Metabolite profiles of Populus in response to pathogen stress

Editing Metabolism, Sex, and Microbiome: How Can We Help Poplar Resist Pathogens?

Poplar (Populus) is a genus of woody plants of great economic value. Due to the growing economic importance of poplar, there is a need to ensure its stable growth by increasing its resistance to pathogens. Genetic engineering can create organisms with improved traits faster than traditional methods, and with the development of CRISPR/Cas-based genome editing systems, scientists have a new highly effective tool for creating valuable genotypes. In this review, we summarize the latest research data on poplar diseases, the biology of their pathogens and how these plants resist pathogens. In the final section, we propose to plant male or mixed poplar populations; consider the genes of the MLO group, transcription factors of the WRKY and MYB families and defensive proteins BbChit1, LJAMP2, MsrA2 and PtDef as the most promising targets for genetic engineering; and also pay attention to the possibility of microbiome engineering.

Comparative Analysis of the Wood Metabolites of Three Poplar Clones Using UPLC-Triple-TOF-MS

Poplar, a woody tree species, is widely used for industrial production and as a protective forest belt. Different clones of poplar exhibit clear variation in terms of morphological and physiological features, however, the impact of the genetic variation on the composition and abundance of wood metabolite have not been fully determined. In this study, ultra-high pressure liquid chromatography-triple time of flight-mass spectrometer (UPLC-Triple-TOF-MS) was used to explore the metabolite changes in poplar wood from three clones, including Populus deltoides CL. '55/65', P. deltoides CL. 'Danhong', and P. nigra CL. 'N179'. A total of 699 metabolites were identified. Clustering analysis and principal component analysis display that the metabolic differences of wood have allowed distinguishing different species of poplar. Meanwhile, eight significantly different metabolites were screened between P. deltoides and P. nigra, which may be considered as valuable markers for chemotaxonomy. In addition, the highly discriminant 352 metabolites were obtained among the three clones, and those may be closely related to the distinction in unique properties (e.g., growth, rigidity and tolerance) of the poplar wood cultivars. This study provides a foundation for further studies on wood metabolomics in poplar, and offers chemotaxonomic markers that will stimulate the early screening of potentially superior trees.

Integrated transcriptomic and metabolomic profiles reveal adaptive responses of three poplar varieties against the bacterial pathogen Lonsdalea populi

Different poplar varieties vary in their tolerance to certain pathogens. However, knowledge about molecular regulation and critical responses of resistant poplars during pathogen infection remains scarce. To investigate adaptive responses to canker disease caused by the bacterium Lonsdalea populi, we screened three poplar varieties with contrasting tolerance, including Populus deltoides. 'Zhonglin 2025' (2025), Populus × Euramericana. '74/76' (107) and Populus tomentosa cv 'henan' (P. tomentosa). Transcriptomic analysis revealed significant changes in the expression levels of defence-related genes in different poplar varieties in response to infection, which reshaped the PTI and ETI processes. Intriguingly, photosynthesis-related genes were found to be highly expressed in the resistant variety, whereas the opposite was observed in the susceptible variety. Susceptible poplars maintained the activation of defence-related genes during early period of onset, which restricted the expression of photosynthesis-related and auxin signal-related genes. Furthermore, combined with metabolomic analysis, differences in the content of antibacterial substances and key differentially expressed genes in phenylpropane and flavonoid biosynthesis pathways were identified. Delayed induction of catechin in the susceptible variety and it's in vitro antibacterial activity were considered to be one of the important reasons for the differences in resistance to L. populi compared with the resistant variety, which is of practical interest for tree breeding. Moreover, the trade-off between growth and defence observed among the three poplar varieties during infection provides new insights into the multilevel regulatory circuits in tree-pathogen interactions.

Studying tree response to biotic stress using a multi-disciplinary approach: The pine pitch canker case study

In an era of climate change and global trade, forests sustainability is endangered by several biotic threats. Pine pitch canker (PPC), caused by Fusarium circinatum, is one of the most important disease affecting conifers worldwide. To date, no effective control measures have been found for this disease. Earlier studies on PPC were mainly focused on the pathogen itself or on determining the levels of susceptibility of different hosts to F. circinatum infection. However, over the last years, plenty of information on the mechanisms that may explain the susceptibility or resistance to PPC has been published. This data are useful to better understand tree response to biotic stress and, most importantly, to aid the development of innovative and scientific-based disease control measures. This review gathers and discusses the main advances on PPC knowledge, especially focusing on multi-disciplinary studies investigating the response of pines with different levels of susceptibility to PPC upon infection. After an overview of the general knowledge of the disease, the importance of integrating information from physiological and Omics studies to unveil the mechanisms behind PPC susceptibility/resistance and to develop control strategies is explored. An extensive review of the main host responses to PPC was performed, including changes in water relations, signalling (ROS and hormones), primary metabolism, and defence (resin, phenolics, and PR proteins). A general picture of pine response to PPC is suggested according to the host susceptibility level and the next steps and gaps on PPC research are pointed out.

Expression Profiling of Flavonoid Biosynthesis Genes and Secondary Metabolites Accumulation in Populus under Drought Stress

Flavonoids are key secondary metabolites that are biologically active and perform diverse functions in plants such as stress defense against abiotic and biotic stress. In addition to its importance, no comprehensive information has been available about the secondary metabolic response of Populus tree, especially the genes that encode key enzymes involved in flavonoid biosynthesis under drought stress. In this study, the quantitative real-time polymerase chain reaction (qRT-PCR) analysis revealed that the expression of flavonoid biosynthesis genes (PtPAL, Pt4-CL, PtCHS, PtFLS-1, PtF3H, PtDFR, and PtANS) gradually increased in the leaves of hybrid poplar (P. tremula × P. alba), corresponding to the drought stress duration. In addition, the activity and capacity of antioxidants have also increased, which is positively correlated with the increment of phenolic, flavonoid, anthocyanin, and carotenoid compounds under drought stress. As the drought stress prolonged, the level of reactive oxygen species such as hydrogen peroxide (H2O2) and singlet oxygen (O2-) too increased. The concentration of phytohormone salicylic acid (SA) also increased significantly in the stressed poplar leaves. Our research concluded that drought stress significantly induced the expression of flavonoid biosynthesis genes in hybrid poplar plants and enhanced the accumulation of phenolic and flavonoid compounds with resilient antioxidant activity.

Mass spectrometry-based forest tree metabolomics

Research in forest tree species has advanced slowly when compared with other agricultural crops and model organisms, mainly due to the long-life cycles, large genome sizes, and lack of genomic tools. Additionally, trees are complex matrices, and the presence of interferents (e.g., oleoresins and cellulose) challenges the analysis of tree tissues with mass spectrometry (MS)-based analytical platforms. In this review, advances in MS-based forest tree metabolomics are discussed. Given their economic and ecological significance, particular focus is given to Pinus, Quercus, and Eucalyptus forest tree species to better understand their metabolite responses to abiotic and biotic stresses in the current climate change scenario. Furthermore, MS-based metabolomics technologies produce large and complex datasets that require expertize to adequately manage, process, analyze, and store the data in dedicated repositories. To ensure that the full potential of forest tree metabolomics data are translated into new knowledge, these data should comply with the FAIR principles (i.e., Findable, Accessible, Interoperable, and Re-usable). It is essential that adequate standards are implemented to annotate metadata from forest tree metabolomics studies as is already required by many science and governmental agencies and some major scientific publishers. © 2019 John Wiley & Sons Ltd. Mass Spec Rev 40:126-157, 2021.

Fungal canker pathogens trigger carbon starvation by inhibiting carbon metabolism in poplar stems

Carbon starvation is the current leading hypothesis of plant mortality mechanisms under drought stress; recently, it is also used to explain tree die-off in plant diseases. However, the molecular biology of the carbon starvation pathway is unclear. Here, using a punch inoculation system, we conducted transcriptome and physiological assays to investigate pathogen response in poplar stems at the early stages of Botryosphaeria and Valsa canker diseases. Transcriptome assays showed that the majority of differentially expressed genes (DEGs) in stem phloem and xylem, such as genes involved in carbon metabolism and transportation, aquaporin genes (in xylem) and genes related to the biosynthesis of secondary metabolites and the phenylpropanoid pathway (related to lignin synthesis), were downregulated at 7 days after inoculation (DAI). Results also showed that the expression of the majority of disease-resistance genes upregulated in poplar stems, which may be connected with the downregulation expression of the majority of WRKY family genes. Physiological assays showed that transpiration rate decreased but WUE (water use efficiency) increased the 3 and 7 DAI, while the net photosynthetic rate decreased at 11 DAI in Botryosphaeria infected poplars (ANOVA, P < 0.05). The NSC (non-structural carbohydrates) content assays showed that the soluble sugar content of stem phloem samples increased at 3, 7, and 11 DAI that might due to the impede of pathogen infection. However, soluble sugar content of stem xylem and root samples decreased at 11 DAI; in contrast, the starch content unchanged. Therefore, results revealed a chronological order of carbon related molecular and physiological performance: declination of genes involved in carbon and starch metabolism first (at least at 7 DAI), declination of assimilation and carbon reserve (at 11 DAI) second. Results implied a potential mechanism that affects the host carbon reserve, by directly inhibiting the expression of genes involved in carbon metabolism and transport.

Variations in Accumulation of Lignin and Cellulose and Metabolic Changes in Seed Hull Provide Insight into Dehulling Characteristic of Tartary Buckwheat Seeds

Tartary buckwheat (Fagopyrum tataricum) is considered a profitable crop that possesses medicinal properties, because of its flavonoid compounds. However, the dehulling issue is becoming the bottleneck for consumption of Tartary buckwheat seed. In this study, we investigated the relation between dehulling efficiency and content of lignin and cellulose in the seed hull. Moreover, the untargeted metabolomics analysis, including partial least squares discriminant analysis (PLS-DA) and principal component analysis (PCA), were performed to examine the pattern of metabolic changes in the hull of Tartary buckwheat seeds, XQ 1 and MQ 1, during seed development using gas chromatography mass spectrometry (GC-MS). In mature seed hull the accumulation of highest lignin and lowest cellulose were observed in the hull of MQ 1 seed, a dehulling-friendly variety with highest dehulling efficiency (93%), than that in other dehulling recalcitrant varieties, such as XQ 1 with a range of dehulling efficiency from 2% to 6%. During seed development, the total content of lignin and cellulose increased. MQ 1 and XQ 1 displayed a similar trend in the change of lignin and cellulose that the content was decreased in lignin and increased in cellulose. PCA result showed the metabolic differentiations between MQ 1 and XQ 1 during seed development. The results of our study suggest the compensatory regulation of lignin and cellulose deposition in the hull of mature and developing seed, and deviation of MQ 1 from the ratio of lignin to cellulose of other dehulling recalcitrant varieties may have been a contributing factor that resulted in the dehulling differentia.

Comparative metabolomics of scab-resistant and susceptible apple cell cultures in response to scab fungus elicitor treatment

Apple scab disease caused by the fungus Venturia inaequalis is a devastating disease that seriously affects quality and yield of apples. In order to understand the mechanisms involved in scab resistance, we performed gas chromatography-mass spectrometry based metabolomics analysis of the cell culture of scab resistant cultivar 'Florina' and scab susceptible cultivar 'Vista Bella' both prior -to and -following treatment with V. inaequalis elicitor (VIE). A total 21 metabolites were identified to be altered significantly in 'Florina' cell cultures upon VIE-treatment. Among 21 metabolites, formation of three new specialized metabolites aucuparin, noraucuparin and eriobofuran were observed only in resistant cultivar 'Florina' after the elicitor treatment. The score plots of principal component analysis (PCA) exhibited clear discrimination between untreated and VIE-treated samples. The alteration in metabolite levels correlated well with the changes in the transcript levels of selected secondary metabolite biosynthesis genes. Aucuparin, noraucuparin and eriobofuran isolated from the 'Florina' cultures showed significant inhibitory effect on the conidial germination of V. inaequalis. The results expand our understanding of the metabolic basis of scab-resistance in apple and therefore are of interest in apple breeding programs to fortify scab resistance potential of commercially grown apple cultivars.

Transcriptome analysis reveals the role of nitric oxide in Pleurotus eryngii responses to Cd2+ stress

Pleurotus eryngii is widely cultivated in China. However, our understanding of its transcriptional response to heavy metal stress and the underlying mechanism of nitric oxide (NO) in enhancing its tolerance to heavy metals is limited. In the present study, RNA-seq was used to generate large transcript sequences from P. eryngii exposed to cadmium chloride (CdCl₂) and exogenous NO. A total of 45,833 unigenes were assembled from the P. eryngii transcriptome, of which 32,333 (70.54%) unigenes matched known proteins in the nr database. Transcriptional analysis revealed that putative genes encoding heat shock proteins (HSPs) and genes participating in glycerolipid metabolism and steroid biosynthesis were significantly up-regulated in P. eryngii exposed to 50 μM Cd (P < 0.05). P. eryngii mycelia exposed to extremely high levels of heavy metals showed an increase in biomass when exogenous NO was added to the culture. The collaboration of putative oxidoreductase, dehydrogenase, reductase, transferase genes and transcription factors such as "GTPase activator activity", "transcription factor complex", "ATP binding", "GTP binding", and "enzyme activator activity", which were significantly up-regulated in samples induced by exogenous NO, contributed to the enhancement of P. eryngii tolerance to extremely high levels of heavy metals. The study provides a new insight into the transcriptional response of P. eryngii to extremely high levels of heavy metals and the mechanism of NO in enhancing heavy metal tolerance.