Mining biosynthetic gene clusters in Paenibacillus genomes to discover novel antibiotics.

Background: Bacterial antimicrobial resistance poses a severe threat to humanity, necessitating the urgent development of new antibiotics. Recent advances in genome sequencing offer new avenues for antibiotic discovery. Paenibacillus genomes encompass a considerable array of antibiotic biosynthetic gene clusters (BGCs), rendering these species as good candidates for genome-driven novel antibiotic exploration.

Production of a major metabolite of niclosamide using bacterial cytochrome P450 enzymes.

Niclosamide has been proposed as a possible candidate for a Covid-19 drug. However, the metabolites of niclosamide are difficult to investigate because they are usually not available commercially or they are quite expensive in the commercial market. In this study, the major metabolite of niclosamide in human liver microsomes (HLMs) was confirmed to be 3-OH niclosamide.

Bacillus integrative plasmid system combining a synthetic gene circuit for efficient genetic modifications of undomesticated Bacillus strains.

Background: Owing to CRISPR-Cas9 and derivative technologies, genetic studies on microorganisms have dramatically increased. However, the CRISPR-Cas9 system is still difficult to utilize in many wild-type Bacillus strains owing to Cas9 toxicity. Moreover, less toxic systems, such as cytosine base editors, generate unwanted off-target mutations that can interfere with the genetic studies of wild-type strains.

Elicitation of Innate Immunity by a Bacterial Volatile 2-Nonanone at Levels below Detection Limit in Tomato Rhizosphere.

Bacterial volatile compounds (BVCs) exert beneficial effects on plant protection both directly and indirectly. Although BVCs have been detected in vitro, their detection in situ remains challenging. The purpose of this study was to investigate the possibility of BVCs detection under in situ condition and estimate the potentials of in situ BVC to plants at below detection limit.

Cell Factory Engineering of Undomesticated Strains Using a Modified Integrative and Conjugative Element for Efficient Plasmid Delivery.

A large number of strains have been isolated from various environments and many of them have great potential as cell factories. However, they have been rarely developed as cell factories due to their poor transformation efficiency. In this study, we developed a highly efficient plasmid delivery system for undomesticated strains using a modified integrative and conjugative element (MICE), which was designed to be activated by an inducer, prevent self-transfer, and deliver desired plasmids to the recipient cells.

Cytosine Base Editor-Mediated Multiplex Genome Editing to Accelerate Discovery of Novel Antibiotics in and .

Genome-based identification of new antibiotics is emerging as an alternative to traditional methods. However, uncovering hidden antibiotics under the background of known antibiotics remains a challenge. To over this problem using a quick and effective genetic approach, we developed a multiplex genome editing system using a cytosine base editor (CBE).

Regioselective Hydroxylation of Phloretin, a Bioactive Compound from Apples, by Human Cytochrome P450 Enzymes.

Phloretin, the major polyphenol compound in apples and apple products, is interesting because it shows beneficial effects on human health. It is mainly found as a form of glucoside, phlorizin. However, the metabolic pathway of phloretin in humans has not been reported.

Bacillus subtilis spore vaccines displaying protective antigen induce functional antibodies and protective potency.

Background: Bacillus anthracis is the causative agent of anthrax, a disease of both humans and various animal species, and can be used as a bioterror agent. Effective vaccines are available, but those could benefit from improvements, including increasing the immunity duration, reducing the shot frequency and adverse reactions. In addition, more sophisticated antigen delivery and potentiation systems are urgently required.

Programmed gRNA Removal System for CRISPR-Cas9-Mediated Multi-Round Genome Editing in .

CRISPR/Cas9 has become a simple and powerful genome editing tool for many organisms. However, multi-round genome editing should replace single-guide RNA (sgRNA) every round, which is laborious and time-consuming. Here, we have developed a multi-round genome editing system in which genome editing and the programmed removal of the sgRNA have sequentially occurred in a growth-dependent manner in .

Chronicle of a Soil Bacterium: E681 as a Tiny Guardian of Plant and Human Health.

The Gram-positive rhizosphere bacterium promotes plant growth and produces various antibiotics. Herein, we review research on this species over the past two and a half decades, and focus on the mechanisms of strain E681, isolated from barley roots in the South Korea in 1995. Strain E681 has outstanding growth-promoting effects on barley, cucumber, pepper, sesame, and and produces antimicrobial compounds that protect plants against pathogenic fungi, oomycetes, and bacteria.

Expansion of antibacterial spectrum of xanthorrhizol against Gram-negatives in combination with PMBN and food-grade antimicrobials.

Xanthorrhizol (XTZ), isolated from Curcuma xanthorrhiza, has potent antifungal and antibacterial activity. It shows very strong activity against Gram-positive bacteria, such as Streptococcus mutans and Staphylococcus aureus, but is generally not active against Gram-negative bacteria. In this study, we explored the possibility of using a combination strategy for expanding the antimicrobial spectrum of XTZ against Gram-negative bacteria.

Complete Genome Sequence of Bacillus subtilis Strain WB800N, an Extracellular Protease-Deficient Derivative of Strain 168.

Bacillus subtilis WB800N is a genetically engineered variant of B. subtilis 168, such that all extracellular proteases are disrupted, which enables WB800N to be widely used for the expression of secretory proteins. Here, we report the 4.

Genome Sequence of the Probiotic Strain Bacillus velezensis Variant polyfermenticus GF423.

The genome sequence of the commercial probiotic strain "Bacillus polyfermenticus" GF423 was determined. Comparison of the 4.1-Mb genome sequence revealed Bacillus velezensis FZB42 as its closest relative.

Scarless Genomic Point Mutation to Construct a Strain Displaying Increased Antibiotic Plipastatin Production.

strains produce various types of antibiotics, and random mutagenesis has traditionally been used to overproduce these natural metabolites. However, this method leads to the accumulation of unwanted mutations in the genome. Here, we rationally designed a single nucleotide substitution in the gene to generate a strain displaying increased plipastatin production in a foreign DNA-free manner.

Random knock-in expression system for high yield production of heterologous protein in Bacillus subtilis.

Chromosome-integrated recombinant protein expression in bacteria has advantages for the stable maintenance of genes without any use of antibiotics during large-scale fermentation. Even though different levels of gene expression were reported, depending upon their chromosomal position in bacterial species, only a limited number of integration sites have been used in B. subtilis.

A Highly Efficient CRISPR-Cas9-Mediated Large Genomic Deletion in .

In , large genomic deletions have been carried out for genome reduction, antibiotic overproduction, and heterologous protein overexpression. In view of the eco-friendliness of , it is critical that engineering preserves its food-grade status and avoids leaving foreign DNA in the genome. Existing methods of generating large genomic deletions leave antibiotic resistance markers or display low mutation efficiency.

Genome Sequences of Bacillus thuringiensis Serovar kurstaki Strain BP865 and B. thuringiensis Serovar aizawai Strain HD-133.

We report the draft genome sequences of two insecticidal strains against lepidopteran pests, Bacillus thuringiensis serovar kurstaki strain BP865, an isolate from the South Korean phylloplane, and strain HD-133, a reference strain of B. thuringiensis serovar aizawai.

Draft Genome Sequences of Four Plant Probiotic Bacillus Strains.

Here, we report the whole-genome sequences of four Bacillus strains that exhibit plant probiotic activities. Three of them are the type strains of Bacillus endophyticus, "Bacillus gaemokensis," and Bacillus trypoxylicola, and the other, Bacillus sp. strain KCTC 13219, should be reclassified into a species belonging to the genus Lysinibacillus.

Genome Sequence of Antibiotic-Producing Bacillus amyloliquefaciens Strain KCTC 13012.

We report the 4.0-Mb draft genome sequence of Bacillus amyloliquefaciens (syn. Bacillus velezensis) KCTC 13012, which exhibits a broad spectrum of antagonistic activity against bacteria and fungi and promotes plant growth as well.

Deciphering the conserved genetic loci implicated in plant disease control through comparative genomics of Bacillus amyloliquefaciens subsp. plantarum.

To understand the growth-promoting and disease-inhibiting activities of plant growth-promoting rhizobacteria (PGPR) strains, the genomes of 12 Bacillus subtilis group strains with PGPR activity were sequenced and analyzed. These B. subtilis strains exhibited high genomic diversity, whereas the genomes of B.

Biosynthesis of Polymyxins B, E, and P Using Genetically Engineered Polymyxin Synthetases in the Surrogate Host Bacillus subtilis.

The development of diverse polymyxin derivatives is needed to solve the toxicity and resistance problems of polymyxins. However, no platform has generated polymyxin derivatives by genetically engineering a polymyxin synthetase, which is a nonribosomal peptide synthetase. In this study, we present a two-step approach for the construction of engineered polymyxin synthetases by substituting the adenylation (A) domains of polymyxin A synthetase, which is encoded by the pmxABCDE gene cluster of Paenibacillus polymyxa E681.

Complete Genome Sequence of Bacillus subtilis Strain ATCC 6051a, a Potential Host for High-Level Secretion of Industrial Enzymes.

Bacillus subtilis ATCC 6051a (=KCTC 1028), which is less domesticated than strain 168, is widely used for the secretory expression of industrial enzymes. Herein, we present the complete genome sequence of the Bacillus subtilis strain ATCC 6051a.

Genome engineering using a synthetic gene circuit in Bacillus subtilis.

Genome engineering without leaving foreign DNA behind requires an efficient counter-selectable marker system. Here, we developed a genome engineering method in Bacillus subtilis using a synthetic gene circuit as a counter-selectable marker system. The system contained two repressible promoters (B.

Genome Sequence of the Plant Endophyte Bacillus pumilus INR7, Triggering Induced Systemic Resistance in Field Crops.

Bacillus pumilus INR7 is an endophytic bacterium that has been commercialized as a biological control product against soilborne pathogens as well as foliar pathogens by direct antagonism and induction of systemic resistance. In the current study, we provide the genome sequence and a possible explanation of the function of strain INR7.