1
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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. Plant J 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] [What about the content of this article? (0)] [Affiliation(s)] [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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2
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Prall W, Ganguly DR, Gregory BD. The covalent nucleotide modifications within plant mRNAs: What we know, how we find them, and what should be done in the future. Plant Cell 2023; 35:1801-1816. [PMID: 36794718 PMCID: PMC10226571 DOI: 10.1093/plcell/koad044] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 12/16/2022] [Accepted: 01/09/2023] [Indexed: 05/30/2023]
Abstract
Although covalent nucleotide modifications were first identified on the bases of transfer RNAs (tRNAs) and ribosomal RNAs (rRNAs), a number of these epitranscriptome marks have also been found to occur on the bases of messenger RNAs (mRNAs). These covalent mRNA features have been demonstrated to have various and significant effects on the processing (e.g. splicing, polyadenylation, etc.) and functionality (e.g. translation, transport, etc.) of these protein-encoding molecules. Here, we focus our attention on the current understanding of the collection of covalent nucleotide modifications known to occur on mRNAs in plants, how they are detected and studied, and the most outstanding future questions of each of these important epitranscriptomic regulatory signals.
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Affiliation(s)
- Wil Prall
- Department of Biology, University of Pennsylvania, School of Arts and Sciences, 433 S. University Ave., Philadelphia, PA 19104, USA
| | - Diep R Ganguly
- Department of Biology, University of Pennsylvania, School of Arts and Sciences, 433 S. University Ave., Philadelphia, PA 19104, USA
| | - Brian D Gregory
- Department of Biology, University of Pennsylvania, School of Arts and Sciences, 433 S. University Ave., Philadelphia, PA 19104, USA
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3
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Chen L, Ganguly DR, Shafik SH, Danila F, Grof CPL, Sharwood RE, Furbank RT. The role of SWEET4 proteins in the post-phloem sugar transport pathway of Setaria viridis sink tissues. J Exp Bot 2023; 74:2968-2986. [PMID: 36883216 PMCID: PMC10560085 DOI: 10.1093/jxb/erad076] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Accepted: 03/06/2023] [Indexed: 05/21/2023]
Abstract
In the developing seeds of all higher plants, filial cells are symplastically isolated from the maternal tissue supplying photosynthate to the reproductive structure. Photoassimilates must be transported apoplastically, crossing several membrane barriers, a process facilitated by sugar transporters. Sugars Will Eventually be Exported Transporters (SWEETs) have been proposed to play a crucial role in apoplastic sugar transport during phloem unloading and the post-phloem pathway in sink tissues. Evidence for this is presented here for developing seeds of the C4 model grass Setaria viridis. Using immunolocalization, SvSWEET4 was detected in various maternal and filial tissues within the seed along the sugar transport pathway, in the vascular parenchyma of the pedicel, and in the xylem parenchyma of the stem. Expression of SvSWEET4a in Xenopus laevis oocytes indicated that it functions as a high-capacity glucose and sucrose transporter. Carbohydrate and transcriptional profiling of Setaria seed heads showed that there were some developmental shifts in hexose and sucrose content and consistent expression of SvSWEET4 homologues. Collectively, these results provide evidence for the involvement of SWEETs in the apoplastic transport pathway of sink tissues and allow a pathway for post-phloem sugar transport into the seed to be proposed.
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Affiliation(s)
- Lily Chen
- Research School of Biology, ARC Centre of Excellence for Translational Photosynthesis, Australian National University, Canberra, Australian Capital Territory 2601, Australia
- Hawkesbury Institute for the Environment, Western Sydney University, Hawkesbury Campus, New South Wales 2753, Australia
| | - Diep R Ganguly
- Research School of Biology, ARC Centre of Excellence in Plant Energy Biology, Australian National University, Canberra, Australian Capital Territory 2601, Australia
- CSIRO Synthetic Biology Future Science Platform, Canberra, Australian Capital Territory 2601, Australia
| | - Sarah H Shafik
- Research School of Biology, Australian National University, Canberra, Australian Capital Territory 2601, Australia
| | - Florence Danila
- Research School of Biology, ARC Centre of Excellence for Translational Photosynthesis, Australian National University, Canberra, Australian Capital Territory 2601, Australia
| | - Christopher P L Grof
- Centre for Plant Science, School of Environmental and Life Sciences, College of Engineering Science and Environment, University of Newcastle, Callaghan, New South Wales 2308, Australia
| | - Robert E Sharwood
- Hawkesbury Institute for the Environment, Western Sydney University, Hawkesbury Campus, New South Wales 2753, Australia
| | - Robert T Furbank
- Research School of Biology, ARC Centre of Excellence for Translational Photosynthesis, Australian National University, Canberra, Australian Capital Territory 2601, Australia
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4
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Ganguly DR, Hickey LT, Crisp PA. Harnessing genetic variation at regulatory regions to fine-tune traits for climate-resilient crops. Mol Plant 2022; 15:222-224. [PMID: 34968735 DOI: 10.1016/j.molp.2021.12.011] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 12/21/2021] [Accepted: 12/22/2021] [Indexed: 06/14/2023]
Affiliation(s)
- Diep R Ganguly
- Australian Research Council Centre of Excellence in Plant Energy Biology, Research School of Biology, The Australian National University, Acton, Canberra, ACT 2601, Australia; CSIRO Synthetic Biology Future Science Platform, Canberra, ACT, Australia
| | - Lee T Hickey
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Peter A Crisp
- School of Agriculture and Food Sciences, The University of Queensland, Brisbane, QLD 4072, Australia.
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5
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Chen L, Ganguly DR, Shafik SH, Ermakova M, Pogson BJ, Grof CPL, Sharwood RE, Furbank RT. Elucidating the role of SWEET13 in phloem loading of the C 4 grass Setaria viridis. Plant J 2022; 109:615-632. [PMID: 34780111 DOI: 10.1111/tpj.15581] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 10/11/2021] [Accepted: 11/08/2021] [Indexed: 06/13/2023]
Abstract
Photosynthetic efficiency and sink demand are tightly correlated with rates of phloem loading, where maintaining low cytosolic sugar concentrations is paramount to prevent the downregulation of photosynthesis. Sugars Will Eventually be Exported Transporters (SWEETs) are thought to have a pivotal role in the apoplastic phloem loading of C4 grasses. SWEETs have not been well studied in C4 species, and their investigation is complicated by photosynthesis taking place across two cell types and, therefore, photoassimilate export can occur from either one. SWEET13 homologues in C4 grasses have been proposed to facilitate apoplastic phloem loading. Here, we provide evidence for this hypothesis using the C4 grass Setaria viridis. Expression analyses on the leaf gradient of C4 species Setaria and Sorghum bicolor show abundant transcript levels for SWEET13 homologues. Carbohydrate profiling along the Setaria leaf shows total sugar content to be significantly higher in the mature leaf tip compared with the younger tissue at the base. We present the first known immunolocalization results for SvSWEET13a and SvSWEET13b using novel isoform-specific antisera. These results show localization to the bundle sheath and phloem parenchyma cells of both minor and major veins. We further present the first transport kinetics study of C4 monocot SWEETs by using a Xenopus laevis oocyte heterologous expression system. We demonstrate that SvSWEET13a and SvSWEET13b are high-capacity transporters of glucose and sucrose, with a higher apparent Vmax for sucrose, compared with glucose, typical of clade III SWEETs. Collectively, these results provide evidence for an apoplastic phloem loading pathway in Setaria and possibly other C4 species.
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Affiliation(s)
- Lily Chen
- Research School of Biology, ARC Centre of Excellence for Translational Photosynthesis, Australian National University, Canberra, Australian Capital Territory, 2601, Australia
- School of Science, Hawkesbury Institute for the Environment, Western Sydney University, Hawkesbury Campus, New South Wales, 2753, Australia
| | - Diep R Ganguly
- ARC Centre of Excellence in Plant Energy Biology, Research School of Biology, Australian National University, Canberra, Australian Capital Territory, 2601, Australia
- CSIRO Synthetic Biology Future Science Platform, Canberra, Australian Capital Territory, 2601, Australia
| | - Sarah H Shafik
- Research School of Biology, Australian National University, Canberra, Australian Capital Territory, 2601, Australia
| | - Maria Ermakova
- Research School of Biology, ARC Centre of Excellence for Translational Photosynthesis, Australian National University, Canberra, Australian Capital Territory, 2601, Australia
| | - Barry J Pogson
- ARC Centre of Excellence in Plant Energy Biology, Research School of Biology, Australian National University, Canberra, Australian Capital Territory, 2601, Australia
| | - Christopher P L Grof
- Centre for Plant Science, School of Environmental and Life Sciences, College of Engineering Science and Environment, University of Newcastle, Callaghan, New South Wales, 2308, Australia
| | - Robert E Sharwood
- Research School of Biology, ARC Centre of Excellence for Translational Photosynthesis, Australian National University, Canberra, Australian Capital Territory, 2601, Australia
- School of Science, Hawkesbury Institute for the Environment, Western Sydney University, Hawkesbury Campus, New South Wales, 2753, Australia
| | - Robert T Furbank
- Research School of Biology, ARC Centre of Excellence for Translational Photosynthesis, Australian National University, Canberra, Australian Capital Territory, 2601, Australia
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6
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Wijerathna-Yapa A, Signorelli S, Fenske R, Ganguly DR, Stroeher E, Li L, Pogson BJ, Duncan O, Millar AH. Autophagy mutants show delayed chloroplast development during de-etiolation in carbon limiting conditions. Plant J 2021; 108:459-477. [PMID: 34365695 DOI: 10.1111/tpj.15452] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2021] [Revised: 07/30/2021] [Accepted: 08/04/2021] [Indexed: 06/13/2023]
Abstract
Autophagy is a conserved catabolic process that plays an essential role under nutrient starvation conditions and influences different developmental processes. We observed that seedlings of autophagy mutants (atg2, atg5, atg7, and atg9) germinated in the dark showed delayed chloroplast development following illumination. The delayed chloroplast development was characterized by a decrease in photosynthetic and chlorophyll biosynthetic proteins, lower chlorophyll content, reduced chloroplast size, and increased levels of proteins involved in lipid biosynthesis. Confirming the biological impact of these differences, photosynthetic performance was impaired in autophagy mutants 12 h post-illumination. We observed that while gene expression for photosynthetic machinery during de-etiolation was largely unaffected in atg mutants, several genes involved in photosystem assembly were transcriptionally downregulated. We also investigated if the delayed chloroplast development could be explained by lower lipid import to the chloroplast or lower triglyceride (TAG) turnover. We observed that the limitations in the chloroplast lipid import imposed by trigalactosyldiacylglycerol1 are unlikely to explain the delay in chloroplast development. However, we found that lower TAG mobility in the triacylglycerol lipase mutant sugardependent1 significantly affected de-etiolation. Moreover, we showed that lower levels of carbon resources exacerbated the slow greening phenotype whereas higher levels of carbon resources had an opposite effect. This work suggests a lack of autophagy machinery limits chloroplast development during de-etiolation, and this is exacerbated by limited lipid turnover (lipophagy) that physically or energetically restrains chloroplast development.
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Affiliation(s)
- Akila Wijerathna-Yapa
- ARC Centre of Excellence in Plant Energy Biology, School of Molecular Science, The University of Western Australia, 6009, Crawley, WA, Australia
| | - Santiago Signorelli
- ARC Centre of Excellence in Plant Energy Biology, School of Molecular Science, The University of Western Australia, 6009, Crawley, WA, Australia
- Laboratorio de Bioquímica, Departamento de Biología Vegetal, Facultad de Agronomía, Universidad de la República, Uruguay
| | - Ricarda Fenske
- ARC Centre of Excellence in Plant Energy Biology, School of Molecular Science, The University of Western Australia, 6009, Crawley, WA, Australia
| | - Diep R Ganguly
- ARC Centre of Excellence in Plant Energy Biology, Research School of Biology, The Australian National University, Canberra, ACT, Australia
| | - Elke Stroeher
- ARC Centre of Excellence in Plant Energy Biology, School of Molecular Science, The University of Western Australia, 6009, Crawley, WA, Australia
| | - Lei Li
- ARC Centre of Excellence in Plant Energy Biology, School of Molecular Science, The University of Western Australia, 6009, Crawley, WA, Australia
- Department of Plant Biology and Ecology, College of Life Sciences, Nankai University, 300071, Tianjin, PR China
| | - Barry J Pogson
- ARC Centre of Excellence in Plant Energy Biology, Research School of Biology, The Australian National University, Canberra, ACT, Australia
| | - Owen Duncan
- ARC Centre of Excellence in Plant Energy Biology, School of Molecular Science, The University of Western Australia, 6009, Crawley, WA, Australia
| | - A Harvey Millar
- ARC Centre of Excellence in Plant Energy Biology, School of Molecular Science, The University of Western Australia, 6009, Crawley, WA, Australia
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7
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Eichten SR, Srivastava A, Reddiex AJ, Ganguly DR, Heussler A, Streich JC, Wilson PB, Borevitz JO. Extending the Genotype in Brachypodium by Including DNA Methylation Reveals a Joint Contribution with Genetics on Adaptive Traits. G3 (Bethesda) 2020; 10:1629-1637. [PMID: 32132166 PMCID: PMC7202021 DOI: 10.1534/g3.120.401189] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Epigenomic changes have been considered a potential missing link underlying phenotypic variation in quantitative traits but is potentially confounded with the underlying DNA sequence variation. Although the concept of epigenetic inheritance has been discussed in depth, there have been few studies attempting to directly dissect the amount of epigenomic variation within inbred natural populations while also accounting for genetic diversity. By using known genetic relationships between Brachypodium lines, multiple sets of nearly identical accession families were selected for phenotypic studies and DNA methylome profiling to investigate the dual role of (epi)genetics under simulated natural seasonal climate conditions. Despite reduced genetic diversity, appreciable phenotypic variation was still observable in the measured traits (height, leaf width and length, tiller count, flowering time, ear count) between as well as within the inbred accessions. However, with reduced genetic diversity there was diminished variation in DNA methylation within families. Mixed-effects linear modeling revealed large genetic differences between families and a minor contribution of DNA methylation variation on phenotypic variation in select traits. Taken together, this analysis suggests a limited but significant contribution of DNA methylation toward heritable phenotypic variation relative to genetic differences.
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Affiliation(s)
- Steven R Eichten
- Australian Research Council Centre of Excellence in Plant Energy Biology, Research School of Biology, Australian National University, Canberra, Acton, Australian Capital Territory 2601, Australia
| | - Akanksha Srivastava
- Australian Research Council Centre of Excellence in Plant Energy Biology, Research School of Biology, Australian National University, Canberra, Acton, Australian Capital Territory 2601, Australia
| | - Adam J Reddiex
- Australian Research Council Centre of Excellence in Plant Energy Biology, Research School of Biology, Australian National University, Canberra, Acton, Australian Capital Territory 2601, Australia
| | - Diep R Ganguly
- Australian Research Council Centre of Excellence in Plant Energy Biology, Research School of Biology, Australian National University, Canberra, Acton, Australian Capital Territory 2601, Australia
| | - Alison Heussler
- Australian Research Council Centre of Excellence in Plant Energy Biology, Research School of Biology, Australian National University, Canberra, Acton, Australian Capital Territory 2601, Australia
| | - Jared C Streich
- Australian Research Council Centre of Excellence in Plant Energy Biology, Research School of Biology, Australian National University, Canberra, Acton, Australian Capital Territory 2601, Australia
| | - Pip B Wilson
- Australian Research Council Centre of Excellence in Plant Energy Biology, Research School of Biology, Australian National University, Canberra, Acton, Australian Capital Territory 2601, Australia
| | - Justin O Borevitz
- Australian Research Council Centre of Excellence in Plant Energy Biology, Research School of Biology, Australian National University, Canberra, Acton, Australian Capital Territory 2601, Australia
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8
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Ganguly DR, Stone BAB, Bowerman AF, Eichten SR, Pogson BJ. Excess Light Priming in Arabidopsis thaliana Genotypes with Altered DNA Methylomes. G3 (Bethesda) 2019; 9:3611-3621. [PMID: 31484672 PMCID: PMC6829136 DOI: 10.1534/g3.119.400659] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Accepted: 08/31/2019] [Indexed: 01/17/2023]
Abstract
Plants must continuously react to the ever-fluctuating nature of their environment. Repeated exposure to stressful conditions can lead to priming, whereby prior encounters heighten a plant's ability to respond to future events. A clear example of priming is provided by the model plant Arabidopsis thaliana (Arabidopsis), in which photosynthetic and photoprotective responses are enhanced following recurring light stress. While there are various post-translational mechanisms underpinning photoprotection, an unresolved question is the relative importance of transcriptional changes toward stress priming and, consequently, the potential contribution from DNA methylation - a heritable chemical modification of DNA capable of influencing gene expression. Here, we systematically investigate the potential molecular underpinnings of physiological priming against recurring excess-light (EL), specifically DNA methylation and transcriptional regulation: the latter having not been examined with respect to EL priming. The capacity for physiological priming of photosynthetic and photoprotective parameters following a recurring EL treatment was not impaired in Arabidopsis mutants with perturbed establishment, maintenance, or removal of DNA methylation. Importantly, no differences in development or basal photoprotective capacity were identified in the mutants that may confound the above result. Little evidence for a causal transcriptional component of physiological priming was identified; in fact, most alterations in primed plants presented as a transcriptional 'dampening' in response to an additional EL exposure, likely a consequence of physiological priming. However, a set of transcripts uniquely regulated in primed plants provide preliminary evidence for a novel transcriptional component of recurring EL priming, independent of physiological changes. Thus, we propose that physiological priming of recurring EL in Arabidopsis occurs independently of DNA methylation; and that the majority of the associated transcriptional alterations are a consequence, not cause, of this physiological priming.
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Affiliation(s)
- Diep R Ganguly
- Australian Research Council Centre of Excellence in Plant Energy Biology, Research School of Biology, The Australian National University Canberra, Acton, ACT, 2601, Australia
| | - Bethany A B Stone
- Australian Research Council Centre of Excellence in Plant Energy Biology, Research School of Biology, The Australian National University Canberra, Acton, ACT, 2601, Australia
| | - Andrew F Bowerman
- Australian Research Council Centre of Excellence in Plant Energy Biology, Research School of Biology, The Australian National University Canberra, Acton, ACT, 2601, Australia
| | - Steven R Eichten
- Australian Research Council Centre of Excellence in Plant Energy Biology, Research School of Biology, The Australian National University Canberra, Acton, ACT, 2601, Australia
| | - Barry J Pogson
- Australian Research Council Centre of Excellence in Plant Energy Biology, Research School of Biology, The Australian National University Canberra, Acton, ACT, 2601, Australia
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9
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Crisp PA, Smith AB, Ganguly DR, Murray KD, Eichten SR, Millar AA, Pogson BJ. RNA Polymerase II Read-Through Promotes Expression of Neighboring Genes in SAL1-PAP-XRN Retrograde Signaling. Plant Physiol 2018; 178:1614-1630. [PMID: 30301775 PMCID: PMC6288732 DOI: 10.1104/pp.18.00758] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Accepted: 09/25/2018] [Indexed: 05/07/2023]
Abstract
In plants, the molecular function(s) of the nucleus-localized 5'-3' EXORIBONUCLEASES (XRNs) are unclear; however, their activity is reported to have a significant effect on gene expression and SAL1-mediated retrograde signaling. Using parallel analysis of RNA ends, we documented a dramatic increase in uncapped RNA substrates of the XRNs in both sal1 and xrn2xrn3 mutants. We found that a major consequence of reducing SAL1 or XRN activity was RNA Polymerase II 3' read-through. This occurred at 72% of expressed genes, demonstrating a major genome-wide role for the XRN-torpedo model of transcription termination in Arabidopsis (Arabidopsis thaliana). Read-through is speculated to have a negative effect on transcript abundance; however, we did not observe this. Rather, we identified a strong association between read-through and increased transcript abundance of tandemly orientated downstream genes, strongly correlated with the proximity (less than 1,000 bp) and expression of the upstream gene. We observed read-through in the proximity of 903 genes up-regulated in the sal1-8 retrograde signaling mutant; thus, this phenomenon may account directly for up to 23% of genes up-regulated in sal1-8 Using APX2 and AT5G43770 as exemplars, we genetically uncoupled read-through loci from downstream genes to validate the principle of read-through-mediated mRNA regulation, providing one mechanism by which an ostensibly posttranscriptional exoribonuclease that targets uncapped RNAs could modulate gene expression.
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Affiliation(s)
- Peter A Crisp
- Australian Research Council Centre of Excellence in Plant Energy Biology, Research School of Biology, Australian National University Canberra, Acton, Australian Capital Territory 0200, Australia
- Department of Plant and Microbial Biology, University of Minnesota, Saint Paul, Minnesota 55108
| | - Aaron B Smith
- Australian Research Council Centre of Excellence in Plant Energy Biology, Research School of Biology, Australian National University Canberra, Acton, Australian Capital Territory 0200, Australia
| | - Diep R Ganguly
- Australian Research Council Centre of Excellence in Plant Energy Biology, Research School of Biology, Australian National University Canberra, Acton, Australian Capital Territory 0200, Australia
| | - Kevin D Murray
- Australian Research Council Centre of Excellence in Plant Energy Biology, Research School of Biology, Australian National University Canberra, Acton, Australian Capital Territory 0200, Australia
| | - Steven R Eichten
- Australian Research Council Centre of Excellence in Plant Energy Biology, Research School of Biology, Australian National University Canberra, Acton, Australian Capital Territory 0200, Australia
| | - Anthony A Millar
- Research School of Biology, Australian National University Canberra, Acton, Australian Capital Territory 0200, Australia
| | - Barry J Pogson
- Australian Research Council Centre of Excellence in Plant Energy Biology, Research School of Biology, Australian National University Canberra, Acton, Australian Capital Territory 0200, Australia
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10
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Ganguly DR, Crisp PA, Eichten SR, Pogson BJ. Maintenance of pre-existing DNA methylation states through recurring excess-light stress. Plant Cell Environ 2018; 41:1657-1672. [PMID: 29707792 DOI: 10.1111/pce.13324] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2018] [Revised: 04/16/2018] [Accepted: 04/17/2018] [Indexed: 05/23/2023]
Abstract
The capacity for plant stress priming and memory and the notion of this being underpinned by DNA methylation-mediated memory is an appealing hypothesis for which there is mixed evidence. We previously established a lack of drought-induced methylome variation in Arabidopsis thaliana (Arabidopsis); however, this was tied to only minor observations of physiological memory. There are numerous independent observations demonstrating that photoprotective mechanisms, induced by excess-light stress, can lead to robust programmable changes in newly developing leaf tissues. Although key signalling molecules and transcription factors are known to promote this priming signal, an untested question is the potential involvement of chromatin marks towards the maintenance of light stress acclimation, or memory. Thus, we systematically tested our previous hypothesis of a stress-resistant methylome using a recurring excess-light stress, then analysing new, emerging, and existing tissues. The DNA methylome showed negligible stress-associated variation, with the vast majority attributable to stochastic differences. Yet, photoacclimation was evident through enhanced photosystem II performance in exposed tissues, and nonphotochemical quenching and fluorescence decline ratio showed evidence of mitotic transmission. Thus, we have observed physiological acclimation in new and emerging tissues in the absence of substantive DNA methylome changes.
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Affiliation(s)
- Diep R Ganguly
- Australian Research Council Centre of Excellence in Plant Energy Biology, Division of Plant Sciences, Research School of Biology, Australian National University, Acton, ACT 2601, Australia
| | - Peter A Crisp
- Department of Plant and Microbial Biology, University of Minnesota, Saint Paul, MN, 55108, USA
| | - Steven R Eichten
- Australian Research Council Centre of Excellence in Plant Energy Biology, Division of Plant Sciences, Research School of Biology, Australian National University, Acton, ACT 2601, Australia
| | - Barry J Pogson
- Australian Research Council Centre of Excellence in Plant Energy Biology, Division of Plant Sciences, Research School of Biology, Australian National University, Acton, ACT 2601, Australia
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11
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Ganguly DR, Crisp PA, Eichten SR, Pogson BJ. The Arabidopsis DNA Methylome Is Stable under Transgenerational Drought Stress. Plant Physiol 2017; 175:1893-1912. [PMID: 28986422 PMCID: PMC5717726 DOI: 10.1104/pp.17.00744] [Citation(s) in RCA: 82] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Accepted: 10/03/2017] [Indexed: 05/08/2023]
Abstract
Improving the responsiveness, acclimation, and memory of plants to abiotic stress holds substantive potential for improving agriculture. An unresolved question is the involvement of chromatin marks in the memory of agriculturally relevant stresses. Such potential has spurred numerous investigations yielding both promising and conflicting results. Consequently, it remains unclear to what extent robust stress-induced DNA methylation variation can underpin stress memory. Using a slow-onset water deprivation treatment in Arabidopsis (Arabidopsis thaliana), we investigated the malleability of the DNA methylome to drought stress within a generation and under repeated drought stress over five successive generations. While drought-associated epi-alleles in the methylome were detected within a generation, they did not correlate with drought-responsive gene expression. Six traits were analyzed for transgenerational stress memory, and the descendants of drought-stressed lineages showed one case of memory in the form of increased seed dormancy, and that persisted one generation removed from stress. With respect to transgenerational drought stress, there were negligible conserved differentially methylated regions in drought-exposed lineages compared with unstressed lineages. Instead, the majority of observed variation was tied to stochastic or preexisting differences in the epigenome occurring at repetitive regions of the Arabidopsis genome. Furthermore, the experience of repeated drought stress was not observed to influence transgenerational epi-allele accumulation. Our findings demonstrate that, while transgenerational memory is observed in one of six traits examined, they are not associated with causative changes in the DNA methylome, which appears relatively impervious to drought stress.
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Affiliation(s)
- Diep R Ganguly
- Australian Research Council Centre of Excellence in Plant Energy Biology, Research School of Biology, Australian National University, Acton, Australian Capital Territory 2601, Australia
| | - Peter A Crisp
- Department of Plant and Microbial Biology, University of Minnesota, Saint Paul, Minnesota 55108
| | - Steven R Eichten
- Australian Research Council Centre of Excellence in Plant Energy Biology, Research School of Biology, Australian National University, Acton, Australian Capital Territory 2601, Australia
| | - Barry J Pogson
- Australian Research Council Centre of Excellence in Plant Energy Biology, Research School of Biology, Australian National University, Acton, Australian Capital Territory 2601, Australia
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Crisp PA, Ganguly DR, Smith AB, Murray KD, Estavillo GM, Searle I, Ford E, Bogdanović O, Lister R, Borevitz JO, Eichten SR, Pogson BJ. Rapid Recovery Gene Downregulation during Excess-Light Stress and Recovery in Arabidopsis. Plant Cell 2017; 29:1836-1863. [PMID: 28705956 PMCID: PMC5590493 DOI: 10.1105/tpc.16.00828] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2016] [Revised: 06/22/2017] [Accepted: 07/11/2017] [Indexed: 05/19/2023]
Abstract
Stress recovery may prove to be a promising approach to increase plant performance and, theoretically, mRNA instability may facilitate faster recovery. Transcriptome (RNA-seq, qPCR, sRNA-seq, and PARE) and methylome profiling during repeated excess-light stress and recovery was performed at intervals as short as 3 min. We demonstrate that 87% of the stress-upregulated mRNAs analyzed exhibit very rapid recovery. For instance, HSP101 abundance declined 2-fold every 5.1 min. We term this phenomenon rapid recovery gene downregulation (RRGD), whereby mRNA abundance rapidly decreases promoting transcriptome resetting. Decay constants (k) were modeled using two strategies, linear and nonlinear least squares regressions, with the latter accounting for both transcription and degradation. This revealed extremely short half-lives ranging from 2.7 to 60.0 min for 222 genes. Ribosome footprinting using degradome data demonstrated RRGD loci undergo cotranslational decay and identified changes in the ribosome stalling index during stress and recovery. However, small RNAs and 5'-3' RNA decay were not essential for recovery of the transcripts examined, nor were any of the six excess light-associated methylome changes. We observed recovery-specific gene expression networks upon return to favorable conditions and six transcriptional memory types. In summary, rapid transcriptome resetting is reported in the context of active recovery and cellular memory.
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Affiliation(s)
- Peter A Crisp
- Australian Research Council Centre of Excellence in Plant Energy Biology, Research School of Biology, Australian National University Canberra, Acton ACT 0200, Australia
- Department of Plant and Microbial Biology, University of Minnesota, Saint Paul, Minnesota 55108
| | - Diep R Ganguly
- Australian Research Council Centre of Excellence in Plant Energy Biology, Research School of Biology, Australian National University Canberra, Acton ACT 0200, Australia
| | - Aaron B Smith
- Australian Research Council Centre of Excellence in Plant Energy Biology, Research School of Biology, Australian National University Canberra, Acton ACT 0200, Australia
| | - Kevin D Murray
- Australian Research Council Centre of Excellence in Plant Energy Biology, Research School of Biology, Australian National University Canberra, Acton ACT 0200, Australia
| | - Gonzalo M Estavillo
- Australian Research Council Centre of Excellence in Plant Energy Biology, Research School of Biology, Australian National University Canberra, Acton ACT 0200, Australia
- CSIRO Agriculture and Food, Black Mountain, Canberra ACT 2601, Australia
| | - Iain Searle
- School of Biological Sciences, The University of Adelaide, SA 5005, Australia
| | - Ethan Ford
- Australian Research Council Centre of Excellence in Plant Energy Biology, The University of Western Australia, Perth WA 6009, Australia
| | - Ozren Bogdanović
- Australian Research Council Centre of Excellence in Plant Energy Biology, The University of Western Australia, Perth WA 6009, Australia
- Harry Perkins Institute of Medical Research, Perth WA 6009, Australia
| | - Ryan Lister
- Australian Research Council Centre of Excellence in Plant Energy Biology, The University of Western Australia, Perth WA 6009, Australia
- Harry Perkins Institute of Medical Research, Perth WA 6009, Australia
| | - Justin O Borevitz
- Australian Research Council Centre of Excellence in Plant Energy Biology, Research School of Biology, Australian National University Canberra, Acton ACT 0200, Australia
| | - Steven R Eichten
- Australian Research Council Centre of Excellence in Plant Energy Biology, Research School of Biology, Australian National University Canberra, Acton ACT 0200, Australia
| | - Barry J Pogson
- Australian Research Council Centre of Excellence in Plant Energy Biology, Research School of Biology, Australian National University Canberra, Acton ACT 0200, Australia
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