iTRAQ-based quantitative proteomic analysis gives insight into sexually different metabolic processes of poplars under nitrogen and phosphorus deficiencies

Facilitated remediation of heavy metals contaminated land using Quercus spp. with different strategies: Variations in amendments and experiment periods

Phytoremediation using trees combined with soil amendments has gained much attention for its highly cost-effective trait. In natural field conditions, however, the results may not reflect the true performance of amendments based on short-term laboratory studies. In this three-year field trial, various soil amendments such as rice straw biochar, palygorskite, a combined biochar of rice straw biochar and palygorskite, and hydroxyapatite were used to systematically study the potential of the low-accumulator (Quercus fabri Hance) and high-accumulator (Quercus texana Buckley) for cadmium (Cd) and zinc (Zn) to remediate severely contaminated soils. Soil amendments enhanced the dendroremediation capacity of Quercus as the growth period prolonged. In 2021, the rice straw biochar treatment increased Cd and Zn accumulation by 1.76 and 2.09 times in Q. fabri, respectively, compared to the control. Cd and Zn accumulation increased to 1.78 and 2.10 times, respectively, under combined biochar treatment for Q. texana compared to the control. Metals accumulation was mainly enhanced by soil amendments through increasing the growth biomass of Q. fabri and improving the biomass and bioconcentration ability of Q. texana. Overall, soil amendments effectively improved the phytoremediation efficiency of Quercus in the long term, and selecting suitable amendments should be fully considered in phytoremediation.

Integrated physiological, proteome and gene expression analyses provide new insights into nitrogen remobilization in citrus trees

Nitrogen (N) remobilization is an important physiological process that supports the growth and development of trees. However, in evergreen broad-leaved tree species, such as citrus, the mechanisms of N remobilization are not completely understood. Therefore, we quantified the potential of N remobilization from senescing leaves of spring shoots to mature leaves of autumn shoots of citrus trees under different soil N availabilities and further explored the underlying N metabolism characteristics by physiological, proteome and gene expression analyses. Citrus exposed to low N had an approximately 38% N remobilization efficiency (NRE), whereas citrus exposed to high N had an NRE efficiency of only 4.8%. Integrated physiological, proteomic and gene expression analyses showed that photosynthesis, N and carbohydrate metabolism interact with N remobilization. The improvement of N metabolism and photosynthesis, the accumulation of proline and arginine, and delayed degradation of storage protein in senescing leaves are the result of sufficient N supply and low N remobilization. Proteome further showed that energy generation proteins and glutamate synthase were hub proteins affecting N remobilization. In addition, N requirement of mature leaves is likely met by soil supply at high N nutrition, thereby resulting in low N remobilization. These results provide insight into N remobilization mechanisms of citrus that are of significance for N fertilizer management in orchards.

Role of female-predominant MYB39-bHLH13 complex in sexually dimorphic accumulation of taxol in Taxus media

Taxus trees are major natural sources for the extraction of taxol, an anti-cancer agent used worldwide. Taxus media is a dioecious woody tree with high taxol yield. However, the sexually dimorphic accumulation of taxoids in T. media is largely unknown. Our study revealed high accumulation of taxoids in female T. media trees using a UPLC-MS/MS method. Thereafter, many differential metabolites and genes between female and male T. media trees were identified using metabolomic and transcriptomic analyses, respectively. Most of the taxol-related genes were predominantly expressed in female trees. A female-specific R2R3-MYB transcription factor gene, TmMYB39, was identified. Furthermore, bimolecular fluorescence complementation and yeast two-hybrid assays suggested the potential interaction between TmMYB39 and TmbHLH13. Several taxol biosynthesis-related promoter sequences were isolated and used for the screening of MYB recognition elements. The electrophoretic mobility shift assay indicated that TmMYB39 could bind to the promoters of the GGPPS, T10OH, T13OH, and TBT genes. Interaction between TmMYB39 and TmbHLH13 transactivated the expression of the GGPPS and T10OH genes. TmMYB39 might function in the transcriptional regulation of taxol biosynthesis through an MYB-bHLH module. Our results give a potential explanation for the sexually dimorphic biosynthesis of taxol in T. media.

Differences in carbon and nitrogen metabolism between male and female Populus cathayana in response to deficient nitrogen

Sexual dimorphism occurs regarding carbon and nitrogen metabolic processes in response to nitrogen supply. Differences in fixation and remobilization of carbon and allocation and assimilation of nitrogen between sexes may differ under severe defoliation. The dioecious species Populus cathayana was studied after two defoliation treatments with two N levels. Males had a higher capacity of carbon fixation because of higher gas exchange and fluorescence traits of leaves after severe long-term defoliation under deficient N. Males had higher leaf abscisic acid, stomatal conductance and leaf sucrose phosphate synthase activity increasing transport of sucrose to sinks. Males had a higher carbon sink than females, because under N-deficient conditions, males accumulated >131.10% and 90.65% root starch than males in the control, whereas females accumulated >40.55% and 52.81%, respectively, than females in the control group. Males allocated less non-protein N (NNon-p) to leaves, having higher nitrogen use efficiency (photosynthetic nitrogen use efficiency), higher glutamate dehydrogenase (GDH) and higher leaf GDH expression, even after long-term severe defoliation under deficient N. Females had higher leaf jasmonic acid concentration and NNon-p. The present study suggested that females allocated more carbon and nitrogen to defense chemicals than males after long-term severe defoliation under deficient N.

Phosphoproteomic and Metabolomic Analyses Reveal Sexually Differential Regulatory Mechanisms in Poplar to Nitrogen Deficiency

Nitrogen (N) is a key factor impacting physiological processes in plants. Many proteins have been investigated in male and female poplars under N limitation. However, little is known about sex differences in the protein modifications and metabolites that occur in poplar leaves in response to N deficiency. In this study, as compared to N-deficient males, N-deficient females suffered greater damage from N deficiency, including chloroplast disorganization and lipid peroxidation of cellular membranes. Male poplars had greater osmotic adjustment ability than did females, allowing greater accumulation of soluble metabolites. In addition, as compared to that in N-deficient males, glycolysis was less suppressed in N-deficient females for increased enzyme activities to consume excess energy. Moreover, we found that pronounced protein phosphorylation occurred during carbon metabolism and substance transport processes in both sexes of poplar under N-limiting conditions. Sex-specific metabolites mainly included intermediates in glycolysis, amino acids, and phenylpropanoid-derived metabolites. This study provides new molecular evidence that female poplars suffer greater negative effects from N deficiency than do male poplars.

Sexually differential gene expressions in poplar roots in response to nitrogen deficiency

Nitrogen (N) is a key nutrient impacting plant growth and physiological processes. However, the supply of N is often not sufficient to meet the requirements of trees in many terrestrial ecosystems. Because of differences in production costs, male and female plants have evolved different stress resistance strategies for N limitation. However, little is known about differential gene expression according to sex in poplars responding to N limitation. To explore sex-related constitutive defenses, Populus cathayana Rehder transcriptomic, proteomic and metabolic analyses were performed on the roots of male and female Populus cathayana. We detected 16,816 proteins and 37,286 transcripts, with 2797 overlapping proteins and mRNAs in the roots. In combination with the identification of 90 metabolites, we found that N deficiency greatly altered gene expression related to N metabolism as well as carbohydrate metabolism, secondary metabolism and stress-related processes in both sexes. Nitrogen-deficient P. cathayana females exhibited greater root biomass and less inhibition of citric acid production and glycolysis as well as higher secondary metabolic activity and abscisic acid contents than N-deficient P. cathayana males. Interestingly, males presented a better osmotic adjustment ability and higher expression of resistance genes, suggesting that P. cathayana males exhibit a better stress tolerance ability and can invest fewer resources in defense compared with females. Therefore, our study provides new molecular evidence that P. cathayana males and females adopt different resistance strategies to cope with N deficiency in their roots.

Metabolic and physiological analyses reveal that Populus cathayana males adopt an energy-saving strategy to cope with phosphorus deficiency

Dioecious trees have evolved sex-specific adaptation strategies to cope with inorganic phosphorus (Pi) limitation. Yet, little is known about the effects of Pi limitation on plant metabolism, particularly in dioecious woody plants. To identify potential gender-specific metabolites appearing in response to Pi limitation in poplars, we studied the metabolic and ionomic responses in the roots and leaves of Populus cathayana Rehd males and females exposed to a 60-day period of Pi deficiency. Besides significant decreases in phosphorus contents in both Pi-deficient roots and leaves, the calcium level decreased significantly and the sulfur content increased significantly in Pi-deficient male roots, while the zinc and ferrum contents increased significantly in Pi-deficient female roots. Inorganic P deficiency caused a smaller change in the abscisic acid content, but a significant increase in the jasmonic acid content was detected in both leaves and roots. Salicylic acid significantly decreased under Pi deficiency in male leaves and female roots. Changes were found in phospholipids and phosphorylated metabolites (e.g., fructose-6-phosphate, glycerol-3-phosphate, glucose-6-phosphate, phosphoric acid and inositol-1-phosphate) in roots and leaves. Both P. cathayana males and females relied on inorganic pyrophosphate-dependent but not on Pi-dependent glycolysis under Pi-deficient conditions. Sex-specific metabolites in leaves were primarily in the category of primary metabolites (e.g., amino acids), while in roots primarily in the category of secondary metabolites (e.g., organic acids) and sugars. The metabolome analysis revealed that sexually different pathways occurred mainly in amino acid metabolism, and the tissue-related differences were in the shikimate pathway and glycolysis. We observed changes in carbon flow, reduced root biomass and increased amino acid contents in P. cathayana males but not in females, which indicated that males have adopted an energy-saving strategy to adapt to Pi deficiency. Thus, this study provides new insights into sex-specific metabolic responses to Pi deficiency.

Proteome and transcriptome profiling of equine myofibrillar myopathy identifies diminished peroxiredoxin 6 and altered cysteine metabolic pathways

Equine myofibrillar myopathy (MFM) causes exertional muscle pain and is characterized by myofibrillar disarray and ectopic desmin aggregates of unknown origin. To investigate the pathophysiology of MFM, we compared resting and 3 h postexercise transcriptomes of gluteal muscle and the resting skeletal muscle proteome of MFM and control Arabian horses with RNA sequencing and isobaric tags for relative and absolute quantitation analyses. Three hours after exercise, 191 genes were identified as differentially expressed (DE) in MFM vs. control muscle with >1 log₂ fold change (FC) in genes involved in sulfur compound/cysteine metabolism such as cystathionine-beta-synthase ( CBS, ↓4.51), a cysteine and neutral amino acid membrane transporter ( SLC7A10, ↓1.80 MFM), and a cationic transporter (SLC24A1, ↓1.11 MFM). In MFM vs. control at rest, 284 genes were DE with >1 log₂ FC in pathways for structure morphogenesis, fiber organization, tissue development, and cell differentiation including > 1 log₂ FC in cardiac alpha actin ( ACTC1 ↑2.5 MFM), cytoskeletal desmoplakin ( DSP ↑2.4 MFM), and basement membrane usherin ( USH2A ↓2.9 MFM). Proteome analysis revealed significantly lower antioxidant peroxiredoxin 6 content (PRDX6, ↓4.14 log₂ FC MFM), higher fatty acid transport enzyme carnitine palmitoyl transferase (CPT1B, ↑3.49 MFM), and lower sarcomere protein tropomyosin (TPM2, ↓3.24 MFM) in MFM vs. control muscle at rest. We propose that in MFM horses, altered cysteine metabolism and a deficiency of cysteine-containing antioxidants combined with a high capacity to oxidize fatty acids and generate ROS during aerobic exercise causes chronic oxidation and aggregation of key proteins such as desmin.

iTRAQ-based analysis of the Arabidopsis proteome reveals insights into the potential mechanisms of anthocyanin accumulation regulation in response to phosphate deficiency

Phosphate (Pi) deficiency significantly limits plant growth in natural and agricultural systems. Accumulation of anthocyanins in shoots is a common response of Arabidopsis thaliana to Pi deficiency. To elucidate the mechanisms underlying Pi deficiency-induced anthocyanin accumulation, we employed a proteomic approach based on isobaric tags for relative and absolute quantification (iTRAQ) to investigate protein expression profiles of Arabidopsis thaliana seedlings subjected to Pi deficiency for 7 days. In total, 5,106 proteins were identified, of which 156 displayed significant changes in abundance upon Pi deficiency. Bioinformatics analysis indicated that flavonoid biosynthesis was the most significantly elevated metabolic process under Pi deficiency. We further examined the potential role of the flavonoid biosynthetic pathway using a dihydroflavonol 4-reductase (DFR) mutant (tt3) and quantitative RT-PCR (qRT-PCR) analysis, and found that the tt3 mutant was deprived of transcriptional up-regulation of three genes related to anthocyanin biosynthesis, modification and transport under Pi deficiency. These results showed that Pi deficiency probably enhances the anthocyanin accumulation by promoting the flavonoid biosynthesis. The exact functions of these proteins remain to be examined. Nevertheless, our study increases the understanding of the mechanisms implicated in the anthocyanin accumulation induced by Pi deficiency and adaptive responses of plants to Pi starvation.

Proteomic and genomic responses of plants to nutritional stress

Minerals or trace elements in small amount are essential nutrients for every plant, but when the internal concentration exceeds the threshold, these essential elements do create phytotoxicity. Plant responses to elemental stresses are very common due to different anthropogenic activities; however it is a complex phenomenon with individual characteristics for various species. To cope up with the situation, a plant produces a group of strategies both in proteomic and genomic level to overcome it. Controlling the metal stress is known to activate a multigene response resulting in the changes in various proteins, which directly affects almost all biological processes in a living cell. Therefore, proteomic and genomic approaches can be useful for elucidating the molecular responses under metal stress. For this, it is tried to provide the latest knowledge and techniques used in proteomic and genomic study during nutritional stress and is represented here in review form.

Transcriptional profiling reveals mechanisms of sexually dimorphic responses of Populus cathayana to potassium deficiency

Potassium (K) deficiency causes a series of physiological and metabolic disorders in plants, and dioecious species exhibit different responses based on sex. Our previous morphological and physiological observations indicated that Populus cathayana males were more tolerant to K⁺ deficiency than females. To continue this work, comparative transcriptome analyses were carried out to investigate sexually differentially expressed genes (DEGs) in this study. The results indicate that 10 weeks of K⁺ deficiency result in 111 and 181 DEGs in males and females, respectively. These DEGs are mainly involved in photosynthesis, cell wall biosynthesis, secondary metabolism, transport, stress responses, gene expression regulation and protein synthesis and degradation. Comparing between sexes, P. cathayana females showed more changes in response to K⁺ deficiency than males with regard to photosynthesis, gene expression regulation and posttranslational modification but fewer changes in secondary metabolism, stress responses and redox homeostasis. These results provide evidence that P. cathayana females are more susceptible to K⁺ deficiency than males. Therefore, there are sex-related molecular strategies in response to K⁺ deficiency between sexes.

Sex-Specific Response to Stress in Populus

Populus is an effective model for genetic studies in trees. The genus Populus includes dioecious species, and the differences exhibited in males and females have been intensively studied. This review focused on the distinctions between male and female poplar and aspen plants under stress conditions, such as drought, salinity, heavy metals, and nutrient deficiency on morphological, physiological, proteome, and gene expression levels. In most studies, males of Populus species were more adaptive to the majority of the stress conditions and showed less damage, better growth, and higher photosynthetic capacity and antioxidant activity than that of the females. However, in two recent studies, no differences in non-reproductive traits were revealed for male and female trees. This discrepancy of the results could be associated with experimental design: different species and genotypes, stress conditions, types of plant materials, sampling sizes. Knowledge of sex-specific differences is crucial for basic and applied research in Populus species.

Describing the Diapause-Preparatory Proteome of the Beetle Colaphellus bowringi and Identifying Candidates Affecting Lipid Accumulation Using Isobaric Tags for Mass Spectrometry-Based Proteome Quantification (iTRAQ)

Prior to entering diapause, insects must prepare themselves physiologically to withstand the stresses of arresting their development for a lengthy period. While studies describing the biochemical and cellular milieu of the maintenance phase of diapause are accumulating, few studies have taken an “omics” approach to describing molecular events during the diapause preparatory phase. We used isobaric tags and mass spectrometry (iTRAQ) to quantitatively compare the expression profiles of proteins identified during the onset of diapause preparation phase in the heads of adult female cabbage beetles, Colaphellus bowringi. A total of 3,175 proteins were identified, 297 of which were differentially expressed between diapause-destined and non-diapause-destined female adults and could therefore be involved in diapause preparation in this species. Comparison of identified proteins with protein function databases shows that many of these differentially expressed proteins enhanced in diapause destined beetles are involved in energy production and conversion, carbohydrate metabolism and transport, and lipid metabolism. Further hand annotation of differentially abundant peptides nominates several associated with stress hardiness, including HSPs and antioxidants, as well as neural development. In contrast, non-diapause destined beetles show substantial increases in cuticle proteins, suggesting additional post-emergence growth. Using RNA interference to silence a fatty acid-binding protein (FABP) that was highly abundant in the head of diapause-destined females prevented the accumulation of lipids in the fat body, a common product of diapause preparation in this species and others. Surprisingly, RNAi against the FABP also affected the transcript abundance of several heat shock proteins. These results suggest that the identified differentially expressed proteins that play vital roles in lipid metabolism may also contribute somehow to enhanced hardiness to environmental stress that is characteristic of diapause.