A Pair of Arabidopsis Diacylglycerol Kinases Essential for Gametogenesis and Endoplasmic Reticulum Phospholipid Metabolism in Leaves and Flowers

Angkawijaya, Artik Elisa; Nguyen, Van Cam; Gunawan, Farrel; Nakamura, Yuki

doi:10.1105/tpc.20.00251

Cited by 23 publications

(24 citation statements)

References 51 publications

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“…Co-expression of binary combinations of differentially tagged constructs of SYT3, SYT1 and MAPPER (Figure 3C, Figure S4C, Figure S4D), produced a highly overlapping pattern. When we co-expressed SYT3-GFP with the ER localized proteins DGK2-mCherry (Angkawijaya et al, 2020) or FaFAH1-mCherry (Sánchez-Sevilla et al, 2014) we found that SYT3-GFP was mainly located in ER tubules and at the edges of ER sheets (Figure 3D, Figure S4E and Figure S4F). This localization is similar to that of Arabidopsis SYT1 (Ishikawa et al, 2018) and yeast Tcbs (Collado et al, 2019; Hoffmann et al, 2019), which have been reported to have important implications in the formation of the tubular ER network and in the formation of peaks of extreme curvature respectively.…”

Section: Resultsmentioning

confidence: 99%

Synaptotagmins Maintain Diacylglycerol Homeostasis at Endoplasmic Reticulum-Plasma Membrane Contact Sites during Abiotic Stress

Ruiz-López

Pérez-Sancho

Valle

et al. 2020

Preprint

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SUMMARYEndoplasmic Reticulum-Plasma Membrane contact sites (ER-PM CS) play fundamental roles in all eukaryotic cells. Arabidopsis mutants lacking the ER-PM protein tether synaptotagmin1 (SYT1) exhibit decreased plasma membrane (PM) integrity under multiple abiotic stresses such as freezing, high salt, osmotic stress and mechanical damage. Here, we show that, together with SYT1, the stress-induced SYT3 is an ER-PM tether that also functions in maintaining PM integrity. The ER-PM CS localization of SYT1 and SYT3 is dependent on PM phosphatidylinositol-4-phosphate and is regulated by abiotic stress. Lipidomic analysis revealed that cold stress increased the accumulation of diacylglycerol at the PM in a syt1/3 double mutant relative to WT while the levels of most glycerolipid species remain unchanged. Additionally, SYT1-GFP preferentially binds diacylglycerol in vivo with little affinity for polar glycerolipids. Our work uncovers a crucial SYT-dependent mechanism of stress adaptation counteracting the detrimental accumulation of diacylglycerol at the PM produced during episodes of abiotic stress.

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Section: Resultsmentioning

confidence: 99%

Synaptotagmins Maintain Diacylglycerol Homeostasis at Endoplasmic Reticulum-Plasma Membrane Contact Sites during Abiotic Stress

Ruiz-López

Pérez-Sancho

Valle

et al. 2020

Preprint

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“…Bioinformatics analysis revealed that some of plant GCs possess highly conserved heme-NO and oxygen−binding (H-NOX) domains ( Mulaudzi et al, 2011 ; Gehring and Turek, 2017 ). Recent reports showed that diacylglycerol kinase 4 (DGK4) from A. thaliana contains the GC domain modulating NO responses ( Vaz Dias et al, 2019 ; Angkawijaya et al, 2020 ; Wong et al, 2020 ). The authors confirmed that DGK4 is a link between NO, cNMP and Ca 2+ signaling in pollen tube guidance.…”

Section: Cooperation Of Ca 2+ and Adenylyl/guanylymentioning

confidence: 99%

Cross Talk Between Cyclic Nucleotides and Calcium Signaling Pathways in Plants–Achievements and Prospects

et al. 2021

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A variety of plant cellular activities are regulated through mechanisms controlling the level of signal molecules, such as cyclic nucleotides (cNMPs, e.g., cyclic adenosine 3′:5′-monophosphate, cAMP, and cyclic guanosine 3′:5′- monophosphate, cGMP) and calcium ions (Ca2+). The mechanism regulating cNMP levels affects their synthesis, degradation, efflux and cellular distribution. Many transporters and the spatiotemporal pattern of calcium signals, which are transduced by multiple, tunable and often strategically positioned Ca2+-sensing elements, play roles in calcium homeostasis. Earlier studies have demonstrated that while cNMPs and Ca2+ can act separately in independent transduction pathways, they can interact and function together. Regardless of the context, the balance between Ca2+ and cNMP is the most important consideration. This balance seems to be crucial for effectors, such as phosphodiesterases, cyclic nucleotide gated channels and cyclase activity. Currently, a wide range of molecular biology techniques enable thorough analyses of cellular cross talk. In recent years, data have indicated relationships between calcium ions and cyclic nucleotides in mechanisms regulating specific signaling pathways. The purpose of this study is to summarize the current knowledge on nucleotide-calcium cross talk in plants.

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“…(Swiezawska et al, 2015(Swiezawska et al, , 2017 and Japanese morning glory (Szmidt-Jaworska et al, 2009) and in the monocot grass model Brachypodium (Swiezawska et al, 2020), as well as in a human immune-responsive protein IRAK3 (Freihat et al, 2019), have demonstrated the robustness of this approach and its significance in biological discoveries across different systems. Furthermore, the method enables candidate selections for follow-up in vivo and in planta studies that will eventually reveal the biological roles of these functional centers such as those reported in Joudoi et al (2013), Shen et al (2019), Vaz Dias et al (2019, Angkawijaya et al (2020), Lee et al (2020), andTurek et al (2020). We foresee that emerging experimental data will inform and strengthen motif refinement efforts, and enable the development of modern machine learning techniques that incorporate multiple features ranging from the classical physicochemical properties of protein domains and protein-protein interaction (PPI) networks to GO based function predictions, to not only automate annotations for uncharacterized proteins, but also to identify hidden functional centers in complex multi-functional proteins (Rifaioglu et al, 2019;Bonetta and Valentino, 2020;Cai et al, 2020;Littmann et al, 2021).…”

Section: Conclusion and Future Perspectivementioning

confidence: 99%

Computational Identification of Functional Centers in Complex Proteins: A Step-by-Step Guide With Examples

et al. 2021

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In proteins, functional centers consist of the key amino acids required to perform molecular functions such as catalysis, ligand-binding, hormone- and gas-sensing. These centers are often embedded within complex multi-domain proteins and can perform important cellular signaling functions that enable fine-tuning of temporal and spatial regulation of signaling molecules and networks. To discover hidden functional centers, we have developed a protocol that consists of the following sequential steps. The first is the assembly of a search motif based on the key amino acids in the functional center followed by querying proteomes of interest with the assembled motif. The second consists of a structural assessment of proteins that harbor the motif. This approach, that relies on the application of computational tools for the analysis of data in public repositories and the biological interpretation of the search results, has to-date uncovered several novel functional centers in complex proteins. Here, we use recent examples to describe a step-by-step guide that details the workflow of this approach and supplement with notes, recommendations and cautions to make this protocol robust and widely applicable for the discovery of hidden functional centers.

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A Pair of Arabidopsis Diacylglycerol Kinases Essential for Gametogenesis and Endoplasmic Reticulum Phospholipid Metabolism in Leaves and Flowers

Cited by 23 publications

References 51 publications

Synaptotagmins Maintain Diacylglycerol Homeostasis at Endoplasmic Reticulum-Plasma Membrane Contact Sites during Abiotic Stress

Synaptotagmins Maintain Diacylglycerol Homeostasis at Endoplasmic Reticulum-Plasma Membrane Contact Sites during Abiotic Stress

Cross Talk Between Cyclic Nucleotides and Calcium Signaling Pathways in Plants–Achievements and Prospects

Computational Identification of Functional Centers in Complex Proteins: A Step-by-Step Guide With Examples

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