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1.
Suppression of External NADPH Dehydrogenase-NDB1 in Arabidopsis thaliana Confers Improved Tolerance to Ammonium Toxicity via Efficient Glutathione/Redox Metabolism.
Podgórska, A, Ostaszewska-Bugajska, M, Borysiuk, K, Tarnowska, A, Jakubiak, M, Burian, M, Rasmusson, AG, Szal, B
International journal of molecular sciences. 2018;(5)
Abstract
Environmental stresses, including ammonium (NH₄⁺) nourishment, can damage key mitochondrial components through the production of surplus reactive oxygen species (ROS) in the mitochondrial electron transport chain. However, alternative electron pathways are significant for efficient reductant dissipation in mitochondria during ammonium nutrition. The aim of this study was to define the role of external NADPH-dehydrogenase (NDB1) during oxidative metabolism of NH₄⁺-fed plants. Most plant species grown with NH₄⁺ as the sole nitrogen source experience a condition known as “ammonium toxicity syndrome”. Surprisingly, transgenic Arabidopsis thaliana plants suppressing NDB1 were more resistant to NH₄⁺ treatment. The NDB1 knock-down line was characterized by milder oxidative stress symptoms in plant tissues when supplied with NH₄⁺. Mitochondrial ROS accumulation, in particular, was attenuated in the NDB1 knock-down plants during NH₄⁺ treatment. Enhanced antioxidant defense, primarily concerning the glutathione pool, may prevent ROS accumulation in NH₄⁺-grown NDB1-suppressing plants. We found that induction of glutathione peroxidase-like enzymes and peroxiredoxins in the NDB1-surpressing line contributed to lower ammonium-toxicity stress. The major conclusion of this study was that NDB1 suppression in plants confers tolerance to changes in redox homeostasis that occur in response to prolonged ammonium nutrition, causing cross tolerance among plants.
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2.
PROMIS, global analysis of PROtein-metabolite interactions using size separation in Arabidopsis thaliana.
Veyel, D, Sokolowska, EM, Moreno, JC, Kierszniowska, S, Cichon, J, Wojciechowska, I, Luzarowski, M, Kosmacz, M, Szlachetko, J, Gorka, M, et al
The Journal of biological chemistry. 2018;(32):12440-12453
Abstract
Small molecules not only represent cellular building blocks and metabolic intermediates, but also regulatory ligands and signaling molecules that interact with proteins. Although these interactions affect cellular metabolism, growth, and development, they have been largely understudied. Herein, we describe a method, which we named PROtein-Metabolite Interactions using Size separation (PROMIS), that allows simultaneous, global analysis of endogenous protein-small molecule and of protein-protein complexes. To this end, a cell-free native lysate from Arabidopsis thaliana cell cultures was fractionated by size-exclusion chromatography, followed by quantitative metabolomic and proteomic analyses. Proteins and small molecules showing similar elution behavior, across protein-containing fractions, constituted putative interactors. Applying PROMIS to an A. thaliana extract, we ascertained known protein-protein (PPIs) and protein-metabolite (PMIs) interactions and reproduced binding between small-molecule protease inhibitors and their respective proteases. More importantly, we present examples of two experimental strategies that exploit the PROMIS dataset to identify novel PMIs. By looking for similar elution behavior of metabolites and enzymes belonging to the same biochemical pathways, we identified putative feedback and feed-forward regulations in pantothenate biosynthesis and the methionine salvage cycle, respectively. By combining PROMIS with an orthogonal affinity purification approach, we identified an interaction between the dipeptide Tyr-Asp and the glycolytic enzyme glyceraldehyde-3-phosphate dehydrogenase. In summary, we present proof of concept for a powerful experimental tool that enables system-wide analysis of PMIs and PPIs across all biological systems. The dataset obtained here comprises nearly 140 metabolites and 5000 proteins, which can be mined for putative interactors.
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3.
Pumping up the volume - vacuole biogenesis in Arabidopsis thaliana.
Krüger, F, Schumacher, K
Seminars in cell & developmental biology. 2018;:106-112
Abstract
Plant architecture follows the need to collect CO2, solar energy, water and mineral nutrients via large surface areas. It is by the presence of a central vacuole that fills much of the cell volume that plants manage to grow at low metabolic cost. In addition vacuoles buffer the fluctuating supply of essential nutrients and help to detoxify the cytosol when plants are challenged by harmful molecules. Despite their large size and multiple important functions, our knowledge of vacuole biogenesis and the machinery underlying their amazing dynamics is still fragmentary. In this review, we try to reconcile past and present models for vacuole biogenesis with the current knowledge of multiple parallel vacuolar trafficking pathways and the molecular machineries driving membrane fusion and organelle shape.
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4.
VirD5 is required for efficient Agrobacterium infection and interacts with Arabidopsis VIP2.
Wang, Y, Zhang, S, Huang, F, Zhou, X, Chen, Z, Peng, W, Luo, M
The New phytologist. 2018;(2):726-738
Abstract
During Agrobacterium (Agrobacterium tumefaciens) infection, the translocated virulence proteins (VirD2, VirE2, VirE3, VirF and VirD5) play crucial roles. It is thought that, through protein-protein interactions, Agrobacterium uses and abuses host plant factors and systems to facilitate its infection. Although some molecular functions have been revealed, the roles of VirD5 still need to be further elucidated. Here, plant transformation and tumorigenesis mediated by genetically modified Agrobacterium strains were performed to examine VirD5 roles. In addition, protein-protein interaction-associated molecular and biochemistry technologies were used to reveal and elucidate VirD5 interaction with Arabidopsis VirE2 interacting protein 2 (VIP2). Our results showed that deleting virD5 from Agrobacterium reduced its tumor formation ability and stable transformation efficiency but did not affect the transient transformation efficiency. We also found that VirD5 can interact with Arabidopsis VIP2. Further experiments demonstrated that VirD5 can affect VIP2 binding to cap-binding proteins (CBP20 and CBP80). The tumorigenesis efficiency for cbp80 mutant was not significantly changed, but that for cbp20, cbp20cbp80 mutants were significantly increased. This work demonstrates experimentally that VirD5 is required for efficient Agrobacterium infection and may promote this process by competitive interaction with Arabidopsis VIP2. CBP20 is involved in the Agrobacterium infection process and its effect can be synergistically enhanced by CBP80.
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5.
NPR1 in JazzSet with Pathogen Effectors.
Sun, Y, Detchemendy, TW, Pajerowska-Mukhtar, KM, Mukhtar, MS
Trends in plant science. 2018;(6):469-472
Abstract
NON-EXPRESSOR OF PATHOGENESIS-RELATED GENES 1 (NPR1) is a master regulator of salicylic acid (SA)-mediated systemic acquired resistance (SAR), a broad-spectrum disease resistance mechanism in plants. NPR1 controls approximately 90% of SA-dependent transcriptome in Arabidopsis. Here, we discuss how pathogen effectors manipulate NPR1 functions in different cellular compartments to establish disease.
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6.
Dynamic modeling of subcellular phenylpropanoid metabolism in Arabidopsis lignifying cells.
Guo, L, Wang, P, Jaini, R, Dudareva, N, Chapple, C, Morgan, JA
Metabolic engineering. 2018;:36-46
Abstract
Lignin is a polymer that significantly inhibits saccharification of plant feedstocks. Adjusting the composition or reducing the total lignin content have both been demonstrated to result in an increase in sugar yield from biomass. However, because lignin is essential for plant growth, it cannot be manipulated with impunity. Thus, it is important to understand the control of carbon flux towards lignin biosynthesis such that optimal modifications to it can be made precisely. Phenylalanine (Phe) is the common precursor for all lignin subunits and it is commonly accepted that all biosynthetic steps, spanning multiple subcellular compartments, are known, yet an in vivo model of how flux towards lignin is controlled is lacking. To address this deficiency, we formulated and parameterized a kinetic model based on data from feeding Arabidopsis thaliana basal lignifying stems with ring labeled [13C6]-Phe. Several candidate models were compared by an information theoretic approach to select the one that best matched the experimental observations. Here we present a dynamic model of phenylpropanoid metabolism across several subcellular compartments that describes the allocation of carbon towards lignin biosynthesis in wild-type Arabidopsis stems. Flux control coefficients for the enzymes in the pathway starting from arogenate dehydratase through 4-coumarate: CoA ligase were calculated and show that the plastidial cationic amino-acid transporter has the highest impact on flux.
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7.
Engineering Rubisco activase from thermophilic cyanobacteria into high-temperature sensitive plants.
Ogbaga, CC, Stepien, P, Athar, HU, Ashraf, M
Critical reviews in biotechnology. 2018;(4):559-572
Abstract
In the past decade, various strategies to improve photosynthesis and crop yield, such as leaf morphology, light interception and use efficiency, biochemistry of light reactions, stomatal conductance, carboxylation efficiency, and source to sink regulation, have been discussed at length. Leaf morphology and physiology are tightly coupled to light capturing efficiency, gas exchange capacity, and temperature regulation. However, apart from the photoprotective mechanism of photosystem-II (PSII), i.e. non-photochemical quenching, very low genetic variation in the components of light reactions has been observed in plants. In the last decade, biochemistry-based enhancement of carboxylation efficiency that improves photosynthesis in plants was one of the potential strategies for improving plant biomass production. Enhancement of activation of the ubiquitous enzyme ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco; EC 4.1.1.39) by Rubisco activase may be another potential strategy for improving a photosynthesis-driven increase in crop yield. Rubisco activase modifies the conformation of the active center in Rubisco by removing tightly bound inhibitors, thereby contributing to enzyme activation and rapid carboxylation. Thermophilic cyanobacteria are oxygenic photosynthetic bacteria that thrive in high-temperature environments. This critical review discusses the prospects for and the potential of engineering Rubisco activase from thermophilic cyanobacteria into temperature-sensitive plants, to increase the threshold temperature and survival of these plants in arid regions.
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8.
Rapid and reversible root growth inhibition by TIR1 auxin signalling.
Fendrych, M, Akhmanova, M, Merrin, J, Glanc, M, Hagihara, S, Takahashi, K, Uchida, N, Torii, KU, Friml, J
Nature plants. 2018;(7):453-459
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Abstract
The phytohormone auxin is the information carrier in a plethora of developmental and physiological processes in plants1. It has been firmly established that canonical, nuclear auxin signalling acts through regulation of gene transcription2. Here, we combined microfluidics, live imaging, genetic engineering and computational modelling to reanalyse the classical case of root growth inhibition3 by auxin. We show that Arabidopsis roots react to addition and removal of auxin by extremely rapid adaptation of growth rate. This process requires intracellular auxin perception but not transcriptional reprogramming. The formation of the canonical TIR1/AFB-Aux/IAA co-receptor complex is required for the growth regulation, hinting to a novel, non-transcriptional branch of this signalling pathway. Our results challenge the current understanding of root growth regulation by auxin and suggest another, presumably non-transcriptional, signalling output of the canonical auxin pathway.
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9.
Large-scale docking predicts that sORF-encoded peptides may function through protein-peptide interactions in Arabidopsis thaliana.
Hazarika, RR, Sostaric, N, Sun, Y, van Noort, V
PloS one. 2018;(10):e0205179
Abstract
Several recent studies indicate that small Open Reading Frames (sORFs) embedded within multiple eukaryotic non-coding RNAs can be translated into bioactive peptides of up to 100 amino acids in size. However, the functional roles of the 607 Stress Induced Peptides (SIPs) previously identified from 189 Transcriptionally Active Regions (TARs) in Arabidopsis thaliana remain unclear. To provide a starting point for functional annotation of these plant-derived peptides, we performed a large-scale prediction of peptide binding sites on protein surfaces using coarse-grained peptide docking. The docked models were subjected to further atomistic refinement and binding energy calculations. A total of 530 peptide-protein pairs were successfully docked. In cases where a peptide encoded by a TAR is predicted to bind at a known ligand or cofactor-binding site within the protein, it can be assumed that the peptide modulates the ligand or cofactor-binding. Moreover, we predict that several peptides bind at protein-protein interfaces, which could therefore regulate the formation of the respective complexes. Protein-peptide binding analysis further revealed that peptides employ both their backbone and side chain atoms when binding to the protein, forming predominantly hydrophobic interactions and hydrogen bonds. In this study, we have generated novel predictions on the potential protein-peptide interactions in A. thaliana, which will help in further experimental validation.
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10.
Novel DNAJ-related proteins in Arabidopsis thaliana.
Pulido, P, Leister, D
The New phytologist. 2018;(2):480-490
Abstract
Classical DNAJ proteins are co-chaperones that together with HSP70s control protein homeostasis. All three classical types of DNAJ proteins (DNAJA, DNAJB and DNAJC types) possess the J-domain for interaction with HSP70. DNAJA proteins contain, in addition, both the zinc-finger motif and the C-terminal domain which are involved in substrate binding, while DNAJB retains only the latter and DNAJC comprises only the J-domain. There is increasing evidence that some of the activities of DNAJ proteins do not require the J-domain, highlighting the functional significance of the other two domains. Indeed, the so-called DNAJ-like proteins with a degenerate J-domain have been previously coined as DNAJD proteins, and also proteins containing only a DNAJ-like zinc-finger motif appear to be involved in protein homeostasis. Therefore, we propose to extend the classification of DNAJ-related proteins into three different groups. The DNAJD type comprises proteins with a J-like domain only, and has 15 members in Arabidopsis thaliana, whereas proteins of the DNAJE (33 Arabidopsis members) and DNAJF (three Arabidopsis members) types contain a DNAJA-like zinc-finger domain and DNAJA/B-like C-terminal domain, respectively. Here, we provide an overview of the entire repertoire of these proteins in A. thaliana with respect to their physiological function and possible evolutionary origin.