Simple and Rapid Non-ribosomal Peptide Synthetase Gene Assembly Using the SEAM-OGAB Method

Combinatorial Nonribosomal Peptide Synthetase Libraries Using the SEAM-Combi-OGAB Method

To overcome the difficulty of building large nonribosomal peptide synthetase (NRPS) gene cluster libraries, an efficient one-pot method using Bacillus subtilis was developed. This new method, named Seamed Express Assembly Method (SEAM)-combi-Ordered Gene Assembly in Bacillus subtilis (OGAB), combines the SEAM-OGAB approach for NRPS gene cluster construction with the combi-OGAB method for combinatorial DNA library construction to randomly swap DNA fragments for NRPS modules. In this study, NRPS gene clusters of plipastatin and gramicidin S were used as the starting material. The full length of each gene cluster was prepared as plasmid DNA by introducing restriction enzyme SfiI sites into the module border according to SEAM-OGAB. These two plasmids were mixed, digested with SfiI, ligated in a tandem repeat form, and used to transform B. subtilis according to the combi-OGAB method. While 64 of all the possible combinations were used in the calculation, 32 types of plasmid DNA were obtained from 50 randomly selected transformants. These transformants produced at least 30 types of peptides, including cyclic and linear variations with lengths ranging from 5 to 10 amino acids. Thus, this method enabled an efficient construction of NRPS gene cluster libraries with more than five module members, making it advantageous for applications in peptide libraries.

In Vivo Quantification of Surfactin Nonribosomal Peptide Synthetase Complexes in Bacillus subtilis

Surfactin, a potent biosurfactant produced by Bacillus subtilis, is synthesized using a non-ribosomal peptide synthetase (NRPS) encoded by the srfAA-AD operon. Despite its association with quorum sensing via the ComX pheromone, the dynamic behavior and in vivo quantification of the NRPS complex remain underexplored. This study established an in vivo quantification system using fluorescence labeling to monitor the availability of surfactin-forming NRPS subunits (SrfAA, SrfAB, SrfAC, and SrfAD) during bioprocesses. Four Bacillus subtilis sensor strains were constructed by fusing these subunits with the megfp gene, resulting in strains BMV25, BMV26, BMV27, and BMV28. These strains displayed growth and surfactin productivity similar to those of the parental strain, BMV9. Fluorescence signals indicated varying NRPS availability, with BMV27 showing the highest and BMV25 showing the lowest relative fluorescence units (RFUs). RFUs were converted to the relative number of NRPS molecules using open-source FPCountR package. During bioprocesses, NRPS availability peaked at the end of the exponential growth phase and declined in the stationary phase, suggesting reduced NRPS productivity under nutrient-limited conditions and potential post-translational regulation. This study provides a quantitative framework for monitoring NRPS dynamics in vivo, offering insights into optimizing surfactin production. The established sensor strains and quantification system enable the real-time monitoring of NRPS availability, aiding bioprocess optimization for industrial applications of surfactin and potentially other non-ribosomal peptides.

A simple and cost-effective transformation system for Porphyromonas gingivalis via natural competence

Porphyromonas gingivalis is a major oral bacterial pathogen responsible for severe periodontal diseases. Numerous studies have used genetic approaches to elucidate the molecular mechanisms underlying its pathogenicity. Typically, electroporation and conjugation are utilized for mutagenesis of P. gingivalis; however, these techniques require specialized equipment such as high-voltage electroporators, conjugative plasmids and donor strains. In this study, we present a simple, cost-effective transformation method for P. gingivalis without any special equipment by exploiting its natural DNA competence. P. gingivalis ATCC 33277 was grown to the early-exponential phase and mixed with a donor DNA cassette. This mixture was then spotted onto a BHI-HM blood-agar plate and incubated for one day to promote colony biofilm formation. The resulting colony biofilm was suspended in a liquid medium and spread onto antibiotic-containing agar plates. Transformants appeared within 4 to 5 days, achieving a maximum efficiency of 7.7 × 106 CFU/μg. Although we optimized the transformation conditions using a representative strain ATCC 33277, but the method was also effective for other P. gingivalis strains, W83 and TDC60. Additionally, we discovered that deletion of PGN_0421 or PGN_0519, encoding putative ComEA and ComEC, abolished competency, indicating that these gene products are essential for the natural competence.

Bacillus subtilis as a host for natural product discovery and engineering of biosynthetic gene clusters

Covering: up to October 2023Many bioactive natural products are synthesized by microorganisms that are either difficult or impossible to cultivate under laboratory conditions, or that produce only small amounts of the desired compound. By transferring biosynthetic gene clusters (BGCs) into alternative host organisms that are more easily cultured and engineered, larger quantities can be obtained and new analogues with potentially improved biological activity or other desirable properties can be generated. Moreover, expression of cryptic BGCs in a suitable host can facilitate the identification and characterization of novel natural products. Heterologous expression therefore represents a valuable tool for natural product discovery and engineering as it allows the study and manipulation of their biosynthetic pathways in a controlled setting, enabling innovative applications. Bacillus is a genus of Gram-positive bacteria that is widely used in industrial biotechnology as a host for the production of proteins from diverse origins, including enzymes and vaccines. However, despite numerous successful examples, Bacillus species remain underexploited as heterologous hosts for the expression of natural product BGCs. Here, we review important advantages that Bacillus species offer as expression hosts, such as high secretion capacity, natural competence for DNA uptake, and the increasing availability of a wide range of genetic tools for gene expression and strain engineering. We evaluate different strain optimization strategies and other critical factors that have improved the success and efficiency of heterologous natural product biosynthesis in B. subtilis. Finally, future perspectives for using B. subtilis as a heterologous host are discussed, identifying research gaps and promising areas that require further exploration.

An Engineered Microbial Consortium Provides Precursors for Fengycin Production by Bacillus subtilis

Fengycin has great potential for applications in biological control because of its biosafety and degradability. In this study, the addition of exogenous precursors increased fengycin production by Bacillus subtilis. Corynebacterium glutamicum was engineered to produce high levels of precursors (Thr, Pro, Val, and Ile) to promote the biosynthesis of fengycin. Furthermore, recombinant C. glutamicum and Yarrowia lipolytica providing amino acid and fatty acid precursors were co-cultured to improve fengycin production by B. subtilis in a three-strain artificial consortium, in which fengycin production was 2100 mg·L-1. In addition, fengycin production by the consortium in a 5 L bioreactor reached 3290 mg·L-1. Fengycin had a significant antifungal effect on Rhizoctonia solani, which illustrates its potential as a food preservative. Taken together, this work provides a new strategy for improving fengycin production by a microbial consortium and metabolic engineering.