Carbon Fixation In Photosynthetic Organisms Research Articles

Integrated metabolomics and proteomics analyses reveal the molecular mechanism underlying the yellow leaf phenotype of Camellia sinensis

The tea plant cultivar ‘Zhonghuang 2’ (ZH2) possesses albino-induced yellow leaves that contain low levels of catechins but high contents of amino acids. However, the molecular mechanism underlying the yellow leaf phenotype of ZH2 has not been elucidated clearly. In the current research, the yellow shoots (ZH2-Y) and naturally converted green shoots (ZH2-G) of ZH2 were studied using metabolic and proteomic profiling for a better understanding of the mechanism underlying phenotype formation. In total, 107 differentially changed metabolites (DCMs) were identified from the GC‒MS-based metabolomics, and 189 differentially accumulated proteins (DAPs) were identified from the tandem mass tag (TMT)-based quantitative proteomics. Subsequently, integrated analysis revealed that ‘porphyrin and chlorophyll metabolism’, ‘carbon fixation in photosynthetic organisms’, and ‘phenylpropanoid biosynthesis’ pathways were commonly enriched for DAPs and DCMs. We further found that the inhibition of chlorophyll biosynthesis, the deficiency of photosynthetic proteins and the imbalance of the ROS-scavenging system were the crucial reasons responsible for the chlorosis, chloroplast abnormality and photooxidative damage of ZH2 leaves. Altogether, our research combines metabolomics and proteomics approaches to uncover the molecular mechanism leading to the yellow leaf phenotype of tea plants.

Transcriptome analysis revealed changes in multiple genes in Larimichthys crocea under starvation stress

To identify important functional genes of the large yellow croaker (Larimichthys crocea) under starvation stress, the expression changes of genes in muscles tissue of fish fasted for 0, 4, 8, 12, 16, and 20 d were analyzed with RNA-seq technology. Sequencing results showed that a total of 507 million clean reads were generated. Totals of 662, 998, 1015, 1260, and 1122 of differentially expressed genes (DEGs) were obtained at 4, 8, 12, 16, and 20 d, respectively, using starvation 0 d as control. Gene ontology (GO) classification and analysis showed that DEGs could be classified into 42 categories of biological processes, cellular components, and molecular functions. Of these, DEGs are enriched in regulations such as metabolic process, cellular process and single-organism process. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis showed that DEGs involved a total of 22 pathways, eight of which were metabolic pathways. With fewer pathways enrichment entry in early starvation stages, but more pathways enrichment entry in late starvation stages (such as at 16 days of starvation), DEGs were significantly enriched in glycolysis/gluconeogenesis, biosynthesis of amino acids, carbon metabolism, fructose and mannose metabolism, methane metabolism and carbon fixation in photosynthetic organisms. After 20 days of starvation, DEGs began to be significantly enriched in the immune pathway, indicating that at this time, fish began to show an immunomodulatory response. This study systematically disclosed the changes of muscle tissue genes in large yellow croaker under starvation stress. The obtained results contribute to research on environmental stress in teleost fish.

Effects of Potassium-Containing Fertilizers on Sugar and Organic Acid Metabolism in Grape Fruits.

To identify suitable potassium fertilizers for grape (Vitis vinifera L.) production and study their mechanism of action, the effects of four potassium-containing fertilizers (complex fertilizer, potassium nitrate, potassium sulfate, and potassium dihydrogen phosphate) on sugar and organic acid metabolism in grape fruits were investigated. Potassium-containing fertilizers increased the activity of sugar and organic acid metabolism-related enzymes at all stages of grape fruit development. During the later stages of fruit development, potassium-containing fertilizers increased the total soluble solid content and the sugar content of the different sugar fractions and decreased the titratable acid content and organic acid content of the different organic acid fractions. At the ripening stage of grape fruit, compared with the control, complex fertilizer, potassium nitrate, potassium sulfate, and potassium dihydrogen phosphate increased the total soluble solid content by 1.5, 1.2, 3.5, and 3.4 percentage points, decreased the titratable acid content by 0.09, 0.06, 0.18, and 0.17 percentage points, respectively, and also increased the total potassium content in grape fruits to a certain degree. Transcriptome analysis of the differentially expressed genes (DEGs) in the berries showed that applying potassium-containing fertilizers enriched the genes in pathways involved in fruit quality, namely, carbon metabolism, carbon fixation in photosynthetic organisms, glycolysis and gluconeogenesis, and fructose and mannose metabolism. Potassium-containing fertilizers affected the expression levels of genes regulating sugar metabolism and potassium ion uptake and transport. Overall, potassium-containing fertilizers can promote sugar accumulation and reduce acid accumulation in grape fruits, and potassium sulfate and potassium dihydrogen phosphate had the best effects among the fertilizers tested.

Changes in Phytohormones and Transcriptomic Reprogramming in Strawberry Leaves under Different Light Qualities.

Strawberry plants require light for growth, but the frequent occurrence of low-light weather in winter can lead to a decrease in the photosynthetic rate (Pn) of strawberry plants. Light-emitting diode (LED) systems could be used to increase Pn. However, the changes in the phytohormones and transcriptomic reprogramming in strawberry leaves under different light qualities are still unclear. In this study, we treated strawberry plants with sunlight, sunlight covered with a 50% sunshade net, no light, blue light (460 nm), red light (660 nm), and a 50% red/50% blue LED light combination for 3 days and 7 days. Our results revealed that the light quality has an effect on the contents of Chl a and Chl b, the minimal fluorescence (F0), and the Pn of strawberry plants. The light quality also affected the contents of abscisic acid (ABA), auxin (IAA), trans-zeatin-riboside (tZ), jasmonic acid (JA), and salicylic acid (SA). RNA sequencing (RNA-seq) revealed that differentially expressed genes (DEGs) are significantly enriched in photosynthesis antenna proteins, photosynthesis, carbon fixation in photosynthetic organisms, porphyrin and chlorophyll metabolisms, carotenoid biosynthesis, tryptophan metabolism, phenylalanine metabolism, zeatin biosynthesis, and linolenic acid metabolism. We then selected the key DEGs based on the results of a weighted gene co-expression network analysis (WGCNA) and drew nine metabolic heatmaps and protein-protein interaction networks to map light regulation.

Distinct microbial communities under different rock-associated microhabitats in the Qaidam Desert

Hypolithic communities, which occupy highly specialised microhabitats beneath translucent rocks in desert and arid environments, have assembly mechanisms and ecosystem functions are not fully understood. Thus, in this study, we aimed to examine the microbial community structure, assembly, and function of light-accessible (under quartz, calcite, and hypolithic lichen-dominated biocrusts) and light-inaccessible microhabitats (under basalt and adjacent soil) in the Qaidam Desert, China. The results showed that hypolithic communities have different characteristics compared with microbial communities of light-inaccessible microhabitats. Notably, hypolithic bacterial communities were dominated by Cyanobacteria, whereas light-inaccessible microhabitats showed a predominance of Bacteroidetes and Proteobacteria. Although the class Dothideomycetes (phylum: Ascomycota) dominated the fungal communities between the two microhabitat types, Sordariomycetes were more prevalent in light-accessible microhabitats. Network and robustness analyses showed that hypolithic communities were less complex and more resilient than microbial communities in light-inaccessible microhabitats. Our results indicated that deterministic processes, specifically homogeneous selection, govern the establishment of bacterial and fungal communities in light-accessible and light-inaccessible microhabitats. The hypolithic community showed an increased frequency of phylotypes that exhibited increased tolerance to functional stress response pathways. In contrast to light-inaccessible microhabitats, light-accessible microhabitats showed a slight decrease and a notable increase in the prevalence of carbon fixation pathways in prokaryotes and carbon fixation in photosynthetic organisms, respectively. For fungi, light-accessible microhabitats enriched saprotrophic and ectomycorrhizal groups. These results highlight the importance of complex and diverse microhabitats in desert regions, which serve as vital shelters for microbes. Combining future research on interactions between hypolithic communities and environments may enhance our current understanding of their pivotal roles in sustaining desert ecosystems. This knowledge then be applied to design and implement informed conservation efforts to preserve these unique rock-associated microhabitats in desert ecosystems.

Comparison of the transcriptome and metabolome of wheat (Triticum aestivum L.) proteins content during grain formation provides insight.

Wheat is a food crop with a large global cultivation area, and the content and quality of wheat glutenin accumulation are important indicators of the quality of wheat flour. To elucidate the gene expression regulation and metabolic characteristics related to the gluten content during wheat grain formation, transcriptomic and metabolomic analyses were performed for the high gluten content of the Xinchun 26 cultivar and the low proteins content of the Xinchun 34 cultivar at three periods (7 d, 14 d and 21 d) after flowering. Transcriptomic analysis revealed that 5573 unique differentially expressed genes (DEGs) were divided into two categories according to their expression patterns during the three periods. The metabolites detected were mainly divided into 12 classes. Lipid and lipid-like molecule levels and phenylpropanoid and polyketide levels were the highest, and the difference analysis revealed a total of 10 differentially regulated metabolites (DRMs) over the three periods. Joint analysis revealed that the DEGs and DRMs were significantly enriched in starch and sucrose metabolism; the citrate cycle; carbon fixation in photosynthetic organisms; and alanine, aspartate and glutamate metabolism pathways. The genes and contents of the sucrose and gluten synthesis pathways were analysed, and the correlation between gluten content and its related genes was calculated. Based on weighted correlation network analysis (WGCNA), by constructing a coexpression network, a total of 5 specific modules and 8 candidate genes that were strongly correlated with the three developmental stages of wheat grain were identified. This study provides new insights into the role of glutenin content in wheat grain formation and reveals potential regulatory pathways and candidate genes involved in this developmental process.

Abiotic stress tolerance in pearl millet: Unraveling molecular mechanisms via transcriptomics.

Pearl millet (Pennisetum glaucum (L.)) is a vital cereal crop renowned for its ability to thrive in challenging environmental conditions; however, the molecular mechanisms governing its salt stress tolerance remain poorly understood. To address this gap, next-generation RNA sequencing was conducted to compare gene expression patterns in pearl millet seedlings exposed to salt stress with those grown under normal conditions. Our RNA sequencing analysis focused on shoots from 13-day-old pearl millet plants subjected to either salinity stress (150 mmol of NaCl for 3 days) or thermal stress (50°C for 60 s). Of 36,041 genes examined, 17,271 genes with fold changes ranging from 2.2 to 19.6 were successfully identified. Specifically, 2388 genes were differentially upregulated in response to heat stress, whereas 4327 genes were downregulated. Under salt stress conditions, 2013 genes were upregulated and 4221 genes were downregulated. Transcriptomic analysis revealed four common abiotic KEGG pathways that play crucial roles in the response of pearl millet to salt and heat stress: phenylpropanoid biosynthesis, photosynthesis-antenna proteins, photosynthesis, and plant hormone signal transduction. These metabolic pathways are necessary for pearl millet to withstand and adapt to abiotic stresses caused by salt and heat. Moreover, the pearl millet shoot heat stress group showed specific transcriptomics related to KEEG metabolic pathways such as cytochrome P450, cutin, suberine, and wax biosynthesis, zeatin biosynthesis, crocin biosynthesis, ginsenoside biosynthesis, saponin biosynthesis, and biosynthesis of various plant secondary metabolites. In contrast, pearl millet shoots exposed to salinity stress exhibited transcriptomic changes associated with KEEG metabolic pathways related to carbon fixation in photosynthetic organisms, mismatch repair, and nitrogen metabolism. Our findings underscore the remarkable cross-tolerance of pearl millet to simultaneous salt and heat stress, elucidated through the activation of shared abiotic KEGG pathways. This study emphasizes the pivotal role of transcriptomics analysis in unraveling the molecular responses of pearl millet under abiotic stress conditions.

Protein profile analysis of tension wood development in response to artificial bending and gravitational stimuli in Betula platyphylla

Betula platyphylla Suk (birch) is an excellent short-term hardwood species with growth and wood characteristics well suited to wood industries. To investigate the molecular mechanism of wood development in birch, a tension wood (TW) induced system was used to explore the regulatory mechanism at the protein level and identify the key proteins involved in xylem development in birch. The results of dyeing with Safranin O-Fast Green indicated that the cellulose content of TW was significantly higher than that of opposite wood (OW) or normal wood (NW), and the lignin content in TW was significantly lower than that in OW and NW after artificial bending of birch stems. Protein profile analysis of TW, NW and OW by iTRAQ revealed that there were 639 and 460 differentially expressed proteins (DEPs) between TW/OW and TW/NW, respectively. The DEPs were mainly enriched in tyrosine metabolism, glycolysis/gluconeogenesis, phenylalanine and tyrosine metabolism, phenylpropanoid and pyruvate metabolism, the pentose phosphate pathway, the citrate cycle (TCA cycle), fructose and mannose metabolism, carbon fixation in photosynthetic organisms, fatty acid biosynthesis, photosynthesis proteins and other pathways. The proteins in the citrate cycle were upregulated. The expression levels of PGI, PGM and FRK proteins related to cellulose synthesis increased and the expression levels of PAL, 4CL and COMT related to lignin synthesis decreased, leading to an increase in cellulose content and decreased lignin levels in TW. PPI analysis revealed that key DEPs interact with each other, indicating that these proteins form complexes to implement this function, which may provide important insights for wood formation at the molecular level.

RNA-Sequencing Analysis Revealed Genes Associated with Sweet Potato (Ipomoea batatas (L.) Lam.) Responses to Stem Rot during Different Infection Stages.

The sweet potato, which is an important tuber crop in China, is susceptible to a variety of pathogens and insect pests during cultivation and production. Stem rot is a common sweet potato disease that seriously affects tuber yield and quality. Unfortunately, there have been relatively few studies on the mechanism mediating the stem rot resistance of sweet potatoes. In this study, a transcriptome sequencing analysis was completed using Xushu 48 samples at different stages (T1, T2, and T3) of the stem rot infection. The T1 vs. T2, T1 vs. T3, and T2 vs. T3 comparisons detected 44,839, 81,436, and 61,932 differentially expressed genes (DEGs), respectively. The DEGs encoded proteins primarily involved in alanine, aspartate, and glutamate metabolism (ko00250), carbon fixation in photosynthetic organisms (ko00710), and amino sugar and nucleotide sugar metabolism (ko00520). Furthermore, some candidate genes induced by phytopathogen infections were identified, including gene-encoding receptor-like protein kinases (RLK5 and RLK7), an LRR receptor-like serine/threonine protein kinase (SERK1), and transcription factors (bHLH137, ERF9, MYB73, and NAC053). The results of this study provide genetic insights that are relevant to future explorations of sweet potato stem rot resistance, while also providing the theoretical basis for breeding sweet potato varieties that are resistant to stem rot and other diseases.

Kernel Transcriptome Profiles of Susceptible Wheat Genotypes in Response to Wheat Dwarf Bunt.

Wheat dwarf bunt is caused by Tilletia controversa J. G. Kühn (TCK), which is a serious fungal diseases affecting kernels of wheat. In order to identify candidate genes involved in the abnormal development of kernels in wheat, we used RNA sequencing technology to analyze the transcriptome of the abnormal and healthy kernels of a susceptible variety (Yili053) at the mid-filling stage, late-filling stage, and maturity stage, respectively. The differentially expressed genes (DEGs) were analyzed, and there were 3930 DEGs, 28,422 DEGs, and 20,874 DEGs found at the mid-filling stage, late-filling stage, and maturity stage in Yili053, respectively. A total of 1592 DEGs (506 DEGs up-regulated) showed continuously differential expression in the three stages. Gene ontology analysis showed that these DEGs were related to biological regulation, metabolic processes, and the response to stimulus. Kyoto Encyclopedia of Genes and Genomes enrichment analysis showed that these DEGs play major roles in pathways including photosynthesis, carbon metabolism, carbon fixation in photosynthetic organisms, and glyoxylate and dicarboxylate metabolism. Moreover, we predicted that 13 MADS-MIKC transcription factors, which were continuously up-regulated, were crucial for regulating the maturation and senescence of eukaryotes. Some 21 genes related to the plant hormone signaling transduction pathway and 61 genes related to the response to stimulus were analyzed. A total of 26 of them were successful validated with a qPCR analysis. These genes were thought to be involved in the abnormal development of kernels infected by TCK. A transcriptomics analysis of wheat kernels in response to TCK will contribute to understanding the interaction of TCK and wheat, and may provide a basis for knowledge of molecular events in the abnormal development of kernels, which will be helpful for more efficient TCK management.

Changes in bacterial community structure and root metabolites in Themeda japonica habitat under slight and strong karst rocky desertification

Microorganisms can quickly respond to vegetation succession, and plants also regulate the structure of microbial community through root exudates or by affecting soil nutrients. Themeda japonica is a dominant plant species in karst rocky desertification (KRD) regions, but it is currently unclear the role of soil bacterial communities, interact with T. japonica during the KRD process. The purpose of this study is to explore the variation of soil metal element content, soil enzyme activity, soil bacterial communities and soil environment factor/root metabolites of T. japonica, and the relationship between soil bacterial communities and root metabolites in different degrees of KRD. Our results showed that the significant changes was found in soil metal element content and soil enzyme activity from slight KRD to strong KRD. Metabolic analysis demonstrated that the strong KRD environment increased the organic acid content of T. japonica roots, decreased the amino acids and sugars content. The specific metabolic pathways of Citrate cycle (TCA cycle), carbon fixation in photosynthetic organisms, glyoxylate and dicarboxylate metabolism and pyruvate metabolism were altered to help T. japonica adapt to the harsh environment. In addition, there was significant difference in beta diversity among bulk soil, rhizosphere and root endophytic bacterial community. With the aggravation of KRD, the abundance of Proteobacteria was decreased, while the abundance of Actinobacteria was increased. KRD also enhanced positive interactions between bacterial communities, and made the inter species associations of endophytic bacteria more sensitive. Mantel analysis showed that potassium (K), magnesium (Mg), cadmium (Cd) lead (Pb) and invertase (Inv), alkaline phosphatase (Alp), catalase (Cat), and aconitic acid, alanine, fructose, glucose, L-malic acid, palmitic acid, saccharic acid and serine significantly influence bacterial communities in bulk soil and rhizosphere. These results implied that root metabolites and soil characteristics might jointly affect the bacterial community in KRD area during the process of T. japonica in adapting to different rocky desertification.

Transcriptomic analysis of the effect of shaking and tumbling degree on quality formation of Wuyi rock tea.

Shaking and tumbling are extremely important for the formation of the special flavor of Wuyi rock tea. In this study, we analyzed the effects of different shaking and tumbling degrees on the quality index content of tea leaves and determined changes in gene expression in tea leaves using RNA sequencing technology. On this basis, the correlation between gene expression intensities in tea leaves and tea quality index content was analyzed. The results showed that heavy shaking and tumbling (MW3) increased gene expression of metabolic pathways, biosynthesis of secondary metabolites, starch and sucrose metabolism, biosynthesis of amino acids, glycine, serine, and threonine metabolism, alpha-linolenic acid metabolism pathways and decreased gene expression of flavonoid biosynthesis, carbon fixation in photosynthetic organisms, phenylpropanoid biosynthesis, and plant hormone signal transduction pathways in tea leaves, which in turn increased the content of caffeine, soluble sugar, amino acid and decreased the content of flavone, tea polyphenol, catechin component in tea leaves; the opposite was true for light shaking and tumbling. Second, this study found that MW3 was more beneficial in improving the mellowness, sweetness, and fresh and brisk taste of tea leaves and reducing the bitterness of tea leaves. This study provides some references to guide the processing of Wuyi rock tea with different flavors. PRACTICAL APPLICATION: Heavy shaking and tumbling was more beneficial in improving the mellowness, sweetness, and fresh and brisk taste of tea leaves and reducing the bitterness of tea leaves. Therefore, the degree of shaking and tumbling in Wuyi production can be appropriately improved to produce high-quality tea and improve the economic benefits of tea.

Effects of Xanthomonas campestris pv. campestris on the photosynthesis of cabbage in the early stage of infection

Cabbage is one of the most important cruciferous vegetables. Black rot, caused by Xanthomonas campestris pv. campestris (Xcc) seriously affects cabbage production; therefore, it is important to study the resistance mechanism to black rot in cabbage. In this study, cabbage photosynthetic physiology changes in the early stages of Xcc infection were analyzed using physiological index determination and transcriptome analysis. The results showed that the Xcc infection can lead the chlorophyll degradation and decreased the net photosynthetic rate (Pn), and the decrease in Pn was mainly due to non-stomatal factors. In addition, the maximum photosynthetic efficiency (Fv/Fm), actual photosynthetic efficiency of photosystem II (PSII) gradually decreased, and the OJIP curve tended to be flat, indicating that Xcc infection reduced the activity of the PSII reaction center and affected the chlorophyll fluorescence intensity. Moreover, the primary photochemical reaction of cabbage leaves was damaged, and electron transfer on the PSII receptor side was inhibited after Xcc infection. NADP-GAPDH and FBPase activities in the Calvin cycle decreased after Xcc invasion. Using transcriptome analysis, 173, 77, 63, and 53 differentially expressed genes (DEGs) were enriched in "carbon metabolism", "photosynthesis", "carbon fixation in photosynthetic organisms", and "metabolism of porphyrins and chlorophyll" metabolic processes, respectively. These results suggest that Xcc infection affects cabbage photosynthesis via multiple pathways. Our results provide a theoretical basis for further research on black rot-resistant breeding and cabbage resistance mechanisms.

Integrated Transcriptome and Proteome Analysis Revealed the Regulatory Mechanism of Hypocotyl Elongation in Pakchoi.

Hypocotyl length is a critical determinant for the efficiency of mechanical harvesting in pakchoi production, but the knowledge on the molecular regulation of hypocotyl growth is very limited. Here, we report a spontaneous mutant of pakchoi, lhy7.1, and identified its characteristics. We found that it has an elongated hypocotyl phenotype compared to the wild type caused by the longitudinal growth of hypocotyl cells. Different light quality treatments, transcriptome, and proteomic analyses were performed to reveal the molecular mechanisms of hypocotyl elongation. The data showed that the hypocotyl length of lhy7.1 was significantly longer than that of WT under red, blue, and white lights but there was no significant difference under dark conditions. Furthermore, we used transcriptome and label-free proteome analyses to investigate differences in gene and protein expression levels between lhy7.1 and WT. At the transcript level, 4568 differentially expressed genes (DEGs) were identified, which were mainly enriched in "plant hormone signal transduction", "photosynthesis", "photosynthesis-antenna proteins", and "carbon fixation in photosynthetic organisms" pathways. At the protein level, 1007 differentially expressed proteins (DEPs) were identified and were mainly enriched in photosynthesis-related pathways. The comprehensive transcriptome and proteome analyses revealed a regulatory network of hypocotyl elongation involving plant hormone signal transduction and photosynthesis-related pathways. The findings of this study help elucidate the regulatory mechanisms of hypocotyl elongation in lhy7.1.

Physiological and molecular responses of Trollius chinensis seedlings to waterlogging stress and subsequent drainage

Waterlogging led by extreme rainfall events is one of the major natural disasters under the global climate change context, putting plants under water stress. However, systematical studies on the response mechanisms in leaves to waterlogging are limited. We explored major leaf characteristics of oxidative stress and scavenging, photosynthesis, and osmotic regulations of Trollius chinensis. Two levels of waterlogging serverities (moderate level, W1, and severe level, W2) were studied on the 1st (D1), 5th (D5), 10th (D10), and 15th day (D15) upon waterlogging and on the subsequent 10th day after drainage (R10). In addition, based on physiological indicators, the leaves in control and W2 on D10 were selected for RNA-Seq. We found that most of physiological characteristics presented the greatest differences between control and waterlogging groups on D10 such as O2.-, SOD, and proline, while some other characteristics such as H2O2, POD, and GR showed highest change from control on D15. Furthermore, on R10, most of the physiologcial characteristics recovered in different levels, which indicates that this species is relative waterlogging-tolerant. The results also showed that out of 1182 differentially expressed genes (307 up-regulated and 875 down-regulated) obtained in W2 vs control, ‘photosynthesis’, ‘plastid’, ‘chloroplast’, ‘thylakoid’, and ‘chlorophyll-binding’ were the Gene Ontology (GO) enrichment hotspots, and ‘photosynthesis’, ‘photosynthesis-antenna proteins’, and ‘carbon fixation in photosynthetic organisms’ were the most enriched Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. The expression of genes related to the photosynthesis, amylase, calcineurin interacting protein kinases (CIPKs), glutathione-S-transferase (GST), and ethylene response factor (ERF) decreased, while the expression of some genes related to antioxidation, osmoregulation, and transcription factors belonging to MYB (Myb proto-oncogene protein) and NAC ((NAM, ATAF1/2, and CUC2) families increased, implying that these genes play key roles in T. chinensis to cope with waterlogging stress. We conclude that T. chinensis is a waterlogging-tolerant species and 10 days of severe waterlogging has induced changes of antioxidant, photosynthesis, and osmoregulation in physiological and transcriptome level. The present study provides candidate genes that can be used for waterlogging-resistant breeding in T. chinensis.

Design, Synthesis, Antibacterial Activity, and Mechanism of Novel Mesoionic Compounds Based on Natural Pyrazole Isolated from an Endophytic Fungus Colletotrichum gloeosporioides.

Xanthomonas oryzae pv. oryzicola (Xoo) is a type of bacteria that causes bacterial leaf blight disease in rice plants. This disease is substantially harmful, and the current prevention and control measures are facing challenges. This study has investigated the effectiveness of the control activity that the endophytic fungus NS7 fermented from Dendrobium candidum possessed against Xoo. Twenty-eight novel mesoionic compounds were designed and synthesized based on the natural compound D. These compounds displayed moderate to excellent anti-Xoo activity in vitro. Notably, compound 24 exhibited prominent anti-Xoo activity in vitro with an EC50 value of 40.3 mg/L, which was better than that of the positive control thiodiazole copper (TC)(71.2 mg/L) and the lead compound D (108.1 mg/L). In vivo pot experiments on Xoo showed that compound 24 exhibited protective and curative activities of 39.4 and 30.4%, respectively, which were better than those of TC (35.7 and 28.8%, respectively). Further, a preliminary mechanism study indicated that compound 24 could enhance the activity of defense enzymes to improve the ability for anti-Xoo. Meanwhile, compound 24 could also regulate the carbon fixation in photosynthetic organisms, which might be related to the enhanced immune function of rice. This study offers a new strategy for discovering antibacterial agents based on natural products.

Studying the effect of light intensity on the photosynthetic mechanism of pepper leaf yellowing mutants by proteomics and phosphoproteomics

The leaf is an important plant organ and is closely related to agricultural yield. Photosynthesis plays a critical role in promoting plant growth and development. Understanding the mechanism of leaf photosynthesis regulation will help improve crop yield. In this study, the pepper yellowing mutant was used as the experimental material, and the photosynthetic changes of pepper leaves (yl1 and 6421) under different light intensities were analyzed by chlorophyll fluorimeter and photosynthesis meter. Changes in proteins and enrichment of phosphopeptides in pepper leaves were determined. The results showed that different light intensities had significant effects on the chlorophyll fluorescence and photosynthetic parameters of pepper leaves. The differentially expressed proteins (DEPs) and differentially expressed phosphorylated proteins (DEPPs) were mainly involved in photosynthesis, photosynthesis-antenna proteins, and carbon fixation in photosynthetic organisms. In yl1 leaves, the phosphorylation levels of photosynthesis and photosynthesis-antenna proteins LHCA2, LHCA3, PsbC, PsbO, and PsbP were lower under low light treatment, but significantly higher under high light intensity compared with wild-type leaves. In addition, many proteins involved in the carbon assimilation pathway, including TKT, Rubisco, and PGK, were phosphorylated, and this modification level was significantly higher in yl1 than in the wild type under high light intensity. These results provide a new perspective for studying the photosynthesis mechanism of pepper under different light intensities.

Transcriptomic analysis of Cucumis sativus uncovers putative genes related to hormone signaling under low temperature (LT) and high humidity (HH) stress

Climate change has caused changes in environmental conditions, leading to both low temperature (LT) and high humidity (HH) stress on crops worldwide. Therefore, there is a growing need to enhance our understanding of the physiological and molecular mechanisms underlying LT and HH stress tolerance in cucumbers, given the significance of climate change. The findings of this study offer a comprehensive understanding of how the transcriptome and hormone profiles of cucumbers respond to LT and HH stress. In this study, cucumber seedlings were subjected to LT and HH stress (9/5 °C day/night temperature, 95% humidity) as well as control (CK) conditions (25/18 °C day/night temperature, 80% humidity) for 24, 48, and 72 h. It was observed that the LT and HH stress caused severe damage to the morphometric traits of the plants compared to the control treatment. The concentrations of phytohormones IAA, ethylene, and GA were lower, while ABA and JA were higher during LT and HH stress at most time points. To gain insights into the molecular mechanisms underlying this stress response, RNA-sequencing was performed. The analysis revealed a total of 10,459 differentially expressed genes (DEGs) with annotated pathways. These pathways included plant hormone signal transduction, protein processing in the endoplasmic reticulum, MAPK signaling pathway, carbon fixation in photosynthetic organisms, and glycerolipid metabolism. Furthermore, 123 DEGs associated with hormone signaling pathways were identified, and their responses to LT and HH stress were thoroughly discussed. Overall, this study sheds light on the LT and HH tolerance mechanisms in cucumbers, particularly focusing on the genes involved in the LT and HH response and the signaling pathways of endogenous phytohormones.

An ancient metabolite damage-repair system sustains photosynthesis in plants

Ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) is the major catalyst in the conversion of carbon dioxide into organic compounds in photosynthetic organisms. However, its activity is impaired by binding of inhibitory sugars such as xylulose-1,5-bisphosphate (XuBP), which must be detached from the active sites by Rubisco activase. Here, we show that loss of two phosphatases in Arabidopsis thaliana has detrimental effects on plant growth and photosynthesis and that this effect could be reversed by introducing the XuBP phosphatase from Rhodobacter sphaeroides. Biochemical analyses revealed that the plant enzymes specifically dephosphorylate XuBP, thus allowing xylulose-5-phosphate to enter the Calvin-Benson-Bassham cycle. Our findings demonstrate the physiological importance of an ancient metabolite damage-repair system in degradation of by-products of Rubisco, and will impact efforts to optimize carbon fixation in photosynthetic organisms.

The effect of manure-borne doxycycline combined with different types of oversized microplastic contamination layers on carbon and nitrogen metabolism in sandy loam

The different forms and properties of microplastics (MPs) have different effects on the elemental cycles in soil ecosystems, and this is further complicated when the soil contains antibiotics; meanwhile, oversized microplastic (OMP) in soil is always ignored in studies of environmental behavior. In the context of antibiotic action, the effects of OMP on soil carbon (C) and nitrogen (N) cycling have rarely been explored. In this study, we created four types of oversized microplastic (thick fibers, thin fibers, large debris, and small debris) composite doxycycline (DOX) contamination layers (5–10 cm) in sandy loam, hoping to reveal the effects on soil C and N cycling and potential microbial mechanisms when exposed to the combination of manure-borne DOX and different types of OMP from the perspective of metagenomics in the longitudinal soil layer (0–30 cm). The results showed that all different forms of OMP, when combined with DOX, reduced the soil C content in each layer, but only reduced the soil N content in the upper layer of the OMP contamination layer. The microbial structure of the surface soil (0–10 cm) was more noteworthy than that of the deeper soil (10–30 cm). The genera Chryseolinea and Ohtaekwangia were key microbes involved in C and N cycling in the surface layer and regulated carbon fixation in photosynthetic organisms (K00134), carbon fixation pathways in prokaryotes (K00031), methane metabolism (K11212 and K14941), assimilatory nitrate reduction (K00367), and denitrification (K00376 and K04561). The present study is the first to reveal the potential microbial mechanism of C and N cycling under OMP combined with DOX in different layers, mainly the OMP contamination layer and its upper layer, and the OMP shape plays an important role in this process.