Comprehensive genome-wide analysis of the pear (Pyrus bretschneideri) laccase gene (PbLAC) family and functional identification of PbLAC1 involved in lignin biosynthesis

A Combined Metabolome and Transcriptome Reveals the Lignin Metabolic Pathway during the Developmental Stages of Peel Coloration in the 'Xinyu' Pear

Sand pear is the main cultivated pear species in China, and brown peel is a unique feature of sand pear. The formation of brown peel is related to the activity of the cork layer, of which lignin is an important component. The formation of brown peel is intimately associated with the biosynthesis and accumulation of lignin; however, the regulatory mechanism of lignin biosynthesis in pear peel remains unclear. In this study, we used a newly bred sand pear cultivar 'Xinyu' as the material to investigate the biosynthesis and accumulation of lignin at nine developmental stages using metabolomic and transcriptomic methods. Our results showed that the 30 days after flowering (DAF) to 50DAF were the key periods of lignin accumulation according to data analysis from the assays of lignin measurement, scanning electron microscope (SEM) observation, metabolomics, and transcriptomics. Through weighted gene co-expression network analysis (WGCNA), positively correlated modules with lignin were identified. A total of nine difference lignin components were identified and 148 differentially expressed genes (DEGs), including 10 structural genes (PAL1, C4H, two 4CL genes, HCT, CSE, two COMT genes, and two CCR genes) and MYB, NAC, ERF, and TCP transcription factor genes were involved in lignin metabolism. An analysis of RT-qPCR confirmed that these DEGs were involved in the biosynthesis and regulation of lignin. These findings further help us understand the mechanisms of lignin biosynthesis and provide a theoretical basis for peel color control and quality improvement in pear breeding and cultivation.

Cell size and xylem differentiation regulating genes from Salicornia europaea contribute to plant salt tolerance

Cell wall is involved in plant growth and plays pivotal roles in plant adaptation to environmental stresses. Cell wall remodelling may be crucial to salt adaptation in the euhalophyte Salicornia europaea. However, the mechanism underlying this process is still unclear. Here, full-length transcriptome indicated cell wall-related genes were comprehensively regulated under salinity. The morphology and cell wall components in S. europaea shoot were largely modified under salinity. Through the weighted gene co-expression network analysis, SeXTH2 encoding xyloglucan endotransglucosylase/hydrolases, and two SeLACs encoding laccases were focused. Meanwhile, SeEXPB was focused according to expansin activity and the expression profiling. Function analysis in Arabidopsis validated the functions of these genes in enhancing salt tolerance. SeXTH2 and SeEXPB overexpression led to larger cells and leaves with hemicellulose and pectin content alteration. SeLAC1 and SeLAC2 overexpression led to more xylem vessels, increased secondary cell wall thickness and lignin content. Notably, SeXTH2 transgenic rice exhibited enhanced salt tolerance and higher grain yield. Altogether, these genes may function in the succulence and lignification process in S. europaea. This work throws light on the regulatory mechanism of cell wall remodelling in S. europaea under salinity and provides potential strategies for improving crop salt tolerance and yields.

The Analysis, Description, and Examination of the Maize LAC Gene Family's Reaction to Abiotic and Biotic Stress

Laccase (LAC) is a diverse group of genes found throughout the plant genome essential for plant growth and the response to stress by converting monolignin into intricate lignin formations. However, a comprehensive investigation of maize laccase has not yet been documented. A bioinformatics approach was utilized in this research to conduct a thorough examination of maize (Zea mays L.), resulting in the identification and categorization of 22 laccase genes (ZmLAC) into six subfamilies. The gene structure and motifs of each subgroup were largely consistent. The distribution of the 22 LAC genes was uneven among the maize chromosomes, with the exception of chromosome 9. The differentiation of the genes was based on fragment replication, and the differentiation time was about 33.37 million years ago. ZmLAC proteins are primarily acidic proteins. There are 18 cis-acting elements in the promoter sequences of the maize LAC gene family associated with growth and development, stress, hormones, light response, and stress response. The analysis of tissue-specific expression revealed a high expression of the maize LAC gene family prior to the V9 stage, with minimal expression at post-V9. Upon reviewing the RNA-seq information from the publicly available transcriptome, it was discovered that ZmLAC5, ZmLAC10, and ZmLAC17 exhibited significant expression levels when exposed to various biotic and abiotic stress factors, suggesting their crucial involvement in stress responses and potential value for further research. This study offers an understanding of the functions of the LAC genes in maize's response to biotic and abiotic stress, along with a theoretical basis for comprehending the molecular processes at play.

The Laccase Family Gene CsLAC37 Participates in Resistance to Colletotrichum gloeosporioides Infection in Tea Plants

Fungal attacks have become a major obstacle in tea plantations. Colletotrichum gloeosporioides is one of the most devastating fungal pathogens in tea plantations that can severely affect tea yield and quality. However, the molecular mechanism of resistance genes involved in anthracnose is still largely unknown in tea plants. Here, we found that the laccase gene CsLAC37 was involved in the response to fungal infection based on a transcriptome analysis. The full-length CDS of CsLAC37 was cloned, and its protein sequence had the closest relationship with the Arabidopsis AtLAC15 protein compared to other AtLACs. Tissue-specific expression analysis showed that CsLAC37 had higher expression levels in mature leaves and stems than in the other tissues. Subcellular localization showed that the CsLAC37 protein was predominantly localized in the cell membrane. The expression levels of CsLAC37 were upregulated at different time points under cold, salt, SA, and ABA treatments. qRT-PCR confirmed that CsLAC37 responded to both Pestalotiopsis-like species and C. gloeosporioides infections. Functional validation showed that the hydrogen peroxide (H2O2) content increased significantly, and POD activity decreased in leaves after antisense oligonucleotide (AsODN) treatment compared to the controls. The results demonstrated that CsLAC37 may play an important role in resistance to anthracnose, and the findings provide a theoretical foundation for molecular breeding of tea varieties with resistance to fungal diseases.

Transcriptome analysis reveals that PbMYB61 and PbMYB308 are involved in the regulation of lignin biosynthesis in pear fruit stone cells

Pear fruit stone cells have thick walls and are formed by the secondary deposition of lignin in the primary cell wall of thin-walled cells. Their content and size seriously affect fruit characteristics related to edibility. To reveal the regulatory mechanism underlying stone cell formation during pear fruit development and to identify hub genes, we examined the stone cell and lignin contents of 30 'Shannongsu' pear flesh samples and analyzed the transcriptomes of 15 pear flesh samples collected at five developmental stages. On the basis of the RNA-seq data, 35 874 differentially expressed genes were detected. Additionally, two stone cell-related modules were identified according to a WGCNA. A total of 42 lignin-related structural genes were subsequently obtained. Furthermore, nine hub structural genes were identified in the lignin regulatory network. We also identified PbMYB61 and PbMYB308 as candidate transcriptional regulators of stone cell formation after analyzing co-expression networks and phylogenetic relationships. Finally, we experimentally validated and characterized the candidate transcription factors and revealed that PbMYB61 regulates stone cell lignin formation by binding to the AC element in the PbLAC1 promoter to upregulate expression. However, PbMYB308 negatively regulates stone cell lignin synthesis by binding to PbMYB61 to form a dimer that cannot activate PbLAC1 expression. In this study, we explored the lignin synthesis-related functions of MYB family members. The results presented herein are useful for elucidating the complex mechanisms underlying lignin biosynthesis during pear fruit stone cell development.

Stone cell formation in the pedicel of pears and apples

MAIN CONCLUSION

For the first time, stone cells in pear and apple pedicel were studied. The lignification of the pedicel outer part was correlated with flesh, and the secondary cell wall biosynthesis genes were activated. Fruit pedicels act as bridges between the fruit and the shoot. They have secondary thickened cell walls that presumably function in mechanical support, water and nutrient transport. Stone cells are cells with a secondary cell wall thickening. In pears, yet not in apples, the stone cells affect the flesh texture. There have been few reports on stone cell formation in pear and apple pedicels; therefore, we studied these cells for the first time. The apple pedicel had few stone cells in the cortex. The formation of stone cells in pear continued until seven weeks after flowering (WAF), and the density was significantly higher than in apple. The stone cell formation degree (SFD) of pear was 3.6-7.1 times higher than that of apple. Total lignin and lignin non-condensed structure (G and S units) content in the pear pedicle outer part was 1.5-2.7 times higher than that of the apple at harvest. The SFD of the pedicel outer part had a positive correlation with the G and S units content of the flesh. The total lignin and G and S units content between flesh and the pedicel outer part were positively correlated. Correlation analysis revealed a positive relationship between fruit and pedicel formation of the stone cells. The WGCNA showed that NST3 was linked to NAC028, MYB46, CESA, POD, LAC, and VSR6. These genes were highly expressed in the outer part of the pear pedicel, while they were suppressed in that issue of the apple at 4 WAF.

Transcriptome and Physiological Analysis Highlight Lignin Metabolism of the Fruit Dots Disordering during Postharvest Cold Storage in 'Danxiahong' Pear

Pear (Pyrus L.) is one of the most important fruits in the world. Fruit dots are an important trait that affects pear quality. Abnormal fruit dots usually reduce the merchantability of pears. In this research, during cold storage, 'Danxiahong' pear fruit exhibited protrudent fruit dots on the peels. Microscopy system measurement showed that fruit dots size and height on the abnormal fruit peel were bigger and higher than the normal ones. Likewise, scanning electron microscopy observations indicated that the abnormal fruit peel, in contrast to the normal pear peel, exhibited an abnormal cell structure and fruit dots. Physiological analysis showed that the lignin content in abnormal fruit peel was significantly higher than in normal fruit peel. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analysis revealed that the top-enriched pathways were mainly associated with lignin synthesis and metabolism. The transcripts of lignin biosynthesis-associated genes were analyzed, and the results showed that the expression of a cascade of structural genes, including PpyPAL, PpyCCR, PpyC3H, PpyC4H, PpyHCT, PpyCAD, PpyLAC, and PpyPOD, was significantly induced in the protrudent peels. Furthermore, the expression of regulatory genes involved in lignin biosynthesis, especially the NAC-MYB-based gene regulatory network, was significantly upregulated in the abnormal peels. Real-time quantitative PCR (RT-qPCR) analysis confirmed the induction of lignin biosynthesis genes. Overall, this research revealed that the abnormal fruit surface was caused by fruit dots disorder during cold storage. This research provides insights into the fine regulation pathways in the prevention of fruit dots protrusion, especially in modulating lignin synthesis and metabolism during postharvest storage.

Overexpression of a laccase gene, DiLAC17, from Davidia involucrata causes severe seed abortion in Arabidopsis

Seed abortion is a common phenomenon in woody plants, especially in rare and endangered species. Serious seed abortion occurs in the dove tree and largely restricts its natural reproduction. A number of differentially expressed genes (DEGs) between normal and aborted seeds of the dove tree have been previously identified through transcriptome profiling. Among these, most DEGs encoding laccase showed significant upregulation in the aborted seeds. In this study, the laccase gene with the highest expression level in aborted seeds, DiLAC17, was cloned from the dove tree genome and further verified. Overexpression of the DiLAC17 gene in Arabidopsis resulted in retarded growth, deformed siliques, and severe seed abortion. Most Arabidopsis genes involved in seed development, such as AtLEC2, AtANT1, and AtRGE1, were suppressed in the transgenic lines. Laccase activity and lignin content were significantly improved in transgenic lines under ectopic overexpression of the DiLAC17 gene. Excessive lignin accumulation in the early developmental stage was assumed to be a key cause of restricting silique growth and seed expansion, which ultimately led to seed abortion. These results indicate a laccase-mediated pathway for seed abortion, which might be a strategy adopted by this rare and endangered species to reduce the reproductive load.

Comprehensive analysis of the laccase gene family in tea plant highlights its roles in development and stress responses

BACKGROUND

Laccase (LAC) is the pivotal enzyme responsible for the polymerization of monolignols and stress responses in plants. However, the roles of LAC genes in plant development and tolerance to diverse stresses are still largely unknown, especially in tea plant (Camellia sinensis), one of the most economically important crops worldwide.

RESULTS

In total, 51 CsLAC genes were identified, they were unevenly distributed on different chromosomes and classified into six groups based on phylogenetic analysis. The CsLAC gene family had diverse intron-exon patterns and a highly conserved motif distribution. Cis-acting elements in the promoter demonstrated that promoter regions of CsLACs encode various elements associated with light, phytohormones, development and stresses. Collinearity analysis identified some orthologous gene pairs in C. sinensis and many paralogous gene pairs among C. sinensis, Arabidopsis and Populus. Tissue-specific expression profiles revealed that the majority of CsLACs had high expression in roots and stems and some members had specific expression patterns in other tissues, and the expression patterns of six genes by qRT‒PCR were highly consistent with the transcriptome data. Most CsLACs showed significant variation in their expression level under abiotic (cold and drought) and biotic (insect and fungus) stresses via transcriptome data. Among them, CsLAC3 was localized in the plasma membrane and its expression level increased significantly at 13 d under gray blight treatment. We found that 12 CsLACs were predicted to be targets of cs-miR397a, and most CsLACs showed opposite expression patterns compared to cs-miR397a under gray blight infection. Additionally, 18 highly polymorphic SSR markers were developed, these markers can be widely used for diverse genetic studies of tea plants.

CONCLUSIONS

This study provides a comprehensive understanding of the classification, evolution, structure, tissue-specific profiles, and (a)biotic stress responses of CsLAC genes. It also provides valuable genetic resources for functional characterization towards enhancing tea plant tolerance to multiple (a)biotic stresses.

A large-scale proteogenomic atlas of pear

Pear is an important fruit tree that is widely distributed around the world. The first pear genome map was reported from our laboratory approximately 10 years ago. To further study global protein expression patterns in pear, we generated pear proteome data based on 24 major tissues. The tissue-resolved profiles provided evidence of the expression of 17 953 proteins. We identified 4294 new coding events and improved the pear genome annotation via the proteogenomic strategy based on 18 090 peptide spectra with peptide spectrum matches >1. Among the eight randomly selected new short coding open reading frames that were expressed in the style, four promoted and one inhibited the growth of pear pollen tubes. Based on gene coexpression module analysis, we explored the key genes associated with important agronomic traits, such as stone cell formation in fruits. The network regulating the synthesis of lignin, a major component of stone cells, was reconstructed, and receptor-like kinases were implicated as core factors in this regulatory network. Moreover, we constructed the online database PearEXP (http://www.peardb.org.cn) to enable access to the pear proteogenomic resources. This study provides a paradigm for in-depth proteogenomic studies of woody plants.

Characterization of plant laccase genes and their functions

Laccase is a copper-containing polyphenol oxidase found in different organisms. The multigene family that encodes laccases is widely distributed in plant genomes. Plant laccases oxidize monolignols to produce lignin which is important for plant growth and stress responses. Industrial applications of fungal and bacterial laccases are extensively explored and addressed. Recently many studies have focused on the significance of plant laccase, particularly in crop yield, and its functions in different environmental conditions. This review summarizes the transcriptional and posttranscriptional regulation of plant laccase genes and their functions in plant growth and development. It especially describes the responses of laccase genes to various stresses and their contributions to plant biotic and abiotic stress resistance. In-depth explanations and scientific advances will serve as foundations for research into plant laccase genes' function, mechanism, and possible applications.

Genome-wide analysis of the laccase gene family in wheat and relationship with arbuscular mycorrhizal colonization

We identified 156 laccase genes belonging to 11 subfamilies in the wheat genome, and the natural variation of laccase genes significantly affected the development of wheat-arbuscular mycorrhizal symbiosis. Laccases (LACs) have a variety of functions in plant lignification, cell elongation and stress responses. This study aimed to reveal the phylogeny, chromosomal spatial distribution, coexpression and evolution of LAC genes in the wheat genome and to investigate the possible roles of LAC genes during arbuscular mycorrhizal (AM) symbiosis. The genomic characteristics of LAC genes were analyzed by using bioinformatics analysis methods, and the polymorphisms of LAC genes were analyzed by using a diverse wheat panel composed of 289 wheat cultivars. We identified 156 LAC genes belonging to 11 subfamilies in the wheat genome, and segmental duplication dominated the amplification of the LAC gene family in the wheat genome. LACs are dominantly located in the R2 region of wheat chromosomes. Some LACs are collinear with the characterized LACs in Arabidopsis thaliana or rice. A number of genes encoding transcription factors, kinases, and phosphatases were coexpressed with LAC genes in wheat. TaLACs may be potential targets for some miRNAs. Most TaLACs are mainly expressed in the roots and stems of plants. The expression of TaLACs could be regulated by the inoculation of Fusarium graminearum or AM fungi. The polymorphisms of TaLACs mainly accumulate by random drift instead of by selection. Through candidate gene association analysis, we found that the natural variations in TaLACs significantly affected root colonization by AM fungi. The present study provides useful information for further study of the biological functions of LAC genes in wheat, especially the roles of LAC genes during the development of AM symbiosis.

Overexpression of SmLAC25 promotes lignin accumulation and decreases salvianolic acid content in Salvia miltiorrhiza

Laccase (LAC) is a blue multicopper oxidase that contains four copper ions, which is involved in lignin polymerization and flavonoid biosynthesis in plants. Although dozens of LAC genes have been identified in Salvia miltiorrhiza Bunge (a model medicinal plant), most have not been functionally characterized. Here, we explored the expression patterns and the functionality of SmLAC25 in S. miltiorrhiza. SmLAC25 has a higher expression level in roots and responds to methyl jasmonate, auxin, abscisic acid, and gibberellin stimuli. The SmLAC25 protein is localized in the cytoplasm and chloroplasts. Recombinant SmLAC25 protein could oxidize coniferyl alcohol and sinapyl alcohol, two monomers of G-lignin and S-lignin. To investigate its function, we generated SmLAC25-overexpressed S. miltiorrhiza plantlets and hairy roots. The lignin content increased significantly in all SmLAC25-overexpressed plantlets and hairy roots, compared with the controls. However, the concentrations of rosmarinic acid and salvianolic acid B decreased significantly in all the SmLAC25-overexpressed lines. Further studies revealed that the transcription levels of some key enzyme genes in the lignin synthesis pathway (e.g., SmCCR and SmCOMT) were significantly improved in the SmLAC25-overexpressed lines, while the expression levels of multiple enzyme genes in the salvianolic acid biosynthesis pathway were inhibited. We speculated that the overexpression of SmLAC25 promoted the metabolic flux of lignin synthesis, which resulted in a decreased metabolic flux to the salvianolic acid biosynthesis pathway.

Comparative genomic analysis of the COBRA genes in six Rosaceae species and expression analysis in Chinese white pear (Pyrus bretschneideri)

COBRA-Like (COBL) genes encode a glycosylphosphatidylinositol (GPI) anchoring protein unique to plants. In current study, 87 COBRA genes were identified in 6 Rosaceae species, including Pyrus bretschneideri (16 genes), Malus domestica (22 genes), Fragaria vesca (13 genes), Prunus mume (11 genes), Rubus occidentalis (13 genes) and Prunus avium (12 genes). We revealed the evolution of the COBRA gene in six Rosaceae species by phylogeny, gene structure, conservative sequence, hydrophobicity analysis, gene replication events and sliding window analysis. In addition, based on the analysis of expression patterns in pear fruit combined with bioinformatics, we identified PbCOBL12 and PbCOBL13 as potential genes regulating secondary cell wall (SCW) formation during pear stone cell development. This study aimed to understand the evolutionary relationship of the COBRA gene in Rosaceae species, clarify the potential function of COBRA in pear fruit development, and provide essential theoretical basis and gene resources for improving pear fruit quality through genetical modification mechanism.

Pear genetics: Recent advances, new prospects, and a roadmap for the future

Pear, belonging to the genus Pyrus, is one of the most economically important temperate fruit crops. Pyrus is an important genus of the Rosaceae family, subfamily Maloideae, and has at least 22 different species with over 5000 accessions maintained or identified worldwide. With the release of draft whole-genome sequences for Pyrus, opportunities for pursuing studies on the evolution, domestication, and molecular breeding of pear, as well as for conducting comparative genomics analyses within the Rosaceae family, have been greatly expanded. In this review, we highlight key advances in pear genetics, genomics, and breeding driven by the availability of whole-genome sequences, including whole-genome resequencing efforts, pear domestication, and evolution. We cover updates on new resources for undertaking gene identification and molecular breeding, as well as for pursuing functional validation of genes associated with desirable economic traits. We also explore future directions for "pear-omics".

Laccases as green and versatile biocatalysts: from lab to enzyme market-an overview

Laccases are multi-copper oxidase enzymes that catalyze the oxidation of different compounds (phenolics and non-phenolics). The scientific literature on laccases is quite extensive, including many basic and applied research about the structure, functions, mechanism of action and a variety of biotechnological applications of these versatile enzymes. Laccases can be used in various industries/sectors, from the environmental field to the cosmetics industry, including food processing and the textile industry (dyes biodegradation and synthesis). Known as eco-friendly or green enzymes, the application of laccases in biocatalytic processes represents a promising sustainable alternative to conventional methods. Due to the advantages granted by enzyme immobilization, publications on immobilized laccases increased substantially in recent years. Many patents related to the use of laccases are available, however, the real industrial or environmental use of laccases is still challenged by cost-benefit, especially concerning the feasibility of producing this enzyme on a large scale. Although this is a compelling point and the enzyme market is heated, articles on the production and application of laccases usually neglect the economic assessment of the processes. In this review, we present a description of laccases structure and mechanisms of action including the different sources (fungi, bacteria, and plants) for laccases production and tools for laccases evolution and prediction of potential substrates. In addition, we both compare approaches for scaling-up processes with an emphasis on cost reduction and productivity and critically review several immobilization methods for laccases. Following the critical view on production and immobilization, we provide a set of applications for free and immobilized laccases based on articles published within the last five years and patents which may guide future strategies for laccase use and commercialization.

Plant Copper Metalloenzymes As Prospects for New Metabolism Involving Aromatic Compounds

Copper is an important transition metal cofactor in plant metabolism, which enables diverse biocatalysis in aerobic environments. Multiple classes of plant metalloenzymes evolved and underwent genetic expansions during the evolution of terrestrial plants and, to date, several representatives of these copper enzyme classes have characterized mechanisms. In this review, we give an updated overview of chemistry, structure, mechanism, function and phylogenetic distribution of plant copper metalloenzymes with an emphasis on biosynthesis of aromatic compounds such as phenylpropanoids (lignin, lignan, flavonoids) and cyclic peptides with macrocyclizations via aromatic amino acids. We also review a recent addition to plant copper enzymology in a copper-dependent peptide cyclase called the BURP domain. Given growing plant genetic resources, a large pool of copper biocatalysts remains to be characterized from plants as plant genomes contain on average more than 70 copper enzyme genes. A major challenge in characterization of copper biocatalysts from plant genomes is the identification of endogenous substrates and catalyzed reactions. We highlight some recent and future trends in filling these knowledge gaps in plant metabolism and the potential for genomic discovery of copper-based enzymology from plants.

The Laccase Gene Family Mediate Multi-Perspective Trade-Offs during Tea Plant (Camellia sinensis) Development and Defense Processes

Laccase (LAC) plays important roles in different plant development and defense processes. In this study, we identified laccase genes (CsLACs) in Camellia sinensis cv ‘Longjing43′ cultivars, which were classified into six subclades. The expression patterns of CsLACs displayed significant spatiotemporal variations across different tissues and developmental stages. Most members in subclades II, IV and subclade I exhibited contrasting expression patterns during leaf development, consistent with a trade-off model for preferential expression in the early and late developmental stages. The extensive transcriptional changes of CsLACs under different phytohormone and herbivore treatment were observed and compared, with the expression of most genes in subclades I, II and III being downregulated but genes in subclades IV, V and VI being upregulated, suggesting a growth and defense trade-off model between these subclades. Taken together, our research reveal that CsLACs mediate multi-perspective trade-offs during tea plant development and defense processes and are involved in herbivore resistance in tea plants. More in-depth research of CsLACs upstream regulation and downstream targets mediating herbivore defense should be conducted in the future.

The role of JrLACs in the lignification of walnut endocarp

BACKGROUND

The walnut shell, which is composed of a large number of sclereids originating from the lignified parenchyma of the endocarp, plays an important role in fruit development and during harvesting and storage. The physical and chemical properties of walnut shells are closely related to the lignin content. Laccase is the key enzyme responsible for lignin biosynthesis by the polymerization of monolignols and plays crucial roles in secondary cell wall formation in plants. In this study, we screened and identified laccase family genes from the walnut genome and investigated the expression of laccase during endocarp lignification in walnut.

RESULTS

A total of 37 laccase genes were screened from the walnut genome and distributed on nine chromosomes and classified into 6 subfamilies, among which subfamily IV showed distinct expansion. We observed that endocarp lignification started 44 days after flowering (DAF), and at later periods, the lignin content increased rapidly, with growth peaks at 44-50 DAF and 100-115 DAF. The lignification of the endocarp proceeded from the outside to the inside, as demonstrated by section staining in combination with endocarp staining. Furthermore, the changes in the expression of laccase family genes in the endocarp at different developmental stages were studied, and JrLACs showed different expression trends. The expression of nine genes showed significant increase after 44 DAF, and among these, JrLAC12-1, JrLAC12-2 and JrLAC16 showed a significant change in expression at the lignification stage. A study of the expression of JrLACs in different tissues and at various endocarp developmental stages revealed, that most JrLACs were expressed at low levels in mature tissues and at high levels in young tissues, in particular, JrLAC12-1 showed high expression in the young stems. A significant positive correlation was found between the expression of JrLAC12-1 and the variation in the lignin content in the endocarp.

CONCLUSION

Laccase genes play an important role in the lignification of the walnut endocarp, and JrLACs play different roles during fruit development. This study shows that JrLAC12-1 may play a key role in the lignification of endocarp.

A gene that underwent adaptive evolution, LAC2 (LACCASE), in Populus euphratica improves drought tolerance by improving water transport capacity

Drought severely limits plant development and growth; accordingly, plants have evolved strategies to prevent water loss and adapt to water deficit conditions. However, experimental cases that corroborate these evolutionary processes are limited. The LACCASEs (LACs) family is involved in various plant development and growth processes. Here, we performed an evolutionary analysis of LACs from Populus euphratica and characterized the functions of LACs in Arabidopsis and poplar. The results showed that in PeuLACs, multiple gene duplications led to apparent functional redundancy as the result of various selective pressures. Among them, PeuLAC2 underwent strong positive selection. Heterologous expression analyses showed that the overexpression of PeuLAC2 alters the xylem structure of plants, including thickening the secondary cell wall (SCW) and increasing the fiber cell length and stem tensile strength. Altogether, these changes improve the water transport capacity of plants. The analysis of the physiological experimental results showed that PeuLAC2-OE lines exhibited a stronger antioxidant response and greater drought tolerance than WT. Three genes screened by transcriptome analysis, NAC025, BG1, and UGT, that are associated with SCW synthesis and drought stress were all upregulated in the PeuLAC2-OE lines, implying that the overexpression of PeuLAC2 thickened the SCW, improved the water transport capacity of the plant, and further enhanced its drought tolerance. Our study highlights that genes that have undergone adaptive evolution may participate in the development of adaptive traits in P. euphratica and that PeuLAC2 could be a candidate gene for molecular genetic breeding in trees.

Substrate Specificity of LACCASE8 Facilitates Polymerization of Caffeyl Alcohol for C-Lignin Biosynthesis in the Seed Coat of Cleome hassleriana

Catechyl lignin (C-lignin) is a linear homopolymer of caffeyl alcohol found in the seed coats of diverse plant species. Its properties make it a natural source of carbon fibers and high-value chemicals, but the mechanism of in planta polymerization of caffeyl alcohol remains unclear. In the ornamental plant Cleome hassleriana, lignin biosynthesis in the seed coat switches from guaiacyl lignin to C-lignin at ∼12 d after pollination. Here we found that the transcript profile of the laccase gene ChLAC8 parallels the accumulation of C-lignin during seed coat development. Recombinant ChLAC8 oxidizes caffeyl and sinapyl alcohols, generating their corresponding dimers or trimers in vitro, but cannot oxidize coniferyl alcohol. We propose a basis for this substrate preference based on molecular modeling/docking experiments. Suppression of ChLAC8 expression led to significantly reduced C-lignin content in the seed coats of transgenic Cleome plants. Feeding of ¹³C-caffeyl alcohol to the Arabidopsis (Arabidopsis thaliana) caffeic acid o-methyltransferase mutant resulted in no incorporation of ¹³C into C-lignin, but expressing ChLAC8 in this genetic background led to appearance of C-lignin with >40% label incorporation. These results indicate that ChLAC8 is required for C-lignin polymerization and determines lignin composition when caffeyl alcohol is available.

Genome-wide identification of miRNAs and their targets during early somatic embryogenesis in Dimocarpus longan Lour

miRNAs are endogenous regulatory factors that play pivotal roles in post-transcriptional regulation. However, their specific roles in early somatic embryogenesis (SE) remain unclear. Study of the SE system is fundamental for clarifying the molecular mechanisms in Dimocarpus longan. We identified 289 known miRNAs from 106 different miRNA families and 1087 novel miRNAs during early longan SE, including embryogenic callus (EC), incomplete pro-embryogenic culture (ICpEC), globular embryo (GE), and non-embryogenic callus (NEC). The abundances of known miRNAs were concentrated in GE. The differentially expression (DE) miRNAs showed five expression patterns during early SE. Largely miRNAs were expressed highly and specially in EC, ICpEC, and GE, respectively. Some miRNAs and putative target genes were enriched in lignin metabolism. Most potential targets were related to the pathways of plant hormone signal transduction, alternative splicing, tyrosine metabolism and sulfur metabolism in early longan SE. The regulatory relationships between dlo-miR166a-3p and DlHD-zip8, dlo-miR397a and DlLAC7, dlo-miR408-3p and DlLAC12 were confirmed by RNA ligase-mediated rapid amplification of cDNA ends. The expression patterns of eight DE miRNAs detected by qRT-PCR were consistent with RNA-seq. Finally, the miRNA regulatory network in early SE was constructed, which provided new insight into molecular mechanism of early SE in longan.

Correction: Comprehensive genome-wide analysis of the pear (Pyrus bretschneideri) laccase gene (PbLAC) family and functional identification of PbLAC1 involved in lignin biosynthesis

[This corrects the article DOI: 10.1371/journal.pone.0210892.].

Transcriptomic analysis of early fruit development in Chinese white pear (Pyrus bretschneideri Rehd.) and functional identification of PbCCR1 in lignin biosynthesis

BACKGROUND

The content of stone cells and lignin is one of the key factors affecting the quality of pear fruit. In a previous study, we determined the developmental regularity of stone cells and lignin in 'Dangshan Su' pear fruit 15-145 days after pollination (DAP). However, the development of fruit stone cells and lignin before 15 DAP has not been heavily researched.

RESULTS

In this study, we found that primordial stone cells began to appear at 7 DAP and that the fruit had formed a large number of stone cells at 15 DAP. Subsequently, transcriptome sequencing was performed on fruits at 0, 7, and 15 DAP and identified 3834 (0 vs. 7 DAP), 4049 (7 vs. 15 DAP) and 5763 (0 vs. 15 DAP) DEGs. During the 7-15 DAP period, a large number of key enzyme genes essential for lignin biosynthesis are gradually up-regulated, and their expression pattern is consistent with the accumulation of lignin in this period. Further analysis found that the biosynthesis of S-type lignin in 'Dangshan Su' pear does not depend on the catalytic activity of PbSAD but is primarily generated by the catalytic activity of caffeoyl-CoA through CCoAOMT, CCR, F5H, and CAD. We cloned PbCCR1, 2 and analysed their functions in Chinese white pear lignin biosynthesis. PbCCR1 and 2 have a degree of functional redundancy; both demonstrate the ability to participate in lignin biosynthesis. However, PbCCR1 may be the major gene for lignin biosynthesis, while PbCCR2 has little effect on lignin biosynthesis.

CONCLUSIONS

Our results revealed that 'Dangshan Su' pear began to form a large number of stone cells and produce lignin after 7 DAP and mainly accumulated materials from 0 to 7 DAP. PbCCR1 is mainly involved in the biosynthesis of lignin in 'Dangshan Su' pear and plays a positive role in lignin biosynthesis.

Analysis of the laccase gene family and miR397-/miR408-mediated posttranscriptional regulation in Salvia miltiorrhiza

Salvia miltiorrhiza is one of the most commonly used traditional Chinese medicine materials. It contains important bioactive phenolic compounds, such as salvianolic acids, flavonoids and anthocyanins. Elucidation of phenolic compound biosynthesis and its regulatory mechanism is of great significance for S. miltiorrhiza quality improvement. Laccases (LACs) are multicopper-containing enzymes potentially involved in the polymerization of phenolic compounds. So far, little has been known about LAC genes in S. miltiorrhiza. Through systematic investigation of the whole genome sequence and transcriptomes of S. miltiorrhiza, we identified 65 full-length SmLAC genes (SmLAC1–SmLAC65). Phylogenetic analysis showed that 62 of the identified SmLACs clustered with LACs from Arabidopsis and Populus trichocarpa in seven clades (C1–C7), whereas the other three fell into one S. miltiorrhiza-specific clade (C8). All of the deduced SmLAC proteins contain four conserved signature sequences and three typical Cu-oxidase domains, and gene structures of most LACs from S. miltiorrhiza, Arabidopsis and P. trichocarpa were highly conserved, however SmLACs encoding C8 proteins showed distinct intron-exon structures. It suggests the conservation and diversity of plant LACs in gene structures. The majority of SmLACs exhibited tissue-specific expression patterns, indicates manifold functions of SmLACs played in S. miltiorrhiza. Analysis of high-throughput small RNA sequences and degradome data and experimental validation using the 5′ RACE method showed that 23 SmLACs were targets of Smi-miR397. Among them, three were also targeted by Smi-miR408. It suggests the significance of miR397 and miR408 in posttranscriptional regulation of SmLAC genes. Our results provide a foundation for further demonstrating the functions of SmLACs in the production of bioactive phenolic compounds in S. miltiorrhiza.

In Silico Genome-Wide Analysis of Respiratory Burst Oxidase Homolog (RBOH) Family Genes in Five Fruit-Producing Trees, and Potential Functional Analysis on Lignification of Stone Cells in Chinese White Pear

: The accumulation of lignin in fruit has a significant negative impact on the quality of fruit-producing trees, and in particular the lignin formation stimulates the development of stone cells in pear fruit. Reactive oxygen species (ROS) are essential for lignin polymerization. However, knowledge of the RBOH family, a key enzyme in ROS metabolism, remains unknown in most fruit trees. In this study, a total of 40 RBOHs were identified from five fruit-producing trees (Pyrusbretschneideri, Prunuspersica, Citrussinensis, Vitisvinifera, and Prunusmume), and 10 of these sequences came from Pyrusbretschneideri. Multiple sequence alignments revealed that all 10 PbRBOHs contained the NADPH_Ox domain and the six alpha-helical transmembrane domains (TM-I to TM-VI). Chromosome localization and interspecies phylogenetic tree analysis showed that 10 PbRBOHs irregularly distributed on 8 chromosomes and 3 PbRBOHs (PbRBOHA, PbRBOHB, and PbRBOHD) are closely related to known lignification-related RBOHs. Furthermore, hormone response pattern analysis showed that the transcription of PbRBOHs is regulated by SA, ABA and MeJA. Reverse transcription-quantitative real-time polymerase chain reaction (qRT-PCR) and transcriptome sequencing analysis showed that PbRBOHA, PbRBOHB, and PbRBOHD accumulated high transcript abundance in pear fruit, and the transcriptional trends of PbRBOHA and PbRBOHD was consistent with the change of stone cell content during fruit development. In addition, subcellular localization revealed that PbRBOHA and PbRBOHD are distributed on the plasma membrane. Combining the changes of apoplastic superoxide (O2.-) content and spatio-temporal expression analysis, these results indicate that PbRBOHA and PbRBOHD, which are candidate genes, may play an important role in ROS metabolism during the lignification of pear stone cells. This study not only provided insight into the molecular characteristics of the RBOH family in fruit-producing trees, but also lays the foundation for studying the role of ROS in plant lignification.