Genetic, transcriptional, and regulatory landscape of monolignol biosynthesis pathway in Miscanthus × giganteus

Exploring the role of the LkABCG36 transporter in lignin accumulation

Lignin is a complex biopolymer formed through the condensation of three monomeric precursors known as monolignols. However, the mechanism underlying lignin precursor transport remains elusive, with uncertainty over whether it occurs through passive diffusion or an active energized process. ATP-binding cassette 36 (ABCG36) plays important roles in abiotic stress resistance. In this study, we investigated the transport functions of LkABCG36 (Larix kaempferi) for lignin precursors and the potential effects of LkABCG36 overexpression in plants. LkABCG36 enhanced the ability of tobacco (Nicotiana tabacum) bright yellow-2 (BY-2) cells to resist monolignol alcohol stress. Furthermore, LkABCG36 overexpression promoted lignin deposition in tobacco plant stem tissue. To understand the underlying mechanism, we measured the BY-2 cell ability to export lignin monomers and the uptake of monolignol precursors in inside-out (inverted) plasma membrane vesicles. We found that the transport of coniferyl and sinapyl alcohols is an ATP-dependent process. Our data suggest that LkABCG36 contributes to lignin accumulation in tobacco stem tissues through a mechanism involving the active transport of lignin precursors to the cell wall. These findings shed light on the lignin biosynthesis process, with important implications for enhancing lignin deposition in plants, potentially leading to improved stress tolerance and biomass production.

Integrative analysis of metabolome, proteome, and transcriptome for identifying genes influencing total lignin content in Populus trichocarpa

Lignin, a component of plant cell walls, possesses significant research potential as a renewable energy source to replace carbon-based products and as a notable pollutant in papermaking processes. The monolignol biosynthetic pathway has been elucidated and it is known that not all monolignol genes influence the total lignin content. However, it remains unclear which monolignol genes are more closely related to the total lignin content and which potential genes influence the total lignin content. In this study, we present a combination of t-test, differential gene expression analysis, correlation analysis, and weighted gene co-expression network analysis to identify genes that regulate the total lignin content by utilizing multi-omics data from transgenic knockdowns of the monolignol genes that includes data related to the transcriptome, proteome, and total lignin content. Firstly, it was discovered that enzymes from the PtrPAL, Ptr4CL, PtrC3H, and PtrC4H gene families are more strongly correlated with the total lignin content. Additionally, the co-downregulation of three genes, PtrC3H3, PtrC4H1, and PtrC4H2, had the greatest impact on the total lignin content. Secondly, GO and KEGG analysis of lignin-related modules revealed that the total lignin content is not only influenced by monolignol genes, but also closely related to genes involved in the "glutathione metabolic process", "cellular modified amino acid metabolic process" and "carbohydrate catabolic process" pathways. Finally, the cinnamyl alcohol dehydrogenase genes CAD1, CADL3, and CADL8 emerged as potential contributors to total lignin content. The genes HYR1 (UDP-glycosyltransferase superfamily protein) and UGT71B1 (UDP-glucosyltransferase), exhibiting a close relationship with coumarin, have the potential to influence total lignin content by regulating coumarin metabolism. Additionally, the monolignol genes PtrC3H3, PtrC4H1, and PtrC4H2, which belong to the cytochrome P450 genes, may have a significant impact on the total lignin content. Overall, this study establishes connections between gene expression levels and total lignin content, effectively identifying genes that have a significant impact on total lignin content and offering novel perspectives for future lignin research endeavours.

Development of energy plants from hybrids between Miscanthus sacchariflorus and M. lutarioriparius grown on reclaimed mine land in the Loess Plateau of China

Miscanthus, a promising bioenergy plant, has a high biomass yield with high cellulose content suitable for biofuel production. However, harsh climatic and poor soil conditions, such as barren lands or abandoned mines, pose a challenge to the survival and yield of Miscanthus feedstock on the marginal land. The selection from the interspecific hybrids of Miscanthus might combine high survival rates and high yield, which benefits energy crop development in multi-stressful environments. A total of 113 F₁ hybrids between Miscanthus sacchariflorus and M. lutarioriparius together with the parents were planted and evaluated for multiple morphological and physiological traits on the mine land of the Loess Plateau of China. The majority of hybrids had higher establishment rates than M. sacchariflorus while M. lutarioriparius failed to survive for the first winter. Nearly all hybrid genotypes outperformed M. lutarioriparius for yield-related traits including plant height, tiller number, tiller diameter, and leaf area. The average biomass of the hybrids was 20 times higher than that of surviving parent, M. sacchariflorus. Furthermore, the photosynthetic rates and water use efficiency of the hybrids were both significantly higher than those of the parents, which might be partly responsible for their higher yield. A total of 29 hybrids with outstanding traits related to yield and stress tolerance were identified as candidates. The study investigated for the first time the hybrids between local individuals of M. sacchariflorus and high-biomass M. lutarioriparius, suggesting that this could be an effective approach for high-yield energy crop development on vast of marginal lands.

MYB transcription factors-master regulators of phenylpropanoid biosynthesis and diverse developmental and stress responses

Phenylpropanoids, the largest class of natural products including flavonoids, anthocyanins, monolignols and tannins perform multiple functions ranging from photosynthesis, nutrient uptake, regulating growth, cell division, maintenance of redox homeostasis and biotic and abiotic stress responses. Being sedentary life forms, plants possess several regulatory modules that increase their performance in varying environments by facilitating activation of several signaling cascades upon perception of developmental and stress signals. Of the various regulatory modules, those involving MYB transcription factors are one of the extensive groups involved in regulating the phenylpropanoid metabolic enzymes in addition to other genes. R2R3 MYB transcription factors are a class of plant-specific transcription factors that regulate the expression of structural genes involved in anthocyanin, flavonoid and monolignol biosynthesis which are indispensable to several developmental pathways and stress responses. The aim of this review is to present the regulation of the phenylpropanoid pathway by MYB transcription factors via Phospholipase D/phosphatidic acid signaling, downstream activation of the structural genes, leading to developmental and/or stress responses. Specific MYB transcription factors inducing or repressing specific structural genes of anthocyanin, flavonoid and lignin biosynthetic pathways are discussed. Further the roles of MYB in activating biotic and abiotic stress responses are delineated. While several articles have reported the role of MYB's in stress responses, they are restricted to two or three specific MYB factors. This review is a consolidation of the diverse roles of different MYB transcription factors involved both in induction and repression of anthocyanin, flavonoid, and lignin biosynthesis.

Bioengineering and Molecular Biology of Miscanthus

Miscanthus is a perennial wild plant that is vital for the production of paper and roofing, as well as horticulture and the development of new high-yielding crops in temperate climates. Chromosome-level assembly of the ancient tetraploid genome of miscanthus chromosomes is reported to provide resources that can link its chromosomes to related diploid sorghum and complex polyploid sugarcane. Analysis of Miscanthus sinensis and Miscanthus sacchariflorus showed intense mixing and interspecific hybridization and documented the origin of a high-yielding triploid bioenergetic plant, Miscanthus × giganteus. The Miscanthus genome expands comparative genomics functions to better understand the main abilities of Andropogoneae herbs. Miscanthus × giganteus is widely regarded as a promising lignocellulosic biomass crop due to its high-biomass yield, which does not emit toxic compounds into the environment, and ability to grow in depleted lands. The high production cost of lignocellulosic bioethanol limits its commercialization. The main components that inhibit the enzymatic reactions of fermentation and saccharification are lignin in the cell wall and its by-products released during the pre-treatment stage. One approach to overcoming this barrier could be to genetically modify the genes involved in lignin biosynthesis, manipulating the lignin content and composition of miscanthus.

Breeding Targets to Improve Biomass Quality in Miscanthus

Lignocellulosic crops are attractive bioresources for energy and chemicals production within a sustainable, carbon circular society. Miscanthus is one of the perennial grasses that exhibits great potential as a dedicated feedstock for conversion to biobased products in integrated biorefineries. The current biorefinery strategies are primarily focused on polysaccharide valorization and require severe pretreatments to overcome the lignin barrier. The need for such pretreatments represents an economic burden and impacts the overall sustainability of the biorefinery. Hence, increasing its efficiency has been a topic of great interest. Inversely, though pretreatment will remain an essential step, there is room to reduce its severity by optimizing the biomass composition rendering it more exploitable. Extensive studies have examined the miscanthus cell wall structures in great detail, and pinpointed those components that affect biomass digestibility under various pretreatments. Although lignin content has been identified as the most important factor limiting cell wall deconstruction, the effect of polysaccharides and interaction between the different constituents play an important role as well. The natural variation that is available within different miscanthus species and increased understanding of biosynthetic cell wall pathways have specified the potential to create novel accessions with improved digestibility through breeding or genetic modification. This review discusses the contribution of the main cell wall components on biomass degradation in relation to hydrothermal, dilute acid and alkaline pretreatments. Furthermore, traits worth advancing through breeding will be discussed in light of past, present and future breeding efforts.

Genetic Improvement of Arundo donax L.: Opportunities and Challenges

Arundo donax L., the giant reed-being a long-duration, low-cost, non-food energy crop able to grow in marginal lands-has emerged as a potential alternative to produce biomass for both energy production, with low carbon emissions, and industrial bioproducts. In recent years, pioneering efforts have been made to genetically improve this very promising energy crop. This review analyses the recent advances and challenges encountered in using clonal selection, mutagenesis/somaclonal variation and transgenesis/genome editing. Attempts to improve crop yield, in vitro propagation efficiency, salt and heavy metal tolerance by clonal selection were carried out, although limited by the species' low genetic diversity and availability of mutants. Mutagenesis and somaclonal variation have also been attempted on this species; however, since Arundo donax is polyploid, it is very difficult to induce and select promising mutations. In more recent years, genomics and transcriptomics data are becoming available in Arundo, closing the gap to make possible the genetic manipulation of this energy crop in the near future. The challenge will regard the functional characterization of the genes/sequences generated by genomic sequencing and transcriptomic analysis in a complex polyploid genome.