Transcriptomics and Proteomics Reveal the Cellulose and Pectin Metabolic Processes in the Tension Wood (Non-G-Layer) of Catalpa bungei

Comparative proteomics analysis of Shiraia bambusicola revealed a variety of regulatory systems on conidiospore formation

Shiraia bambusicola is a typical parasitic medicinal fungus of the family Shiraiaceae. The fruiting bodies of S. bambusicola cannot be cultivated artificially, and active substances can be effectively produced via fermentation. The mechanism of conidia production is a research hotspot in the industrial utilization and growth development of S. bambusicola. This study is the first to systematically study the proteomics of conidiospore formation from S. bambusicola. Near-spherical conidia were observed and identified by internal transcribed spacer (ITS) sequence detection. A total of 2,840 proteins were identified and 1,976 proteins were quantified in the mycelia and conidia of S. bambusicola. Compared with mycelia, 445 proteins were differentially expressed in the conidia of S. bambusicola, with 165 proteins being upregulated and 280 proteins being downregulated. The Gene Ontology (GO) annotation results of differential proteomics showed that the biological process of S. bambusicola sporulation is complex. The Kyoto Encyclopedia of Genes and Genomes (KEGG) metabolic pathway analysis showed that the differential proteins were mainly involved in starch and sucrose metabolism, biosynthesis of secondary metabolites, microbial metabolism in diverse environments, and other processes. Our in-depth speculative analysis showed that proteins related to carbohydrate metabolism were differentially expressed in conidiospore formation of S. bambusicola, suggesting the involvement of saccharides. Conidiation may increase the synthesis and release of ethanol and polysaccharide proteins such as glycoside hydrolase (GH), suppress host immunity, and facilitate S. bambusicola to infect and colonize of the host. In-depth analysis of differential proteomes will help reveal the molecular mechanism underlying the conidiospore formation of S. bambusicola, which has strong theoretical and practical significance.

Pectin-Coated Iron-Based Metal-Organic Framework Nanoparticles for Enhanced Foliar Adhesion and Targeted Delivery of Fungicides

Conventional agrochemicals are underutilized due to their large particle sizes, poor foliar retention rates, and difficult translocation in plants, and the development of functional nanodelivery carriers with high adhesion to the plant body surface and efficient uptake and translocation in plants remains challenging. In this study, a nanodelivery system based on a pectin-encapsulated iron-based MOF (TF@Fe-MOF-PT NPs) was constructed to enhance the utilization of thifluzamide (TF) in rice plants by taking advantage of the pectin affinity for plant cell walls. The prepared TF@Fe-MOF-PT NPs exhibited an average particle size of 126.55 nm, a loading capacity of 27.41%, and excellent dual-stimulus responses to reactive oxygen species and pectinase. Foliar washing experiments showed that the TF@Fe-MOF-PT NPs were efficiently adhered to the surfaces of rice leaves and stems. Confocal laser scanning microscopy showed that fluorescently labeled TF@Fe-MOF-PT NPs were bidirectionally delivered through vascular bundles in rice plants. The in vitro bactericidal activity of the TF@Fe-MOF-PT NPs showed better inhibitory activity than that of a TF suspension (TF SC), with an EC50 of 0.021 mg/L. A greenhouse test showed that the TF@Fe-MOF-PT NPs were more effective than TF SC at 7 and 14 d, with control effects of 85.88 and 78.59%, respectively. It also reduced the inhibition of seed stem length and root length by TF SC and promoted seedling growth. These results demonstrated that TF@Fe-MOF-PT NPs can be used as a pesticide nanodelivery system for efficient delivery and intelligent release in plants and applied for sustainable control of pests and diseases.

Cell Wall Pectin Content Refers to Favored Delivery of Negatively Charged Carbon Dots in Leaf Cells

In this work, we systematically investigated how cell wall and cell wall components affect the delivery of charged carbon quantum dots (CDs, from -34 to +41 mV) to leaf cells of cucumber and Arabidopsis plants. Four different types of leaf cells in cucumber and Arabidopsis were used, i.e., protoplasts (without cell wall), isolated individual cells (cell wall hydrolyzed with pectinase), regenerated individual cells (cell wall regenerated from protoplast), and intact leaf cells (intact cell wall, in planta). Leaf cells were incubated with charged CDs (0.5 mg/mL) for 2 h. Confocal imaging results showed that protoplasts, regenerated individual cells, and leaf cells showed favored uptake of the negatively charged CDs (-34 mV) compared to the PEI (polyethylenimine) coated and positively charged carbon dots [PEI600-CDs (17 mV) and PEI10K-CDs (41 mV)], while in isolated individual cells, the trend is opposite. The results of the content of the cell wall components showed that no significant changes in the total cell wall content were found between isolated individual cells and regenerated individual cells (1.28 vs 1.11 mg/106 cells), while regenerated individual cells showed significant higher pectin content [water-soluble pectin (0.13 vs 0.06 mg/106 cells, P < 0.01), chelator-soluble pectin (0.04 vs 0.01 mg/106 cells, P < 0.01), and alkaline pectin (0.02 vs 0.01 mg/106 cells, P < 0.01)] and significant lower cellulose content (0.13 vs 0.32 mg/106 cells, P < 0.01) than the isolated individual cells. No difference of the hemicellulose content was found between isolated individual cells and regenerated individual cells (0.20 vs 0.21 mg/106 cells). Our results suggest that compared with cellulose and hemicellulose in the cell wall, the pectin is a more important factor referring to the favored uptake of negatively charged carbon dots in leaf cells. Overall, this work provides a method to study the role of cell wall components in the uptake of nanoparticles in plant cells and also points out the importance of understanding the interactions between cell barriers and nanoparticles to design nanoparticles for agricultural use.

Seasonal Developing Xylem Transcriptome Analysis of Pinus densiflora Unveils Novel Insights for Compression Wood Formation

Wood is the most important renewable resource not only for numerous practical utilizations but also for mitigating the global climate crisis by sequestering atmospheric carbon dioxide. The compressed wood (CW) of gymnosperms, such as conifers, plays a pivotal role in determining the structure of the tree through the reorientation of stems displaced by environmental forces and is characterized by a high content of lignin. Despite extensive studies on many genes involved in wood formation, the molecular mechanisms underlying seasonal and, particularly, CW formation remain unclear. This study examined the seasonal dynamics of two wood tissue types in Pinus densiflora: CW and opposite wood (OW). RNA sequencing of developing xylem for two consecutive years revealed comprehensive transcriptome changes and unique differences in CW and OW across seasons. During growth periods, such as spring and summer, we identified 2255 transcripts with differential expression in CW, with an upregulation in lignin biosynthesis genes and significant downregulation in stress response genes. Notably, among the laccases critical for monolignol polymerization, PdeLAC17 was found to be specifically expressed in CW, suggesting its vital role in CW formation. PdeERF4, an ERF transcription factor preferentially expressed in CW, seems to regulate PdeLAC17 activity. This research provides an initial insight into the transcriptional regulation of seasonal CW development in P. densiflora, forming a foundation for future studies to enhance our comprehension of wood formation in gymnosperms.

Identification of a Comprehensive Gene Co-Expression Network Associated with Autotetraploid Potato (Solanum tuberosum L.) Development Using WGCNA Analysis

The formation and development of potato tissues and organs is a complex process regulated by a variety of genes and environmental factors. The regulatory mechanisms underlying the growth and development are still unclear. In this work, we aimed to explore the changes in gene expression patterns and genetic characteristics of potato tissues throughout different developmental stages. To achieve this, we used autotetraploid potato JC14 as an experimental subject to analyze the transcriptome of the root, stem, and leaf at the seedling, tuber formation, and tuber expansion stages. The results revealed thousands of differentially expressed genes, predominantly involved in defense response and carbohydrate metabolism according to KEGG pathway enrichment analysis. Weighted gene co-expression network analysis (WGCNA) revealed a total of 12 co-expressed gene modules, with 4 modules showing the highest correlation with potato stem development. By calculating the connectivity of genes within the module, hub genes were identified, and functional annotations were subsequently performed. A total of 40 hub genes from the four modules were identified, and their functions were found to be related to carbohydrate metabolism, defense response, and transcription factors. These findings provide important insights for further understanding of the molecular regulation and genetic mechanisms involved in potato tissue development.

VDR Regulates BNP Promoting Neurite Growth and Survival of Cochlear Spiral Ganglion Neurons through cGMP-PKG Signaling Pathway

Spiral ganglion neurons (SGNs) are important for hearing, and their peripheral and central processes connect sensory cells of the Corti organ to the central nervous system. The resulting network forms a point-to-point auditory conduction. As a cardiac hormone, brain natriuretic peptide (BNP) binds to natriuretic peptide receptor type A leading to diuresis, vasodilatation, inhibition of renin and aldosterone production, and cardiac and vascular myocyte growth. This study primarily aimed to explore the expression and function of BNP in the rat's inner ear and elucidate its regulatory mechanism. We determined the expression and function of BNP and found that the vitamin D receptor (VDR) could upregulate the expression of BNP and enhance its function. In SGNs of the rat inner ear, BNP promotes neuron survival and prolongs neurite length through the cGMP-PKG signaling pathway, which could be regulated by VDR and provide a novel approach for neuronal regeneration therapy. To the best of our knowledge, this is the first study to report this potential transcriptional regulatory relationship and will act as a reference for research on neuronal regeneration therapy for SGNs injury.

Integrated Transcriptome and Proteome Analysis Provides Insight into the Ribosome Inactivating Proteins in Plukenetia volubilis Seeds

Plukenetia volubilis is a highly promising plant with high nutritional and economic values. In our previous studies, the expression levels of ricin encoded transcripts were the highest in the maturation stage of P. volubilis seeds. The present study investigated the transcriptome and proteome profiles of seeds at two developmental stages (Pv-1 and Pv-2) using RNA-Seq and iTRAQ technologies. A total of 53,224 unigenes and 6026 proteins were identified, with functional enrichment analyses, including GO, KEGG, and KOG annotations. At two development stages of P. volubilis seeds, 8815 unique differentially expressed genes (DEGs) and 4983 unique differentially abundant proteins (DAPs) were identified. Omics-based association analysis showed that ribosome-inactivating protein (RIP) transcripts had the highest expression and abundance levels in Pv-2, and those DEGs/DAPs of RIPs in the GO category were involved in hydrolase activity. Furthermore, 21 RIP genes and their corresponding amino acid sequences were obtained from libraries produced with transcriptome analysis. The analysis of physicochemical properties showed that 21 RIPs of P. volubilis contained ricin, the ricin_B_lectin domain, or RIP domains and could be divided into three subfamilies, with the largest number for type II RIPs. The expression patterns of 10 RIP genes indicated that they were mostly highly expressed in Pv-2 and 4 transcripts encoding ricin_B_like lectins had very low expression levels during the seed development of P. volubilis. This finding would represent valuable evidence for the safety of oil production from P. volubilis for human consumption. It is also notable that the expression level of the Unigene0030485 encoding type I RIP was the highest in roots, which would be related to the antiviral activity of RIPs. This study provides a comprehensive analysis of the physicochemical properties and expression patterns of RIPs in different organs of P. volubilis and lays a theoretical foundation for further research and utilization of RIPs in P. volubilis.

Comprehensive Transcriptome Analysis of Stem-Differentiating Xylem Upon Compression Stress in Cunninghamia Lanceolata

Compression wood (CW) in gymnosperm brings great difficulties to wood industry using wood as raw materials since CW presents special wood structure and have different physical and chemical properties from those of normal wood (NW). Chinese fir (Cunninghamia lanceolata) is widely distributed in China. However, global transcriptome profiling of coding and long non-coding RNA in response to compression stress has not been reported in the gymnosperm species. In this study, we revealed that CW in Chinese fir exhibited distinct morphology and cytology properties compared with those of NW, including high lignin content, thick and round tracheid cells. Furthermore, we combined both PacBio long-read SMRT sequencing (Iso-Seq) and Illumina short-read RNA-Seq to reveal the transcriptome in stem-differentiating xylem (SDX) under different time points (2, 26, and 74 h) upon compression stress in NW, CW, and OW (opposite wood), respectively. Iso-Seq was successfully assembled into 41,253 de-novo full-length transcriptome reference (average length 2,245 bp). Moreover, there were striking differences in expression upon compression stress, which were involved 13 and 7 key enzyme genes in the lignin and cellulose synthesis, respectively. Especially, we revealed 11 secondary growth-related transcription factors show differential expression under compression stress, which was further validated by qRT-PCR. Finally, the correlation between 6,533 differentially expressed coding genes and 372 differentially expressed long non-coding RNAs (lncRNAs) indicates that these lncRNAs may affect cell wall biogenesis and xyloglucan metabolism. In conclusion, our results provided comprehensive cytology properties and full-length transcriptome profiling of wood species upon compression stress. Especially we explored candidate genes, including both coding and long non-coding genes, and provided a theoretical basis for further research on the formation mechanism of CW in gymnosperm Chinese fir.

A PtrLBD39-mediated transcriptional network regulates tension wood formation in Populus trichocarpa

Tension wood (TW) is a specialized xylem tissue formed in angiosperm trees under gravitational stimulus or mechanical stresses (e.g., bending). The genetic regulation that underlies this important mechanism remains poorly understood. Here, we used laser capture microdissection of stem xylem cells coupled with full transcriptome RNA-sequencing to analyze TW formation in Populus trichocarpa. After tree bending, PtrLBD39 was the most significantly induced transcription factor gene; it has a phylogenetically paired homolog, PtrLBD22. CRISPR-based knockout of PtrLBD39/22 severely inhibited TW formation, reducing cellulose and increasing lignin content. Transcriptomic analyses of CRISPR-based PtrLBD39/22 double mutants showed that these two genes regulate a set of TW-related genes. Chromatin immunoprecipitation sequencing (ChIP-seq) was used to identify direct targets of PtrLBD39. We integrated transcriptomic analyses and ChIP-seq assays to construct a transcriptional regulatory network (TRN) mediated by PtrLBD39. In this TRN, PtrLBD39 directly regulates 26 novel TW-responsive transcription factor genes. Our work suggests that PtrLBD39 and PtrLBD22 specifically control TW formation by mediating a TW-specific TRN in Populus.

Efficient Transformation of Catalpa bungei Shows Crystal Genes Conferring Resistance to the Shoot Borer Omphisa plagialis

Although Catalpa bungei is a forest plant with considerable economic and ornamental value in China, its wood and decorative qualities are constrained by insect pests such as the shoot borer Omphisa plagialis (Lepidoptera). Overexpressing insect resistance genes such as crystal genes to develop an insect-resistant variety of C. bungei is an environmental and ecological approach. However, genotype limitations and low regeneration rates of embryogenic calli (EC) inhibit the development of transformation and the insect-resistant gene expression system in C. bungei. Here, we first established embryogenic callus induction and regeneration systems of five genotypes using mature seed and stem segment explants; the highest induction and regeneration rates of EC were 39.89 and 100%, respectively. Next, an efficient and stable Agrobacterium-mediated genetic transformation system was developed from EC and its positive frequency was up to 92.31%. Finally, using the transformation system, 15 and 22 transgenic C. bungei lines that expressed Cry2A and Cry9Aa-like were generated, respectively. These transgenic lines that exhibited significantly higher resistance to O. plagialis in the laboratory and field have great promise for meeting the challenge of future pest management under changing climatic conditions. Additionally, this efficient, fast, and stable transformation system could be a potential tool for gene function analysis and forest tree genetic improvement.

Transcriptomic, Proteomic, and Metabolic Profiles of Catalpa bungei Tension Wood Reveal New Insight Into Lignin Biosynthesis Involving Transcription Factor Regulation

Lignin is a complex polymer in plant cell walls whose proportion is second only to that of cellulose and plays an important role in the mechanical properties of wood and stress resistance of plants. Here, we induced tension wood (TW) formation in Catalpa bungei by artificial bending and analyzed the lignin metabolism of the TW. LC-MS analysis showed that a significantly higher content of coniferyl aldehyde was observed in the TW cell wall than in the opposite wood (OW) and normal wood (NW) cell walls. TW had significantly lower contents of coniferyl alcohol than OW and NW. Raman spectroscopy results indicated that TW had lower total lignin than OW and NW. The transcription and translation levels of most of the differentially expressed genes (DEGs) involved in lignin monomer biosynthesis indicated upregulation in TW/OW and TW/NW. We found no significant difference in the transcription levels of three collision gases (CADs) between TW and OW or between NW, but their translation levels were significantly downregulated in TW, suggesting post-transcriptional control for CAD. We predicted and analyzed transcription factors that could target DEGs involved in lignin monomer biosynthesis in TW. Based on the analysis of the relationships of targeting and coexpression, we found that NAC (evm.model.group1.695) could potentially target 4CLs and CCoAOMT, that HD-Zip (evm.model.group7.1157) had potential targeting relationships with CCoAOMT, F5H, and CCR, and that their expression levels were significantly positive. It is speculated that the upregulation of NAC and HD-ZIP transcription factors activates the expression of downstream target genes, which leads to a significant increase in coniferyl aldehyde in TW. However, the decrease in total lignin in TW may be caused by the significant downregulation of CAD translation and the significant decrease in precursors (coniferyl alcohol). Whether the expression of CAD genes is regulated by post-transcriptional control and affects TW lignin metabolism needs further study.

Genome-wide analysis of lncRNA and mRNA expression and endogenous hormone regulation during tension wood formation in Catalpa bungei

BACKGROUND

Phytohormones are the key factors regulating vascular development in plants, and they are also involved in tension wood (TW) formation. Although the theory of hormone distribution in TW formation is widely supported, the effects of endogenous hormones on TW formation have not yet been assessed. In this study, TW formation was induced in Catalpa bungei by artificial bending. The phytohormone content of TW, opposite wood (OW) and normal wood (NW) was determined using liquid chromatography-mass spectrometry (LC-MS), and transcriptome sequencing was performed. The hormone content and related gene expression data were comprehensively analyzed.

RESULTS

The results of analyses of the plant hormone contents indicated significantly higher levels of cis-zeatin (cZ), indoleacetic acid (IAA) and abscisic acid (ABA) in TW than in OW. Genes involved in the IAA and ABA synthesis pathways, such as ALDH (evm.

MODEL

group5.1511) and UGT (evm.

MODEL

scaffold36.20), were significantly upregulated in TW. and the expression levels of ARF (evm.

MODEL

group5.1332), A-ARR (evm.

MODEL

group0.1600), and TCH4 (evm.

MODEL

group2.745), which participate in IAA, cZ and Brassinolide (BR) signal transduction, were significantly increased in TW. In particular, ARF expression may be regulated by long noncoding RNAs (lncRNAs) and the HD-ZIP transcription factor ATHB-15.

CONCLUSIONS

We constructed a multiple hormone-mediated network of C. bungei TW formation based on hormone levels and transcriptional expression profiles were identified during TW formation.

Plant Cell and Organism Development

Plants represent a unique and fascinating group of living organisms [...].

Multi-omics sequencing provides insight into floral transition in Catalpa bungei. C.A. Mey

BACKGROUND

Floral transition plays an important role in development, and proper time is necessary to improve the value of valuable ornamental trees. The molecular mechanisms of floral transition remain unknown in perennial woody plants. "Bairihua" is a type of C. bungei that can undergo floral transition in the first planting year.

RESULTS

Here, we combined short-read next-generation sequencing (NGS) and single-molecule real-time (SMRT) sequencing to provide a more complete view of transcriptome regulation during floral transition in C. bungei. The circadian rhythm-plant pathway may be the critical pathway during floral transition in early flowering (EF) C. bungei, according to horizontal and vertical analysis in EF and normal flowering (NF) C. bungei. SBP and MIKC-MADS-box were seemingly involved in EF during floral transition. A total of 61 hub genes were associated with floral transition in the MEturquoise model with Weighted Gene Co-expression Network Analysis (WGCNA). The results reveal that ten hub genes had a close connection with the GASA homologue gene (Cbu.gene.18280), and the ten co-expressed genes belong to five flowering-related pathways. Furthermore, our study provides new insights into the complexity and regulation of alternative splicing (AS). The ratio or number of isoforms of some floral transition-related genes is different in different periods or in different sub-genomes.

CONCLUSIONS

Our results will be a useful reference for the study of floral transition in other perennial woody plants. Further molecular investigations are needed to verify our sequencing data.