Functional analysis of the Arabidopsis PAL gene family in plant growth, development, and response to environmental stress

Biosynthesis and Pharmacological Activities of Flavonoids, Triterpene Saponins and Polysaccharides Derived from Astragalus membranaceus

Astragalus membranaceus (A. membranaceus), a well-known traditional herbal medicine, has been widely used in ailments for more than 2000 years. The main bioactive compounds including flavonoids, triterpene saponins and polysaccharides obtained from A. membranaceus have shown a wide range of biological activities and pharmacological effects. These bioactive compounds have a significant role in protecting the liver, immunomodulation, anticancer, antidiabetic, antiviral, antiinflammatory, antioxidant and anti-cardiovascular activities. The flavonoids are initially synthesized through the phenylpropanoid pathway, followed by catalysis with corresponding enzymes, while the triterpenoid saponins, especially astragalosides, are synthesized through the universal upstream pathways of mevalonate (MVA) and methylerythritol phosphate (MEP), and the downstream pathway of triterpenoid skeleton formation and modification. Moreover, the Astragalus polysaccharide (APS) possesses multiple pharmacological activities. In this review, we comprehensively discussed the biosynthesis pathway of flavonoids and triterpenoid saponins, and the structural features of polysaccharides in A. membranaceus. We further systematically summarized the pharmacological effects of bioactive ingredients in A. membranaceus, which laid the foundation for the development of clinical candidate agents. Finally, we proposed potential strategies of heterologous biosynthesis to improve the industrialized production and sustainable supply of natural products with pharmacological activities from A. membranaceus, thereby providing an important guide for their future development trend.

The plant protection preparation GZM improves crop immunity, yield, and quality

Lauryl alcohol, a natural compound found in plants and other organisms, is widely used to make surfactants, food, and pharmaceuticals. GZM, a plant protection preparation with lauryl alcohol as its major component is thought to establish a physical barrier on the plant surface, but its physiological functions are unknown. Here, we show that GZM improves the performance of peanut (Arachis hypogaea) plants in both the laboratory and the field. We demonstrate that the treatment with GZM or lauryl alcohol raises the contents of several specific lysophospholipids and induces the biosynthesis of phenylpropanoids, flavonoids, and wax in various plant species. In the field, GZM improves crop immunity, yield, and quality. In addition, GZM and lauryl alcohol can inhibit the growth of some pathogenic fungi. Our findings provide insights into the physiological and biological effects of GZM treatment on plants and show that GZM and lauryl alcohol are promising preparations in agricultural production.

Supplementation of the Plant Conditioner ELICE Vakcina® Product with β-Aminobutyric Acid and Salicylic Acid May Lead to Trans-Priming Signaling in Barley (Hordeum vulgare)

Plant immunological memory, priming, is a defense mechanism that can be triggered by external stimuli, leading to the activation of biochemical pathways and preparing plants for disease resistance. Plant conditioners improve yield and crop quality through nutrient efficiency and abiotic stress tolerance, which is enhanced by the addition of resistance- and priming-induced compounds. Based on this hypothesis, this study aimed to investigate plant responses to priming actives of different natures, including salicylic acid and beta-aminobutyric acid, in combination with the plant conditioning agent ELICE Vakcina^®. Phytotron experiments and RNA-Seq analyses of differentially expressed genes using the combinations of these three investigated compounds were performed in a barley culture to investigate possible synergistic relationships in the genetic regulatory network. The results indicated a strong regulation of defense responses, which was enhanced by supplemental treatments; however, both synergistic and antagonistic effects were enhanced with one or two components, depending on the supplementation. The overexpressed transcripts were functionally annotated to assess their involvement in jasmonic acid and salicylic acid signaling; however, their determinant genes were highly dependent on the supplemental treatments. Although the effects overlapped, the potential effects of trans-priming the two supplements tested could be largely separated.

Potential pathways and genes expressed in Chrysanthemum in response to early fusarium oxysporum infection

BACKGROUND

Chrysanthemum Fusarium wilt is a common fungal disease caused by Fusarium oxysporum, which causes continuous cropping obstacles and huge losses to the chrysanthemum industry. The defense mechanism of chrysanthemum against F. oxysporum remains unclear, especially during the early stages of the disease. Therefore, in the present study, we analyzed chrysanthemum 'Jinba' samples inoculated with F. oxysporum at 0, 3, and 72 h using RNA-seq.

RESULTS

The results revealed that 7985 differentially expressed genes (DEGs) were co-expressed at 3 and 72 h after F. oxysporum infection. We analyzed the identified DEGs using Kyoto Encyclopedia of Genes and Genomes and Gene Ontology. The DEGs were primarily enriched in "Plant pathogen interaction", "MAPK signaling pathway", "Starch and sucrose metabolism", and "Biosynthesis of secondary metabolites". Genes related to the synthesis of secondary metabolites were upregulated in chrysanthemum early during the inoculation period. Furthermore, peroxidase, polyphenol oxidase, and phenylalanine ammonia-lyase enzymes were consistently produced to accumulate large amounts of phenolic compounds to resist F. oxysporum infection. Additionally, genes related to the proline metabolic pathway were upregulated, and proline levels accumulated within 72 h, regulating osmotic balance in chrysanthemum. Notably, the soluble sugar content in chrysanthemum decreased early during the inoculation period; we speculate that this is a self-protective mechanism of chrysanthemums for inhibiting fungal reproduction by reducing the sugar content in vivo. In the meantime, we screened for transcription factors that respond to F. oxysporum at an early stage and analyzed the relationship between WRKY and DEGs in the "Plant-pathogen interaction" pathway. We screened a key WRKY as a research target for subsequent experiments.

CONCLUSION

This study revealed the relevant physiological responses and gene expression changes in chrysanthemum in response to F. oxysporum infection, and provided a relevant candidate gene pool for subsequent studies on chrysanthemum Fusarium wilt.

Genome-wide identification and expression analyses of phenylalanine ammonia-lyase gene family members from tomato (Solanum lycopersicum) reveal their role in root-knot nematode infection

Phenylalanine ammonia-lyase (PAL) is a key enzyme and rate-limiting enzyme of phenylpropanoid metabolism, which is a very important pathway in plants, and the secondary products it produces play an important role in plant growth and development, disease resistance, and stress resistance responses. However, PALs still lack systematic characterization in tomato. Based on a bioinformatics methods, PAL family genes were identified and characterized from tomato. qRT-PCR was used to study the expression of PAL genes in cultivated tomato after root-knot nematode infection. In this study, 14 and 11 PAL genes were identified in cultivated and wild tomatoes, and phylogenetic analysis classified them into three subfamilies, with different subfamilies of PAL proteins evolving in different directions in monocotyledonous and dicotyledonous plants. The extensive presence of stress, growth, hormone, and light response elements in the promoter sequences of SlPAL (Solanum lycopersicum) and SpenPAL (Solanum pennellii) genes suggests that this family has a critical role in abiotic stress. Collinearity indicates that members of the tomato and Arabidopsis PAL genes family are from the same ancestor, and the SlPAL10 gene is directly homologous to monocotyledonous rice and maize, suggesting that the SlPAL10 gene was present before monocotyledonous differentiation. Two co-expressed gene modules containing PAL genes were screened by WGCNA, and the core genes in the network were mined and functionally annotated by calculating the connectivity of genes within the modules. In addition, the expression of some genes changed significantly after root-knot nematode infection, with up-regulation of 4 genes and down-regulation of 3 genes. This result provides a data reference for the study of PAL family gene functions in tomato, and also provides a potential application for the subsequent selection of PAL genes in tomato for root-knot nematode resistance.

Integrative analysis of the multi-omics reveals the stripe rust fungus resistance mechanism of the TaPAL in wheat

Wheat is one of the major food crops in the world. However, stripe rust fungus significantly decreases wheat yield and quality. In the present study, transcriptomic and metabolite analyses were conducted in R88 (resistant line) and CY12 (susceptible cultivar) during Pst-CYR34 infection due to the limited availability of information regarding the underlying mechanisms governing wheat-pathogen interactions. The results revealed that Pst infection promoted the genes and metabolites involved in phenylpropanoid biosynthesis. The key enzyme gene TaPAL to regulate lignin and phenolic synthesis has a positive resistance contribution to Pst in wheat, which was verified by the virus-induced gene silencing (VIGS) technique. The distinctive resistance of R88 is regulated by the selective expression of genes involved in the fine-tuning of wheat-Pst interactions. Furthermore, metabolome analysis suggested that lignin biosynthesis-related metabolite accumulation was significantly affected by Pst. These results help to elucidate the regulatory networks of wheat-Pst interactions and pave the way for durable resistance breeding in wheat, which may ease environmental and food crises around the world.

Salicylic acid regulates two photosystem II protection pathways in tomato under chilling stress mediated by ETHYLENE INSENSITIVE 3-like proteins

Chilling stress seriously impairs photosynthesis and activates a series of molecular responses in plants. Previous studies have shown that ETHYLENE INSENSITIVE 3 (EIN3) and EIN3-like (SlEIL) proteins mediate ethylene signaling and reduce plant tolerance to freezing in tomato (Solanum lycopersicum). However, the specific molecular mechanisms underlying an EIN3/EILs-mediated photoprotection pathway under chilling stress are unclear. Here, we discovered that salicylic acid (SA) participates in photosystem II (PSII) protection via SlEIL2 and SlEIL7. Under chilling stress, the phenylalanine ammonia-lyase gene SlPAL5 plays an important role in the production of SA, which also induces WHIRLY1 (SlWHY1) transcription. The resulting accumulation of SlWHY1 activates SlEIL7 expression under chilling stress. SlEIL7 then binds to and blocks the repression domain of the heat shock factor SlHSFB-2B, releasing its inhibition of HEAT SHOCK PROTEIN 21 (HSP21) expression to maintain PSII stability. In addition, SlWHY1 indirectly represses SlEIL2 expression, allowing the expression of l-GALACTOSE-1-PHOSPHATE PHOSPHATASE3 (SlGPP3). The ensuing higher SlGPP3 abundance promotes the accumulation of ascorbic acid (AsA), which scavenges reactive oxygen species produced upon chilling stress and thus protects PSII. Our study demonstrates that SlEIL2 and SlEIL7 protect PSII under chilling stress via two different SA response mechanisms: one involving the antioxidant AsA and the other involving the photoprotective chaperone protein HSP21.

Autophagy and multivesicular body pathways cooperate to protect sulfur assimilation and chloroplast functions

Autophagy and multivesicular bodies (MVBs) represent 2 closely related lysosomal/vacuolar degradation pathways. In Arabidopsis (Arabidopsis thaliana), autophagy is stress-induced, with deficiency in autophagy causing strong defects in stress responses but limited effects on growth. LYST-INTERACTING PROTEIN 5 (LIP5) is a key regulator of stress-induced MVB biogenesis, and mutation of LIP5 also strongly compromises stress responses with little effect on growth in Arabidopsis. To determine the functional interactions of these 2 pathways in Arabidopsis, we generated mutations in both the LIP5 and AUTOPHAGY-RELATED PROTEIN (ATG) genes. atg5/lip5 and atg7/lip5 double mutants displayed strong synergistic phenotypes in fitness characterized by stunted growth, early senescence, reduced survival, and greatly diminished seed production under normal growth conditions. Transcriptome and metabolite analysis revealed that chloroplast sulfate assimilation was specifically downregulated at early seedling stages in the atg7/lip5 double mutant prior to the onset of visible phenotypes. Overexpression of adenosine 5'-phosphosulfate reductase 1, a key enzyme in sulfate assimilation, substantially improved the growth and fitness of the atg7/lip5 double mutant. Comparative multi-omic analysis further revealed that the atg7/lip5 double mutant was strongly compromised in other chloroplast functions including photosynthesis and primary carbon metabolism. Premature senescence and reduced survival of atg/lip5 double mutants were associated with increased accumulation of reactive oxygen species and overactivation of stress-associated programs. Blocking PHYTOALEXIN DEFICIENT 4 and salicylic acid signaling prevented early senescence and death of the atg7/lip5 double mutant. Thus, stress-responsive autophagy and MVB pathways play an important cooperative role in protecting essential chloroplast functions including sulfur assimilation under normal growth conditions to suppress salicylic-acid-dependent premature cell-death and promote plant growth and fitness.

Ethylene signals modulate the survival of Arabidopsis leaf explants

BACKGROUND

Leaf explants are major materials in plant tissue cultures. Incubation of detached leaves on phytohormone-containing media, which is an important process for producing calli and regenerating plants, change their cell fate. Although hormone signaling pathways related to cell fate transition have been widely studied, other molecular and physiological events occurring in leaf explants during this process remain largely unexplored.

RESULTS

Here, we identified that ethylene signals modulate expression of pathogen resistance genes and anthocyanin accumulation in leaf explants, affecting their survival during culture. Anthocyanins accumulated in leaf explants, but were not observed near the wound site. Ethylene signaling mutant analysis revealed that ethylene signals are active and block anthocyanin accumulation in the wound site. Moreover, expression of defense-related genes increased, particularly near the wound site, implying that ethylene induces defense responses possibly by blocking pathogenesis via wounding. We also found that anthocyanin accumulation in non-wounded regions is required for drought resistance in leaf explants.

CONCLUSIONS

Our study revealed the key roles of ethylene in the regulation of defense gene expression and anthocyanin biosynthesis in leaf explants. Our results suggest a survival strategy of detached leaves, which can be applied to improve the longevity of explants during tissue culture.

Integrated Multi-Omics Reveals Significant Roles of Non-Additively Expressed Small RNAs in Heterosis for Maize Plant Height

Heterosis is a complex biological phenomenon regulated by genetic variations and epigenetic changes. However, the roles of small RNAs (sRNAs), an important epigenetic regulatory element, on plant heterosis are still poorly understood. Here, an integrative analysis was performed with sequencing data from multi-omics layers of maize hybrids and their two homologous parental lines to explore the potential underlying mechanisms of sRNAs in plant height (PH) heterosis. sRNAome analysis revealed that 59 (18.61%) microRNAs (miRNAs) and 64,534 (54.00%) 24-nt small interfering RNAs (siRNAs) clusters were non-additively expressed in hybrids. Transcriptome profiles showed that these non-additively expressed miRNAs regulated PH heterosis through activating genes involved in vegetative growth-related pathways while suppressing those related to reproductive and stress response pathways. DNA methylome profiles showed that non-additive methylation events were more likely to be induced by non-additively expressed siRNA clusters. Genes associated with low-parental expression (LPE) siRNAs and trans-chromosomal demethylation (TCdM) events were enriched in developmental processes as well as nutrients and energy metabolism, whereas genes associated with high-parental expression (HPE) siRNAs and trans-chromosomal methylation (TCM) events were gathered in stress response and organelle organization pathways. Our results provide insights into the expression and regulation patterns of sRNAs in hybrids and help to elucidate their potential targeting pathways contributing to PH heterosis.

Evaluation of inducing activity of CIP elicitors from diverse sources based on monosaccharide composition and physiological indicators

Application of elicitors can greatly enhance plant immune resistance against pathogens. However, it is still obscure whether elicitor activity is influenced by diverse sources. This study investigated the effect of foliar spraying of 19 batches of Chrysanthemum indicum polysaccharides (CIPs) on the disease resistance of Atractylodes macrocephala Koidz. (A. macrocephala) and explored the main reasons for the differences of inducing activity of CIP elicitors. PCA, OPLS-DA, grey relational analysis and entropy weight method had good predictability for the activity evaluation of CIP elicitors and other plant-derived elicitors. The results showed that 19 batches of CIPs had definite regional differences in inducing activity and monosaccharide content. CIP elicitors with high inducing activity could significantly increase the accumulation of Atractylenolide Ⅱ and Atractylenolide Ⅲ, the mRNA relative transcription level of CAT, POD, PAL genes, the amount of pH change in the medium and effectively reduce the disease index of A. macrocephala. Furthermore, CIP with high inducing activity exhibited the high contents of Rha, Ara and GalA, which might be the main contributor to their high activity. The evaluation procedure developed in this work can be applied for screening CIP elicitors with high inducing activity, and it lays a foundation for identifying more functional elicitors related to plant immune resistance.

The MYB59 transcription factor negatively regulates salicylic acid- and jasmonic acid-mediated leaf senescence

Leaf senescence is the final stage of leaf development and is affected by various exogenous and endogenous factors. Transcriptional regulation is essential for leaf senescence, however, the underlying molecular mechanisms remain largely unclear. In this study, we report that the transcription factor MYB59, which was predominantly expressed in early senescent rosette leaves, negatively regulates leaf senescence in Arabidopsis (Arabidopsis thaliana). RNA sequencing revealed a large number of differentially expressed genes involved in several senescence-related biological processes in myb59-1 rosette leaves. Chromatin immunoprecipitation and transient dual-luciferase reporter assays demonstrated that MYB59 directly repressed the expression of SENESCENCE ASSOCIATED GENE 18 and indirectly inhibited the expression of several other senescence-associated genes to delay leaf senescence. Moreover, MYB59 was induced by salicylic acid (SA) and jasmonic acid (JA). MYB59 inhibited SA production by directly repressing the expression of ISOCHORISMATE SYNTHASE 1 and PHENYLALANINE AMMONIA-LYASE 2 and restrained JA biosynthesis by directly suppressing the expression of LIPOXYGENASE 2, thus forming two negative feedback regulatory loops with SA and JA and ultimately delaying leaf senescence. These results help us understand the novel function of MYB59 and provide insights into the regulatory network controlling leaf senescence in Arabidopsis.

The Influence of Methyl Jasmonate on Expression Patterns of Rosmarinic Acid Biosynthesis Genes, and Phenolic Compounds in Different Species of Salvia subg. Perovskia Kar L

Salvia yangii B.T. Drew and Salvia abrotanoides Kar are two important fragrant and medicinal plants that belong to the subgenus Perovskia. These plants have therapeutic benefits due to their high rosmarinic acid (RA) content. However, the molecular mechanisms behind RA generation in two species of Salvia plants are still poorly understood. As a first report, the objectives of the present research were to determine the effects of methyl jasmonate (MeJA) on the rosmarinic acid (RA), total flavonoid and phenolic contents (TFC and TPC), and changes in the expression of key genes involved in their biosynthesis (phenylalanine ammonia lyase (PAL), 4-coumarate-CoA ligase (4CL), and rosmarinic acid synthase (RAS)). The results of High-performance liquid chromatography (HPLC) analysis indicated that MeJA significantly increased RA content in S. yungii and S. abrotanoides species (to 82 and 67 mg/g DW, respectively) by 1.66- and 1.54-fold compared with untreated plants. After 24 h, leaves of Salvia yangii and Salvia abrotanoides species treated with 150 M MeJA had the greatest TPC and TFC (80 and 42 mg TAE/g DW, and 28.11 and 15.14 mg QUE/g DW, respectively), which was in line with the patterns of gene expression investigated. Our findings showed that MeJA dosages considerably enhanced the RA, TPC, and TFC contents in both species compared with the control treatment. Since increased numbers of transcripts for PAL, 4CL, and RAS were also detected, the effects of MeJA are probably caused by the activation of genes involved in the phenylpropanoid pathway.

Salicylic acid biosynthesis is not from phenylalanine in Arabidopsis

The phytohormone salicylic acid (SA) regulates biotic and abiotic stress responses in plants. Two distinct biosynthetic pathways for SA have been well documented in plants: the isochorismate (IC) pathway in the chloroplast and the phenylalanine ammonia-lyase (PAL) pathway in the cytosol. However, there has been no solid evidence that the PAL pathway contributes to SA biosynthesis. Here, we report that feeding Arabidopsis thaliana with Ring-¹³ C-labeled phenylalanine (¹³ C₆ -Phe) resulted in incorporation of the ¹³ C label not into SA, but into its isomer 4-hydroxybenzoic acid (4-HBA) instead. We obtained similar results when feeding ¹³ C₆ -Phe to the SA-deficient ics1 ics2 mutant and the SA-hyperaccumulating mutant s3h s5h. Notably, we detected ¹³ C₆ -SA when ¹³ C₆ -benzoic acid (BA) was provided, suggesting that SA can be synthesized from BA. Furthermore, despite the substantial accumulation of SA upon pathogen infection, we did not observe incorporation of ¹³ C label from Phe into SA. We also did not detect ¹³ C₆ -SA in PAL-overexpressing lines in the kfb01 kfb02 kfb39 kfb50 background after being fed ¹³ C₆ -Phe, although endogenous PAL levels were dramatically increased. Based on these combined results, we propose that SA biosynthesis is not from Phe in Arabidopsis. These results have important implications for our understanding of the SA biosynthetic pathway in land plants.

Identification and analysis of lignin biosynthesis genes related to fruit ripening and stress response in banana (Musa acuminata L. AAA group, cv. Cavendish)

BACKGROUND

Lignin is a key component of the secondary cell wall of plants, providing mechanical support and facilitating water transport as well as having important impact effects in response to a variety of biological and abiotic stresses.

RESULTS

In this study, we identified 104 genes from ten enzyme gene families related to lignin biosynthesis in Musa acuminata genome and found the number of MaCOMT gene family was the largest, while MaC3Hs had only two members. MaPALs retained the original members, and the number of Ma4CLs in lignin biosynthesis was significantly less than that of flavonoids. Segmental duplication existed in most gene families, except for MaC3Hs, and tandem duplication was the main way to expand the number of MaCOMTs. Moreover, the expression profiles of lignin biosynthesis genes during fruit development, postharvest ripening stages and under various abiotic and biological stresses were investigated using available RNA-sequencing data to obtain fruit ripening and stress response candidate genes. Finally, a co-expression network of lignin biosynthesis genes was constructed by weighted gene co-expression network analysis to elucidate the lignin biosynthesis genes that might participate in lignin biosynthesis in banana during development and in response to stresses.

CONCLUSION

This study systematically identified the lignin biosynthesis genes in the Musa acuminata genome, providing important candidate genes for further functional analysis. The identification of the major genes involved in lignin biosynthesis in banana provides the basis for the development of strategies to improve new banana varieties tolerant to biological and abiotic stresses with high yield and high quality.

Molecular identification of phenylalanine ammonia lyase-encoding genes EfPALs and EfPAL2-interacting transcription factors in Euryale ferox

Flavonoids are one of the most important secondary metabolites in plants, and phenylalanine ammonia-lyase (PAL) is the first rate-limiting enzyme for their biosynthesis. However, detailed information on the regulation of PAL in plants is still little. In this study, PAL in E. ferox was identified and functionally analyzed, and its upstream regulatory network was investigated. Through genome-wide identification, we obtained 12 putative PAL genes from E. ferox. Phylogenetic tree and synteny analysis revealed that PAL in E. ferox was expanded and mostly preserved. Subsequently, enzyme activity assays demonstrated that EfPAL1 and EfPAL2 both catalyzed the production of cinnamic acid from phenylalanine only, with EfPAL2 exhibiting a superior enzyme activity. Overexpression of EfPAL1 and EfPAL2 in Arabidopsis thaliana, respectively, both enhanced the biosynthesis of flavonoids. Furthermore, two transcription factors, EfZAT11 and EfHY5, were identified by yeast one-hybrid library assays as binding to the promoter of EfPAL2, and further luciferase (LUC) activity analysis indicated that EfZAT11 promoted the expression of EfPAL2, while EfHY5 repressed the expression of EfPAL2. These results suggested that EfZAT11 and EfHY5 positively and negatively regulate flavonoid biosynthesis, respectively. Subcellular localization revealed that EfZAT11 and EfHY5 were localized in the nucleus. Our findings clarified the key EfPAL1 and EfPAL2 of flavonoid biosynthesis in E. ferox and established the upstream regulatory network of EfPAL2, which would provide novel information for the study of flavonoid biosynthesis mechanism.

SCL14 Inhibits the Functions of the NAC043-MYB61 Signaling Cascade to Reduce the Lignin Content in Autotetraploid Populus hopeiensis

Whole-genome duplication often results in a reduction in the lignin content in autopolyploid plants compared with their diploid counterparts. However, the regulatory mechanism underlying variation in the lignin content in autopolyploid plants remains unclear. Here, we characterize the molecular regulatory mechanism underlying variation in the lignin content after the doubling of homologous chromosomes in Populus hopeiensis. The results showed that the lignin content of autotetraploid stems was significantly lower than that of its isogenic diploid progenitor throughout development. Thirty-six differentially expressed genes involved in lignin biosynthesis were identified and characterized by RNA sequencing analysis. The expression of lignin monomer synthase genes, such as PAL, COMT, HCT, and POD, was significantly down-regulated in tetraploids compared with diploids. Moreover, 32 transcription factors, including MYB61, NAC043, and SCL14, were found to be involved in the regulatory network of lignin biosynthesis through weighted gene co-expression network analysis. We inferred that SCL14, a key repressor encoding the DELLA protein GAI in the gibberellin (GA) signaling pathway, might inhibit the NAC043-MYB61 signaling functions cascade in lignin biosynthesis, which results in a reduction in the lignin content. Our findings reveal a conserved mechanism in which GA regulates lignin synthesis after whole-genome duplication; these results have implications for manipulating lignin production.

Exogenous abscisic acid and sodium nitroprusside regulate flavonoid biosynthesis and photosynthesis of Nitraria tangutorum Bobr in alkali stress

Abscisic acid (ABA) and nitric oxide (NO) are involved in mediating abiotic stress-induced plant physiological responses. Nitraria tangutorum Bobr is a typical salinized desert plant growing in an arid environment. In this study, we investigated the effects of ABA and NO on N.tangutorum seedlings under alkaline stress. Alkali stress treatment caused cell membrane damage, increased electrolyte leakage, and induced higher production of reactive oxygen species (ROS), which caused growth inhibition and oxidative stress in N.tangutorum seedlings. Exogenous application of ABA (15μm) and Sodium nitroprusside (50μm) significantly increased the plant height, fresh weight, relative water content, and degree of succulency in N.tangutorum seedlings under alkali stress. Meanwhile, the contents of ABA and NO in plant leaves were significantly increased. ABA and SNP can promote stomatal closure, decrease the water loss rate, increase leaf surface temperature and the contents of osmotic regulator proline, soluble protein, and betaine under alkali stress. Meanwhile, SNP more significantly promoted the accumulation of chlorophyll a/b and carotenoids, increased quantum yield of photosystem II (φPSII) and electron transport rate (ETRII) than ABA, and decreased photochemical quenching (qP), which improved photosynthetic efficiency and accelerated the accumulation of soluble sugar, glucose, fructose, sucrose, starch, and total sugar. However, compared with exogenous application of SNP in the alkaline stress, ABA significantly promoted the transcription of NtFLS/NtF3H/NtF3H/NtANR genes and the accumulation of naringin, quercetin, isorhamnetin, kaempferol, and catechin in the synthesis pathway of flavonoid metabolites, and isorhamnetin content was the highest. These results indicate that both ABA and SNP can reduce the growth inhibition and physiological damage caused by alkali stress. Among them, SNP has a better effect on the improvement of photosynthetic efficiency and the regulation of carbohydrate accumulation than ABA, while ABA has a more significant effect on the regulation of flavonoid and anthocyanin secondary metabolite accumulation. Exogenous application of ABA and SNP also improved the antioxidant capacity and the ability to maintain Na⁺/K⁺ balance of N. tangutorum seedlings under alkali stress. These results demonstrate the beneficial effects of ABA and NO as stress hormones and signaling molecules that positively regulate the defensive response of N. tangutorum to alkaline stress.

A reference-grade genome assembly for Astragalus mongholicus and insights into the biosynthesis and high accumulation of triterpenoids and flavonoids in its roots

Astragalus membranaceus var. mongholicus (AMM), a member of the Leguminosae, is one of the most important medicinal plants worldwide. The dried roots of AMM have a wide range of pharmacological effects and are a traditional Chinese medicine. Here, we report the first chromosome-level reference genome of AMM, comprising nine pseudochromosomes with a total size of 1.47 Gb and 27 868 protein-encoding genes. Comparative genomic analysis reveals that AMM has not experienced an independent whole-genome duplication (WGD) event after the WGD event shared by the Papilionoideae species. Analysis of long terminal repeat retrotransposons suggests a recent burst of these elements at approximately 0.13 million years ago, which may explain the large size of the AMM genome. Multiple gene families involved in the biosynthesis of triterpenoids and flavonoids were expanded, and our data indicate that tandem duplication has been the main driver for expansion of these families. Among the expanded families, the phenylalanine ammonia-lyase gene family was primarily expressed in the roots of AMM, suggesting their roles in the biosynthesis of phenylpropanoid compounds. The functional versatility of 2,3-oxidosqualene cyclase genes in cluster III may play a critical role in the diversification of triterpenoids in AMM. Our findings provide novel insights into triterpenoid and flavonoid biosynthesis and can facilitate future research on the genetics and medical applications of AMM.

Exogenous application of salicylic acid improves freezing stress tolerance in alfalfa

Freezing stress is one of the most detrimental environmental factors that can seriously impact the growth, development, and distribution of alfalfa (Medicago sativa L.). Exogenous salicylic acid (SA) has been revealed as a cost-effective method of improving defense against freezing stress due to its predominant role in biotic and abiotic stress resistance. However, how the molecular mechanisms of SA improve freezing stress resistance in alfalfa is still unclear. Therefore, in this study, we used leaf samples of alfalfa seedlings pretreatment with 200 μM and 0 μM SA, which were exposed to freezing stress (-10°C) for 0, 0.5, 1, and 2h and allowed to recover at normal temperature in a growth chamber for 2 days, after which we detect the changes in the phenotypical, physiological, hormone content, and performed a transcriptome analysis to explain SA influence alfalfa in freezing stress. The results demonstrated that exogenous SA could improve the accumulation of free SA in alfalfa leaves primarily through the phenylalanine ammonia-lyase pathway. Moreover, the results of transcriptome analysis revealed that the mitogen-activated protein kinase (MAPK) signaling pathway-plant play a critical role in SA alleviating freezing stress. In addition, the weighted gene co-expression network analysis (WGCNA) found that MPK3, MPK9, WRKY22 (downstream target gene of MPK3), and TGACG-binding factor 1 (TGA1) are candidate hub genes involved in freezing stress defense, all of which are involved in the SA signaling pathway. Therefore, we conclude that SA could possibly induce MPK3 to regulate WRKY22 to participate in freezing stress to induced gene expression related to SA signaling pathway (NPR1-dependent pathway and NPR1-independent pathway), including the genes of non-expresser of pathogenesis-related gene 1 (NPR1), TGA1, pathogenesis-related 1 (PR1), superoxide dismutase (SOD), peroxidase (POD), ascorbate peroxidase (APX), glutathione-S-transferase (GST), and heat shock protein (HSP). This enhanced the production of antioxidant enzymes such as SOD, POD, and APX, which increases the freezing stress tolerance of alfalfa plants.

Transcriptome analysis identifies differentially expressed genes involved in lignin biosynthesis in barley

Lignin is an essential metabolite for plant growth but negatively affects the quality of forage barley. Genetic modification of quality traits to improve the forage digestibility requires an understanding of the molecular mechanism of lignin biosynthesis. RNA-Seq was used to quantify transcripts differentially expressed among leaf, stem and spike tissues from two barley genotypes. A total of 13,172 differentially expressed genes (DEGs) were identified, of which much more up-regulated DEGs were detected from the contrasting groups of leaf vs spike (L-S) and stem vs spike (S-S), and down-regulated DEGs were dominant in the group of stem vs leaf (S-L). 47 DEGs were successfully annotated to the monolignol pathway and six of them were candidate genes regulating the lignin biosynthesis. The qRT-PCR assay verified the expression profiles of the six candidate genes. Among them, four genes might positively regulate the lignin biosynthesis during forage barley development in terms of the consistency of their expression levels and changes of lignin content among the tissues, while the other two genes may have the reverse effects. These findings provide target genes for further investigations on molecular regulatory mechanisms of lignin biosynthesis and genetic resources for improvement of forage quality in barley molecular breeding programme.

Nitrogen application improves salt tolerance of grape seedlings via regulating hormone metabolism

Salt stress is a dominant environmental factor that restricts the growth and yield of crops. Nitrogen is an essential mineral element for plants, regulates various physiological and biochemical processes, and has been reported to enhance salt tolerance in plants. However, the crosstalk between salt and nitrogen in grapes is not well understood. In this study, we found that nitrogen supplementation (0.01 and 0.1 mol L-1 NH4 NO3 ) significantly increased the accumulation of proline, chlorophyll, Na+ , NH4 + , and NO3 - , while it reduced the malondialdehyde content and inhibited photosynthetic performance under salt stress conditions (200 mmol L-1 NaCl). Further transcriptome and metabolome analyses showed that a total of 4890 differentially expressed genes (DEGs) and 753 differently accumulated metabolites (DAMs) were identified. Joint omics results revealed that plant hormone signal transduction pathway connected the DEGs and DAMs. In-depth analysis revealed that nitrogen supplementation increased the levels of endogenous abscisic acid, salicylic acid, and jasmonic acid by inducing the expression of 11, 4, and 13 genes related to their respective biosynthesis pathway. In contrast, endogenous indoleacetic acid content was significantly reduced due to the remarkable regulation of seven genes of its biosynthetic pathway. The modulation in hormone contents subsequently activated the differential expression of 13, 10, 12, and 29 genes of the respective downstream hormone signaling transduction pathways. Overall, all results indicate that moderate nitrogen supplementation could improve salt tolerance by regulating grape physiology and endogenous hormone homeostasis, as well as the expression of key genes in signaling pathways, which provides new insights into the interactions between mineral elements and salt stress.

Molecular regulation of immunity in tea plants

Tea, which is mainly produced using the young leaves and buds of tea plants (Camellia sinensis (L.) O. Kuntze), is one of the most common non-alcoholic beverages consumed in the world. The standard of tea mostly depends on the variety and quality of tea plants, which generally grow in subtropical areas, where the warm and humid conditions are also conducive to the occurrence of diseases. In fighting against pathogens, plants rely on their sophisticated innate immune systems which has been extensively studied in model plants. Many components involved in pathogen associated molecular patterns (PAMPs) triggered immunity (PTI) and effector triggered immunity (ETI) have been found. Nevertheless, the molecular regulating network against pathogens (e.g., Pseudopestalotiopsis sp., Colletotrichum sp. and Exobasidium vexans) causing widespread disease (such as grey blight disease, anthracnose, and blister blight) in tea plants is still unclear. With the recent release of the genome data of tea plants, numerous genes involved in tea plant immunity have been identified, and the molecular mechanisms behind tea plant immunity is being studied. Therefore, the recent achievements in identifying and cloning functional genes/gene families, in finding crucial components of tea immunity signaling pathways, and in understanding the role of secondary metabolites have been summarized and the opportunities and challenges in the future studies of tea immunity are highlighted in this review.

Molecular module of CmMYB15-like-Cm4CL2 regulating lignin biosynthesis of chrysanthemum (Chrysanthemum morifolium) in response to aphid (Macrosiphoniella sanborni) feeding

Lignin is a major component of plant cell walls and a conserved basic defense mechanism in higher plants deposited in response to aphid infection. However, the molecular mechanisms of lignin biosynthesis in response to aphid infection and the effect of lignin on aphid feeding behavior remain unclear. We report that 4-Coumarate:coenzyme A ligase 2 (Cm4CL2), a gene encoding a key enzyme in the lignin biosynthesis pathway, is induced by aphid feeding, resulting in lignin deposition and reduced aphid attack. Upstream regulator analysis showed that the expression of Cm4CL2 in response to aphid feeding was directly upregulated by CmMYB15-like, an SG2-type R2R3-MYB transcription factor. CmMYB15-like binds directly to the AC cis-element in the promoter region of Cm4CL2. Genetic validation demonstrated that CmMYB15-like was induced by aphid infection and contributed to lignin deposition and cell wall thickening, which consequently enhanced aphid resistance in a Cm4CL2-dependent manner. This study is the first to show that the CmMYB15-like-Cm4CL2 module regulates lignin biosynthesis in response to aphid feeding.

Endogenous salicylic acid suppresses de novo root regeneration from leaf explants

Plants can regenerate new organs from damaged or detached tissues. In the process of de novo root regeneration (DNRR), adventitious roots are frequently formed from the wound site on a detached leaf. Salicylic acid (SA) is a key phytohormone regulating plant defenses and stress responses. The role of SA and its acting mechanisms during de novo organogenesis is still unclear. Here, we found that endogenous SA inhibited the adventitious root formation after cutting. Free SA rapidly accumulated at the wound site, which was accompanied by an activation of SA response. SA receptors NPR3 and NPR4, but not NPR1, were required for DNRR. Wounding-elevated SA compromised the expression of AUX1, and subsequent transport of auxin to the wound site. A mutation in AUX1 abolished the enhanced DNRR in low SA mutants. Our work elucidates a role of SA in regulating DNRR and suggests a potential link between biotic stress and tissue regeneration.

Salicylic Acid and Mobile Regulators of Systemic Immunity in Plants: Transport and Metabolism

Systemic acquired resistance (SAR) occurs when primary infected leaves produce several SAR-inducing chemical or mobile signals that are transported to uninfected distal parts via apoplastic or symplastic compartments and activate systemic immunity. The transport route of many chemicals associated with SAR is unknown. Recently, it was demonstrated that pathogen-infected cells preferentially transport salicylic acid (SA) through the apoplasts to uninfected areas. The pH gradient and deprotonation of SA may lead to apoplastic accumulation of SA before it accumulates in the cytosol following pathogen infection. Additionally, SA mobility over a long distance is essential for SAR, and transpiration controls the partitioning of SA into apoplasts and cuticles. On the other hand, glycerol-3-phosphate (G3P) and azelaic acid (AzA) travel via the plasmodesmata (PD) channel in the symplastic route. In this review, we discuss the role of SA as a mobile signal and the regulation of SA transport in SAR.

Emerging Roles of Salicylic Acid in Plant Saline Stress Tolerance

One of the most important phytohormones is salicylic acid (SA), which is essential for the regulation of plant growth, development, ripening, and defense responses. The role of SA in plant-pathogen interactions has attracted a lot of attention. Aside from defense responses, SA is also important in responding to abiotic stimuli. It has been proposed to have great potential for improving the stress resistance of major agricultural crops. On the other hand, SA utilization is dependent on the dosage of the applied SA, the technique of application, and the status of the plants (e.g., developmental stage and acclimation). Here, we reviewed the impact of SA on saline stress responses and the associated molecular pathways, as well as recent studies toward understanding the hubs and crosstalk between SA-induced tolerances to biotic and saline stress. We propose that elucidating the mechanism of the SA-specific response to various stresses, as well as SA-induced rhizosphere-specific microbiome modeling, may provide more insights and support in coping with plant saline stress.

Regulation of Salicylic Acid and N-Hydroxy-Pipecolic Acid in Systemic Acquired Resistance

In plants, salicylic acid (SA) is a central immune signal that is involved in both local and systemic acquired resistance (SAR). In addition to SA, several other chemical signals are also involved in SAR and these include N-hydroxy-pipecolic acid (NHP), a newly discovered plant metabolite that plays a crucial role in SAR. Recent discoveries have led to a better understanding of the biosynthesis of SA and NHP and their signaling during plant defense responses. Here, I review the recent progress in role of SA and NHP in SAR. In addition, I discuss how these signals cooperate with other SAR-inducing chemicals to regulate SAR.

A Joint Transcriptomic and Metabolomic Analysis Reveals the Regulation of Shading on Lignin Biosynthesis in Asparagus

Asparagus belongs to the Liliaceae family and has important economic and pharmacological value. Lignin plays a crucial role in cell wall structural integrity, stem strength, water transport, mechanical support and plant resistance to pathogens. In this study, various biological methods were used to study the mechanism of shading on the asparagus lignin accumulation pathway. The physiological results showed that shading significantly reduced stem diameter and cell wall lignin content. Microstructure observation showed that shading reduced the number of vascular bundles and xylem area, resulting in decreased lignin content, and thus reducing the lignification of asparagus. Cinnamic acid, caffeic acid, ferulic acid and sinapyl alcohol are crucial intermediate metabolites in the process of lignin synthesis. Metabolomic profiling showed that shading significantly reduced the contents of cinnamic acid, caffeic acid, ferulic acid and sinapyl alcohol. Transcriptome profiling identified 37 differentially expressed genes related to lignin, including PAL, C4H, 4CL, CAD, CCR, POD, CCoAOMT, and F5H related enzyme activity regulation genes. The expression levels of POD, CCoAOMT, and CCR genes were significantly decreased under shading treatment, while the expression levels of CAD and F5H genes exhibited no significant difference with increased shading. The downregulation of POD, CCoAOMT genes and the decrease in CCR gene expression levels inhibited the activities of the corresponding enzymes under shading treatment, resulting in decreased downstream content of caffeic acid, ferulic acid, sinaperol, chlorogenic acid and coniferin. A significant decrease in upstream cinnamic acid content was observed with shading, which also led to decreased downstream metabolites and reduced asparagus lignin content. In this study, transcriptomic and metabolomic analysis revealed the key regulatory genes and metabolites of asparagus lignin under shading treatment. This study provides a reference for further understanding the mechanism of lignin biosynthesis and the interaction of related genes.

MePAL6 regulates lignin accumulation to shape cassava resistance against two-spotted spider mite

INTRODUCTION

The two-spotted spider mite (TSSM) is a devastating pest of cassava production in China. Lignin is considered as an important defensive barrier against pests and diseases, several genes participate in lignin biosynthesis, however, how these genes modulate lignin accumulation in cassava and shape TSSM-resistance is largely unknown.

METHODS

To fill this knowledge gap, while under TSSM infestation, the cassava lignin biosynthesis related genes were subjected to expression pattern analysis followed by family identification, and genes with significant induction were used for further function exploration.

RESULTS

Most genes involved in lignin biosynthesis were up-regulated when the mite-resistant cassava cultivars were infested by TSSM, noticeably, the MePAL gene presented the most vigorous induction among these genes. Therefore, we paid more attention to dissect the function of MePAL gene during cassava-TSSM interaction. Gene family identification showed that there are 6 MePAL members identified in cassava genome, further phylogenetic analysis, gene duplication, cis-elements and conserved motif prediction speculated that these genes may probably contribute to biotic stress responses in cassava. The transcription profile of the 6 MePAL genes in TSSM-resistant cassava cultivar SC9 indicated a universal up-regulation pattern. To further elucidate the potential correlation between MePAL expression and TSSM-resistance, the most strongly induced gene MePAL6 were silenced using virus-induced gene silencing (VIGS) assay, we found that silencing of MePAL6 in SC9 not only simultaneously suppressed the expression of other lignin biosynthesis genes such as 4-coumarate--CoA ligase (4CL), hydroxycinnamoyltransferase (HCT) and cinnamoyl-CoA reductase (CCR), but also resulted in decrease of lignin content. Ultimately, the suppression of MePAL6 in SC9 can lead to significant deterioration of TSSM-resistance.

DISCUSSION

This study accurately identified MePAL6 as critical genes in conferring cassava resistance to TSSM, which could be considered as promising marker gene for evaluating cassava resistance to insect pest.

G protein signaling and metabolic pathways as evolutionarily conserved mechanisms to combat calcium deficiency

Calcium (Ca) deficiency causes necrotic symptoms of foliar edges known as tipburn; however, the underlying cellular mechanisms have been poorly understood due to the lack of an ideal plant model and research platform. Using a phenotyping system that quantitates growth and tipburn traits in the model bryophyte Marchantia polymorpha, we evaluated metabolic compounds and the Gβ-null mutant (gpb1) that modulate the occurrence and expansion of the tipburn. Transcriptomic comparisons between wild-type and gpb1 plants revealed the phenylalanine/phenylpropanoid biosynthesis pathway and reactive oxygen species (ROS) important for Ca deficiency responses. gpb1 plants reduced ROS production possibly through transcriptomic regulations of class III peroxidases and induced the expression of phenylpropanoid pathway enzymes without changing downstream lignin contents. Supplementation of intermediate metabolites and chemical inhibitors further confirmed the cell-protective mechanisms of the phenylpropanoid and ROS pathways. Marchantia polymorpha, Arabidopsis thaliana, and Lactuca sativa showed comparable transcriptomic changes where genes related to phenylpropanoid and ROS pathways were enriched in response to Ca deficiency. In conclusion, our study demonstrated unresolved signaling and metabolic pathways of Ca deficiency response. The phenotyping platform can speed up the discovery of chemical and genetic pathways, which could be widely conserved between M. polymorpha and angiosperms.

Cell dehydration of intergeneric hybrid induces subgenome-related specific responses

The aim was to identify subgenome-related specific responses in two types of triticale, that is, of the wheat-dominated genome (WDG) and rye-dominated genome (RDG), to water stress induced in the early phase (tillering) of plant growth. Higher activity of the primary metabolism of carbohydrates is a feature of the WDG type, while the dominance of the rye genome is associated with a higher activity of the secondary metabolism of phenolic compounds in the RDG type. The study analyzed carbohydrates and key enzymes of their synthesis, free phenolic compounds and carbohydrate-related components of the cell wall, monolignols, and shikimic acid (ShA), which is a key link between the primary and secondary metabolism of phenolic compounds. Under water stress, dominance of the wheat genome in the WDG type was manifested by an increased accumulation of the large subunit of Rubisco and sucrose phosphate synthase and a higher content of raffinose and stachyose compared with the RDG type. In dehydrated RDG plants, higher activity of L-phenylalanine ammonia lyase (PAL) and L-tyrosine ammonia lyase (TAL), as well as a higher level of ShA, free and cell wall-bound p-hydroxybenzoic acid, free homovanillic acid, free sinapic acid, and cell wall-bound syringic acid can be considered biochemical indicators of the dominance of the rye genome.

Efficacy of endophytic SB10 and glycine betaine duo in alleviating phytotoxic impact of combined heat and salinity in Glycine max L. via regulation of redox homeostasis and physiological and molecular responses

Adverse environmental stresses occurring simultaneously exhibit a lethal effect on crop productivity at the global level. Here, we investigated the individual and synergistic effects of endophytic T. virens SB10 and glycine betaine (GB) on the physiological and biochemical responses of Glycine max L. to alleviate the devastating effects of combined heat and salinity (HS) stress. Screening against HS stress tolerance showed that SB10 has significant tolerance against heat stress and produces hormones such as gibberellins and indole-3-acetic acid upon GB amendment of the growth medium under HS stress. Moreover, the current findings illustrated that the synergistic application of SB10 and GB was effective in alleviating the negative effects of HS stress on plant growth and physiology. The findings revealed that SB10 + GB led to a reduction in proline accumulation and Na⁺ uptake. It also maintained a high K⁺/Na ⁺ ratio by regulating GmHKT1 and GmSOS1 expression and enhanced macronutrient uptake (N, Ca, K) in plants. In turn, plants exhibited a higher growth rate and gaseous exchange attributes coupled with the upregulation of APX, SOD, POD, and GSH antioxidant activities and transcript accumulation of GmSOD1 and GmAPX1 to overcome HS-induced oxidative damage. Furthermore, SB10 + GB downregulated DREB2, DREB1B, and GmNCED3 expression and resulted in the reduced accumulation of endogenous ABA while enhancing endogenous SA accumulation via upregulation of PAL genes. In addition, enhanced accumulation of bioactive gibberellins (GA1, GA3, GA4, and GA7) was detected under HS stress in the SB10 + GB treatment group. Moreover, SB10 + GB also significantly regulated GmHsp90A2 and GmHsfA2 expression in tolerance against HS stress. The combination of SB10 and GB was shown to be an effective and alternative approach for growing G. max at high temperature coupled with saline conditions for sustainable agriculture.

Genome-wide studies of PAL genes in sorghum and their responses to aphid infestation

Phenylalanine ammonia-lyase (PAL, EC 4.3.1.25) plays a crucial role in plant adaptation to biotic and abiotic stresses. However, the current knowledge about PAL proteins in sorghum is essentially lacking. Thus, in this study we aimed to analyze the PAL family genes in sorghum using a genome-wide approach and to explore the role of PAL genes in host plant resistance to aphids via SA-mediated defense signaling. Here, we report gene structural features of 8 PAL (SbPAL) genes in sorghum (Sorghum bicolor), their phylogeny, protein motifs and promoter analysis. Furthermore, we demonstrated that the SbPAL genes were induced by sugarcane aphid (SCA) infestation and SbPAL exhibited differential gene expression in susceptible and resistant genotypes. PAL activity assays further validated upregulated expression of the SbPAL genes in a resistant genotype. In addition, exogenous application of SA reduced plant damage and suppressed aphid population growth and fecundity in susceptible genotype, suggesting that those SbPAL genes act as positive regulator of the SA-mediated defense signaling pathway to combat aphid pests in sorghum. This study provides insights for further examination of the defense role of PAL in sorghum against other pests and pathogens.

Effect of Heavy Metal Stress on Phenolic Compounds Accumulation in Winter Wheat Plants

Heavy metal stress can lead to many adverse effects that inhibit cellular processes at various levels of metabolism, causing a decrease in plant productivity. In response to environmental stressors, phenolic compounds fulfill significant molecular and biochemical functions in plants. Increasing the biosynthesis of phenolic compounds in plants subjected to heavy metal stress helps protect plants from oxidative stress. A pot experiment was carried out to determine the effect of the accumulation of copper (Cu) and lead (Pb) salts at concentrations of 200, 500, and 1000 ppm on seed germination, the activity of enzymes in the phenylalanine ammonia-lyase pathway (PAL) and tyrosine ammonia-lyase (TAL), along with the total phenol and flavonoid contents in seedlings of hybrid Triticum aestivum L. (winter wheat) cultivars. The accumulation of heavy metals, especially Cu, had a negative impact on the seed germination process. The cultivar "Hyacinth" reacted most strongly to heavy metal stress, which was confirmed by obtaining the lowest values of the germination parameters. Heavy metal stress caused an increase in the activity of PAL and TAL enzymes and an increase in the accumulation of phenolic compounds. Under the influence of Cu, the highest activity was shown in cv. "Hyvento" (especially at 200 ppm) and, due to the accumulation of Pb, in cv. "Hyacinth" (1000 ppm) and cv. "Hyking" (200 ppm). The cultivar "Hyking" had the highest content of phenolic compounds, which did not increase with the application of higher concentrations of metals. In other cultivars, the highest content of total phenols and flavonoids was usually observed at the lowest concentration (200 ppm) of the tested heavy metals, Cu and Pb.

Plant Cell Wall Integrity Perturbations and Priming for Defense

A plant cell wall is a highly complex structure consisting of networks of polysaccharides, proteins, and polyphenols that dynamically change during growth and development in various tissues. The cell wall not only acts as a physical barrier but also dynamically responds to disturbances caused by biotic and abiotic stresses. Plants have well-established surveillance mechanisms to detect any cell wall perturbations. Specific immune signaling pathways are triggered to contrast biotic or abiotic forces, including cascades dedicated to reinforcing the cell wall structure. This review summarizes the recent developments in molecular mechanisms underlying maintenance of cell wall integrity in plant-pathogen and parasitic interactions. Subjects such as the effect of altered expression of endogenous plant cell-wall-related genes or apoplastic expression of microbial cell-wall-modifying enzymes on cell wall integrity are covered. Targeted genetic modifications as a tool to study the potential of cell wall elicitors, priming of signaling pathways, and the outcome of disease resistance phenotypes are also discussed. The prime importance of understanding the intricate details and complete picture of plant immunity emerges, ultimately to engineer new strategies to improve crop productivity and sustainability.

Transcriptomic and metabolomic analyses reveal the mechanism of uniconazole inducing hypocotyl dwarfing by suppressing BrbZIP39-BrPAL4 module mediating lignin biosynthesis in flowering Chinese cabbage

Uniconazole, a triazole plant growth regulator, is widely used to regulate plant height and prevent the overgrowth of seedlings. However, the underlying molecular mechanism of uniconazole in inhibiting the hypocotyl elongation of seedlings is still largely unclear, and there has been little research on the integration of transcriptomic and metabolomic data to investigate the mechanisms of hypocotyl elonga-tion. Herein we observed that the hypocotyl elongation of flowering Chinese cabbage seedings was significantly inhibited by uniconazole. Interestingly, based on combined transcriptome and metabolome analyses, we found that the "phenylpropanoid biosynthesis" pathway was significantly affected by uniconazole. In this pathway, only one member of the portal enzyme gene family, named BrPAL4, was remarkably downregulated, which was related to lignin biosynthesis. Furthermore, the yeast one-hybrid and dual-luciferase assays showed that BrbZIP39 could directly bind to the promoter region of BrPAL4 and activate its transcript. The virus-induced gene silencing system further demonstrated that BrbZIP39 could positively regulate hypocotyl elongation and the lignin biosynthesis of hypocotyl. Our findings provide a novel insight into the molecular regulatory mechanism of uniconazole inhibiting hypocotyl elongation in flowering Chinese cabbage and confirm, for the first time, that uniconazole decreases lignin content through repressing the BrbZIP39-BrPAL4 module-mediated phenylpropanoid biosynthesis, which leads to the hypocotyl dwarfing of flowering Chinese cabbage seedlings.

A Protective Role of Phenylalanine Ammonia-Lyase from Astragalus membranaceus against Saline-Alkali Stress

Phenylalanine ammonia-lyase (PAL, E.C.4.3.1.5) catalyzes the benzene propane metabolism and is the most extensively studied enzyme of the phenylpropanoid pathway. However, the role of PAL genes in Astragalus membranaceus, a non-model plant showing high capability toward abiotic stress, is less studied. Here, we cloned AmPAL and found that it encodes a protein that resides in the cytoplasmic membrane. The mRNA of AmPAL was strongly induced by NaCl or NaHCO₃ treatment, especially in the root. Overexpressing AmPAL in Nicotiana tabacum resulted in higher PAL enzyme activities, lower levels of malondialdehyde (MDA), and better root elongation in the seedlings under stress treatment compared to the control plants. The protective role of AmPAL under saline-alkali stress was also observed in 30-day soil-grown plants, which showed higher levels of superoxide dismutase (SOD), proline, and chlorophyll compared to wild-type N. Tabacum. Collectively, we provide evidence that AmPAL is responsive to multiple abiotic stresses and that manipulating the expression of AmPAL can be used to increase the tolerance to adverse environmental factors in plants.

Reduced Expression of PRX2/ATPRX1, PRX8, PRX35, and PRX73 Affects Cell Elongation, Vegetative Growth, and Vasculature Structures in Arabidopsis thaliana

Class III peroxidases (PRXs) are involved in a broad spectrum of physiological and developmental processes throughout the life cycle of plants. However, the specific function of each PRX member in the family remains largely unknown. In this study, we selected four class III peroxidase genes (PRX2/ATPRX1, PRX8, PRX35, and PRX73) from a previous genome-wide transcriptome analysis, and performed phenotypic and morphological analyses, including histochemical staining, in PRX2RNAi, PRX8RNAi, PRX35RNAi, and PRX73RNAi plants. The reduced mRNA levels of corresponding PRX genes in PRX2RNAi, PRX8RNAi, PRX35RNAi, and PRX73RNAi seedlings resulted in elongated hypocotyls and roots, and slightly faster vegetative growth. To investigate internal structural changes in the vasculature, we performed histochemical staining, which revealed alterations in cell wall structures in the main vasculature of hypocotyls, stems, and roots of each PRXRNAi plant compared to wild-type (Col-0) plants. Furthermore, we found that PRX35RNAi plants displayed the decrease in the cell wall in vascular regions, which are involved in downregulation of lignin biosynthesis and biosynthesis-regulated genes' expression. Taken together, these results indicated that the reduced expression levels of PRX2/ATPRX1, PRX8, PRX35, and PRX73 affected hypocotyl and root elongation, vegetative growth, and the vasculature structures in hypocotyl, stem, and root tissues, suggesting that the four class III PRX genes play roles in plant developmental processes.

Transcription factor OsNAC055 regulates GA-mediated lignin biosynthesis in rice straw

Crop straws represent enormous biomass resource that mainly contain secondary cell walls (SCWs) consisting of cellulose, hemicelluloses and lignin. Nevertheless, the regulatory mechanism of SCW biosynthesis still needs to be well understood. In this study, we identified a rice NAC (NAM, ATAF1/2, CUC2) transcription factor OsNAC055 that regulates GA-mediated lignin biosynthesis. As a nucleus-localized transcription factor, OsNAC055 exhibits the transcriptional activation activity. Overexpression of OsNAC055 increases the lignin content in rice straw. Transcriptomic analyses showed that the expression of multiple lignin biosynthetic genes was increased in OsNAC055-overexpressing plants. Further ChIP-qPCR analysis and transient transactivation assays indicated that OsNAC055 directly activates rice lignin biosynthetic genes CINNAMOYL-CoA REDUCTASE 10 (OsCCR10) and CINNAMYL ALCOHOL DEHYDROGENASE 2 (OsCAD2) by binding to their promoters. On the other hand, phytohormone measurement showed that OsNAC055 overexpression significantly increased exogenous GA3 levels in rice plants by regulating GA biosynthetic gene OsGA20ox2. Moreover, yeast two-hybrid and bimolecular fluorescence complement (BiFC) assays indicated that OsNAC055 interacts with SLENDER RICE1 (SLR1), the repressor in GA signaling. More importantly, exogenous GA treatment markedly enhanced the transcription of OsCCR10 and OsCAD2, suggesting the role of GA in lignin biosynthesis. Together, our results provide the evidence that OsNAC055 functions as an essential transcription factor to regulate the GA-mediated lignin biosynthesis, which provides a strategy for manipulating lignin production.

The function of the plant cell wall in plant-microbe interactions

The plant cell wall is an interface of plant-microbe interactions. The ability of microbes to decompose cell wall polysaccharides contributes to microbial pathogenicity. Plants have evolved mechanisms to prevent cell wall degradation. However, the role of the cell wall in plant-microbe interactions is not well understood. Here, we discuss four functions of the plant cell wall-physical defence, storage of antimicrobial compounds, production of cell wall-derived elicitors, and provision of carbon sources-in the context of plant-microbe interactions. In addition, we discuss the four families of cell surface receptors associated with plant cell walls (malectin-like receptor kinase family, wall-associated kinase family, leucine-rich repeat receptor-like kinase family, and lysin motif receptor-like kinase family) that have been the subject of several important studies in recent years. This review summarises the findings on both plant cell wall and plant immunity, improving our understanding and may provide impetus to various researchers.

Chitosan-Salicylic acid and Zinc sulphate nano-formulations defend against yellow rust in wheat by activating pathogenesis-related genes and enzymes

Stripe rust instigated by Puccinia striiformis f. sp. tritici causes major yield loss in wheat. In this study, disease resistance was induced in wheat by pre-activation of pathogenesis related (PR) genes using two different nano-formulations (NFs) i.e. Chitosan- Salicylic acid (SA) NFs (CH-NFs) and Zinc sulphate NFs (Zn-NFs). These NFs were synthesized using green approach and were characterized using various techniques. Both NFs effectively controlled stripe rust in wheat genotypes (WH 711 and WH 1123) by significantly increasing activities of phenylalanine ammonia lyase, tyrosine ammonia lyase and polyphenol oxidase enzymes when compared with disease free-control and diseased plants. Total soluble sugar (TSS) level was highest in CH-NF treated plants. TSS was also relatively higher in diseased plants than disease free-control as well as Zn-NF treated plants. Both CH-NFs and Zn-NFs induced the expression of PR genes. In CH-NF treated plants, the relative expression of PR genes was higher on the 3rd day after spraying (DAS) of NFs as compared to diseased and Zn-NF treated plants in both the genotypes. While in case of Zn-NF treated plants, relative expression of PR genes was higher on 5th DAS as compared to diseased and disease free-control plants. Early rise in expression of PR genes due to NF treatments was responsible for disease resistance in both the wheat genotypes as evidenced by a lower average coefficient of infection. These NFs can be synthesized easily with low cost input, are eco-friendly and can be effectively used against yellow rust as well as other wheat diseases.

A draft genome of the medicinal plant Cremastra appendiculata (D. Don) provides insights into the colchicine biosynthetic pathway

Cremastra appendiculata (D. Don) Makino is a rare terrestrial orchid with a high market value as an ornamental and Chinese traditional medicinal herb with a wide range of pharmacological properties. The pseudobulbs of C. appendiculata are one of the primary sources of the famous traditional Chinese medicine "Shancigu", which has been clinically used for treating many diseases, especially, as the main component to treat gout. The lack of genetic research and genome data restricts the modern development and clinical use of C. appendiculata. Here, we report a 2.3 Gb chromosome-level genome of C. appendiculata. We identify a series of candidates of 35 candidate genes responsible for colchicine biosynthesis, among which O-methyltransferase (OMT) gene exhibits an important role in colchicine biosynthesis. Co-expression analysis reveal purple and green-yellow module have close relationships with pseudobulb parts and comprise most of the colchicine pathway genes. Overall, our genome data and the candidate genes reported here set the foundation to decipher the colchicine biosynthesis pathways in medicinal plants.

Phenylalanine Ammonia Lyase GmPAL1.1 Promotes Seed Vigor under High-Temperature and -Humidity Stress and Enhances Seed Germination under Salt and Drought Stress in Transgenic Arabidopsis

Seed vigor is an important agronomic attribute, essentially associated with crop yield. High-temperature and humidity (HTH) stress directly affects seed development of plants, resulting in the decrease of seed vigor. Therefore, it is particularly important to discover HTH-tolerant genes related to seed vigor. Phenylalanine ammonia lyase (PAL, EC 4.3.1.24) is the first rate-limiting enzyme in the phenylpropanoid biosynthesis pathway and a key enzyme involved in plant growth and development and environmental adaptation. However, the biological function of PAL in seed vigor remains unknown. Here, GmPAL1.1 was cloned from soybean, and its protein was located in the cytoplasm and cell membrane. GmPAL1.1 was significantly induced by HTH stress in developing seeds. The overexpression of GmPAL1.1 in Arabidopsis (OE) accumulated lower level of ROS in the developing seeds and in the leaves than the WT at the physiological maturity stage under HTH stress, and the activities of SOD, POD, and CAT and flavonoid contents were significantly increased, while MDA production was markedly reduced in the leaves of the OE lines than in those of the WT. The germination rate and viability of mature seeds of the OE lines harvested after HTH stress were higher than those of the WT. Compared to the control, the overexpression of GmPAL1.1 in Arabidopsis enhanced the tolerance to salt and drought stresses during germination. Our results suggested the overexpression of GmPAL1.1 in Arabidopsis promoted seed vigor at the physiological maturation period under HTH stress and increased the seeds' tolerance to salt and drought during germination.

Flooding and herbivory: the effect of concurrent stress factors on plant volatile emissions and gene expression in two heirloom tomato varieties

BACKGROUND

In nature and in cultivated fields, plants encounter multiple stress factors. Nonetheless, our understanding of how plants actively respond to combinatorial stress remains limited. Among the least studied stress combination is that of flooding and herbivory, despite the growing importance of these stressors in the context of climate change. We investigated plant chemistry and gene expression changes in two heirloom tomato varieties: Cherokee Purple (CP) and Striped German (SG) in response to flooding, herbivory by Spodoptera exigua, and their combination.

RESULTS

Volatile organic compounds (VOCs) identified in tomato plants subjected to flooding and/or herbivory included several mono- and sesquiterpenes. Flooding was the main factor altering VOCs emission rates, and impacting plant biomass accumulation, while different varieties had quantitative differences in their VOC emissions. At the gene expression levels, there were 335 differentially expressed genes between the two tomato plant varieties, these included genes encoding for phenylalanine ammonia-lyase (PAL), cinnamoyl-CoA-reductase-like, and phytoene synthase (Psy1). Flooding and variety effects together influenced abscisic acid (ABA) signaling genes with the SG variety showing higher levels of ABA production and ABA-dependent signaling upon flooding. Flooding downregulated genes associated with cytokinin catabolism and general defense response and upregulated genes associated with ethylene biosynthesis, anthocyanin biosynthesis, and gibberellin biosynthesis. Combining flooding and herbivory induced the upregulation of genes including chalcone synthase (CHS), PAL, and genes encoding BAHD acyltransferase and UDP-glucose iridoid glucosyltransferase-like genes in one of the tomato varieties (CP) and a disproportionate number of heat-shock proteins in SG. Only the SG variety had measurable changes in gene expression due to herbivory alone, upregulating zeatin, and O-glucosyltransferase and thioredoxin among others.

CONCLUSION

Our results suggest that both heirloom tomato plant varieties differ in their production of secondary metabolites including phenylpropanoids and terpenoids and their regulation and activation of ABA signaling upon stress associated with flooding. Herbivory and flooding together had interacting effects that were evident at the level of plant chemistry (VOCs production), gene expression and biomass markers. Results from our study highlight the complex nature of plant responses to combinatorial stresses and point at specific genes and pathways that are affected by flooding and herbivory combined.

Lignin engineering in forest trees: From gene discovery to field trials

Wood is an abundant and renewable feedstock for the production of pulp, fuels, and biobased materials. However, wood is recalcitrant toward deconstruction into cellulose and simple sugars, mainly because of the presence of lignin, an aromatic polymer that shields cell-wall polysaccharides. Hence, numerous research efforts have focused on engineering lignin amount and composition to improve wood processability. Here, we focus on results that have been obtained by engineering the lignin biosynthesis and branching pathways in forest trees to reduce cell-wall recalcitrance, including the introduction of exotic lignin monomers. In addition, we draw general conclusions from over 20 years of field trial research with trees engineered to produce less or altered lignin. We discuss possible causes and solutions for the yield penalty that is often associated with lignin engineering in trees. Finally, we discuss how conventional and new breeding strategies can be combined to develop elite clones with desired lignin properties. We conclude this review with priorities for the development of commercially relevant lignin-engineered trees.

MsMYB741 is involved in alfalfa resistance to aluminum stress by regulating flavonoid biosynthesis

Aluminum (Al) toxicity severely restricts plant growth in acidic soils (pH < 5.0). In this study, an R2R3-MYB transcription factor (TF) gene, MsMYB741, was cloned from alfalfa. Its function and gene regulatory pathways were studied via overexpression and RNA interference of MsMYB741 in alfalfa seedlings. Results showed that root elongation increased as a result of MsMYB741 overexpression (MsMYB741-OE) and decreased with MsMYB741 RNA interference (MsMYB741-RNAi) in alfalfa seedlings compared with the wild-type under Al stress. These were attributed to the reduced Al content in MsMYB741-OE lines, and increased Al content in MsMYB741-RNAi lines. MsMYB741 positively activated the expression of phenylalanine ammonia-lyase 1 (MsPAL1) and chalcone isomerase (MsCHI) by binding to MYB and ABRE elements in their promoters, respectively, which directly affected flavonoid accumulation in roots and secretion from root tips in plants under Al stress, eventually affecting Al accumulation in alfalfa. Additionally, MsABF2 TF directly activated the expression of MsMYB741 by binding to the ABRE element in its promoter. Taken together, our results indicate that MsMYB741 transcriptionally activates MsPAL1 and MsCHI expression to increase flavonoid accumulation in roots and secretion from root tips, leading to increased resistance of alfalfa to Al stress.

Integrative analysis in Pinus revealed long-term heat stress splicing memory

Due to the current climate change, many studies have described main drivers in abiotic stress. Recent findings suggest that alternative splicing (AS) has a critical role in controlling plant responses to high temperature. AS is a mechanism that allows organisms to create an assortment of RNA transcripts and proteins using a single gene. However, the most important roles of AS in stress could not be rigorously addressed because research has been focused on model species, covering only a narrow phylogenetic and lifecycle spectrum. Thus, AS degree of diversification among more dissimilar taxa in heat response is still largely unknown. To fill this gap, the present study employs a systems biology approach to examine how the AS landscape responds to and 'remembers' heat stress in conifers, a group which has received little attention even though their position can solve key evolutionary questions. Contrary to angiosperms, we found that potential intron retention may not be the most prevalent type of AS. Furthermore, our integrative analysis with metabolome and proteome data places splicing as the main source of variation during the response. Finally, we evaluated possible acquired long-term splicing memory in a diverse subset of events, and although this mechanism seems to be conserved in seed plants, AS dynamics are divergent. These discoveries reveal the particular way of remembering past temperature changes in long-lived plants and open the door to include species with unique features to determine the extent of conservation in gene expression regulation.

AIG2A and AIG2B limit the activation of salicylic acid-regulated defenses by tryptophan-derived secondary metabolism in Arabidopsis

Chemical defense systems involving tryptophan-derived secondary metabolites (TDSMs) and salicylic acid (SA) are induced by general nonself signals and pathogen signals, respectively, in Arabidopsis thaliana. Whether and how these chemical defense systems are connected and balanced is largely unknown. In this study, we identified the AVRRPT2-INDUCED GENE2A (AIG2A) and AIG2B genes as gatekeepers that prevent activation of SA defense systems by TDSMs. These genes also were identified as important contributors to natural variation in disease resistance among A. thaliana natural accessions. The loss of AIG2A and AIG2B function leads to upregulation of both SA and TDSM defense systems. Suppressor screens and genetic analysis revealed that a functional TDSM system is required for the upregulation of the SA pathway in the absence of AIG2A and AIG2B, but not vice versa. Furthermore, the AIG2A and AIG2B genes are co-induced with TDSM biosynthesis genes by general pathogen elicitors and nonself signals, thereby functioning as a feedback control of the TDSM defense system, as well as limiting activation of the SA defense system by TDSMs. Thus, this study uncovers an AIG2A- and AIG2B-mediated mechanism that fine-tunes and balances SA and TDSM chemical defense systems in response to nonpathogenic and pathogenic microbes.