| 1. |
- Bozhkov, Peter, et al.
(författare)
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Autophagy-related approaches for improving nutrient use efficiency and crop yield protection
- 2018
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Ingår i: Journal of Experimental Botany. - : Oxford University Press (OUP). - 0022-0957 .- 1460-2431. ; 69, s. 1335-1353
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Forskningsöversikt (refereegranskat)abstract
- Autophagy is a eukaryotic catabolic pathway essential for growth and development. In plants, it is activated in response to environmental cues or developmental stimuli. However, in contrast to other eukaryotic systems, we know relatively little regarding the molecular players involved in autophagy and the regulation of this complex pathway. In the framework of the COST (European Cooperation in Science and Technology) action TRANSAUTOPHAGY (2016-2020), we decided to review our current knowledge of autophagy responses in higher plants, with emphasis on knowledge gaps. We also assess here the potential of translating the acquired knowledge to improve crop plant growth and development in a context of growing social and environmental challenges for agriculture in the near future.
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| 2. |
- Elander, Pernilla, et al.
(författare)
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Autophagy in turnover of lipid stores: trans-kingdom comparison
- 2018
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Ingår i: Journal of Experimental Botany. - : Oxford University Press (OUP). - 0022-0957 .- 1460-2431. ; 69, s. 1301-1311
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Forskningsöversikt (refereegranskat)abstract
- Lipids and their cellular utilization are essential for life. Not only are lipids energy storage molecules, but their diverse structural and physical properties underlie various aspects of eukaryotic biology, such as membrane structure, signalling, and trafficking. In the ever-changing environment of cells, lipids, like other cellular components, are regularly recycled to uphold the housekeeping processes required for cell survival and organism longevity. The ways in which lipids are recycled, however, vary between different phyla. For example, animals and plants have evolved distinct lipid degradation pathways. The major cell recycling system, autophagy, has been shown to be instrumental for both differentiation of specialized fat storing-cells, adipocytes, and fat degradation in animals. Does plant autophagy play a similar role in storage and degradation of lipids? In this review, we discuss and compare implications of bulk autophagy and its selective route, lipophagy, in the turnover of lipid stores in animals, fungi, and plants.
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| 3. |
- Elander, Pernilla, et al.
(författare)
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Interactome of Arabidopsis ATG5 Suggests Functions beyond Autophagy
- 2023
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Ingår i: International Journal of Molecular Sciences. - 1661-6596 .- 1422-0067. ; 24
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Tidskriftsartikel (refereegranskat)abstract
- Autophagy is a catabolic pathway capable of degrading cellular components ranging from individual molecules to organelles. Autophagy helps cells cope with stress by removing superfluous or hazardous material. In a previous work, we demonstrated that transcriptional upregulation of two autophagy-related genes, ATG5 and ATG7, in Arabidopsis thaliana positively affected agronomically important traits: biomass, seed yield, tolerance to pathogens and oxidative stress. Although the occurrence of these traits correlated with enhanced autophagic activity, it is possible that autophagy-independent roles of ATG5 and ATG7 also contributed to the phenotypes. In this study, we employed affinity purification and LC-MS/MS to identify the interactome of wild-type ATG5 and its autophagy-inactive substitution mutant, ATG5(K128R) Here we present the first interactome of plant ATG5, encompassing not only known autophagy regulators but also stress-response factors, components of the ubiquitin-proteasome system, proteins involved in endomembrane trafficking, and potential partners of the nuclear fraction of ATG5. Furthermore, we discovered post-translational modifications, such as phosphorylation and acetylation present on ATG5 complex components that are likely to play regulatory functions. These results strongly indicate that plant ATG5 complex proteins have roles beyond autophagy itself, opening avenues for further investigations on the complex roles of autophagy in plant growth and stress responses.
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| 4. |
- Elander, Pernilla
(författare)
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Living through hard times: Dispose of or sequester? Plant subcellular strategies for stress resilience
- 2022
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Extreme weather events have become the new normal due to climate change and global warming. This damages crop harvests, threatening global food production. One of the many measures to ensure food security is to develop stress-resilient plants, but to do that we need to understand how plants respond to stress factors. In this work, we studied two cellular mechanisms underlying plant resilience, autophagy and formation of stress granules (SGs). Autophagy is an evolutionarily conserved vesicle trafficking pathway which at the time of stress disposes of cellular constituents which might be superfluous, hazardous or dysfunctional by degrading them in the lysosome (animals) or vacuole (fungi and plants). In our studies we have focused on autophagy-related proteins ATG5 and ATG7, the core components of the ATG8 and ATG5-12 conjugation systems. Overexpression of ATG5 or ATG7 led to increased lipidation of ATG8 and enhanced autophagic recycling without affecting the transcription level of other components of the conjugation systems, indicating that ATG5 and ATG7 are ratelimiting steps of the autophagy pathway. Plants with enhanced levels of either ATG5 or ATG7 showed improved fitness for a broad range of agronomically important traits, such as, increased vegetative biomass, delayed senescence and increased seed set. Surprisingly, these plants also displayed improved tolerance to necrotrophic pathogens and oxidative stress. Our findings can be used for growing resilient crops with improved productivity. A follow up study addressed the roles of ATG5 unrelated to autophagy, by isolating interactomes of the wild-type ATG5 and its point mutant which does not conjugate to ATG12. LC-MS/MS analysis yielded 104 interactor hits for the wild-type ATG5, 78 for the mutant and 97 hits shared by the wild-type and the mutant. Further functional studies are required to understand the roles of ATG5 and its interactors of autophagy-unrelated pathways in plants. SGs are membraneless protein-mRNA biomolecular condensates formed via phase separation under stress, which selectively sequester or concentrate proteins and mRNAs. The sequestration of proteins can result in activation or suppression of biochemical pathways. We investigated the interactome of the Tudor staphylococcal nuclease (TSN) protein. TSN is a multifunctional and evolutionary conserved regulator of gene expression, previously shown to stably associate with SGs under heat stress. We found that TSN functions as a docking platform for SG components and its localization to SGs is essential for the activation of a major regulator of energy homeostasis in the cell, SnRK1 (a homolog of AMPK/SNF1). Our work provides a proteome-wide resource of SG components and sheds light on the signalling role of stress granules in plant physiology.
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| 5. |
- Elander, Pernilla, et al.
(författare)
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Tudor staphylococcal nuclease is a docking platform for stress granule components and is essential for SnRK1 activation in Arabidopsis
- 2021
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Ingår i: The Embo Journal. - : EMBO. - 0261-4189 .- 1460-2075. ; 40
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Tidskriftsartikel (refereegranskat)abstract
- Tudor staphylococcal nuclease (TSN; also known as Tudor-SN, p100, or SND1) is a multifunctional, evolutionarily conserved regulator of gene expression, exhibiting cytoprotective activity in animals and plants and oncogenic activity in mammals. During stress, TSN stably associates with stress granules (SGs), in a poorly understood process. Here, we show that in the model plant Arabidopsis thaliana, TSN is an intrinsically disordered protein (IDP) acting as a scaffold for a large pool of other IDPs, enriched for conserved stress granule components as well as novel or plant-specific SG-localized proteins. While approximately 30% of TSN interactors are recruited to stress granules de novo upon stress perception, 70% form a protein-protein interaction network present before the onset of stress. Finally, we demonstrate that TSN and stress granule formation promote heat-induced activation of the evolutionarily conserved energy-sensing SNF1-related protein kinase 1 (SnRK1), the plant orthologue of mammalian AMP-activated protein kinase (AMPK). Our results establish TSN as a docking platform for stress granule proteins, with an important role in stress signalling.
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| 6. |
- Minina, Alyona, et al.
(författare)
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The Arabidopsis homolog of Scc4/MAU2 is essential for embryogenesis
- 2017
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Ingår i: Journal of Cell Science. - : The Company of Biologists. - 0021-9533 .- 1477-9137. ; 130, s. 1051-1063
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Tidskriftsartikel (refereegranskat)abstract
- Factors regulating dynamics of chromatin structure have direct impact on expression of genetic information. Cohesin is a multi-subunit protein complex that is crucial for pairing sister chromatids during cell division, DNA repair and regulation of gene transcription and silencing. In non-plant species, cohesin is loaded on chromatin by the Scc2-Scc4 complex (also known as the NIBPL-MAU2 complex). Here, we identify the Arabidopsis homolog of Scc4, which we denote Arabidopsis thaliana (At) SCC4, and show that it forms a functional complex with AtSCC2, the homolog of Scc2. We demonstrate that AtSCC2 and AtSCC4 act in the same pathway, and that both proteins are indispensable for cell fate determination during early stages of embryo development. Mutant embryos lacking either of these proteins develop only up to the globular stage, and show the suspensor overproliferation phenotype preceded by ectopic auxin maxima distribution. We further establish a new assay to reveal the AtSCC4-dependent dynamics of cohesin loading on chromatin in vivo. Our findings define the Scc2-Scc4 complex as an evolutionary conserved machinery controlling cohesin loading and chromatin structure maintenance, and provide new insight into the plant-specific role of this complex in controlling cell fate during embryogenesis.
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| 7. |
- Minina, Alyona, et al.
(författare)
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Transcriptional stimulation of rate-limiting components of the autophagic pathway improves plant fitness
- 2018
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Ingår i: Journal of Experimental Botany. - : Oxford University Press (OUP). - 0022-0957 .- 1460-2431. ; 69, s. 1415-1432
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Tidskriftsartikel (refereegranskat)abstract
- Autophagy is a major catabolic process whereby autophagosomes deliver cytoplasmic content to the lytic compartment for recycling. Autophagosome formation requires two ubiquitin-like systems conjugating Atg12 with Atg5, and Atg8 with lipid phosphatidylethanolamine (PE), respectively. Genetic suppression of these systems causes autophagy-deficient phenotypes with reduced fitness and longevity. We show that Atg5 and the E1-like enzyme, Atg7, are rate-limiting components of Atg8-PE conjugation in Arabidopsis. Overexpression of ATG5 or ATG7 stimulates Atg8 lipidation, autophagosome formation, and autophagic flux. It also induces transcriptional changes opposite to those observed in atg5 and atg7 mutants, favoring stress resistance and growth. As a result, ATG5-or ATG7-over-expressing plants exhibit increased resistance to necrotrophic pathogens and oxidative stress, delayed aging and enhanced growth, seed set, and seed oil content. This work provides an experimental paradigm and mechanistic insight into genetic stimulation of autophagy in planta and shows its efficiency for improving plant productivity.
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| 8. |
- Ohlsson, Jonas A., et al.
(författare)
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SPIRO : the automated Petri plate imaging platform designed by biologists, for biologists
- 2024
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Ingår i: The Plant Journal. - : John Wiley & Sons. - 0960-7412 .- 1365-313X. ; 118:2, s. 584-600
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Tidskriftsartikel (refereegranskat)abstract
- Phenotyping of model organisms grown on Petri plates is often carried out manually, despite the procedures being time-consuming and laborious. The main reason for this is the limited availability of automated phenotyping facilities, whereas constructing a custom automated solution can be a daunting task for biologists. Here, we describe SPIRO, the Smart Plate Imaging Robot, an automated platform that acquires time-lapse photographs of up to four vertically oriented Petri plates in a single experiment, corresponding to 192 seedlings for a typical root growth assay and up to 2500 seeds for a germination assay. SPIRO is catered specifically to biologists' needs, requiring no engineering or programming expertise for assembly and operation. Its small footprint is optimized for standard incubators, the inbuilt green LED enables imaging under dark conditions, and remote control provides access to the data without interfering with sample growth. SPIRO's excellent image quality is suitable for automated image processing, which we demonstrate on the example of seed germination and root growth assays. Furthermore, the robot can be easily customized for specific uses, as all information about SPIRO is released under open-source licenses. Importantly, uninterrupted imaging allows considerably more precise assessment of seed germination parameters and root growth rates compared with manual assays. Moreover, SPIRO enables previously technically challenging assays such as phenotyping in the dark. We illustrate the benefits of SPIRO in proof-of-concept experiments which yielded a novel insight on the interplay between autophagy, nitrogen sensing, and photoblastic response.
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