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.

NnLAC17, a Gene Related to Lignin Synthesis, is Involved in Adventitious Root Formation in the Seedlings of Lotus (Nelumbo Nucifera Gaertn)

BarkgroundAdventitious roots (ARs), which are considered as an important member of root system, have an unmatched status in plant growth and metabolism due to the degeneration of primary roots in lotus. The regulation of AR formation was previously revealed and multiple factors were recognized to be involved in this biological process. ResultsIn the present study, we sought to assess the effect of sucrose on AR formation. Based on our results, lignin metabolism, which is regulated by the sucrose signal transduction pathway, is involved in AR development. The lignification degree of the AR primordium was weaker in plants treated with 20 g/L sucrose than in control plants. However, based on the microstructural observation of the AR developmental process, 50 g/L sucrose promoted the lignification process. Lignin content, including monomer and polymer lignin, was determined in the present study. Compared with control plants, the monomer (containing 30%–45% S type and 55%–70% G type) and polymer lignin contents were lower in plants treated with 20 g/L sucrose and higher in plants treated with 50 g/L sucrose. The precursors of monomer lignin were identified in four libraries of differential developmental stages in seedlings using LC-MS/MS technique. The contents of four metabolites, including p-coumaric acid, caffeate, sinapinal aldehyde and ferulic acid for monomer lignin synthsis were lower in the GL50 library than in the GL20 library. Further analysis revealed that the gene expression of these four metabolites had no novel difference in the GL50/GL20 libraries. However, NnLAC17, a gene involved in polymer lignin synthesis, had a higher expression in the GL50 library than in the GL20 library. ConclusionsTherefore, NnLAC17 was cloned, and the overexpression of NnLAC17 was found to directly result in a decrease in AR number in transgenic Arabidopsis plants. These findings suggest that NnLAC17, which is relevant to lignin synthesis, is involved in AR formation in lotus seedlings.

Preharvest Application of Chitosan Improves the Postharvest Life of ‘Garmrok’ Kiwifruit through the Modulation of Genes Related to Ethylene Biosynthesis, Cell Wall Modification and Lignin Metabolism

The influence of the preharvest application of chitosan on physicochemical properties and changes in gene expression of ‘Garmrok’ kiwifruit during postharvest cold storage (0 °C; RH 90–95%; 90 days) was investigated. Preharvest treatment of chitosan increased the fruit weight but had no significant effect on fruit size. The chitosan treatment suppressed the ethylene production and respiration rate of kiwifruit during the cold storage. The reduction of ethylene production of chitosan-treated kiwifruit was accompanied with the suppressed expression of ethylene biosynthesis genes. Moreover, preharvest application of chitosan diminished weight loss and delayed the changes in physicochemical properties that include firmness, soluble solids content, titratable acidity, total sugars, total acids, total phenols, and total lignin. As a result, the preharvest application of chitosan delayed the maturation and ripening of fruit. Expression of genes related to cell wall modification was down-regulated during the early maturation (ripening) period, while those related to gene expression for lignin metabolism were up-regulated at the later stages of ripening. These results demonstrate that the preharvest application of chitosan maintained the fruit quality and extends the postharvest life of ‘Garmrok’ kiwifruit, possibly through the modulation of genes related to ethylene biosynthesis, cell wall modification, and lignin metabolism.

Effects of Multiple Planting Densities on Lignin Metabolism and Lodging Resistance of the Strip Intercropped Soybean Stem

The shading of maize and self-shading are the key factors affecting the stem lignin biosynthesis and lodging resistance of soybean at middle and later growth stages in the strip intercropping system. A study was designed to explore the regulation mechanism of lignin metabolism and different planting densities; PD1, PD2, and PD3 were used having a total number of 17 plants m−2, 20 plants m−2, and 25 plants m−2, respectively, on the lodging resistance of strip intercropped soybean stem. Our results depicted that the lower planting density (PD1) appropriately promoted the leaf photosynthesis activities (Pn), increase the activity of lignin-related enzymes and the accumulation of carbohydrates in stems, and eventually enhanced the lodging resistance of the strip intercropped soybean stem. Correlation analysis also showed that the lodging resistance index of soybean stem was significantly correlated with the available light for soybean canopy and Pn strip intercropped soybean stem characteristics and activities of enzymes related to lignin synthesis among the different planting densities. The findings of our research will be useful in future studies to understand the relationship between different light environment, planting densities, and lodging resistance of intercropped soybean and also guide the optimum planting density in maize–soybean intercropping system.

Exploring the complexity of soybean (Glycine max) transcriptional regulation using global gene co-expression networks

ABSTRACTSoybean (Glycine max (L.) Merr.) is one of the most important crops worldwide, constituting a major source of protein and edible oil. Gene co-expression networks (GCN) have been extensively used to study transcriptional regulation and evolution of genes and genomes. Here, we report a soybean GCN using 1,284 publicly available RNA-Seq samples from 15 distinct tissues. We found modules that are differentially regulated in specific tissues, comprising processes such as photosynthesis, gluconeogenesis, lignin metabolism, and response to biotic stress. We identified transcription factors among intramodular hubs, which probably integrate different pathways and shape the transcriptional landscape in different conditions. The top hubs for each module tend to encode proteins with critical roles, such as succinate dehydrogenase and RNA polymerase subunits. Importantly, gene essentiality was strongly correlated with degree centrality and essential hubs enriched in genes involved in nucleic acids metabolism and regulation of cell replication. By using a using a guilt-by-association approach, we predicted functions for 93 of 106 hubs without functional description in soybean. Most of the duplicated genes had different transcriptional profiles, supporting their functional divergence, although paralogs originating from whole-genome duplications (WGD) are more often preserved in the same module than those from other mechanisms. Together, our results highlight the importance of GCN analysis in unraveling key functional aspects of the soybean genome, in particular those associated with hub genes and WGD events.

Global analysis insights into coupling relationship between lignan and lignin metabolism of flax

Background: Flax ( Linum usitatissimum L.) is one of the most important economic crops in the world. The lignin content of flax stems directly determines the quality of flax fibers. Flax seeds contain lignans of highly beneficial for human health.Results: To elucidate the metabolic relationship between these compounds and the regulatory nodes of their metabolic processes, third generation (PacBio Iso-Seq) and second generation (Illumina) sequencing technologies were used to sequence the transcriptomes of a pair of flax cultivars with significant differences in lignan content. It was discovered that the differential expressed genes (DEGs) are significantly enriched in the lignin and lignan biosynthesis pathways. Furthermore, there are seven genes with significant differences in expression that were annotated as UDP-glucosyl transferases ( UGTs ). We found that lignan and lignin content is significantly negatively correlated with each other. SEM observations on flax bast fibers provided further evidence of this relationship.Conclusions: This is the first full-length transcriptome analysis on flax plants using third-generation sequencing technologies, and it is also the first study to observe a negative correlation between lignin and lignan content of flax plants. Furthermore, it was found that UGTs are likely to be regulatory node genes for lignan and lignin metabolism.

Effects of Metaxenia on Stone Cell Formation in Pear (Pyrus bretschneideri) Based on Transcriptomic Analysis and Functional Characterization of the Lignin-Related Gene PbC4H2

The deposition of lignin in flesh parenchyma cells for pear stone cells, and excessive stone cells reduce the taste and quality of the fruit. The effect of metaxenia on the quality of fruit has been heavily studied, but the effect of metaxenia on stone cell formation has not been fully elucidated to date. This study used P. bretschneideri (Chinese white pear) cv. ‘Yali’ (high-stone cell content) and P. pyrifolia (Sand pear) cv. ‘Cuiguan’ (low-stone cell content) as pollination trees to pollinate P. bretschneideri cv. ‘Lianglizaosu’ separately to fill this gap in the literature. The results of quantitative determination, histochemical staining and electron microscopy indicated that the content of stone cells and lignin in YL fruit (‘Yali’ (pollen parent) × ‘Lianglizaosu’ (seed parent)) was significantly higher than that in CL fruit (‘Cuiguan’ (pollen parent) × ‘Lianglizaosu’ (seed parent)). The transcriptome sequencing results that were obtained from the three developmental stages of the two types of hybrid fruits indicated that a large number of differentially expressed genes (DEGs) related to auxin signal transduction (AUX/IAAs and ARFs), lignin biosynthesis, and lignin metabolism regulation (MYBs, LIMs, and KNOXs) between the CL and YL fruits at the early stage of fruit development. Therefore, metaxenia might change the signal transduction process of auxin in pear fruit, thereby regulating the expression of transcription factors (TFs) related to lignin metabolism, and ultimately affecting lignin deposition and stone cell development. In addition, we performed functional verification of a differentially expressed gene, PbC4H2 (cinnamate 4-hydroxylase). Heterologous expression of PbC4H2 in the c4h mutant not only restored its collapsed cell wall, but also significantly increased the lignin content in the inflorescence stem. The results of our research help to elucidate the metaxenia-mediated regulation of pear stone cell development and clarify the function of PbC4H2 in cell wall development and lignin synthesis, which establishes a foundation for subsequent molecular breeding.