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Necroptosis is a promising novel target for cervical cancer therapy. Nevertheless, differentially expressed necroptosis-related genes (NRGs) in cervical cancer and their associations with prognosis are far from fully clarified. In this study, differentially expressed NRGs (DE-NRGs) were screened out and their bio-function was elucidated. Subsequently, a prognostic scoring model based on the regression coefficients of the screened out NRGs and their corresponding mRNA expressions were constructed and validated. Finally, the survival probability of cervical cancer patients based on the constructed prognostic scoring model in 3 and 5 years was predicted and assessed. We found 17 DE-NRGs in cervical cancer tissues which were closely related to cancer progression, and most of them were significantly highly expressed. Furthermore, 3 NRG were confirmed as the prognostic signature genes from 17 DE-NRGs by regression analysis. Overall survival predicted through our prognostic scoring model was lower in the high-risk group than in the low-risk group (p 0.05) in both the TCGA cohort and the external GEO44001 validation cohort. What's more, the prediction performance of our prognostic scoring models well verified by the ROC curve, and the risk score calculated could act as an independent prognostic factor for cervical cancer patients. The calibration curve and C-index (0.776) of the nomogram analysis suggested that the predictive performance of the nomogram was satisfactory. Our study identified and validated a necroptosis-related prognostic signature in cervical cancer, which could well predict the prognosis for cervical cancer patients.

Reaction selectivity and yield prediction are important for chemical synthesis. Most existing computational methods use either computational expensive and complicated quantum mechanics-based models that are not easy for experimental chemists to use or black-box deep learning models that do not generalize well outside of the training space and lack explanation. Herein, using convenient physics-based electronic descriptors and structure-based steric descriptors, we developed an explainable machine learning platform, Reaxtica, that outperformed previous methods in four different reaction types and tasks, including regioselectivity, site-selectivity, enantioselectivity, and yield predictions. Further descriptor analysis helps understand reaction mechanisms behind the data. As a practical and robust toolbox, Reaxtica can be easily applied to different chemical reactions and extended to out-of-sample reaction. To assist chemists’ daily research, we further built an easy-to-use webserver, which only takes seconds to run and can be accessed at http://www.pkumdl.cn:8000/reaxtica/.

The production of patchoulol in the patchouli (

Farnesyl pyrophosphate synthase (FPPS) plays an important role in the synthesis of plant secondary metabolites, but its function and molecular regulation mechanism remain unclear in

Background Patchouli alcohol is an effective component of the medicinal plant patchouli. Similar to other secondary metabolites, its synthesis is also regulated by transcription factors. Although the biosynthetic pathway of patchouli alcohol has been characterized, the regulatory mechanism of patchouli alcohol has not been fully revealed. Results This study combined the transcriptome data of patchouli leaves treated with different hormones and WGCNA to complete the coexpression network. The modules related to patchouli alcohol were identified, and PcMYB25 played a crucial role in regulating patchouli alcohol biosynthesis. The overexpression of PcMYB25 can promote the expression of PTS , thereby increasing the content of patchouli alcohol. Conclusions This is the first reporter that MYB25 regulates the secondary metabolism of patchouli. These experimental results lay the foundation for further analysis of the regulatory mechanism of patchouli alcohol synthesis.

Andrographis paniculata (Burm. f.) Nees is one of the most important economic crops for its various medicinal properties, which has been widely used as medicinal herb in several folk medicine systems all over the world. A. paniculata suffers from continuous cropping problem in cultivation; however, effects of continuous cropping on A. paniculata and the underlying mechanism at molecular level are rarely understood. In this study, Illumina paired-end RNA-seq was performed for de novo transcriptome construction of A. paniculata leaf with or without 2-years continuous cropping, to identify gene expression in response to continuous cropping stress. A total of 43,683 Unigenes were obtained by de novo assembly of 231.53 million paired-end clean reads. RNA-seq based gene expression profiling showed a total of 6193 Unigenes was significantly up-/down-regulated after continuous cropping. Integrating the GO and KEGG enrichment analysis of differentially expressed genes (DEGs) revealed that A. paniculata could alter enzyme genes expression to adjust the complicated metabolic pathways to tolerate the continuous cropping stress. Specially, accorded with the downtrend of active component contents in A. paniculata, majority of genes involved in the terpenoids biosynthesis, phenylpropanoid biosynthesis and flavonoids biosynthesis pathways were down-regulated, indicating that continuous cropping led to a declined synthesis of active ingredients through repressing the expression levels of genes involved in these metabolites’ biosynthesis pathways. The transcriptome profiling will deepen the understanding of A. paniculata under continuous cropping stress at transcriptional level, and provide useful genomic resource for further interpretation on the regulation mechanism.

Background Changes of soil microbial communities are one of the main factors of continuous cropping problem. Andrographis paniculata has been reported to have replant problem in cultivation. However, little is known about the variations of rhizosphere soil microbial communities of A. paniculata under a continuous cropping system. Here, Illumina MiSeq was used to investigate the shifts of rhizospheric bacterial and fungal communities after continuous cropping of A. paniculata. Results The bacterial diversity increased whereas the fungal diversity decreased in rhizosphere soil after consecutive A. paniculata monoculture; and the soil microbial community structure differed between newly plant soil and continuous cropped soil. Taxonomic analyses further revealed that the bacterial phyla Proteobacteria, Acidobacteria and Bacteroidetes and the fungal phyla Zygomycota, Ascomycota and Cercozoa were the dominant phyla across all soil samples. The relative abundance of phyla Acidobacteria and Zygomycota were significantly increased after continuous cropping. Additionally, the most abundant bacterial genus Pseudolabrys significantly decreased, while the predominant fungal genus Mortierella increased considerably in abundance after continuous cropping. Conclusions Our results revealed the changes on diversity and composition of bacterial and fungal communities in rhizospheric soil under continuous cropping of A. paniculata. These data contributed to the understanding of soil micro-ecological environments in the rhizosphere of A. paniculata.

Additional file 1: Table S1. Sequencing output of soil bacterial sequences. Table S2. Sequencing output of soil fungal sequences. Fig. S1. Rarefaction curves of soil microbial communities based on OTUs at the 97% similarity cut-off level for individual samples. (a) and (b) are the rarefaction curves of OTU for bacterial and fungal communities, respectively. AP0, AP1 and AP2 represent soil with continuously cropping histories of A. paniculata for 0, 1 and 2 years. “a” and “b” mean the two replicates.

The JASMONATE ZIM DOMAIN (JAZ) proteins act as negative regulators in the jasmonic acid (JA) signaling pathways of plants, and these proteins have been reported to play key roles in plant secondary metabolism mediated by JA. In this study, we firstly isolated one JAZ from P. cablin, PatJAZ6, which was characterized and revealed based on multiple alignments and a phylogenic tree analysis. The result of subcellular localization indicated that the PatJAZ6 protein was located in the nucleus of plant protoplasts. The expression level of PatJAZ6 was significantly induced by the methyl jasmonate (MeJA). Furthermore, by means of yeast two-hybrid screening, we identified two transcription factors that interact with the PatJAZ6, the PatMYC2b1 and PatMYC2b2. Virus-induced gene silencing (VIGS) of PatJAZ6 caused a decrease in expression abundance, resulting in a significant increase in the accumulation of patchouli alcohol. Moreover, we overexpressed PatJAZ6 in P. cablin, which down-regulated the patchoulol synthase expression, and then suppressed the biosynthesis of patchouli alcohol. The results demonstrate that PatJAZ6 probably acts as a repressor in the regulation of patchouli alcohol biosynthesis, contributed to a model proposed for the potential JA signaling pathway in P. cablin.

Lysine succinylation is a novel, naturally occurring posttranslational modification (PTM) in living organisms. Global lysine succinylation identification has been performed at the proteomic level in various species; however, the study of lysine succinylation in plant species is relatively limited. Patchouli plant (P. cablin (Blanco) Benth., Lamiaceae) is a globally important industrial plant and medicinal herb. In the present study, lysine succinylome analysis was carried out in patchouli plants to determine the potential regulatory role of lysine succinylation in patchouli growth, development, and physiology. The global succinylation sites and proteins in patchouli plants were screened with an immunoprecipitation affinity enrichment technique and advanced mass spectrometry-based proteomics. Several bioinformatic analyses, such as function classification and enrichment, subcellular location predication, metabolic pathway enrichment and protein−protein interaction networking, were conducted to characterize the functions of the identified sites and proteins. In total, 1097 succinylation sites in 493 proteins were detected in patchouli plants, among which 466 succinylation sites in 241 proteins were repeatedly identified within three independent experiments. The functional characterization of these proteins indicated that the tricarboxylic acid (TCA) cycle, oxidative phosphorylation, photosynthesis processes, and amino acid biosynthesis may be regulated by lysine succinylation. In addition, these succinylated proteins showed a wide subcellular location distribution, although the chloroplast and cytoplasm were the top two preferred cellular components. Our study suggested the important role of lysine succinylation in patchouli plant physiology and biology and could serve as a useful reference for succinylation studies in other medicinal plants.

Figure S1. Morphology characteristics of different Pogostemon cablin cultivars, including (a) P. cablin cv. ‘Zhanxiang’, (b) P. cablin cv. ‘Yangjiang’, and (c) P. cablin cv. ‘Indonesia’. (DOCX 458 kb)

Figure S3. Homologous species distribution of P. cablin annotated in Nr database. (DOCX 152 kb)

Trihelix (TH) transcription factors (TFs) actively function in regulating growth and development of plant. Moreover, members of this gene family regulate environment-responsive secondary metabolism. Here, members of trihelix family were explored based on the full-length transcriptome of Pogostemon cablin (Blanco) Benth. (patchouli), an extensively used medicinal plant. Among them, 16 PatTHs exhibited complete opening reading frame (ORF) were successfully cloned, and were classified according to their structural properties into four subfamilies (GT-1, GT-2, SH4, and SIP1). The expression patterns of PatTHs varied in various P. cablin tissues, and most of the PatTHs were induced by methyl jasmonate (MeJA). On exposure to abiotic stresses, including salt, drought, and cold condition, each PatTH responded to at least one of the stresses. In addition, the promoter of patchouli HMGR gene was bound and repressed by PatGT-1, a homologous protein of Arabidopsis transcription factor GT-1. According to subcellular localization results, PatGT-1 is a nuclear-localized protein. Once PatGT-1 was transiently overexpressed, it significantly lowered the production of patchoulol via repressing genes in patchoulol biosynthetic pathway. In this study, PatTHs and their putative functions were identified from P. cablin, and PatGT-1 was revealed as a negative regulator in patchoulol synthesis. Our findings improve the understanding of trihelix family in patchouli and contribute to the future study on this family.

Patchoulol, the major active ingredient in Pogostemon cablin (Blanco) Benth., has considerable clinical and industrial value. A number of genes that participate in the patchoulol biosynthesis pathway have been identified; however, little is known about the transcription factors involved in regulating patchoulol synthesis. In this study, PatSWC4, a homologous protein of Arabidopsis SWC4 belonging to the MYB (v-myb avian myeloblastosis viral oncogene homolog)-related transcription factor family, was identified and characterized. Subcellular localization showed that PatSWC4 protein localized in the nucleus. The highest expression level of PatSWC4 gene was found in old leaves of P. cablin and it was significantly induced by methyl jasmonate (MeJA). Additionally, yeast one-hybrid (Y1H) and dual-luciferase (dual-LUC) assays revealed that PatSWC4 could bind to the promoter of PatPTS gene to increase its transcriptional activity. Yeast two-hybrid (Y2H) assays also confirmed the interaction between PatSWC4 and PatJAZ4 proteins, indicating that PatSWC4 might function in the JA response network. Moreover, transient overexpression of PatSWC4 gene in P. cablin leaves markedly increased the production of patchoulol, and qRT-PCR analysis further revealed that genes in the patchoulol biosynthesis pathway were significantly upregulated at the transcriptional level. Ultimately, we proposed a work model depicting how JA signaling regulates PatPTS via the interaction between PatSWC4 and PatJAZ4, thereby regulating the biosynthesis of patchoulol. Our findings not only help to elucidate the regulatory mechanism governing JA-induced patchoulol biosynthesis, but also lay a foundation for future studies on improving patchoulol production through genetic and metabolic engineering.

Exogenous hormone application is an effective and feasible method to regulate production of economic plant and synthesis of high-value natural medical products. Jasmonate and ethylene are two crucial plant hormones regulate growth and development, secondary metabolism, and stress responses in Pogostemon cablin. However, the regulatory mechanism of these phytohormones in this important medicinal plant has not been elucidated to date. In the present study, alterations of secondary metabolites and photosynthesis of P. cablin leaves treated with exogenous methyl jasmonate (MeJA), ethrel (ETH), and simultaneously with both MeJA and ETH, respectively, were explored. To uncover the potential protein functional network involved in the hormone-induction mechanism, we performed a proteomic analysis of differently treated leaves using isobaric tags for relative and absolute quantification (iTRAQ). In P. cablin leaves before and after three different treatments, 254, 229 and 400 differentially expressed proteins (DEPs) involving a wide range of physiological processes were clearly identified respectively. The quantitative data were further validated by parallel reaction monitoring (PRM) and qRT-PCR. Functional enrichment analysis indicated photosynthesis-related proteins showed a significant increase expression in P. cablin leaves after MeJA treatment, while proteins involved in secondary metabolite biosynthesis and thiamine metabolism were significantly down-regulated. Exogenous ETH mainly repressed the expression of proteins related to carbohydrate and energy metabolism in P. cablin leaves while markedly raised protein abundance in photosynthesis and protein processing in the endoplasmic reticulum. Regarding P. cablin leaves treated with both MeJA and ETH, expression of proteins related to carbohydrate and energy metabolism, secondary metabolite biosynthesis, tyrosine metabolism, thiamine metabolism and lipid metabolism were significantly down-regulated, while that of proteins involved in photosynthesis, phenylpropanoid biosynthesis and nitrogen metabolism were considerably up-regulated. This is the first study using iTRAQ-based proteomics approach to comprehensively elucidate exogenous hormone response of P. cablin, providing important pathways/proteins involved in secondary metabolism regulation, which will contribute to potential genetic improvement of medical constituents.