Comparative proteomics analysis of Arabidopsis thaliana response to light-emitting diode of narrow wavelength 450 nm, 595 nm, and 650 nm

Abstract

Incident light is a central modulator of plant growth and development. However, there are still open questions surrounding wavelength-specific plant proteomic responses. Here we applied tandem mass tag based quantitative proteomics technology to acquire an in-depth view of proteome changes in Arabidopsis thaliana response to narrow wavelength blue (B; 450 nm), amber (A; 595 nm), and red (R; 650 nm) light treatments. A total of 16,707 proteins were identified with 9120 proteins quantified across all three light treatments in three biological replicates. This enabled examination of changes in the abundance for proteins with low abundance and important regulatory roles including transcription factors and hormone signaling. Importantly, 18% (1631 proteins) of the A. thaliana proteome is differentially abundant in response to narrow wavelength lights, and changes in proteome correlate well with different morphologies exhibited by plants. To showcase the usefulness of this resource, data were placed in the context of more than thirty published datasets, providing orthogonal validation and further insights into light-specific biological pathways, including Systemic Acquired Resistance and Shade Avoidance Syndrome. This high-resolution resource for A. thaliana provides baseline data and a tool for defining molecular mechanisms that control fundamental aspects of plant response to changing light conditions, with implications in plant development and adaptation. SIGNIFICANCE: Understanding of molecular mechanisms involved in wavelength-specific response of plant is question of widespread interest both to basic researchers and to those interested in applying such knowledge to the engineering of novel proteins, as well as targeted lighting systems. Here we sought to generate a high-resolution proteomic profile of plant leaves, based on exposure to specific narrow-wavelength lights. Although changes in plant physiology in response to light spectral composition is well documented, there is limited knowledge on the roles of specific light wavelengths and their impact. Most previous studies have utilized relatively broad wavebands in their experiments. Such multi-wavelengths lights trigger diverse and complex signaling networks that pose major challenges in inference of wavelength-specific molecular processes that underly the plant response. Moreover, most studies have compared the effect of blue and red wavelengths comparing with FL, as control. As FL light consists the mixed spectra composition of both red and blue as well as numerous other wavelengths, comparing undeniably results in inconsistent and overlapping responses that will hamper effects to elucidate the plant response to specific wavelengths [1, 2]. Monitoring plant proteome response to specific wavelengths and further contrasting the changes with one another, rather than comparing plants proteome to FL, is thus necessary to gain detailed insights on underlying biological pathways and their consequences in plant physiology. Here, we employed narrow wavelength LED lights in our design to eliminate a potential overlap in molecular responses by ensuring non-overlapping wavelengths in the light treatments. We further applied TMT-labeling technology to gain a high-resolution view on the proteome changes. Our proteomics data provides an in-depth coverage suitable for system-wide analyses, providing deep insights on plant molecular response particularly because of the tremendous increase in the coverage of identified proteins which outreach the other biological data.

Keywords: A. thaliana; Development and Adaptation; Narrow Wavelength; Proteome Profiling; Shade-Avoidance; Systemic Acquired Resistance; TMT-labeling Technology.