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Dong Y, Gupta S, Wargent JJ, Putterill J, Macknight RC, Gechev TS, Mueller-Roeber B, Dijkwel PP. Comparative Transcriptomics of Multi-Stress Responses in Pachycladon cheesemanii and Arabidopsis thaliana. Int J Mol Sci 2023; 24:11323. [PMID: 37511083 PMCID: PMC10379395 DOI: 10.3390/ijms241411323] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Revised: 06/26/2023] [Accepted: 07/06/2023] [Indexed: 07/30/2023] Open
Abstract
The environment is seldom optimal for plant growth and changes in abiotic and biotic signals, including temperature, water availability, radiation and pests, induce plant responses to optimise survival. The New Zealand native plant species and close relative to Arabidopsis thaliana, Pachycladon cheesemanii, grows under environmental conditions that are unsustainable for many plant species. Here, we compare the responses of both species to different stressors (low temperature, salt and UV-B radiation) to help understand how P. cheesemanii can grow in such harsh environments. The stress transcriptomes were determined and comparative transcriptome and network analyses discovered similar and unique responses within species, and between the two plant species. A number of widely studied plant stress processes were highly conserved in A. thaliana and P. cheesemanii. However, in response to cold stress, Gene Ontology terms related to glycosinolate metabolism were only enriched in P. cheesemanii. Salt stress was associated with alteration of the cuticle and proline biosynthesis in A. thaliana and P. cheesemanii, respectively. Anthocyanin production may be a more important strategy to contribute to the UV-B radiation tolerance in P. cheesemanii. These results allowed us to define broad stress response pathways in A. thaliana and P. cheesemanii and suggested that regulation of glycosinolate, proline and anthocyanin metabolism are strategies that help mitigate environmental stress.
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Affiliation(s)
- Yanni Dong
- School of Natural Sciences, Massey University, Tennent Drive, Palmerston North 4474, New Zealand
| | - Saurabh Gupta
- Department Molecular Biology, Institute of Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Straße 24-25, Haus 20, 14476 Potsdam, Germany
| | - Jason J Wargent
- School of Agriculture & Environment, Massey University, Palmerston North 4442, New Zealand
| | - Joanna Putterill
- School of Biological Sciences, University of Auckland, Auckland 1142, New Zealand
| | - Richard C Macknight
- Biochemistry Department, School of Biomedical Sciences, University of Otago, Dunedin 9016, New Zealand
| | - Tsanko S Gechev
- Center of Plant Systems Biology and Biotechnology (CPSBB), 139 Ruski Blvd., 4000 Plovdiv, Bulgaria
- Department of Plant Physiology and Plant Molecular Biology, University of Plovdiv, 24 Tsar Assen Str., 4000 Plovdiv, Bulgaria
| | - Bernd Mueller-Roeber
- Department Molecular Biology, Institute of Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Straße 24-25, Haus 20, 14476 Potsdam, Germany
- Center of Plant Systems Biology and Biotechnology (CPSBB), 139 Ruski Blvd., 4000 Plovdiv, Bulgaria
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam, Germany
| | - Paul P Dijkwel
- School of Natural Sciences, Massey University, Tennent Drive, Palmerston North 4474, New Zealand
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Shirzadian-Khorramabad R, Moazzenzadeh T, Sajedi RH, Jing HC, Hille J, Dijkwel PP. A mutation in Arabidopsis SAL1 alters its in vitro activity against IP 3 and delays developmental leaf senescence in association with lower ROS levels. Plant Mol Biol 2022; 108:549-563. [PMID: 35122174 DOI: 10.1007/s11103-022-01245-0] [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: 08/10/2021] [Accepted: 01/21/2022] [Indexed: 06/14/2023]
Abstract
Our manuscript is the first to find a link between activity of SAL1/OLD101 against IP3 and plant leaf senescence regulation and ROS levels assigning a potential biological role for IP3. Leaf senescence is a genetically programmed process that limits the longevity of a leaf. We identified and analyzed the recessive Arabidopsis stay-green mutation onset of leaf death 101 (old101). Developmental leaf longevity is extended in old101 plants, which coincided with higher peroxidase activity and decreased H2O2 levels in young 10-day-old, but not 25-day-old plants. The old101 phenotype is caused by a point mutation in SAL1, which encodes a bifunctional enzyme with inositol polyphosphate-1-phosphatase and 3' (2'), 5'-bisphosphate nucleotidase activity. SAL1 activity is highly specific for its substrates 3-polyadenosine 5-phosphate (PAP) and inositol 1, 4, 5-trisphosphate (IP3), where it removes the 1-phosphate group from the IP3 second messenger. The in vitro activity of recombinant old101 protein against its substrate IP3 was 2.5-fold lower than that of wild type SAL1 protein. However, the in vitro activity of recombinant old101 mutant protein against PAP remained the same as that of the wild type SAL1 protein. The results open the possibility that the activity of SAL1 against IP3 may affect the redox balance of young seedlings and that this delays the onset of leaf senescence.
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Affiliation(s)
- Reza Shirzadian-Khorramabad
- Department of Agricultural Biotechnology, Faculty of Agricultural Sciences, University of Guilan, Rasht, Iran.
- Molecular Biology of Plants, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Kerklaan 30, 9751 NN, Haren, The Netherlands.
- School of Fundamental Sciences, Massey University, Private Bag 11222, Palmerston North, New Zealand.
| | - Taghi Moazzenzadeh
- Department of Agricultural Biotechnology, Faculty of Agricultural Sciences, University of Guilan, Rasht, Iran
- MESA+ Institute for Nanotechnology, University of Twente, P.O. Box 217, 7500 AE, Enschede, The Netherlands
| | - Reza H Sajedi
- Department of Biochemistry, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Hai-Chun Jing
- Molecular Biology of Plants, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Kerklaan 30, 9751 NN, Haren, The Netherlands
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Jacques Hille
- Molecular Biology of Plants, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Kerklaan 30, 9751 NN, Haren, The Netherlands
| | - Paul P Dijkwel
- Molecular Biology of Plants, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Kerklaan 30, 9751 NN, Haren, The Netherlands
- School of Fundamental Sciences, Massey University, Private Bag 11222, Palmerston North, New Zealand
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3
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Xu X, Jibran R, Wang Y, Dong L, Flokova K, Esfandiari A, McLachlan ARG, Heiser A, Sutherland-Smith AJ, Brummell DA, Bouwmeester HJ, Dijkwel PP, Hunter DA. Strigolactones regulate sepal senescence in Arabidopsis. J Exp Bot 2021; 72:5462-5477. [PMID: 33970249 DOI: 10.1093/jxb/erab199] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [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: 02/28/2021] [Accepted: 05/08/2021] [Indexed: 05/07/2023]
Abstract
Flower sepals are critical for flower development and vary greatly in life span depending on their function post-pollination. Very little is known about what controls sepal longevity. Using a sepal senescence mutant screen, we identified two Arabidopsis mutants with delayed senescence directly connecting strigolactones with senescence regulation in a novel floral context that hitherto has not been explored. The mutations were in the strigolactone biosynthetic gene MORE AXILLARY GROWTH1 (MAX1) and in the strigolactone receptor gene DWARF14 (AtD14). The mutation in AtD14 changed the catalytic Ser97 to Phe in the enzyme active site, which is the first mutation of its kind in planta. The lesion in MAX1 was in the haem-iron ligand signature of the cytochrome P450 protein, converting the highly conserved Gly469 to Arg, which was shown in a transient expression assay to substantially inhibit the activity of MAX1. The two mutations highlighted the importance of strigolactone activity for driving to completion senescence initiated both developmentally and in response to carbon-limiting stress, as has been found for the more well-known senescence-associated regulators ethylene and abscisic acid. Analysis of transcript abundance in excised inflorescences during an extended night suggested an intricate relationship among sugar starvation, senescence, and strigolactone biosynthesis and signalling.
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Affiliation(s)
- Xi Xu
- Massey University, School of Fundamental Sciences, Palmerston North, New Zealand
- The New Zealand Institute for Plant and Food Research Limited, Palmerston North, New Zealand
| | - Rubina Jibran
- The New Zealand Institute for Plant and Food Research Limited, Palmerston North, New Zealand
| | - Yanting Wang
- Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, The Netherlands
| | - Lemeng Dong
- Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, The Netherlands
| | - Kristyna Flokova
- Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, The Netherlands
| | - Azadeh Esfandiari
- The New Zealand Institute for Plant and Food Research Limited, Palmerston North, New Zealand
| | - Andrew R G McLachlan
- The New Zealand Institute for Plant and Food Research Limited, Palmerston North, New Zealand
| | - Axel Heiser
- Hopkirk Research Institute, AgResearch Limited, Palmerston North, New Zealand
| | | | - David A Brummell
- The New Zealand Institute for Plant and Food Research Limited, Palmerston North, New Zealand
| | - Harro J Bouwmeester
- Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, The Netherlands
| | - Paul P Dijkwel
- Massey University, School of Fundamental Sciences, Palmerston North, New Zealand
| | - Donald A Hunter
- The New Zealand Institute for Plant and Food Research Limited, Palmerston North, New Zealand
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Kanojia A, Gupta S, Benina M, Fernie AR, Mueller-Roeber B, Gechev T, Dijkwel PP. Developmentally controlled changes during Arabidopsis leaf development indicate causes for loss of stress tolerance with age. J Exp Bot 2020; 71:6340-6354. [PMID: 32720687 PMCID: PMC7586751 DOI: 10.1093/jxb/eraa347] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [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: 05/24/2020] [Accepted: 07/22/2020] [Indexed: 05/26/2023]
Abstract
Leaf senescence is the final stage of leaf development and is induced by the gradual occurrence of age-related changes (ARCs). The process of leaf senescence has been well described, but the cellular events leading to this process are still poorly understood. By analysis of progressively ageing, but not yet senescing, Arabidopsis thaliana rosette leaves, we aimed to better understand processes occurring prior to the onset of senescence. Using gene expression analysis, we found that as leaves mature, genes responding to oxidative stress and genes involved in stress hormone biosynthesis and signalling were up-regulated. A decrease in primary metabolites that provide protection against oxidative stress was a possible explanation for the increased stress signature. The gene expression and metabolomics changes occurred concomitantly to a decrease in drought, salinity, and dark stress tolerance of individual leaves. Importantly, stress-related genes showed elevated expression in the early ageing mutant old5 and decreased expression in the delayed ageing mutant ore9. We propose that the decreased stress tolerance with age results from the occurrence of senescence-inducing ARCs that is integrated into the leaf developmental programme, and that this ensures a timely and certain death.
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Affiliation(s)
- Aakansha Kanojia
- School of Fundamental Sciences, Massey University, Palmerston North, New Zealand
- Center of Plant Systems Biology and Biotechnology, Plovdiv, Bulgaria
| | - Saurabh Gupta
- Department Molecular Biology, Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| | - Maria Benina
- Center of Plant Systems Biology and Biotechnology, Plovdiv, Bulgaria
| | - Alisdair R Fernie
- Center of Plant Systems Biology and Biotechnology, Plovdiv, Bulgaria
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| | - Bernd Mueller-Roeber
- Center of Plant Systems Biology and Biotechnology, Plovdiv, Bulgaria
- Department Molecular Biology, Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Tsanko Gechev
- Center of Plant Systems Biology and Biotechnology, Plovdiv, Bulgaria
- Department of Plant Physiology and Molecular Biology, University of Plovdiv, Plovdiv, Bulgaria
| | - Paul P Dijkwel
- School of Fundamental Sciences, Massey University, Palmerston North, New Zealand
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5
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Kondratev N, Denton-Giles M, Bradshaw RE, Cox MP, Dijkwel PP. Camellia Plant Resistance and Susceptibility to Petal Blight Disease Are Defined by the Timing of Defense Responses. Mol Plant Microbe Interact 2020; 33:982-995. [PMID: 32223579 DOI: 10.1094/mpmi-10-19-0304-r] [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] [Indexed: 06/10/2023]
Abstract
The family Sclerotiniaceae includes important phytopathogens, such as Botrytis cinerea and Sclerotinia sclerotiorum, that activate plant immune responses to facilitate infection propagation. The mechanisms of plant resistance to these necrotrophic pathogens are still poorly understood. To discover mechanisms of resistance, we used the Ciborinia camelliae (Sclerotiniaceae)-Camellia spp. pathosystem. This fungus induces rapid infection of the blooms of susceptible cultivar Nicky Crisp (Camellia japonica × Camellia pitardii var. pitardii), while Camellia lutchuensis is highly resistant. Genome-wide analysis of gene expression in resistant plants revealed fast modulation of host transcriptional activity 6 h after ascospore inoculation. Ascospores induced the same defense pathways in the susceptible Camellia cultivar but much delayed and coinciding with disease development. We next tested the hypothesis that differences in defense timing influences disease outcome. We induced early defense in the susceptible cultivar using methyl jasmonate and this strongly reduced disease development. Conversely, delaying the response in the resistant species, by infecting it with actively growing fungal mycelium, increased susceptibility. The same plant defense pathways, therefore, contribute to both resistance and susceptibility, suggesting that defense timing is a critical factor in plant health, and resistance against necrotrophic pathogens may occur during the initial biotrophy-like stages.
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Affiliation(s)
- Nikolai Kondratev
- School of Fundamental Sciences, Massey University, Palmerston North, New Zealand
- Bio-Protection Research Centre, Massey University, Palmerston North, New Zealand
| | - Matthew Denton-Giles
- School of Fundamental Sciences, Massey University, Palmerston North, New Zealand
| | - Rosie E Bradshaw
- School of Fundamental Sciences, Massey University, Palmerston North, New Zealand
- Bio-Protection Research Centre, Massey University, Palmerston North, New Zealand
| | - Murray P Cox
- School of Fundamental Sciences, Massey University, Palmerston North, New Zealand
- Bio-Protection Research Centre, Massey University, Palmerston North, New Zealand
| | - Paul P Dijkwel
- School of Fundamental Sciences, Massey University, Palmerston North, New Zealand
- Bio-Protection Research Centre, Massey University, Palmerston North, New Zealand
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6
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Faisal MB, Gechev TS, Mueller-Roeber B, Dijkwel PP. Putative alternative translation start site-encoding nucleotides of CPR5 regulate growth and resistance. BMC Plant Biol 2020; 20:295. [PMID: 32600419 PMCID: PMC7322872 DOI: 10.1186/s12870-020-02485-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Accepted: 06/09/2020] [Indexed: 06/11/2023]
Abstract
BACKGROUND The Arabidopsis CONSTITUTIVE EXPRESSER of PATHOGENESIS-RELATED GENES 5 (CPR5) has recently been shown to play a role in gating as part of the nuclear pore complex (NPC). Mutations in CPR5 cause multiple defects, including aberrant trichomes, reduced ploidy levels, reduced growth and enhanced resistance to bacterial and fungal pathogens. The pleiotropic nature of cpr5 mutations implicates that the CPR5 protein affects multiple pathways. However, little is known about the structural features that allow CPR5 to affect the different pathways. RESULTS Our in silico studies suggest that in addition to three clusters of putative nuclear localization signals and four or five transmembrane domains, CPR5 contains two putative alternative translation start sites. To test the role of the methionine-encoding nucleotides implicated in those sites, metCPR5 cDNAs, in which the relevant nucleotides were changed to encode glutamine, were fused to the CPR5 native promoter and the constructs transformed to cpr5-2 plants to complement cpr5-compromised phenotypes. The control and metCPR5 constructs were able to complement all cpr5 phenotypes, although the extent of complementation depended on the specific complementing plant lines. Remarkably, plants transformed with metCPR5 constructs showed larger leaves and displayed reduced resistance when challenged to Pseudomonas syringae pv Pst DC3000, as compared to control plants. Thus, the methionine-encoding nucleotides regulate growth and resistance. We propose that structural features of the CPR5 N-terminus are implicated in selective gating of proteins involved in regulating the balance between growth and resistance. CONCLUSION Plants need to carefully balance the amount of resources used for growth and resistance. The Arabidopsis CPR5 protein regulates plant growth and immunity. Here we show that N-terminal features of CPR5 are involved in the regulation of the balance between growth and resistance. These findings may benefit efforts to improve plant yield, while maintaining optimal levels of disease resistance.
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Affiliation(s)
- Muhammad B Faisal
- School of Fundamental Sciences, Massey University, Palmerston North, New Zealand
| | - Tsanko S Gechev
- Center of Plant Systems Biology and Biotechnology, 4000, Plovdiv, Bulgaria
| | - Bernd Mueller-Roeber
- Center of Plant Systems Biology and Biotechnology, 4000, Plovdiv, Bulgaria
- Department of Molecular Biology, Institute of Biochemistry and Biology, University of Potsdam, 14476, Potsdam, Germany
| | - Paul P Dijkwel
- School of Fundamental Sciences, Massey University, Palmerston North, New Zealand.
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Denton‐Giles M, McCarthy H, Sehrish T, Dijkwel Y, Mesarich CH, Bradshaw RE, Cox MP, Dijkwel PP. Conservation and expansion of a necrosis-inducing small secreted protein family from host-variable phytopathogens of the Sclerotiniaceae. Mol Plant Pathol 2020; 21:512-526. [PMID: 32061186 PMCID: PMC7060139 DOI: 10.1111/mpp.12913] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [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: 10/07/2019] [Revised: 12/19/2019] [Accepted: 12/21/2019] [Indexed: 05/02/2023]
Abstract
Fungal effector proteins facilitate host-plant colonization and have generally been characterized as small secreted proteins (SSPs). We classified and functionally tested SSPs from the secretomes of three closely related necrotrophic phytopathogens: Ciborinia camelliae, Botrytis cinerea, and Sclerotinia sclerotiorum. Alignment of predicted SSPs identified a large protein family that share greater than 41% amino acid identity and that have key characteristics of previously described microbe-associated molecular patterns (MAMPs). Strikingly, 73 of the 75 SSP family members were predicted within the secretome of the host-specialist C. camelliae with single-copy homologs identified in the secretomes of the host generalists S. sclerotiorum and B. cinerea. To explore the potential function of this family of SSPs, 10 of the 73 C. camelliae proteins, together with the single-copy homologs from S. sclerotiorum (SsSSP3) and B. cinerea (BcSSP2), were cloned and expressed as recombinant proteins. Infiltration of SsSSP3 and BcSSP2 into host tissue induced rapid necrosis. In contrast, only one of the 10 tested C. camelliae SSPs was able to induce a limited amount of necrosis. Analysis of chimeric proteins consisting of domains from both a necrosis-inducing and a non-necrosis-inducing SSP demonstrated that the C-terminus of the S. sclerotiorum SSP is essential for necrosis-inducing function. Deletion of the BcSSP2 homolog from B. cinerea did not affect growth or pathogenesis. Thus, this research uncovered a family of highly conserved SSPs present in diverse ascomycetes that exhibit contrasting necrosis-inducing functions.
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Affiliation(s)
- Matthew Denton‐Giles
- Centre for Crop and Disease ManagementCurtin UniversityPerthAustralia
- School of Fundamental SciencesMassey UniversityPalmerston NorthNew Zealand
| | - Hannah McCarthy
- School of Fundamental SciencesMassey UniversityPalmerston NorthNew Zealand
| | - Tina Sehrish
- School of Fundamental SciencesMassey UniversityPalmerston NorthNew Zealand
| | - Yasmin Dijkwel
- School of Fundamental SciencesMassey UniversityPalmerston NorthNew Zealand
| | - Carl H. Mesarich
- School of Agriculture and EnvironmentMassey UniversityPalmerston NorthNew Zealand
| | - Rosie E. Bradshaw
- School of Fundamental SciencesMassey UniversityPalmerston NorthNew Zealand
| | - Murray P. Cox
- School of Fundamental SciencesMassey UniversityPalmerston NorthNew Zealand
| | - Paul P. Dijkwel
- School of Fundamental SciencesMassey UniversityPalmerston NorthNew Zealand
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8
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Forte FP, Schmid J, Dijkwel PP, Nagy I, Hume DE, Johnson RD, Simpson WR, Monk SM, Zhang N, Sehrish T, Asp T. Fungal Endophyte Colonization Patterns Alter Over Time in the Novel Association Between Lolium perenne and Epichloë Endophyte AR37. Front Plant Sci 2020; 11:570026. [PMID: 33193501 PMCID: PMC7658011 DOI: 10.3389/fpls.2020.570026] [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] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Accepted: 09/22/2020] [Indexed: 05/16/2023]
Abstract
Infection of the pasture grass Lolium perenne with the seed-transmitted fungal endophyte Epichloë festucae enhances its resilience to biotic and abiotic stress. Agricultural benefits of endophyte infection can be increased by generating novel symbiotic associations through inoculating L. perenne with selected Epichloë strains. Natural symbioses have coevolved over long periods. Thus, artificial symbioses will probably not have static properties, but symbionts will coadapt over time improving the fitness of the association. Here we report for the first time on temporal changes in a novel association of Epichloë strain AR37 and the L. perenne cultivar Grasslands Samson. Over nine generations, a seed maintenance program had increased the endophyte seed transmission rates to > 95% (from an initial 76%). We observed an approximately fivefold decline in endophyte biomass concentration in vegetative tissues over time (between generations 2 and 9). This indicates strong selection pressure toward reducing endophyte-related fitness costs by reducing endophyte biomass, without compromising the frequency of endophyte transmission to seed. We observed no obvious changes in tillering and only minor transcriptomic changes in infected plants over time. Functional analysis of 40 plant genes, showing continuously decreasing expression over time, suggests that adaptation of host metabolism and defense mechanisms are important for increasing the fitness of this association, and possibly fitness of such symbioses in general. Our results indicate that fitness of novel associations is likely to improve over time and that monitoring changes in novel associations can assist in identifying key features of endophyte-mediated enhancement of host fitness.
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Affiliation(s)
- Flavia Pilar Forte
- Center for Quantitative Genetics and Genomics, Aarhus University, Slagelse, Denmark
- School of Fundamental Sciences, Massey University, Palmerston North, New Zealand
- *Correspondence: Flavia Pilar Forte,
| | - Jan Schmid
- School of Fundamental Sciences, Massey University, Palmerston North, New Zealand
- Ferguson Street Laboratories, Palmerston North, New Zealand
| | - Paul P. Dijkwel
- School of Fundamental Sciences, Massey University, Palmerston North, New Zealand
| | - Istvan Nagy
- Center for Quantitative Genetics and Genomics, Aarhus University, Slagelse, Denmark
| | - David E. Hume
- AgResearch, Grasslands Research Centre, Palmerston North, New Zealand
| | | | - Wayne R. Simpson
- AgResearch, Grasslands Research Centre, Palmerston North, New Zealand
| | | | - Ningxin Zhang
- School of Fundamental Sciences, Massey University, Palmerston North, New Zealand
| | - Tina Sehrish
- School of Fundamental Sciences, Massey University, Palmerston North, New Zealand
| | - Torben Asp
- Center for Quantitative Genetics and Genomics, Aarhus University, Slagelse, Denmark
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9
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Berry D, Mace W, Grage K, Wesche F, Gore S, Schardl CL, Young CA, Dijkwel PP, Leuchtmann A, Bode HB, Scott B. Efficient nonenzymatic cyclization and domain shuffling drive pyrrolopyrazine diversity from truncated variants of a fungal NRPS. Proc Natl Acad Sci U S A 2019; 116:25614-25623. [PMID: 31801877 PMCID: PMC6926027 DOI: 10.1073/pnas.1913080116] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Nonribosomal peptide synthetases (NRPSs) generate the core peptide scaffolds of many natural products. These include small cyclic dipeptides such as the insect feeding deterrent peramine, which is a pyrrolopyrazine (PPZ) produced by grass-endophytic Epichloë fungi. Biosynthesis of peramine is catalyzed by the 2-module NRPS, PpzA-1, which has a C-terminal reductase (R) domain that is required for reductive release and cyclization of the NRPS-tethered dipeptidyl-thioester intermediate. However, some PpzA variants lack this R domain due to insertion of a transposable element into the 3' end of ppzA We demonstrate here that these truncated PpzA variants utilize nonenzymatic cyclization of the dipeptidyl thioester to a 2,5-diketopiperazine (DKP) to synthesize a range of novel PPZ products. Truncation of the R domain is sufficient to subfunctionalize PpzA-1 into a dedicated DKP synthetase, exemplified by the truncated variant, PpzA-2, which has also evolved altered substrate specificity and reduced N-methyltransferase activity relative to PpzA-1. Further allelic diversity has been generated by recombination-mediated domain shuffling between ppzA-1 and ppzA-2, resulting in the ppzA-3 and ppzA-4 alleles, each of which encodes synthesis of a unique PPZ metabolite. This research establishes that efficient NRPS-catalyzed DKP biosynthesis can occur in vivo through nonenzymatic dipeptidyl cyclization and presents a remarkably clean example of NRPS evolution through recombinant exchange of functionally divergent domains. This work highlights that allelic variants of a single NRPS can result in a surprising level of secondary metabolite diversity comparable to that observed for some gene clusters.
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Affiliation(s)
- Daniel Berry
- School of Fundamental Sciences, Massey University, Palmerston North 4442, New Zealand
- Bioprotection Research Centre, Massey University, Palmerston North 4442, New Zealand
| | - Wade Mace
- Grasslands Research Centre, AgResearch Ltd., Palmerston North 4442, New Zealand
| | - Katrin Grage
- School of Fundamental Sciences, Massey University, Palmerston North 4442, New Zealand
| | - Frank Wesche
- Fachbereich Biowissenschaften, Molekulare Biotechnologie, Goethe Universität Frankfurt, 60438 Frankfurt am Main, Germany
| | - Sagar Gore
- Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute, 07745 Jena, Germany
| | | | | | - Paul P Dijkwel
- School of Fundamental Sciences, Massey University, Palmerston North 4442, New Zealand
- Bioprotection Research Centre, Massey University, Palmerston North 4442, New Zealand
| | - Adrian Leuchtmann
- Institute of Integrative Biology, ETH Zürich, CH-8092 Zürich, Switzerland
| | - Helge B Bode
- Fachbereich Biowissenschaften, Molekulare Biotechnologie, Goethe Universität Frankfurt, 60438 Frankfurt am Main, Germany;
- Buchmann Institute for Molecular Life Sciences, Goethe-Universität, 60438 Frankfurt am Main, Germany
- Landes-Offensive zur Entwicklung Wissenschaftlich-Ökonomischer Exzellenz (LOEWE) Centre for Translational Biodiversity Genomics, 60325 Frankfurt am Main, Germany
| | - Barry Scott
- School of Fundamental Sciences, Massey University, Palmerston North 4442, New Zealand;
- Bioprotection Research Centre, Massey University, Palmerston North 4442, New Zealand
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10
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Dong Y, Gupta S, Sievers R, Wargent JJ, Wheeler D, Putterill J, Macknight R, Gechev T, Mueller-Roeber B, Dijkwel PP. Genome draft of the Arabidopsis relative Pachycladon cheesemanii reveals novel strategies to tolerate New Zealand's high ultraviolet B radiation environment. BMC Genomics 2019; 20:838. [PMID: 31718535 PMCID: PMC6849220 DOI: 10.1186/s12864-019-6084-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Accepted: 09/06/2019] [Indexed: 11/10/2022] Open
Abstract
Background Pachycladon cheesemanii is a close relative of Arabidopsis thaliana and is an allotetraploid perennial herb which is widespread in the South Island of New Zealand. It grows at altitudes of up to 1000 m where it is subject to relatively high levels of ultraviolet (UV)-B radiation. To gain first insights into how Pachycladon copes with UV-B stress, we sequenced its genome and compared the UV-B tolerance of two Pachycladon accessions with those of two A. thaliana accessions from different altitudes. Results A high-quality draft genome of P. cheesemanii was assembled with a high percentage of conserved single-copy plant orthologs. Synteny analysis with genomes from other species of the Brassicaceae family found a close phylogenetic relationship of P. cheesemanii with Boechera stricta from Brassicaceae lineage I. While UV-B radiation caused a greater growth reduction in the A. thaliana accessions than in the P. cheesemanii accessions, growth was not reduced in one P. cheesemanii accession. The homologues of A. thaliana UV-B radiation response genes were duplicated in P. cheesemanii, and an expression analysis of those genes indicated that the tolerance mechanism in P. cheesemanii appears to differ from that in A. thaliana. Conclusion Although the P. cheesemanii genome shows close similarity with that of A. thaliana, it appears to have evolved novel strategies allowing the plant to tolerate relatively high UV-B radiation.
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Affiliation(s)
- Yanni Dong
- School of Fundamental Sciences, Massey University, Tennent Drive, Palmerston North, 4410, New Zealand
| | - Saurabh Gupta
- Department Molecular Biology, Institute of Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Straße 24-25, Haus 20, 14476, Potsdam, Germany
| | - Rixta Sievers
- School of Agriculture & Environment, Massey University, Palmerston North, 4442, New Zealand
| | - Jason J Wargent
- School of Agriculture & Environment, Massey University, Palmerston North, 4442, New Zealand
| | - David Wheeler
- School of Fundamental Sciences, Massey University, Tennent Drive, Palmerston North, 4410, New Zealand
| | - Joanna Putterill
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Richard Macknight
- Biochemistry Department, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand
| | - Tsanko Gechev
- Department of Plant Physiology and Molecular Biology, University of Plovdiv, 24 Tsar Assen str, 4000, Plovdiv, Bulgaria.,Center of Plant Systems Biology and Biotechnology (CPSBB), 139 Ruski Blvd, 4000, Plovdiv, Bulgaria
| | - Bernd Mueller-Roeber
- Department Molecular Biology, Institute of Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Straße 24-25, Haus 20, 14476, Potsdam, Germany.,Center of Plant Systems Biology and Biotechnology (CPSBB), 139 Ruski Blvd, 4000, Plovdiv, Bulgaria.,Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam, Germany
| | - Paul P Dijkwel
- School of Fundamental Sciences, Massey University, Tennent Drive, Palmerston North, 4410, New Zealand.
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11
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Berry D, Mace W, Rehner SA, Grage K, Dijkwel PP, Young CA, Scott B. Orthologous peramine and pyrrolopyrazine-producing biosynthetic gene clusters in Metarhizium rileyi, Metarhizium majus and Cladonia grayi. Environ Microbiol 2018; 21:928-939. [PMID: 30452111 DOI: 10.1111/1462-2920.14483] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Revised: 11/09/2018] [Accepted: 11/13/2018] [Indexed: 12/17/2022]
Abstract
Peramine is a non-ribosomal peptide-derived pyrrolopyrazine (PPZ)-containing molecule with anti-insect properties. Peramine is known to be produced by fungi from genus Epichloë, which form mutualistic endophytic associations with cool-season grass hosts. Peramine biosynthesis has been proposed to require only the two-module non-ribosomal peptide synthetase (NRPS) peramine synthetase (PerA), which is encoded by the 8.3 kb gene perA, though this has not been conclusively proven. Until recently, both peramine and perA were thought to be exclusive to fungi of genus Epichloë; however, a putative perA homologue was recently identified in the genome of the insect-pathogenic fungus Metarhizium rileyi. We use a heterologous expression system and a hydrophilic interaction chromatography-based analysis method to confirm that PerA is the only pathway-specific protein required for peramine biosynthesis. The perA homologue from M. rileyi (MR_perA) is shown to encode a functional peramine synthetase, establishing a precedent for distribution of perA orthologs beyond genus Epichloë. Furthermore, perA is part of a larger seven-gene PPZ cluster in M. rileyi, Metarhizium majus and the stalked-cup lichen fungus Cladonia grayi. These PPZ genes encode proteins predicted to derivatize peramine into more complex PPZ metabolites, with the orphaned perA gene of Epichloë spp. representing an example of reductive evolution.
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Affiliation(s)
- Daniel Berry
- Institute of Fundamental Sciences, Massey University, Palmerston North, New Zealand.,Bio-Protection Research Centre, Massey University, Palmerston North, New Zealand
| | - Wade Mace
- AgResearch Ltd., Grasslands Research Center, Palmerston North, New Zealand
| | - Stephen A Rehner
- Mycology and Nematology Genetic Diversity and Biology Laboratory, USDA-ARS, Beltsville, MD, USA
| | - Katrin Grage
- Institute of Fundamental Sciences, Massey University, Palmerston North, New Zealand
| | - Paul P Dijkwel
- Institute of Fundamental Sciences, Massey University, Palmerston North, New Zealand
| | | | - Barry Scott
- Institute of Fundamental Sciences, Massey University, Palmerston North, New Zealand.,Bio-Protection Research Centre, Massey University, Palmerston North, New Zealand
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12
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Dhanushkodi R, Matthew C, McManus MT, Dijkwel PP. Drought-induced senescence of Medicago truncatula nodules involves serpin and ferritin to control proteolytic activity and iron levels. New Phytol 2018; 220:196-208. [PMID: 29974467 DOI: 10.1111/nph.15298] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [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: 02/19/2018] [Accepted: 05/20/2018] [Indexed: 05/09/2023]
Abstract
Drought is a major constraint for legume growth and yield. Senescence of nitrogen-fixing nodules is one of the early drought responses and may cause nutrient stress in addition to water stress in legumes. For nodule senescence to function as part of a drought-survival strategy, we propose that the intrinsically destructive senescence process must be tightly regulated. Medicago truncatula protease inhibitor and iron scavenger-encoding genes, possibly involved in controlling nodule senescence, were identified. RNA interference (RNAi) lines were constructed in which expression of a serpin or ferritins was knocked down. Both wild-type and RNAi lines were subjected to drought stress and nodule activity and plant physiological responses were measured. Drought caused M. truncatula to initiate nodule senescence before plant growth was affected and before an increase in papain-like proteolytic activity and free iron levels was apparent. Knock-down expression of serpin6 and ferritins caused increased protease activity, free iron levels, early nodule senescence and reduced plant growth. The results suggest that M. truncatula nodule-expressed serpin6 and ferritins mediate ordered drought-induced senescence by regulating papain-like cysteine protease activity and free iron levels. This strategy may allow the drought-stressed plants to benefit maximally from residual nitrogen fixation and nutrient recovery resulting from break down of macromolecules.
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Affiliation(s)
- Ramadoss Dhanushkodi
- Institute of Fundamental Sciences, Massey University, Private Bag 11-222, Palmerston North, New Zealand
| | - Cory Matthew
- Institute of Agriculture and Environment, Massey University, Private Bag 11-222, Palmerston North, New Zealand
| | - Michael T McManus
- Institute of Fundamental Sciences, Massey University, Private Bag 11-222, Palmerston North, New Zealand
| | - Paul P Dijkwel
- Institute of Fundamental Sciences, Massey University, Private Bag 11-222, Palmerston North, New Zealand
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13
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Durgud M, Gupta S, Ivanov I, Omidbakhshfard MA, Benina M, Alseekh S, Staykov N, Hauenstein M, Dijkwel PP, Hörtensteiner S, Toneva V, Brotman Y, Fernie AR, Mueller-Roeber B, Gechev TS. Molecular Mechanisms Preventing Senescence in Response to Prolonged Darkness in a Desiccation-Tolerant Plant. Plant Physiol 2018; 177:1319-1338. [PMID: 29789435 PMCID: PMC6053018 DOI: 10.1104/pp.18.00055] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2018] [Accepted: 05/09/2018] [Indexed: 05/28/2023]
Abstract
The desiccation-tolerant plant Haberlea rhodopensis can withstand months of darkness without any visible senescence. Here, we investigated the molecular mechanisms of this adaptation to prolonged (30 d) darkness and subsequent return to light. H. rhodopensis plants remained green and viable throughout the dark treatment. Transcriptomic analysis revealed that darkness regulated several transcription factor (TF) genes. Stress- and autophagy-related TFs such as ERF8, HSFA2b, RD26, TGA1, and WRKY33 were up-regulated, while chloroplast- and flowering-related TFs such as ATH1, COL2, COL4, RL1, and PTAC7 were repressed. PHYTOCHROME INTERACTING FACTOR4, a negative regulator of photomorphogenesis and promoter of senescence, also was down-regulated. In response to darkness, most of the photosynthesis- and photorespiratory-related genes were strongly down-regulated, while genes related to autophagy were up-regulated. This occurred concomitant with the induction of SUCROSE NON-FERMENTING1-RELATED PROTEIN KINASES (SnRK1) signaling pathway genes, which regulate responses to stress-induced starvation and autophagy. Most of the genes associated with chlorophyll catabolism, which are induced by darkness in dark-senescing species, were either unregulated (PHEOPHORBIDE A OXYGENASE, PAO; RED CHLOROPHYLL CATABOLITE REDUCTASE, RCCR) or repressed (STAY GREEN-LIKE, PHEOPHYTINASE, and NON-YELLOW COLORING1). Metabolite profiling revealed increases in the levels of many amino acids in darkness, suggesting increased protein degradation. In darkness, levels of the chloroplastic lipids digalactosyldiacylglycerol, monogalactosyldiacylglycerol, phosphatidylglycerol, and sulfoquinovosyldiacylglycerol decreased, while those of storage triacylglycerols increased, suggesting degradation of chloroplast membrane lipids and their conversion to triacylglycerols for use as energy and carbon sources. Collectively, these data show a coordinated response to darkness, including repression of photosynthetic, photorespiratory, flowering, and chlorophyll catabolic genes, induction of autophagy and SnRK1 pathways, and metabolic reconfigurations that enable survival under prolonged darkness.
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Affiliation(s)
- Meriem Durgud
- Center of Plant Systems Biology and Biotechnology, Plovdiv 4000, Bulgaria
- Institute of Molecular Biology and Biotechnology, Plovdiv 4000, Bulgaria
- Department of Plant Physiology and Molecular Biology, University of Plovdiv, Plovdiv 4000, Bulgaria
| | - Saurabh Gupta
- Department Molecular Biology, Institute of Biochemistry and Biology, University of Potsdam, 14476 Potsdam, Germany
| | - Ivan Ivanov
- Center of Plant Systems Biology and Biotechnology, Plovdiv 4000, Bulgaria
- Institute of Molecular Biology and Biotechnology, Plovdiv 4000, Bulgaria
| | - M Amin Omidbakhshfard
- Department Molecular Biology, Institute of Biochemistry and Biology, University of Potsdam, 14476 Potsdam, Germany
- Department Willmitzer, Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam, Germany
| | - Maria Benina
- Center of Plant Systems Biology and Biotechnology, Plovdiv 4000, Bulgaria
| | - Saleh Alseekh
- Center of Plant Systems Biology and Biotechnology, Plovdiv 4000, Bulgaria
- Department Willmitzer, Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam, Germany
| | - Nikola Staykov
- Center of Plant Systems Biology and Biotechnology, Plovdiv 4000, Bulgaria
- Institute of Molecular Biology and Biotechnology, Plovdiv 4000, Bulgaria
| | - Mareike Hauenstein
- Department of Plant and Microbial Biology, University of Zurich, CH-8008 Zurich, Switzerland
| | - Paul P Dijkwel
- Institute of Fundamental Sciences, Massey University, 4474 Palmerston North, New Zealand
| | - Stefan Hörtensteiner
- Department of Plant and Microbial Biology, University of Zurich, CH-8008 Zurich, Switzerland
| | - Valentina Toneva
- Center of Plant Systems Biology and Biotechnology, Plovdiv 4000, Bulgaria
- Institute of Molecular Biology and Biotechnology, Plovdiv 4000, Bulgaria
- Department of Plant Physiology and Molecular Biology, University of Plovdiv, Plovdiv 4000, Bulgaria
| | - Yariv Brotman
- Department of Life Sciences, Ben Gurion University of the Negev, Beersheva, Israel
| | - Alisdair R Fernie
- Center of Plant Systems Biology and Biotechnology, Plovdiv 4000, Bulgaria
- Department Willmitzer, Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam, Germany
| | - Bernd Mueller-Roeber
- Center of Plant Systems Biology and Biotechnology, Plovdiv 4000, Bulgaria
- Department Molecular Biology, Institute of Biochemistry and Biology, University of Potsdam, 14476 Potsdam, Germany
| | - Tsanko S Gechev
- Center of Plant Systems Biology and Biotechnology, Plovdiv 4000, Bulgaria
- Institute of Molecular Biology and Biotechnology, Plovdiv 4000, Bulgaria
- Department of Plant Physiology and Molecular Biology, University of Plovdiv, Plovdiv 4000, Bulgaria
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14
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Kanojia A, Dijkwel PP. Abiotic Stress Responses are Governed by Reactive Oxygen Species and Age. Annual Plant Reviews online 2018:295-326. [PMID: 0 DOI: 10.1002/9781119312994.apr0611] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
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15
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Miret JA, Munné‐Bosch S, Dijkwel PP. ABA signalling manipulation suppresses senescence of a leafy vegetable stored at room temperature. Plant Biotechnol J 2018; 16:530-544. [PMID: 28703416 PMCID: PMC5787841 DOI: 10.1111/pbi.12793] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [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: 04/10/2017] [Revised: 06/23/2017] [Accepted: 07/10/2017] [Indexed: 05/16/2023]
Abstract
Postharvest senescence and associated stresses limit the shelf life and nutritional value of vegetables. Improved understanding of these processes creates options for better management. After harvest, controlled exposure to abiotic stresses and/or exogenous phytohormones can enhance nutraceutical, organoleptic and commercial longevity traits. With leaf senescence, abscisic acid (ABA) contents progressively rise, but the actual biological functions of this hormone through senescence still need to be clarified. Postharvest senescence of detached green cabbage leaves (Brassica oleracea var. capitata) was characterized under cold (4 °C) and room temperature (25 °C) storage conditions. Hormonal profiling of regions of the leaf blade (apical, medial, basal) revealed a decrease in cytokinins contents during the first days under both conditions, while ABA only increased at 25 °C. Treatments with ABA and a partial agonist of ABA (pyrabactin) for 8 days did not lead to significant effects on water and pigment contents, but increased cell integrity and altered 1-aminocyclopropane-1-carboxylic acid (ACC) and cytokinins contents. Transcriptome analysis showed transcriptional regulation of ABA, cytokinin and ethylene metabolism and signalling; proteasome components; senescence regulation; protection of chloroplast functionality and cell homeostasis; and suppression of defence responses (including glucosinolates and phenylpropanoids metabolism). It is concluded that increasing the concentration of ABA (or its partial agonist pyrabactin) from the start of postharvest suppresses senescence of stored leaves, changes the transcriptional regulation of glucosinolates metabolism and down-regulates biotic stress defence mechanisms. These results suggest a potential for manipulating ABA signalling for improving postharvest quality of leafy vegetables stored at ambient temperature.
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Affiliation(s)
- Javier A. Miret
- Department of Evolutionary BiologyEcology and Environmental SciencesPlant Physiology Section, Faculty of BiologyBarcelona UniversityBarcelonaSpain
| | - Sergi Munné‐Bosch
- Department of Evolutionary BiologyEcology and Environmental SciencesPlant Physiology Section, Faculty of BiologyBarcelona UniversityBarcelonaSpain
| | - Paul P. Dijkwel
- Institute of Fundamental SciencesMassey UniversityPalmerston NorthNew Zealand
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16
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Jibran R, Tahir J, Cooney J, Hunter DA, Dijkwel PP. Arabidopsis AGAMOUS Regulates Sepal Senescence by Driving Jasmonate Production. Front Plant Sci 2017; 8:2101. [PMID: 29312374 PMCID: PMC5732193 DOI: 10.3389/fpls.2017.02101] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2017] [Accepted: 11/27/2017] [Indexed: 05/29/2023]
Abstract
The signal that initiates the age-regulated senescence program in flowers is still unknown. Here we propose for the ephemeral Arabidopsis thaliana flower that it dies because of continued expression of the MADS-box transcription factor AGAMOUS (AG). AG is necessary for specifying the reproductive structures of the flower. Flowers of ag-1, which lack AG, exhibited delayed sepal senescence and abscission. The flowers also had reduced jasmonic acid (JA) content. Other anther-defective sterile mutants deficient in JA, defective in anther dehiscence 1 (dad1) and delayed dehiscence 2 (dde2), exhibited delayed sepal senescence and abscission as well. Manually pollinated dad1 flowers produced siliques but still had delayed senescence, demonstrating that absence of pollination does not cause delayed senescence. When ag-1, dad1 and dde2 flowers were sprayed with 100 μM methyl jasmonate, the sepal senescence and abscission phenotypes were rescued, suggesting that JA has a role in these processes. Our study uncovers a novel role for AG in determining the timing of death of the flower it helps develop and highlights a role for JA in sepal senescence.
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Affiliation(s)
- Rubina Jibran
- The New Zealand Institute for Plant and Food Research Limited, Palmerston North, New Zealand
- Institute of Fundamental Sciences, Massey University, Palmerston North, New Zealand
| | - Jibran Tahir
- The New Zealand Institute for Plant and Food Research Limited, Palmerston North, New Zealand
- Institute of Fundamental Sciences, Massey University, Palmerston North, New Zealand
| | - Janine Cooney
- The New Zealand Institute for Plant and Food Research Limited, Hamilton, New Zealand
| | - Donald A. Hunter
- The New Zealand Institute for Plant and Food Research Limited, Palmerston North, New Zealand
| | - Paul P. Dijkwel
- Institute of Fundamental Sciences, Massey University, Palmerston North, New Zealand
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17
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Islam A, Leung S, Nikmatullah A, Dijkwel PP, McManus MT. Kunitz Proteinase Inhibitors Limit Water Stress Responses in White Clover ( Trifolium repens L.) Plants. Front Plant Sci 2017; 8:1683. [PMID: 29046678 PMCID: PMC5632647 DOI: 10.3389/fpls.2017.01683] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Accepted: 09/13/2017] [Indexed: 05/22/2023]
Abstract
The response of plants to water deficiency or drought is a complex process, the perception of which is triggered at the molecular level before any visible morphological responses are detected. It was found that different groups of plant proteinase inhibitors (PIs) are induced and play an active role during abiotic stress conditions such as drought. Our previous work with the white clover (Trifolium repens L.) Kunitz Proteinase Inhibitor (Tr-KPI) gene family showed that Tr-KPIs are differentially regulated to ontogenetic and biotic stress associated cues and that, at least some members of this gene family may be required to maintain cellular homeostasis. Altered cellular homeostasis may also affect abiotic stress responses and therefore, we aimed to understand if distinct Tr-PKI members function during drought stress. First, the expression level of three Tr-KPI genes, Tr-KPI1, Tr-KPI2, and Tr-KPI5, was measured in two cultivars and one white clover ecotype with differing capacity to tolerate drought. The expression of Tr-KPI1 and Tr-KPI5 increased in response to water deficiency and this was exaggerated when the plants were treated with a previous period of water deficiency. In contrast, proline accumulation and increased expression of Tr-NCED1, a gene encoding a protein involved in ABA biosynthesis, was delayed in plants that experienced a previous drought period. RNAi knock-down of Tr-KPI1 and Tr-KPI5 resulted in increased proline accumulation in leaf tissue of plants grown under both well-watered and water-deficit conditions. In addition, increased expression of genes involved in ethylene biosynthesis was found. The data suggests that Tr-KPIs, particularly Tr-KPI5, have an explicit function during water limitation. The results also imply that the Tr-KPI family has different in planta proteinase targets and that the functions of this protein family are not solely restricted to one of storage proteins or in response to biotic stress.
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Affiliation(s)
| | | | | | - Paul P. Dijkwel
- Institute of Fundamental Sciences, Massey University, Palmerston North, New Zealand
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18
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Islam A, Leung S, Burgess EPJ, Laing WA, Richardson KA, Hofmann RW, Dijkwel PP, McManus MT. Knock-down of transcript abundance of a family of Kunitz proteinase inhibitor genes in white clover (Trifolium repens) reveals a redundancy and diversity of gene function. New Phytol 2015; 208:1188-201. [PMID: 26377591 DOI: 10.1111/nph.13543] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [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: 10/23/2014] [Accepted: 06/01/2015] [Indexed: 06/05/2023]
Abstract
The transcriptional regulation of four phylogenetically distinct members of a family of Kunitz proteinase inhibitor (KPI) genes isolated from white clover (Trifolium repens; designated Tr-KPI1, Tr-KPI2, Tr-KPI4 and Tr-KPI5) has been investigated to determine their wider functional role. The four genes displayed differential transcription during seed germination, and in different tissues of the mature plant, and transcription was also ontogenetically regulated. Heterologous over-expression of Tr-KPI1, Tr-KPI2, Tr-KPI4 and Tr-KPI5 in Nicotiana tabacum retarded larval growth of the herbivore Spodoptera litura, and an increase in the transcription of the pathogenesis-related genes PR1 and PR4 was observed in the Tr-KPI1 and Tr-KPI4 over-expressing lines. RNA interference (RNAi) knock-down lines in white clover displayed significantly altered vegetative growth phenotypes with inhibition of shoot growth and a stimulation of root growth, while knock-down of Tr-KPI1, Tr-KPI2 and Tr-KPI5 transcript abundance also retarded larval growth of S. litura. Examination of these RNAi lines revealed constitutive stress-associated phenotypes as well as altered transcription of cellular signalling genes. These results reveal a functional redundancy across members of the KPI gene family. Further, the regulation of transcription of at least one member of the family, Tr-KPI2, may occupy a central role in the maintenance of a cellular homeostasis.
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Affiliation(s)
- Afsana Islam
- Institute of Fundamental Sciences, Massey University, Private Bag 11-222, Palmerston North, New Zealand
| | - Susanna Leung
- Institute of Fundamental Sciences, Massey University, Private Bag 11-222, Palmerston North, New Zealand
| | | | - William A Laing
- Plant & Food Research, Private Bag 92169, Auckland, 1142, New Zealand
| | - Kim A Richardson
- AgResearch Grasslands, Private Bag 11-008, Palmerston North, New Zealand
| | - Rainer W Hofmann
- Faculty of Agriculture and Life Sciences, Lincoln University, PO Box 85084, Lincoln, 7647, New Zealand
| | - Paul P Dijkwel
- Institute of Fundamental Sciences, Massey University, Private Bag 11-222, Palmerston North, New Zealand
| | - Michael T McManus
- Institute of Fundamental Sciences, Massey University, Private Bag 11-222, Palmerston North, New Zealand
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19
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Jibran R, Sullivan KL, Crowhurst R, Erridge ZA, Chagné D, McLachlan ARG, Brummell DA, Dijkwel PP, Hunter DA. Staying green postharvest: how three mutations in the Arabidopsis chlorophyll b reductase gene NYC1 delay degreening by distinct mechanisms. J Exp Bot 2015; 66:6849-6862. [PMID: 26261268 DOI: 10.1093/jxb/erv390] [Citation(s) in RCA: 13] [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] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Stresses such as energy deprivation, wounding and water-supply disruption often contribute to rapid deterioration of harvested tissues. To uncover the genetic regulation behind such stresses, a simple assessment system was used to detect senescence mutants in conjunction with two rapid mapping techniques to identify the causal mutations. To demonstrate the power of this approach, immature inflorescences of Arabidopsis plants that contained ethyl methanesulfonate-induced lesions were detached and screened for altered timing of dark-induced senescence. Numerous mutant lines displaying accelerated or delayed timing of senescence relative to wild type were discovered. The underlying mutations in three of these were identified using High Resolution Melting analysis to map to a chromosomal arm followed by a whole-genome sequencing-based mapping method, termed 'Needle in the K-Stack', to identify the causal lesions. All three mutations were single base pair changes and occurred in the same gene, NON-YELLOW COLORING1 (NYC1), a chlorophyll b reductase of the short-chain dehydrogenase/reductase (SDR) superfamily. This was consistent with the mutants preferentially retaining chlorophyll b, although substantial amounts of chlorophyll b were still lost. The single base pair mutations disrupted NYC1 function by three distinct mechanisms, one by producing a termination codon, the second by interfering with correct intron splicing and the third by replacing a highly conserved proline with a non-equivalent serine residue. This non-synonymous amino acid change, which occurred in the NADPH binding domain of NYC1, is the first example of such a mutation in an SDR protein inhibiting a physiological response in plants.
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Affiliation(s)
- Rubina Jibran
- The New Zealand Institute for Plant & Food Research Limited, Private Bag 11600, Palmerston North 4442, New Zealand Institute of Fundamental Sciences, Massey University, Private Bag 11222, Palmerston North, New Zealand
| | - Kerry L Sullivan
- The New Zealand Institute for Plant & Food Research Limited, Private Bag 11600, Palmerston North 4442, New Zealand
| | - Ross Crowhurst
- The New Zealand Institute for Plant & Food Research Limited, Private Bag 92169, Auckland 1142, New Zealand
| | - Zoe A Erridge
- The New Zealand Institute for Plant & Food Research Limited, Private Bag 11600, Palmerston North 4442, New Zealand
| | - David Chagné
- The New Zealand Institute for Plant & Food Research Limited, Private Bag 11600, Palmerston North 4442, New Zealand
| | - Andrew R G McLachlan
- The New Zealand Institute for Plant & Food Research Limited, Private Bag 11600, Palmerston North 4442, New Zealand
| | - David A Brummell
- The New Zealand Institute for Plant & Food Research Limited, Private Bag 11600, Palmerston North 4442, New Zealand
| | - Paul P Dijkwel
- Institute of Fundamental Sciences, Massey University, Private Bag 11222, Palmerston North, New Zealand
| | - Donald A Hunter
- The New Zealand Institute for Plant & Food Research Limited, Private Bag 11600, Palmerston North 4442, New Zealand
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20
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Islam A, Mercer CF, Leung S, Dijkwel PP, McManus MT. Transcription of Biotic Stress Associated Genes in White Clover (Trifolium repens L.) Differs in Response to Cyst and Root-Knot Nematode Infection. PLoS One 2015; 10:e0137981. [PMID: 26393362 PMCID: PMC4578895 DOI: 10.1371/journal.pone.0137981] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2014] [Accepted: 08/24/2015] [Indexed: 11/25/2022] Open
Abstract
The transcription of four members of the Kunitz proteinase inhibitor (KPI) gene family of white clover (Trifolium repens L.), designated as Tr-KPI1, Tr-KPI2, Tr-KPI4 and Tr-KPI5, was investigated at both local infection (roots) and systemic (leaf tissue) sites in white clover in response to infection with the clover root knot nematode (CRKN) Meloidogyne trifoliophila and the clover cyst nematode (CCN) Heterodera trifolii. Invasion by the CRKN resulted in a significant decrease in transcript abundance of Tr-KPI4 locally at both 4 days post-infection (dpi) and at 8 dpi, and an increase in transcription of Tr-KPI1 systemically at 8 dpi. In contrast, an increase in transcript abundance of all four Tr-KPI genes locally at 4 and 8 dpi, and an increase of Tr-KPI1, Tr-KPI2, and Tr-KPI5 at 8 dpi systemically was observed in response to infection with the CCN. Challenge of a resistant (R) genotype and a susceptible (S) genotype of white clover with the CCN revealed a significant increase in transcript abundance of all four Tr-KPI genes locally in the R genotype, while an increase in abundance of only Tr-KPI1, Tr-KPI2, and Tr-KPI5 was observed in the S genotype, and only at 4 dpi. The transcript abundance of a member of the1-AMINOCYCLOPROPANE-1-CARBOXYLATE (ACC) SYNTHASE gene family from white clover (Tr-ACS1) was significantly down-regulated locally in response to CRKN infection at 4 and 8 dpi and at 4 dpi, systemically, while abundance increased locally and systemically at 8 dpi in response to CCN challenge. Conversely, the abundance of the jasmonic acid (JA) signalling gene, CORONATINE-INSENSITIVE PROTEIN 1 from white clover (Tr-COI1) increased significantly at 8 dpi locally in response to CRKN infection, but decreased at 8 dpi in response to CCN infection. The significance of this differential regulation of transcription is discussed with respect to differences in infection strategy of the two nematode species.
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Affiliation(s)
- Afsana Islam
- Institute of Fundamental Sciences, Massey University, Palmerston North, New Zealand
- * E-mail: (AI); (PPD)
| | | | - Susanna Leung
- Institute of Fundamental Sciences, Massey University, Palmerston North, New Zealand
| | - Paul P. Dijkwel
- Institute of Fundamental Sciences, Massey University, Palmerston North, New Zealand
- * E-mail: (AI); (PPD)
| | - Michael T. McManus
- Institute of Fundamental Sciences, Massey University, Palmerston North, New Zealand
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Abstract
Circadian clocks have emerged to tune the physiology of organisms to periodic changes in the environment in a dynamic fashion. Negative implications of circadian disruptions in humans, animals and plants have encouraged extensive studies of clock-controlled biological processes in various model species. Recently, it has been shown that the transcription-dependent and -independent biological oscillators are largely driven by cellular oxidative cycles that are intrinsically linked with metabolism. Essentially, the clock is viewed as an integrated network that encompasses cytosolic, genetic and metabolic dimensions. Furthermore, in multicellular organisms, the clock network is organized in a tissue-specific manner. Here we discuss questions that remain unanswered: How do these dimensions communicate with each other and how do tissue-specific clocks exchange temporal information within multicellular organisms?
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Jibran R, A Hunter D, P Dijkwel P. Hormonal regulation of leaf senescence through integration of developmental and stress signals. Plant Mol Biol 2013; 82:547-61. [PMID: 23504405 DOI: 10.1007/s11103-013-0043-2] [Citation(s) in RCA: 172] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2012] [Accepted: 03/07/2013] [Indexed: 05/18/2023]
Abstract
Leaf senescence is a genetically controlled dismantling programme that enables plants to efficiently remobilise nutrients to new growing sinks. It involves substantial metabolic reprogramming whose timing is affected by developmental and environmental signals. Plant hormones have long been known to affect the timing of leaf senescence, but they also affect plant development and stress responses. It has therefore been difficult to tease apart how the different hormones regulate the onset and progression of leaf senescence, i.e., whether they directly affect leaf senescence or affect it indirectly by altering the developmental programme or by altering plants' response to stress. Here we review research on hormonal regulation of leaf senescence and propose that hormones affect senescence through differential responses to developmental and environmental signals. We suggest that leaf senescence strictly depends on developmental changes, after which senescence can be induced, depending on the type of hormonal and environmental cues.
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Affiliation(s)
- Rubina Jibran
- Institute of Fundamental Sciences, Massey University, Palmerston North, New Zealand
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23
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Denton-Giles M, Bradshaw RE, Dijkwel PP. Ciborinia camelliae (Sclerotiniaceae) induces variable plant resistance responses in selected species of Camellia. Phytopathology 2013; 103:725-732. [PMID: 23406433 DOI: 10.1094/phyto-11-12-0289-r] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Ciborinia camelliae is the causal agent of Camellia flower blight. This fungal pathogen is a significant pest of the Camellia floriculture industry because it specifically infects the floral tissue of ornamental camellia cultivars leading to the rapid development of necrotic lesions and blight. This study aims to characterize natural resistance to Ciborinia camelliae within a selection of Camellia spp. Based on macroscopic lesion development, Camellia 'Nicky Crisp' and Camellia lutchuensis were chosen as compatible and incompatible hosts, respectively. Microscopic analyses of the incompatible Camellia lutchuensis-Ciborinia camelliae interaction revealed several hallmarks of induced plant resistance, including papillae formation, H2O2 accumulation, and localized cell death. The compatible Camellia Nicky Crisp-Ciborinia camelliae interaction failed to trigger a similar resistance response. Ciborinia camelliae growth in compatible tissue demonstrated a switch from biotrophy to necrotrophy, evident from the simultaneous development of secondary hyphae and necrotic lesions. Extension of resistance analyses to 39 additional Camellia spp. identified variable levels of resistance within the Camellia genus. The evidence presented supports a resistance breeding strategy for controlling Ciborinia camelliae on ornamental Camellia hybrids.
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Affiliation(s)
- Matthew Denton-Giles
- Institute of Molecular Biosciences, Massey University, Palmerston North, New Zealand
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24
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Tahir J, Watanabe M, Jing HC, Hunter DA, Tohge T, Nunes-Nesi A, Brotman Y, Fernie AR, Hoefgen R, Dijkwel PP. Activation of R-mediated innate immunity and disease susceptibility is affected by mutations in a cytosolic O-acetylserine (thiol) lyase in Arabidopsis. Plant J 2013; 73:118-30. [PMID: 22974487 DOI: 10.1111/tpj.12021] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [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: 06/08/2012] [Revised: 09/05/2012] [Accepted: 09/10/2012] [Indexed: 05/09/2023]
Abstract
O-acetylserine (thiol) lyases (OASTLs) are evolutionarily conserved proteins among many prokaryotes and eukaryotes that perform sulfur acquisition and synthesis of cysteine. A mutation in the cytosolic OASTL-A1 protein ONSET OF LEAF DEATH3 (OLD3) was previously shown to reduce the OASTL activity of the old3-1 protein in vitro and cause auto-necrosis in specific Arabidopsis accessions. Here we investigated why a mutation in this protein causes auto-necrosis in some but not other accessions. The auto-necrosis was found to depend on Recognition of Peronospora Parasitica 1 (RPP1)-like disease resistance R gene(s) from an evolutionarily divergent R gene cluster that is present in Ler-0 but not the reference accession Col-0. RPP1-like gene(s) show a negative epistatic interaction with the old3-1 mutation that is not linked to reduced cysteine biosynthesis. Metabolic profiling and transcriptional analysis further indicate that an effector triggered-like immune response and metabolic disorder are associated with auto-necrosis in old3-1 mutants, probably activated by an RPP1-like gene. However, the old3-1 protein in itself results in largely neutral changes in primary plant metabolism, stress defence and immune responses. Finally, we showed that lack of a functional OASTL-A1 results in enhanced disease susceptibility against infection with virulent and non-virulent Pseudomonas syringae pv. tomato DC3000 strains. These results reveal an interaction between the cytosolic OASTL and components of plant immunity.
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Affiliation(s)
- Jibran Tahir
- Institute of Molecular BioSciences, Massey University, Private Bag 11222, Palmerston North, New Zealand
| | - Mutsumi Watanabe
- Max-Planck-Institut fuer Molekulare Pflanzenphysiologie, Wissenschaftspark Golm, Am Muehlenberg 1, Potsdam-Golm, 14476, Germany
| | - Hai-Chun Jing
- Centre for Bioenergy Plants Research and Development, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China, and
| | - Donald A Hunter
- The New Zealand Institute for Plant & Food Research Limited, Private Bag 11600, Palmerston North, 4442, New Zealand
| | - Takayuki Tohge
- Max-Planck-Institut fuer Molekulare Pflanzenphysiologie, Wissenschaftspark Golm, Am Muehlenberg 1, Potsdam-Golm, 14476, Germany
| | - Adriano Nunes-Nesi
- Max-Planck-Institut fuer Molekulare Pflanzenphysiologie, Wissenschaftspark Golm, Am Muehlenberg 1, Potsdam-Golm, 14476, Germany
| | - Yariv Brotman
- Max-Planck-Institut fuer Molekulare Pflanzenphysiologie, Wissenschaftspark Golm, Am Muehlenberg 1, Potsdam-Golm, 14476, Germany
| | - Alisdair R Fernie
- Max-Planck-Institut fuer Molekulare Pflanzenphysiologie, Wissenschaftspark Golm, Am Muehlenberg 1, Potsdam-Golm, 14476, Germany
| | - Rainer Hoefgen
- Max-Planck-Institut fuer Molekulare Pflanzenphysiologie, Wissenschaftspark Golm, Am Muehlenberg 1, Potsdam-Golm, 14476, Germany
| | - Paul P Dijkwel
- Institute of Molecular BioSciences, Massey University, Private Bag 11222, Palmerston North, New Zealand
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Trivellini A, Jibran R, Watson LM, O’Donoghue EM, Ferrante A, Sullivan KL, Dijkwel PP, Hunter DA. Carbon deprivation-driven transcriptome reprogramming in detached developmentally arresting Arabidopsis inflorescences. Plant Physiol 2012; 160:1357-72. [PMID: 22930749 PMCID: PMC3490613 DOI: 10.1104/pp.112.203083] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2012] [Accepted: 08/24/2012] [Indexed: 05/22/2023]
Abstract
Senescence is genetically controlled and activated in mature tissues during aging. However, immature plant tissues also display senescence-like symptoms when continuously exposed to adverse energy-depleting conditions. We used detached dark-held immature inflorescences of Arabidopsis (Arabidopsis thaliana) to understand the metabolic reprogramming occurring in immature tissues transitioning from rapid growth to precocious senescence. Macroscopic growth of the detached inflorescences rapidly ceased upon placement in water in the dark at 21°C. Inflorescences were completely degreened by 120 h of dark incubation and by 24 h had already lost 24% of their chlorophyll and 34% of their protein content. Comparative transcriptome profiling at 24 h revealed that inflorescence response at 24 h had a large carbon-deprivation component. Genes that positively regulate developmental senescence (ARABIDOPSIS NAC DOMAIN CONTAINING PROTEIN92) and shade-avoidance syndrome (PHYTOCHROME INTERACTING FACTOR4 [PIF4] and PIF5) were up-regulated within 24 h. Mutations in these genes delayed degreening of the inflorescences. Their up-regulation was suppressed in dark-held inflorescences by glucose treatment, which promoted macroscopic growth and development and inhibited degreening of the inflorescences. Detached inflorescences held in the dark for 4 d were still able to reinitiate development to produce siliques upon being brought out to the light, indicating that the transcriptional reprogramming at 24 h was adaptive and reversible. Our results suggest that the response of detached immature tissues to dark storage involves interactions between carbohydrate status sensing and light deprivation signaling and that the dark-adaptive response of the tissues appears to utilize some of the same key regulators as developmental senescence.
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Affiliation(s)
- Alice Trivellini
- The New Zealand Institute for Plant Food Research Limited, Private Bag 11600, Palmerston North 4442, New Zealand (A.T., R.J., L.M.W., E.M.O., K.L.S., D.A.H.); Department of Crop Biology, University of Pisa, 56124 Pisa, Italy (A.T.); Institute of Molecular BioSciences, Massey University, Private Bag 11222, Palmerston North, New Zealand (R.J., P.P.D.); and Department of Plant Production, Università degli Studi di Milano, 20133 Milan, Italy (A.F.)
| | - Rubina Jibran
- The New Zealand Institute for Plant Food Research Limited, Private Bag 11600, Palmerston North 4442, New Zealand (A.T., R.J., L.M.W., E.M.O., K.L.S., D.A.H.); Department of Crop Biology, University of Pisa, 56124 Pisa, Italy (A.T.); Institute of Molecular BioSciences, Massey University, Private Bag 11222, Palmerston North, New Zealand (R.J., P.P.D.); and Department of Plant Production, Università degli Studi di Milano, 20133 Milan, Italy (A.F.)
| | - Lyn M. Watson
- The New Zealand Institute for Plant Food Research Limited, Private Bag 11600, Palmerston North 4442, New Zealand (A.T., R.J., L.M.W., E.M.O., K.L.S., D.A.H.); Department of Crop Biology, University of Pisa, 56124 Pisa, Italy (A.T.); Institute of Molecular BioSciences, Massey University, Private Bag 11222, Palmerston North, New Zealand (R.J., P.P.D.); and Department of Plant Production, Università degli Studi di Milano, 20133 Milan, Italy (A.F.)
| | - Erin M. O’Donoghue
- The New Zealand Institute for Plant Food Research Limited, Private Bag 11600, Palmerston North 4442, New Zealand (A.T., R.J., L.M.W., E.M.O., K.L.S., D.A.H.); Department of Crop Biology, University of Pisa, 56124 Pisa, Italy (A.T.); Institute of Molecular BioSciences, Massey University, Private Bag 11222, Palmerston North, New Zealand (R.J., P.P.D.); and Department of Plant Production, Università degli Studi di Milano, 20133 Milan, Italy (A.F.)
| | - Antonio Ferrante
- The New Zealand Institute for Plant Food Research Limited, Private Bag 11600, Palmerston North 4442, New Zealand (A.T., R.J., L.M.W., E.M.O., K.L.S., D.A.H.); Department of Crop Biology, University of Pisa, 56124 Pisa, Italy (A.T.); Institute of Molecular BioSciences, Massey University, Private Bag 11222, Palmerston North, New Zealand (R.J., P.P.D.); and Department of Plant Production, Università degli Studi di Milano, 20133 Milan, Italy (A.F.)
| | - Kerry L. Sullivan
- The New Zealand Institute for Plant Food Research Limited, Private Bag 11600, Palmerston North 4442, New Zealand (A.T., R.J., L.M.W., E.M.O., K.L.S., D.A.H.); Department of Crop Biology, University of Pisa, 56124 Pisa, Italy (A.T.); Institute of Molecular BioSciences, Massey University, Private Bag 11222, Palmerston North, New Zealand (R.J., P.P.D.); and Department of Plant Production, Università degli Studi di Milano, 20133 Milan, Italy (A.F.)
| | - Paul P. Dijkwel
- The New Zealand Institute for Plant Food Research Limited, Private Bag 11600, Palmerston North 4442, New Zealand (A.T., R.J., L.M.W., E.M.O., K.L.S., D.A.H.); Department of Crop Biology, University of Pisa, 56124 Pisa, Italy (A.T.); Institute of Molecular BioSciences, Massey University, Private Bag 11222, Palmerston North, New Zealand (R.J., P.P.D.); and Department of Plant Production, Università degli Studi di Milano, 20133 Milan, Italy (A.F.)
| | - Donald A. Hunter
- The New Zealand Institute for Plant Food Research Limited, Private Bag 11600, Palmerston North 4442, New Zealand (A.T., R.J., L.M.W., E.M.O., K.L.S., D.A.H.); Department of Crop Biology, University of Pisa, 56124 Pisa, Italy (A.T.); Institute of Molecular BioSciences, Massey University, Private Bag 11222, Palmerston North, New Zealand (R.J., P.P.D.); and Department of Plant Production, Università degli Studi di Milano, 20133 Milan, Italy (A.F.)
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Lai AG, Denton-Giles M, Mueller-Roeber B, Schippers JHM, Dijkwel PP. Positional information resolves structural variations and uncovers an evolutionarily divergent genetic locus in accessions of Arabidopsis thaliana. Genome Biol Evol 2011; 3:627-40. [PMID: 21622917 PMCID: PMC3157834 DOI: 10.1093/gbe/evr038] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Genome sequencing of closely related individuals has yielded valuable insights that link genome evolution to phenotypic variations. However, advancement in sequencing technology has also led to an escalation in the number of poor quality–drafted genomes assembled based on reference genomes that can have highly divergent or haplotypic regions. The self-fertilizing nature of Arabidopsis thaliana poses an advantage to sequencing projects because its genome is mostly homozygous. To determine the accuracy of an Arabidopsis drafted genome in less conserved regions, we performed a resequencing experiment on a ∼371-kb genomic interval in the Landsberg erecta (Ler-0) accession. We identified novel structural variations (SVs) between Ler-0 and the reference accession Col-0 using a long-range polymerase chain reaction approach to generate an Illumina data set that has positional information, that is, a data set with reads that map to a known location. Positional information is important for accurate genome assembly and the resolution of SVs particularly in highly duplicated or repetitive regions. Sixty-one regions with misassembly signatures were identified from the Ler-0 draft, suggesting the presence of novel SVs that are not represented in the draft sequence. Sixty of those were resolved by iterative mapping using our data set. Fifteen large indels (>100 bp) identified from this study were found to be located either within protein-coding regions or upstream regulatory regions, suggesting the formation of novel alleles or altered regulation of existing genes in Ler-0. We propose future genome-sequencing experiments to follow a clone-based approach that incorporates positional information to ultimately reveal haplotype-specific differences between accessions.
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Affiliation(s)
- Alvina G Lai
- Institute of Molecular BioSciences, Massey University, Private Bag 11-222, Palmerston North 4442, New Zealand
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27
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Simpson GG, Laurie RE, Dijkwel PP, Quesada V, Stockwell PA, Dean C, Macknight RC. Noncanonical translation initiation of the Arabidopsis flowering time and alternative polyadenylation regulator FCA. Plant Cell 2010; 22:3764-77. [PMID: 21075770 PMCID: PMC3015108 DOI: 10.1105/tpc.110.077990] [Citation(s) in RCA: 14] [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] [Indexed: 05/03/2023]
Abstract
The RNA binding protein FCA regulates the floral transition and is required for silencing RNAs corresponding to specific noncoding sequences in the Arabidopsis thaliana genome. Through interaction with the canonical RNA 3' processing machinery, FCA affects alternative polyadenylation of many transcripts, including antisense RNAs at the locus encoding the floral repressor FLC. This potential for widespread alteration of gene regulation clearly needs to be tightly regulated, and we have previously shown that FCA expression is autoregulated through poly(A) site choice. Here, we show distinct layers of FCA regulation that involve sequences within the 5' region that regulate noncanonical translation initiation and alter the expression profile. FCA translation in vivo occurs exclusively at a noncanonical CUG codon upstream of the first in-frame AUG. We fully define the upstream flanking sequences essential for its selection, revealing features that distinguish this from other non-AUG start site mechanisms. Bioinformatic analysis identified 10 additional Arabidopsis genes that likely initiate translation at a CUG codon. Our findings reveal further unexpected complexity in the regulation of FCA expression with implications for its roles in regulating flowering time and gene expression and more generally show plant mRNA exceptions to AUG translation initiation.
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Affiliation(s)
- Gordon G. Simpson
- Department of Cell and Developmental Biology, John Innes Centre, Norfolk NR4 7UH, United Kingdom
| | - Rebecca E. Laurie
- Department of Cell and Developmental Biology, John Innes Centre, Norfolk NR4 7UH, United Kingdom
- Department of Biochemistry, University of Otago, Dunedin 9054, New Zealand
| | - Paul P. Dijkwel
- Department of Cell and Developmental Biology, John Innes Centre, Norfolk NR4 7UH, United Kingdom
| | - Victor Quesada
- Department of Cell and Developmental Biology, John Innes Centre, Norfolk NR4 7UH, United Kingdom
| | - Peter A. Stockwell
- Department of Biochemistry, University of Otago, Dunedin 9054, New Zealand
| | - Caroline Dean
- Department of Cell and Developmental Biology, John Innes Centre, Norfolk NR4 7UH, United Kingdom
| | - Richard C. Macknight
- Department of Biochemistry, University of Otago, Dunedin 9054, New Zealand
- Address correspondence to
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Shirzadian-Khorramabad R, Jing HC, Everts GE, Schippers JHM, Hille J, Dijkwel PP. A mutation in the cytosolic O-acetylserine (thiol) lyase induces a genome-dependent early leaf death phenotype in Arabidopsis. BMC Plant Biol 2010; 10:80. [PMID: 20429919 PMCID: PMC2890954 DOI: 10.1186/1471-2229-10-80] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2009] [Accepted: 04/29/2010] [Indexed: 05/24/2023]
Abstract
BACKGROUND Cysteine is a component in organic compounds including glutathione that have been implicated in the adaptation of plants to stresses. O-acetylserine (thiol) lyase (OAS-TL) catalyses the final step of cysteine biosynthesis. OAS-TL enzyme isoforms are localised in the cytoplasm, the plastids and mitochondria but the contribution of individual OAS-TL isoforms to plant sulphur metabolism has not yet been fully clarified. RESULTS The seedling lethal phenotype of the Arabidopsis onset of leaf death3-1 (old3-1) mutant is due to a point mutation in the OAS-A1 gene, encoding the cytosolic OAS-TL. The mutation causes a single amino acid substitution from Gly162 to Glu162, abolishing old3-1 OAS-TL activity in vitro. The old3-1 mutation segregates as a monogenic semi-dominant trait when backcrossed to its wild type accession Landsberg erecta (Ler-0) and the Di-2 accession. Consistent with its semi-dominant behaviour, wild type Ler-0 plants transformed with the mutated old3-1 gene, displayed the early leaf death phenotype. However, the old3-1 mutation segregates in an 11:4:1 (wild type: semi-dominant: mutant) ratio when backcrossed to the Colombia-0 and Wassilewskija accessions. Thus, the early leaf death phenotype depends on two semi-dominant loci. The second locus that determines the old3-1 early leaf death phenotype is referred to as odd-ler (for old3 determinant in the Ler accession) and is located on chromosome 3. The early leaf death phenotype is temperature dependent and is associated with increased expression of defence-response and oxidative-stress marker genes. Independent of the presence of the odd-ler gene, OAS-A1 is involved in maintaining sulphur and thiol levels and is required for resistance against cadmium stress. CONCLUSIONS The cytosolic OAS-TL is involved in maintaining organic sulphur levels. The old3-1 mutation causes genome-dependent and independent phenotypes and uncovers a novel function for the mutated OAS-TL in cell death regulation.
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Affiliation(s)
- Reza Shirzadian-Khorramabad
- Molecular Biology of Plants, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Kerklaan 30, 9751 NN, Haren, The Netherlands
- University of Guilan, Department of Agronomy and Plant Breeding, P.O. Box 41635-1314, Rasht, Iran
| | - Hai-Chun Jing
- Molecular Biology of Plants, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Kerklaan 30, 9751 NN, Haren, The Netherlands
- Centre for Bioenergy Plants Research and Development, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Gerja E Everts
- Molecular Biology of Plants, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Kerklaan 30, 9751 NN, Haren, The Netherlands
| | - Jos HM Schippers
- Molecular Biology of Plants, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Kerklaan 30, 9751 NN, Haren, The Netherlands
- University of Potsdam, Department of Molecular Biology, Karl-Liebknecht-Str. 24-25, Haus 20, 14476 Potsdam-Golm, Germany
| | - Jacques Hille
- Molecular Biology of Plants, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Kerklaan 30, 9751 NN, Haren, The Netherlands
| | - Paul P Dijkwel
- Molecular Biology of Plants, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Kerklaan 30, 9751 NN, Haren, The Netherlands
- Institute of Molecular BioSciences (IMBS), Massey University, Private Bag 11222, Palmerston North, New Zealand
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Schippers JHM, Nunes-Nesi A, Apetrei R, Hille J, Fernie AR, Dijkwel PP. The Arabidopsis onset of leaf death5 mutation of quinolinate synthase affects nicotinamide adenine dinucleotide biosynthesis and causes early ageing. Plant Cell 2008; 20:2909-25. [PMID: 18978034 PMCID: PMC2590718 DOI: 10.1105/tpc.107.056341] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2007] [Revised: 10/03/2008] [Accepted: 10/15/2008] [Indexed: 05/18/2023]
Abstract
Leaf senescence in Arabidopsis thaliana is a strict, genetically controlled nutrient recovery program, which typically progresses in an age-dependent manner. Leaves of the Arabidopsis onset of leaf death5 (old5) mutant exhibit early developmental senescence. Here, we show that OLD5 encodes quinolinate synthase (QS), a key enzyme in the de novo synthesis of NAD. The Arabidopsis QS was previously shown to carry a Cys desulfurase domain that stimulates reconstitution of the oxygen-sensitive Fe-S cluster that is required for QS activity. The old5 lesion in this enzyme does not affect QS activity but it decreases its Cys desulfurase activity and thereby the long-term catalytic competence of the enzyme. The old5 mutation causes increased NAD steady state levels that coincide with increased activity of enzymes in the NAD salvage pathway. NAD plays a key role in cellular redox reactions, including those of the tricarboxylic acid cycle. Broad-range metabolite profiling of the old5 mutant revealed that it contains higher levels of tricarboxylic acid cycle intermediates and nitrogen-containing amino acids. The mutant displays a higher respiration rate concomitant with increased expression of oxidative stress markers. We postulate that the alteration in the oxidative state is integrated into the plant developmental program, causing early ageing of the mutant.
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Affiliation(s)
- Jos H M Schippers
- Molecular Biology of Plants, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9751 NN Haren, The Netherlands
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30
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Jing HC, Hebeler R, Oeljeklaus S, Sitek B, Stühler K, Meyer HE, Sturre MJG, Hille J, Warscheid B, Dijkwel PP. Early leaf senescence is associated with an altered cellular redox balance in Arabidopsis cpr5/old1 mutants. Plant Biol (Stuttg) 2008; 10 Suppl 1:85-98. [PMID: 18721314 DOI: 10.1111/j.1438-8677.2008.00087.x] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Reactive oxygen species (ROS) are the inevitable by-products of essential cellular metabolic and physiological activities. Plants have developed sophisticated gene networks of ROS generation and scavenging systems. However, ROS regulation is still poorly understood. Here, we report that mutations in the Arabidopsis CPR5/OLD1 gene may cause early senescence through deregulation of the cellular redox balance. Genetic analysis showed that blocking stress-related hormonal signalling pathways, such as ethylene, salicylic acid, jasmonic acid, abscisic acid and sugar, did not affect premature cell death and leaf senescence. We took a bioinformatics approach and analysed publicly available transcriptome data of presymptomatic cpr5/old1 mutants. The results demonstrate that many genes in the ROS gene network show at least fivefold increases in transcripts in comparison with those of wild-type plants, suggesting that presymptomatic cpr5/old1 mutants are in a state of high-cellular oxidative stress. This was further confirmed by a comparative, relative quantitative proteomics study of Arabidopsis wild-type and cpr5/old1 mutant plants, which demonstrated that several Phi family members of glutathione s-transferases significantly increased in abundance. In summary, our genetic, transcriptomic and relative quantitative proteomics analyses indicate that CPR5 plays a central role in regulating redox balance in Arabidopsis.
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Affiliation(s)
- H-C Jing
- Department of Molecular Biology of Plants, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Haren, The Netherlands
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Abstract
In our recent paper in Journal of Experimental Botany, we examined the effects of cpr5/old1 mutations and CPR5 overexpression on Arabidopsis growth and development.1 We found that CPR5 is important for early plant growth but promotes senescence at late development and hence proposed it as a senescence-regulatory gene as predicted by the Evolutionary Theory of Senescence derived from studies on animal ageing. One of the key unsolved issues is how CPR5 contributes to the early plant growth and development. Here we discuss the possible cellular functions of CPR5.
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Affiliation(s)
- Hai-Chun Jing
- Centre for Sustainable Pest and Disease Management; Department of Plant Pathology and Microbiology; Rothamsted Research; Harpenden, UK
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Hebeler R, Oeljeklaus S, Reidegeld KA, Eisenacher M, Stephan C, Sitek B, Stühler K, Meyer HE, Sturre MJG, Dijkwel PP, Warscheid B. Study of Early Leaf Senescence in Arabidopsis thaliana by Quantitative Proteomics Using Reciprocal 14N/15N Labeling and Difference Gel Electrophoresis. Mol Cell Proteomics 2008; 7:108-20. [PMID: 17878269 DOI: 10.1074/mcp.m700340-mcp200] [Citation(s) in RCA: 75] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Leaf senescence represents the final stage of leaf development and is associated with fundamental changes on the level of the proteome. For the quantitative analysis of changes in protein abundance related to early leaf senescence, we designed an elaborate double and reverse labeling strategy simultaneously employing fluorescent two-dimensional DIGE as well as metabolic (15)N labeling followed by MS. Reciprocal (14)N/(15)N labeling of entire Arabidopsis thaliana plants showed that full incorporation of (15)N into the proteins of the plant did not cause any adverse effects on development and protein expression. A direct comparison of DIGE and (15)N labeling combined with MS showed that results obtained by both quantification methods correlated well for proteins showing low to moderate regulation factors. Nano HPLC/ESI-MS/MS analysis of 21 protein spots that consistently exhibited abundance differences in nine biological replicates based on both DIGE and MS resulted in the identification of 13 distinct proteins and protein subunits that showed significant regulation in Arabidopsis mutant plants displaying advanced leaf senescence. Ribulose 1,5-bisphosphate carboxylase/oxygenase large and three of its four small subunits were found to be down-regulated, which reflects the degradation of the photosynthetic machinery during leaf senescence. Among the proteins showing higher abundance in mutant plants were several members of the glutathione S-transferase family class phi and quinone reductase. Up-regulation of these proteins fits well into the context of leaf senescence since they are generally involved in the protection of plant cells against reactive oxygen species which are increasingly generated by lipid degradation during leaf senescence. With the exception of one glutathione S-transferase isoform, none of these proteins has been linked to leaf senescence before.
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Affiliation(s)
- Romano Hebeler
- Medizinisches Proteom-Center, Zentrum fuer klinische Forschung, Ruhr-Universitaet Bochum, Universitaetsstrasse 150, 44780 Bochum, Germany
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Jing HC, Anderson L, Sturre MJG, Hille J, Dijkwel PP. Arabidopsis CPR5 is a senescence-regulatory gene with pleiotropic functions as predicted by the evolutionary theory of senescence. J Exp Bot 2007; 58:3885-94. [PMID: 18033818 DOI: 10.1093/jxb/erm237] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Evolutionary theories of senescence predict that genes with pleiotropic functions are important for senescence regulation. In plants there is no direct molecular genetic test for the existence of such senescence-regulatory genes. Arabidopsis cpr5 mutants exhibit multiple phenotypes including hypersensitivity to various signalling molecules, constitutive expression of pathogen-related genes, abnormal trichome development, spontaneous lesion formation, and accelerated leaf senescence. These indicate that CPR5 is a beneficial gene which controls multiple facets of the Arabidopsis life cycle. Ectopic expression of CPR5 restored all the mutant phenotypes. However, in transgenic plants with increased CPR5 transcripts, accelerated leaf senescence was observed in detached leaves and at late development around 50 d after germination, as illustrated by the earlier onset of senescence-associated physiological and molecular markers. Thus, CPR5 has early-life beneficial effects by repressing cell death and insuring normal plant development, but late-life deleterious effects by promoting developmental senescence. As such, CPR5 appears to function as a typical senescence-regulatory gene as predicted by the evolutionary theories of senescence.
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Affiliation(s)
- Hai-Chun Jing
- Molecular Biology of Plants, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Kerklaan 30, 9751 NN, Haren, The Netherlands
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Jing HC, Schippers JHM, Hille J, Dijkwel PP. Ethylene-induced leaf senescence depends on age-related changes and OLD genes in Arabidopsis. J Exp Bot 2005; 56:2915-23. [PMID: 16172137 DOI: 10.1093/jxb/eri287] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Ethylene can only induce senescence in leaves that have reached a defined age. Thus, ethylene-induced senescence depends on age-related changes (ARCs) of individual leaves. The relationship between ethylene and age in the induction of leaf senescence was tested in Arabidopsis Ler-0, Col-0, and Ws-0 accessions as well as in eight old (onset of leaf death) mutants, isolated from the Ler-0 background. Plants with a constant final age of 24 d were exposed to ethylene for 3-16 d. The wild-type accessions showed a common response to the ethylene treatment. Increasing ethylene treatments of 3-12 d caused an increase in the number of yellow leaves. However, an ethylene exposure time of 16 d resulted in a decrease in the amount of yellowing. Thus, ethylene can both positively and negatively influence ARCs and the subsequent induction of leaf senescence, depending on the length of the treatment. The old mutants showed altered responses to the ethylene treatments. old1 and old11 were hypersensitive to ethylene in the triple response assay and a 12-d ethylene exposure resulted in a decrease in the amount of yellow leaves. The other six mutants did not show a decrease in yellow leaves with an ethylene treatment of 16 d. The results revealed that the effect of ethylene on the induction of senescence can be modified by at least eight genes.
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Affiliation(s)
- Hai-Chun Jing
- Molecular Biology of Plants, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Kerklaan 30, 9751 NN, Haren, The Netherlands
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Bagherieh-Najjar MB, de Vries OMH, Hille J, Dijkwel PP. Arabidopsis RecQI4A suppresses homologous recombination and modulates DNA damage responses. Plant J 2005; 43:789-98. [PMID: 16146519 DOI: 10.1111/j.1365-313x.2005.02501.x] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
The DNA damage response and DNA recombination are two interrelated mechanisms involved in maintaining the integrity of the genome, but in plants they are poorly understood. RecQ is a family of genes with conserved roles in the regulation of DNA recombination in eukaryotes; there are seven members in Arabidopsis. Here we report on the functional analysis of the Arabidopsis RecQl4A gene. Ectopic expression of Arabidopsis RecQl4A in yeast RecQ-deficient cells suppressed their hypersensitivity to the DNA-damaging drug methyl methanesulfonate (MMS) and enhanced their rate of homologous recombination (HR). Analysis of three recQl4A mutant alleles revealed no obvious developmental defects or telomere deregulation in plants grown under standard growth conditions. Compared with wild-type Arabidopsis, the recQl4A mutant seedlings were found to be hypersensitive to UV light and MMS, and more resistant to mitomycin C. The average frequency of intrachromosomal HR in recQl4A mutant plants was increased 7.5-fold over that observed in wild-type plants. The data reveal roles for Arabidopsis RecQl4A in maintenance of genome stability by modulation of the DNA damage response and suppression of HR.
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Affiliation(s)
- Mohammad B Bagherieh-Najjar
- Molecular Biology of Plants, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Kerklaan 30, 9751 NN Haren, The Netherlands
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Abstract
Plants control their flowering time in order to ensure that they reproduce under favourable conditions. The components involved in this complex process have been identified using a molecular genetic approach in Arabidopsis and classified into genetically separable pathways. The autonomous pathway controls the level of mRNA encoding a floral repressor, FLC, and comprises three RNA-binding proteins, FCA, FPA and FLK. FCA interacts with the 3'-end RNA-processing factor FY to autoregulate its own expression post-transcriptionally and to control FLC. Other components of the autonomous pathway, FVE and FLD, regulate FLC epigenetically. This combination of epigenetic and post-transcriptional control gives precision to the control of FLC expression and flowering time.
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Affiliation(s)
- G G Simpson
- Cell and Developmental Biology, John Innes Centre, Norfolk NR4 7UH, UK.
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Simpson GG, Dijkwel PP, Quesada V, Henderson I, Dean C. FY is an RNA 3' end-processing factor that interacts with FCA to control the Arabidopsis floral transition. Cell 2003; 113:777-87. [PMID: 12809608 DOI: 10.1016/s0092-8674(03)00425-2] [Citation(s) in RCA: 337] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
The nuclear RNA binding protein, FCA, promotes Arabidopsis reproductive development. FCA contains a WW protein interaction domain that is essential for FCA function. We have identified FY as a protein partner for this domain. FY belongs to a highly conserved group of eukaryotic proteins represented in Saccharomyces cerevisiae by the RNA 3' end-processing factor, Pfs2p. FY regulates RNA 3' end processing in Arabidopsis as evidenced through its role in FCA regulation. FCA expression is autoregulated through the use of different polyadenylation sites within the FCA pre-mRNA, and the FCA/FY interaction is required for efficient selection of the promoter-proximal polyadenylation site. The FCA/FY interaction is also required for the downregulation of the floral repressor FLC. We propose that FCA controls 3' end formation of specific transcripts and that in higher eukaryotes, proteins homologous to FY may have evolved as sites of association for regulators of RNA 3' end processing.
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Affiliation(s)
- Gordon G Simpson
- Department of Cell and Developmental Biology, John Innes Centre, Norwich, United Kingdom
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Bagherieh-Najjar MB, de Vries OMH, Kroon JTM, Wright EL, Elborough KM, Hille J, Dijkwel PP. Arabidopsis RecQsim, a plant-specific member of the RecQ helicase family, can suppress the MMS hypersensitivity of the yeast sgs1 mutant. Plant Mol Biol 2003; 52:273-284. [PMID: 12856935 DOI: 10.1023/a:1023968429220] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
The Arabidopsis genome contains seven genes that belong to the RecQ family of ATP-dependent DNA helicases. RecQ members in Saccharomyces cerevisiae (SGS1) and man (WRN, BLM and RecQL4) are involved in DNA recombination, repair and genome stability maintenance, but little is known about the function of their plant counterparts. The Arabidopsis thaliana RecQsim gene is remarkably different from the other RecQ-like genes due to an insertion in its helicase domain. We isolated the AtRecQsim orthologues from rice and rape and established the presence of a similar insertion in their helicase domain, which suggests a plant specific function for the insert. The expression pattern of the AtRecQsim gene was compared with the other Arabidopsis RecQ-like members in different tissues and in response to stress. The transcripts of the AtRecQsim gene were found in all plant organs and its accumulation was higher in roots and seedlings, as compared to the other AtRecQ-like members. In contrast to most AtRecQ-like genes, the examined environmental cues did not have a detectable effect on the accumulation of the AtRecQsim transcripts. The budding yeast sgs1 mutant, which is known to be hypersensitive to the DNA-damaging drug MMS, was transformed with the AtRecQsim cDNA. The AtRecQsim gene suppressed the MMS hypersensitivity phenotype of the sgs1 cells. We propose that the Arabidopsis RecQsim gene, despite its unusual structure, exhibits an evolutionary conserved function.
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Affiliation(s)
- Mohammad B Bagherieh-Najjar
- Molecular Biology of Plants, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Kerklaan 30, 9751 NN Haren, The Netherlands
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Abstract
The onset of leaf senescence is controlled by leaf age and ethylene can promote leaf senescence within a specific age window. We exploited the interaction between leaf age and ethylene and isolated mutants with altered leaf senescence that are named as onset of leaf death (old) mutants. Early leaf senescence mutants representing three genetic loci were selected and their senescence syndromes were characterised using phenotypical, physiological and molecular markers. old1 is represented by three recessive alleles and displayed earlier senescence both in air and upon ethylene exposure. The etiolated old1 seedlings exhibited a hypersensitive triple response. old2 is a dominant trait and the mutant plants were indistinguishable from the wild-type when grown in air but showed an earlier senescence syndrome upon ethylene treatment. old3 is a semi-dominant trait and its earlier onset of senescence is independent of ethylene treatment. Analyses of the chlorophyll degradation, ion leakage and SAG expression showed that leaf senescence was advanced in ethylene-treated old2 plants and in both air-grown and ethylene-treated old1 and old3 plants. Epistatic analysis indicated that OLD1 might act downstream of OLD2 and upstream of OLD3 and mediate the interaction between leaf age and ethylene. A genetic model was proposed that links the three OLD genes and ethylene into a regulatory pathway controlling the onset of leaf senescence.
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Affiliation(s)
- Hai-Chun Jing
- Molecular Biology of Plants, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Kerklaan 30, 9751 NN, Haren, The Netherlands
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Dijkwel PP, Rook F, Smeekens SC. [12] Analysis of light-regulated gene expression. Methods Enzymol 1998. [DOI: 10.1016/s0076-6879(98)97014-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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41
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Abstract
Many plant genes are responsive to sugars but the mechanisms used by plants to sense sugars are unknown. A genetic approach has been used in Arabidopsis to identify genes involved in perception and transduction of sugar signals. For this purpose, an in vivo reporter system was established consisting of the light- and sugar-regulated plastocyanin promoter, fused to the luciferase coding sequence (PC-LUC construct). At the seedling stage, expression of the PC-LUC gene is repressed by sucrose, and a number of sucrose-uncoupled (sun) mutants were selected in which sucrose is unable to repress the activity of the PC promoter. Three mutants have been characterized in more detail. The sugar analog 2-deoxy-D-glucose (2DG) was used to repress whole plant photosynthesis, PC-LUC gene expression and total ribulose-1,5-bisphosphate activity. It was found that the sun6 mutation makes plants unresponsive to these 2DG-induced effects. Moreover, unlike wild-type plants, sun6 mutants are insensitive to elevated levels of glucose in the growth medium. These findings suggest that the SUN6 gene is active in a hexose-activated signal transduction pathway.
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Affiliation(s)
- J J Van Oosten
- Laboratoire du Métabolisme Carboné, DEVM CEA, St Paul Lez Durance, France.
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Abstract
The expression of the Arabidopsis plastocyanin (PC) gene is developmentally controlled and regulated by light. During seedling development, PC gene expression is transiently induced, and this induction can be repressed by sucrose. In transgenic seedlings carrying a PC promoter-luciferase fusion gene, the luciferase-induced in vivo luminescence was similarly repressed by sucrose. From a mutagenized population of such transgenic seedlings, we selected for mutant seedlings that displayed a high luminescence level when grown on a medium with 3% sucrose. This screening of mutants resulted in the isolation of several sucrose-uncoupled (sun) mutants showing reduced repression of luminescence by sucrose. Analysis of the sun mutants revealed that the accumulation of PC and chlorophyll a/b binding protein (CAB) mRNA was also sucrose uncoupled, although the extent of uncoupling varied. The effect of sucrose on far-red light high-irradiance responses was studied in wild-type, sun1, sun6, and sun7 seedlings. In wild-type seedlings, sucrose repressed the far-red light-induced cotyledon opening and inhibition of hypocotyl elongation. sun7 seedlings showed reduced repression of these responses. Sucrose also repressed the far-red light-induced block of greening in wild-type seedlings, and both sun6 and sun7 were affected in this response. The results provide evidence for a close interaction between sucrose and light signaling pathways. Moreover, the sun6 and sun7 mutants genetically identify separate branches of phytochrome A-dependent signal transduction pathways.
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Affiliation(s)
- P P Dijkwel
- Department of Molecular Cell Biology, University of Utrecht, The Netherlands
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