Auxin response factors fine-tune lignin biosynthesis in response to mechanical bending in bamboo

PtrVINV2 is dispensable for cellulose synthesis but essential for salt tolerance in Populus trichocarpa Torr. and Gray

Invertase (EC.3.2.1.26), a key enzyme in sucrose breakdown, is crucial for cellulose synthesis. However, the function of the vacuolar invertase (VINV) in woody plants remains unclear. In this study, transgenic lines of Populus trichocarpa Torr. and Gray were generated to investigate the role of PtrVINV2 in wood formation and under high salinity stress. Compared to wild-type (WT), VINV activity in the developing xylem of knockout lines was reduced, resulting in a decrease in lignin content and an increase in hemicellulose content, while cellulose content remained unaffected. These changes in structural carbohydrate content were accompanied by reductions in xylem width and fibre cell wall thickness. The overexpression lines of the developing xylem exhibited opposite trends. Transcriptome analyses of developing xylem indicated that the expression level of PtrVINV2 affects the expression of genes involved in hemicellulose and lignin biosynthesis pathways, such as AXS, UAMs, HCT, COMT, CAD and peroxidases, while CesA expression remained unaffected. WGCNA analysis revealed that Potri.001G219100, Potri.009G106600 and Potri.002G081000 serve as 'hub' transcription factor genes within the structural/non-structural carbohydrate modules of PtrVINV2 transgenic lines, potentially involved in plant salt tolerance. Additionally, under 200 mmol/L NaCl treatment, the knockout lines exhibited increased salt sensitivity compared to WT. This increased sensitivity was accompanied by elevated activities of SOD, CAT and MDA, as well as higher sucrose content and reduced contents of glucose and fructose. The findings indicate that although PtrVINV2 is not essential for cellulose synthesis, it enhances salt tolerance in poplar and presents a promising candidate gene for breeding salt-tolerant poplar.

PtrCWINV3 encoding a cell wall invertase regulates carbon flow to wood in Populus trichocarpa

Cell wall invertase (CWINV) catalyzes the hydrolysis of sucrose into glucose and fructose in the apoplastic unloading pathway, with carbon sources provided for sink tissues. However, its role in wood formation remains undetermined. Therefore, transgenic lines overexpressing PtrCWINV3 or with knocked-out PtrCWINV3 expression were generated in Populus trichocarpa. Compared with wild type, the PtrCWINV3-knockout lines showed decreased CWINV activity (by 7.4 %-10.8 %), which resulted in a 1.5 %-1.8 % decrease in cellulose content, a 0.82 %-0.98 % decrease in hemicellulose content, and an increase in lignin content (by 2.9 %-4.7 %). These changes in structural carbohydrate contents were accompanied with anomalies in the late stages of secondary xylem development, characterized by reduced width of the secondary xylem, fewer cell layers in secondary xylem, and thinner fiber cell walls. The lines overexpressing PtrCWINV3 under the control of the DX15 promoter in the developing xylem showed the opposite phenotype. Transcriptome data from the developing xylem indicated that PtrCWINV3 regulated the expression of genes involved in the biosynthesis of cellulose (CesA, EG, and CB), hemicellulose/pectin (UGD, AXS, GATL, UAM, PAE, and GAUT), and starch (GBSS), which suggested its involvement in multiple polysaccharide metabolic pathways. Ultimately, this facilitated the synthesis of structural carbohydrate components such as cellulose and hemicellulose, which promoted the later stages of secondary xylem development. These findings not only demonstrate the significant role of CWINV activity in wood formation, but also highlight an excellent candidate gene for breeding new poplar varieties with high cellulose and low lignin contents.

Advances in bamboo genomics: Growth and development, stress tolerance, and genetic engineering

Bamboo is a fast-growing and ecologically significant plant with immense economic value due to its applications in construction, textiles, and bioenergy. However, research on bamboo has been hindered by its long vegetative period, unpredictable flowering cycles, and challenges in genetic transformation. Recent developments in advanced sequencing and genetic engineering technologies have provided new insights into bamboo's evolutionary history, developmental biology, and stress resilience, paving the way for improved conservation and sustainable utilization. This review synthesizes the latest findings on bamboo's genomics, biotechnology, and the molecular mechanisms governing its growth, development, and stress response. Key genes and regulatory pathways controlling its rapid growth, internode elongation, rhizome development, culm lignification, flowering, and abiotic stress responses have been identified through multi-omics and functional studies. Complex interactions among transcription factors, epigenetic regulators, and functionally important genes shape bamboo's unique growth characteristics. Moreover, progress in genetic engineering techniques, including clustered regularly interspaced short palindromic repeats-based genome editing, has opened new avenues for targeted genetic improvements. However, technical challenges, particularly the complexity of polyploid bamboo genomes and inefficient regeneration systems, remain significant barriers to functional studies and large-scale breeding efforts. By integrating recent genomic discoveries with advancements in biotechnology, this review proposes potential strategies to overcome existing technological limitations and to accelerate the development of improved bamboo varieties. Continued efforts in multi-omics research, gene-editing applications, and sustainable cultivation practices will be essential for harnessing bamboo as a resilient and renewable resource for the future. The review presented here not only deepens our understanding of bamboo's genetic architecture but also provides a foundation for future research aimed at optimizing its ecological and industrial potential.

Identification and characterization of auxin response factor (ARF) gene family in five Bambusoideae species reveals the role of PedARF 23 in regulating lignin synthesis through auxin signaling

Auxin plays a critical role in plant growth and development, mediating responses to environmental stimuli and directing organ growth by establishing and maintaining auxin concentration gradients. Auxin Response Factors (ARFs) are key transcription factors that regulate the expression of auxin-responsive genes. Different ARF genes can act as transcriptional activators or repressors, functioning through various auxin signaling pathways at different developmental stages and under various environmental conditions. Studying the ARF gene family in bamboo is essential for uncovering the molecular mechanisms underlying rapid growth, maintenance of apical dominance, and root development in bamboo. However, research on the function of ARF genes in bamboo is still limited. In this study, we utilized the latest bamboo genome data to comprehensively analyze the genomes of five representative bamboo species, identifying a total of 216 ARF genes and classifying them into 12 subfamilies based on phylogenetic relationships. Through a combination of transcriptome date and RT-qPCR analysis, we observed that the PedARF23 gene in Moso bamboo was significantly upregulated following NAA treatment. To further explore the mechanisms by which PedARF23 modulates plant growth and development via auxin signaling, we developed PedARF23 overexpression lines. By measuring auxin and lignin levels, the expression of key genes (4CL3, 4CL7, and CCoAOMT1) in the lignin biosynthesis pathway in both Moso bamboo and transgenic Arabidopsis, as well as the Yeast one-hybrid assay and LUC activation assay, study discovered that PedARF23 could enhances auxin synthesis and activates the auxin signaling pathway, thereby regulating lignin biosynthesis. Overall, this study provides a foundation for understanding the classification, characteristics, and functions of the ARF gene family in the Bambusoideae. It elucidates the role of ARFs in regulating lignin synthesis, offering valuable insights into the regulation of lignin content in bamboo.

Identification and characterization of the auxin-response factor family in moso bamboo reveals that PeARF41 negatively regulates second cell wall formation

Auxin response factors (ARFs) are key transcriptional factors mediating the transcriptional of auxin-related genes that play crucial roles in a range of plant metabolic activities. The characteristics of 47 PeARFs, identified in moso bamboo and divided into three classes, were evaluated. Structural feature analysis showed that intron numbers ranged from 3 to 14, while Motif 1, 2, 7 and 10 were highly conserved, altogether forming DNA-binding and ARF domains. Analysis of RNA-seq from different tissues revealed that PeARFs showed tissue-specificity. Additionally, abundant hormone-response and stress-related elements were enriched in promoters of PeARFs, supporting the hypothesis that the expression of PeARFs was significantly activated or inhibited by ABA and cold treatments. Further, PeARF41 overexpression inhibited SCW formation by reducing hemicellulose, cellulose and lignin contents. Moreover, a co-expression network, containing 28 genes with PeARF41 at its core was predicted, and the results of yeast one hybridization (Y1H), electrophoretic mobility shift assay (EMSA) and dual-luciferase (Dul-LUC) assays showed that PeARF41 bound the PeSME1 promoter to inhibit its expression. We conclude that a 'PeARF41-PeSME1' regulatory cascade mediates SCW formation. Our findings provided a solid theoretical foundation for further research on the role of PeARFs.

Subgenome asymmetry of gibberellins-related genes plays important roles in regulating rapid growth of bamboos

Rapid growth is an innovative trait of woody bamboos that has been widely studied. However, the genetic basis and evolution of this trait are poorly understood. Taking advantage of genomic resources of 11 representative bamboos at different ploidal levels, we integrated morphological, physiological, and transcriptomic datasets to investigate rapid growth. In particular, these bamboos include two large-sized and a small-sized woody species, compared with a diploid herbaceous species. Our results showed that gibberellin A1 was important for the rapid shoot growth of the world's largest bamboo, Dendrocalamus sinicus, and indicated that two gibberellins (GAs)-related genes, KAO and SLRL1, were key to the rapid shoot growth and culm size in woody bamboos. The expression of GAs-related genes exhibited significant subgenome asymmetry with subgenomes A and C demonstrating expression dominance in the large-sized woody bamboos while the generally submissive subgenomes B and D dominating in the small-sized species. The subgenome asymmetry was found to be correlated with the subgenome-specific gene structure, particularly UTRs and core promoters. Our study provides novel insights into the molecular mechanism and evolution of rapid shoot growth following allopolyploidization in woody bamboos, particularly via subgenome asymmetry. These findings are helpful for understanding of how polyploidization in general and subgenome asymmetry in particular contributed to the origin of innovative traits in plants.

Optimization of vegetation carbon content parameters and their application in carbon storage estimation in China

As a key parameter for C pool and flux assessments, vegetation carbon (C) content can be used in ecological models to predict climate-induced changes in the C sequestration capacity of vegetation. However, the differences in methods for upscaling C content from the organ to the community scale and their impact on regional C stock estimates have been ignored. Based on a comprehensive community structure survey of 72 typical natural ecosystems in China and 27,905 measured samples of plant organs (leaves, twigs, trunks, and roots), we first quantified the differences among scaling-up methods for vegetation C content. These methods included the community or dominant species-weighted mean, geometric mean, arithmetic mean, and traditional empirical coefficients (45 % and 50 %), and their impact on C storage estimation at the regional scale. Comparing the accuracy, variability, and response patterns of the different scaling-up methods, the dominant C species biomass-weighted mean (CDWM) method had the highest similarity to the community-weighted C mean (CCWM) method. Concerning vegetation C storage estimation in China's natural terrestrial ecosystems, the relative errors of the other methods ranged from -2.6 % to 8.22 % compared with that of the CCWM method (18.39 Pg C). The empirical coefficients had the highest uncertainty, with a 45 % empirical coefficient underestimating the vegetation C stock by 2.60 %, and a 50 % empirical coefficient overestimating it by 8.22 %. The CDWM method proposed here has high reliability for C storage estimation (overestimated by only 0.44 %), making it a preferable sampling and scaling-up method for regional C content and stock assessment. Additionally, our study provided the C content of plant organs for China's provinces and typical vegetation types based on the CCWM, which could be used for regional C stock assessment and C cycle models.

Characterization and expression analysis of the B3 gene family during seed development in Akebia trifoliata

BACKGROUND

B3 genes encode transcription factors that play key roles in plant growth and development. However, the specific B3 genes involved in the seed development of Akebia trifoliata remain unexplored.

RESULTS

A total of 72 AktB3 genes were identified and classified into five subfamilies (ARF, LAV, RAV, HSI, and REM) based on phylogenetic analysis. These 72 AktB3 genes were unevenly distributed across 16 chromosomes. Collinear analysis indicated that segmental duplication has played a significant role in the evolution of AktB3 genes, and underwent purification selection. Expression profiling across seed development stages revealed that seven AktB3 genes, particularly from the LAV subfamily (AktABI3, AktFUS3, AktLEC2), were up-regulated at 70 days after flowering (DAF). Notably, the expression of oleosin exhibited a strong positive correlation with LAV subfamily genes, highlighting their potential roles as hub genes in lipid metabolism and seed development. Yeast two-hybrid (Y2H) and yeast one-hybrid (Y1H) experiments confirmed that AktFUS3-1, AktFUS3-2, and AktLEC2 form protein complexes and individually bind to the AktOLE1 promoter, thereby regulating downstream gene expression. These results provide direct evidence of the cooperative role these transcription factors play in controlling lipid metabolism, particularly related to oleosin proteins. Additionally, miRNA sequencing across three seed developmental stages identified 591 miRNAs and 1,673 target gene pairs. A total of 23 AktB3 genes were predicted to be targets of 20 miRNAs, with 11 miRNAs specifically targeting the ARF subfamily genes. Particularly, miR160-x, miR160-z, and miR167-z were predicted to target ARF subfamily genes, potentially influencing seed development. Moreover, the miRNA-B3 regulatory modules, especially involving ARF genes and miR160/167, require further study to clarify their roles in seed development.

CONCLUSIONS

These findings contribute valuable resources for future functional studies of the molecular regulatory networks governing seed development in A. trifoliata.

Comparison analysis of ABCG subfamily in bamboo and the potential function of PeABCG15 in monolignol transport

Lignin is a principal component of secondary cell wall and plays vital roles in various biological processes. In this study, 68 and 42 members of ABC transporter G subfamily (ABCG) were identified in Bambusa amplexicaulis and Olyra latifolia, which were less than that of 77 in moso bamboo (Phyllostachys edulis). Collinearity analysis showed that ABCGs had undergone robust purifying selection with lower functional differentiation. These ABCGs were clustered into two clades of WBC and PDR. Notably, PeABCG15 was highly expressed with the lignification of bamboo shoot. The WGCNA revealed that PeABCG15 was co-expressed with eight MYB genes, among which PeMYB203 was able to activate PeABCG15 validated by Y1H, DLR, and GUS assays. Furthermore, over-expressing PeABCG15 significantly enhanced the content of lignin and the expression levels of monolignol biosynthetic genes in Arabidopsis thaliana, conferring improved tolerance to exogenous coniferyl alcohol. Collectively, our findings elucidated the prospective contribution of PeABCG15 to monolignol transport, providing insights into the lignin biosynthesis mechanism in bamboo.

Impaired Brown midrib12 function orchestrates sorghum resistance to aphids via an auxin conjugate indole-3-acetic acid-aspartic acid

Lignin, a complex heterogenous polymer present in virtually all plant cell walls, plays a critical role in protecting plants from various stresses. However, little is known about how lignin modifications in sorghum will impact plant defense against sugarcane aphids (SCA), a key pest of sorghum. We utilized the sorghum brown midrib (bmr) mutants, which are impaired in monolignol synthesis, to understand sorghum defense mechanisms against SCA. We found that loss of Bmr12 function and overexpression (OE) of Bmr12 provided enhanced resistance and susceptibility to SCA, respectively, as compared with wild-type (WT; RTx430) plants. Monitoring of the aphid feeding behavior indicated that SCA spent more time in reaching the first sieve element phase on bmr12 plants compared with RTx430 and Bmr12-OE plants. A combination of transcriptomic and metabolomic analyses revealed that bmr12 plants displayed altered auxin metabolism upon SCA infestation and specifically, elevated levels of auxin conjugate indole-3-acetic acid-aspartic acid (IAA-Asp) were observed in bmr12 plants compared with RTx430 and Bmr12-OE plants. Furthermore, exogenous application of IAA-Asp restored resistance in Bmr12-OE plants, and artificial diet aphid feeding trial bioassays revealed that IAA-Asp is associated with enhanced resistance to SCA. Our findings highlight the molecular underpinnings that contribute to sorghum bmr12-mediated resistance to SCA.

Rice CHD3/Mi-2 chromatin remodeling factor RFS regulates vascular development and root formation by modulating the transcription of auxin-related genes NAL1 and OsPIN1

The vascular system in plants facilitates long-distance transportation of water and nutrients through the xylem and phloem, while also providing mechanical support for vertical growth. Although many genes that regulate vascular development in rice have been identified, the mechanism by which epigenetic regulators control vascular development remains unclear. This study found that Rolled Fine Striped (RFS), a Chromodomain Helicase DNA-binding 3 (CHD3)/Mi-2 subfamily protein, regulates vascular development in rice by affecting the initiation and development of primordia. The rfs mutant was found to affect auxin-related genes, as revealed by RNA sequencing and reverse transcription-quantitative PCR analysis. The transcript levels of OsPIN1 and NAL1 genes were downregulated in rfs mutant, compared to the wild-type plant. The chromatin immunoprecipitation assays showed lower levels of H3K4me3 in the OsPIN1a and NAL1 genes in rfs mutant. Furthermore, exogenous auxin treatment partially rescued the reduced adventitious root vascular development in rfs mutant. Subsequently, exogenous treatments with auxin or an auxin-transport inhibitor revealed that the expression of OsPIN1a and NAL1 is mainly affected by auxin. These results provide strong evidence that RFS plays an important role in vascular development and root formation through the auxin signaling pathway in rice. [BMB Reports 2024; 57(10): 441-446].

Unveiling the mechanisms of Moso bamboo's motor function and internal growth stress

Bamboo, a renewable resource with rapid growth and an impressive height-to-diameter ratio, faces mechanical instability due to its slender structure. Despite this, bamboo maintains its posture without breaking in its battle against environmental and gravitational forces. But what drives this motor function in bamboo? This study subjected Moso bamboo (Phyllostachys edulis) to gravitational stimulation, compelling it to grow at a 45° angle instead of upright. Remarkably, the artificially inclined bamboo exhibited astonishing shape control and adjustment capabilities. The growth strain was detected at both macroscopic and microscopic levels, providing evidence for the presence of internal stress, namely growth stress. The high longitudinal tensile stress on the upper side, along with a significant asymmetry in stress distribution in tilted bamboo, plays a pivotal role in maintaining its mechanical stability. Drawing upon experimental findings, it can be deduced that the growth stress primarily originates from the broad layers of fiber cells. Bamboo could potentially regulate the magnitude of growth stress by modifying the number of fiber cell layers during its maturation process. Additionally, the microfibril angle and lignin disposition may decisively influence the generation of growth stress.

Stem lodging Resistance-1 controls stem strength by positively regulating the biosynthesis of cell wall components in Capsicum annuum L

Lodging presents a significant challenge in cultivating high-yield crops with extensive above-ground biomass, yet the molecular mechanisms underlying this phenomenon in the Solanaceae family remain largely unexplored. In this study, we identified a gene, CaSLR1 (Capsicum annuum Stem Lodging Resistance 1), which encodes a MYELOBLASTOSIS (MYB) family transcription factor, from a lodging-affected C. annuum EMS mutant. The suppression of CaSLR1 expression in pepper led to notable stem lodging, reduced thickness of the secondary cell wall, and decreased stem strength. A similar phenotype was observed in tomato with the knockdown of SlMYB61, the orthologous gene to CaSLR1. Further investigations demonstrated that CaNAC6, a gene involved in secondary cell wall (SCW) formation, is co-expressed with CaSLR1 and acts as a positive regulator of its expression, as confirmed through yeast one-hybrid, dual-luciferase reporter assays, and electrophoretic mobility shift assays. These findings elucidate the CaNAC6-CaSLR1 module that contributes to lodging resistance, emphasizing the critical role of CaSLR1 in the lodging resistance regulatory network.

Identification of the function of a key gene NnHCT1 in lignin synthesis in petioles of Nelumbo nucifera

Leaf petiole or stem strength is an important agronomic trait affecting the growth of underground organs as a channel for material exchange and plays a vital role in the quality and yield of crops and vegetables. There are two different types of petioles in lotus, floating leaf petioles and vertical leaf petioles; however, the internal difference mechanism between these petioles is unclear. In this study, we investigated the differences between the initial vertical leaf petioles and the initial floating leaf petioles based on RNA sequencing (RNA-seq), and >2858 differentially expressed genes were annotated. These genes were chiefly enriched in phenylpropanoid biosynthesis, which is the source of the lignin and cellulose in petioles and stems. Lignin biology-related gene NnHCT1 was identified, and subsequent biological function validation demonstrated that the transient overexpression of NnHCT1 significantly increased the lignin and cellulose contents in lotus petioles and tobacco leaves. In contrast, silencing NnHCT1 through virus-induced gene silencing significantly reduced petiole lignin synthesis. Additionally, differentially up-regulated MYB family transcription factors were identified using RNA-seq. Yeast-one-hybrid and dual-luciferase reporter assays demonstrated that MYB4 could bind to the NnHCT1 promoter and up-regulate NnHCT1 expression. These findings demonstrate the significant potential of NnHCT1 to enhance lignin synthesis, thereby improving stem or petiole resistance to stunting and explaining the need for the study of differential petiole relationships in plants.

Integrating Physiological Features and Proteomic Analyses Provides New Insights in Blue/Red Light-Treated Moso Bamboo (Phyllostachys edulis)

Bamboo is one of the most important nontimber forestry products in the world. Light is not only the most critical source of energy for plant photosynthesis but also involved in regulating the biological processes of plants. However, there are few reports on how blue/red light affects Moso bamboo. This study investigated the growth status and physiological responses of Moso bamboo (Phyllostachys edulis) to blue/red light treatments. The growth status of the bamboo plants was evaluated, revealing that both blue- and red-light treatments promoted plant height and overall growth. Gas exchange parameters, chlorophyll fluorescence, and enzyme activity were measured to assess the photosystem response of Moso bamboo to light treatments. Additionally, the blue light treatment led to a higher chlorophyll content and enzyme activities compared to the red light treatment. A tandem mass tag quantitative proteomics approach identified significant changes in protein abundance under different light conditions with specific response proteins associated with distinct pathways, such as photosynthesis and starch metabolism. Overall, this study provides valuable insights into the physiological and proteomic responses of Moso bamboo to blue/red light treatments, highlighting their potential impact on growth and development.