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Baraniecka P, Seibt W, Groten K, Kessler D, McGale E, Gase K, Baldwin IT, Pannell JR. Prezygotic mate selection is only partially correlated with the expression of NaS-like RNases and affects offspring phenotypes. THE NEW PHYTOLOGIST 2024; 242:2832-2844. [PMID: 38581189 DOI: 10.1111/nph.19741] [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: 12/18/2023] [Accepted: 03/21/2024] [Indexed: 04/08/2024]
Abstract
Nicotiana attenuata styles preferentially select pollen from among accessions with corresponding expression patterns of NaS-like-RNases (SLRs), and the postpollination ethylene burst (PPEB) is an accurate predictor of seed siring success. However, the ecological consequences of mate selection, its effect on the progeny, and the role of SLRs in the control of ethylene signaling remain unknown. We explored the link between the magnitude of the ethylene burst and expression of the SLRs in a set of recombinant inbred lines (RILs), dissected the genetic underpinnings of mate selection through genome-wide association study (GWAS), and examined its outcome for phenotypes in the next generation. We found that high levels of PPEB are associated with the absence of SLR2 in most of the tested RILs. We identified candidate genes potentially involved in the control of mate selection and showed that pollination of maternal genotypes with their favored pollen donors produces offspring with longer roots. When the maternal genotypes are only able to select against nonfavored pollen donors, the selection for such positive traits is abolished. We conclude that plants' ability of mate choice contributes to measurable changes in progeny phenotypes and is thus likely a target of selection.
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Affiliation(s)
| | - Wibke Seibt
- MPI for Chemical Ecology, Hans-Knöll-Str. 8, Jena, 07745, Germany
| | - Karin Groten
- MPI for Chemical Ecology, Hans-Knöll-Str. 8, Jena, 07745, Germany
| | - Danny Kessler
- MPI for Chemical Ecology, Hans-Knöll-Str. 8, Jena, 07745, Germany
| | - Erica McGale
- Department of Ecology and Evolution, University of Lausanne, Lausanne, CH-1015, Switzerland
| | - Klaus Gase
- MPI for Chemical Ecology, Hans-Knöll-Str. 8, Jena, 07745, Germany
| | - Ian T Baldwin
- MPI for Chemical Ecology, Hans-Knöll-Str. 8, Jena, 07745, Germany
| | - John R Pannell
- Department of Ecology and Evolution, University of Lausanne, Lausanne, CH-1015, Switzerland
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2
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Blagojevic A, Baldrich P, Schiaffini M, Lechner E, Baumberger N, Hammann P, Elmayan T, Garcia D, Vaucheret H, Meyers BC, Genschik P. Heat stress promotes Arabidopsis AGO1 phase separation and association with stress granule components. iScience 2024; 27:109151. [PMID: 38384836 PMCID: PMC10879784 DOI: 10.1016/j.isci.2024.109151] [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: 08/31/2023] [Revised: 12/17/2023] [Accepted: 02/01/2024] [Indexed: 02/23/2024] Open
Abstract
In Arabidopsis thaliana, ARGONAUTE1 (AGO1) plays a central role in microRNA (miRNA) and small interfering RNA (siRNA)-mediated silencing. AGO1 associates to the rough endoplasmic reticulum to conduct miRNA-mediated translational repression, mRNA cleavage, and biogenesis of phased siRNAs. Here, we show that a 37°C heat stress (HS) promotes AGO1 protein accumulation in cytosolic condensates where it colocalizes with components of siRNA bodies and of stress granules. AGO1 contains a prion-like domain in its poorly characterized N-terminal Poly-Q domain, which is sufficient to undergo phase separation independently of the presence of SGS3. HS only moderately affects the small RNA repertoire, the loading of AGO1 by miRNAs, and the signatures of target cleavage, suggesting that its localization in condensates protects AGO1 rather than promoting or impairing its activity in reprogramming gene expression during stress. Collectively, our work sheds new light on the impact of high temperature on a main effector of RNA silencing in plants.
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Affiliation(s)
- Aleksandar Blagojevic
- Institut de Biologie Moléculaire des Plantes, CNRS, Université de Strasbourg, 12, rue du Général Zimmer, 67084 Strasbourg, France
| | | | - Marlene Schiaffini
- Institut de Biologie Moléculaire des Plantes, CNRS, Université de Strasbourg, 12, rue du Général Zimmer, 67084 Strasbourg, France
| | - Esther Lechner
- Institut de Biologie Moléculaire des Plantes, CNRS, Université de Strasbourg, 12, rue du Général Zimmer, 67084 Strasbourg, France
| | - Nicolas Baumberger
- Institut de Biologie Moléculaire des Plantes, CNRS, Université de Strasbourg, 12, rue du Général Zimmer, 67084 Strasbourg, France
| | - Philippe Hammann
- Plateforme Protéomique Strasbourg Esplanade du CNRS, Université de Strasbourg, 67084 Strasbourg, France
| | - Taline Elmayan
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), 78000 Versailles, France
| | - Damien Garcia
- Institut de Biologie Moléculaire des Plantes, CNRS, Université de Strasbourg, 12, rue du Général Zimmer, 67084 Strasbourg, France
| | - Hervé Vaucheret
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), 78000 Versailles, France
| | - Blake C. Meyers
- Donald Danforth Plant Science Center, Saint Louis, MO 63132, USA
- Division of Plant Science and Technology, University of Missouri, Columbia, MO 65211, USA
| | - Pascal Genschik
- Institut de Biologie Moléculaire des Plantes, CNRS, Université de Strasbourg, 12, rue du Général Zimmer, 67084 Strasbourg, France
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3
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Luha R, Rana V, Vainstein A, Kumar V. Nonsense-mediated mRNA decay pathway in plants under stress: general gene regulatory mechanism and advances. PLANTA 2024; 259:51. [PMID: 38289504 DOI: 10.1007/s00425-023-04317-7] [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: 05/02/2023] [Accepted: 12/23/2023] [Indexed: 02/01/2024]
Abstract
MAIN CONCLUSION Nonsense-mediated mRNA decay in eukaryotes is vital to cellular homeostasis. Further knowledge of its putative role in plant RNA metabolism under stress is pivotal to developing fitness-optimizing strategies. Nonsense-mediated mRNA decay (NMD), part of the mRNA surveillance pathway, is an evolutionarily conserved form of gene regulation in all living organisms. Degradation of mRNA-bearing premature termination codons and regulation of physiological RNA levels highlight NMD's role in shaping the cellular transcriptome. Initially regarded as purely a tool for cellular RNA quality control, NMD is now considered to mediate various aspects of plant developmental processes and responses to environmental changes. Here we offer a basic understanding of NMD in eukaryotes by explaining the concept of premature termination codon recognition and NMD complex formation. We also provide a detailed overview of the NMD mechanism and its role in gene regulation. The potential role of effectors, including ABCE1, in ribosome recycling during the translation process is also explained. Recent reports of alternatively spliced variants of corresponding genes targeted by NMD in Arabidopsis thaliana are provided in tabular format. Detailed figures are also provided to clarify the NMD concept in plants. In particular, accumulating evidence shows that NMD can serve as a novel alternative strategy for genetic manipulation and can help design RNA-based therapies to combat stress in plants. A key point of emphasis is its function as a gene regulatory mechanism as well as its dynamic regulation by environmental and developmental factors. Overall, a detailed molecular understanding of the NMD mechanism can lead to further diverse applications, such as improving cellular homeostasis in living organisms.
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Affiliation(s)
- Rashmita Luha
- Department of Botany, School for Basic Sciences, Central University of Punjab, Bathinda, India
- Centre for Biosystems Science and Engineering, Indian Institute of Science Bangalore, Bangaluru, India
| | - Varnika Rana
- Department of Botany, School for Basic Sciences, Central University of Punjab, Bathinda, India
| | - Alexander Vainstein
- Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Vinay Kumar
- Department of Botany, School for Basic Sciences, Central University of Punjab, Bathinda, India.
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James AB, Sharples C, Laird J, Armstrong EM, Guo W, Tzioutziou N, Zhang R, Brown JWS, Nimmo HG, Jones MA. REVEILLE2 thermosensitive splicing: a molecular basis for the integration of nocturnal temperature information by the Arabidopsis circadian clock. THE NEW PHYTOLOGIST 2024; 241:283-297. [PMID: 37897048 DOI: 10.1111/nph.19339] [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: 05/07/2023] [Accepted: 09/27/2023] [Indexed: 10/29/2023]
Abstract
Cold stress is one of the major environmental factors that limit growth and yield of plants. However, it is still not fully understood how plants account for daily temperature fluctuations, nor how these temperature changes are integrated with other regulatory systems such as the circadian clock. We demonstrate that REVEILLE2 undergoes alternative splicing after chilling that increases accumulation of a transcript isoform encoding a MYB-like transcription factor. We explore the biological function of REVEILLE2 in Arabidopsis thaliana using a combination of molecular genetics, transcriptomics, and physiology. Disruption of REVEILLE2 alternative splicing alters regulatory gene expression, impairs circadian timing, and improves photosynthetic capacity. Changes in nuclear gene expression are particularly apparent in the initial hours following chilling, with chloroplast gene expression subsequently upregulated. The response of REVEILLE2 to chilling extends our understanding of plants immediate response to cooling. We propose that the circadian component REVEILLE2 restricts plants responses to nocturnal reductions in temperature, thereby enabling appropriate responses to daily environmental changes.
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Affiliation(s)
- Allan B James
- School of Molecular Biosciences, University of Glasgow, Glasgow, G12 8QQ, UK
| | - Chantal Sharples
- School of Molecular Biosciences, University of Glasgow, Glasgow, G12 8QQ, UK
- RNA Biology and Molecular Physiology, Faculty for Biology, Bielefeld University, Universitaetsstrasse 25, 33615, Bielefeld, Germany
| | - Janet Laird
- School of Molecular Biosciences, University of Glasgow, Glasgow, G12 8QQ, UK
| | - Emily May Armstrong
- School of Molecular Biosciences, University of Glasgow, Glasgow, G12 8QQ, UK
| | - Wenbin Guo
- Information and Computational Sciences, The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, UK
| | - Nikoleta Tzioutziou
- Plant Sciences Division, College of Life Sciences, University of Dundee, Invergowrie, Dundee, DD2 5DA, UK
- Cell and Molecular Sciences, The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, UK
| | - Runxuan Zhang
- Information and Computational Sciences, The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, UK
| | - John W S Brown
- Plant Sciences Division, College of Life Sciences, University of Dundee, Invergowrie, Dundee, DD2 5DA, UK
- Cell and Molecular Sciences, The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, UK
| | - Hugh G Nimmo
- School of Molecular Biosciences, University of Glasgow, Glasgow, G12 8QQ, UK
| | - Matthew A Jones
- School of Molecular Biosciences, University of Glasgow, Glasgow, G12 8QQ, UK
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5
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Du Y, Cao L, Wang S, Guo L, Tan L, Liu H, Feng Y, Wu W. Differences in alternative splicing and their potential underlying factors between animals and plants. J Adv Res 2023:S2090-1232(23)00354-5. [PMID: 37981087 DOI: 10.1016/j.jare.2023.11.017] [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: 05/07/2023] [Revised: 08/16/2023] [Accepted: 11/14/2023] [Indexed: 11/21/2023] Open
Abstract
BACKGROUND Alternative splicing (AS), a posttranscriptional process, contributes to the complexity of transcripts from a limited number of genes in a genome, and AS is considered a great source of genetic and phenotypic diversity in eukaryotes. In animals, AS is tightly regulated during the processes of cell growth and differentiation, and its dysregulation is involved in many diseases, including cancers. Likewise, in plants, AS occurs in all stages of plant growth and development, and it seems to play important roles in the rapid reprogramming of genes in response to environmental stressors. To date, the prevalence and functional roles of AS have been extensively reviewed in animals and plants. However, AS differences between animals and plants, especially their underlying molecular mechanisms and impact factors, are anecdotal and rarely reviewed. AIM OF REVIEW This review aims to broaden our understanding of AS roles in a variety of biological processes and provide insights into the underlying mechanisms and impact factors likely leading to AS differences between animals and plants. KEY SCIENTIFIC CONCEPTS OF REVIEW We briefly summarize the roles of AS regulation in physiological and biochemical activities in animals and plants. Then, we underline the differences in the process of AS between plants and animals and especially analyze the potential impact factors, such as gene exon/intron architecture, 5'/3' untranslated regions (UTRs), spliceosome components, chromatin dynamics and transcription speeds, splicing factors [serine/arginine-rich (SR) proteins and heterogeneous nuclear ribonucleoproteins (hnRNPs)], noncoding RNAs, and environmental stimuli, which might lead to the differences. Moreover, we compare the nonsense-mediated mRNA decay (NMD)-mediated turnover of the transcripts with a premature termination codon (PTC) in animals and plants. Finally, we summarize the current AS knowledge published in animals versus plants and discuss the potential development of disease therapies and superior crops in the future.
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Affiliation(s)
- Yunfei Du
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin'an, 311300, Hangzhou, China
| | - Lu Cao
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin'an, 311300, Hangzhou, China
| | - Shuo Wang
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin'an, 311300, Hangzhou, China
| | - Liangyu Guo
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin'an, 311300, Hangzhou, China
| | - Lingling Tan
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin'an, 311300, Hangzhou, China
| | - Hua Liu
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin'an, 311300, Hangzhou, China
| | - Ying Feng
- Key Laboratory of Nutrition, Metabolism and Food Safety, Shanghai Institute of Nutrition and Health (SINH), Chinese Academy of Sciences (CAS), Shanghai 200032, China.
| | - Wenwu Wu
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin'an, 311300, Hangzhou, China.
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6
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Dwivedi SL, Quiroz LF, Reddy ASN, Spillane C, Ortiz R. Alternative Splicing Variation: Accessing and Exploiting in Crop Improvement Programs. Int J Mol Sci 2023; 24:15205. [PMID: 37894886 PMCID: PMC10607462 DOI: 10.3390/ijms242015205] [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: 09/02/2023] [Revised: 10/09/2023] [Accepted: 10/10/2023] [Indexed: 10/29/2023] Open
Abstract
Alternative splicing (AS) is a gene regulatory mechanism modulating gene expression in multiple ways. AS is prevalent in all eukaryotes including plants. AS generates two or more mRNAs from the precursor mRNA (pre-mRNA) to regulate transcriptome complexity and proteome diversity. Advances in next-generation sequencing, omics technology, bioinformatics tools, and computational methods provide new opportunities to quantify and visualize AS-based quantitative trait variation associated with plant growth, development, reproduction, and stress tolerance. Domestication, polyploidization, and environmental perturbation may evolve novel splicing variants associated with agronomically beneficial traits. To date, pre-mRNAs from many genes are spliced into multiple transcripts that cause phenotypic variation for complex traits, both in model plant Arabidopsis and field crops. Cataloguing and exploiting such variation may provide new paths to enhance climate resilience, resource-use efficiency, productivity, and nutritional quality of staple food crops. This review provides insights into AS variation alongside a gene expression analysis to select for novel phenotypic diversity for use in breeding programs. AS contributes to heterosis, enhances plant symbiosis (mycorrhiza and rhizobium), and provides a mechanistic link between the core clock genes and diverse environmental clues.
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Affiliation(s)
| | - Luis Felipe Quiroz
- Agriculture and Bioeconomy Research Centre, Ryan Institute, University of Galway, University Road, H91 REW4 Galway, Ireland
| | - Anireddy S N Reddy
- Department of Biology and Program in Cell and Molecular Biology, Colorado State University, Fort Collins, CO 80523, USA
| | - Charles Spillane
- Agriculture and Bioeconomy Research Centre, Ryan Institute, University of Galway, University Road, H91 REW4 Galway, Ireland
| | - Rodomiro Ortiz
- Department of Plant Breeding, Swedish University of Agricultural Sciences, 23053 Alnarp, SE, Sweden
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7
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McHugh E, Bulloch MS, Batinovic S, Patrick CJ, Sarna DK, Ralph SA. Nonsense-mediated decay machinery in Plasmodium falciparum is inefficient and non-essential. mSphere 2023; 8:e0023323. [PMID: 37366629 PMCID: PMC10449492 DOI: 10.1128/msphere.00233-23] [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: 05/07/2023] [Accepted: 05/15/2023] [Indexed: 06/28/2023] Open
Abstract
Nonsense-mediated decay (NMD) is a conserved mRNA quality control process that eliminates transcripts bearing a premature termination codon. In addition to its role in removing erroneous transcripts, NMD is involved in post-transcriptional regulation of gene expression via programmed intron retention in metazoans. The apicomplexan parasite Plasmodium falciparum shows relatively high levels of intron retention, but it is unclear whether these variant transcripts are functional targets of NMD. In this study, we use CRISPR-Cas9 to disrupt and epitope-tag the P. falciparum orthologs of two core NMD components: PfUPF1 (PF3D7_1005500) and PfUPF2 (PF3D7_0925800). We localize both PfUPF1 and PfUPF2 to puncta within the parasite cytoplasm and show that these proteins interact with each other and other mRNA-binding proteins. Using RNA-seq, we find that although these core NMD orthologs are expressed and interact in P. falciparum, they are not required for degradation of nonsense transcripts. Furthermore, our work suggests that the majority of intron retention in P. falciparum has no functional role and that NMD is not required for parasite growth ex vivo. IMPORTANCE In many organisms, the process of destroying nonsense transcripts is dependent on a small set of highly conserved proteins. We show that in the malaria parasite, these proteins do not impact the abundance of nonsense transcripts. Furthermore, we demonstrate efficient CRISPR-Cas9 editing of the malaria parasite using commercial Cas9 nuclease and synthetic guide RNA, streamlining genomic modifications in this genetically intractable organism.
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Affiliation(s)
- Emma McHugh
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, Victoria, Australia
| | - Michaela S. Bulloch
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, Victoria, Australia
| | - Steven Batinovic
- Department of Physiology, Anatomy and Microbiology, La Trobe University, Bundoora, Victoria, Australia
| | - Cameron J. Patrick
- School of Mathematics and Statistics, The University of Melbourne, Parkville, Victoria, Australia
| | - Drishti K. Sarna
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, Victoria, Australia
| | - Stuart A. Ralph
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, Victoria, Australia
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8
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Schwarze J, Carolan JC, Stewart GS, McCabe PF, Kacprzyk J. The boundary of life and death: changes in mitochondrial and cytosolic proteomes associated with programmed cell death of Arabidopsis thaliana suspension culture cells. FRONTIERS IN PLANT SCIENCE 2023; 14:1194866. [PMID: 37593044 PMCID: PMC10431908 DOI: 10.3389/fpls.2023.1194866] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Accepted: 06/22/2023] [Indexed: 08/19/2023]
Abstract
Introduction Despite the critical role of programmed cell death (PCD) in plant development and defense responses, its regulation is not fully understood. It has been proposed that mitochondria may be important in the control of the early stages of plant PCD, but the details of this regulation are currently unknown. Methods We used Arabidopsis thaliana cell suspension culture, a model system that enables induction and precise monitoring of PCD rates, as well as chemical manipulation of this process to generate a quantitative profile of the alterations in mitochondrial and cytosolic proteomes associated with early stages of plant PCD induced by heat stress. The cells were subjected to PCD-inducing heat levels (10 min, 54°C), with/without the calcium channel inhibitor and PCD blocker LaCl3. The stress treatment was followed by separation of cytosolic and mitochondrial fractions and mass spectrometry-based proteome analysis. Results Heat stress induced rapid and extensive changes in protein abundance in both fractions, with release of mitochondrial proteins into the cytosol upon PCD induction. In our system, LaCl3 appeared to act downstream of cell death initiation signal, as it did not affect the release of mitochondrial proteins, but instead partially inhibited changes occurring in the cytosolic fraction, including upregulation of proteins with hydrolytic activity. Discussion We characterized changes in protein abundance and localization associated with the early stages of heat stress-induced PCD. Collectively, the generated data provide new insights into the regulation of cell death and survival decisions in plant cells.
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Affiliation(s)
- Johanna Schwarze
- School of Biology and Environmental Science, University College Dublin, Dublin, Ireland
| | | | - Gavin S. Stewart
- School of Biology and Environmental Science, University College Dublin, Dublin, Ireland
| | - Paul F. McCabe
- School of Biology and Environmental Science, University College Dublin, Dublin, Ireland
| | - Joanna Kacprzyk
- School of Biology and Environmental Science, University College Dublin, Dublin, Ireland
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9
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McCombe CL, Catanzariti AM, Greenwood JR, Desai AM, Outram MA, Yu DS, Ericsson DJ, Brenner SE, Dodds PN, Kobe B, Jones DA, Williams SJ. A rust-fungus Nudix hydrolase effector decaps mRNA in vitro and interferes with plant immune pathways. THE NEW PHYTOLOGIST 2023; 239:222-239. [PMID: 36631975 DOI: 10.1111/nph.18727] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Accepted: 01/02/2023] [Indexed: 06/02/2023]
Abstract
To infect plants, pathogenic fungi secrete small proteins called effectors. Here, we describe the catalytic activity and potential virulence function of the Nudix hydrolase effector AvrM14 from the flax rust fungus (Melampsora lini). We completed extensive in vitro assays to characterise the enzymatic activity of the AvrM14 effector. Additionally, we used in planta transient expression of wild-type and catalytically dead AvrM14 versions followed by biochemical assays, phenotypic analysis and RNA sequencing to unravel how the catalytic activity of AvrM14 impacts plant immunity. AvrM14 is an extremely selective enzyme capable of removing the protective 5' cap from mRNA transcripts in vitro. Homodimerisation of AvrM14 promoted biologically relevant mRNA cap cleavage in vitro and this activity was conserved in related effectors from other Melampsora spp. In planta expression of wild-type AvrM14, but not the catalytically dead version, suppressed immune-related reactive oxygen species production, altered the abundance of some circadian-rhythm-associated mRNA transcripts and reduced the hypersensitive cell-death response triggered by the flax disease resistance protein M1. To date, the decapping of host mRNA as a virulence strategy has not been described beyond viruses. Our results indicate that some fungal pathogens produce Nudix hydrolase effectors with in vitro mRNA-decapping activity capable of interfering with plant immunity.
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Affiliation(s)
- Carl L McCombe
- Plant Sciences Division, Research School of Biology, The Australian National University, Canberra, ACT, 2601, Australia
| | - Ann-Maree Catanzariti
- Plant Sciences Division, Research School of Biology, The Australian National University, Canberra, ACT, 2601, Australia
| | - Julian R Greenwood
- Plant Sciences Division, Research School of Biology, The Australian National University, Canberra, ACT, 2601, Australia
| | - Anna M Desai
- Plant and Microbial Biology Department, University of California, Berkeley, CA, 94720, USA
| | - Megan A Outram
- Plant Sciences Division, Research School of Biology, The Australian National University, Canberra, ACT, 2601, Australia
| | - Daniel S Yu
- Plant Sciences Division, Research School of Biology, The Australian National University, Canberra, ACT, 2601, Australia
| | - Daniel J Ericsson
- Australian Synchrotron, Macromolecular Crystallography, Clayton, Vic., 3168, Australia
| | - Steven E Brenner
- Plant and Microbial Biology Department, University of California, Berkeley, CA, 94720, USA
| | - Peter N Dodds
- Black Mountain Science and Innovation Park, CSIRO Agriculture and Food, Canberra, ACT, 2601, Australia
| | - Bostjan Kobe
- School of Chemistry and Molecular Biosciences, Institute for Molecular Bioscience and Australian Infectious Diseases Research Centre, University of Queensland, Brisbane, Qld, 4072, Australia
| | - David A Jones
- Plant Sciences Division, Research School of Biology, The Australian National University, Canberra, ACT, 2601, Australia
| | - Simon J Williams
- Plant Sciences Division, Research School of Biology, The Australian National University, Canberra, ACT, 2601, Australia
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10
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Berthelier J, Furci L, Asai S, Sadykova M, Shimazaki T, Shirasu K, Saze H. Long-read direct RNA sequencing reveals epigenetic regulation of chimeric gene-transposon transcripts in Arabidopsis thaliana. Nat Commun 2023; 14:3248. [PMID: 37277361 DOI: 10.1038/s41467-023-38954-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Accepted: 05/21/2023] [Indexed: 06/07/2023] Open
Abstract
Transposable elements (TEs) are accumulated in both intergenic and intragenic regions in plant genomes. Intragenic TEs often act as regulatory elements of associated genes and are also co-transcribed with genes, generating chimeric TE-gene transcripts. Despite the potential impact on mRNA regulation and gene function, the prevalence and transcriptional regulation of TE-gene transcripts are poorly understood. By long-read direct RNA sequencing and a dedicated bioinformatics pipeline, ParasiTE, we investigated the transcription and RNA processing of TE-gene transcripts in Arabidopsis thaliana. We identified a global production of TE-gene transcripts in thousands of A. thaliana gene loci, with TE sequences often being associated with alternative transcription start sites or transcription termination sites. The epigenetic state of intragenic TEs affects RNAPII elongation and usage of alternative poly(A) signals within TE sequences, regulating alternative TE-gene isoform production. Co-transcription and inclusion of TE-derived sequences into gene transcripts impact regulation of RNA stability and environmental responses of some loci. Our study provides insights into TE-gene interactions that contributes to mRNA regulation, transcriptome diversity, and environmental responses in plants.
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Grants
- JP20H02995 Ministry of Education, Culture, Sports, Science and Technology (MEXT)
- JP22H00364 Ministry of Education, Culture, Sports, Science and Technology (MEXT)
- JP20H05909 Ministry of Education, Culture, Sports, Science and Technology (MEXT)
- JP20H05913 Ministry of Education, Culture, Sports, Science and Technology (MEXT)
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Affiliation(s)
- Jérémy Berthelier
- Plant Epigenetics Unit, Okinawa Institute of Science and Technology Graduate University (OIST), 1919-1 Tancha, Onna-son, Kunigami-gun, Okinawa, 904-0495, Japan.
| | - Leonardo Furci
- Plant Epigenetics Unit, Okinawa Institute of Science and Technology Graduate University (OIST), 1919-1 Tancha, Onna-son, Kunigami-gun, Okinawa, 904-0495, Japan
| | - Shuta Asai
- Center for Sustainable Resource Science, RIKEN, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, Kanagawa, 230-0045, Japan
| | - Munissa Sadykova
- Plant Epigenetics Unit, Okinawa Institute of Science and Technology Graduate University (OIST), 1919-1 Tancha, Onna-son, Kunigami-gun, Okinawa, 904-0495, Japan
| | - Tomoe Shimazaki
- Plant Epigenetics Unit, Okinawa Institute of Science and Technology Graduate University (OIST), 1919-1 Tancha, Onna-son, Kunigami-gun, Okinawa, 904-0495, Japan
| | - Ken Shirasu
- Center for Sustainable Resource Science, RIKEN, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, Kanagawa, 230-0045, Japan
| | - Hidetoshi Saze
- Plant Epigenetics Unit, Okinawa Institute of Science and Technology Graduate University (OIST), 1919-1 Tancha, Onna-son, Kunigami-gun, Okinawa, 904-0495, Japan.
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11
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Nagarajan VK, Stuart CJ, DiBattista AT, Accerbi M, Caplan JL, Green PJ. RNA degradome analysis reveals DNE1 endoribonuclease is required for the turnover of diverse mRNA substrates in Arabidopsis. THE PLANT CELL 2023; 35:1936-1955. [PMID: 37070465 PMCID: PMC10226599 DOI: 10.1093/plcell/koad085] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Revised: 03/01/2023] [Accepted: 03/04/2023] [Indexed: 05/30/2023]
Abstract
In plants, cytoplasmic mRNA decay is critical for posttranscriptionally controlling gene expression and for maintaining cellular RNA homeostasis. Arabidopsis DCP1-ASSOCIATED NYN ENDORIBONUCLEASE 1 (DNE1) is a cytoplasmic mRNA decay factor that interacts with proteins involved in mRNA decapping and nonsense-mediated mRNA decay (NMD). There is limited information on the functional role of DNE1 in RNA turnover, and the identities of its endogenous targets are unknown. In this study, we utilized RNA degradome approaches to globally investigate DNE1 substrates. Monophosphorylated 5' ends, produced by DNE1, should accumulate in mutants lacking the cytoplasmic exoribonuclease XRN4, but be absent from DNE1 and XRN4 double mutants. In seedlings, we identified over 200 such transcripts, most of which reflect cleavage within coding regions. While most DNE1 targets were NMD-insensitive, some were upstream ORF (uORF)-containing and NMD-sensitive transcripts, indicating that this endoribonuclease is required for turnover of a diverse set of mRNAs. Transgenic plants expressing DNE1 cDNA with an active-site mutation in the endoribonuclease domain abolished the in planta cleavage of transcripts, demonstrating that DNE1 endoribonuclease activity is required for cleavage. Our work provides key insights into the identity of DNE1 substrates and enhances our understanding of DNE1-mediated mRNA decay.
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Affiliation(s)
- Vinay K Nagarajan
- Delaware Biotechnology Institute, University of Delaware,
Newark, DE 19713-1316, USA
| | - Catherine J Stuart
- Delaware Biotechnology Institute, University of Delaware,
Newark, DE 19713-1316, USA
| | - Anna T DiBattista
- Delaware Biotechnology Institute, University of Delaware,
Newark, DE 19713-1316, USA
| | - Monica Accerbi
- Delaware Biotechnology Institute, University of Delaware,
Newark, DE 19713-1316, USA
| | - Jeffrey L Caplan
- Bio-Imaging Center, Delaware Biotechnology Institute, University of
Delaware, Newark, DE 19713-1316, USA
| | - Pamela J Green
- Delaware Biotechnology Institute, University of Delaware,
Newark, DE 19713-1316, USA
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12
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Misra CS, Sousa AGG, Barros PM, Kermanov A, Becker JD. Cell-type-specific alternative splicing in the Arabidopsis germline. PLANT PHYSIOLOGY 2023; 192:85-101. [PMID: 36515615 PMCID: PMC10152659 DOI: 10.1093/plphys/kiac574] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 09/30/2022] [Accepted: 11/23/2022] [Indexed: 05/03/2023]
Abstract
During sexual reproduction in flowering plants, the two haploid sperm cells (SCs) embedded within the cytoplasm of a growing pollen tube are carried to the embryo sac for double fertilization. Pollen development in flowering plants is a dynamic process that encompasses changes at transcriptome and epigenome levels. While the transcriptome of pollen and SCs in Arabidopsis (Arabidopsis thaliana) is well documented, previous analyses have mostly been based on gene-level expression. In-depth transcriptome analysis, particularly the extent of alternative splicing (AS) at the resolution of SC and vegetative nucleus (VN), is still lacking. Therefore, we performed RNA-seq analysis to generate a spliceome map of Arabidopsis SCs and VN isolated from mature pollen grains. Based on our de novo transcriptome assembly, we identified 58,039 transcripts, including 9,681 novel transcripts, of which 2,091 were expressed in SCs and 3,600 in VN. Four hundred and sixty-eight genes were regulated both at gene and splicing levels, with many having functions in mRNA splicing, chromatin modification, and protein localization. Moreover, a comparison with egg cell RNA-seq data uncovered sex-specific regulation of transcription and splicing factors. Our study provides insights into a gamete-specific AS landscape at unprecedented resolution.
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Affiliation(s)
- Chandra Shekhar Misra
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB NOVA), 2780-157 Oeiras, Portugal
- Instituto Gulbenkian de Ciência, 2780-156 Oeiras, Portugal
| | | | - Pedro M Barros
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB NOVA), 2780-157 Oeiras, Portugal
| | - Anton Kermanov
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB NOVA), 2780-157 Oeiras, Portugal
- Instituto Gulbenkian de Ciência, 2780-156 Oeiras, Portugal
| | - Jörg D Becker
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB NOVA), 2780-157 Oeiras, Portugal
- Instituto Gulbenkian de Ciência, 2780-156 Oeiras, Portugal
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13
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Muhammad S, Xu X, Zhou W, Wu L. Alternative splicing: An efficient regulatory approach towards plant developmental plasticity. WILEY INTERDISCIPLINARY REVIEWS. RNA 2023; 14:e1758. [PMID: 35983878 DOI: 10.1002/wrna.1758] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Revised: 06/28/2022] [Accepted: 07/19/2022] [Indexed: 05/13/2023]
Abstract
Alternative splicing (AS) is a gene regulatory mechanism that plants adapt to modulate gene expression (GE) in multiple ways. AS generates alternative isoforms of the same gene following various development and environmental stimuli, increasing transcriptome plasticity and proteome complexity. AS controls the expression levels of certain genes and regulates GE networks that shape plant adaptations through nonsense-mediated decay (NMD). This review intends to discuss AS modulation, from interaction with noncoding RNAs to the established roles of splicing factors (SFs) in response to endogenous and exogenous cues. We aim to gather such studies that highlight the magnitude and impact of AS, which are not always clear from individual articles, when AS is increasing in individual genes and at a global level. This work also anticipates making plant researchers know that AS is likely to occur in their investigations and that dynamic changes in AS and their effects must be frequently considered. We also review our understanding of AS-mediated posttranscriptional modulation of plant stress tolerance and discuss its potential application in crop improvement in the future. This article is categorized under: RNA Processing > Splicing Regulation/Alternative Splicing RNA Processing > Splicing Mechanisms RNA-Based Catalysis > RNA Catalysis in Splicing and Translation.
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Affiliation(s)
- Sajid Muhammad
- Hainan Yazhou Bay Seed Laboratory, Hainan Institute of Zhejiang University, Sanya, Hainan, China
- State Key Laboratory of Rice Biology, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, Zhejiang, China
| | - Xiaoli Xu
- Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Weijun Zhou
- State Key Laboratory of Rice Biology, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, Zhejiang, China
| | - Liang Wu
- Hainan Yazhou Bay Seed Laboratory, Hainan Institute of Zhejiang University, Sanya, Hainan, China
- State Key Laboratory of Rice Biology, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, Zhejiang, China
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14
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Li X, Li C, Zhu J, Zhong S, Zhu H, Zhang X. Functions and mechanisms of RNA helicases in plants. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:2295-2310. [PMID: 36416783 PMCID: PMC10082930 DOI: 10.1093/jxb/erac462] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Accepted: 11/21/2022] [Indexed: 05/21/2023]
Abstract
RNA helicases (RHs) are a family of ubiquitous enzymes that alter RNA structures and remodel ribonucleoprotein complexes typically using energy from the hydrolysis of ATP. RHs are involved in various aspects of RNA processing and metabolism, exemplified by transcriptional regulation, pre-mRNA splicing, miRNA biogenesis, liquid-liquid phase separation, and rRNA biogenesis, among other molecular processes. Through these mechanisms, RHs contribute to vegetative and reproductive growth, as well as abiotic and biotic stress responses throughout the life cycle in plants. In this review, we systematically characterize RH-featured domains and signature motifs in Arabidopsis. We also summarize the functions and mechanisms of RHs in various biological processes in plants with a focus on DEAD-box and DEAH-box RNA helicases, aiming to present the latest understanding of RHs in plant biology.
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Affiliation(s)
- Xindi Li
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA
| | - Changhao Li
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA
| | - Jiaying Zhu
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA
| | - Songxiao Zhong
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA
| | - Hongliang Zhu
- College of Food Science and Nutritional Engineering, China Agricultural University, 100083 Beijing, China
| | - Xiuren Zhang
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA
- Department of Biology, College of Science, Texas A&M University, College Station, TX 77843, USA
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15
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The biological functions of nonsense-mediated mRNA decay in plants: RNA quality control and beyond. Biochem Soc Trans 2023; 51:31-39. [PMID: 36695509 DOI: 10.1042/bst20211231] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Revised: 01/11/2023] [Accepted: 01/13/2023] [Indexed: 01/26/2023]
Abstract
Nonsense-mediated mRNA decay (NMD) is an evolutionarily conserved quality control pathway that inhibits the expression of transcripts containing premature termination codon. Transcriptome and phenotypic studies across a range of organisms indicate roles of NMD beyond RNA quality control and imply its involvement in regulating gene expression in a wide range of physiological processes. Studies in moss Physcomitrella patens and Arabidopsis thaliana have shown that NMD is also important in plants where it contributes to the regulation of pathogen defence, hormonal signalling, circadian clock, reproduction and gene evolution. Here, we provide up to date overview of the biological functions of NMD in plants. In addition, we discuss several biological processes where NMD factors implement their function through NMD-independent mechanisms.
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16
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Boulanger HG, Guo W, Monteiro LDFR, Calixto CPG. Co-expression network of heat-response transcripts: A glimpse into how splicing factors impact rice basal thermotolerance. Front Mol Biosci 2023; 10:1122201. [PMID: 36818043 PMCID: PMC9932781 DOI: 10.3389/fmolb.2023.1122201] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Accepted: 01/23/2023] [Indexed: 02/05/2023] Open
Abstract
To identify novel solutions to improve rice yield under rising temperatures, molecular components of thermotolerance must be better understood. Alternative splicing (AS) is a major post-transcriptional mechanism impacting plant tolerance against stresses, including heat stress (HS). AS is largely regulated by splicing factors (SFs) and recent studies have shown their involvement in temperature response. However, little is known about the splicing networks between SFs and AS transcripts in the HS response. To expand this knowledge, we constructed a co-expression network based on a publicly available RNA-seq dataset that explored rice basal thermotolerance over a time-course. Our analyses suggest that the HS-dependent control of the abundance of specific transcripts coding for SFs might explain the widespread, coordinated, complex, and delicate AS regulation of critical genes during a plant's inherent response to extreme temperatures. AS changes in these critical genes might affect many aspects of plant biology, from organellar functions to cell death, providing relevant regulatory candidates for future functional studies of basal thermotolerance.
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Affiliation(s)
- Hadrien Georges Boulanger
- Université Paris-Saclay, Gif-sur-Yvette, France,École Nationale Supérieure d'Informatique pour l'Industrie et l’Entreprise, Evry-Courcouronnes, France,Department of Botany, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
| | - Wenbin Guo
- Information and Computational Sciences, The James Hutton Institute, Dundee, United Kingdom
| | | | - Cristiane Paula Gomes Calixto
- Department of Botany, Institute of Biosciences, University of São Paulo, São Paulo, Brazil,*Correspondence: Cristiane Paula Gomes Calixto,
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17
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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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18
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Hoffmann G, Mahboubi A, Bente H, Garcia D, Hanson J, Hafrén A. Arabidopsis RNA processing body components LSM1 and DCP5 aid in the evasion of translational repression during Cauliflower mosaic virus infection. THE PLANT CELL 2022; 34:3128-3147. [PMID: 35511183 PMCID: PMC9338796 DOI: 10.1093/plcell/koac132] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Accepted: 04/24/2022] [Indexed: 06/14/2023]
Abstract
Viral infections impose extraordinary RNA stress, triggering cellular RNA surveillance pathways such as RNA decapping, nonsense-mediated decay, and RNA silencing. Viruses need to maneuver among these pathways to establish infection and succeed in producing high amounts of viral proteins. Processing bodies (PBs) are integral to RNA triage in eukaryotic cells, with several distinct RNA quality control pathways converging for selective RNA regulation. In this study, we investigated the role of Arabidopsis thaliana PBs during Cauliflower mosaic virus (CaMV) infection. We found that several PB components are co-opted into viral factories that support virus multiplication. This pro-viral role was not associated with RNA decay pathways but instead, we established that PB components are helpers in viral RNA translation. While CaMV is normally resilient to RNA silencing, dysfunctions in PB components expose the virus to this pathway, which is similar to previous observations for transgenes. Transgenes, however, undergo RNA quality control-dependent RNA degradation and transcriptional silencing, whereas CaMV RNA remains stable but becomes translationally repressed through decreased ribosome association, revealing a unique dependence among PBs, RNA silencing, and translational repression. Together, our study shows that PB components are co-opted by the virus to maintain efficient translation, a mechanism not associated with canonical PB functions.
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Affiliation(s)
- Gesa Hoffmann
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences, Uppsala 75007, Sweden
- Linnean Center for Plant Biology, Uppsala 75007, Sweden
| | - Amir Mahboubi
- Department of Plant Physiology, Umeå Plant Science Centre, Umeå University, Umeå, Sweden
| | - Heinrich Bente
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences, Uppsala 75007, Sweden
- Linnean Center for Plant Biology, Uppsala 75007, Sweden
| | - Damien Garcia
- Institut de Biologie Moléculaire des Plantes, CNRS, Université de Strasbourg, Strasbourg, France
| | - Johannes Hanson
- Department of Plant Physiology, Umeå Plant Science Centre, Umeå University, Umeå, Sweden
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19
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Lu P, Chen D, Qi Z, Wang H, Chen Y, Wang Q, Jiang C, Xu JR, Liu H. Landscape and regulation of alternative splicing and alternative polyadenylation in a plant pathogenic fungus. THE NEW PHYTOLOGIST 2022; 235:674-689. [PMID: 35451076 DOI: 10.1111/nph.18164] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2021] [Accepted: 03/30/2022] [Indexed: 06/14/2023]
Abstract
Alternative splicing (AS) and alternative polyadenylation (APA) contribute significantly to the regulation of gene expression in higher eukaryotes. Their biological impact in filamentous fungi, however, is largely unknown. Here we combine PacBio Isoform-Sequencing and strand-specific RNA-sequencing of multiple tissues and mutant characterization to reveal the landscape and regulation of AS and APA in Fusarium graminearum. We generated a transcript annotation comprising 51 617 isoforms from 17 189 genes. In total, 4997 and 11 133 genes are alternatively spliced and polyadenylated, respectively. Majority of the AS events alter coding sequences. Unexpectedly, the AS transcripts containing premature-termination codons are not sensitive to nonsense-mediated messenger RNA decay. Unlike in yeasts and animals, distal APA sites have strong signals, but proximal APA isoforms are highly expressed in F. graminearum. The 3'-end processing factors FgRNA15, FgHRP1, and FgFIP1 play roles in promoting proximal APA site usage and intron splicing. A genome-wide increase in intron inclusion and distal APA site usage and downregulation of the spliceosomal and 3'-end processing factors were observed in older and quiescent tissues, indicating intron inclusion and 3'-untranslated region lengthening as novel mechanisms in regulating aging and dormancy in fungi. This study provides new insights into the complexity and regulation of AS and APA in filamentous fungi.
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Affiliation(s)
- Ping Lu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Daipeng Chen
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, 712100, China
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN, 47907, USA
| | - Zhaomei Qi
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Haoming Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Yitong Chen
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Qinhu Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Cong Jiang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Jin-Rong Xu
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN, 47907, USA
| | - Huiquan Liu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, 712100, China
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20
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Raxwal VK, Singh S, Agarwal M, Riha K. Transcriptional and post-transcriptional regulation of young genes in plants. BMC Biol 2022; 20:134. [PMID: 35676681 PMCID: PMC9178820 DOI: 10.1186/s12915-022-01339-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Accepted: 05/30/2022] [Indexed: 12/03/2022] Open
Abstract
Background New genes continuously emerge from non-coding DNA or by diverging from existing genes, but most of them are rapidly lost and only a few become fixed within the population. We hypothesized that young genes are subject to transcriptional and post-transcriptional regulation to limit their expression and minimize their exposure to purifying selection. Results We performed a protein-based homology search across the tree of life to determine the evolutionary age of protein-coding genes present in the rice genome. We found that young genes in rice have relatively low expression levels, which can be attributed to distal enhancers, and closed chromatin conformation at their transcription start sites (TSS). The chromatin in TSS regions can be re-modeled in response to abiotic stress, indicating conditional expression of young genes. Furthermore, transcripts of young genes in Arabidopsis tend to be targeted by nonsense-mediated RNA decay, presenting another layer of regulation limiting their expression. Conclusions These data suggest that transcriptional and post-transcriptional mechanisms contribute to the conditional expression of young genes, which may alleviate purging selection while providing an opportunity for phenotypic exposure and functionalization. Supplementary Information The online version contains supplementary material available at 10.1186/s12915-022-01339-7.
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Affiliation(s)
- Vivek Kumar Raxwal
- Department of Botany, University of Delhi, Delhi, 110007, India. .,Central European Institute of Technology (CEITEC), Masaryk University, Brno, Czech Republic.
| | - Somya Singh
- Department of Botany, University of Delhi, Delhi, 110007, India
| | - Manu Agarwal
- Department of Botany, University of Delhi, Delhi, 110007, India.
| | - Karel Riha
- Central European Institute of Technology (CEITEC), Masaryk University, Brno, Czech Republic.
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21
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Lapin D, Johanndrees O, Wu Z, Li X, Parker JE. Molecular innovations in plant TIR-based immunity signaling. THE PLANT CELL 2022; 34:1479-1496. [PMID: 35143666 PMCID: PMC9153377 DOI: 10.1093/plcell/koac035] [Citation(s) in RCA: 42] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 01/27/2022] [Indexed: 05/19/2023]
Abstract
A protein domain (Toll and Interleukin-1 receptor [TIR]-like) with homology to animal TIRs mediates immune signaling in prokaryotes and eukaryotes. Here, we present an overview of TIR evolution and the molecular versatility of TIR domains in different protein architectures for host protection against microbial attack. Plant TIR-based signaling emerges as being central to the potentiation and effectiveness of host defenses triggered by intracellular and cell-surface immune receptors. Equally relevant for plant fitness are mechanisms that limit potent TIR signaling in healthy tissues but maintain preparedness for infection. We propose that seed plants evolved a specialized protein module to selectively translate TIR enzymatic activities to defense outputs, overlaying a more general function of TIRs.
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Affiliation(s)
- Dmitry Lapin
- Department of Plant-Microbe Interactions, Max Planck Institute for Plant Breeding Research, Cologne 50829, Germany
- Plant-Microbe Interactions, Department of Biology, Utrecht University, Utrecht 3584 CH, The Netherlands
- Author for correspondence: (D.L.), (J.E.P.)
| | - Oliver Johanndrees
- Department of Plant-Microbe Interactions, Max Planck Institute for Plant Breeding Research, Cologne 50829, Germany
| | - Zhongshou Wu
- Michael Smith Labs and Department of Botany, University of British Columbia, Vancouver BC V6T 1Z4, Canada
| | - Xin Li
- Michael Smith Labs and Department of Botany, University of British Columbia, Vancouver BC V6T 1Z4, Canada
| | - Jane E Parker
- Department of Plant-Microbe Interactions, Max Planck Institute for Plant Breeding Research, Cologne 50829, Germany
- Cluster of Excellence on Plant Sciences (CEPLAS), Duesseldorf 40225, Germany
- Author for correspondence: (D.L.), (J.E.P.)
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22
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Sui S, Wang Z, Cui X, Jin L, Zhu C. The biological behavior of tRNA-derived fragment tRF-Leu-AAG in pancreatic cancer cells. Bioengineered 2022; 13:10617-10628. [PMID: 35442152 PMCID: PMC9161985 DOI: 10.1080/21655979.2022.2064206] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Revised: 03/29/2022] [Accepted: 04/05/2022] [Indexed: 01/01/2023] Open
Abstract
Pancreatic cancer (PC) is a life-threatening cancer with increasing incidence in developed countries. Reports indicate that tRNA-derived fragments (tRFs) are possible therapeutic targets and biomarkers for cancer treatment. Nonetheless, the effect of tRF-Leu-AAG on PC is unclear. This study aims to explore the role of tRF-Leu-AAG and upstream frameshift mutant 1 (UPF1) in the development of PC and its potential underlying mechanisms. High-throughput second-generation sequencing techniques were used to detect the expression of tRFs in cancerous and adjacent normal tissues from PC patients. The role of tRF-Leu-AAG proliferation in PC cells was investigated via the Cell Counting Kit-8 (CCK8) assay. The effect of tRF-Leu-AAG on the invasion and migration ability of PC cells was also determined by the transwell assay. Thereafter, the downstream target genes of tRF-Leu-AAG were comprehensively predicted using bioinformatics analysis databases. We also used the Dual-Luciferase Reporter assay to assess the nexus between tRF-Leu-AAG and UPF1. Eventually, Western Blot was used to validate the expression of UPF1 in PC cells. A total of 33 tRF expressions significantly varied from PC patients. RT-qPCR confirmed that the expression of tRF-Leu-AAG was observably up-regulated in PC cells as compared to the control cells. Importantly, knockdown of tRF-Leu-AAG observably inhibited cell proliferation, migration, and invasion. Furthermore, according to the predicted frameshift database results, the UPF1 acted as downstream target genes for tRF-Leu-AAG and significantly down-regulated UPF1 expression.
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Affiliation(s)
- Shizhen Sui
- Graduate School of Dalian Medical University, Dalian Medical University, Dalian, Liaoning, China
| | - Zhihuai Wang
- Graduate School of Dalian Medical University, Dalian Medical University, Dalian, Liaoning, China
| | - Xiaohan Cui
- Department of Hepatobiliary Surgery, The Affiliated Changzhou No. 2 People’s Hospital of Nanjing Medical University, Changzhou, Jiangsu, China
| | - Lei Jin
- Department of Hepatobiliary Surgery, The Affiliated Changzhou No. 2 People’s Hospital of Nanjing Medical University, Changzhou, Jiangsu, China
| | - Chunfu Zhu
- Department of Hepatobiliary Surgery, The Affiliated Changzhou No. 2 People’s Hospital of Nanjing Medical University, Changzhou, Jiangsu, China
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Jin J, She Y, Qiu P, Lin W, Zhang W, Zhang J, Wu Z, Du Z. The cap-snatching frequency of a plant bunyavirus from nonsense mRNAs is low but is increased by silencing of UPF1 or SMG7. MOLECULAR PLANT PATHOLOGY 2022; 23:576-582. [PMID: 34954877 PMCID: PMC8916216 DOI: 10.1111/mpp.13179] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Revised: 12/13/2021] [Accepted: 12/13/2021] [Indexed: 06/02/2023]
Abstract
Bunyaviruses cleave host cellular mRNAs to acquire cap structures for their own mRNAs in a process called cap-snatching. How bunyaviruses interact with cellular mRNA surveillance pathways such as nonsense-mediated decay (NMD) during cap-snatching remains poorly understood, especially in plants. Rice stripe virus (RSV) is a plant bunyavirus threatening rice production in East Asia. Here, with a newly developed system allowing us to present defined mRNAs to RSV in Nicotiana benthamiana, we found that the frequency of RSV to target nonsense mRNAs (nsRNAs) during cap-snatching was much lower than its frequency to target normal mRNAs. The frequency of RSV to target nsRNAs was increased by virus-induced gene silencing of UPF1 or SMG7, each encoding a protein component involved in early steps of NMD (in an rdr6 RNAi background). Coincidently, RSV accumulation was increased in the UPF1- or SMG7-silenced plants. These data indicated that the frequency of RSV to target nsRNAs during cap-snatching is restricted by NMD. By restricting the frequency of RSV to target nsRNAs, NMD may impose a constraint to the overall cap-snatching efficiency of RSV. Besides a deeper understanding for the cap-snatching of RSV, these findings point to a novel role of NMD in plant-bunyavirus interactions.
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Affiliation(s)
- Jing Jin
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan CropsFuzhouChina
| | - Yuanyuan She
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan CropsFuzhouChina
| | - Ping Qiu
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan CropsFuzhouChina
| | - Wenzhong Lin
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan CropsFuzhouChina
| | - Wenwen Zhang
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan CropsFuzhouChina
| | - Jie Zhang
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan CropsFuzhouChina
| | - Zujian Wu
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan CropsFuzhouChina
- Plant Virus Research InstituteFujian Agricultural and Forestry UniversityFuzhouChina
| | - Zhenguo Du
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan CropsFuzhouChina
- Plant Virus Research InstituteFujian Agricultural and Forestry UniversityFuzhouChina
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24
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Chen H, Ma J, Kong F, Song N, Wang C, Ma X. UPF1 contributes to the maintenance of endometrial cancer stem cell phenotype by stabilizing LINC00963. Cell Death Dis 2022; 13:257. [PMID: 35318304 PMCID: PMC8940903 DOI: 10.1038/s41419-022-04707-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Revised: 02/15/2022] [Accepted: 03/03/2022] [Indexed: 12/15/2022]
Abstract
Endometrial cancer stem cells (ECSCs) play a vital role in endometrial cancer (EC) metastasis, relapse, and chemoresistance. However, the molecular mechanisms that sustain ECSCs remain elusive. Here, we showed that the expression of UPF1 was upregulated in EC tissues and ECSCs and correlated with poor clinicopathological characteristics. UPF1 silencing suppressed ECSC hallmarks, such as sphere formation ability, carboplatin resistance, migration and invasion, and cell cycle progression. UPF1 regulated the behavior and fate of ECSCs by stabilizing LINC00963. LINC00963 further shares the same miRNA response element with the core transcription factor SOX2 and relieved the suppression of SOX2 by miR-508-5p in self-renewing ECSCs. Notably, inhibition of UPF1 and LINC00963 in combination severely impaired the in vivo tumorigenic potential of ECSCs. We demonstrate that the UPF1/LINC00963/miR-508-5p/SOX2 axis has potential value in modulating ECSC maintenance, chemoresistance, and tumorigenesis in EC, which highlights a novel promising target for EC treatment.
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25
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Liu W, Sun Y, Qiu X, Meng C, Song C, Tan L, Liao Y, Liu X, Ding C. Genome-Wide Analysis of Alternative Splicing during Host-Virus Interactions in Chicken. Viruses 2021; 13:v13122409. [PMID: 34960678 PMCID: PMC8703359 DOI: 10.3390/v13122409] [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: 09/28/2021] [Revised: 11/19/2021] [Accepted: 11/19/2021] [Indexed: 11/16/2022] Open
Abstract
The chicken is a model animal for the study of evolution, immunity and development. In addition to their use as a model organism, chickens also represent an important agricultural product. Pathogen invasion has already been shown to modulate the expression of hundreds of genes, but the role of alternative splicing in avian virus infection remains unclear. We used RNA-seq data to analyze virus-induced changes in the alternative splicing of Gallus gallus, and found that a large number of alternative splicing events were induced by virus infection both in vivo and in vitro. Virus-responsive alternative splicing events preferentially occurred in genes involved in metabolism and transport. Many of the alternatively spliced transcripts were also expressed from genes with a function relating to splicing or immune response, suggesting a potential impact of virus infection on pre-mRNA splicing and immune gene regulation. Moreover, exon skipping was the most frequent AS event in chickens during virus infection. This is the first report describing a genome-wide analysis of alternative splicing in chicken and contributes to the genomic resources available for studying host-virus interaction in this species. Our analysis fills an important knowledge gap in understanding the extent of genome-wide alternative splicing dynamics occurring during avian virus infection and provides the impetus for the further exploration of AS in chicken defense signaling and homeostasis.
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Affiliation(s)
- Weiwei Liu
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai 200241, China; (W.L.); (Y.S.); (X.Q.); (C.M.); (C.S.); (L.T.); (Y.L.)
| | - Yingjie Sun
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai 200241, China; (W.L.); (Y.S.); (X.Q.); (C.M.); (C.S.); (L.T.); (Y.L.)
| | - Xusheng Qiu
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai 200241, China; (W.L.); (Y.S.); (X.Q.); (C.M.); (C.S.); (L.T.); (Y.L.)
| | - Chunchun Meng
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai 200241, China; (W.L.); (Y.S.); (X.Q.); (C.M.); (C.S.); (L.T.); (Y.L.)
| | - Cuiping Song
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai 200241, China; (W.L.); (Y.S.); (X.Q.); (C.M.); (C.S.); (L.T.); (Y.L.)
| | - Lei Tan
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai 200241, China; (W.L.); (Y.S.); (X.Q.); (C.M.); (C.S.); (L.T.); (Y.L.)
| | - Ying Liao
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai 200241, China; (W.L.); (Y.S.); (X.Q.); (C.M.); (C.S.); (L.T.); (Y.L.)
| | - Xiufan Liu
- School of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China;
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, China
| | - Chan Ding
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai 200241, China; (W.L.); (Y.S.); (X.Q.); (C.M.); (C.S.); (L.T.); (Y.L.)
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, China
- Correspondence: ; Tel.: +86-21-3429-3441
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A CENH3 mutation promotes meiotic exit and restores fertility in SMG7-deficient Arabidopsis. PLoS Genet 2021; 17:e1009779. [PMID: 34591845 PMCID: PMC8509889 DOI: 10.1371/journal.pgen.1009779] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Revised: 10/12/2021] [Accepted: 08/16/2021] [Indexed: 01/21/2023] Open
Abstract
Meiosis in angiosperm plants is followed by mitotic divisions to form multicellular haploid gametophytes. Termination of meiosis and transition to gametophytic development is, in Arabidopsis, governed by a dedicated mechanism that involves SMG7 and TDM1 proteins. Mutants carrying the smg7-6 allele are semi-fertile due to reduced pollen production. We found that instead of forming tetrads, smg7-6 pollen mother cells undergo multiple rounds of chromosome condensation and spindle assembly at the end of meiosis, resembling aberrant attempts to undergo additional meiotic divisions. A suppressor screen uncovered a mutation in centromeric histone H3 (CENH3) that increased fertility and promoted meiotic exit in smg7-6 plants. The mutation led to inefficient splicing of the CENH3 mRNA and a substantial decrease of CENH3, resulting in smaller centromeres. The reduced level of CENH3 delayed formation of the mitotic spindle but did not have an apparent effect on plant growth and development. We suggest that impaired spindle re-assembly at the end of meiosis limits aberrant divisions in smg7-6 plants and promotes formation of tetrads and viable pollen. Furthermore, the mutant with reduced level of CENH3 was very inefficient haploid inducer indicating that differences in centromere size is not the key determinant of centromere-mediated genome elimination. Meiosis is a reductional cell division that halves number of chromosomes during two successive rounds of chromosome segregation without intervening DNA replication. Such mode of chromosome segregation requires extensive reprogramming of the cell division machinery at the entry to meiosis, and inactivation of the meiotic program upon the formation of haploid spores. Here we showed that Arabidopsis partially deficient in the RNA decay factor SMG7 fail to exit meiosis and continue with attempts to undergo additional cycles of post-meiotic chromosome segregations without genome replication. This results in a reduced number of viable pollen and diminished fertility. To find genes involved in meiotic exit, we performed a suppressor screen for the SMG7-deicient plants that re-gain fertility. We found that reducing the amount of centromeric histone partially restores pollen formation and fertility in smg7 mutants. This is likely due to inefficient formation of centromere-microtubule interactions that impairs spindle reassembly and re-entry into aberrant rounds of post-meiotic chromosome segregation.
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Decoding co-/post-transcriptional complexities of plant transcriptomes and epitranscriptome using next-generation sequencing technologies. Biochem Soc Trans 2021; 48:2399-2414. [PMID: 33196096 DOI: 10.1042/bst20190492] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Revised: 10/06/2020] [Accepted: 10/22/2020] [Indexed: 12/12/2022]
Abstract
Next-generation sequencing (NGS) technologies - Illumina RNA-seq, Pacific Biosciences isoform sequencing (PacBio Iso-seq), and Oxford Nanopore direct RNA sequencing (DRS) - have revealed the complexity of plant transcriptomes and their regulation at the co-/post-transcriptional level. Global analysis of mature mRNAs, transcripts from nuclear run-on assays, and nascent chromatin-bound mRNAs using short as well as full-length and single-molecule DRS reads have uncovered potential roles of different forms of RNA polymerase II during the transcription process, and the extent of co-transcriptional pre-mRNA splicing and polyadenylation. These tools have also allowed mapping of transcriptome-wide start sites in cap-containing RNAs, poly(A) site choice, poly(A) tail length, and RNA base modifications. The emerging theme from recent studies is that reprogramming of gene expression in response to developmental cues and stresses at the co-/post-transcriptional level likely plays a crucial role in eliciting appropriate responses for optimal growth and plant survival under adverse conditions. Although the mechanisms by which developmental cues and different stresses regulate co-/post-transcriptional splicing are largely unknown, a few recent studies indicate that the external cues target spliceosomal and splicing regulatory proteins to modulate alternative splicing. In this review, we provide an overview of recent discoveries on the dynamics and complexities of plant transcriptomes, mechanistic insights into splicing regulation, and discuss critical gaps in co-/post-transcriptional research that need to be addressed using diverse genomic and biochemical approaches.
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28
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Zhang X, Huang Q, Wang P, Liu F, Luo M, Li X, Wang Z, Wan L, Yang G, Hong D. A 24,482-bp deletion is associated with increased seed weight in Brassica napus L. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2021; 134:2653-2669. [PMID: 34002254 DOI: 10.1007/s00122-021-03850-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Accepted: 04/29/2021] [Indexed: 06/12/2023]
Abstract
A major QTL for seed weight was fine-mapped in rapeseed, and a 24,482-bp deletion likely mediates the effect through multiple pathways. Exploration of the genes controlling seed weight is critical to the improvement of crop yield and elucidation of the mechanisms underlying seed formation in rapeseed (Brassica napus L.). We previously identified the quantitative trait locus (QTL) qSW.C9 for the thousand-seed weight (TSW) in a double haploid population constructed from F1 hybrids between the parental accessions HZ396 and Y106. Here, we confirmed the phenotypic effects associated with qSW.C9 in BC3F2 populations and fine-mapped the candidate causal locus to a 266-kb interval. Sequence and expression analyses revealed that a 24,482-bp deletion in HZ396 containing six predicted genes most likely underlies qSW.C9. Differential gene expression analysis and cytological observations suggested that qSW.C9 affects both cell proliferation and cell expansion through multiple signaling pathways. After genotyping of a rapeseed diversity panel to define the haplotype structure, it could be concluded that the selection of germplasm with two specific markers may be effective in improving the seed weight of rapeseed. This study provides a solid foundation for the identification of the causal gene of qSW.C9 and offers a promising target for the breeding of higher-yielding rapeseed.
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Affiliation(s)
- Xiaohui Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Qiyang Huang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Pengfei Wang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Feiyang Liu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Mudan Luo
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Xiang Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Zhuanrong Wang
- Institute of Crops, Wuhan Academy of Agricultural Sciences, Wuhan, 430065, Hubei, China
| | - Lili Wan
- Institute of Crops, Wuhan Academy of Agricultural Sciences, Wuhan, 430065, Hubei, China
| | - Guangsheng Yang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Dengfeng Hong
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, Hubei, China.
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29
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HopA1 Effector from Pseudomonas syringae pv syringae Strain 61 Affects NMD Processes and Elicits Effector-Triggered Immunity. Int J Mol Sci 2021; 22:ijms22147440. [PMID: 34299060 PMCID: PMC8306789 DOI: 10.3390/ijms22147440] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 06/29/2021] [Accepted: 06/30/2021] [Indexed: 01/25/2023] Open
Abstract
Pseudomonas syringae-secreted HopA1 effectors are important determinants in host range expansion and increased pathogenicity. Their recent acquisitions via horizontal gene transfer in several non-pathogenic Pseudomonas strains worldwide have caused alarming increase in their virulence capabilities. In Arabidopsis thaliana, RESISTANCE TO PSEUDOMONAS SYRINGAE 6 (RPS6) gene confers effector-triggered immunity (ETI) against HopA1pss derived from P. syringae pv. syringae strain 61. Surprisingly, a closely related HopA1pst from the tomato pathovar evades immune detection. These responsive differences in planta between the two HopA1s represents a unique system to study pathogen adaptation skills and host-jumps. However, molecular understanding of HopA1′s contribution to overall virulence remain undeciphered. Here, we show that immune-suppressive functions of HopA1pst are more potent than HopA1pss. In the resistance-compromised ENHANCED DISEASE SUSCEPTIBILITY 1 (EDS1) null-mutant, transcriptomic changes associated with HopA1pss-elicited ETI are still induced and carry resemblance to PAMP-triggered immunity (PTI) signatures. Enrichment of HopA1pss interactome identifies proteins with regulatory roles in post-transcriptional and translational processes. With our demonstration here that both HopA1 suppress reporter-gene translations in vitro imply that the above effector-associations with plant target carry inhibitory consequences. Overall, with our results here we unravel possible virulence role(s) of HopA1 in suppressing PTI and provide newer insights into its detection in resistant plants.
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30
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Nasim Z, Fahim M, Gawarecka K, Susila H, Jin S, Youn G, Ahn JH. Role of AT1G72910, AT1G72940, and ADR1-LIKE 2 in Plant Immunity under Nonsense-Mediated mRNA Decay-Compromised Conditions at Low Temperatures. Int J Mol Sci 2020; 21:E7986. [PMID: 33121126 PMCID: PMC7663611 DOI: 10.3390/ijms21217986] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Revised: 10/23/2020] [Accepted: 10/23/2020] [Indexed: 01/26/2023] Open
Abstract
Nonsense-mediated mRNA decay (NMD) removes aberrant transcripts to avoid the accumulation of truncated proteins. NMD regulates nucleotide-binding, leucine-rich repeat (NLR) genes to prevent autoimmunity; however, the function of a large number of NLRs still remains poorly understood. Here, we show that three NLR genes (AT1G72910, AT1G72940, and ADR1-LIKE 2) are important for NMD-mediated regulation of defense signaling at lower temperatures. At 16 °C, the NMD-compromised up-frameshift protein1 (upf1) upf3 mutants showed growth arrest that can be rescued by the artificial miRNA-mediated knockdown of the three NLR genes. mRNA levels of these NLRs are induced by Pseudomonas syringae inoculation and exogenous SA treatment. Mutations in AT1G72910, AT1G72940, and ADR1-LIKE 2 genes resulted in increased susceptibility to Pseudomonas syringae, whereas their overexpression resulted in severely stunted growth, which was dependent on basal disease resistance genes. The NMD-deficient upf1 upf3 mutants accumulated higher levels of NMD signature-containing transcripts from these NLR genes at 16 °C. Furthermore, mRNA degradation kinetics showed that these NMD signature-containing transcripts were more stable in upf1 upf3 mutants. Based on these findings, we propose that AT1G72910, AT1G72940, and ADR1-LIKE 2 are directly regulated by NMD in a temperature-dependent manner and play an important role in modulating plant immunity at lower temperatures.
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Affiliation(s)
- Zeeshan Nasim
- Department of Life Sciences, Korea University, Seoul 02841, Korea; (Z.N.); (K.G.); (H.S.); (S.J.); (G.Y.)
| | - Muhammad Fahim
- Centre for Omic Sciences, Islamia College University, Peshawar 25120, Pakistan;
| | - Katarzyna Gawarecka
- Department of Life Sciences, Korea University, Seoul 02841, Korea; (Z.N.); (K.G.); (H.S.); (S.J.); (G.Y.)
| | - Hendry Susila
- Department of Life Sciences, Korea University, Seoul 02841, Korea; (Z.N.); (K.G.); (H.S.); (S.J.); (G.Y.)
| | - Suhyun Jin
- Department of Life Sciences, Korea University, Seoul 02841, Korea; (Z.N.); (K.G.); (H.S.); (S.J.); (G.Y.)
| | - Geummin Youn
- Department of Life Sciences, Korea University, Seoul 02841, Korea; (Z.N.); (K.G.); (H.S.); (S.J.); (G.Y.)
| | - Ji Hoon Ahn
- Department of Life Sciences, Korea University, Seoul 02841, Korea; (Z.N.); (K.G.); (H.S.); (S.J.); (G.Y.)
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31
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Shahid S. On UPF Proteins, Baking Cookies, and the Many Targets of Nonsense-Mediated RNA Decay. THE PLANT CELL 2020; 32:2665-2666. [PMID: 32732310 PMCID: PMC7474293 DOI: 10.1105/tpc.20.00602] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Affiliation(s)
- Saima Shahid
- Donald Danforth Plant Science CenterSt. Louis, Missouri
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