Genome-Wide Transcriptional Profiling and Metabolic Analysis Uncover Multiple Molecular Responses of the Grass Species Lolium perenne Under Low-Intensity Xenobiotic Stress

Abstract

Lolium perenne, which is a major component of pastures, lawns, and grass strips, can be exposed to xenobiotic stresses due to diffuse and residual contaminations of soil. L. perenne was recently shown to undergo metabolic adjustments in response to sub-toxic levels of xenobiotics. To gain insight in such chemical stress responses, a de novo transcriptome analysis was carried out on leaves from plants subjected at the root level to low levels of xenobiotics, glyphosate, tebuconazole, and a combination of the two, leading to no adverse physiological effect. Chemical treatments influenced significantly the relative proportions of functional categories and of transcripts related to carbohydrate processes, to signaling, to protein-kinase cascades, such as Serine/Threonine-protein kinases, to transcriptional regulations, to responses to abiotic or biotic stimuli and to responses to phytohormones. Transcriptomics-based expressions of genes encoding different types of SNF1 (sucrose non-fermenting 1)-related kinases involved in sugar and stress signaling or encoding key metabolic enzymes were in line with specific qRT-PCR analysis or with the important metabolic and regulatory changes revealed by metabolomic analysis. The effects of pesticide treatments on metabolites and gene expression strongly suggest that pesticides at low levels, as single molecule or as mixture, affect cell signaling and functioning even in the absence of major physiological impact. This global analysis of L. perenne therefore highlighted the interactions between molecular regulation of responses to xenobiotics, and also carbohydrate dynamics, energy dysfunction, phytohormones and calcium signaling.

Herbicide-related signaling in plants reveals novel insights for herbicide use strategies, environmental risk assessment and global change assessment challenges

“…Transcriptomics and metabolomics studies Qian et al, 2011Qian et al, , 2012Ramel et al, 2007Ramel et al, , 2012Serra et al, 2013Serra et al, , 2015aSerra et al, , 2015bVivancos et al, 2011;Zhang et al, 2016) demonstrate that herbicide action is integrated within a larger cellular and molecular context involving expression regulation of hundreds of genes covering fundamental structural and physiological functions: transcription, translation, cellular communication and signaling, central metabolism, energy metabolism, biogenesis, stress responses, programmed cell death, cell homeostasis, senescence. However, as pointed out by Zhou et al (2015), sensing and signal transduction mechanisms that underlie xenobiotic-related gene regulation remain elusive in plants, in contrast with mammalian cells and yeast where xenobiotic sensors have been characterized.…”

“…Conversely, treatments with hormones such as auxins (Kerchev et al, 2015), brassinosteroids (Zhou et al, 2015), or salicylate (Cui et al, 2010) can interfere with the effects of herbicides or pesticides. Brassinosteroids (Zhou et al, 2015) and salicylate (Cui et al, 2010) directly regulate genes that are related to herbicide detoxification, and activation of auxin signaling (Kerchev et al, 2015) counteracts the cell death effects of photorespiration, which is involved in the responses to several herbicides (Serra et al, , 2015a(Serra et al, , 2015bVivancos et al, 2011). Analysis of transcriptomic, proteomic or metabolomic modifications also shows that herbicide treatments have major impacts on genes and proteins involved in stress and nutrition signaling pathways: ROS signaling, membrane stress signaling, photosystem and light stress signaling, endoplasmic reticulum stress signaling, drought and salinity signaling, nutritional starvation signaling, and cell death signaling (Duhoux et al, 2015;Faus et al, 2015;Gaines et al, 2014;Goossens et al, 2001;Horn et al, 2013;Li et al, 2015;Ozgur et al, 2014;Ramel et al, 2007Ramel et al, , 2009aSerra et al, 2013Serra et al, , 2015aSerra et al, , 2015bWalley et al, 2015;.…”

“…Some of these effectors interact with master regulators of metabolism, such as the SNF1 (sucrose non-fermenting 1)-related kinase 1 (SnRK1) (Baena-González et al, 2007;Emanuelle et al, 2015;Tomé et al, 2014) and the target-ofrapamycin (TOR) kinase (Tomé et al, 2014;Xiong et al, 2013), which exert major controls on the regulation of genes involved in catabolic processes (proteolysis, amino acid catabolism, sugar degradation, lipid catabolism) that can compensate low carbohydrate and low energy situations. In Arabidopsis, SnRK1 acts through the activation of bZIP transcription factors on asparagine biosynthesis and branched-chain amino acid metabolism (Dietrich et al, 2011), and the dynamics of these important amino acids is affected by chemically-and functionally-diverse herbicides, such as acetolactate synthase inhibitors (Duhoux et al, 2015), glyphosate (Serra et al, , 2015a(Serra et al, , 2015bVivancos et al, 2011), or atrazine , by the atrazine derivative hydroxyatrazine (Serra et al, , 2015a, and by the glyphosate derivative aminomethylphosphonic acid (AMPA) (Serra et al, , 2015a.…”

“…However, as pointed out by Zhou et al (2015), sensing and signal transduction mechanisms that underlie xenobiotic-related gene regulation remain elusive in plants, in contrast with mammalian cells and yeast where xenobiotic sensors have been characterized. Moreover, even herbicide metabolites that are considered to be inactive cause major metabolomic and molecular modifications under conditions of no observable adverse effects (Serra et al, , 2015a(Serra et al, , 2015b and non-herbicidal synthetic compounds used as herbicide safeners in some monocotyledonous crops (Riechers et al, 2010) provide protection through induction of plant defence and detoxification gene expression (Ramel et al, 2012;Riechers et al, 2010). On the other hand, field studies and empirical evidence have shown that environmental physicochemical factors (cold, heat, drought) and growth and development parameters significantly influence plant sensitivity to herbicide treatment (Klingaman et al, 1992;Vila-Aiub et al, 2013), thus emphasising potential involvement of complex physiological mechanisms in the outcomes of herbicide treatments.…”

“…Herbicide treatments modify metabolic networks that include generegulating metabolic signals (Ramel et al, 2007(Ramel et al, , 2009aSerra et al, , 2015aSerra et al, , 2015bVivancos et al, 2011), such as sucrose, glucose, trehalose, serine, or leucine, which are major effectors of the sensing mechanisms that integrate metabolism, stress and development (Emanuelle et al, 2015;Tomé et al, 2014). Some of these effectors interact with master regulators of metabolism, such as the SNF1 (sucrose non-fermenting 1)-related kinase 1 (SnRK1) (Baena-González et al, 2007;Emanuelle et al, 2015;Tomé et al, 2014) and the target-ofrapamycin (TOR) kinase (Tomé et al, 2014;Xiong et al, 2013), which exert major controls on the regulation of genes involved in catabolic processes (proteolysis, amino acid catabolism, sugar degradation, lipid catabolism) that can compensate low carbohydrate and low energy situations.…”