperature fluctuations, known as heat stress response and heat stress memory. Although the transcriptional regulatory network of plant heat stress response has been established, little is known about the genome-wide transcriptional changes occurring within the first several minutes after heat shock. Here, we investigated the nascent RNA and mature messenger RNA (mRNA) from plant leaf tissues exposed to 5 min of heat shock treatment using global run-on sequencing and RNA sequencing methods. Only a small group of genes were up- or downregulated at both the nascent RNA and mRNA levels. Primed plants that were already exposed to mild heat stress exhibited a more drastic alteration at multiple transcriptional steps than naïve plants that had not experienced heat stress. Upon heat shock, we also observed the following: (i) engaged RNA polymerase II accumulated downstream of transcription start sites; (ii) 5' pausing release was a rate-limiting step for the induction of some heat shock protein genes; (iii) numerous genes switched transcription modes; (iv) pervasive read-through was induced at terminators; and (v) heat stress memory occurs at multiple steps of the transcription cycle, such as at Pol II recruitment, 5' pausing, elongation, and termination.
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Affiliation(s)
- Min Liu
- Innovative Center of Molecular Genetics and Evolution, Guangzhou Higher Education Mega Center, School of Life Sciences, Guangzhou University, Guangzhou, 510006, China
| | - Jiafu Zhu
- Innovative Center of Molecular Genetics and Evolution, Guangzhou Higher Education Mega Center, School of Life Sciences, Guangzhou University, Guangzhou, 510006, China
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, South China Botanical Garden, the Chinese Academy of Sciences, Guangzhou, 510650, China
| | - Zhicheng Dong
- Innovative Center of Molecular Genetics and Evolution, Guangzhou Higher Education Mega Center, School of Life Sciences, Guangzhou University, Guangzhou, 510006, China
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16
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Wang L, Leister D, Kleine T. Chloroplast development and genomes uncoupled signaling are independent of the RNA-directed DNA methylation pathway. Sci Rep 2020; 10:15412. [PMID: 32963291 PMCID: PMC7508864 DOI: 10.1038/s41598-020-71907-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Accepted: 08/21/2020] [Indexed: 01/18/2023] Open
Abstract
The Arabidopsis genome is methylated in CG and non-CG (CHG, and CHH in which H stands for A, T, or C) sequence contexts. DNA methylation has been suggested to be critical for seed development, and CHH methylation patterns change during stratification and germination. In plants, CHH methylation occurs mainly through the RNA-directed DNA methylation (RdDM) pathway. To test for an involvement of the RdDM pathway in chloroplast development, we analyzed seedling greening and the maximum quantum yield of photosystem II (Fv/Fm) in Arabidopsis thaliana seedlings perturbed in components of that pathway. Neither seedling greening nor Fv/Fm in seedlings and adult plants were affected in this comprehensive set of mutants, indicating that alterations in the RdDM pathway do not affect chloroplast development. Application of inhibitors like lincomycin or norflurazon inhibits greening of seedlings and represses the expression of photosynthesis-related genes including LIGHT HARVESTING CHLOROPHYLL A/B BINDING PROTEIN1.2 (LHCB1.2) in the nucleus. Our results indicate that the LHCB1.2 promoter is poorly methylated under both control conditions and after inhibitor treatment. Therefore no correlation between LHCB1.2 mRNA transcription and methylation changes of the LHCB1.2 promoter could be established. Moreover, we conclude that perturbations in the RdDM pathway do not interfere with gun signaling.
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Affiliation(s)
- Liangsheng Wang
- Plant Molecular Biology (Botany), Department Biology I, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
| | - Dario Leister
- Plant Molecular Biology (Botany), Department Biology I, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
| | - Tatjana Kleine
- Plant Molecular Biology (Botany), Department Biology I, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany.
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17
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Unal D, García-Caparrós P, Kumar V, Dietz KJ. Chloroplast-associated molecular patterns as concept for fine-tuned operational retrograde signalling. Philos Trans R Soc Lond B Biol Sci 2020; 375:20190443. [PMID: 32362264 DOI: 10.1098/rstb.2019.0443] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Chloroplasts compose about one-quarter of the mesophyll cell volume and contain about 60% of the cell protein. Photosynthetic carbon assimilation is the dominating metabolism in illuminated leaves. To optimize the resource expenditure in these costly organelles and to control and adjust chloroplast metabolism, an intensive transfer of information between nucleus-cytoplasm and chloroplasts occurs in both directions as anterograde and retrograde signalling. Recent research identified multiple retrograde pathways that use metabolite transfer and include reaction products of lipids and carotenoids with reactive oxygen species (ROS). Other pathways use metabolites of carbon, sulfur and nitrogen metabolism, low molecular weight antioxidants and hormone precursors to carry information between the cell compartments. This review focuses on redox- and ROS-related retrograde signalling pathways. In analogy to the microbe-associated molecular pattern, we propose the term 'chloroplast-associated molecular pattern' which connects chloroplast performance to extrachloroplast processes such as nuclear gene transcription, posttranscriptional processing, including translation, and RNA and protein fate. This article is part of the theme issue 'Retrograde signalling from endosymbiotic organelles'.
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Affiliation(s)
- Dilek Unal
- Biochemistry and Physiology of Plants, Bielefeld University, 33501 Bielefeld, Germany.,Molecular Biology and Genetic, Faculty of Science and Letter, Bilecik Seyh Edebali University, 11230 Bilecik, Turkey
| | - Pedro García-Caparrós
- Biochemistry and Physiology of Plants, Bielefeld University, 33501 Bielefeld, Germany.,Department of Agronomy, University of Almeria, Higher Engineering School, Agrifood Campus of International Excellence ceiA3, Carretera de Sacramento s/n, La Cañada de San Urbano 04120, Almeria, Spain
| | - Vijay Kumar
- Biochemistry and Physiology of Plants, Bielefeld University, 33501 Bielefeld, Germany
| | - Karl-Josef Dietz
- Biochemistry and Physiology of Plants, Bielefeld University, 33501 Bielefeld, Germany
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18
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Wang Y, Selinski J, Mao C, Zhu Y, Berkowitz O, Whelan J. Linking mitochondrial and chloroplast retrograde signalling in plants. Philos Trans R Soc Lond B Biol Sci 2020; 375:20190410. [PMID: 32362265 PMCID: PMC7209950 DOI: 10.1098/rstb.2019.0410] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Retrograde signalling refers to the regulation of nuclear gene expression in response to functional changes in organelles. In plants, the two energy-converting organelles, mitochondria and chloroplasts, are tightly coordinated to balance their activities. Although our understanding of components involved in retrograde signalling has greatly increased in the last decade, studies on the regulation of the two organelle signalling pathways have been largely independent. Thus, the mechanism of how mitochondrial and chloroplastic retrograde signals are integrated is largely unknown. Here, we summarize recent findings on the function of mitochondrial signalling components and their links to chloroplast retrograde responses. From this, a picture emerges showing that the major regulators are integrators of both organellar retrograde signalling pathways. This article is part of the theme issue 'Retrograde signalling from endosymbiotic organelles'.
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Affiliation(s)
- Yan Wang
- Department of Animal, Plant and Soil Sciences, Australian Research Council Centre of Excellence in Plant Energy Biology, School of Life Sciences, La Trobe University, Bundoora, Victoria, Australia
| | - Jennifer Selinski
- Department of Animal, Plant and Soil Sciences, Australian Research Council Centre of Excellence in Plant Energy Biology, School of Life Sciences, La Trobe University, Bundoora, Victoria, Australia
| | - Chunli Mao
- Department of Animal, Plant and Soil Sciences, Australian Research Council Centre of Excellence in Plant Energy Biology, School of Life Sciences, La Trobe University, Bundoora, Victoria, Australia.,Department of Animal Science and Technology, Grassland Science, China Agricultural University, Beijing 100193, People's Republic of China
| | - Yanqiao Zhu
- Department of Animal, Plant and Soil Sciences, Australian Research Council Centre of Excellence in Plant Energy Biology, School of Life Sciences, La Trobe University, Bundoora, Victoria, Australia.,Department of Animal Science and Technology, Grassland Science, China Agricultural University, Beijing 100193, People's Republic of China
| | - Oliver Berkowitz
- Department of Animal, Plant and Soil Sciences, Australian Research Council Centre of Excellence in Plant Energy Biology, School of Life Sciences, La Trobe University, Bundoora, Victoria, Australia
| | - James Whelan
- Department of Animal, Plant and Soil Sciences, Australian Research Council Centre of Excellence in Plant Energy Biology, School of Life Sciences, La Trobe University, Bundoora, Victoria, Australia
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19
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FIERY1 promotes microRNA accumulation by suppressing rRNA-derived small interfering RNAs in Arabidopsis. Nat Commun 2019; 10:4424. [PMID: 31562313 PMCID: PMC6765019 DOI: 10.1038/s41467-019-12379-z] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Accepted: 09/06/2019] [Indexed: 01/29/2023] Open
Abstract
Plant microRNAs (miRNAs) associate with ARGONAUTE1 (AGO1) to direct post-transcriptional gene silencing and regulate numerous biological processes. Although AGO1 predominantly binds miRNAs in vivo, it also associates with endogenous small interfering RNAs (siRNAs). It is unclear whether the miRNA/siRNA balance affects miRNA activities. Here we report that FIERY1 (FRY1), which is involved in 5'-3' RNA degradation, regulates miRNA abundance and function by suppressing the biogenesis of ribosomal RNA-derived siRNAs (risiRNAs). In mutants of FRY1 and the nuclear 5'-3' exonuclease genes XRN2 and XRN3, we find that a large number of 21-nt risiRNAs are generated through an endogenous siRNA biogenesis pathway. The production of risiRNAs correlates with pre-rRNA processing defects in these mutants. We also show that these risiRNAs are loaded into AGO1, causing reduced loading of miRNAs. This study reveals a previously unknown link between rRNA processing and miRNA accumulation.
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20
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Chan KX, Phua SY, Van Breusegem F. Secondary sulfur metabolism in cellular signalling and oxidative stress responses. JOURNAL OF EXPERIMENTAL BOTANY 2019; 70:4237-4250. [PMID: 30868163 DOI: 10.1093/jxb/erz119] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2018] [Accepted: 03/08/2019] [Indexed: 05/27/2023]
Abstract
The sulfur metabolism pathway in plants produces a variety of compounds that are central to the acclimation response to oxidative stresses such as drought and high light. Primary sulfur assimilation provides the amino acid cysteine, which is utilized in protein synthesis and as a precursor for the cellular redox buffer glutathione. In contrast, the secondary sulfur metabolism pathway produces sulfated compounds such as glucosinolates and sulfated peptides, as well as a corresponding by-product 3'-phosphoadenosine 5'-phosphate (PAP). Emerging evidence over the past decade has shown that secondary sulfur metabolism also has a crucial engagement during oxidative stress. This occurs across various cellular, tissue, and organismal levels including chloroplast-to-nucleus retrograde signalling events mediated by PAP, modulation of hormonal signalling by sulfated compounds and PAP, control of physiological responses such as stomatal closure, and potential regulation of plant growth. In this review, we examine the contribution of the different components of plant secondary metabolism to oxidative stress homeostasis, and how this pathway is metabolically regulated. We further outline the key outstanding questions in the field that are necessary to understand how and why this 'specialized' metabolic pathway plays significant roles in plant oxidative stress tolerance.
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Affiliation(s)
- Kai Xun Chan
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Technologiepark, Ghent, Belgium
- VIB Center for Plant Systems Biology, Technologiepark, Ghent, Belgium
| | - Su Yin Phua
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Technologiepark, Ghent, Belgium
- VIB Center for Plant Systems Biology, Technologiepark, Ghent, Belgium
| | - Frank Van Breusegem
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Technologiepark, Ghent, Belgium
- VIB Center for Plant Systems Biology, Technologiepark, Ghent, Belgium
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21
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Shapiguzov A, Vainonen JP, Hunter K, Tossavainen H, Tiwari A, Järvi S, Hellman M, Aarabi F, Alseekh S, Wybouw B, Van Der Kelen K, Nikkanen L, Krasensky-Wrzaczek J, Sipari N, Keinänen M, Tyystjärvi E, Rintamäki E, De Rybel B, Salojärvi J, Van Breusegem F, Fernie AR, Brosché M, Permi P, Aro EM, Wrzaczek M, Kangasjärvi J. Arabidopsis RCD1 coordinates chloroplast and mitochondrial functions through interaction with ANAC transcription factors. eLife 2019; 8:43284. [PMID: 30767893 PMCID: PMC6414205 DOI: 10.7554/elife.43284] [Citation(s) in RCA: 93] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Accepted: 02/14/2019] [Indexed: 01/17/2023] Open
Abstract
Reactive oxygen species (ROS)-dependent signaling pathways from chloroplasts and mitochondria merge at the nuclear protein RADICAL-INDUCED CELL DEATH1 (RCD1). RCD1 interacts in vivo and suppresses the activity of the transcription factors ANAC013 and ANAC017, which mediate a ROS-related retrograde signal originating from mitochondrial complex III. Inactivation of RCD1 leads to increased expression of mitochondrial dysfunction stimulon (MDS) genes regulated by ANAC013 and ANAC017. Accumulating MDS gene products, including alternative oxidases (AOXs), affect redox status of the chloroplasts, leading to changes in chloroplast ROS processing and increased protection of photosynthetic apparatus. ROS alter the abundance, thiol redox state and oligomerization of the RCD1 protein in vivo, providing feedback control on its function. RCD1-dependent regulation is linked to chloroplast signaling by 3'-phosphoadenosine 5'-phosphate (PAP). Thus, RCD1 integrates organellar signaling from chloroplasts and mitochondria to establish transcriptional control over the metabolic processes in both organelles. Most plant cells contain two types of compartments, the mitochondria and the chloroplasts, which work together to supply the chemical energy required by life processes. Genes located in another part of the cell, the nucleus, encode for the majority of the proteins found in these compartments. At any given time, the mitochondria and the chloroplasts send specific, ‘retrograde’ signals to the nucleus to turn on or off the genes they need. For example, mitochondria produce molecules known as reactive oxygen species (ROS) if they are having problems generating energy. These molecules activate several regulatory proteins that move into the nucleus and switch on MDS genes, a set of genes which helps to repair the mitochondria. Chloroplasts also produce ROS that can act as retrograde signals. It is still unclear how the nucleus integrates signals from both chloroplasts and mitochondria to ‘decide’ which genes to switch on, but a protein called RCD1 may play a role in this process. Indeed, previous studies have found that Arabidopsis plants that lack RCD1 have defects in both their mitochondria and chloroplasts. In these mutant plants, the MDS genes are constantly active and the chloroplasts have problems making ROS. To investigate this further, Shapiguzov, Vainonen et al. use biochemical and genetic approaches to study RCD1 in Arabidopsis. The experiments confirm that this protein allows a dialog to take place between the retrograde signals of both mitochondria and chloroplasts. On one hand, RCD1 binds to and inhibits the regulatory proteins that usually activate the MDS genes under the control of mitochondria. This explains why, in the absence of RCD1, the MDS genes are always active, which is ultimately disturbing how these compartments work. On the other hand, RCD1 is also found to be sensitive to the ROS that chloroplasts produce. This means that chloroplasts may be able to affect when mitochondria generate energy by regulating the protein. Finally, further experiments show that MDS genes can affect both mitochondria and chloroplasts: by influencing how these genes are regulated, RCD1 therefore acts on the two types of compartments. Overall, the work by Shapiguzov, Vainonen et al. describes a new way Arabidopsis coordinates its mitochondria and chloroplasts. Further studies will improve our understanding of how plants regulate these compartments in different environments to produce the energy they need. In practice, this may also help plant breeders create new varieties of crops that produce energy more efficiently and which better resist to stress.
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Affiliation(s)
- Alexey Shapiguzov
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland.,Viikki Plant Science Center, University of Helsinki, Helsinki, Finland.,Institute of Plant Physiology, Russian Academy of Sciences, Moscow, Russia
| | - Julia P Vainonen
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland.,Viikki Plant Science Center, University of Helsinki, Helsinki, Finland
| | - Kerri Hunter
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland.,Viikki Plant Science Center, University of Helsinki, Helsinki, Finland
| | - Helena Tossavainen
- Program in Structural Biology and Biophysics, Institute of Biotechnology, University of Helsinki, Helsinki, Finland.,Department of Chemistry, Nanoscience Center, University of Jyväskylä, Jyväskylä, Finland
| | - Arjun Tiwari
- Department of Biochemistry / Molecular Plant Biology, University of Turku, Turku, Finland
| | - Sari Järvi
- Department of Biochemistry / Molecular Plant Biology, University of Turku, Turku, Finland
| | - Maarit Hellman
- Department of Chemistry, Nanoscience Center, University of Jyväskylä, Jyväskylä, Finland
| | - Fayezeh Aarabi
- Max-Planck Institute for Molecular Plant Physiology, Potsdam, Germany
| | - Saleh Alseekh
- Max-Planck Institute for Molecular Plant Physiology, Potsdam, Germany.,Center of Plant System Biology and Biotechnology, Plovdiv, Bulgaria
| | - Brecht Wybouw
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium.,VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Katrien Van Der Kelen
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium.,VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Lauri Nikkanen
- Department of Biochemistry / Molecular Plant Biology, University of Turku, Turku, Finland
| | - Julia Krasensky-Wrzaczek
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland.,Viikki Plant Science Center, University of Helsinki, Helsinki, Finland
| | - Nina Sipari
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland.,Viikki Metabolomics Unit, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Markku Keinänen
- Department of Environmental and Biological Sciences, University of Eastern Finland, Joensuu, Finland
| | - Esa Tyystjärvi
- Department of Biochemistry / Molecular Plant Biology, University of Turku, Turku, Finland
| | - Eevi Rintamäki
- Department of Biochemistry / Molecular Plant Biology, University of Turku, Turku, Finland
| | - Bert De Rybel
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium.,VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Jarkko Salojärvi
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland.,Viikki Plant Science Center, University of Helsinki, Helsinki, Finland
| | - Frank Van Breusegem
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium.,VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Alisdair R Fernie
- Max-Planck Institute for Molecular Plant Physiology, Potsdam, Germany.,Center of Plant System Biology and Biotechnology, Plovdiv, Bulgaria
| | - Mikael Brosché
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland.,Viikki Plant Science Center, University of Helsinki, Helsinki, Finland.,Institute of Technology, University of Tartu, Tartu, Estonia
| | - Perttu Permi
- Program in Structural Biology and Biophysics, Institute of Biotechnology, University of Helsinki, Helsinki, Finland.,Department of Chemistry, Nanoscience Center, University of Jyväskylä, Jyväskylä, Finland.,Department of Biological and Environmental Science, Nanoscience Center, University of Jyväskylä, Jyväskylä, Finland
| | - Eva-Mari Aro
- Department of Biochemistry / Molecular Plant Biology, University of Turku, Turku, Finland
| | - Michael Wrzaczek
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland.,Viikki Plant Science Center, University of Helsinki, Helsinki, Finland
| | - Jaakko Kangasjärvi
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland.,Viikki Plant Science Center, University of Helsinki, Helsinki, Finland
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