Transcriptomic analysis of topping-induced axillary shoot outgrowth in Nicotiana tabacum

Transcriptome analysis reveals the key network of axillary bud outgrowth modulated by topping in citrus

Topping, an important tree shaping and pruning technique, can promote the outgrowth of citrus axillary buds. However, the underlying molecular mechanism is still unclear. In this study, spring shoots of Citrus reticulata 'Huagan No.2' were topped and transcriptome was compared between axillary buds of topped and untopped shoots at 6 and 11 days after topping (DAT). 1944 and 2394 differentially expressed genes (DEGs) were found at 6 and 11 DAT, respectively. KEGG analysis revealed that many DEGs were related to starch and sucrose metabolism, signal transduction of auxin, cytokinin and abscisic acid. Specially, transcript levels of auxin synthesis, transport, and signaling-related genes (SAURs and ARF5), cytokinin signal transduction related genes (CRE1, AHP and Type-A ARRs), ABA signal responsive genes (PYL and ABF) were up-regulated by topping; while transcript levels of auxin receptor TIR1, auxin responsive genes AUX/IAAs, ABA signal transduction related gene PP2Cs and synthesis related genes NCED3 were down-regulated. On the other hand, the contents of sucrose and fructose in axillary buds of topped shoots were significantly higher than those in untopped shoots; transcript levels of 16 genes related to sucrose synthase, hexokinase, sucrose phosphate synthase, endoglucanase and glucosidase, were up-regulated in axillary buds after topping. In addition, transcript levels of genes related to trehalose 6-phosphate metabolism and glycolysis/tricarboxylic acid (TCA) cycle, as well to some transcription factors including Pkinase, Pkinase_Tyr, Kinesin, AP2/ERF, P450, MYB, NAC and Cyclin_c, significantly responded to topping. Taken together, the present results suggested that topping promoted citrus axillary bud outgrowth through comprehensively regulating plant hormone and carbohydrate metabolism, as well as signal transduction. These results deepened our understanding of citrus axillary bud outgrowth by topping and laid a foundation for further research on the molecular mechanisms of citrus axillary bud outgrowth.

Integrative proteome and metabolome unveil the central role of IAA alteration in axillary bud development following topping in tobacco

Axillary bud is an important aspect of plant morphology, contributing to the final tobacco yield. However, the mechanisms of axillary bud development in tobacco remain largely unknown. To investigate this aspect of tobacco biology, the metabolome and proteome of the axillary buds before and after topping were compared. A total of 569 metabolites were differentially abundant before and 1, 3, and 5 days after topping. KEGG analyses further revealed that the axillary bud was characterized by a striking enrichment of metabolites involved in flavonoid metabolism, suggesting a strong flavonoid biosynthesis activity in the tobacco axillary bud after topping. Additionally, 9035 differentially expressed proteins (DEPs) were identified before and 1, 3, and 5 days after topping. Subsequent GO and KEGG analyses revealed that the DEPs in the axillary bud were enriched in oxidative stress, hormone signal transduction, MAPK signaling pathway, and starch and sucrose metabolism. The integrated proteome and metabolome analysis revealed that the indole-3-acetic acid (IAA) alteration in buds control dormancy release and sustained growth of axillary bud by regulating proteins involved in carbohydrate metabolism, amino acid metabolism, and lipid metabolism. Notably, the proteins related to reactive oxygen species (ROS) scavenging and flavonoid biosynthesis were strongly negatively correlated with IAA content. These findings shed light on a critical role of IAA alteration in regulating axillary bud outgrowth, and implied a potential crosstalk among IAA alteration, ROS homeostasis, and flavonoid biosynthesis in tobacco axillary bud under topping stress, which could improve our understanding of the IAA alteration in axillary bud as an important regulator of axillary bud development.

Comparative transcriptome analysis reveals nicotine metabolism is a critical component for enhancing stress response intensity of innate immunity system in tobacco

The pyridine alkaloid nicotine acts as one of best-studied plant resistant traits in tobacco. Previous research has shown that NtERF199 and NtERF189, acting as master regulators within the NIC1 and NIC2 locus, quantitatively contribute to nicotine accumulation levels in N. tabacum. Genome editing-created Nic1(Nterf199) and Nic2 (Nterf189) double mutant provides an ideal platform for precisely dissecting the defensive role of nicotine and the connection between the nicotine biosynthetic pathway with other putative metabolic networks. Taking this advantage, we performed a comparative transcriptomic analysis to reevaluate the potential physiological and metabolic changes in response to nicotine synthesis defect by comparing the nic1nic2 and NIC1NIC2 plants. Our findings revealed that nicotine reduction could systematically diminishes the expression intensities of genes associated with stimulus perception, signal transduction and regulation, as well as secondary metabolic flux. Consequently, this global expression reduction might compromise tobacco adaptions to environmental fitness, herbivore resistances, and plant growth and development. The up-regulation of a novel set of stress-responsive and metabolic pathway genes might signify a newly established metabolic reprogramming to tradeoff the detrimental effect of nicotine loss. These results offer additional compelling evidence regarding nicotine's critical defensive role in nature and highlights the tight link between nicotine biosynthesis and gene expression levels of quantitative resistance-related genes for better environmental adaptation.

H2O2 promotes trimming-induced tillering by regulating energy supply and redox status in bermudagrass

Tillering/branching pattern plays a significant role in determining the structure and diversity of grass, and trimming has been found to induce tillering in turfgrass. Recently, it has been reported that hydrogen peroxide (H2O2) regulates axillary bud development. However, the role of H2O2 in trimming-induced tillering in bermudagrass, a kind of turfgrass, remains unclear. Our study unveils the significant impact of trimming on promoting the sprouting and growth of tiller buds in stolon nodes, along with an increase in the number of tillers in the main stem. This effect is accompanied by spatial-temporal changes in cytokinin and sucrose content, as well as relevant gene expression in axillary buds. In addition, the partial trimming of new-born tillers results in an increase in sucrose and starch reserves in their leaves, which can be attributed to the enhanced photosynthesis capacity. Importantly, trimming promotes a rapid H2O2 burst in the leaves of new-born tillers and axillary stolon buds. Furthermore, exogenous application of H2O2 significantly increases the number of tillers after trimming by affecting the expression of cytokinin-related genes, bolstering photosynthesis potential, energy reserves and antioxidant enzyme activity. Taken together, these results indicate that both endogenous production and exogenous addition of H2O2 enhance the inductive effects of trimming on the tillering process in bermudagrass, thus helping boost energy supply and maintain the redox state in newly formed tillers.

Genome-wide identification and expression analysis of the ADH gene family under diverse stresses in tobacco (Nicotiana tabacum L.)

BACKGROUND

Alcohol dehydrogenases (ADHs) are the crucial enzymes that can convert ethanol into acetaldehyde. In tobacco, members of ADH gene family are involved in various stresses tolerance reactions, lipid metabolism and pathways related to plant development. It will be of great application significance to analyze the ADH gene family and expression profile under various stresses in tobacco.

RESULTS

A total of 53 ADH genes were identified in tobacco (Nicotiana tabacum L.) genome and were grouped into 6 subfamilies based on phylogenetic analysis. Gene structure (exon/intron) and protein motifs were highly conserved among the NtADH genes, especially the members within the same subfamily. A total of 5 gene pairs of tandem duplication, and 3 gene pairs of segmental duplication were identified based on the analysis of gene duplication events. Cis-regulatory elements of the NtADH promoters participated in cell development, plant hormones, environmental stress, and light responsiveness. The analysis of expression profile showed that NtADH genes were widely expressed in topping stress and leaf senescence. However, the expression patterns of different members appeared to be diverse. The qRT-PCR analysis of 13 NtADH genes displayed their differential expression pattern in response to the bacterial pathogen Ralstonia solanacearum L.

INFECTION

Metabolomics analysis revealed that NtADH genes were primarily associated with carbohydrate metabolism, and moreover, four NtADH genes (NtADH20/24/48/51) were notably involved in the pathway of alpha-linolenic acid metabolism which related to the up-regulation of 9-hydroxy-12-oxo-10(E), 15(Z)-octadecadienoic acid and 9-hydroxy-12-oxo-15(Z)-octadecenoic acid.

CONCLUSION

The genome-wide identification, evolutionary analysis, expression profiling, and exploration of related metabolites and metabolic pathways associated with NtADH genes have yielded valuable insights into the roles of these genes in response to various stresses. Our results could provide a basis for functional analysis of NtADH gene family under stressful conditions.

Genome-wide identification of MAXs genes for strigolactones synthesis/signaling in solanaceous plants and analysis of their potential functions in tobacco

The more axillary growth (MAX) gene family is a group of key genes involved in the synthesis and signal transduction of strigolactones (SLs) in plants. Although MAX genes play vital roles in plant growth and development, characterization of the MAX gene family has been limited in solanaceous crops, especially in tobacco. In this study, 74 members of the MAX family were identified in representative Solanaceae crops and classified into four groups. The physicochemical properties, gene structure, conserved protein structural domains, cis-acting elements, and expression patterns could be clearly distinguished between the biosynthetic and signal transduction subfamilies; furthermore, MAX genes in tobacco were found to be actively involved in the regulation of meristem development by responding to hormones. MAX genes involved in SL biosynthesis were more responsive to abiotic stresses than genes involved in SL signaling. Tobacco MAX genes may play an active role in stress resistance. The results of this study provide a basis for future in-depth analysis of the molecular mechanisms of MAX genes in tobacco meristem development and stress resistance.

Topping and grafting affect the alkaloid content and gene expression patterns of tobacco (Nicotiana tabacum L.)

In this study, we aimed to determine molecular mechanisms underlying the effects of topping and grafting in tobacco (Nicotiana tabacum L.) by comparing the alkaloid contents and enrichment pathways of differentially expressed genes (DEGs) among plants subjected to different combinations of topping and grafting treatments. Plants of the tobacco variety "Zhongyan 100" and eggplant (Solanum melongena L.) were grafted in four combinations as scions and rootstocks, respectively. The four treatment groups were tobacco with topping, tobacco without topping, topped tobacco grafted onto an eggplant rootstock, and non-topped tobacco grafted onto an eggplant rootstock. Tobacco leaves were collected on the day of topping, at 7 days after topping, and after flue curing, the alkaloid contents of the collected leaves were determined. Leaves of plants subjected to the different treatments were collected for RNA sequencing and screened for DEGs, which were subsequently subjected to functional enrichment analyses. Analyses revealed reductions in the leaf alkaloid contents of tobacco subjected to combined topping and eggplant grafting. Gene annotation indicated that topping influences biological processes such as starch metabolism and stress response, whereas grafting affected the biosynthesis and metabolic pathways of secondary metabolites. Downregulated DEGs between non-topped tobacco and eggplant-grafted topped tobacco and between topped and non-topped tobacco are mainly involved in inositol phosphate metabolic and biosynthetic processes. Downregulated DEGs between different grafting methods (eggplant-grafted non-topped tobacco vs. non-topped tobacco and eggplant-grafted topped tobacco vs. topped tobacco) are mainly involved in sesquiterpene synthase activity and photosynthesis. The findings of this study provide important insights into the molecular mechanisms underlying the effects of topping and grafting on tobacco plants.

A Practical Guide to the Management of Oral Candidiasis in Patients with Plaque Psoriasis Receiving Treatments That Target Interleukin-17

Plaque psoriasis is an immune-mediated inflammatory skin disease associated with the dysregulation of cytokines, especially those involved in the interleukin (IL)-23/IL-17 pathways. In recent years, there has been growing interest in developing biologic therapies that target these pathways. However, inhibition of the cytokines of the IL-23/IL-17 pathways may increase patients' risk of developing fungal infections, particularly oral candidiasis. Therefore, it is important that dermatology practitioners can effectively diagnose and treat oral candidiasis. In this review, we examine the role of the IL-23/IL-17 pathways in antifungal host defense, and provide a practical guide to the diagnosis and treatment of oral candidiasis in patients with psoriasis. Overall, while treatment with anti-IL-17 medications leads to an increased incidence of oral candidiasis in patients with psoriasis, these cases are typically mild or moderate in severity and can be managed with standard antifungal therapy without discontinuing treatment for psoriasis. If applicable, patients with psoriasis should also be advised to practice good oral hygiene and manage or control co-existing diabetes, and should be provided with information on smoking cessation to prevent oral candidiasis.

Genome-wide identification of the tobacco GDSL family and apical meristem-specific expression conferred by the GDSL promoter

BACKGROUND

GDSL esterases/lipases are a large protein subfamily defined by the distinct GDSL motif, and play important roles in plant development and stress responses. However, few studies have reported on the role of GDSLs in the growth and development of axillary buds. This work aims to identify the GDSL family members in tobacco and explore whether the NtGDSL gene contributes to development of the axillary bud in tobacco.

RESULTS

One hundred fifty-nine GDSL esterase/lipase genes from cultivated tobacco (Nicotiana tabacum) were identified, and the dynamic changes in the expression levels of 93 of these genes in response to topping, as assessed using transcriptome data of topping-induced axillary shoots, were analysed. In total, 13 GDSL esterase/lipase genes responded with changes in expression level. To identify genes and promoters that drive the tissue-specific expression in tobacco apical and axillary buds, the expression patterns of these 13 genes were verified using qRT-PCR. GUS activity and a lethal gene expression pattern driven by the NtGDSL127 promoter in transgenic tobacco demonstrated that NtGDSL127 is specifically expressed in apical buds, axillary buds, and flowers. Three separate deletions in the NtGDSL127 promoter demonstrated that a minimum upstream segment of 235 bp from the translation start site can drive the tissue-specific expression in the apical meristem. Additionally, NtGDSL127 responded to phytohormones, providing strategies for improving tobacco breeding and growth.

CONCLUSION

We propose that in tobacco, the NtGDSL127 promoter directs expression specifically in the apical meristem and that expression is closely correlated with axillary bud development.

Signaling network regulating plant branching: Recent advances and new challenges

Auxin alone or supplemented with cytokinins and strigolactones were long considered as the main player(s) in the control of apical dominance (AD) and correlative inhibition of the lateral bud outgrowth, the processes that shape the plant phenotype. However, past decade data indicate a more sophisticated pathways of AD regulation, with the involvement of mobile carbohydrates which perform both signal and trophic functions. Here we provide a critical comprehensive overview of the current status of the AD problem. This includes insight into intimate mechanisms regulating directed auxin transport in axillary buds with participation of phytohormones and sugars. Also roles of auxin, cytokinin and sugars in the dormancy or sustained growth of the lateral meristems were assigned. This review not only provides the latest data on implicated phytohormone crosstalk and its relationship with the signaling of sugars and abscisic acid, new AD players, but also focuses on the emerging biochemical mechanisms, at first positive feedback loops involving both sugars and hormones, that ensure the sustained bud growth. Data show that sugars act in concert with cytokinins but antagonistically to strigolactone signaling. A complex bud growth regulating network is demonstrated and unresolved issues regarding the hormone-carbohydrate regulation of AD are highlighted.

Genome-wide identification of the ARRs gene family in tobacco (Nicotiana tabacum)

BACKGROUND

The growth of axillary buds determines the shoot branching and morphology of plants, and its initiation and development are regulated by a series of hormonal signals, such as cytokinin. Arabidopsis response regulators (ARRs) can regulate the growth and development, disease resistance and stress resistance of plants by participating in cytokinin signaling.

OBJECTIVE

To explore the distribution and expression pattern of ARR members in tobacco.

METHODS

The identification, isoelectric points, molecular weights, protein subcellular localization prediction, multiple sequence alignment, phylogenetic analysis, protein motifs and structures, chromosome distributions of deduced ARR proteins were conducted. The gene expression profiling of various tissues in response to topping, low temperature and drought were analyzed by RNA-seq and qRT-PCR.

RESULTS

59 ARR genes from cultivated tobacco (Nicotiana tabacum) were identified, namely NtARRs, including 21 type A NtARRs and 38 type B NtARRs. The 59 NtARRs were expressed mainly in all organs except the fruits. Some representative NtARRs may participate in axillary bud initiation and development, as well as in stress resistance through cytokinin signal transduction.

CONCLUSION

Understanding the roles of NtARRs in the molecular mechanisms responsible for axillary bud growth and stress tolerance could aid in targeted breeding in crops.

Genomic diversity analysis and identification of novel SSR markers in four tobacco varieties by high-throughput resequencing

Genome resequencing was carried out on two varieties of flue-cured tobacco (LY1306 and Qinyan 96), one variety of sun-cured tobacco (Wanmao 3), and one variety of air-cured Maryland tobacco (Wufeng 1), for a comparative analysis of genomic variation across the four varieties. Single nucleotide polymorphisms (SNPs), insertions and deletions (InDels), structural variations (SVs), and copy-number variations (CNVs) were then identified in each tobacco variety. Furthermore, a functional analysis of mutated genes was carried out. Through in-depth comparative analysis of genomes of different tobacco varieties, we identified genome variations in a number of SNPs, InDels, SVs, and CNVs, respectively. Computational analysis to predict the function of mutated genes containing these differential SNPs, InDels, SVs, and CNVs showed that they were mainly involved in different functions, such as carbohydrate metabolism and secondary metabolites biosynthesis. We mainly focused on genes that were involved in the biosynthesis of secondary metabolites and nicotine metabolism. In addition, we identified five simple sequence repeat (SSR)-based markers and verified them by PCR amplification in 10 tobacco varieties. Taken together, our study increases the understanding of genetic differences between tobacco types or varieties and identifies five SSR markers to classify tobacco varieties or types.

Integrating transcriptome and metabolome reveals molecular networks involved in genetic and environmental variation in tobacco

Tobacco (Nicotiana tabacum) is one of the most widely cultivated commercial non-food crops with significant social and economic impacts. Here we profiled transcriptome and metabolome from 54 tobacco samples (2-3 replicates; n = 151 in total) collected from three varieties (i.e. genetic factor), three locations (i.e. environmental factor), and six developmental stages (i.e. developmental process). We identified 3,405 differentially expressed (DE) genes (DEGs) and 371 DE metabolites, respectively. We used quantitative real-time PCR to validate 20 DEGs, and confirmed 18/20 (90%) DEGs between three locations and 16/20 (80%) with the same trend across developmental stages. We then constructed nine co-expression gene modules and four co-expression metabolite modules , and defined seven de novo regulatory networks, including nicotine- and carotenoid-related regulatory networks. A novel two-way Pearson correlation approach was further proposed to integrate co-expression gene and metabolite modules to identify joint gene-metabolite relations. Finally, we further integrated DE and network results to prioritize genes by its functional importance and identified a top-ranked novel gene, LOC107773232, as a potential regulator involved in the carotenoid metabolism pathway. Thus, the results and systems-biology approaches provide a new avenue to understand the molecular mechanisms underlying complex genetic and environmental perturbations in tobacco.

hsa_circRNA_100873 upregulation is associated with increased lymphatic metastasis of esophageal squamous cell carcinoma

Circular RNAs (circRNAs) are a type of endogenous non-coding RNA with multiple binding sites that specifically bind to microRNAs (miRNAs) and serve an important role in cellular regulatory networks. Patients exhibit varying levels of lymphatic metastasis in a clinical setting. The present study investigated the association between circRNAs and lymphatic metastasis in esophageal squamous cell carcinoma (ESCC). The tissue samples were divided into three groups, including early tumor stage associated with advanced nodal stage (T1 group), advanced tumor stage associated with early nodal stage (T2 group) and healthy esophageal epithelial tissues as the control group (C group). Gene chip analysis identified circRNAs, and those with possible regulatory functions were validated by reverse transcription-quantitative polymerase chain reaction analysis (RT-qPCR). circRNAs containing miRNA response element (MRE) sequences were obtained, and circRNA/miRNA prediction software was used to predict miRNAs that may interact with circRNA. A total of 12,275 circRNAs were detected, including 861 with statistically significant differences. A comparison between the T1 and C groups identified 152 upregulated circRNAs and 431 downregulated ones, while a comparison between the T2 and C groups identified 187 upregulated and 481 downregulated circRNAs. A T1/T2 group comparison revealed that four circRNAs were upregulated and seven were downregulated (fold change >1.5; P<0.05). The RT-qPCR data and gene chip analysis consistently identified hsa_circRNA_100873 as differentially expressed among the examined groups. A total of five potential MREs and complementary sequences were selected for hsa_circRNA_100873. The results of the present study indicated that multiple differentially expressed circRNAs are involved in the pathogenesis of ESCC, and that upregulation of hsa_circRNA_100873 may be associated with increased lymphatic metastases in ESCC.

Bioinformatics identification of lncRNA biomarkers associated with the progression of esophageal squamous cell carcinoma

The poor outcome of patients with esophageal squamous cell carcinoma (ESCC) highlights the importance of the identification of novel effective prognostic biomarkers. Long non-coding RNAs (lncRNAs) serve regulatory roles in various types of cancer. The aim of the present study was to investigate the lncRNA expression profile in ESCC and to identify lncRNAs associated with the prognosis of ESCC by performing comprehensive bioinformatics analyses. The RNA-sequencing (Seq) expression dataset GSE53625 generated from ESCC samples was used as a training dataset. Additional RNA-Seq datasets relative to ESCC samples were downloaded from The Cancer Genome Atlas and used as a validation dataset. Data were screened using the limma package, and differentially expressed lncRNAs between early- and late-stage ESCC were identified. A random forest algorithm was used to select the optimal lncRNA biomarkers, which were then analyzed using the support vector machine (SVM) algorithm with R software. The identified lncRNA biomarkers were examined in the validation dataset by bidirectional hierarchical clustering and using an SVM classifier. Subsequently, univariate and multivariate Cox regression analyses were performed to analyze the potential ability lncRNAs to predict the survival rate of patients with ESCC. By examining the training group, 259 deregulated lncRNAs between early- and advanced-stage ESCC were identified. Further bioinformatics analyses identified a nine-lncRNA signature, including AC098973, AL133493, RP11-51M24, RP11-317N8, RP11-834C11, RP11-69C17, LINC00471, LINC01193 and RP1-124C. This nine-lncRNA signature was used to predict the tumor stage and patient survival rate with high reliability and accuracy in the training and validation datasets. Furthermore, these nine lncRNA biomarkers were primarily involved in regulating the cell cycle and DNA replication, and these processes were previously identified to be associated with the progression of ESCC. The identified nine-lncRNA signature was identified to be associated with the tumor stage, and could be used as predictor of the survival rate of patients with ESCC.

Dysregulated long non‑coding RNAs in pleomorphic adenoma tissues of pleomorphic adenoma gene 1 transgenic mice

Long non-coding RNAs (lncRNAs) have been proven to serve vital roles in various human diseases. However, their involvement in the development of pleomorphic adenoma (PA) in the salivary gland has yet to be examined. In the present study, microarray analysis of the lncRNA and mRNA expression profiles in pleomorphic adenoma gene 1 (PLAG1) transgenic mice was performed. Next, bioinformatics tools were used to predict the differentially expressed genes associated with PA, including Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment and lncRNA-mRNA co-expression network analyses. Comparison of the transgenic and control mice demonstrated that a total of 9,110 lncRNAs and 7,750 mRNAs were significantly differentially expressed (fold change >2; P<0.05). Subsequently, six lncRNAs were randomly selected for further analysis, and five of these were validated as differentially expressed in PA by quantitative polymerase chain reaction, supporting the methodology employed in the current study. The GO and KEGG enrichment analysis of the differentially expressed mRNAs revealed that these mRNAs were closely associated with a number of processes involved in the development of PA. Furthermore, the lncRNA-mRNA co-expression network indicated that certain lncRNAs may serve vital roles in the pathogenesis of PA by interacting with a number of core genes. Taken together, these results indicated that lncRNAs and mRNAs were differentially expressed in PA tissues obtained from PLAG1 transgenic mice as compared with those from control mice. These differentially expressed lncRNAs may act as novel biomarkers and therapeutic targets for PA.