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Zhou J, Wu G, Zheng J, Abdalmegeed D, Wang M, Sun S, Sedjoah RCAA, Shao Y, Sun S, Xin Z. Research on the Regulation of Plipastatin Production by the Quorum-Sensing ComQXPA System of Bacillus amyloliquefaciens. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023. [PMID: 37427858 DOI: 10.1021/acs.jafc.3c03120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/11/2023]
Abstract
Plipastatin is a cyclic lipopeptide synthesized by non-ribosomal peptide synthetases (NRPS), which has a diverse range of applications in postharvest preservation of fruits and vegetables, biological control, and feed processing. Whereas the yield of plipastatin in wild Bacillus sp. is low, its chemical structure is complex and challenging to synthesize, significantly limiting its production and application. ComQXPA-PsrfA, a quorum-sensing (QS) circuit from Bacillus amyloliquefaciens, was constructed in this study. Two QS promoters MuPsrfA and MtPsrfA, with 35 and 100% increased activity, respectively, were obtained by mutating the original promoter PsrfA. Thus, the natural promoter of plipastatin was replaced by a QS promoter to achieve the dynamic regulation of plipastatin, which increased the yield of plipastatin by 3.5 times. Integrating ComQXPA into plipastatin mono-producing M-24:MtPsrfA increased the yield of plipastatin to 3850 mg/L, representing the highest yield reported to date. Four new plipastatins were identified via UPLC-ESI-MS/MS and GC-MS analysis of fermentation products of mono-producing engineered strains. Among them, three plipastatins contained two double bonds in the fatty acid side chain, representing the first example of a new type of plipastatin. Our results indicate that the QS system ComQXPA-PsrfA of Bacillus can dynamically regulate plipastatin production, and the pipeline could be extended to the other strains to regulate target products dynamically.
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Affiliation(s)
- Jingjie Zhou
- Key Laboratory of Food Processing and Quality Control, College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, P. R. China
| | - Guojun Wu
- Key Laboratory of Food Processing and Quality Control, College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, P. R. China
| | - Jie Zheng
- Key Laboratory of Food Processing and Quality Control, College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, P. R. China
| | - Dyaaaldin Abdalmegeed
- Key Laboratory of Food Processing and Quality Control, College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, P. R. China
| | - Mengxi Wang
- Key Laboratory of Food Processing and Quality Control, College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, P. R. China
| | - Shengwei Sun
- Key Laboratory of Food Processing and Quality Control, College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, P. R. China
| | - Rita-Cindy Aye-Ayire Sedjoah
- Key Laboratory of Food Processing and Quality Control, College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, P. R. China
| | - Yuting Shao
- Key Laboratory of Food Processing and Quality Control, College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, P. R. China
| | - Sen Sun
- Key Laboratory of Food Processing and Quality Control, College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, P. R. China
| | - Zhihong Xin
- Key Laboratory of Food Processing and Quality Control, College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, P. R. China
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2
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Zhang P, Lv Z, Lu Z, Ma W, Bie X. Effects of the deletion and substitution of thioesterase on bacillomycin D synthesis. Biotechnol Lett 2023:10.1007/s10529-023-03373-z. [PMID: 37266877 DOI: 10.1007/s10529-023-03373-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2022] [Revised: 03/04/2023] [Accepted: 03/31/2023] [Indexed: 06/03/2023]
Abstract
OBJECTIVES The importance of thioesterase domains on bacillomycin D synthesis and the ability of different thioesterase domains to selectively recognize and catalyze peptide chain hydrolysis and cyclization were studied by deleting and substituting thioesterase domains. RESULTS No bacillomycin D analogs were found in the thioesterase-deleted strain fmbJ-ΔTE, indicating that the TE domain was essential for bacillomycin D synthesis. Then the thioesterase in bacillomycin D synthetases was replaced by the thioesterase in bacillomycin F, iturin A, mycosubtilin, plipastatin and surfactin synthetases. Except for fmbJ-S-TE, all others were able to synthesize bacillomycin D homologs because a suitable recombination site was selected, which maintained the integrity of NRPSs. In particular, the yield of bacillomycin D in fmbJ-IA-TE, fmbJ-M-TE and fmbJ-P-TE was significantly increased. CONCLUSION This study expands our understanding of the TE domain in bacillomycin D synthetases and shows that thioesterase has excellent potential in the chemical-enzymatic synthesis of natural products or their analogs.
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Affiliation(s)
- Ping Zhang
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China
| | - Ziyan Lv
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China
| | - Zhaoxin Lu
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China
| | - Wenjie Ma
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China
| | - Xiaomei Bie
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China.
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3
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Wu G, Zhou J, Zheng J, Abdalmegeed D, Tian J, Wang M, Sun S, Sedjoah RCAA, Shao Y, Sun S, Xin Z. Construction of lipopeptide mono-producing Bacillus strains and comparison of their antimicrobial activity. FOOD BIOSCI 2023; 53:102813. [DOI: 10.1016/j.fbio.2023.102813] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/15/2024]
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4
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Danaeifar M, Mazlomi MA. Combinatorial biosynthesis: playing chess with the metabolism. JOURNAL OF ASIAN NATURAL PRODUCTS RESEARCH 2023; 25:171-190. [PMID: 35435779 DOI: 10.1080/10286020.2022.2065265] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2022] [Accepted: 04/07/2022] [Indexed: 06/14/2023]
Abstract
Secondary metabolites are a group of natural products that produced by bacteria, fungi and plants. Many applications of these compounds from medicine to industry have been discovered. However, some changes in their structure and biosynthesis mechanism are necessary for their properties to be more suitable and also for their production to be profitable. The main and most useful method to achieve this goal is combinatorial biosynthesis. This technique uses the multi-unit essence of the secondary metabolites biosynthetic enzymes to make changes in their order, structure and also the organism that produces them.
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Affiliation(s)
- Mohsen Danaeifar
- Department of Medical Biotechnology, School of Advanced Technologies in Medicine, Tehran University of Medical Sciences, Tehran 1416753955, Iran
| | - Mohammad Ali Mazlomi
- Department of Medical Biotechnology, School of Advanced Technologies in Medicine, Tehran University of Medical Sciences, Tehran 1416753955, Iran
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5
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Jagadeesh V, Yoshida T, Uraji M, Okahashi N, Matsuda F, Vavricka CJ, Tsuge K, Kondo A. Simple and Rapid Non-ribosomal Peptide Synthetase Gene Assembly Using the SEAM-OGAB Method. ACS Synth Biol 2023; 12:305-318. [PMID: 36563322 DOI: 10.1021/acssynbio.2c00565] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Recombination of biosynthetic gene clusters including those of non-ribosomal peptide synthetases (NRPSs) is essential for understanding the mechanisms of biosynthesis. Due to relatively huge gene cluster sizes ranging from 10 to 150 kb, the prevalence of sequence repeats, and inability to clearly define optimal points for manipulation, functional characterization of recombinant NRPSs with maintained activity has been hindered. In this study, we introduce a simple yet rapid approach named "Seamed Express Assembly Method (SEAM)" coupled with Ordered Gene Assembly in Bacillus subtilis (OGAB) to reconstruct fully functional plipastatin NRPS. This approach is enabled by the introduction of restriction enzyme sites as seams at module borders. SEAM-OGAB is then first demonstrated by constructing the ppsABCDE NRPS (38.4 kb) to produce plipastatin, a cyclic decapeptide in B. subtilis. The introduced amino acid level seams do not hinder the NRPS function and enable successful production of plipastatin at a commensurable titer. It is challenging to modify the plipastatin NRPS gene cluster due to the presence of three long direct-repeat sequences; therefore, this study demonstrates that SEAM-OGAB can be readily applied towards the recombination of various NRPSs. Compared to previous NRPS gene assembly methods, the advantage of SEAM-OGAB is that it readily enables the shuffling of NRPS gene modules, and therefore, chimeric NRPSs can be rapidly constructed for the production of novel peptides. This chimeric assembly application of SEAM-OGAB is demonstrated by swapping plipastatin NRPS and surfactin NRPS modules to produce two novel lipopeptides in B. subtilis.
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Affiliation(s)
- Varada Jagadeesh
- Graduate School of Science, Technology, and Innovation, Kobe University, 1-1, Rokkodai-cho, Nada-ku, Kobe 657-8501, Japan
| | - Takanobu Yoshida
- Graduate School of Science, Technology, and Innovation, Kobe University, 1-1, Rokkodai-cho, Nada-ku, Kobe 657-8501, Japan
| | - Misugi Uraji
- Graduate School of Science, Technology, and Innovation, Kobe University, 1-1, Rokkodai-cho, Nada-ku, Kobe 657-8501, Japan
| | - Nobuyuki Okahashi
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, 1-5 Yamadaoka, Suita 565-0871, Japan.,Department of Biotechnology, Osaka University Shimadzu Analytical Innovation Research Laboratory, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita 565-0871, Japan
| | - Fumio Matsuda
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, 1-5 Yamadaoka, Suita 565-0871, Japan.,Department of Biotechnology, Osaka University Shimadzu Analytical Innovation Research Laboratory, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita 565-0871, Japan
| | - Christopher J Vavricka
- Department of Biotechnology and Life Science, Graduate School of Engineering, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan
| | - Kenji Tsuge
- Graduate School of Science, Technology, and Innovation, Kobe University, 1-1, Rokkodai-cho, Nada-ku, Kobe 657-8501, Japan
| | - Akihiko Kondo
- Graduate School of Science, Technology, and Innovation, Kobe University, 1-1, Rokkodai-cho, Nada-ku, Kobe 657-8501, Japan
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6
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Translocation of subunit PPSE in plipastatin synthase and synthesis of novel lipopeptides. Synth Syst Biotechnol 2022; 7:1173-1180. [PMID: 36204332 PMCID: PMC9519435 DOI: 10.1016/j.synbio.2022.09.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Revised: 08/01/2022] [Accepted: 09/07/2022] [Indexed: 11/20/2022] Open
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7
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Addressing artifacts of colorimetric anticancer assays for plant-based drug development. MEDICAL ONCOLOGY (NORTHWOOD, LONDON, ENGLAND) 2022; 39:198. [PMID: 36071299 DOI: 10.1007/s12032-022-01791-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2022] [Accepted: 07/06/2022] [Indexed: 10/14/2022]
Abstract
Cancer has become the silent killer in less-developed countries and the most significant cause of morbidity worldwide. The accessible and frequently used treatments include surgery, radiotherapy, chemotherapy, and immunotherapy. Chemotherapeutic drugs traditionally involve using plant-based medications either in the form of isolated compounds or as scaffolds for synthetic drugs. To launch a drug in the market, it has to pass through several intricate steps. The multidrug resistance in cancers calls for novel drug discovery and development. Every year anticancer potential of several plant-based compounds and extracts is reported but only a few advances to clinical trials. The false-positive or negative results impact the progress of the cell-based anticancer assays. There are several cell-based assays but the widely used include MTT, MTS, and XTT. In this article, we have discussed various pitfalls and workable solutions.
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Han P, Chen Z, Liu Y, Ma A, Li S, Jia Y. Structural Organization of Brevilaterin Biosynthesis in Brevibacillus laterosporus S62-9: A Novel MbtH-Independent Cationic Antimicrobial Peptide Synthetase System. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:7471-7478. [PMID: 35675382 DOI: 10.1021/acs.jafc.2c01143] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Cationic antimicrobial peptides, produced by nonribosomal peptide synthetases (NRPSs), have received great attention in different applications, including as biocontrol and antimicrobial agents against foodborne pathogenic bacteria. Also, Brevibacillus spp. is a competent microorganism to produce cationic antimicrobial peptides yet has received little attention. Herein, Brevibacillus laterosporus S62-9 genome mining revealed an integrated cationic antimicrobial peptide synthetase system that synthesized brevilaterin. Combining biochemical analysis with bioinformatics elucidated that the A domain from this system was the MbtH-independent enzyme and showed activity against the same amino acid in the structure of brevilaterin. Moreover, the creations of the first three and position 12 residues in the sequence were targeted to bre261, bre270, bre2691A, and bre2662, respectively. Further analysis of the specificity-conferring code of the A domain suggested that a tiny difference would make the activity of the A domain very diverse and the range of substrate selection would be enlarged or narrowed by changing some residues in the code. The dissection of this biosynthesis mechanism would contribute to the successful realization of reasonable artificial design and the modification of bioactive peptides, and this capable organism also would be more fully utilized.
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Affiliation(s)
- Panpan Han
- School of Food and Health, Beijing Technology and Business University, No.33 Fucheng Road, Haidian District, Beijing 100048, China
| | - Zhou Chen
- School of Food and Health, Beijing Technology and Business University, No.33 Fucheng Road, Haidian District, Beijing 100048, China
| | - Yangliu Liu
- School of Food and Health, Beijing Technology and Business University, No.33 Fucheng Road, Haidian District, Beijing 100048, China
| | - Aijin Ma
- School of Food and Health, Beijing Technology and Business University, No.33 Fucheng Road, Haidian District, Beijing 100048, China
| | - Siting Li
- School of Food and Health, Beijing Technology and Business University, No.33 Fucheng Road, Haidian District, Beijing 100048, China
| | - Yingmin Jia
- School of Food and Health, Beijing Technology and Business University, No.33 Fucheng Road, Haidian District, Beijing 100048, China
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9
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Abati E, Manini A, Comi GP, Corti S. Inhibition of myostatin and related signaling pathways for the treatment of muscle atrophy in motor neuron diseases. Cell Mol Life Sci 2022; 79:374. [PMID: 35727341 PMCID: PMC9213329 DOI: 10.1007/s00018-022-04408-w] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 05/16/2022] [Accepted: 06/01/2022] [Indexed: 11/26/2022]
Abstract
Myostatin is a negative regulator of skeletal muscle growth secreted by skeletal myocytes. In the past years, myostatin inhibition sparked interest among the scientific community for its potential to enhance muscle growth and to reduce, or even prevent, muscle atrophy. These characteristics make it a promising target for the treatment of muscle atrophy in motor neuron diseases, namely, amyotrophic lateral sclerosis (ALS) and spinal muscular atrophy (SMA), which are rare neurological diseases, whereby the degeneration of motor neurons leads to progressive muscle loss and paralysis. These diseases carry a huge burden of morbidity and mortality but, despite this unfavorable scenario, several therapeutic advancements have been made in the past years. Indeed, a number of different curative therapies for SMA have been approved, leading to a revolution in the life expectancy and outcomes of SMA patients. Similarly, tofersen, an antisense oligonucleotide, is now undergoing clinical trial phase for use in ALS patients carrying the SOD1 mutation. However, these therapies are not able to completely halt or reverse progression of muscle damage. Recently, a trial evaluating apitegromab, a myostatin inhibitor, in SMA patients was started, following positive results from preclinical studies. In this context, myostatin inhibition could represent a useful strategy to tackle motor symptoms in these patients. The aim of this review is to describe the myostatin pathway and its role in motor neuron diseases, and to summarize and critically discuss preclinical and clinical studies of myostatin inhibitors in SMA and ALS. Then, we will highlight promises and pitfalls related to the use of myostatin inhibitors in the human setting, to aid the scientific community in the development of future clinical trials.
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Affiliation(s)
- Elena Abati
- Department of Pathophysiology and Transplantation (DEPT), Dino Ferrari Centre, Neuroscience Section, Neurology Unit, Fondazione IRCCS Ca' Granda-Ospedale Maggiore Policlinico, University of Milan, Milan, Italy
- Neurology Unit, Department of Neuroscience, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Arianna Manini
- Department of Pathophysiology and Transplantation (DEPT), Dino Ferrari Centre, Neuroscience Section, Neurology Unit, Fondazione IRCCS Ca' Granda-Ospedale Maggiore Policlinico, University of Milan, Milan, Italy
| | - Giacomo Pietro Comi
- Department of Pathophysiology and Transplantation (DEPT), Dino Ferrari Centre, Neuroscience Section, Neurology Unit, Fondazione IRCCS Ca' Granda-Ospedale Maggiore Policlinico, University of Milan, Milan, Italy
- Neurology Unit, Department of Neuroscience, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
- Neuromuscular and Rare Diseases Unit, Department of Neuroscience, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Stefania Corti
- Department of Pathophysiology and Transplantation (DEPT), Dino Ferrari Centre, Neuroscience Section, Neurology Unit, Fondazione IRCCS Ca' Granda-Ospedale Maggiore Policlinico, University of Milan, Milan, Italy.
- Neurology Unit, Department of Neuroscience, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy.
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10
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Ku JT, Chen AY, Lan EI. Metabolic engineering of Escherichia coli for efficient biosynthesis of butyl acetate. Microb Cell Fact 2022; 21:28. [PMID: 35193559 PMCID: PMC8864926 DOI: 10.1186/s12934-022-01755-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Accepted: 02/07/2022] [Indexed: 11/30/2022] Open
Abstract
Background Butyl acetate is a versatile compound that is widely used in the chemical and food industry. The conventional butyl acetate synthesis via Fischer esterification of butanol and acetic acid using catalytic strong acids under high temperature is not environmentally benign. Alternative lipase-catalyzed ester formation requires a significant amount of organic solvent which also presents another environmental challenge. Therefore, a microbial cell factory capable of producing butyl acetate through fermentation of renewable resources would provide a greener approach to butyl acetate production. Result Here, we developed a metabolically engineered strain of Escherichia coli that efficiently converts glucose to butyl acetate. A modified Clostridium CoA-dependent butanol production pathway was used to synthesize butanol which was then condensed with acetyl-CoA through an alcohol acetyltransferase. Optimization of alcohol acetyltransferase expression and redox balance with auto-inducible fermentative controlled gene expression led to an effective titer of 22.8 ± 1.8 g/L butyl acetate produced in a bench-top bioreactor. Conclusion Building on the well-developed Clostridium CoA-dependent butanol biosynthetic pathway, expression of an alcohol acetyltransferase converts the butanol produced into butyl acetate. The results from this study provided a strain of E. coli capable of directly producing butyl acetate from renewable resources at ambient conditions. Supplementary Information The online version contains supplementary material available at 10.1186/s12934-022-01755-y.
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Affiliation(s)
- Jason T Ku
- Institute of Molecular Medicine and Bioengineering, National Chiao Tung University, 1001 Daxue Road, Hsinchu City, 300, Taiwan.,Institute of Molecular Medicine and Bioengineering, National Yang Ming Chiao Tung University, 1001 Daxue Road, Hsinchu City, 300, Taiwan
| | - Arvin Y Chen
- Institute of Molecular Medicine and Bioengineering, National Chiao Tung University, 1001 Daxue Road, Hsinchu City, 300, Taiwan.,Institute of Molecular Medicine and Bioengineering, National Yang Ming Chiao Tung University, 1001 Daxue Road, Hsinchu City, 300, Taiwan
| | - Ethan I Lan
- Department of Biological Science and Technology, National Chiao Tung University, 1001 Daxue Road, Hsinchu City, 300, Taiwan. .,Department of Biological Science and Technology, National Yang Ming Chiao Tung University, 1001 Daxue Road, Hsinchu City, 300, Taiwan.
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11
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Microbial Lipopeptide-Producing Strains and Their Metabolic Roles under Anaerobic Conditions. Microorganisms 2021; 9:microorganisms9102030. [PMID: 34683351 PMCID: PMC8540375 DOI: 10.3390/microorganisms9102030] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Revised: 09/09/2021] [Accepted: 09/10/2021] [Indexed: 01/17/2023] Open
Abstract
The lipopeptide produced by microorganisms is one of the representative biosurfactants and is characterized as a series of structural analogues of different families. Thirty-four families covering about 300 lipopeptide compounds have been reported in the last decades, and most of the reported lipopeptides produced by microorganisms were under aerobic conditions. The lipopeptide-producing strains under anaerobic conditions have attracted much attention from both the academic and industrial communities, due to the needs and the challenge of their applications in anaerobic environments, such as in oil reservoirs and in microbial enhanced oil recovery (MEOR). In this review, the fifty-eight reported bacterial strains, mostly isolated from oil reservoirs and dominated by the species Bacillus subtilis, producing lipopeptide biosurfactants, and the species Pseudomonas aeruginosa, producing glycolipid biosurfactants under anaerobic conditions were summarized. The metabolic pathway and the non-ribosomal peptide synthetases (NRPSs) of the strain Bacillus subtilis under anaerobic conditions were analyzed, which is expected to better understand the key mechanisms of the growth and production of lipopeptide biosurfactants of such kind of bacteria under anaerobic conditions, and to expand the industrial application of anaerobic biosurfactant-producing bacteria.
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12
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Kim M, Bae M, Jung Y, Kim JM, Hwang S, Song MC, Ban YH, Bae ES, Hong S, Lee SK, Cha S, Oh D, Yoon YJ. Unprecedented Noncanonical Features of the Nonlinear Nonribosomal Peptide Synthetase Assembly Line for WS9326A Biosynthesis. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202103872] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Myoun‐Su Kim
- Natural Products Research Institute College of Pharmacy Seoul National University 1 Gwanak-ro, Gwanak-gu Seoul 08826 Republic of Korea
| | - Munhyung Bae
- Natural Products Research Institute College of Pharmacy Seoul National University 1 Gwanak-ro, Gwanak-gu Seoul 08826 Republic of Korea
| | - Ye‐Eun Jung
- Department of Chemistry and Nanoscience Ewha Womans University 52 Ewhayeodae-gil, Seodaemun-gu Seoul 03760 Republic of Korea
| | - Jung Min Kim
- Natural Products Research Institute College of Pharmacy Seoul National University 1 Gwanak-ro, Gwanak-gu Seoul 08826 Republic of Korea
| | - Sunghoon Hwang
- Natural Products Research Institute College of Pharmacy Seoul National University 1 Gwanak-ro, Gwanak-gu Seoul 08826 Republic of Korea
| | - Myoung Chong Song
- Natural Products Research Institute College of Pharmacy Seoul National University 1 Gwanak-ro, Gwanak-gu Seoul 08826 Republic of Korea
| | - Yeon Hee Ban
- Natural Products Research Institute College of Pharmacy Seoul National University 1 Gwanak-ro, Gwanak-gu Seoul 08826 Republic of Korea
| | - Eun Seo Bae
- Natural Products Research Institute College of Pharmacy Seoul National University 1 Gwanak-ro, Gwanak-gu Seoul 08826 Republic of Korea
| | - Suckchang Hong
- Research Institute of Pharmaceutical Sciences College of Pharmacy Seoul National University 1 Gwanak-ro, Gwanak-gu Seoul 08826 Republic of Korea
| | - Sang Kook Lee
- Natural Products Research Institute College of Pharmacy Seoul National University 1 Gwanak-ro, Gwanak-gu Seoul 08826 Republic of Korea
| | - Sun‐Shin Cha
- Department of Chemistry and Nanoscience Ewha Womans University 52 Ewhayeodae-gil, Seodaemun-gu Seoul 03760 Republic of Korea
| | - Dong‐Chan Oh
- Natural Products Research Institute College of Pharmacy Seoul National University 1 Gwanak-ro, Gwanak-gu Seoul 08826 Republic of Korea
| | - Yeo Joon Yoon
- Natural Products Research Institute College of Pharmacy Seoul National University 1 Gwanak-ro, Gwanak-gu Seoul 08826 Republic of Korea
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13
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Kim M, Bae M, Jung Y, Kim JM, Hwang S, Song MC, Ban YH, Bae ES, Hong S, Lee SK, Cha S, Oh D, Yoon YJ. Unprecedented Noncanonical Features of the Nonlinear Nonribosomal Peptide Synthetase Assembly Line for WS9326A Biosynthesis. Angew Chem Int Ed Engl 2021; 60:19766-19773. [DOI: 10.1002/anie.202103872] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Revised: 05/04/2021] [Indexed: 12/21/2022]
Affiliation(s)
- Myoun‐Su Kim
- Natural Products Research Institute College of Pharmacy Seoul National University 1 Gwanak-ro, Gwanak-gu Seoul 08826 Republic of Korea
| | - Munhyung Bae
- Natural Products Research Institute College of Pharmacy Seoul National University 1 Gwanak-ro, Gwanak-gu Seoul 08826 Republic of Korea
| | - Ye‐Eun Jung
- Department of Chemistry and Nanoscience Ewha Womans University 52 Ewhayeodae-gil, Seodaemun-gu Seoul 03760 Republic of Korea
| | - Jung Min Kim
- Natural Products Research Institute College of Pharmacy Seoul National University 1 Gwanak-ro, Gwanak-gu Seoul 08826 Republic of Korea
| | - Sunghoon Hwang
- Natural Products Research Institute College of Pharmacy Seoul National University 1 Gwanak-ro, Gwanak-gu Seoul 08826 Republic of Korea
| | - Myoung Chong Song
- Natural Products Research Institute College of Pharmacy Seoul National University 1 Gwanak-ro, Gwanak-gu Seoul 08826 Republic of Korea
| | - Yeon Hee Ban
- Natural Products Research Institute College of Pharmacy Seoul National University 1 Gwanak-ro, Gwanak-gu Seoul 08826 Republic of Korea
| | - Eun Seo Bae
- Natural Products Research Institute College of Pharmacy Seoul National University 1 Gwanak-ro, Gwanak-gu Seoul 08826 Republic of Korea
| | - Suckchang Hong
- Research Institute of Pharmaceutical Sciences College of Pharmacy Seoul National University 1 Gwanak-ro, Gwanak-gu Seoul 08826 Republic of Korea
| | - Sang Kook Lee
- Natural Products Research Institute College of Pharmacy Seoul National University 1 Gwanak-ro, Gwanak-gu Seoul 08826 Republic of Korea
| | - Sun‐Shin Cha
- Department of Chemistry and Nanoscience Ewha Womans University 52 Ewhayeodae-gil, Seodaemun-gu Seoul 03760 Republic of Korea
| | - Dong‐Chan Oh
- Natural Products Research Institute College of Pharmacy Seoul National University 1 Gwanak-ro, Gwanak-gu Seoul 08826 Republic of Korea
| | - Yeo Joon Yoon
- Natural Products Research Institute College of Pharmacy Seoul National University 1 Gwanak-ro, Gwanak-gu Seoul 08826 Republic of Korea
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Production of Diverse Beauveriolide Analogs in Closely Related Fungi: a Rare Case of Fungal Chemodiversity. mSphere 2020; 5:5/5/e00667-20. [PMID: 32878933 PMCID: PMC7471007 DOI: 10.1128/msphere.00667-20] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
Fungal chemodiversity is well known in part due to the production of diverse analogous compounds by a single biosynthetic gene cluster (BGC). Usually, similar or the same metabolites are produced by closely related fungal species under a given condition, the foundation of fungal chemotaxonomy. Here, we report a rare case of the production of the cyclodepsipeptide beauveriolides (BVDs) in three insect-pathogenic fungi. We found that the more closely related fungi Beauveria bassiana and Beauveria brongniartii produced structurally distinct analogs of BVDs, whereas the less-close relatives B. brongniartii and Cordyceps militaris biosynthesized structurally similar congeners under the same growth condition. It was verified that a conserved BGC containing four genes is responsible for BVD biosynthesis in three fungi, including a polyketide synthase (PKS) for the production of 3-hydroxy fatty acids (FAs) with chain length variations. In contrast to BVD production patterns, phylogenetic analysis of the BGC enzymes or enzyme domains largely resulted in the congruence relationship with fungal speciation. Feeding assays demonstrated that an FA with a chain length of eight carbon atoms was preferentially utilized, whereas an FA with a chain longer than 10 carbon atoms could not be used as a substrate for BVD biosynthesis. Insect survival assays suggested that the contribution of BVDs to fungal virulence might be associated with the susceptibility of insect species. The results of this study enrich the knowledge of fungal secondary metabolic diversity that can question the reliability of fungal chemotaxonomy.IMPORTANCE Fungal chemotaxonomy is an approach to classify fungi based on the fungal production profile of metabolites, especially the secondary metabolites. We found an atypical example that could question the reliability of fungal chemical classifications in this study, i.e., the more closely related entomopathogenic species Beauveria bassiana and Beauveria brongniartii produced structurally different congeners of the cyclodepsipeptide beauveriolides, whereas the rather divergent species B. brongniartii and Cordyceps militaris biosynthesized similar analogs under the same growth condition. The conserved biosynthetic gene cluster (BGC) containing four genes present in each species is responsible for beauveriolide production. In contrast to the compound formation profiles, the phylogenies of biosynthetic enzymes or enzymatic domains show associations with fungal speciation. Dependent on the insect species, production of beauveriolides may contribute to fungal virulence against the susceptible insect hosts. The findings in this study augment the diversity of fungal secondary metabolisms.
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Key elements and regulation strategies of NRPSs for biosynthesis of lipopeptides by Bacillus. Appl Microbiol Biotechnol 2020; 104:8077-8087. [DOI: 10.1007/s00253-020-10801-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Revised: 04/08/2020] [Accepted: 07/27/2020] [Indexed: 10/23/2022]
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Penha RO, Vandenberghe LPS, Faulds C, Soccol VT, Soccol CR. Bacillus lipopeptides as powerful pest control agents for a more sustainable and healthy agriculture: recent studies and innovations. PLANTA 2020; 251:70. [PMID: 32086615 DOI: 10.1007/s00425-020-03357-7] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Accepted: 02/05/2020] [Indexed: 05/27/2023]
Abstract
Lipopeptides could help to overcome a large concern in agriculture: resistance against chemical pesticides. These molecules have activity against various phytopathogens and a potential to be transformed by genetic engineering. The exponential rise of pest resistances to different chemical pesticides and the global appeal of consumers for a sustainable agriculture and healthy nutrition have led to the search of new solutions for pest control. Furthermore, new laws require a different stance of producers. Based on that, bacteria of the genus Bacillus present a great agricultural potential, producing lipopeptides (LPs) that have high activity against insects, mites, nematodes, and/or phytopathogens that are harmful to plant cultures. Biopesticide activity can be found mainly in three families of Bacillus lipopeptides: surfactin, iturin, and fengycin. These molecules have an amphiphilic nature, interfering with biological membrane structures. Their antimicrobial properties include activity against bacteria, fungi, oomycetes, and viruses. Recent studies also highlight the ability of these compounds to stimulate defense mechanisms of plants and biofilm formation, which is a key factor for the successful colonization of biocontrol organisms. The use of molecular biology has also recently been researched for continuous advances and discoveries of new LPs, avoiding possible future problems of resistance against these molecules. As a consequence of the properties and possibilities of LPs, numerous studies and developments as well as the attention of large companies in the field is expected in the near future.
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Affiliation(s)
- Rafaela O Penha
- Bioprocess Engineering and Biotechnology Department, Federal University of Paraná, Centro Politécnico, CP 19011, Curitiba, PR, 81531-908, Brazil
| | - Luciana P S Vandenberghe
- Bioprocess Engineering and Biotechnology Department, Federal University of Paraná, Centro Politécnico, CP 19011, Curitiba, PR, 81531-908, Brazil
| | - Craig Faulds
- Aix-Marseille Université, POLYTECH Marseille, UMR 1163 Biotechnologie Des Champignons Filamenteux, 163 Avenue de Luminy, 13288, Marseille Cedex 09, France
| | - Vanete T Soccol
- Bioprocess Engineering and Biotechnology Department, Federal University of Paraná, Centro Politécnico, CP 19011, Curitiba, PR, 81531-908, Brazil
| | - Carlos R Soccol
- Bioprocess Engineering and Biotechnology Department, Federal University of Paraná, Centro Politécnico, CP 19011, Curitiba, PR, 81531-908, Brazil.
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Steiniger C, Hoffmann S, Süssmuth RD. Probing Exchange Units for Combining Iterative and Linear Fungal Nonribosomal Peptide Synthetases. Cell Chem Biol 2019; 26:1526-1534.e2. [DOI: 10.1016/j.chembiol.2019.08.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Revised: 07/08/2019] [Accepted: 08/09/2019] [Indexed: 11/30/2022]
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Robinson SL, Christenson JK, Wackett LP. Biosynthesis and chemical diversity of β-lactone natural products. Nat Prod Rep 2019; 36:458-475. [PMID: 30191940 DOI: 10.1039/c8np00052b] [Citation(s) in RCA: 84] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Covering: up to 2018 β-Lactones are strained rings that are useful organic synthons and pharmaceutical warheads. Over 30 core scaffolds of β-lactone natural products have been described to date, many with potent bioactivity against bacteria, fungi, or human cancer cell lines. β-Lactone natural products are chemically diverse and have high clinical potential, but production of derivatized drug leads has been largely restricted to chemical synthesis partly due to gaps in biochemical knowledge about β-lactone biosynthesis. Here we review recent discoveries in enzymatic β-lactone ring closure via ATP-dependent synthetases, intramolecular cyclization from seven-membered rings, and thioesterase-mediated cyclization during release from nonribosomal peptide synthetase assembly lines. We also comprehensively cover the diversity and taxonomy of source organisms for β-lactone natural products including their isolation from bacteria, fungi, plants, insects, and marine sponges. This work identifies computational and experimental bottlenecks and highlights future directions for genome-based discovery of biosynthetic gene clusters that may produce novel compounds with β-lactone rings.
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Affiliation(s)
- Serina L Robinson
- BioTechnology Institute, University of Minnesota - Twin Cities 140 Gortner Laboratory, 1479 Gortner Avenue, Saint Paul, MN 55108, USA.
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Hu Y, Nan F, Maina SW, Guo J, Wu S, Xin Z. Clone of plipastatin biosynthetic gene cluster by transformation-associated recombination technique and high efficient expression in model organism Bacillus subtilis. J Biotechnol 2018; 288:1-8. [DOI: 10.1016/j.jbiotec.2018.10.006] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Revised: 10/01/2018] [Accepted: 10/16/2018] [Indexed: 11/16/2022]
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Rütschlin S, Böttcher T. Dissecting the Mechanism of Oligomerization and Macrocyclization Reactions of NRPS-Independent Siderophore Synthetases. Chemistry 2018; 24:16044-16051. [DOI: 10.1002/chem.201803494] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Revised: 09/03/2018] [Indexed: 12/19/2022]
Affiliation(s)
- Sina Rütschlin
- Konstanz Research School Chemical Biology, Zukunftskolleg; Chemistry Department; University of Konstanz; Universitätsstrasse 10 78457 Konstanz Germany
| | - Thomas Böttcher
- Konstanz Research School Chemical Biology, Zukunftskolleg; Chemistry Department; University of Konstanz; Universitätsstrasse 10 78457 Konstanz Germany
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Gao L, Guo J, Fan Y, Ma Z, Lu Z, Zhang C, Zhao H, Bie X. Module and individual domain deletions of NRPS to produce plipastatin derivatives in Bacillus subtilis. Microb Cell Fact 2018; 17:84. [PMID: 29855381 PMCID: PMC5984369 DOI: 10.1186/s12934-018-0929-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2017] [Accepted: 05/11/2018] [Indexed: 12/04/2022] Open
Abstract
Background Plipastatin, an antifungal lipopeptide, is synthesized by a non-ribosomal peptide synthetase (NRPS) in Bacillus subtilis. However, little information is available on the combinatorial biosynthesis strategies applied in plipastatin biosynthetic pathway. In this study, we applied module or individual domain deletion strategies to engineer the plipastatin biosynthetic pathway, and investigated the effect of deletions on the plipastatin assembly line, as well as revealed the synthetic patterns of novel lipopeptides. Results Module deletion inactivated the entire enzyme complex, whereas individual domain (A/T domain) deletion within module 7 truncated the assembly line, resulting in truncated linear hexapeptides (C16~17β-OHFA-Glu-Orn-Tyr-Thr-Glu-Ala/Val). Interestingly, within the module 6 catalytic unit, the effect of thiolation domain deletion differed from that of adenylation deletion. Absence of the T6-domain resulted in a nonproductive strain, whereas deletion of the A6-domain resulted in multiple assembly lines via module-skipping mechanism, generating three novel types of plipastatin derivatives, pentapeptides (C16~17β-OHFA-Glu-Orn-Tyr-Thr-Glu), hexapeptides (C16~17β-OHFA-Glu-Orn-Tyr-Thr-Glu-Ile), and octapeptides (C16~17β-OHFA-Glu-Orn-Tyr-Thr-Glu-Gln-Tyr-Ile). Conclusions Notably, a unique module-skipping process occurred following deletion of the A6-domain, which has not been previously reported for engineered NRPS systems. This finding provides new insight into the lipopeptides engineering. It is of significant importance for combinatorial approaches and should be taken into consideration in engineering non-ribosomal peptide biosynthetic pathways for generating novel lipopeptides. Electronic supplementary material The online version of this article (10.1186/s12934-018-0929-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ling Gao
- College of Food Science and Technology, Nanjing Agricultural University, 1 Weigang, Nanjing, 210095, People's Republic of China
| | - Jianping Guo
- College of Food Science and Technology, Nanjing Agricultural University, 1 Weigang, Nanjing, 210095, People's Republic of China
| | - Yun Fan
- College of Food Science and Technology, Nanjing Agricultural University, 1 Weigang, Nanjing, 210095, People's Republic of China
| | - Zhi Ma
- College of Food Science and Technology, Nanjing Agricultural University, 1 Weigang, Nanjing, 210095, People's Republic of China
| | - Zhaoxin Lu
- College of Food Science and Technology, Nanjing Agricultural University, 1 Weigang, Nanjing, 210095, People's Republic of China
| | - Chong Zhang
- College of Food Science and Technology, Nanjing Agricultural University, 1 Weigang, Nanjing, 210095, People's Republic of China
| | - Haizhen Zhao
- College of Food Science and Technology, Nanjing Agricultural University, 1 Weigang, Nanjing, 210095, People's Republic of China
| | - Xiaomei Bie
- College of Food Science and Technology, Nanjing Agricultural University, 1 Weigang, Nanjing, 210095, People's Republic of China.
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Gao L, Han J, Liu H, Qu X, Lu Z, Bie X. Plipastatin and surfactin coproduction by Bacillus subtilis pB2-L and their effects on microorganisms. Antonie van Leeuwenhoek 2017; 110:1007-1018. [PMID: 28477175 DOI: 10.1007/s10482-017-0874-y] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2017] [Accepted: 04/17/2017] [Indexed: 10/19/2022]
Abstract
To convert the lipopeptide non-producer strain Bacillus subtilis pB2 into a plipastatin and surfactin coproducer, a gene expression cassette composed of a constitutive promoter (P43), functional gene sfp, and pleiotropic regulatory gene degQ was integrated into the chromosomal amyE locus of strain B. subtilis pB2 by homologous recombination, which generated a plipastatin and surfactin co-producer. Thirteen plipastatins and fifteen surfactins were identified in lipopeptide extracts using analytical techniques, and their effects on microorganisms were described by microscopic, cytoskeleton analysis and flow-cytometry, respectively. Plipastatins isolated from the engineered strain pB2-L exhibited strong antifungal activity (MIC 16 μg ml-1) by disrupting the cell walls, membranes and cytoskeleton of Fusarium oxysporum f. sp. cucumerinum hyphae. Surfactins affected the cell membrane of Staphylococcus aureus (MIC 20 μg ml-1), resulting in nucleic acid leakage and ultimately, cell death. Based on the convenience of genetic manipulation in the engineering strain, this work could be useful for the rational design of lipopeptide synthetases via the recombination of gene fragments to generate arrays of peptide derivatives and thus expand the diversity of microbial-produced lipopeptides.
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Affiliation(s)
- Ling Gao
- Key Laboratory of Food Processing and Quality Control, Ministry of Agriculture of China, College of Food Science and Technology, Nanjing Agricultural University, 1 Weigang, Nanjing, 210095, People's Republic of China
| | - Jinzhi Han
- Key Laboratory of Food Processing and Quality Control, Ministry of Agriculture of China, College of Food Science and Technology, Nanjing Agricultural University, 1 Weigang, Nanjing, 210095, People's Republic of China
| | - Hongxia Liu
- Key Laboratory of Food Processing and Quality Control, Ministry of Agriculture of China, College of Food Science and Technology, Nanjing Agricultural University, 1 Weigang, Nanjing, 210095, People's Republic of China
| | - Xiaoxu Qu
- Key Laboratory of Food Processing and Quality Control, Ministry of Agriculture of China, College of Food Science and Technology, Nanjing Agricultural University, 1 Weigang, Nanjing, 210095, People's Republic of China
| | - Zhaoxin Lu
- Key Laboratory of Food Processing and Quality Control, Ministry of Agriculture of China, College of Food Science and Technology, Nanjing Agricultural University, 1 Weigang, Nanjing, 210095, People's Republic of China
| | - Xiaomei Bie
- Key Laboratory of Food Processing and Quality Control, Ministry of Agriculture of China, College of Food Science and Technology, Nanjing Agricultural University, 1 Weigang, Nanjing, 210095, People's Republic of China.
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