Regulation of micoRNA2111 and its target IbFBK in sweet potato on wounding

Identification and Network Construction of mRNAs, miRNAs, lncRNAs, and circRNAs in Sweetpotato (Ipomoea batatas L.) Adventitious Roots Under Salt Stress via Whole-Transcriptome RNA Sequencing

Sweetpotato is the seventh largest crop worldwide, and soil salinization is a major environmental stress limiting its yield. Recent studies have shown that noncoding RNAs (ncRNAs) play important regulatory roles in plant responses to abiotic stress. However, ncRNAs in sweetpotato remain largely unexplored. This study analyzed the characteristics of salt-responsive ncRNAs in sweetpotato adventitious roots under salt stress via whole-transcriptome RNA sequencing. The results revealed that 3175 messenger RNAs (mRNAs), 458 microRNAs (miRNAs), 544 long-chain ncRNAs (lncRNAs), and 23 circular RNAs (circRNAs) were differentially expressed. Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis revealed that most differentially expressed mRNAs (DEmRNAs) and miRNAs (DEmiRNAs) were enriched primarily in phenylpropanoid biosynthesis, starch and sucrose metabolism, the Mitogen-Activated Protein Kinase (MAPK) signaling pathway, plant hormone signal transduction, the mRNA surveillance pathway, and ATP-binding cassette (ABC) transporters. Gene Ontology (GO) enrichment analysis revealed that the majority of DEmRNAs, their target DEmiRNAs, and differentially expressed lncRNAs (DElncRNAs) were associated with the cell wall, oxidation-reduction, the plasma membrane, protein phosphorylation, metabolic processes, transcription factor activity, and the regulation of transcription. Additionally, based on the competitive endogenous RNA (ceRNA) hypothesis, we predicted interactions among different RNAs and constructed a salt-responsive ceRNA network comprising 22 DEmiRNAs, 42 DEmRNAs, 27 DElncRNAs, and 10 differentially expressed circRNAs (DEcircRNAs). Some miRNAs, such as miR408, miR169, miR160, miR5139, miR5368, and miR6179, were central to the network, suggesting their crucial roles in the sweetpotato salt response. Our findings provide a foundation for further research into the potential functions of ncRNAs and offer new targets for salt stress resistance improvement through the manipulation of ncRNAs.

The Role of E3 Ubiquitin Ligase Gene FBK in Ubiquitination Modification of Protein and Its Potential Function in Plant Growth, Development, Secondary Metabolism, and Stress Response

As a crucial post-translational modification (PTM), protein ubiquitination mediates the breakdown of particular proteins, which plays a pivotal role in a large number of biological processes including plant growth, development, and stress response. The ubiquitin-proteasome system (UPS) consists of ubiquitin (Ub), ubiquitinase, deubiquitinating enzyme (DUB), and 26S proteasome mediates more than 80% of protein degradation for protein turnover in plants. For the ubiquitinases, including ubiquitin-activating enzyme (E1), ubiquitin-conjugating enzyme (E2), and ubiquitin ligase (E3), the FBK (F-box Kelch repeat protein) is an essential component of multi-subunit E3 ligase SCF (Skp1-Cullin 1-F-box) involved in the specific recognition of target proteins in the UPS. Many FBK genes have been identified in different plant species, which regulates plant growth and development through affecting endogenous phytohormones as well as plant tolerance to various biotic and abiotic stresses associated with changes in secondary metabolites such as phenylpropanoid, phenolic acid, flavonoid, lignin, wax, etc. The review summarizes the significance of the ubiquitination modification of protein, the role of UPS in protein degradation, and the possible function of FBK genes involved in plant growth, development, secondary metabolism, and stress response, which provides a systematic and comprehensive understanding of the mechanism of ubiquitination and potential function of FBKs in plant species.

Post-transcriptional and post-translational regulation of anthocyanin biosynthesis in sweetpotato by Ib-miR2111 and IbKFB: Implications for health promotion

INTRODUCTION

Sweetpotato (Ipomoea batatas (L.) Lam.) is a genetically intricate hexaploid crop. The purple-fleshed variety, enriched with anthocyanin pigments, is an outstanding source for creating high-value functional products. Previous research on anthocyanin biosynthesis has primarily focused on the above-ground plant parts at the transcriptional level. However, the regulatory mechanisms underlying anthocyanin accumulation in underground tuberous roots of sweetpotato remain largely unexplored.

OBJECTIVES

This study aimed to elucidate the post-transcriptional and post-translational mechanisms of Ib-miR2111 and its target gene IbKFB in anthocyanin synthesis in sweetpotato.

METHODS

Genetic manipulation techniques were used to validate the function of Ib-miR2111 and IbKFB in anthocyanin biosynthesis in sweetpotato. To investigate how IbKFB works, a series of protein interaction assays, including yeast two-hybrid (Y2H), bimolecular fluorescence complementation (BiFC), GST pull-down, co-immunoprecipitation (Co-IP), and ubiquitination, were conducted. Additionally, the impact of anthocyanin extracts from the genetically modified sweetpotato lines on inflammatory cells morphology, cytokine expression, and cell proliferation were evaluated using in vitro assays.

RESULTS

Purple-fleshed sweetpotato (PFSP) varieties exhibited elevated Ib-miR2111 expression compared to white-fleshed sweetpotato (WFSP) varieties, with an inverse expression pattern in IbKFB. Genetic manipulations, including overexpression, CRISPR/Cas9 knockouts, and targeted mutations, confirmed their critical roles in anthocyanin modulation. Furthermore, IbKFB's interactions and ubiquitination with phenylalanine ammonia-lyase 1 (IbPAL1) and glyceraldehyde-3-phosphate dehydrogenase 1 (IbGAPCp1) were elucidated, revealing intricate regulatory mechanisms. Enhanced anthocyanin content showed significant effects on inflammatory cell morphology, cytokine expression, and cell proliferation.

CONCLUSION

This study provides new insights into the regulatory mechanisms of Ib-miR2111 and IbKFB in anthocyanin biosynthesis and suggests potential health benefits of anthocyanin-rich sweetpotatoes.

Genome-Wide Identification of the Rehmannia glutinosa miRNA Family and Exploration of Their Expression Characteristics Caused by the Replant Disease Formation-Related Principal Factor

Background/Objectives: Rehmannia glutinosa, a highly valuable medicinal plant in China, is encountering severe replant disease. Replant disease represents a complex stress driven by multiple principal factors (RDFs), including allelochemicals, microbes, and their interactions. miRNAs are recognized as key regulators of plant response to stresses; however, their specific roles within RDFs are not entirely clear. Methods: This study builds six RDF treatments, comprising R. glutinosa continuously planted (SP), normally planted (NP), and NP treated with ferulic acid (FA), Fusarium oxysporum (FO), and a combination of FA with FO (FAFO). sRNA-seq technology was used to identify crucial miRNAs in response to diverse RDFs. Results: In total, 30 sRNA datasets were generated from the SP, NP, FA, FO, and FAFO samples. A total of 160 known and 41 novel miRNAs (RgmiRNAs) were identified in the R. glutinosa genome based on the sRNA database. Abundance analysis revealed that RgmiRNAs in SP exhibited a distinct expression profile in comparison with others. Of these, 124, 86, 86, and 90 RgmiRNAs were differentially expressed in SP, FA, FO, and FAFO compared with NP. Target analysis indicated that RgmiRNAs downregulated in both SP and RDFs impede the organism growth of R. glutinosa. RgmiRNAs upregulated in SP can disrupt root formation and nutrient metabolism, in which, two RgmiR398 were uniquely expressed in SP. It was confirmed to target RgCSD genes. The expression patterns of RgmiR398 and RgCSD indicated that replant disease induces the oxidative damage of R. glutinosa through RgmiR398. Conclusions:RgmiRNA profiling under RDFs provides a theoretical basis for the further clarification of RgmiRNA function in replant disease.

Review: Defense responses in sweetpotato (Ipomoea batatas L.) against biotic stress

Sweetpotato (Ipomoea batatas L.) is regarded as amongst the world's most important crops for food, vegetable, forage, and raw material for starch and alcohol production. Since pest attack and disease infection are the main limiting aspects frequently causing the yield loss and quality degradation of sweetpotato, it is a great demand to develop the effective defense strategies for maintaining productivity. In the past decade, many studies have focused on dynamic analysis at the physiological, biochemical, and molecular responses of sweetpotatoes to environmental challenges. This review offers an overview of the defense mechanisms against biotic stresses in sweetpotato observed so far, particularly insect herbivory and pathogen infections. The defenses of sweetpotato include the regulation of the toxic and anti-digestive proteins, plant-derived compounds, physical barrier formation, and sugar distribution. Ipomoelin and sporamin have been extensively researched for the defense against herbivore wounding. Herbivory-induced plant volatiles, chlorogenic acid, and latex phytochemicals play important roles in defenses for insect herbivory. Induction of IbSWEET10 reduces sugar content to mediate F. oxysporum resistance. Therefore, these researches provide the genetic strategies for improving resistance bioengineering and breeding of sweetpotato crops and future prospects for research in this field.

Regulatory mechanisms and metabolic changes of miRNA during leaf color change in the bud mutation branches of Acer pictum subsp. mono

Acer pictum subsp. mono is a colorful tree species with considerable ornamental and economic value. However, little is known about the metabolism and regulatory mechanism of leaf color change in A. p. subsp. mono. To reveal the molecular mechanism of leaf color change in A. p. subsp. mono, the present study examined the bud mutation branches and compared the metabolites of the red leaves (AR) of the bud mutation branches of A. p. subsp. mono with those of the green leaves (AG) of the wild-type branches. It was found that the chlorophyll and carotenoids content of the red leaves decreased significantly, while anthocyanins, and various antioxidant enzymes increased significantly compared with the green leaves. The glycosides cyanidin, pelargonidin, malvidin, petunidin, delphinidin, and peonidin were detected in AR by liquid chromatography-mass spectrometry. The cyanidin glycosides increased, and cyanidin 3-O-glycoside was significantly upregulated. We analyzed the transcriptome and small RNA of A. p. subsp. mono leaves and detected 4061 differentially expressed mRNAs and 116 differentially expressed miRNAs. Through miRNA-mRNA association analysis, five differentially expressed modules were found; one miRNA targeted three genes, and four miRNAs targeted a single gene. Among them, miR160b, miR6300, and miR396g were found to be the key miRNAs regulating stable anthocyanin accumulation in A. p. subsp. mono leaves. By revealing the physiological response of leaf color change and the molecular regulatory mechanism of the miRNA, this study provides new insight into the molecular regulatory mechanism of leaf color change, thereby offering a foundation for future studies.

Blocking IbmiR319a Impacts Plant Architecture and Reduces Drought Tolerance in Sweet Potato

MicroRNA319 (miR319) plays a key role in plant growth, development, and multiple resistance by repressing the expression of targeted TEOSINTE BRANCHED/CYCLOIDEA/PCF (TCP) genes. Two members, IbmiR319a and IbmiR319c, were discovered in the miR319 gene family in sweet potato (Ipomoea batatas [L.] Lam). Here, we focused on the biological function and potential molecular mechanism of the response of IbmiR319a to drought stress in sweet potato. Blocking IbmiR319a in transgenic sweet potato (MIM319) resulted in a slim and tender phenotype and greater sensitivity to drought stress. Microscopic observations revealed that blocking IbmiR319a decreased the cell width and increased the stomatal distribution in the adaxial leaf epidermis, and also increased the intercellular space in the leaf and petiole. We also found that the lignin content was reduced, which led to increased brittleness in MIM319. Quantitative real-time PCR showed that the expression levels of key genes in the lignin biosynthesis pathway were much lower in the MIM319 lines than in the wild type. Ectopic expression of IbmiR319a-targeted genes IbTCP11 and IbTCP17 in Arabidopsis resulted in similar phenotypes to MIM319. We also showed that the expression of IbTCP11 and IbTCP17 was largely induced by drought stress. Transcriptome analysis indicated that cell growth-related pathways, such as plant hormonal signaling, were significantly downregulated with the blocking of IbmiR319a. Taken together, our findings suggest that IbmiR319a affects plant architecture by targeting IbTCP11/17 to control the response to drought stress in sweet potato.

At the Root of Nodule Organogenesis: Conserved Regulatory Pathways Recruited by Rhizobia

The interaction between legume plants and soil bacteria rhizobia results in the formation of new organs on the plant roots, symbiotic nodules, where rhizobia fix atmospheric nitrogen. Symbiotic nodules represent a perfect model to trace how the pre-existing regulatory pathways have been recruited and modified to control the development of evolutionary "new" organs. In particular, genes involved in the early stages of lateral root development have been co-opted to regulate nodule development. Other regulatory pathways, including the players of the KNOX-cytokinin module, the homologues of the miR172-AP2 module, and the players of the systemic response to nutrient availability, have also been recruited to a unique regulatory program effectively governing symbiotic nodule development. The role of the NIN transcription factor in the recruitment of such regulatory modules to nodulation is discussed in more details.