Tianxing He’s research while affiliated with Chengdu University of Traditional Chinese Medicine and other places

Background O-methyltransferase (OMT) is an important rate-limiting enzyme that plays a vital role in synthesizing various key metabolites, such as benzylisoquinoline alkaloids (BIA). Nevertheless, there is a dearth of extensive research on the analysis of the OMT gene family in Stephania japonica , a main source of cepharanthine with an anti-coronavirus effect. Methods Two OMT family genes, SjCCoAOMT and SjCOMT , were identified from the high-quality genome of S. japonica during this investigation. Further analysis of SjCCoAOMT and SjCOMT genes involved chromosome distribution, gene structure, phylogenetic relationship, conserved motif, expression profile, quantitative reverse transcriptase polymerase chain reaction (qRT-PCR) experiments an d cis -acting elements analysis. Results There are six SjCCoAOMT members and fifty-two SjCOMT members in the genome of S. japonica , which are unevenly distributed on 11 chromosomes. OMTs could be clustered into SjCCoAOMT and SjCOMT subfamilies through phylogenetic relationship, consistent with the conserved motif and gene structure analysis results. The expression profile revealed SjCOMT11 and SjCOMT13 showed specific expression levels mainly in root. SjCOMT21, SjCOMT33 and SjCOMT37 were significantly expressed in the root and slightly expressed in the stem, bud and leaf. SjCOMT15 and SjCOMT45 were not only significantly expressed in root, but also expressed highly in leaf. Significantly enhanced expression of SjCOMT11 , SjCOMT13 , SjCOMT15 , SjCOMT21 , SjCOMT33 , SjCOMT37 , and SjCOMT45 suggested these OMTs are essential for cepharanthine synthesis in the S. japonica roots. Cis -acting element analysis revealed the potential roles of OMTs in S. japonica in growth, development, and resistance to stress. These findings provide insight into understanding the functions and characterization of OMTs from S. japonica and lay a foundation for further revealing the role of the OMT genes in the biosynthesis of cepharanthine.

Introduction Cepharanthine (CEP), a bisbenzylisoquinoline alkaloid (bisBIA) extracted from Stephania japonica, has received significant attention for its anti-coronavirus properties. While ethylene response factors (ERFs) have been reported to regulate the biosynthesis of various alkaloids, their role in regulating CEP biosynthesis remains unexplored. Methods Genome-wide analysis of the ERF genes was performed with bioinformatics technology, and the expression patterns of different tissues, were analyzed by transcriptome sequencing analysis and real-time quantitative PCR verification. The nuclear-localized ERF gene cluster was shown to directly bind to the promoters of several CEP-associated genes, as demonstrated by yeast one-hybrid assays and subcellular localization assays. Results In this work, 59 SjERF genes were identified in the S. japonica genome and further categorized into ten subfamilies. Notably, a SjERF gene cluster containing three SjERF genes was found on chromosome 2. Yeast one-hybrid assays confirmed that the SjERF gene cluster can directly bind to the promoters of several CEP-associated genes, suggesting their crucial role in CEP metabolism. The SjERFs cluster-YFP fusion proteins were observed exclusively in the nuclei of Nicotiana benthamiana leaves. Tissue expression profiling revealed that 13 SjERFs exhibit high expression levels in the root, and the qRT-PCR results of six SjERFs were consistent with the RNA-Seq data. Furthermore, a co-expression network analysis demonstrated that 24 SjERFs were highly positively correlated with the contents of various alkaloids and expression levels of CEP biosynthetic genes. Conclusion This study provides the first systematic identification and analysis of ERF transcription factors in the S.japonica genome, laying the foundation for the future functional research of SjERFs transcription factors.

Cepharanthine, a secondary metabolite isolated from Stephania, has garnered attention for its reported effectiveness against severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2). To discover more cepharanthine analogs with anti-coronavirus properties, we assembled three Stephania genomes, proposed the cepharanthine biosynthetic pathway, and assessed the antiviral potential of compounds involved in the pathway. Nearly perfect telomere-to-telomere assembly with one remaining gap has been obtained for the S. japonica genome. Genome-guided cepharanthine analogs mining in Stephania was performed to identify cepharanthine-related metabolites with anti-coronavirus properties, and seven cepharanthine analogs can broad-spectrum inhibit coronavirus including SARS-CoV-2, GX_P2V, SADS-CoV and PEDV infection. Two other genera that produce cepharanthine analogs, Nelumbo and Thalictrum, are also believed to have potential for antiviral compound discovery. Here, we have systematically assessed anti-coronavirus activity of a series of cepharanthine metabolites from the viewpoint of biosynthesis pathway, our study will provide an opportunity to accelerate broad-spectrum anti-coronavirus drug discovery.

Mentha is a commonly used spice worldwide, which possesses medicinal properties and fragrance. These characteristics are conferred, at least partially, by essential oils such as menthol. In this study, a gap-free assembly with a genome size of 414.3 Mb and 31,251 coding genes was obtained for Mentha suaveolens ‘Variegata’. Based on its high heterozygosity (1.5%), two complete haplotypic assemblies were resolved, with genome sizes of 401.9 Mb and 405.7 Mb, respectively. The telomeres and centromeres of each haplotype were almost fully annotated. In addition, we detected a total of 41,135 structural variations. Enrichment analysis demonstrated that genes involved in terpenoid biosynthesis were affected by these structural variations. Analysis of volatile metabolites showed that Mentha suaveolens mainly produces piperitenone oxide rather than menthol. We identified three genes in the Mentha suaveolens genome which encode isopiperitenone reductase (ISPR), a key rate-limiting enzyme in menthol biosynthesis. However, the transcription levels of ISPR were low. Given that other terpenoid biosynthesis genes were expressed, Mentha suaveolens ISPRs may account for the accumulation of piperitenone oxide in this species. The findings of this study may provide a valuable resource for improving the detection rate and accuracy of genetic variants, thereby enhancing our understanding of their impact on gene function and expression. Moreover, our haplotype-resolved gap-free genome assembly offers novel insights into molecular marker-assisted breeding of Mentha.