Using genome and transcriptome analysis to elucidate biosynthetic pathways

Stressing the importance of plant specialized metabolites: omics-based approaches for discovering specialized metabolism in plant stress responses

Plants produce a diverse range of specialized metabolites that play pivotal roles in mediating environmental interactions and stress adaptation. These unique chemical compounds also hold significant agricultural, medicinal, and industrial values. Despite the expanding knowledge of their functions in plant stress interactions, understanding the intricate biosynthetic pathways of these natural products remains challenging due to gene and pathway redundancy, multifunctionality of proteins, and the activity of enzymes with broad substrate specificity. In the past decade, substantial progress in genomics, transcriptomics, metabolomics, and proteomics has made the exploration of plant specialized metabolism more feasible than ever before. Notably, recent advances in integrative multi-omics and computational approaches, along with other technologies, are accelerating the discovery of plant specialized metabolism. In this review, we present a summary of the recent progress in the discovery of plant stress-related specialized metabolites. Emphasis is placed on the application of advanced omics-based approaches and other techniques in studying plant stress-related specialized metabolism. Additionally, we discuss the high-throughput methods for gene functional characterization. These advances hold great promise for harnessing the potential of specialized metabolites to enhance plant stress resilience in the future.

Recent advances in triterpenoid pathway elucidation and engineering

Triterpenoids are among the most assorted class of specialized metabolites found in all the taxa of living organisms. Triterpenoids are the leading active ingredients sourced from plant species and are utilized in pharmaceutical and cosmetic industries. The triterpenoid precursor 2,3-oxidosqualene, which is biosynthesized via the mevalonate (MVA) pathway is structurally diversified by the oxidosqualene cyclases (OSCs) and other scaffold-decorating enzymes such as cytochrome P450 monooxygenases (P450s), UDP-glycosyltransferases (UGTs) and acyltransferases (ATs). A majority of the bioactive triterpenoids are harvested from the native hosts using the traditional methods of extraction and occasionally semi-synthesized. These methods of supply are time-consuming and do not often align with sustainability goals. Recent advancements in metabolic engineering and synthetic biology have shown prospects for the green routes of triterpenoid pathway reconstruction in heterologous hosts such as Escherichia coli, Saccharomyces cerevisiae and Nicotiana benthamiana, which appear to be quite promising and might lead to the development of alternative source of triterpenoids. The present review describes the biotechnological strategies used to elucidate complex biosynthetic pathways and to understand their regulation and also discusses how the advances in triterpenoid pathway engineering might aid in the scale-up of triterpenoid production in engineered hosts.

Gentamicin resistance to Escherichia coli related to fatty acid metabolism based on transcriptome analysis

Antibiotic overuse and misuse have promoted the emergence and spread of antibiotic-resistant bacteria. Increasing bacterial resistance to antibiotics is a major healthcare problem, necessitating elucidation of antibiotic resistance mechanisms. In this study, we explored the mechanism of gentamicin resistance by comparing the transcriptomes of antibiotic-sensitive and -resistant Escherichia coli. A total of 410 differentially expressed genes were identified, of which 233 (56.83%) were up-regulated and 177 (43.17%) were down-regulated in the resistant strain compared with the sensitive strain. Gene Ontology (GO) analysis classifies differential gene expression into three main categories: biological processes, cellular components, and molecular functions. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis indicated that the up-regulated genes were enriched in eight metabolic pathways, including fatty acid metabolism, which suggests that fatty acid metabolism may be involved in the development of gentamicin resistance in E. coli. This was demonstrated by measuring the acetyl-CoA carboxylase activity, plays a fundamental role in fatty acid metabolism, was increased in gentamicin-resistant E. coli. Treatment of fatty acid synthesis inhibitor, triclosan, promoted gentamicin-mediated killing efficacy to antibiotic-resistant bacteria. We also found that exogenous addition of oleic acid, which involved in fatty acid metabolism, reduced E. coli sensitivity to gentamicin. Overall, our results provide insight into the molecular mechanism of gentamicin resistance development in E. coli.

Saponin extract from Achyranthes bidentata Blume alleviates disuse-induced muscle atrophy through PI3K/Akt signaling pathway

ETHNOPHARMACOLOGICAL RELEVANCE

The roots of Achyranthes bidentata Blume are one of the regularly used herbal drugs in Chinese medicine, and has been applied for strengthening the muscle and bone for a long time. However, its effect on muscle remains unclear.

AIM OF THE STUDY

This paper aims to explore the anti-muscle atrophy effect of A. bidentata, and to clarify the possible signaling pathways involved.

MATERIALS AND METHODS

The saponin extract of the roots of A. bidentata (ABSE) was prepared and analyzed, and its activity on myoblast differentiation was assayed with C2C12 cell culture. ABSE was then orally administered at dosage of 35, 70 and 140 mg/kg/day to disuse-induced muscle atrophy mice. The studies on mice body weight and muscle quality were conducted, and Western blot was used for exploring the possible signaling pathways involved in the muscle protective action aided with transcriptome analysis.

RESULTS

The total saponin content of ABSE was 59.1%. ABSE promoted the C2C12 cells differentiation to myotube in C2C12 differentiation assay. Further study with disuse-induced muscle atrophy mice model demonstrated that ABSE significantly increased muscle fiber diameter as well as the proportion of slow muscle fibers. Possible mechanism study aided with transcriptome analysis revealed that ABSE alleviated muscle atrophy at least through activation of PI3K/Akt pathway in vivo & vitro.

CONCLUSIONS

The saponin extract of the root of A. bidentata (ABSE) has a protective effect on muscle atrophy, and showed a considerable potential in prevention and treatment of muscle atrophy.

Transcriptome analysis reveals key metabolic pathways and gene expression involving in cell wall polysaccharides-disassembling and postharvest fruit softening in custard apple (Annona squamosa L.)

This study aimed to investigate the effect of custard apple cell wall polysaccharides-disassembling on postharvest fruit softening and to explore its key metabolic pathways and gene expression. Custard apple fruit was stored at 15 ± 0.5 °C for 12 days, it was found that the decreased significantly in fruit firmness, contents of Na₂CO₃-soluble pectin, hemicellulose and cellulose, and the increased significantly in water-soluble pectin and CDTA-soluble pectin. The activities of cell wall-degrading relevant enzymes in fruit were improved significantly during storage, including cellulase, polygalacturonase, pectin methyl esterase, neutral xylanase, β-galactosidase, and β-D-glucosidase. The RNA sequencing results revealed 41,545 nonredundant unigenes and 7571 differentially expressed genes (DEGs) in custard apple fruit samples. Functional annotation and DEGs data revealed cell wall degradation potentially involved in starch and sucrose metabolism, amino sugar and nucleotide sugar metabolism, galactose metabolism, pentose and glucuronate interconversions. Specifically, two EG and six β-Glc genes controlled the cellulose decomposition, and one β-xyl and one GATU genes involved in the degradation of hemicellulose, and two PME, one Pel, and four PG genes were the major regulators of pectin disassembling. These results provide a molecular foundation for explaining fruit softening and extending shelf life of custard apple.

Engineering Critical Amino Acid Residues of Lanosterol Synthase to Improve the Production of Triterpenoids in Saccharomyces cerevisiae

Triterpenoids are a subgroup of terpenoids and have wide applications in the food, cosmetics, and pharmaceutical industries. The heterologous production of various triterpenoids in Saccharomyces cerevisiae, as well as other microbes, has been successfully implemented as these production hosts not only produce the precursor of triterpenoids 2,3-oxidosqualene by the mevalonate pathway but also allow simple expression of plant membrane-anchored enzymes. Nevertheless, 2,3-oxidosqualene is natively converted to lanosterol catalyzed by the endogenous lanosterol synthase (Erg7p), causing low production of recombinant triterpenoids. While simple deletion of ERG7 was not effective, in this study, the critical amino acid residues of Erg7p were engineered to lower this critical enzyme activity. The engineered S. cerevisiae indeed accumulated 2,3-oxidosqualene up to 180 mg/L. Engineering triterpenoid synthesis into the ERG7-modified strain resulted in 7.3- and 3-fold increases in the titers of dammarane-type and lupane-type triterpenoids, respectively. This study presents an efficient inducer-free strategy for lowering Erg7p activity, thereby providing 2,3-oxidosqualene for the enhanced production of various triterpenoids.

Comparative transcriptome analysis and identification of candidate genes involved in cucurbitacin IIa biosynthesis in Hemsleya macrosperma

Hemsleya macrosperma (H. macrosperma) is widely used in southwestern China as folk medicine with various bioactivities. Cucurbitacin IIa is the main active component in H. macrosperma and draws increased attention for its potential pharmacological activities. In order to reveal the mechanism of cucurbitacin IIa biosynthesis and regulation in H. macrosperma, transcriptome analysis was performed to compare differentially expressed genes in three tissues (root tuber, stem and leaf). A total of 47 946 unigenes were generated from these tissues and 55 unigenes were identified as candidate genes involved in triterpenoid backbone biosynthesis. Three homologous genes encoding squalene epoxidase (HmSE) were discovered and successfully expressed in a prokaryotic system. HmSE1 was found to be responsible for oxidization of squalene. In addition, several cytochrome P450s and transcription factors were predicted as candidates associated to cucurbitacin IIa biosynthesis. Notably, the expression profiles of those putative genes showed a positive correlation with elevated curcurbitacin IIa production in methyl jasmonate-elicited suspension cells of H. macrosperma., suggesting probable functions of the candidates on curcurbitacin IIa biosynthesis. These findings provide insights on cucurbitacin IIa biosynthesis and regulation in H. macrosperma.

Production of mannosylerythritol lipids: biosynthesis, multi-omics approaches, and commercial exploitation

Compilation of resources regarding MEL biosynthesis, key production parameters; available omics resources and current commercial applications, for smut fungi known to produce MELs.