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

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), or 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 labeling 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. These multi-wavelengths lights function in a complex signaling network, which provide major challenges in inference of wavelength-specific molecular processes that underly the plant response. Besides, 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 compare the changes to one another, rather than comparing plants proteome to FL, is thus necessary to gain the clear insights to specific underlying biological pathways and their effect consequences in plant response. Here, we employed narrow wavelength LED lights in our design to eliminate the 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 associates of proteome changes. Our proteomics data provides an in-depth coverage suitable for system-wide analyses, providing deep insights on plant physiological processes particularly because of the tremendous increase in the amount of identified proteins which outreach the other biological data.

Re-interpreting the photosynthetically action radiation (PAR) curve in plants

The basis of a plant's spectral response of photosynthesis, or the photosynthetically active radiation (PAR) curve, is derived from earlier studies nearly five decades ago. These studies reported that blue and red light were the primary wavelengths; however, shifting within red and blue peaks (10-40 nm) in addition to different PAR curve shapes was observed. In recent years, the McCree curve, which is considered the standard for spectral response of photosynthesis, has been challenged because of experimental design and differences between photosynthetic and whole-plant growth responses. Therefore, this overview provides an amalgamation of all the PAR curve studies, with a focus on narrow spectrum light characteristics, including light measurement units, full width at half maximums (FWHMs) of narrow light spectra, and light intensity levels. While replicating these pioneering works with higher wavelength resolution and narrower light spectrum across the whole visible spectrum is still challenging, we hope that this re-interpretation of PAR curves in plants can elucidate and provide in-depth insight into spectral responses of photosynthesis. We leave the readers with some different perspectives and prospects that need to be considered for future studies.

Photobiology eye safety for horticultural LED lighting: Transmittance performance of eyewear protection using high-irradiant monochromatic LEDs

Light emitting diodes have slowly gained market share as horticultural lighting systems in greenhouses due to their rapid improvement in color performances and light outputs. These advancements have increased the availability of the full spectrum of visible wavelengths and the corresponding irradiance outputs available to plants. However, light emitting diodes owners have limited information on the proper options for personal eyewear protection as the irradiance levels have increased. The objective of this study was to measure the light transmittance performance of 12 eyewear protection including welding goggles, safety goggles, polarized glasses, and sunglasses across the human visible spectrum (380-740 nm) up to an irradiance level of 1500 W·m^-2 from high-irradiant light emitting diodes assemblies. Based on the spectral measurements, certain transmitted spectra exhibited spectrum shifts or an alteration in the bimodal distribution which were different than the light emitting diodes spectra, due to the uneven transmittance efficiencies of the glasses. As for the measured transmittance percentages in two experiments, each type of eyewear protection showed distinct transmittance performances, and the performance of the tested eyewear protection was not impacted by irradiance but was dependent on the wavelength. The mean light transmittance was 1.77% for the welding glasses, 13.12% for the polarized glasses, 15.27% for the safety goggles, and 27.65% for the sunglasses. According to these measured results and the spectral weighting exposure limits from the International Electrotechnical Commission 62471 and EU directive 2006/25, consumers and workers using horticultural lighting can select welding goggles or polarized glasses, to limit the possible ocular impact of the high irradiance of monochromatic light in electrical lighting environment. Sunglasses and safety goggles would not be advised as protection, especially if infrared radiation was used.

Guidelines for measuring and reporting environmental parameters for experiments in greenhouses

BACKGROUND

The importance of appropriate, accurate measurement and reporting of environmental parameters in plant sciences is a significant aspect of quality assurance for all researchers and their research. There is a clear need for ensuring research across the world can be compared, understood and where necessary replicated by fellow researchers. A common set of guidelines to educate, assist and encourage comparativeness is of great importance. On the other hand, the level of effort and attention to detail by an individual researcher should be commensurate with the particular research being conducted. For example, a researcher focusing on interactions of light and temperature should measure all relevant parameters and report a measurement summary that includes sufficient detail allowing for replication. Such detail may be less relevant when the impact of environmental parameters on plant growth and development is not the main research focus. However, it should be noted that the environmental experience of a plant during production can have significant impact when subsequent experiments investigate plants at a molecular, biochemical or genetic level or where species interactions are considered. Thus, researchers are encouraged to make a critical assessment of what parameters are of primary importance in their research and these parameters should be measured and reported.

CONTENT

This paper brings together a collection of parameters that the authors, as members of International Committee on Controlled Environment Guidelines (ICCEG) in consultation with members of our three parent organizations, believe constitute those which should be recorded and reported when publishing scientific data from experiments in greenhouses. It provides recommendations to end users on when, how and where these parameters should be measured along with the appropriate internationally standardized units that should be used.

Temporal analysis of xylose fermentation by Scheffersomyces stipitis using shotgun proteomics

Proteomics and fermentation technology have begun to integrate to investigate fermentation organisms in bioprocess development. This is the first shotgun proteomics study employed to monitor the proteomes of Scheffersomyces stipitis during xylose fermentation under oxygen limitation. We identified 958 nonredundant proteins and observed highly similar proteomes from exponential to early stationary phases. In analyzing the temporal proteome, we identified unique expression patterns in biological processes and metabolic pathways, including alternative respiration salicylhydroxamic acid (SHAM) pathway, activation of glyoxylate cycle, expression of galactose enzymes, and secondary zinc-containing alcohol dehydrogenase and O-glycosyl hydrolases. We identified the expression of a putative, high-affinity xylose sugar transporter Xut1p, but low-affinity xylose transporters were absent. Throughout cell growth, housekeeping processes included oxidative phosphorylation, glycolysis, nonoxidative branch of the pentose phosphate pathway, gluconeogenesis, biosynthesis of amino acids and aminoacyl total RNA (tRNA), protein synthesis and proteolysis, fatty acid metabolism, and cell division. This study emphasized qualitative analysis and demonstrated that shotgun proteomics is capable of monitoring S. stipitis fermentation and identifying physiological states, such as nutrient deficiency.

Shotgun proteomic monitoring of Clostridium acetobutylicum during stationary phase of butanol fermentation using xylose and comparison with the exponential phase

Economically viable production of solvents through acetone–butanol–ethanol (ABE) fermentation requires a detailed understanding of Clostridium acetobutylicum. This study focuses on the proteomic profiling of C. acetobutylicum ATCC 824 from the stationary phase of ABE fermentation using xylose and compares with the exponential growth by shotgun proteomics approach. Comparative proteomic analysis revealed 22.9% of the C. acetobutylicum genome and 18.6% was found to be common in both exponential and stationary phases. The proteomic profile of C. acetobutylicum changed during the ABE fermentation such that 17 proteins were significantly differentially expressed between the two phases. Specifically, the expression of five proteins namely, CAC2873, CAP0164, CAP0165, CAC3298, and CAC1742 involved in the solvent production pathway were found to be significantly lower in the stationary phase compared to the exponential growth. Similarly, the expression of fucose isomerase (CAC2610), xylulose kinase (CAC2612), and a putative uncharacterized protein (CAC2611) involved in the xylose utilization pathway were also significantly lower in the stationary phase. These findings provide an insight into the metabolic behavior of C. acetobutylicum between different phases of ABE fermentation using xylose.

Community proteogenomics highlights microbial strain-variant protein expression within activated sludge performing enhanced biological phosphorus removal

Enhanced biological phosphorus removal (EBPR) selects for polyphosphate accumulating microorganisms to achieve phosphate removal from wastewater. We used high-resolution community proteomics to identify key metabolic pathways in 'Candidatus Accumulibacter phosphatis' (A. phosphatis)-mediated EBPR and to evaluate the contributions of co-existing strains within the dominant population. Overall, 702 proteins from the A. phosphatis population were identified. Results highlight the importance of denitrification, fatty acid cycling and the glyoxylate bypass in EBPR. Strong similarity in protein profiles under anaerobic and aerobic conditions was uncovered (only 3% of A. phosphatis-associated proteins exhibited statistically significant abundance differences). By comprehensive genome-wide alignment of 13,930 orthologous proteins, we uncovered substantial differences in protein abundance for enzyme variants involved in both core-metabolism and EBPR-specific pathways among the A. phosphatis population. These findings suggest an essential role for genetic diversity in maintaining the stable performance of EBPR systems and, hence, demonstrate the power of integrated cultivation-independent genomics and proteomics for the analysis of complex biotechnological systems.

Spinach cultigen variation for tissue carotenoid concentrations influences human serum carotenoid levels and macular pigment optical density following a 12-week dietary intervention

Increasing intakes of carotenoid-rich plant foods can increase serum carotenoid concentrations and macular pigment optical density (MPOD) in most, but not all, individuals. Research objectives for this study were to (1) characterize tissue lutein (L) and beta-carotene (BC) concentrations in carotenoid-rich spinach (Spinacia oleracea L.) cultigens and (2) determine serum carotenoid and MPOD responses in human subjects consuming spinach cultigens differing in tissue L and BC concentrations. Thirteen spinach cultigens were evaluated for carotenoid accumulations over two consecutive growing seasons. "Springer" (8.4 and 6.5 mg/100 g of fresh mass for L and BC, respectively) and "Spinner" (12.1 and 9.2 mg/100 g of fresh mass for L and BC, respectively) spinach cultigens were selected for a dietary intervention study and represented low- and high-L concentrations. The high-L ("Spinner") and low-L ("Springer" ) spinach treatment groups consisted of 10 subject volunteers ingesting five 50-g spinach servings/week during a 12-week intervention. Average serum L concentrations increased by 22% (P = 0.07) from baseline (0.233 micromol/L) to 12 weeks (0.297 micromol/L) for subjects consuming low-L spinach. Subjects consuming high-L spinach showed increases of 33% (P = 0.04) in serum L from baseline (0.202 micromol/L) to 12 weeks (0.300 micromol/L). Average MPOD did not change for the low-L treatment group; however, subjects in the high-L group demonstrated increases (P = 0.02) in MPOD at the 30' eccentricity between baseline (0.343) and 12 weeks (0.374). This study demonstrates that serum carotenoid and MPOD are determined by L concentrations present in the spinach matrix. Results emphasize the role of cultigen selection among vegetable crops in determining phytochemical effects on human health.

Kale carotenoids are unaffected by, whereas biomass production, elemental concentrations, and selenium accumulation respond to, changes in selenium fertility

Selenium (Se) is a micronutrient in mammalian nutrition and is accumulated in kale (Brassica oleracea L. var. acephala), which has high levels of lutein and beta-carotene. Selenium, lutein, and beta-carotene have important human health benefits and possess strong antioxidant properties. The objectives of this study were to determine the influence of different Se [as sodium selenate (Na(2)SeO(4)) and sodium selenite (Na(2)SeO(3))] fertility levels on (1) biomass accumulation, (2) the accumulation patterns of carotenoid pigments, and (3) elemental accumulation in the leaves of kale. Winterbor kale was greenhouse-grown using nutrient solution culture with Se treatment concentrations of 0.0, 0.5, 1.0, 1.5, 2.0, 2.5, 3.0, and 3.5 mg Se/L as Na(2)SeO(4) and 0.0, 0.5, 1.0, 1.5, 2.0, 2.5, and 3.0 mg Se/L as Na(2)SeO(3). Increases in either selenate (SeO(4)(-)(2)) or selenite (SeO(3)(-)(2)) resulted in decreases in kale leaf tissue biomass. Neither of the Se treatments had an effect on the accumulation of lutein or beta-carotene in leaf tissues. Increasing SeO(4)(-)(2) significantly increased the accumulation of kale leaf Se; however, leaf tissue Se did not significantly change over the SeO(3)(-)(2) treatments. Increases in SeO(4)(-)(2) affected the leaf tissue concentrations of P, K, Ca, Mg, S, B, Cu, Mn, and Mo, whereas SeO(3)(-)(2) only affected B and S. Growing kale in the presence of SeO(4)(-)(2) would result in the accumulation of high levels of tissue Se without affecting carotenoid concentrations.