-
1.
Novel pipeline identifies new upstream ORFs and non-AUG initiating main ORFs with conserved amino acid sequences in the 5' leader of mRNAs in Arabidopsis thaliana.
van der Horst, S, Snel, B, Hanson, J, Smeekens, S
RNA (New York, N.Y.). 2019;(3):292-304
Abstract
Eukaryotic mRNAs contain a 5' leader sequence preceding the main open reading frame (mORF) and, depending on the species, 20%-50% of eukaryotic mRNAs harbor an upstream ORF (uORF) in the 5' leader. An unknown fraction of these uORFs encode sequence conserved peptides (conserved peptide uORFs, CPuORFs). Experimentally validated CPuORFs demonstrated to regulate the translation of downstream mORFs often do so in a metabolite concentration-dependent manner. Previous research has shown that most CPuORFs possess a start codon context suboptimal for translation initiation, which turns out to be favorable for translational regulation. The suboptimal initiation context may even include non-AUG start codons, which makes CPuORFs hard to predict. For this reason, we developed a novel pipeline to identify CPuORFs unbiased of start codon using well-annotated sequence data from 31 eudicot plant species and rice. Our new pipeline was able to identify 29 novel Arabidopsis thaliana (Arabidopsis) CPuORFs, conserved across a wide variety of eudicot species of which 15 do not initiate with an AUG start codon. In addition to CPuORFs, the pipeline was able to find 14 conserved coding regions directly upstream and in frame with the mORF, which likely initiate translation on a non-AUG start codon. Altogether, our pipeline identified highly conserved coding regions in the 5' leaders of Arabidopsis transcripts, including in genes with proven functional importance such as LHY, a key regulator of the circadian clock, and the RAPTOR1 subunit of the target of rapamycin (TOR) kinase.
-
2.
Topology of TROL protein in thylakoid membranes of Arabidopsis thaliana.
Vojta, L, Fulgosi, H
Physiologia plantarum. 2019;(1):300-308
Abstract
Thylakoid rhodanase-like protein (TROL) is a nuclear-encoded protein of thylakoid membranes required for tethering of ferredoxin:nicotinamide adenine dinucleotide phosphate (NADPH) oxydoreductase (FNR). It has been proposed that the dynamic interaction of TROL with flavoenzyme FNR, influenced by environmental light conditions, regulates the fate of photosynthetic electrons, directing them either to NADPH synthesis or to other acceptors, including reactive oxygen species detoxification pathways. Inside the chloroplasts, TROL has a dual localization: an inner membrane precursor form and a thylakoid membrane mature form, which has been confirmed by several large-scale chloroplast proteomics studies, as well as protein import experiments. Unlike the localization, the topology of TROL in the membranes, which is a prerequisite for further studies of its properties and function, has not been experimentally confirmed yet. Thermolysin was proven to be a valuable protease to probe the surface of chloroplasts and membranes in general. By treating the total chloroplast membranes using increasing protease concentration, sequential degradation of TROL was observed, indicating protected polypeptides of TROL and possible domain orientation. To further substantiate the obtained results, TROL-overexpressing Arabidopsis line (OX) and line in which the central rhodanase-like domain (RHO) has been partially deleted (ΔRHO), were used as well. While OX line showed the same degradation pattern of TROL as the wild-type, surprisingly, TROL from ΔRHO membranes was not detectable even at the lowest protease concentration applied, indicating the importance of this domain to the integrity of TROL. In conclusion, TROL is a polytopic protein with a stroma-exposed C-terminal FNR-binding region, and the thylakoid lumen-located RHO domain.
-
3.
Developmental Plasticity at High Temperature.
Vu, LD, Xu, X, Gevaert, K, De Smet, I
Plant physiology. 2019;(2):399-411
-
-
Free full text
-
Abstract
Molecular mechanisms controlling the thermal response in Arabidopsis.
-
4.
Anti-Inflammatory Activity of A Polyphenolic Extract from Arabidopsis thaliana in In Vitro and In Vivo Models of Alzheimer's Disease.
Mattioli, R, Francioso, A, d'Erme, M, Trovato, M, Mancini, P, Piacentini, L, Casale, AM, Wessjohann, L, Gazzino, R, Costantino, P, et al
International journal of molecular sciences. 2019;(3)
Abstract
Alzheimer's disease (AD) is the most common neurodegenerative disorder and the primary form of dementia in the elderly. One of the main features of AD is the increase in amyloid-beta (Aβ) peptide production and aggregation, leading to oxidative stress, neuroinflammation and neurodegeneration. Polyphenols are well known for their antioxidant, anti-inflammatory and neuroprotective effects and have been proposed as possible therapeutic agents against AD. Here, we investigated the effects of a polyphenolic extract of Arabidopsis thaliana (a plant belonging to the Brassicaceae family) on inflammatory response induced by Aβ. BV2 murine microglia cells treated with both Aβ25⁻35 peptide and extract showed a lower pro-inflammatory (IL-6, IL-1β, TNF-α) and a higher anti-inflammatory (IL-4, IL-10, IL-13) cytokine production compared to cells treated with Aβ only. The activation of the Nrf2-antioxidant response element signaling pathway in treated cells resulted in the upregulation of heme oxygenase-1 mRNA and in an increase of NAD(P)H:quinone oxidoreductase 1 activity. To establish whether the extract is also effective against Aβ-induced neurotoxicity in vivo, we evaluated its effect on the impaired climbing ability of AD Drosophila flies expressing human Aβ1⁻42. Arabidopsis extract significantly restored the locomotor activity of these flies, thus confirming its neuroprotective effects also in vivo. These results point to a protective effect of the Arabidopsis extract in AD, and prompt its use as a model in studying the impact of complex mixtures derived from plant-based food on neurodegenerative diseases.
-
5.
Arabidopsis acyl-CoA-binding proteins regulate the synthesis of lipid signals.
Lung, SC, Chye, ML
The New phytologist. 2019;(1):113-117
Abstract
Plant lipid signals are crucial developmental modulators and stress response mediators. A family of acyl-CoA-binding proteins (ACBPs) participates in the lipid trafficking of these signals. Isoform-specific functions can arise from differences in their subcellular distribution, tissue-specificity, stress-responsiveness, and ligand selectivity. In lipid-mediated cell signaling, plant ACBPs are not merely transporters but are also important regulators via their interaction with lipid-metabolic enzymes and precursor lipids. In this Insight, the regulatory roles of plant ACBPs in the synthesis of various signaling lipids, including phosphatidic acid, sterols, oxylipins, and sphingolipids, are reviewed. We focus on the functional significance of these lipid signals in plant development and stress responses with an overview of recent work using reverse genetics and transgenic Arabidopsis.
-
6.
Spatiotemporal dynamics of a reaction-diffusion model of pollen tube tip growth.
Tian, C, Shi, Q, Cui, X, Guo, J, Yang, Z, Shi, J
Journal of mathematical biology. 2019;(4):1319-1355
Abstract
A reaction-diffusion model is proposed to describe the mechanisms underlying the spatial distributions of ROP1 and calcium on the pollen tube tip. The model assumes that the plasma membrane ROP1 activates itself through positive feedback loop, while the cytosolic calcium ions inhibit ROP1 via a negative feedback loop. Furthermore it is proposed that lateral movement of molecules on the plasma membrane are depicted by diffusion. It is shown that bistable or oscillatory dynamics could exist even in the non-spatial model, and stationary and oscillatory spatiotemporal patterns are found in the full spatial model which resemble the experimental data of pollen tube tip growth.
-
7.
The alternative splicing of SKU5-Similar3 in Arabidopsis.
Zhou, K
Plant signaling & behavior. 2019;(10):e1651182
-
-
Free full text
-
Abstract
Alternative splicing largely enhanced the diversity of transcriptome and proteome in eukaryas. Along with technological development, more and more genes are reported to be alternatively spliced during mRNA maturation. Here, I report the alternative splicing of SKU5-Similar 3 (SKS3) and its special splicing site in Arabidopsis. SKS3 was predicted to be alternatively transcribed into two variants, SKS3.1 and SKS3.2, which encoded a GPI-anchored protein and a soluble secretory protein, respectively. But, according to experimental data, instead of SKS3.2, a novel variant, SKS3.3, which encodes a protein with a transmembrane region at its C-terminus, was demonstrated. Interestingly, it exhibites a different organ-specific expression pattern with SKS3.1, and an unusual intron splicing site not following 'GT-AG' rule or any reported rule.
-
8.
Enhanced biosynthesis of CdS nanoparticles through Arabidopsis thaliana phytochelatin synthase-modified Escherichia coli with fluorescence effect in detection of pyrogallol and gallic acid.
Zhang, D, Yamamoto, T, Tang, D, Kato, Y, Horiuchi, S, Ogawa, S, Yoshimura, E, Suzuki, M
Talanta. 2019;:447-455
Abstract
In this work, CdS nanoparticles (CdS NPs) biosynthesized through Arabidopsis thaliana phytochelatin synthase-modified Escherichia coli (CdS/AtPCS1-E. coli) with fluorescence (FL) performance for detection of pyrogallol and gallic acid was investigated. Through expression of the AtPCS1 gene inside E. coli cells by pET28b vector, biosynthesis of CdS NPs was greatly enhanced due to generation of phytochelatins (PCs, (γ-Glu-Cys)n-Gly, n ≥ 2) for efficient capture of Cd2+. The expression of AtPCS1 and concentration of glutathione (GSH) and PCs were detected by sodium dodecylsulfate-polyacrylamide gel electrophoresis (SDS-PAGE) and high performance liquid chromatography (HPLC), respectively. The morphology and component were checked through scanning electron microscope (SEM), transmission electron microscopy (TEM) and energy dispersive spectrometer (EDS). FL effect with different experimental conditions were examined. In addition, it is also applied to determination of pyrogallol and gallic acid. These results revealed that multifunctional PCs could effectively facilitate biosynthesis of CdS NPs with higher yield, better distribution and lower cost while stronger FL intensity could be obtained for quantitative analysis.
-
9.
Translating auxin responses into ovules, seeds and yield: Insight from Arabidopsis and the cereals.
Shirley, NJ, Aubert, MK, Wilkinson, LG, Bird, DC, Lora, J, Yang, X, Tucker, MR
Journal of integrative plant biology. 2019;(3):310-336
Abstract
Grain production in cereal crops depends on the stable formation of male and female gametes in the flower. In most angiosperms, the female gamete is produced from a germline located deep within the ovary, protected by several layers of maternal tissue, including the ovary wall, ovule integuments and nucellus. In the field, germline formation and floret fertility are major determinants of yield potential, contributing to traits such as seed number, weight and size. As such, stimuli affecting the timing and duration of reproductive phases, as well as the viability, size and number of cells within reproductive organs can significantly impact yield. One key stimulant is the phytohormone auxin, which influences growth and morphogenesis of female tissues during gynoecium development, gametophyte formation, and endosperm cellularization. In this review we consider the role of the auxin signaling pathway during ovule and seed development, first in the context of Arabidopsis and then in the cereals. We summarize the gene families involved and highlight distinct expression patterns that suggest a range of roles in reproductive cell specification and fate. This is discussed in terms of seed production and how targeted modification of different tissues might facilitate improvements.
-
10.
Molecular tools enabling pennycress (Thlaspi arvense) as a model plant and oilseed cash cover crop.
McGinn, M, Phippen, WB, Chopra, R, Bansal, S, Jarvis, BA, Phippen, ME, Dorn, KM, Esfahanian, M, Nazarenus, TJ, Cahoon, EB, et al
Plant biotechnology journal. 2019;(4):776-788
Abstract
Thlapsi arvense L. (pennycress) is being developed as a profitable oilseed cover crop for the winter fallow period throughout the temperate regions of the world, controlling soil erosion and nutrients run-off on otherwise barren farmland. We demonstrate that pennycress can serve as a user-friendly model system akin to Arabidopsis that is well-suited for both laboratory and field experimentation. We sequenced the diploid genome of the spring-type Spring 32-10 inbred line (1C DNA content of 539 Mb; 2n = 14), identifying variation that may explain phenotypic differences with winter-type pennycress, as well as predominantly a one-to-one correspondence with Arabidopsis genes, which makes translational research straightforward. We developed an Agrobacterium-mediated floral dip transformation method (0.5% transformation efficiency) and introduced CRISPR-Cas9 constructs to produce indel mutations in the putative FATTY ACID ELONGATION1 (FAE1) gene, thereby abolishing erucic acid production and creating an edible seed oil comparable to that of canola. We also stably transformed pennycress with the Euonymus alatus diacylglycerol acetyltransferase (EaDAcT) gene, producing low-viscosity acetyl-triacylglycerol-containing seed oil suitable as a diesel-engine drop-in fuel. Adoption of pennycress as a model system will accelerate oilseed-crop translational research and facilitate pennycress' rapid domestication to meet the growing sustainable food and fuel demands.