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iTRAQ-Based Quantitative Proteomics Analysis Reveals the Mechanism of Golden-Yellow Leaf Mutant in Hybrid Paper Mulberry
No full textPlant growth and development relies on the conversion of light energy into chemical energy, which takes place in the leaves. Chlorophyll mutant variations are important for studying certain physiological processes, including chlorophyll metabolism, chloroplast biogenesis, and photosynthesis. To uncover the mechanisms of the golden-yellow phenotype of the hybrid paper mulberry plant, this study used physiological, cytological, and iTRAQ-based proteomic analyses to compare the green and golden-yellow leaves of hybrid paper mulberry. Physiological results showed that the mutants of hybrid paper mulberry showed golden-yellow leaves, reduced chlorophyll, and carotenoid content, and increased flavonoid content compared with wild-type plants. Cytological observations revealed defective chloroplasts in the mesophyll cells of the mutants. Results demonstrated that 4766 proteins were identified from the hybrid paper mulberry leaves, of which 168 proteins displayed differential accumulations between the green and mutant leaves. The differentially accumulated proteins were primarily involved in chlorophyll synthesis, carotenoid metabolism, and photosynthesis. In addition, differentially accumulated proteins are associated with ribosome pathways and could enable plants to adapt to environmental conditions by regulating the proteome to reduce the impact of chlorophyll reduction on growth and survival. Altogether, this study provides a better understanding of the formation mechanism of the golden-yellow leaf phenotype by combining proteomic approaches
An Efficient and Universal Protoplast Isolation Protocol Suitable for Transient Gene Expression Analysis and Single-Cell RNA Sequencing
No full textThe recent advent of single-cell RNA sequencing (scRNA-seq) has enabled access to the developmental landscape of a complex organ by monitoring the differentiation trajectory of every specialized cell type at the single-cell level. A main challenge in this endeavor is dissociating plant cells from the rigid cell walls and some species are recalcitrant to such cellular isolation. Here, we describe the establishment of a simple and efficient protocol for protoplast preparation in Chirita pumila, which includes two consecutive digestion processes with different enzymatic buffers. Using this protocol, we generated viable cell suspensions suitable for an array of expression analyses, including scRNA-seq. The universal application of this protocol was further tested by successfully isolating high-quality protoplasts from multiple organs (petals, fruits, tuberous roots, and gynophores) from representative species on the key branches of the angiosperm lineage. This work provides a robust method in plant science, overcoming barriers to isolating protoplasts in diverse plant species and opens a new avenue to study cell type specification, tissue function, and organ diversification in plants
The CDC48 complex mediates ubiquitin-dependent degradation of intra-chloroplast proteins in plants
No full textChloroplasts are the site of numerous biochemical reactions including photosynthesis, but they also produce reactive oxygen species (ROS) that negatively affect chloroplast integrity. The chaperone-like CDC48 com-plex plays critical roles in ubiquitin-dependent protein degradation in yeast and mammals, but its function in plants is largely unknown. Here, we show that defects in CDC48A and its cofactors UFD1 and NPL4 lead to the accumulation of ubiquitinated chloroplast proteins in Arabidopsis thaliana. We reveal that two plastid genome-encoded proteins, RbcL and AtpB, associate with the CDC48 complex. Strikingly, RbcL and AtpB are ubiquitinated and degraded by the 26S proteasome pathway upon ROS stress, and these processes are impaired by defects of the CDC48 complex. Functional analysis demonstrates that the CDC48 complex is required for plant tolerance to ROS. This study reveals a role for the plant CDC48 complex in modulating ubiquitin-dependent degradation of intra-chloroplast proteins in response to oxidative stress
Asymmetric structure of the native Rhodobacter sphaeroides dimeric LH1-RC complex
No full textRhodobacter sphaeroides is a model organism for studying bacterial photosynthesis. Here, the authors present structures of its native dimeric and a protein-U-lacking monomeric light-harvesting-reaction center complexes, which reveal asymmetric features for the dimer and an altered shape for the monomer. Rhodobacter sphaeroides is a model organism in bacterial photosynthesis, and its light-harvesting-reaction center (LH1-RC) complex contains both dimeric and monomeric forms. Here we present cryo-EM structures of the native LH1-RC dimer and an LH1-RC monomer lacking protein-U (Delta U). The native dimer reveals several asymmetric features including the arrangement of its two monomeric components, the structural integrity of protein-U, the overall organization of LH1, and rigidities of the proteins and pigments. PufX plays a critical role in connecting the two monomers in a dimer, with one PufX interacting at its N-terminus with another PufX and an LH1 beta-polypeptide in the other monomer. One protein-U was only partially resolved in the dimeric structure, signaling different degrees of disorder in the two monomers. The Delta U LH1-RC monomer was half-moon-shaped and contained 11 alpha- and 10 beta-polypeptides, indicating a critical role for protein-U in controlling the number of alpha beta-subunits required for dimer assembly and stabilization. These features are discussed in relation to membrane topology and an assembly model proposed for the native dimeric complex
Adaptiveness of RGB-image derived algorithms in the measurement of fractional vegetation coverage
No full textBackground: Fractional vegetation coverage (FVC) is a crucial parameter in determining vegetation structure. Automatic measurement of FVC using digital images captured by mobile smart devices is a potential direction for future research on field survey methods in plant ecology, and this algorithm is crucial for accurate FVC measurement. However, there is a lack of insight into the influence of illumination on the accuracy of FVC measurements. Therefore, the main objective of this research is to assess the adaptiveness and performance of different algorithms under varying light conditions for FVC measurements and to deepen our understanding of the influence of illumination on FVC measurement. Methods and results: Based on a literature survey, we selected four algorithms that have been reported to have high accuracy in automatic FVC measurements. The first algorithm (Fun01) identifies green plants based on the combination of R/G, B/G, and ExG (R, G, and B are the actual pixel digital numbers from the images based on each RGB channel, ExG is the abbreviation of the Excess Green index), the second algorithm (Fun02) is a decision tree that uses color properties to discriminate plants from the background, the third algorithm (Fun03) uses ExG - ExR (ExR is the abbreviation of the Excess Red index) to recognize plants in the image, and the fourth algorithm (Fun04) uses ExG and Otsu to separate the plants from the background. Otsu is an algorithm used to determine a threshold to transform the image into a binary image for the vegetation and background. We measured the FVC of several surveyed quadrats using these four algorithms under three scenarios, namely overcast sky, solar forenoon, and solar noon. FVC values obtained using the Photoshop-assisted manual identification method were used as a reference to assess the accuracy of the four algorithms selected. Results indicate that under the overcast sky scenario, Fun01 was more accurate than the other algorithms and the MAPE (mean absolute percentage error), BIAS, relBIAS (relative BIAS), RMSE (root mean square error), and relRMSE (relative RMSE) are 8.68%, 1.3, 3.97, 3.13, and 12.33%, respectively. Under the scenario of the solar forenoon, Fun02 (decision tree) was more accurate than other algorithms, and the MAPE, BIAS, relBIAS, RMSE, and relRMSE are 22.70%, - 2.86, - 7.70, 5.00, and 41.23%. Under the solar noon scenario, Fun02 was also more accurate than the other algorithms, and the MAPE, BIAS, relBIAS, RMSE, and relRMSE are 20.60%, - 6.39, - 20.67, 7.30, and 24.49%, respectively. Conclusions: Given that each algorithm has its own optimal application scenario, among the four algorithms selected, Fun01 (the combination of R/G, B/G, and ExG) can be recommended for measuring FVC on cloudy days. Fun02 (decision tree) is more suitable for measuring the FVC on sunny days. However, it considerably underestimates the FVC in most cases. We expect the findings of this study to serve as a useful reference for automatic vegetation cover measurements
The global carbon sink potential of terrestrial vegetation can be increased substantially by optimal land management
No full textExcessive emissions of greenhouse gases - of which carbon dioxide is the most significant component, are regarded as the primary reason for increased concentration of atmospheric carbon dioxide and global warming. Terrestrial vegetation sequesters 112-169 PgC (1PgC = 10(15)g carbon) each year, which plays a vital role in global carbon recycling. Vegetation carbon sequestration varies under different land management practices. Here we propose an integrated method to assess how much more carbon can be sequestered by vegetation if optimal land management practices get implemented. The proposed method combines remotely sensed time-series of net primary productivity datasets, segmented landscape-vegetation-soil zones, and distance-constrained zonal analysis. We find that the global land vegetation can sequester an extra of 13.74 PgC per year if location-specific optimal land management practices are taken and half of the extra clusters in similar to 15% of vegetated areas. The finding suggests optimizing land management is a promising way to mitigate climate changes
Effects of Straw Mulching Thickness on the Soil Health in a Temperate Organic Vineyard
No full textSoil mulching is one of the common measures applied in organic agricultural production which could replace plastic films and protect the environment. In order to fully evaluate the effects of different straw mulching thicknesses on soil health, maize straw was mulched with the thicknesses of 0 cm (CK), 2 cm, 4 cm and 6 cm on soil surface to assess the effects on soil temperature (ST) and moisture (SM), soil pH, soil organic carbon (SOC), total nitrogen (TN), C/N, soil aggregates and soil bulk density (SBD) in a temperate organic vineyard. We found that straw mulching had a significant regulating effect, with soil moisture being elevated with increasing mulching thickness by 5.8%, 9.0% and 11.1% compared with CK. The soil SOC content increased by 3.0%, 2.4% and 2.3%. Although soil pH and C/N significantly (p 2 mm soil particle size and elevated the mean weight diameter (MWD) and geometric mean diameter (GMD). The increasing mulching thickness prolonged the effect on the stability of soil aggregates. The 4 cm maize straw mulching thickness has the best effect for ecologically and environmentally managing warm-temperate organic vineyards so it may have a great application prospect on a global scale
Phylogeny and evolution of Cupressaceae: Updates on intergeneric relationships and new insights on ancient intergeneric hybridization
No full textAfter the merger of the former Taxodiaceae and Cupressaceae s.s., currently the conifer family Cupressaceae (sensu lato) comprises seven subfamilies and 32 genera, most of which are important components of temperate and mountainous forests. With the exception of a recently published genus-level phylogeny of gymnosperms inferred from sequence analysis of 790 orthologs, previous phylogenetic studies of Cupressaceae were based mainly on morphological characters or a few molecular markers, and did not completely resolve the intergeneric relationships. In this study, we reconstructed a robust and well-resolved phylogeny of Cupressaceae represented by all 32 genera, using 1944 genes (Orthogroups) generated from transcriptome sequencing. Reticulate evolution analyses detected a possible ancient hybridization that occurred between ancestors of two subclades of Cupressoideae, including Microbiota-Platycladus-Tetraclinis (MPT) and Juniperus-Cupressus-Hesperocyparis-Calli-tropsis-Xanthocyparis (JCHCX), although both concatenation and coalescent trees are highly supported. Moreover, divergence time estimation and ancestral area reconstruction indicate that Cupressaceae very likely originated in Asia in the Triassic, and geographic isolation caused by continental separation drove the vicariant evolution of the two subfamilies Cupressoideae and Callitroideae in the northern and southern hemispheres, respectively. Evolutionary analyses of some morphological characters suggest that helically arranged linear-acicular leaves and imbricate bract-scale complexes represent ancestral states, and the shift from linear-acicular leaves to scale -like leaves was associated with the shift from helical to decussate arrangement. Our study sheds new light on phylogeny and evolutionary history of Cupressaceae, and strongly suggests that both dichotomous phylogenetic and reticulate evolution analyses be conducted in phylogenomic studies
China's terrestrial ecosystem carbon balance during the 20th century: an analysis with a process-based biogeochemistry model
No full textBackground China's terrestrial ecosystems play a pronounced role in the global carbon cycle. Here we combine spatially-explicit information on vegetation, soil, topography, climate and land use change with a process-based biogeochemistry model to quantify the responses of terrestrial carbon cycle in China during the 20th century. Results At a century scale, China's terrestrial ecosystems have acted as a carbon sink averaging at 96 Tg C yr(- 1), with large inter-annual and decadal variabilities. The regional sink has been enhanced due to the rising temperature and CO2 concentration, with a slight increase trend in carbon sink strength along with the enhanced net primary production in the century. The areas characterized by C source are simulated to extend in the west and north of the Hu Huanyong line, while the eastern and southern regions increase their area and intensity of C sink, particularly in the late 20th century. Forest ecosystems dominate the C sink in China and are responsible for about 64% of the total sink. On the century scale, the increase in carbon sinks in China's terrestrial ecosystems is mainly contributed by rising CO2. Afforestation and reforestation promote an increase in terrestrial carbon uptake in China from 1950s. Although climate change has generally contributed to the increase of carbon sinks in terrestrial ecosystems in China, the positive effect of climate change has been diminishing in the last decades of the 20th century. Conclusion This study focuses on the impacts of climate, CO2 and land use change on the carbon cycle, and presents the potential trends of terrestrial ecosystem carbon balance in China at a century scale. While a slight increase in carbon sink strength benefits from the enhanced vegetation carbon uptake in China's terrestrial ecosystems during the 20th century, the increase trend may diminish or even change to a decrease trend under future climate change
Pectin Characteristics Affect Root Growth in Spinach under Salinity
No full textIn understanding the role of root cell wall mechanisms in plant tolerance to salinity, it is important to elucidate the changes in the pectin composition and physical properties of the cell wall. Two salt-sensitive (Helan 3 and Prius beta) and one salt-tolerant (R7) spinach cultivars were used to investigate the pectin polysaccharides, the characteristics of pectin, including the degree of pectin methy-lesterification, the HG:RG-I ratio, neutral side chains (galactan/arabinangalactan), and elasticity and viscosity parameters in the root elongation zone under salinity. Root growth was inhibited by salinity, whereas the root diameter was thickened in all cultivars. Salinity significantly reduced cell wall extensibility in all cultivars, and increased cell wall viscosity in Helan 3 and R7 relative to Prius beta. Pectin was significantly increased under salinity stress. Cell wall viscosity was affected by pectin due to the molar proportion of uronic acid and/or pectin characteristics (HG:RG-I ratio). The molar proportion of uronic acid in pectin was reduced in Helan 3 and R7 compared with Prius beta. The length and degree of pectin methy-lesterification of neutral side chains were significantly decreased in the R7 cultivar, with no significant changes in the other two cultivars. Demethylation of pectin could alter root growth and boost salt tolerance in the R7 cultivar. In this study, it is shown that cell wall pectin played important roles in regulating the root growth of Spinacia oleracea L. under salinity stress