Specialized or secondary metabolites are small molecules of biological origin, often showing potent biological activities with applications in agriculture, engineering and medicine. Usually, the biosynthesis of these natural products is governed by sets of co-regulated and physically clustered genes known as biosynthetic gene clusters (BGCs). To share information about BGCs in a standardized and machine-readable way, the Minimum Information about a Biosynthetic Gene cluster (MIBiG) data standard and repository was initiated in 2015. Since its conception, MIBiG has been regularly updated to expand data coverage and remain up to date with innovations in natural product research. Here, we describe MIBiG version 4.0, an extensive update to the data repository and the underlying data standard. In a massive community annotation effort, 267 contributors performed 8304 edits, creating 557 new entries and modifying 590 existing entries, resulting in a new total of 3059 curated entries in MIBiG. Particular attention was paid to ensuring high data quality, with automated data validation using a newly developed custom submission portal prototype, paired with a novel peer-reviewing model. MIBiG 4.0 also takes steps towards a rolling release model and a broader involvement of the scientific community. MIBiG 4.0 is accessible online at https://mibig.secondarymetabolites.org/.
Zearalenone (ZEN) is a toxic secondary metabolite of Fusarium sp. commonly found in wheat, corn, and other crops. In addition to economic losses, ZEN can seriously endanger the health of both humans and livestock, thus presenting an urgent need for ZEN-detoxifying enzymes that function in the extreme heat or pH conditions of industrial fermenters. Here, we identify and characterize the activity of the ZEN-degrading enzyme from Exophiala spinifera, ZHD_LD, which shares 60.15% amino acid identity and a conserved catalytic triad with the well-characterized ZEN-detoxifying protein ZHD101 from Clonostachys rosea. Biochemical activity and stability assays indicated that purified recombinant ZHD_LD exhibited high activity against ZEN with optimal reaction conditions of 50 °C and pH 7.0-10.0. Structural modeling of the ZHD_LD active site and comparison with ZHD101 revealed its likely mechanism of ZEN degradation. This research provides an industrially valuable candidate enzyme for ZEN detoxification in food and livestock feed.
- MeSH
- Fusarium * metabolism MeSH
- Hydrolases metabolism MeSH
- Humans MeSH
- Triticum metabolism MeSH
- Zearalenone * chemistry metabolism MeSH
- Check Tag
- Humans MeSH
- Publication type
- Journal Article MeSH
KEY MESSAGE: The new 4.2-kb transposable insertion in the intron of ZmCCT reversely responded relative to the known 5.1-kb transposable insertion to photoperiods between low- and high-latitude regions. Flowering time is a key trait for cereal adaptation that is controlled by a complex genetic background in maize. The effect of multiple alleles from a quantitative trait locus (QTL) on flowering time remains largely unknown. Here, we fine-mapped a major QTL for flowering time on maize chromosome 10 corresponding to ZmCCT, where a new allele with a 4.2-kilobase (kb) transposable insertion was present in the intron. The known allele with a 5.1-kb transposon insertion in the promoter of ZmCCT enhances flowering in high-latitude regions, but has no effect on flowering time in low-latitude regions in comparison with the null allele lacking this insertion. However, our new allele with a 4.2-kb insertion reduced flowering in the low-latitude region, but produced unchanged flowering time in the high-latitude region relative to the 5.1-kb transposable insertion. Transcription analysis revealed that the new allele with 4.2-kb insertion versus the 5.1-kb insertion repressed and unchanged the transcription of ZmCCT in the low- and high-latitude regions, respectively. Thus, the allele with the 4.2-kb transposable insertion showed a completely opposite response to photoperiods between these two regions. Phylogenetic analysis revealed that the 4.2-kb transposable insertion in the two Northern flint corns originated from tropical maize. RNA-seq analysis and dual-luciferase transient expression assays further identified a conserved gene regulation network of ZmCCT between maize and rice, in which ZmCCT directly repressed the transcription of the florigen gene ZCN8 via ZmEhd1. Our results suggest that transposable elements play an important role in maize adaptation.
- MeSH
- Chromosomes, Plant genetics MeSH
- Phenotype MeSH
- Photoperiod * MeSH
- Adaptation, Physiological MeSH
- Zea mays genetics growth & development radiation effects MeSH
- Flowers genetics growth & development radiation effects MeSH
- Quantitative Trait Loci MeSH
- Chromosome Mapping methods MeSH
- Promoter Regions, Genetic MeSH
- Gene Expression Regulation, Plant * MeSH
- Plant Proteins genetics metabolism MeSH
- DNA Transposable Elements * MeSH
- Publication type
- Journal Article MeSH
Tilmicosin (TMS) is widely used to treat bacterial infections in veterinary medicine, but the clinical effect is limited by its poor solubility, bitterness, gastric instability, and intestinal efflux transport. Nanostructured lipid carriers (NLCs) are nowadays considered to be a promising vector of therapeutic drugs for oral administration. In this study, an orthogonal experimental design was applied for optimizing TMS-loaded NLCs (TMS-NLCs). The ratios of emulsifier to mixed lipids, stearic acid to oleic acid, drugs to mixed lipids, and cold water to hot emulsion were selected as the independent variables, while the hydrodynamic diameter (HD), drug loading (DL), and entrapment efficiency (EE) were the chosen responses. The optimized TMS-NLCs had a small HD, high DL, and EE of 276.85 ± 2.62 nm, 9.14 ± 0.04%, and 92.92 ± 0.42%, respectively. In addition, a low polydispersity index (0.231 ± 0.001) and high negative zeta potential (-31.10 ± 0.00 mV) indicated the excellent stability, which was further demonstrated by uniformly dispersed spherical nanoparticles under transmission electron microscopy. TMS-NLCs exhibited a slow and sustained release behavior in both simulated gastric juice and intestinal fluid. Furthermore, MDCK-chAbcg2/Abcb1 cell monolayers were successfully established to evaluate their absorption efficiency and potential mechanism. The results of biodirectional transport showed that TMS-NLCs could enhance the cellular uptake and inhibit the efflux function of drug transporters against TMS in MDCK-chAbcg2/Abcb1 cells. Moreover, the data revealed that TMS-NLCs could enter the cells mainly via the caveolae/lipid raft-mediated endocytosis and partially via macropinocytosis. Furthermore, TMS-NLCs showed the same antibacterial activity as free TMS. Taken together, the optimized NLCs were the promising oral delivery carrier for overcoming oral administration obstacle of TMS.
- Publication type
- Journal Article MeSH
Banana is one of the most important food and fruit crops in the world and its growth is ceasing at 10-17 °C. However, the mechanisms determining the tolerance of banana to mild (>15 °C) and moderate chilling (10-15 °C) are elusive. Furthermore, the biochemical controls over the photosynthesis in tropical plant species at low temperatures above 10 °C is not well understood. The purpose of this research was to reveal the response of chilling-sensitive banana to mild (16 °C) and moderate chilling stress (10 °C) at the molecular (transcripts, proteins) and physiological levels. The results showed different transcriptome responses between mild and moderate chilling stresses, especially in pathways of plant hormone signal transduction, ABC transporters, ubiquinone, and other terpenoid-quinone biosynthesis. Interestingly, functions related to carbon fixation were assigned preferentially to upregulated genes/proteins, while photosynthesis and photosynthesis-antenna proteins were downregulated at 10 °C, as revealed by both digital gene expression and proteomic analysis. These results were confirmed by qPCR and immunofluorescence labeling methods. Conclusion: Banana responded to the mild chilling stress dramatically at the molecular level. To compensate for the decreased photosynthesis efficiency caused by mild and moderate chilling stresses, banana accelerated its carbon fixation, mainly through upregulation of phosphoenolpyruvate carboxylases.
At present, the traditional methods for the screening of Clostridium butyricum are not sufficiently selective and efficient. Therefore, it is necessary to establish a targeted and efficient screening method for the detection of C. butyricum. Bioinformatics was used in this study to find C. butyricum specific genes, and species-specific primers were designed based on the conserved regions of the targeted genes, followed by optimization of the PCR conditions. Methodological evaluation was carried out, and the results were compared with the traditional screening method based on Trypticase Sulfite Neomycin (TSN) selective medium. A high-efficiency PCR screening method, targeting C. butyricum species-specific primers, was established. The method was confirmed to have high specificity and sensitivity towards C. butyricum cut-off CFU 103. Compared with the traditional method, the screening success rate of C. butyricum strains increased from 0.61 to 81.91%. The PCR screening method could quickly and accurately detect C. butyricum in samples and dramatically improve screening efficiency.
Microbial bioremediation of heavy metal-contaminated soil is a potential technique to reduce heavy metals in crop plants. However, the dynamics and roles of the local microbiota in bioremediation of heavy metal-contaminated soil following microbial application are rarely reported. In this study, we used Pseudomonas chenduensis strain MBR for bioremediation of Cd-contaminated paddy soil and investigated its effects on the dynamics of the local soil bacterial community and Cd accumulation in rice. Cd accumulation in rice grains and roots were significantly reduced by the addition of the strain MBR. The addition of the strain MBR caused greater changes in bacterial communities in rhizosphere soil than in bulk soil. MBR enhanced the roles of microbial communities in transformation of Cd fractions, especially in rhizosphere soil. The strain MBR likely regulated abundant subcommunities more than rare subcommunities to improve Cd bioremediation, especially in rhizosphere soil. Consequently, the dynamics and functional roles of the local microbial communities differed significantly during bioremediation between abundant and rare subcommunities and between rhizosphere soil and bulk soil. This study provides new insight into the microbiota-related mechanisms underlying bioremediation.
