Alkaloid chemophenetics and transcriptomics of the Nicotiana genus

Effects of different fermentation temperatures on microbiomes of cigar tobacco leaves

Introduction

Microbiomes of cigar tobacco leaves play a pivotal role during the fermentation, and fermentation temperature is a key factor in shaping the structure and function of the microbial community. This study aimed to investigate the effects of different temperatures (30°C, 35°C, 40°C, 45°C, and 50°C) on the microbiomes of cigar tobacco leaves, providing insights into the complex interactions among temperature, microbes, and physicochemical metabolites.

Methods

Firstly, the physicochemical metabolites of cigar tobacco leaves under various fermentation temperatures were detected by gas chromatography-mass spectrometry. Subsequently, the impacts of different temperatures on microbial biomass and community structure were revealed by quantitative real-time PCR and amplicon sequencing, and the biomarkers at different fermentation temperatures were identified by LEfSe analysis. Finally, the functional potential of microbes was predicted by correlation analysis.

Results

The bacterial biomass increased initially and peaked at 8.4 × 109 copies/g at 35°C, then decreased as the temperature rose. The fungal biomass exhibited a downward trend with increasing temperature, reaching a maximum of 3.9 × 106 copies/g at 30°C. When the fermentation temperature exceeded 45°C, the growth of both bacteria and fungi was significantly restricted. Amplicon sequencing results indicated that Staphylococcus and Aspergillus genera dominated the bacterial and fungal communities, respectively. As the temperature increased, the relative abundance of Staphylococcus decreased first and then increased (46.1%-98.5%), while that of Aspergillus increased first and then decreased (34.9%-77.4%). Additionally, correlation analysis suggested that microbial communities shaped by different temperatures were responsible for the differences in physicochemical metabolites of cigar leaves. The biomarkers identified in the low-temperature fermentation group, including Staphylococcus, Stemphylium, Sampaiozyma, and Filobasidium, were likely responsible for the production of flavor metabolites, the accumulation of sugars, and the elevated ratio of potassium ions to chloride ions contents. Biomarkers in medium and high-temperature fermentation groups, such as Aspergillus, Neodymella, Acinetobacter, Pelomonas, Brevundimonas, and Alkalihalobacillus, might contribute to the degradation of nitrogen-containing substances and alkaloids.

Discussion

This study revealed the unique microbial community structure shaped at different temperatures and its potential correlation with physicochemical metabolites. These findings will help to further optimize the fermentation process of cigar tobacco leaves and develop functional microorganisms suitable for different fermentation temperatures.

Development of an RNA virus vector for non-transgenic genome editing in tobacco and generation of berberine bridge enzyme-like mutants with reduced nicotine content

Tobacco (Nicotiana tabacum) plants synthesize the psychoactive pyridine alkaloid nicotine, which has sparked growing interest in reducing nicotine levels through genome editing aiming at inactivating key biosynthetic genes. Although stable transformation-mediated genome editing is effective in tobacco, its polyploid nature complicates the complete knockout of genes and the segregation of transgenes from edited plants. In this study, we developed a non-transgenic genome editing method in tobacco by delivering the CRISPR/Cas machinery via an engineered negative-strand RNA rhabdovirus vector, followed by the regeneration of mutant plants through tissue culture. Using this method, we targeted six berberine bridge enzyme-like protein (BBL) family genes for mutagenesis, which are implicated in the last steps of pyridine alkaloid biosynthesis, in the commercial tobacco cultivar Hongda. We generated a panel of 16 mutant lines that were homozygous for mutations in various combinations of BBL genes. Alkaloid profiling revealed that lines homozygous for BBLa and BBLb mutations exhibited drastically reduced nicotine levels, while other BBL members played a minor role in nicotine synthesis. The decline of nicotine content in these lines was accompanied by reductions in anatabine and cotinine levels but increases in nornicotine and its derivative myosmine. Preliminary agronomic evaluation identified two low-nicotine lines with growth phenotypes comparable to those of wild-type plants under greenhouse and field conditions. Our work provides potentially valuable genetic materials for breeding low-nicotine tobacco and enhances our understanding of alkaloid biosynthesis.

Supplementary Information

The online version contains supplementary material available at 10.1007/s42994-024-00188-y.

Genetic regulation and manipulation of nicotine biosynthesis in tobacco: strategies to eliminate addictive alkaloids

Tobacco (Nicotiana tabacum L.) is a widely cultivated crop of the genus Nicotiana. Due to the highly addictive nature of tobacco products, tobacco smoking remains the leading cause of preventable death and disease. There is therefore a critical need to develop tobacco varieties with reduced or non-addictive nicotine levels. Nicotine and related pyridine alkaloids biosynthesized in the roots of tobacco plants are transported to the leaves, where they are stored in vacuoles as a defense against predators. Jasmonate, a defense-related plant hormone, plays a crucial signaling role in activating transcriptional regulators that coordinate the expression of downstream metabolic and transport genes involved in nicotine production. In recent years, substantial progress has been made in molecular and genomics research, revealing many metabolic and regulatory genes involved in nicotine biosynthesis. These advances have enabled us to develop tobacco plants with low or ultra-low nicotine levels through various methodologies, such as mutational breeding, genetic engineering, and genome editing. We review the recent progress on genetic manipulation of nicotine production in tobacco, which serves as an excellent example of plant metabolic engineering with profound social implications.

Chromosome-level genome assemblies of Nicotiana tabacum, Nicotiana sylvestris, and Nicotiana tomentosiformis

The Solanaceae species Nicotiana tabacum, an economically important crop plant cultivated worldwide, is an allotetraploid species that appeared about 200,000 years ago as the result of the hybridization of diploid ancestors of Nicotiana sylvestris and Nicotiana tomentosiformis. The previously published genome assemblies for these three species relied primarily on short-reads, and the obtained pseudochromosomes only partially covered the genomes. In this study, we generated annotated de novo chromosome-level genomes of N. tabacum, N. sylvestris, and N. tomentosiformis, which contain 3.99 Gb, 2.32 Gb, and 1.74 Gb, respectively of sequence data, with 97.6%, 99.5%, and 95.9% aligned in chromosomes, and represent 99.2%, 98.3%, and 98.5% of the near-universal single-copy orthologs Solanaceae genes. The completion levels of these chromosome-level genomes for N. tabacum, N. sylvestris, and N. tomentosiformis are comparable to other reference Solanaceae genomes, enabling more efficient synteny-based cross-species research.

Suppression of pyrrolidine ring biosynthesis and its effects on gene expression and subsequent accumulation of anatabine in leaves of tobacco (N. tabacum L.)

BACKGROUND

Anatabine, although being one of four major tobacco alkaloids, is never accumulated in high quantity in any of the naturally occurring species from the Nicotiana genus. Previous studies therefore focused on transgenic approaches to synthetize anatabine, most notably by generating transgenic lines with suppressed putrescine methyltransferase (PMT) activity. This led to promising results, but the global gene expression of plants with such distinct metabolism has not been analyzed. In the current study, we describe how these plants respond to topping and the downstream effects on alkaloid biosynthesis.

RESULTS

The surge in anatabine accumulation in PMT transgenic lines after topping treatment and its effects on gene expression changes were analyzed. The results revealed increases in expression of isoflavone reductase-like (A622) and berberine bridge-like enzymes (BBLs) oxidoreductase genes, previously shown to be crucial for the final steps of nicotine biosynthesis. We also observed significantly higher methylputrescine oxidase (MPO) expression in all plants subjected to topping treatment. In order to investigate if MPO suppression would have the same effects as that of PMT, we generated transgenic plants. These plants with suppressed MPO expression showed an almost complete drop in leaf nicotine content, whereas leaf anatabine was observed to increase by a factor of ~ 1.6X.

CONCLUSION

Our results are the first concrete evidence that suppression of MPO leads to decreased nicotine in favor of anatabine in tobacco roots and that this anatabine is successfully transported to tobacco leaves. Alkaloid transport in plants remains to be investigated to higher detail due to high variation of its efficiency among Nicotiana species and varieties of tobacco. Our research adds important step to better understand pyrrolidine ring biosynthesis and its effects on gene expression and subsequent accumulation of anatabine.

A critical assessment of the Candida strains isolated from cigar tobacco leaves

Introduction: Candida genus plays a crucial role in cigar fermentation, and strains from different sources might have differences in metabolic characteristics. Therefore, this study conducted directional isolation of Candida strains from cigar tobacco leaves and compared their fermentabilities to screen suitable strains for cigar fermentation, thereby improving the cigar quality. Methods: First, the Candida strains from cigars tobacco leaves in different production areas were directionally isolated by pure culture. Then, the isolated strains were screened based on chemical indexes and flavor component contents. Finally, the fermentabilities of preferred strains were verified by sensory evaluation. Results: Five strains of C. parapsilosis and four strains of C. metapsilosis were obtained through directional isolation. By comparing the physicochemical indexes of nine strains of Candida, it was found that C. parapsilosis P1 and C. metapsilosis M4 not only reduced the alkaloids content (by 25.3% and 32.6%, respectively) but also increased the flavor components content (by 25.2% and 18.9%, respectively). Among them, P1 could raise the content of chlorophyll degradation products, carotenoid degradation products, and Maillard reaction products, and enhance the beany and nutty flavor of cigars. M4 could raise the content of chlorophyll degradation products, cembranoids degradation products, and Maillard reaction products, and improve the baking, nutty, cocoa, and honey flavor of the cigar. Discussion: In this study, the Candida strains were directionally isolated from cigars tobacco leaves in different production areas, and two functional strains suitable for cigar fermentation were screened based on physicochemical indexes and sensory evaluation, which would contribute to the directed regulation of cigar quality and flavor diversification.

Evolutionary metabolomics of specialized metabolism diversification in the genus Nicotiana highlights N-acylnornicotine innovations

Specialized metabolite (SM) diversification is a core process to plants' adaptation to diverse ecological niches. Here, we implemented a computational mass spectrometry-based metabolomics approach to exploring SM diversification in tissues of 20 species covering Nicotiana phylogenetics sections. To markedly increase metabolite annotation, we created a large in silico fragmentation database, comprising >1 million structures, and scripts for connecting class prediction to consensus substructures. Together, the approach provides an unprecedented cartography of SM diversity and section-specific innovations in this genus. As a case study and in combination with nuclear magnetic resonance and mass spectrometry imaging, we explored the distribution of N-acylnornicotines, alkaloids predicted to be specific to Repandae allopolyploids, and revealed their prevalence in the genus, albeit at much lower magnitude, as well as a greater structural diversity than previously thought. Together, the data integration approaches provided here should act as a resource for future research in plant SM evolution.

Quantum-Chemical Study of the Assembly Mechanism of 1-Pyrrolines from N-Benzylaldimines and Arylacetylenes in KOtBu/DMSO Superbasic Medium

By using a quantum-chemical approach, B2PLYP-D2/6-311+G**//B3LYP/6-31+G*, we have carried out a detailed study of the assembly of 1-pyrrolines from N-benzyl-1-phenylmethanimine and phenylacetylene in the superbasic medium KO^tBu/dimethyl sulfoxide (DMSO). In this way, we have considered, both theoretically and experimentally, the mechanisms of the assembly through a concerted and stepwise nucleophilic cycloaddition and have addressed the side processes accompanying the assembly. It is found that the assembly via the concerted cycloaddition is kinetically more favorable than that via the stepwise cycloaddition. At the same time, the reaction of C-vinylation of aldimine with phenylacetylene occurs with a similar activation energy as the concerted cycloaddition and leads to the formation of 2-aza-1,4-pentadiene. The anion of 2-aza-1,4-pentadiene is an intermediate for the side processes leading to the formation of triarylpyridines and 1,3-diarylpropan-1-ones. Triarylpyridines are formed through the concerted cycloaddition of the next phenylacetylene molecule to 2-aza-1,4-pentadiene, while 1,3-diarylpropan-1-ones are formed as a result of the hydrolysis of 2-aza-1,4-pentadienes. It is found out that the mild conditions for the assembly of 1-pyrrolines (60 °C, 15 min) relate to the formation of complexes in the KO^tBu/DMSO superbasic medium, where the anion is readily accessible for the nucleophilic attack by the phenylacetylene molecule.

Morphological Characterization of Nicotiana tabacum Inflorescences and Chemical-Functional Analysis of Extracts Obtained from Its Powder by Using Green Solvents (NaDESs)

The production of smokeable tobacco for use in cigarettes is characterized by the production of pre-harvest and post-harvest waste, with ensuing undesirable effects on the environment. The inflorescences of tobacco after blunting, deflowering, or topping are considered pre-harvest waste and left in the field. Using green and ecofriendly solvents such as Natural deep eutectic solvents (NaDESs), these wastes could be used to obtain antioxidant molecules of interest in cosmetics. Taking into account its potential as plant matrix to obtain metabolites of commercial interest, tobacco inflorescences and inflorescence powders of different particle sizes were characterized by optic and electronic microscopy. Thus, the powdered inflorescences were extracted with four conventional solvents, i.e., distilled water (DW), acetone: distilled water (AW), ethanol 70° (EW), methanol (Me), and five NaDESs, i.e., lactic acid: sucrose (LAS), lactic acid: sucrose: distilled water (SALA), fructose: glucose: sucrose: distilled water (FGS), choline chloride: urea: distilled water (CU), and citric acid: propylene glycol (CAP). Among the tested NADESs, SALA was the most promising solvent; higher extraction yields of total phenolic compound (3420.0 ± 9.4 µg GAE/mL) than conventional solvents were attained and it was the only selective solvent to phenolics. CU was the best solvent for flavonoids and alkaloids extraction (215.3 ± 3.2 µg QE/mL and 392.3 ± 8.0 µg ACE/mL, respectively). All extracts showed antioxidant activity. A heatmap with dendrogram and main component analysis showed that acid-based NaDESs are grouped together, this group being the one with the best performance in H₂O₂ scavenging. The extracts obtained with green solvents could be used directly in cosmetic formulations as antioxidant ingredients because both tobacco flower oil and flower extracts are listed in the cosmetic ingredients database as non-toxic products. Additionally, the demand for sustainable ecological cosmetics is growing. In this sense, NaDESs represent an opportunity to develop innovative extracts with unique phytochemical fingerprints and biological activities.

Development of Candida autochthonous starter for cigar fermentation via dissecting the microbiome

Introduction

The main goal of tobacco fermentation technology is to minimize the alkaloid content while improving flavor substance content.

Methods

This study revealed the microbial community structure and their metabolic functions during cigar leaf fermentation by high-throughput sequencing and correlation analysis, and evaluated the fermentation performance of functional microbes based on in vitro isolation and bioaugmentation fermentation.

Results

The relative abundance of Staphylococcus and Aspergillus increased first but then decreased during the fermentation, and would occupy the dominant position of bacterial and fungal communities, respectively, on the 21st day. Correlation analysis predicted that Aspergillus, Staphylococcus and Filobasidium could contribute to the formation of saccharide compounds, Bacillus might have degradation effects on nitrogenous substances. In particular, Candida, as a co-occurring taxa and biomarker in the later stage of fermentation, could not only degrade nitrogenous substrates and synthesize flavor substances, but also contribute to maintaining the stability of microbial community. Moreover, based on in vitro isolation and bioaugmentation inoculation, it was found that Candida parapsilosis and Candida metapsilosis could significantly reduce the alkaloids content and increase the content of flavor components in tobacco leaves.

Discussion

This study found and validated the critical role of Candida in the fermentation of cigar tobacco leaves through high-throughput sequencing and bioaugmentation inoculation, which would help guide the development of microbial starters and directional regulation of cigar tobacco quality.

Effects of Poty-Potexvirus Synergism on Growth, Photosynthesis and Metabolite Status of Nicotiana benthamiana

Mixed virus infections threaten crop production because interactions between the host and the pathogen mix may lead to viral synergism. While individual infections by potato virus A (PVA), a potyvirus, and potato virus X (PVX), a potexvirus, can be mild, co-infection leads to synergistic enhancement of PVX and severe symptoms. We combined image-based phenotyping with metabolite analysis of single and mixed PVA and PVX infections and compared their effects on growth, photosynthesis, and metabolites in Nicotiana benthamiana. Viral synergism was evident in symptom severity and impaired growth in the plants. Indicative of stress, the co-infection increased leaf temperature and decreased photosynthetic parameters. In contrast, singly infected plants sustained photosynthetic activity. The host's metabolic response differed significantly between single and mixed infections. Over 200 metabolites were differentially regulated in the mixed infection: especially defense-related metabolites and aromatic and branched-chain amino acids increased compared to the control. Changes in the levels of methionine cycle intermediates and a low S-adenosylmethionine/S-adenosylhomocysteine ratio suggested a decline in the methylation potential in co-infected plants. The decreased ratio between reduced glutathione, an important scavenger of reactive oxygen species, and its oxidized form, indicated that severe oxidative stress developed during co-infection. Based on the results, infection-associated oxidative stress is successfully controlled in the single infections but not in the synergistic infection, where activated defense pathways are not sufficient to counter the impact of the infections on plant growth.

Fractionation and Extraction Optimization of Potentially Valuable Compounds and Their Profiling in Six Varieties of Two Nicotiana Species

There is an increasingly urgent call to shift industrial processes from fossil fuel feedstock to sustainable bio-based resources. This change becomes of high importance considering new budget requirements for a carbon-neutral economy. Such a transformation can be driven by traditionally used plants that are able to produce large amounts of valuable biologically relevant secondary metabolites. Tobacco plants can play a leading role in providing value-added products in remote areas of the world. In this study, we propose a non-exhaustive list of compounds with potential economic interest that can be sourced from the tobacco plant. In order to optimize extraction methodologies, we first analyzed their physico-chemical properties using rapid solubility tests and high-resolution microfractionation techniques. Next, to identify an optimal extraction for a selected list of compounds, we compared 13 different extraction method-solvent combinations. We proceeded with profiling some of these compounds in a total of six varieties from Nicotiana tabacum and Nicotiana rustica species, identifying the optimal variety for each. The estimated expected yields for each of these compounds demonstrate that tobacco plants can be a superior source of valuable compounds with diverse applications beyond nicotine. Among the most interesting results, we found high variability of anatabine content between species and varieties, ranging from 287 to 1699 µg/g. In addition, we found that CGA (1305 µg/g) and rutin (7910 µg/g) content are orders of magnitude lower in the Burley variety as compared to all others.

Systems biology reveals anatabine to be an NRF2 activator

Anatabine, an alkaloid present in plants of the Solanaceae family (including tobacco and eggplant), has been shown to ameliorate chronic inflammatory conditions in mouse models, such as Alzheimer’s disease, Hashimoto’s thyroiditis, multiple sclerosis, and intestinal inflammation. However, the mechanisms of action of anatabine remain unclear. To understand the impact of anatabine on cellular systems and identify the molecular pathways that are perturbed, we designed a study to examine the concentration-dependent effects of anatabine on various cell types by using a systems pharmacology approach. The resulting dataset, consisting of measurements of various omics data types at different time points, was analyzed by using multiple computational techniques. To identify concentration-dependent activated pathways, we performed linear modeling followed by gene set enrichment. To predict the functional partners of anatabine and the involved pathways, we harnessed the LINCS L1000 dataset’s wealth of information and implemented integer linear programming on directed graphs, respectively. Finally, we experimentally verified our key computational predictions. Using an appropriate luciferase reporter cell system, we were able to demonstrate that anatabine treatment results in NRF2 (nuclear factor-erythroid factor 2-related factor 2) translocation, and our systematic phosphoproteomic assays showed that anatabine treatment results in activation of MAPK signaling. While there are certain areas to be explored in deciphering the exact anti-inflammatory mechanisms of action of anatabine and other NRF2 activators, we believe that anatabine constitutes an interesting molecule for its therapeutic potential in NRF2-related diseases.

Proteomic and Metabolomic Revealed Differences in the Distribution and Synthesis Mechanism of Aroma Precursors in Yunyan 87 Tobacco Leaf, Stem, and Root at the Seedling Stage

Tobacco, as an important cash crop and model plant, has been the subject of various types of research. The quality of flue-cured tobacco products depends on the compound collection of tobacco leaves, including pigments, carbohydrates, amino acids, polyphenols, and alkaloid aroma precursors. The present study investigates tobacco seedling organs (leaf, stem, and root) with the assistance of label-free proteomic technology and untargeted metabonomic technology. We analyzed 4992 proteins and 298 metabolites obtained in the leaf, stem, and root groups and found that there were significant differences in both primary and secondary metabolism processes involved in aroma precursor biosynthesis, such as carbohydrate metabolism, energy metabolism, and amino acid biosynthesis, and phenylpropanoid, flavonoid, and alkaloid biosynthesis. The findings showed that the contents of alkaloid metabolites such as nornicotine, anatabine, anatalline, and myosmine were significantly higher in tobacco roots than in leaves and stems at the seedling stage.

Organocatalytic Allylic Alkylation of α-(Alkylideneamino)nitriles and Its Application in the Preparation of Multisubstituted 1-Pyrrolines

A synthetic approach for the construction of functionalized diverse 1-pyrrolines incorporating β-quaternary carbon centers under mild reaction conditions has been reported, in which α-allyl α-(alkylideneamino)nitriles generated from a Lewis base-catalyzed allylic alkylation reaction engaged in a Lewis base-mediated tandem intramolecular cyclization to deliver the targeted molecules in a catalytically atom-economic fashion.

The chemotype core collection of genus Nicotiana

Sustainable production of chemicals and improving these biosources by engineering metabolic pathways to create efficient plant-based biofactories relies on the knowledge of available chemical/biosynthetic diversity present in the plant. Nicotiana species are well known for their amenability towards transformation and other new plant breeding techniques. The genus Nicotiana is primarily known through Nicotiana tabacum L., the source of tobacco leaves and all respective tobacco products. Due to the prevalence of the latter, N. tabacum and related Nicotiana species are one of the most extensively studied plants. The majority of studies focused solely on N. tabacum or other individual species for chemotyping. The present study analysed a diversity panel including 17 Nicotiana species and six accessions of Nicotiana benthamiana and created a data set that effectively represents the chemotype core collection of the genus Nicotiana. The utilisation of several analytical platforms and previously published libraries/databases enabled the identification and measurement of over 360 metabolites of a wide range of chemical classes as well as thousands of unknowns with dedicated spectral and chromatographic properties.

Iron-Catalyzed Ring Expansion of Cyclobutanols for the Synthesis of 1-Pyrrolines by Using MsONH3OTf

The synthesis of 1-pyrrolines from cyclobutanol derivatives and an aminating reagent (MsONH₃OTf) has been developed. This one-pot procedure achieves C-N bond/C═N bond formation via ring expansion. A series of 1-pyrroline derivatives are synthesized in moderate to good yields under mild conditions.