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Microbiology Resource Announcements Jun 2024In this study, we have identified and characterized three genomes from bacteria isolated from the rhizosphere of CMAA1738 and CMAA1739 were obtained from the wheat...
In this study, we have identified and characterized three genomes from bacteria isolated from the rhizosphere of CMAA1738 and CMAA1739 were obtained from the wheat landrace Iran 1-29-11334, and CMAA1741 was isolated from the wheat landrace Karakilcik.
PubMed: 38860798
DOI: 10.1128/mra.00036-24 -
Frontiers in Microbiology 2024Banana wilt caused by f. sp. tropical race 4 (Foc TR4) is a devastating fungal disease. Biocontrol strategies hold immense potential for inhibiting the spread of Foc...
Banana wilt caused by f. sp. tropical race 4 (Foc TR4) is a devastating fungal disease. Biocontrol strategies hold immense potential for inhibiting the spread of Foc TR4. Here, 30 actinobacteria were isolated from soils and screened for their antagonistic activity against Foc TR4. Strain SCA4-21 was selected due to its strongest antagonistic activity against Foc TR4. Strain SCA4-21 also exhibited strong antagonistic activity against the other eight phytopathogenic fungi. The strain was identified as the genus according to its physiological, biochemical, and phenotypic characteristics. The phylogenetic trees of 16S rRNA sequences demonstrated that strain SCA4-21 formed a subclade with HM 35 and/or NRRL B-5491 with low bootstrap values. Considering that 16S rRNAs did not provide sufficient resolution for species-level identification, the whole genome of strain SCA4-21 was sequenced. Multilocus sequence analysis (MLSA) based on five housekeeping gene alleles (, , , , and ) revealed that strain SCA4-21 clustered into subsp. NBRC 13472 with 100% of bootstrap value. The analysis of the genome-based phylogeny also approved the results. Average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) were 91.26 and 44.30%, respectively, with values below the respective species level threshold of 95 and 70%. Hence, strain SCA 4-21 represented a novel species within the genus , named sp. nov. The type strain is SCA4-21 (=GDMCC4.340 = JCM36555). By the CAZymes analysis, 348 carbohydrate-active enzymes (CAZymes) were detected, including 15 chitinases and eight β-1,3-glucanases. The fermentation broth of strain SCA4-21, exhibiting strong antagonistic activity against Foc TR4, demonstrated high activities of chitinase and β-1,3-glucanase, which might be involved in antifungal activity. Our results showed an innovative potential biocontrol agent for managing plant fungal diseases, specifically banana wilt.
PubMed: 38860218
DOI: 10.3389/fmicb.2024.1402653 -
Frontiers in Microbiology 2024Transglutaminase (EC 2.3.2.13, TGase), an enzyme that catalyzes the formation of covalent cross-links between protein or peptide molecules, plays a critical role in...
Transglutaminase (EC 2.3.2.13, TGase), an enzyme that catalyzes the formation of covalent cross-links between protein or peptide molecules, plays a critical role in commercial food processing, medicine, and textiles. TGase from is the sole commercial enzyme preparation for cross-linking proteins. In this study, we revealed that the SOS response repressor protein LexA in not only triggers morphological development but also enhances TGase synthesis. The absence of significantly diminished TGase production and sporulation. Although LexA does not bind directly to the promoter region of the TGase gene, it indirectly stimulates transcription of the gene, which encodes TGase. Furthermore, LexA directly enhances the expression of genes associated with protein synthesis and transcription factors, thus favorably influencing TGase synthesis at both the transcriptional and posttranscriptional levels. Moreover, LexA activates four crucial genes involved in morphological differentiation, promoting spore maturation. Overall, our findings suggest that LexA plays a dual role as a master regulator of the SOS response and a significant contributor to TGase regulation and certain aspects of secondary metabolism, offering insights into the cellular functions of LexA and facilitating the strategic engineering of TGase overproducers.
PubMed: 38855760
DOI: 10.3389/fmicb.2024.1397314 -
Microbiology Resource Announcements Jun 2024sp. F41 is a potent insecticidal metabolite producing actinomycetes isolated from the topsoil, and the complete genome sequence was determined. The genome consists of...
sp. F41 is a potent insecticidal metabolite producing actinomycetes isolated from the topsoil, and the complete genome sequence was determined. The genome consists of 8,343,496 bp, with 7,221 genes and a GC content of 71.84%.
PubMed: 38842340
DOI: 10.1128/mra.00306-24 -
Frontiers in Microbiology 2024Desert steppe ecosystems are prone to drought stress, which influences the ecological balance and sustainable development of grasslands. In addition to directly restrict...
BACKGROUND
Desert steppe ecosystems are prone to drought stress, which influences the ecological balance and sustainable development of grasslands. In addition to directly restrict plant growth, drought stress indirectly impacts plant fitness by altering the diversity and function of root-associated microbiomes. This begs the question of whether the functional microbiome of forage plants, represented by synthetic microbial communities (SynComs), can be leveraged to mitigate drought stress in desert steppes and promote the ecological restoration of these fragile ecosystems.
METHODS
A pot experiment was conducted to evaluate the role of SynComs in improving the plant growth and drought stress resistance of (Pall.) Poljak in desert steppe in Inner Mongolia, China. Six SynComs were derived from the rhizosphere and root endosphere of 12 dominant forage species in the desert steppe. Each SynCom comprised two to three bacterial genera (, , and ). We examined the capacities of different SynComs for nutrient solubilization, phytohormone secretion, and enzymatic activity.
RESULTS
Under no water stress (75% soil water holding capacity, WHC), single strains performed better than SynComs in promoting plant growth in terms of stem diameter, root length, and plant dry weight, with the greatest effects observed for ATCC 13740 ( < 0.05). However, under mild to moderate drought stress (55% and 35% WHC), SynComs outperformed single strains in enhancing plant biomass accumulation and inducing the production of resistance-related substances ( < 0.05). No significant effect of single strains and SynComs emerged under extreme drought stress (20% WHC).
CONCLUSION
This study underscores the potential of SynComs in facilitating forage plants to combat drought stress in desert steppe. Mild to moderate drought stress stimulates SynComs to benefit the growth of plants, despite a soil moisture threshold (21% WHC) exists for the microbial effect. The use of SynComs provides a promising strategy for the ecological restoration and sustainable utilization of desert steppes by manipulating the functional microbiome of forage plants.
PubMed: 38841054
DOI: 10.3389/fmicb.2024.1371208 -
Scientific Reports Jun 2024Some of the most metabolically diverse species of bacteria (e.g., Actinobacteria) have higher GC content in their DNA, differ substantially in codon usage, and have...
Some of the most metabolically diverse species of bacteria (e.g., Actinobacteria) have higher GC content in their DNA, differ substantially in codon usage, and have distinct protein folding environments compared to tractable expression hosts like Escherichia coli. Consequentially, expressing biosynthetic gene clusters (BGCs) from these bacteria in E. coli often results in a myriad of unpredictable issues with regard to protein expression and folding, delaying the biochemical characterization of new natural products. Current strategies to achieve soluble, active expression of these enzymes in tractable hosts can be a lengthy trial-and-error process. Cell-free expression (CFE) has emerged as a valuable expression platform as a testbed for rapid prototyping expression parameters. Here, we use a type III polyketide synthase from Streptomyces griseus, RppA, which catalyzes the formation of the red pigment flaviolin, as a reporter to investigate BGC refactoring techniques. We applied a library of constructs with different combinations of promoters and rppA coding sequences to investigate the synergies between promoter and codon usage. Subsequently, we assess the utility of cell-free systems for prototyping these refactoring tactics prior to their implementation in cells. Overall, codon harmonization improves natural product synthesis more than traditional codon optimization across cell-free and cellular environments. More importantly, the choice of coding sequences and promoters impact protein expression synergistically, which should be considered for future efforts to use CFE for high-yield protein expression. The promoter strategy when applied to RppA was not completely correlated with that observed with GFP, indicating that different promoter strategies should be applied for different proteins. In vivo experiments suggest that there is correlation, but not complete alignment between expressing in cell free and in vivo. Refactoring promoters and/or coding sequences via CFE can be a valuable strategy to rapidly screen for catalytically functional production of enzymes from BCGs, which advances CFE as a tool for natural product research.
Topics: Cell-Free System; Promoter Regions, Genetic; Streptomyces griseus; Escherichia coli; Multigene Family; Bacterial Proteins; Polyketide Synthases; Codon; Acyltransferases
PubMed: 38839808
DOI: 10.1038/s41598-024-61376-w -
Food Microbiology Sep 2024To investigate the potential antifungal mechanisms of rhizosphere Actinobacteria against Ceratocystis fimbriata in sweet potato, a comprehensive approach combining...
To investigate the potential antifungal mechanisms of rhizosphere Actinobacteria against Ceratocystis fimbriata in sweet potato, a comprehensive approach combining biochemical analyses and multi-omics techniques was employed in this study. A total of 163 bacterial strains were isolated from the rhizosphere soil of sweet potato. Among them, strain MEPS155, identified as Streptomyces djakartensis, exhibited robust and consistent inhibition of C. fimbriata mycelial growth in in vitro dual culture assays, attributed to both cell-free supernatant and volatile organic compounds. Moreover, strain MEPS155 demonstrated diverse plant growth-promoting attributes, including the production of indole-3-acetic acid, 1-aminocyclopropane-1-carboxylate deaminase, phosphorus solubilization, nitrogen fixation, and enzymatic activities such as cellulase, chitinase, and protease. Notably, strain MEPS155 exhibited efficacy against various sweet potato pathogenic fungi. Following the inoculation of strain MEPS155, a significant reduction (P < 0.05) in malondialdehyde content was observed in sweet potato slices, indicating a potential protective effect. The whole genome of MEPS155 was characterized by a size of 8,030,375 bp, encompassing 7234 coding DNA sequences and 32 secondary metabolite biosynthetic gene clusters. Transcriptomic analysis revealed 1869 differentially expressed genes in the treated group that cultured with C. fimbriata, notably influencing pathways associated with porphyrin metabolism, fatty acid biosynthesis, and biosynthesis of type II polyketide products. These alterations in gene expression are hypothesized to be linked to the production of secondary metabolites contributing to the inhibition of C. fimbriata. Metabolomic analysis identified 1469 potential differently accumulated metabolites (PDAMs) when comparing MEPS155 and the control group. The up-regulated PDAMs were predominantly associated with the biosynthesis of various secondary metabolites, including vanillin, myristic acid, and protocatechuic acid, suggesting potential inhibitory effects on plant pathogenic fungi. Our study underscores the ability of strain S. djakartensis MEPS155 to inhibit C. fimbriata growth through the production of secretory enzymes or secondary metabolites. The findings contribute to a theoretical foundation for future investigations into the role of MEPS155 in postharvest black rot prevention in sweet potato.
Topics: Ipomoea batatas; Streptomyces; Plant Diseases; Ascomycota; Rhizosphere; Soil Microbiology; Antifungal Agents; Multiomics
PubMed: 38839221
DOI: 10.1016/j.fm.2024.104557 -
The Plant Pathology Journal Jun 2024Soybean (Glycine max), a crucial global crop, experiences yearly yield reduction due to diseases such as anthracnose (Colletotrichum truncatum) and root rot (Fusarium...
Soybean (Glycine max), a crucial global crop, experiences yearly yield reduction due to diseases such as anthracnose (Colletotrichum truncatum) and root rot (Fusarium spp.). The use of fungicides, which have traditionally been employed to control these phytopathogens, is now facing challenges due to the emergence of fungicide-resistant strains. Streptomyces bacillaris S8 strain S8 is previously known to produce valinomycin t through a nonribosomal peptide synthetase (NRPS) pathway. The objective of this study was to evaluate the antifungal activity of S. bacillaris S8 against C. truncatum and Fusarium sp., assessing its efficacy against soybean pathogens. The results indicate that strain S8 effectively controlled both above-ground and underground soybean diseases, using the NRPS and NRPS-related compound, suggesting its potential as a biological control in plant-microbe interactions. These findings underscore the pivotal role of the stain S8 in fostering healthy soybean microbial communities and emphasize the significance of microbiota structure studies in unveiling potent biocontrol agents.
PubMed: 38835303
DOI: 10.5423/PPJ.NT.01.2024.0021 -
Biomolecules & Therapeutics Jul 2024genome includes 33 genes encoding monooxygenation-catalyzing cytochrome P450 enzymes. We investigated the structure of CYP107P2 and its interactions with terpenoid...
genome includes 33 genes encoding monooxygenation-catalyzing cytochrome P450 enzymes. We investigated the structure of CYP107P2 and its interactions with terpenoid compounds. The recombinant CYP107P2 protein was expressed in and the purified enzyme exhibited a typical P450 spectrum upon CO-binding in its reduced state. Type-I substrate-binding spectral titrations were observed with various terpenoid compounds, including α-pinene, β-pinene, α-terpinyl acetate, and (+)-3-carene. The calculated binding affinities () ranged from 15.9 to 50.8 μM. The X-ray crystal structure of CYP107P2 was determined at 1.99 Å resolution, with a well-conserved overall P450 folding conformation. The terpenoid compound docking models illustrated that the structural interaction between monoterpenes and CYP107P2, with the distance between heme and terpenes ranging from 3.4 to 5.4 Å, indicates potential substrate binding for P450 enzyme. This study suggests that CYP107P2 is a P450 enzyme capable of catalyzing terpenes as substrates, signifying noteworthy advancements in comprehending a novel P450 enzyme's involvement in terpene reactions.
PubMed: 38835149
DOI: 10.4062/biomolther.2024.045 -
Iranian Journal of Biotechnology Jan 2024Uricase or urate oxidase, as a therapeutic enzyme, is extensively applied to oxidize accumulated uric acid in the body to soluble form to treat related illnesses.
BACKGROUND
Uricase or urate oxidase, as a therapeutic enzyme, is extensively applied to oxidize accumulated uric acid in the body to soluble form to treat related illnesses.
OBJECTIVES
This study was conducted with the aim of searching for potential sources of uricase-producing from Eshtehard salt desert in Alborz province, Iran and heterologous expression, purification and functional assay of the enzyme.
MATERIALS AND METHODS
Main screening was conducted by cultivation of the strains on a medium enriched with 0.3 percent (w/v) uric acid. The uricase gene from the most potent strain was then recombinantly expressed in BL21 (DL3).
RESULTS
Out of the tested strains, only seven showed uricase activity. The highest level of native uricase activity (11.5735 U.mL) belonged to strain 17-1, which had the closest similarity to . A recombinant uricase with a molecular mass of approximately 38 kDa was produced. The purified uricase exhibited a specific activity of about 28.29±0.59 U.mg, which is among the highest level of uricase activity reported by other studies.
CONCLUSIONS
This enzyme is a promising candidate for further applicable investigations and large-scale production in terms of its large volume of soluble expression and selective competitive activity.
PubMed: 38827344
DOI: 10.30498/ijb.2024.379614.3602