FGCD: a database of fungal gene clusters related to secondary metabolism.

Fungal secondary metabolites are not necessary for growth, but they are important for fungal metabolism and ecology because they provide selective advantages for competition, survival and interactions with the environment. These various metabolites are widely used as medicinal precursors and insecticides. Secondary metabolism genes are commonly arranged in clusters along chromosomes, which allow for the coordinate control of complete pathways. In this study, we created the Fungal Gene Cluster Database to store, retrieve, and visualize secondary metabolite gene cluster information across fungal species. The database was created by merging data from RNA sequencing, Basic Local Alignment Search Tool, genome browser, enrichment analysis and the R Shiny web framework to visualize and query putative gene clusters. This database facilitated the rapid and thorough examination of significant gene clusters across fungal species by detecting, defining and graphically displaying the architecture, organization and expression patterns of secondary metabolite gene clusters. In general, this genomic resource makes use of the tremendous chemical variety of the products of these ecologically and biotechnologically significant gene clusters to our further understanding of fungal secondary metabolism. Database URL: https://www.hebaubioinformatics.cn/FungalGeneCluster/.

Maize stalk rot caused by Fusarium graminearum alters soil microbial composition and is directly inhibited by Bacillus siamensis isolated from rhizosphere soil.

Maize stalk rot caused by Fusarium graminearum can reduce the yield of maize and efficiency of mechanized harvesting. Besides, deoxynivalenol and zearalenone toxins produced by F. graminearum can also affect domestic animals and human health. As chemical fungicides are expensive and exert negative effects on the environment, the use of biological control agents has become attractive in recent years. In the present study, we collected rhizosphere soil with severe stalk rot disease (ZDD), the rhizosphere soil with disease-free near by the ZDD (ZDH), and measured rhizosphere microbial diversity and microbial taxonomic composition by amplicon sequencing targeting either bacteria or fungi. The results showed that Fusarium stalk rot caused by the Fusarium species among which F. graminearum is frequent and can reduce the abundance and alpha diversity of rhizosphere microbial community, and shift the beta diversity of microorganisms. Furthermore, a bacterial strain, Bacillus siamensis GL-02, isolated from ZDD, was found to significantly affect growth of F. graminearum. In vitro and in vivo assays demonstrated that B. siamensis GL-02 had good capability to inhibit F. graminearum. These results revealed that B. siamensis GL-02 could be a potential biocontrol agent for the control of maize stalk rot.

Identification and expression analysis of maize NF-YA subunit genes.

NF-YAs encode subunits of the nuclear factor-Y (NF-Y) gene family. NF-YAs represent a kind of conservative transcription factor in plants and are involved in plant growth and development, as well as resistance to biotic and abiotic stress. In this study, 16 maize (Zea mays) NF-YA subunit genes were identified using bioinformatics methods, and they were divided into three categories by a phylogenetic analysis. A conserved domain analysis showed that most contained a CCAAT-binding transcription factor (CBFB) _NF-YA domain. Maize NF-YA subunit genes showed very obvious tissue expression characteristics. The expression level of the NF-YA subunit genes significantly changed under different abiotic stresses, including Fusarium graminearum infection and salicylic acid (SA) or jasmonic acid (JA) treatments. After inoculation with Setosphaeria turcica and Cochliobolus heterostrophus, the lesion areas of nfya01 and nfya06 were significantly larger than that of B73, indicating that ZmNFYA01 and ZmNFYA06 positively regulated maize disease resistance. ZmNFYA01 and ZmNFYA06 may regulated maize disease resistance by affecting the transcription levels of ZmPRs. Thus, NF-YA subunit genes played important roles in promoting maize growth and development and resistance to stress. The results laid a foundation for clarifying the functions and regulatory mechanisms of NF-YA subunit genes in maize.

Global analysis of lysine 2-hydroxyisobutyrylation during Fusarium graminearum infection in maize.

Proteins post-translational modification (PTMs) is necessary in the whole life process of organisms. Among them, lysine 2-hydroxyisobutyrylation (Khib) plays an important role in protein synthesis, transcriptional regulation, and cell metabolism. Khib is a newly identified PTM in several plant species. However, the function of Khib in maize was unclear. In this study, western blotting results showed that Khib modification level increased significantly after Fusarium graminearum infection, and 2,066 Khib modified sites on 728 proteins were identified in maize, among which 24 Khib sites occurred on core histones. Subcellular localization results showed that these Khib modified proteins were localized in cytoplasm, chloroplast, and nucleus. Then, comparative proteomic analysis of the defense response to F. graminearum infection showed that Khib modification participated in plant resistance to pathogen infection by regulating glycolysis, TCA cycle, protein synthesis, peroxisome, and secondary metabolic processes, such as benzoxazinoid biosynthesis, phenylpropanoid biosynthesis, jasmonic acid synthesis, and tyrosine and tryptophan biosynthesis. In addition, we also demonstrated that lysine 2-hydroxyisobutyrylation sites on histones were involved in the gene expression of pathogenesis-related proteins. Our results provide a new perspective for the study of plant disease resistance, and had directive significance of maize disease resistance for molecular breeding.

Functionalized monolithic columns: Recent advancements and their applications for high-efficiency separation and enrichment in food and medicine.

The chromatographic column is the core of a high-performance liquid chromatography (HPLC) system, and must have excellent separation efficiency and selectivity. Therefore, functional modification materials for monolithic columns have been rapidly developed. This study is a systematic review of the recently reported functionalized monolithic columns. In particular, the study reviews the types of functional monomers under different modification conditions, as well as the separation and detection techniques combined with chromatography, and their development prospects. In addition, the applications of functionalized monolithic columns in food analysis, biomedicine, and the analysis of active ingredient of Chinese herbal medicines in recent years are also discussed. Also reviewed are the functionalized monolithic columns for qualitative and quantitative analysis. It provided a reference for further development and application of organic polymer monolithic columns.

Graphene oxide-based a network porous poly (trially isocyanurate-co-methacrylate) monolithic column for HPLC separation of aromatic molecular and lipopeptide antibiotics.

Graphene oxide (GO) was introduced into a monolithic column and a network porous poly (GO-co-TAIC-co-MMA) monolith was prepared by redox polymerization. The internal morphology and pore size distribution of the polymer were observed by scanning electron microscopy, and the nitrogen adsorption-desorption and mercury intrusion methods. After optimization, 8 kinds of aromatic compounds were effectively separated in 5 min, and the theoretical plates number of the monolithic column exceeded 33, 070 plates m-1. Five kinds of main ingredients were separated from the traditional Chinese medicine (Schisandra) ingredients and 26 peaks were successfully separated from the fermentation broth containing natural lipopeptide antibiotics. The addition of GO material enhanced the interaction between the compound and the monolithic column, increased the binding sites, improved the uniformity of the internal pore structure of the monolithic column, and improved the separation performance of the monolith. Methodologic validation of five ingredients in Schisandra showed that the correlation coefficients of the linear regressions were in the range of 0.9987-0.9997. The intra- and inter-day values of the relative standard deviation for precision were in the range of 0.6-4.1% and 1.1-4.8%, respectively. The values of accuracy (expressed as recovery) were in the range of 97.7-103.2%, 100.5-105.0%, 98.2-101.8%, 101.3-104.1%, and 101.2-103.3% for the 5 ingredients in order. In terms of the relative standard deviation of the retention time, the reproducibility of the monolithic column M1 was <3.7%. The monolithic column based on GO has great potential in chromatographic separation.

2-Arylindoles: Concise Syntheses and a Privileged Scaffold for Fungicide Discovery.

Indole is a popular and functional scaffold existing widely in the fields of medicine, pesticides, spices, food and feed additives, dyes, and many others. Among indoles, 2-arylindole represents a particular and interesting subset but has attracted less attention for drug discovery. In this study, we report a general, practical one-pot assembly of a variety of 2-arylindole derivatives. To develop novel fungicide scaffolds, their fungicide activity was also evaluated. The bioassay results showed that many of the synthesized 2-arylindoles exhibited considerable fungicidal activities especially toward Rhizoctonia cerealis, and several demonstrated an inhibition rate of more than 90%. Notably, 4-fluoro-2-phenyl-1H-indole 6e was obtained with a broad spectrum of fungicidal activities, which showed excellent growth inhibition activities against R. cerealis, Rhizoctonia solani, Botrytis cinerea, Magnaporthe oryza, and Sclerotinia sclerotiorum with EC50 values of 2.31, 4.98, 6.78, 10.57, and 17.80 µg/mL, respectively. Preliminary fungicidal mode of action of 6e showed a significant inhibition effect on mycelial growth and spore germination. These results indicated that 2-arylindoles as privileged scaffolds exhibited potential fungicidal activities that deserve further study.

Comparative Proteomic Analysis of the Defense Response to Gibberella Stalk Rot in Maize and Reveals That ZmWRKY83 Is Involved in Plant Disease Resistance.

Fusarium graminearum is the causal agent of Gibberella stalk rot in maize stem, resulting in maize lodging, yield, quality, and mechanical harvesting capacity. To date, little is known about the maize stem defense mechanism in response to the invasion of F. graminearum. This study represents a global proteomic approach to document the infection by F. graminearum. A total of 1,894 differentially expressed proteins (DEPs) were identified in maize stem with F. graminearum inoculation. Functional categorization analysis indicated that proteins involved in plant-pathogen interaction were inducible at the early stages of infection. We also found that the expression of proteins involved in phenylpropanoid, flavonoid, and terpenoid biosynthesis were upregulated in response to F. graminearum infection, which may reflect that these secondary metabolism pathways were important in the protection against the fungal attack in maize stem. In continuously upregulated proteins after F. graminearum infection, we identified a WRKY transcription factor, ZmWRKY83, which could improve the resistance to plant pathogens. Together, the results show that the defense response of corn stalks against F. graminearum infection was multifaceted, involving the induction of proteins from various immune-related pathways, which had a directive significance for molecular genetic breeding of maize disease-resistant varieties.

Effect of Osmotic Stress on the Growth, Development and Pathogenicity of Setosphaeria turcica.

Osmotic stress is a severe condition frequently encountered by microorganisms; however, there is limited knowledge on the influence of hyperosmotic stress on the growth, development and pathogenicity of phytopathogenic fungi. Here, three osmotic conditions (0.4 M NaCl, 0.4 M KCl, and 0.6 M sorbitol supplemented in potato dextrose agar medium) were used to identify the effect of osmotic stress on the growth, development and pathogenicity of Setosphaeria turcica which is a plant pathogenic fungus and causes northern corn leaf blight disease in maize, sorghum, and related grasses. In osmotic stress, the growth rate of mycelium was decreased, and the number of vesicular structures and flocculent secretion outside the hypha cell wall were significantly increased. The qRT-PCR results showed that the osmotic stress quickly activated the HOG-MAPK pathway, up-regulated the expression of the downstream genes, and these genes were most highly expressed within 30 min of exposure to osmotic stress. Furthermore, the germination rate and the yield of conidia were significantly higher under osmotic stress than in the control. A pathogenicity analysis confirmed that pathogenicity of the conidia which were cultured under osmotic stress was significantly enhanced. By analyzing the knock-out mutants of an osmotic stress responsed gene StFPS1, an aquaglyceroporin downstream of the HOG-MAPK pathway, we found that StFPS1 was involved in the formation of appressorium and penetration peg, which affected the penetration ability of S. turcica. In summary, our work explained the correlation between osmotic stress and growth, development, and pathogenicity in S. turcica.

One-Pot Synthesis of N-H-Free Pyrroles from Aldehydes and Alkynes.

The first base-mediated intermolecular cyclization of arylaldehydes and terminal arylacetylenes for the synthesis of a wide range of pyrroles in a single step has been described. The developed methodology used commercially available starting materials and tolerated a broad range of functional groups affording 2,3,5-triaryl-substituted-1H-pyrroles with good yields (up to 92% yield) under mild conditions. The possible mechanism was also discussed.

Influenza virus glycoprotein-reactive human monoclonal antibodies.

Influenza continues to be a significant public health challenge. Two glycoproteins on the surface of influenza virus, hemagglutinin and neuraminidase, play a prominent role in the process of influenza virus infection and release. Monoclonal antibodies targeting glycoproteins can effectively prevent the spread of the virus. In this review, we summarized currently reported human monoclonal antibodies targeting glycoproteins of influenza A and B viruses.

Study on the characteristics and mechanisms of nicosulfuron biodegradation by Bacillus velezensis CF57.

Nicosulfuron is one of the main sulfonylurea herbicides that have been widely used to protect maize crops. A total of 10 nicosulfuron-degrading strains were isolated from the intestine tract of earthworm Eisenia foetida. Among them, Bacillus velezensis CF57 with the highest degradation efficiency was selected and studied in detail. The degradation characteristics of CF57 showed that it was able to effectively degrade nicosulfuron in a wide range of temperature, pH, and a low inoculation amount, and the response surface analysis revealed that the optimum degradation conditions were 30.8 °C, pH 6.31, and inoculation amount 3.04%. Meanwhile, CF57 could degrade high-concentration nicosulfuron efficiently and posed a broad degradation spectrum of other sulfonylurea herbicides. Furthermore, the localization of degradation enzyme indicated that the nicosulfuron-degrading enzyme was an extracellular fraction. By analyzing the metabolites of nicosulfuron, it could be further determined that the degradation of nicosulfuron by strain CF57 was mainly through the extracellular enzyme, and its possible degradation pathway was mainly derived from the cleavage of the C-N bond of the sulfonylurea bridge. These results may provide new insights into bioremediation of nicosulfuron-contaminated environments and enrich the resources of degrading bacteria of sulfonylurea herbicides.

Biotransformation of the herbicide nicosulfuron residues in soil and seven sulfonylurea herbicides by Bacillus subtilis YB1: A climate chamber study.

Bacillus subtilis YB1 is a strain that can efficiently transform nicosulfuron. In order to study its remediation ability and effects on other microorganisms in the soil, indoor biological remediation experiments and rhizosphere microbial diversity analysis were performed. B. subtilis YB1 granules were prepared and applied to the nicosulfuron contaminated soil. The concentration of nicosulfuron was detected by ultra-performance liquid chromatography-mass spectrometry (UPLC-MS) and changes in the physiological indicators of wheat were measured. At the same time, the changes in the rhizosphere soil microbial diversity were determined by 16S RNA sequencing. Results showed that the YB1 granules made a contribution to the transformation of nicosulfuron (0.05 mg kg-1) in the soil within 55 days. The physiological indicators of wheat also showed consistent result about nicosulfuron transformation. Rhizosphere soil microbial diversity results indicated the relative abundance of Firmicutes decreased (3.0%-0.35%) and Acidobacteria first decreased (25.82%-22.38%) and then increased (22.3%-26.1%) with nicosulfuron added (N group). The relative abundance of Acidobacteria first decreased (25.8%-15.3%) and then increased (15.3%-21.7%) while Proteobacteria increased (26.5%-38.08%). At the same time, Firmicutes first increased (2.6%-12.3%) and then decreased to original level (12.3%-0.7%) in the N group with YB1 granules (NYB1 group). Members of the genus Bacillus initially increased and then decreased to the original level as the Control group, therefore, they did not become dominant in the rhizosphere soil. Alpha diversity analyses showed no obvious differences in species diversity among the N, NYB1 and Control groups. So YB1 did not have obvious influence on the rhizosphere microbial community structure during nicosulfuron transformation, which only had some effect on species abundance. This study revealed the successful indoor bioremediation of nicosulfuron in the soil, providing a potential strategy for solving the problem of nicosulfuron contamination.

In silico analysis of maize HDACs with an emphasis on their response to biotic and abiotic stresses.

Histone deacetylases (HDACs) are key epigenetic factors in regulating chromatin structure and gene expression in multiple aspects of plant growth, development, and response to abiotic or biotic stresses. Many studies on systematic analysis and molecular function of HDACs in Arabidopsis and rice have been conducted. However, systematic analysis of HDAC gene family and gene expression in response to abiotic and biotic stresses has not yet been reported. In this study, a systematic analysis of the HDAC gene family in maize was performed and 18 ZmHDACs distributed on nine chromosomes were identified. Phylogenetic analysis of ZmHDACs showed that this gene family could be divided into RPD3/HDA1, SIR2, and HD2 groups. Tissue-specific expression results revealed that ZmHDACs exhibited diverse expression patterns in different tissues, indicating that these genes might have diversified functions in growth and development. Expression pattern of ZmHDACs in hormone treatment and inoculation experiment suggested that several ZmHDACs might be involved in jasmonic acid or salicylic acid signaling pathway and defense response. Interestingly, HDAC genes were downregulated under heat stress, and immunoblotting results demonstrated that histones H3K9ac and H4K5ac levels were increased under heat stress. These results provide insights into ZmHDACs, which could help to reveal their functions in controlling maize development and responses to abiotic or biotic stresses.

Heterologous expression of Stlac2, a laccase isozyme of Setosphearia turcica, and the ability of decolorization of malachite green.

The active laccases of ascomycetous fungus Setosphaeria turcica were identified by Native-PAGE and ESI-MS/MS, and one of these isozymes Stlac2 was heterologous expressed to investigate the decolorization of malachite green. Setosphaeria turcica produced three active laccase isozymes: Stlac1, Stlac2, and Stlac6. Stlac2 was heterologously expressed in both eukaryotic and prokaryotic expression systems. The eukaryotic recombinant Stlac2 expressed in Pichia pastoris was inactive, and also showed a higher molecular weight than predicted because of glycosylation. The depression of laccase activity was attributable to the incorrect glycosylation at Asn97. Stlac2 expressed in Escherichia coli and the recombinant Stlac2 exhibited activity of 28.23 U/mg with 2,2-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid) (ABTS) as the substrate. The highest activity was observed at pH of 4.5 and the temperature of 60 °C. The activity of recombinant Stlac2 was inhibited by 10 mM Na+, Mg2+, Ca2+, Mn2+, and increased by 10 mM of Fe3+ with a relatively activity of 315% compared with no addition. Cu2+ did not affect enzyme activity. Recombinant Stlac2 was capable of decolorizing 67.08% of 20 mg/L malachite green in 15 min without any mediators. CONCLUSIONS: Generally, recombinant protein of fungal laccase Stlac2 was active without glycosylation and decolorize malachite green efficiently, which has potential industrial applications.

[Molecular cloning and characterization of calcineurin A in Setosphaeria turcica].

A Setosphaeria turcica gene encoding the catalytic subunit of calcineurin was cloned using degenerated primers corresponding to conserved domains of Ser/Thr protein phosphatases and its complete cDNA (GenBank accession No. EF 407562) was obtained with RACE method. It's validated single copied model by southern hybridization. Furthermore, the CNA inhibitor Cyclosporin A (CsA) exhibited potent antifungal activity against conidial germination and appressorium formation of S. turcica. The inhibition ratio was positively correlated to CsA concentration. However, appressorium formation was more sensitive than conidium germination to the inhibitor at the same concentration. It was suggested that CNA might play an important role in the pathogenicity of S. turcica.