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), 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.

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.

Comparative Shotgun Proteomic Analysis of Wastewater-Cultured Microalgae: Nitrogen Sensing and Carbon Fixation for Growth and Nutrient Removal in Chlamydomonas reinhardtii.

Chlamydomonas reinhardtii was batch-cultured for 12 days under continuous illumination to investigate nitrogen uptake and metabolic responses to wastewater processing. Our approach compared two conditions: (1) artificial wastewater containing nitrate and ammonia and (2) nutrient-sufficient control containing nitrate as sole form of nitrogen. Treatments did not differ in final biomass; however, comparison of group proteomes revealed significant differences. Label-free shotgun proteomic analysis identified 2358 proteins, of which 92 were significantly differentially abundant. Wastewater cells showed higher relative abundances of photosynthetic antenna proteins, enzymes related to carbon fixation, and biosynthesis of amino acids and secondary metabolites. Control cells showed higher abundances of enzymes and proteins related to nitrogen metabolism and assimilation, synthesis and utilization of starch, amino acid recycling, evidence of oxidative stress, and little lipid biosynthesis. This study of the eukaryotic microalgal proteome response to nitrogen source, availability, and switching highlights tightly controlled pathways essential to the maintenance of culture health and productivity in concert with light absorption and carbon assimilation. Enriched pathways in artificial wastewater, notably, photosynthetic carbon fixation and biosynthesis of plant hormones, and those in nitrate only control, most notably, nitrogen, amino acid, and starch metabolism, represent potential targets for genetic improvement requiring targeted elucidation.

The temporal analysis of yeast exponential phase using shotgun proteomics as a fermentation monitoring technique.

System biology and bioprocess technology can be better understood using shotgun proteomics as a monitoring system during the fermentation. We demonstrated a shotgun proteomic method to monitor the temporal yeast proteome in early, middle and late exponential phases. Our study identified a total of 1389 proteins combining all 2D-LC-MS/MS runs. The temporal Saccharomyces cerevisiae proteome was enriched with proteolysis, radical detoxification, translation, one-carbon metabolism, glycolysis and TCA cycle. Heat shock proteins and proteins associated with oxidative stress response were found throughout the exponential phase. The most abundant proteins observed were translation elongation factors, ribosomal proteins, chaperones and glycolytic enzymes. The high abundance of the H-protein of the glycine decarboxylase complex (Gcv3p) indicated the availability of glycine in the environment. We observed differentially expressed proteins and the induced proteins at mid-exponential phase were involved in ribosome biogenesis, mitochondria DNA binding/replication and transcriptional activator. Induction of tryptophan synthase (Trp5p) indicated the abundance of tryptophan during the fermentation. As fermentation progressed toward late exponential phase, a decrease in cell proliferation was implied from the repression of ribosomal proteins, transcription coactivators, methionine aminopeptidase and translation-associated proteins.

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.

Comparative shotgun proteomic analysis of Clostridium acetobutylicum from butanol fermentation using glucose and xylose.

BACKGROUND: Butanol is a second generation biofuel produced by Clostridium acetobutylicum through acetone-butanol-ethanol (ABE) fermentation process. Shotgun proteomics provides a direct approach to study the whole proteome of an organism in depth. This paper focuses on shotgun proteomic profiling of C. acetobutylicum from ABE fermentation using glucose and xylose to understand the functional mechanisms of C. acetobutylicum proteins involved in butanol production. RESULTS: We identified 894 different proteins in C. acetobutylicum from ABE fermentation process by two dimensional - liquid chromatography - tandem mass spectrometry (2D-LC-MS/MS) method. This includes 717 proteins from glucose and 826 proteins from the xylose substrate. A total of 649 proteins were found to be common and 22 significantly differentially expressed proteins were identified between glucose and xylose substrates. CONCLUSION: Our results demonstrate that flagellar proteins are highly up-regulated with glucose compared to xylose substrate during ABE fermentation. Chemotactic activity was also found to be lost with the xylose substrate due to the absence of CheW and CheV proteins. This is the first report on the shotgun proteomic analysis of C. acetobutylicum ATCC 824 in ABE fermentation between glucose and xylose substrate from a single time data point and the number of proteins identified here is more than any other study performed on this organism up to this report.

Shotgun metaproteomics of the human distal gut microbiota.

The human gut contains a dense, complex and diverse microbial community, comprising the gut microbiome. Metagenomics has recently revealed the composition of genes in the gut microbiome, but provides no direct information about which genes are expressed or functioning. Therefore, our goal was to develop a novel approach to directly identify microbial proteins in fecal samples to gain information about the genes expressed and about key microbial functions in the human gut. We used a non-targeted, shotgun mass spectrometry-based whole community proteomics, or metaproteomics, approach for the first deep proteome measurements of thousands of proteins in human fecal samples, thus demonstrating this approach on the most complex sample type to date. The resulting metaproteomes had a skewed distribution relative to the metagenome, with more proteins for translation, energy production and carbohydrate metabolism when compared to what was earlier predicted from metagenomics. Human proteins, including antimicrobial peptides, were also identified, providing a non-targeted glimpse of the host response to the microbiota. Several unknown proteins represented previously undescribed microbial pathways or host immune responses, revealing a novel complex interplay between the human host and its associated microbes.

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.