Poplar stem transcriptome is massively remodelled in response to single or repeated mechanical stimuli

Pomiès et al. BMC Genomics (2017) 18:300 DOI 10.1186/s12864-017-3670-1 RESEARCH ARTICLE Open Access Poplar stem transcriptome is massively remodelled in response to single or repeated mechanical stimuli Lise Pomiès†, Mélanie Decourteix†, Jérôme Franchel, Bruno Moulia and Nathalie Leblanc-Fournier* Abstract Background: Trees experience mechanical stimuli -like wind- that trigger thigmomorphogenetic syndrome, leading to modifications of plant growth and wood quality. This syndrome affects tree productivity but is also believed to improve tree acclimation to chronic wind. Wind is particularly challenging for trees, because of their stature and perenniality. Climate change forecasts are predicting that the occurrence of high wind will worsen, making it increasingly vital to understand the mechanisms regulating thigmomorphogenesis, especially in perennial plants. By extension, this also implies factoring in the recurring nature of wind episodes. However, data on the molecular processes underpinning mechanoperception and transduction of mechanical signals, and their dynamics, are still dramatically lacking in trees. Results: Here we performed a genome-wide and time-series analysis of poplar transcriptional responsiveness to transitory and recurring controlled stem bending, mimicking wind. The study revealed that 6% of the poplar genome is differentially expressed after a single transient bending. The combination of clustering, Gene Ontology categorization and time-series expression approaches revealed the diversity of gene expression patterns and biological processes affected by stem bending. Short-term transcriptomic responses entailed a rapid stimulation of plant defence and abiotic stress signalling pathways, including ethylene and jasmonic acid signalling but also photosynthesis process regulation. Late transcriptomic responses affected genes involved in cell wall organization and/or wood development. An analysis of the molecular impact of recurring bending found that the vast majority (96%) of the genes differentially expressed after a first bending presented reduced or even net-zero amplitude regulation after the second exposure to bending. Conclusion: This study constitutes the first dynamic characterization of the molecular processes affected by single or repeated stem bending in poplar. Moreover, the global attenuation of the transcriptional responses, observed from as early as after a second bending, indicates the existence of a mechanism governing a fine tuning of plant responsiveness. This points toward several mechanistic pathways that can now be targeted to elucidate the complex dynamics of wind acclimation. Keywords: Mechanotransduction, Time series, Acclimation, Accommodation, microarray, Thigmomorphogenesis, Abiotic stress, Mechanical stimuli * Correspondence: † Equal contributors Université Clermont Auvergne, INRA, PIAF, F-63000 Clermont-Ferrand, France © The Author(s). 2017 Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. Pomiès et al. BMC Genomics (2017) 18:300 Background In their fluctuating environment, plants are constantly exposed to abiotic stimuli to which they are sensitive and responsive. Some of these stimuli, such as wind exposure, count a strong mechanical component that has a major influence on plant growth and development. Exposure to such mechanical stimulations results in the so-called thigmomorphogenetic syndrome characterized by a reduction in stem elongation [1, 2], local stimulation of radial growth [3, 4], and modification of the stem’s mechanical properties [5]. These alterations of plant architecture are thought to improve plant acclimation to chronic wind regimes [6]. Using continuous monitoring techniques [4, 7], the early kinetics of these plant growth responses were studied in tomato and poplar by applying quantified stem bending. In poplar, a single transitory stem bending led first to a short period of secondary growth inhibition (4 h) followed by a massive stimulation of the growth rate over 3 days, and finally a relaxation to normal values [4]. To better understand tree acclimation to wind, it is important to first unravel the processes that regulate thigmomorphogenetic syndrome. However, the way plant cells perceive and transduce mechanical signals is still poorly understood. Two major classes of potential mechanosensors are thought to be involved: plant MechanoSensitive (MS) ion channels and Receptor-Like Kinases (RLK) inserted into the cell wall–plasma membrane–cytoskeleton continuum (see [8] for review). Prior to the advent of transcriptomics, studies had identified a handful of mechanoresponsive genes, including TOUCH genes (TCH) that mainly encode calmodulins or calmodulinlike proteins and Xyloglucan endo-Transglycosylase/ Hydrolase (XTH) [9], genes encoding protein kinases [10, 11], Transcription Factors (TF) [12], genes involved in Jasmonic Acid (JA) and ethylene synthesis [13, 14], and genes involved in antioxidative responses [15]. In 2005, a transcriptome analysis of touch-stimulated Arabidopsis rosette leaves allowed a more global insight into the molecular functions altered after a touch-stimulus. Over 700 genes presented regulated expression 30 min after the stimulus [16], representing over 2.5% of the genome. Among these genes, the vast majority (589/760) were up-regulated. Analysis of the functional categorization of these up-regulated genes revealed enrichment in genes encoding calcium-binding proteins, cell-wall proteins, disease resistance proteins, kinases and TF, and a decline in genes involved in general metabolism and the ubiquitin/protein degradation pathway. For the down-regulated genes, the “transcription factor” and “cell-wall-associated protein” categories were over-represented. In a subsequent transcriptomic study of the effect of a long-term exposure (8 weeks) to low-speed wind in Populus nigra leaves, Fluch et al. found at least 98 up- and 94 down-regulated genes [17], including genes encoding cell-wall modification Page 2 of 16 proteins, proteins with regulatory roles (e.g. kinases, calmodulin, etc.), Reactive Oxygen Species (ROS) producing or scavenging proteins, or constituents of microtubules. Unfortunately, these two transcriptomic studies concern a unique time-point after stimulation, giving a very static view of the molecular response to mechanical stimulus. In 2004, Kimbrough et al. found 1,691 mechanoresponsive genes on root apices that were trans (...truncated)