Genome-Wide Identification of Switchgrass Laccases Involved in Lignin Biosynthesis and Heavy-Metal Responses

Excessive copper induces lignin biosynthesis in the leaves and roots of two citrus species: Physiological, metabolomic and anatomical aspects

Excessive copper (Cu) of rhizosphere inhibited the growth and development of citrus seedlings. Lignin deposition on the cell wall promotes plant Cu tolerance. However, the lignin biosynthesis in citrus leaves and roots that respond to Cu toxicity is not fully understood. In this study, young seedlings of 'Xuegan' [Citrus sinensis (L.) Osbeck, a less Cu-tolerant species] and 'Shatian pomelo' [Citrus grandis (L.) Osbeck, a more Cu-tolerant species] were treated with nutrient solution containing 0.5 (as Control), 100, 300 or 500 µM Cu for 15 weeks in sandy culture. By the end of treatments, citrus leaves and roots were sampled to investigate the biomass allocation, Cu distribution, the lignin biosynthesis and deposition. The results indicated that Cu stress from 100 to 500 µM increased the root/shoot biomass ratio, promoting Cu and lignin accumulation in the leaves and roots of the tested citrus species. Besides, 300 µM Cu stress increased the accumulation of three lignin monomers of citrus species. The metabolomic profile indicated that Cu toxicity altered the lignin components of citrus species. The citrus roots are more prominent in the lignin precursor biosynthesis under Cu toxicity than citrus leaves. The histochemical staining supported that Cu stress improved the deposition of both guaiacy and syringy lignin units in citrus roots. The enzyme activity and gene expression revealed that activating lignin-biosynthetic enzymes, such as L-phenylalanine ammonia-lyase, peroxidase and laccase, played an essential role in lignin biosynthesis. Our results demonstrated that excessive Cu induced lignin biosynthesis in citrus leaves and roots to different extents. The findings from the present study increased our understanding of lignin biosynthesis in Cu-stressed citrus species, which would provide a theoretical basis for the citrus Cu-tolerant mechanisms.

Genome-wide identification, classification, and expression profiling of LAC gene family in sesame

BACKGROUND

Laccases (LACs) are vital plant growth and development enzymes, participating in lignin biopolymerization and responding to stress. However, the role of LAC genes in plant development as well as stress tolerance, is still not well understood, particularly in sesame (Sesamum indicum L.), an important oilseed crop.

RESULTS

In this study, 51 sesame LAC genes (SiLACs) were identified, which were unevenly distributed across different chromosomes. The phylogeny of Arabidopsis LAC (AtLACs) subdivided the SiLAC proteins into seven subgroups (Groups I-VII), of which Group VII contained only sesame LACs. Within the same subgroup, SiLACs exhibit comparable structures and conserved motifs. The promoter region of SiLACs harbors various cis-acting elements that are related to plant growth, phytohormones, and stress responses. Most SiLACs were expressed in the roots and stems, whereas some were expressed specifically in flowers or seeds. RNA-seq analysis revealed that 19 SiLACs exhibited down-regulation and three showed up-regulation in response to drought stress, while 15 SiLACs were down-regulated and four up-regulated under salt stress. Additionally, qRT-PCR analysis showcased that certain SiLAC expression was significantly upregulated as a result of osmotic and salt stress. SiLAC5 and SiLAC17 exhibited the most significant changes in expression under osmotic and salt stresses, indicating that they may serve as potential targets for improving sesame resistance to various stresses.

CONCLUSIONS

Our study offers a thorough comprehension of LAC gene structure, classification, evolution, and abiotic stress response in sesame plants. Furthermore, we provide indispensable genetic resources for sesame functional characterization to enhance its tolerance to various abiotic stresses.

Heterologous expression of AaLac1 gene in hairy roots and its role in secondary metabolism under PEG-induced osmotic stress condition in Artemisia annua L

This study explores the Laccase gene (AaLac) family along with AaLac1 expression in hairy roots of A. annua. 42 AaLacs were identified by detecting three conserved domains: Cu-oxidase, Cu oxidase-2, and Cu oxidase-3. The physicochemical properties show that AaLacs are proteins with 541-1075 amino acids. These proteins are stable, with an instability index less than 40. Phylogenetic and motif studies have shown structural variants in AaLacs, suggesting functional divergence. 22 AaLac cis-regulatory elements were selected for their roles in drought stress, metabolic modulations, defense, and stress responses. A comparison of AtLac and AaLac proteins showed that 11 AtLacs mitigates stress reactions. In silico expression, analysis of 11 AtLacs showed that AtLac84 may function under osmotic stress. Thus, the Homolog AaLac1 was selected by expression profiling. The real-time PCR results showed that AaLac1 enhances osmotic stress tolerance in shoot and root samples. It was also used to analyze AaLac1, ADS, and CYP71AV1 gene expression in hairy roots via induction. The transformed hairy roots exhibited a greater capacity for PEG-induced osmotic stress tolerance in contrast to the untransformed roots. The gene expression analysis also depicted a significant increment in expression of AaLac1, ADS, and CYP71AV1 genes to 3.8, 6.9, and 3.1 folds respectively. The transformed hairy roots exhibited a significant increase of 2.2 and 1.4 fold in flavonoid and phenolic content respectively. Also, lignin content and artemisinin content increased by 7.05 folds and 95.6% with respect to the control. Thus, transformed hairy roots of A. annua under PEG-induced osmotic stress demonstrate the involvement of the AaLac1 gene in stress responses, lignin biosynthesis, and secondary metabolism production.

Supplementary Information

The online version contains supplementary material available at 10.1007/s12298-024-01516-8.

An EIL Family Transcription Factor From Switchgrass Affects Sulphur Assimilation and Root Development in Arabidopsis

Sulphur limitation 1 (SLIM1), a member of ethylene-insensitive3-like (EIN3/EIL) protein family, is recognised as the pivotal transcription factor regulating sulphur assimilation, essential for maintaining sulphur homoeostasis in Arabidopsis. However, the function of its monocot homologues is largely unknown. In this study, we identified PvEIL3a, a homologous gene of AtSLIM1, from switchgrass (Panicum virgatum L.), a significant perennial bioenergy crop. Our results demonstrated that introducing PvEIL3a into Arabidopsis slim1 mutants significantly increased the expression of genes responsive to sulphur deficiency, and transgenic plants exhibited shortened root length and delayed development. Moreover, PvEIL3a activated the expression of AtAPR1, AtSULTR1;1 and AtBGLU30, which plays an important role in sulphur assimilation and glucosinolate metabolism. Results of transcriptome and metabonomic analysis further indicated a perturbation in the metabolic pathways of tryptophan-dependent indole glucosinolates (IGs), camalexin and auxin. In addition, PvEIL3a conservatively regulated sulphur assimilation and the biosynthesis of tryptophan pathway-derived secondary metabolites, which reduced the biosynthesis of indole-3-acetic acid (IAA) and inhibited the root elongation of transgenic Arabidopsis. In conclusion, this study highlights the functional difference of the ethylene-insensitive 3-like (EIL) family gene in monocot and dicot plants, thereby deepening the understanding of the specific biological roles of EIL3 in monocot plant species.

Genome-wide analysis of the common bean (Phaseolus vulgaris) laccase gene family and its functions in response to abiotic stress

BACKGROUND

Laccase (LAC) gene family plays a pivotal role in plant lignin biosynthesis and adaptation to various stresses. Limited research has been conducted on laccase genes in common beans.

RESULTS

29 LAC gene family members were identified within the common bean genome, distributed unevenly in 9 chromosomes. These members were divided into 6 distinct subclades by phylogenetic analysis. Further phylogenetic analyses and synteny analyses indicated that considerable gene duplication and loss presented throughout the evolution of the laccase gene family. Purified selection was shown to be the major evolutionary force through Ka / Ks. Transcriptional changes of PvLAC genes under low temperature and salt stress were observed, emphasizing the regulatory function of these genes in such conditions. Regulation by abscisic acid and gibberellins appears to be the case for PvLAC3, PvLAC4, PvLAC7, PvLAC13, PvLAC14, PvLAC18, PvLAC23, and PvLAC26, as indicated by hormone induction experiments. Additionally, the regulation of PvLAC3, PvLAC4, PvLAC7, and PvLAC14 in response to nicosulfuron and low-temperature stress were identified by virus-induced gene silence, which demonstrated inhibition on growth and development in common beans.

CONCLUSIONS

The research provides valuable genetic resources for improving the resistance of common beans to abiotic stresses and enhance the understanding of the functional roles of the LAC gene family.

Grass lignin: biosynthesis, biological roles, and industrial applications

Lignin is a phenolic heteropolymer found in most terrestrial plants that contributes an essential role in plant growth, abiotic stress tolerance, and biotic stress resistance. Recent research in grass lignin biosynthesis has found differences compared to dicots such as Arabidopsis thaliana. For example, the prolific incorporation of hydroxycinnamic acids into grass secondary cell walls improve the structural integrity of vascular and structural elements via covalent crosslinking. Conversely, fundamental monolignol chemistry conserves the mechanisms of monolignol translocation and polymerization across the plant phylum. Emerging evidence suggests grass lignin compositions contribute to abiotic stress tolerance, and periods of biotic stress often alter cereal lignin compositions to hinder pathogenesis. This same recalcitrance also inhibits industrial valorization of plant biomass, making lignin alterations and reductions a prolific field of research. This review presents an update of grass lignin biosynthesis, translocation, and polymerization, highlights how lignified grass cell walls contribute to plant development and stress responses, and briefly addresses genetic engineering strategies that may benefit industrial applications.

Genome-wide study of Cerrena unicolor 87613 laccase gene family and their mode prediction in association with substrate oxidation

BACKGROUND

Laccases are green biocatalysts with wide industrial applications. The study of efficient and specific laccase producers remains a priority. Cerrena species have been shown to be promising basidiomycete candidates for laccase production. Although two sets of Cerrena genome data have been publicly published, no comprehensive bioinformatics study of laccase gene family in C. unicolor has been reported, particularly concerning the analysis of their three-dimensional (3D) structures and molecular docking to substrates, like ABTS and aflatoxin B1 (AFB1).

RESULTS

In this study, we conducted a comprehensive genome-wide analysis of laccase gene family in C. unicolor 87613. We identified eighteen laccase genes (CuLacs) and classified them into three clades using phylogenetic analysis. We characterized these laccases, including their location in contig 5,6,9,12,15,19,26,27, gene structures of different exon-intron arrangements, molecular weight ranging from 47.89 to 141.41 kDa, acidic pI value, 5-15 conserved protein motifs, signaling peptide of extracellular secretion (harbored by 13 CuLacs) and others. In addition, the analysis of cis-acting element in laccase promoters indicated that the transcription response of CuLac gene family was regulatable and complex under different environmental cues. Furthermore, analysis of transcription pattern revealed that CuLac8, 12 and CuLac2, 13 were the predominant laccases in response to copper ions or oxidative stress, respectively. Finally, we focused on the 3D structure analysis of CuLac proteins. Seven laccases with extra transmembrane domains or special sequences were particularly interesting. Predicted structures of each CuLac protein with or without these extra sequences showed altered interacting amino acid residues and binding sites, leading to varied affinities to both ABTS and AFB1. As far as we know, it is the first time to discuss the influence of the extra sequence on laccase's affinity to substrates.

CONCLUSIONS

Our findings provide robust genetic data for a better understanding of the laccase gene family in C. unicolor 87613, and create a foundation for the molecular redesign of CuLac proteins to enhance their industrial applications.

Genome-wide identification of bZIP transcription factor family in Artemisia annua, its transcriptional profiling and regulatory role in phenylpropanoid metabolism under different light conditions

The basic leucine zipper (bZIP) protein transcription factors are known to modulate development, plant growth, metabolic response, and resistance to several biotic and abiotic stressors and have been widely studied in the model plant Arabidopsis thaliana. However, no comprehensive information about the bZIP transcription factor family in Artemisia annua has been explored to date. In this genome-wide study, we identified 61 bZIP TFs after removing false positives and incomplete sequences from Artemisia annua. Seven highly expressed homolog AabZIP TF genes under UV-B and differential light conditions in different tissues were identified from the publicly available microarray dataset as having their cis-regulatory elements involved in, flavonoids biosynthesis, seed-specific gene regulation, stress responses, and metabolic regulation. In-silico analysis and electrophoretic mobility shift assay (EMSA) confirmed the interaction of AabZIP19 TF over the AaPAL1 promoter in order to regulate the phenolics and flavonoid biosynthesis via the phenylpropanoid pathway. Further, RT-PCR analysis has been carried out to validate the transcript levels of selected AabZIP genes under white light, red light, blue light (45 min), and UV-B exposure (12 and 24 h). These genes have their highest expression levels under UV-B and blue light exposure, in contrast with white light. Therefore, the detection of ROS through staining confirms the accumulation of superoxide radicals and H2O2, and in addition to reducing ROS accumulation under UV-B and blue light irradiation, total phenols and flavonoids are significantly enhanced. This study laid the groundwork for deciphering the possible role of AabZIP TFs under different light stress-responsive conditions and in the regulation of secondary metabolism.

Supplementary Information

The online version contains supplementary material available at 10.1007/s12298-023-01338-0.

The Citrus Laccase Gene CsLAC18 Contributes to Cold Tolerance

Plant laccases, as multicopper oxidases, play an important role in monolignol polymerization, and participate in the resistance response of plants to multiple biotic/abiotic stresses. However, little is currently known about the role of laccases in the cold stress response of plants. In this study, the laccase activity and lignin content of C. sinensis leaves increased after the low-temperature treatment, and cold treatment induced the differential regulation of 21 CsLACs, with 15 genes being upregulated and 6 genes being downregulated. Exceptionally, the relative expression level of CsLAC18 increased 130.17-fold after a 48-h treatment. The full-length coding sequence of CsLAC18 consists of 1743 nucleotides and encodes a protein of 580 amino acids, and is predominantly expressed in leaves and fruits. CsLAC18 was phylogenetically related to AtLAC17, and was localized in the cell membrane. Overexpression of CsLAC18 conferred enhanced cold tolerance on transgenic tobacco; however, virus-induced gene silencing (VIGS)-mediated suppression of CsLAC18 in Poncirus trifoliata significantly impaired resistance to cold stress. As a whole, our findings revealed that CsLAC18 positively regulates a plant's response to cold stress, providing a potential target for molecular breeding or gene editing.

Characterization of Peroxidase and Laccase Gene Families and In Silico Identification of Potential Genes Involved in Upstream Steps of Lignan Formation in Sesame

Peroxidases and laccases are oxidative enzymes involved in physiological processes in plants, covering responses to biotic and abiotic stress as well as biosynthesis of health-promoting specialized metabolites. Although they are thought to be involved in the biosynthesis of (+)-pinoresinol, a comprehensive investigation of this class of enzymes has not yet been conducted in the emerging oil crop sesame and no information is available regarding the potential (+)-pinoresinol synthase genes in this crop. In the present study, we conducted a pan-genome-wide identification of peroxidase and laccase genes coupled with transcriptome profiling of diverse sesame varieties. A total of 83 and 48 genes have been identified as coding for sesame peroxidase and laccase genes, respectively. Based on their protein domain and Arabidopsis thaliana genes used as baits, the genes were classified into nine and seven groups of peroxidase and laccase genes, respectively. The expression of the genes was evaluated using dynamic transcriptome sequencing data from six sesame varieties, including one elite cultivar, white vs black seed varieties, and high vs low oil content varieties. Two peroxidase genes (SiPOD52 and SiPOD63) and two laccase genes (SiLAC1 and SiLAC39), well conserved within the sesame pan-genome and exhibiting consistent expression patterns within sesame varieties matching the kinetic of (+)-pinoresinol accumulation in seeds, were identified as potential (+)-pinoresinol synthase genes. Cis-acting elements of the candidate genes revealed their potential involvement in development, hormonal signaling, and response to light and other abiotic triggers. Transcription factor enrichment analysis of promoter regions showed the predominance of MYB binding sequences. The findings from this study pave the way for lignans-oriented engineering of sesame with wide potential applications in food, health and medicinal domains.