Radioactive contamination of the natural areas is one of the most long-lasting anthropogenic impacts on the environment. Scots pine (Pinus sylvestris L.) is a promising organism for radiation-related ...research because of its high radiosensitivity, but the genome size of Pinacea species has imposed obstacles for high-throughput studies so far. In this work, we conducted the analysis of the de novo assembled transcriptome of Scots pine populations growing in the Chernobyl-affected zone, which is still today contaminated with radionuclides because of the accident at the nuclear power plant in 1986. The transcriptome profiles indicate a clear pattern of adaptive stress response, which seems to be dose-dependent. The transcriptional response indicates a continuous modulation of the cellular redox system, enhanced expression of chaperones and histones, along with the control of ions balance. Interestingly, the activity of transposable element families is inversely correlated to the exposure levels to radiation. These adaptive responses, which are triggered by radiation doses 30 times lower than the one accepted as a safe for biota species by international regulations, suggest that the environmental management in radiation protection should be reviewed.
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•De novo transcriptome assembly of Scots pine trees from Chernobyl affected zone.•The profiles indicate stress adaptation to doses considered as safe for biota species.•The response pattern suggests a sustained control of the redox system and ion balance.•Transposons activity essentially inversely correlated to the levels of irradiation.
De novo transcriptome analysis of chronically irradiated Scots pine trees from Chernobyl affected zone reveals a unique stress response profile.
Key message
The manuscript by Alves et al. entitled “
Genome-wide identification and characterization of tRNA-derived RNA fragments in land plants
” describes the identification and characterization ...of tRNAderived sRNA fragments in plants. By combining bioinformatic analysis and genetic and molecular approaches, we show that tRF biogenesis does not rely on canonical microRNA/siRNA processing machinery (i.e., independent of DICER-LIKE proteins). Moreover, we provide evidences that the Arabidopsis S-like Ribonuclease 1 (RNS1) might be involved in the biogenesis of tRFs. Detailed analyses showed that plant tRFs are sorted into different types of ARGONAUTE proteins and that they have potential target candidate genes. Our work advances the understanding of the tRF biology in plants by providing evidences that plant and animal tRFs shared common features and raising the hypothesis that an interplay between tRFs and other sRNAs might be important to fine-tune gene expression and protein biosynthesis in plant cells.
Small RNA (sRNA) fragments derived from tRNAs (3′-loop, 5′-loop, anti-codon loop), named tRFs, have been reported in several organisms, including humans and plants. Although they may interfere with gene expression, their biogenesis and biological functions in plants remain poorly understood. Here, we capitalized on small RNA sequencing data from distinct species such as
Arabidopsis thaliana, Oryza sativa
, and
Physcomitrella patens
to examine the diversity of plant tRFs and provide insight into their properties.
In silico
analyzes of 19 to 25-nt tRFs derived from 5′ (tRF-5s) and 3′CCA (tRF-3s) tRNA loops in these three evolutionary distant species showed that they are conserved and their abundance did not correlate with the number of genomic copies of the parental tRNAs. Moreover, tRF-5 is the most abundant variant in all three species.
In silico
and in vivo expression analyses unraveled differential accumulation of tRFs in
Arabidopsis
tissues/organs, suggesting that they are not byproducts of tRNA degradation. We also verified that the biogenesis of most
Arabidopsis
19–25 nt tRF-5s and tRF-3s is not primarily dependent on DICER-LIKE proteins, though they seem to be associated with ARGONAUTE proteins and have few potential targets. Finally, we provide evidence that
Arabidopsis
ribonuclease RNS1 might be involved in the processing and/or degradation of tRFs. Our data support the notion that an interplay between tRFs and other sRNAs might be important to fine tune gene expression and protein biosynthesis in plant cells.
The target of rapamycin (TOR) kinase is a conserved energy sensor that regulates growth in response to environmental cues. However, little is known about the TOR signaling pathway in plants. We used ...Arabidopsis lines affected in the lethal with SEC13 protein 8 (LST8-1) gene, a core element of the TOR complex, to search for suppressor mutations. Two suppressor lines with improved growth were isolated that carried mutations in the Yet Another Kinase 1 (AtYAK1) gene encoding a member of the dual-specificity tyrosine phosphorylation-regulated kinase (DYRK) family. Atyak1 mutations partly rescued the developmental defects of lst8-1-1 mutants and conferred resistance to the TOR inhibitor AZD-8055. Moreover, atyak1 mutations suppressed the transcriptomic and metabolic perturbations as well as the abscisic acid (ABA) hypersensitivity of the lst8-1-1 mutants. AtYAK1 interacted with the regulatory-associated protein of TOR (RAPTOR), a component of the TOR complex, and was phosphorylated by TOR. Thus, our findings reveal that AtYAK1 is a TOR effector that probably needs to be switched off to activate plant growth.
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•A screen for suppressors of plant lst8 mutants identifies the AtYAK1 kinase•The AtYAK1 kinase interacts with RAPTOR and is phosphorylated by TOR•AtYAK1 disruption reduces transcriptional and metabolic changes in lst8 mutants•The ABA hypersensitivity of lst8 mutants is reverted by atyak1 mutations
The target of rapamycin (TOR) kinase is conserved in eukaryotes and controls growth and development. Forzani et al. find that mutations of the double-specificity plant YAK1 kinase restore growth of lst8-1 mutants and dampen the effects of TOR deficiency. Moreover, they show that AtYAK1 is phosphorylated by TOR.
Abstract
Shoot growth directly impacts plant productivity. Plants adjust their shoot growth in response to varying environments to maximize resource capture and stress resilience. While several ...factors controlling shoot growth are known, the complexity of the regulation and the input of the environment are not fully understood. We have investigated shoot growth repression induced by low ambient temperatures in hybrids of Arabidopsis thaliana Kro-0 and BG-5 accessions. To continue our previous studies, we confirmed that the Kro-0 allele of DYNAMIN-RELATED PROTEIN 3B causes stunted shoot growth in the BG-5 background. We also found that shoot growth repression was most pronounced near the apex at a lower temperature and that the cells in the hybrid stem failed to elongate correctly. Furthermore, we observed that shoot growth repression in hybrids depended on light availability. Global gene expression analysis indicated the involvement of hormones, especially strigolactone, associated with the dwarf phenotype. Altogether, this study enhances our knowledge on the genetic, physiological and environmental factors associated with shoot growth regulation.
Chronic ionising radiation exposure is a main consequence of radioactive pollution of the environment. The development of functional genomics approaches coupled with morphological and physiological ...studies allows new insights into plant adaptation to life under chronic irradiation. Using morphological, reproductive, physiological, and transcriptomic experiments, we evaluated the way in which
natural accessions from the Chernobyl exclusion zone recover from chronic low-dose and acute high-dose γ-irradiation of seeds. Plants from radioactively contaminated areas were characterized by lower germination efficiency, suppressed growth, decreased chlorophyll fluorescence, and phytohormonal changes. The transcriptomes of plants chronically exposed to low-dose radiation indicated the repression of mobile genetic elements and deregulation of genes related to abiotic stress tolerance. Furthermore, these chronically irradiated natural accessions showed higher tolerance to acute 150 Gy γ-irradiation of seeds, according to transcriptome and phytohormonal profiles. Overall, the lower sensitivity of the accessions from radioactively contaminated areas to acute high-dose irradiation may come at the cost of their growth performance under normal conditions.
Nitrate reductase (NR) has emerged as a potential NO source in plants. Indeed, the Arabidopsis thaliana NR double-deficient mutant (nia1 nia2) produces low NO and develops abnormal susceptibility to ...bacterial infection. We have employed quantitative real-time polymerase chain reactions to analyze the effects of NO gas on the expression of defense-related genes in wild-type and nia1 nial2 A. thaliana plants that were inoculated with an avirulent strain of Pseudomonas syringae pv. tomato. The pathogenesis-related gene 1 (PR1) was up-regulated by bacterial infection, and its expression was higher in the wild type than in nia1 nia2. Fumigation with NO attenuated the expression of PR1 and other salicylic acid-related genes in plants that had been inoculated with P. syringae. Nevertheless, NO inhibited the most intense bacterial growth and disease symptoms in nial nial leaves. The NO fumigation also directly modulated lignin biosynthesisrelated gene expression (CADI) and parts of the auxin (TIR1, ILL1, GH3) and ethylene (ACCS7) pathways, among other defense-related genes, and their modulation was more intense in the NR-deficient mutant. Pathogen inoculation induced delayed but intense H₂O₂ production in mutant leaves in comparison with the wild type. Hydrogen peroxide potentiated the microbicidal effects of NO against bacterial cultures. These results suggest that NO has a direct microbicidal effect in combination with H₂O₂ to allow for the attenuation of the SA-mediated defense response, thereby reducing the energy expenditure associated with defense-related gene transcription. Overall, these results highlight the importance of NR-dependent NO production in the establishment of disease resistance.
Summary
Adjustment to energy starvation is crucial to ensure growth and survival. In Arabidopsis thaliana (Arabidopsis), this process relies in part on the phosphorylation of the circadian clock ...regulator bZIP63 by SUCROSE non‐fermenting RELATED KINASE1 (SnRK1), a key mediator of responses to low energy.
We investigated the effects of mutations in bZIP63 on plant carbon (C) metabolism and growth. Results from phenotypic, transcriptomic and metabolomic analysis of bZIP63 mutants prompted us to investigate the starch accumulation pattern and the expression of genes involved in starch degradation and in the circadian oscillator.
bZIP63 mutation impairs growth under light‐dark cycles, but not under constant light. The reduced growth likely results from the accentuated C depletion towards the end of the night, which is caused by the accelerated starch degradation of bZIP63 mutants. The diel expression pattern of bZIP63 is dictated by both the circadian clock and energy levels, which could determine the changes in the circadian expression of clock and starch metabolic genes observed in bZIP63 mutants.
We conclude that bZIP63 composes a regulatory interface between the metabolic and circadian control of starch breakdown to optimize C usage and plant growth.
The changes in the ability of three fluorescent derivatives of 2-(2′-hydroxyphenyl)benzothiazole to undergo excited-state intramolecular proton transfer (ESIPT) processes have been correlated with ...the rheological properties of four amino-polydimethylsiloxanes with different molar masses and containing different amounts of monomer units with amino pendant groups, in the presence and absence of a cross-linking molecule, CO2. The changes lead to a variety of species (keto, enol, and enolate forms) in both the ground and excited states. Calculations using the density-functional theory/time-dependent density-functional theory method at the CAM-B3LYP/6-311++G(d,p) level helped to identify how ESIPT is involved in the formation of the intermediates. The results demonstrate that proton transfer in 2-(2′-hydroxyphenyl)benzothiazoles is a powerful tool to identify local changes in the viscosity and micropolarity of the environment that are attributed to the structural differences of the amino-polydimethylsiloxanes and their cross-linking.
At low intensity, certain stress conditions may have a positive effect on growth and development of plants (eustress). Growth stimulation of barley plants after gamma irradiation of seeds in low ...doses was observed as an increase in root and shoot lengths. Hydrogen peroxide concentrations in shoots of irradiated plants were significantly higher than in control, while the opposite effect was observed in the roots. To elucidate the molecular basis of growth stimulation after gamma irradiation of barley seeds, we performed the transcriptomic analysis of barley embryos at different stages of seed germination. The transcriptomic data were correlated with morphological parameters and the hydrogen peroxide levels in irradiated and control plants. These data indicate that the growth stimulation by low‐dose irradiation involves the transcriptional control of genes related to phytohormones, antioxidant system, late embryogenesis abundant proteins and cell wall components, with possible involvement of jasmonate and ABA signalling. Gamma irradiation of seeds at dose 100 Gy caused significant growth inhibition and promoted expression changes in transcripts related to cell cycle arrest, DNA damage repair and antioxidant system.
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