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Li X, Zhang M, Lu Y, Wu N, Chen J, Ji Z, Zhan Y, Ma X, Chen J, Cai D, Chen S. Metabolic engineering of Bacillus amyloliquefaciens for efficient production of α-glucosidase inhibitor1-deoxynojirimycin. Synth Syst Biotechnol 2023; 8:378-385. [PMID: 37692204 PMCID: PMC10485785 DOI: 10.1016/j.synbio.2023.05.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 05/13/2023] [Accepted: 05/16/2023] [Indexed: 09/12/2023] Open
Abstract
Owing to the feature of strong α-glucosidase inhibitory activity, 1-deoxynojirimycin (1-DNJ) has broad application prospects in areas of functional food, biomedicine, etc., and this research wants to construct an efficient strain for 1-DNJ production, basing on Bacillus amyloliquefaciens HZ-12. Firstly, using the temperature-sensitive shuttle plasmid T2 (2)-Ori, gene ptsG in phosphotransferase system (PTS) was weakened by homologous recombination, and non-PTS pathway was strengthened by deleting its repressor gene iolR, and 1-DNJ yield of resultant strain HZ-S2 was increased by 4.27-fold, reached 110.72 mg/L. Then, to increase precursor fructose-6-phosphate (F-6-P) supply, phosphofructokinase was weaken, fructose phosphatase GlpX and 6-phosphate glucose isomerase Pgi were strengthened by promoter replacement, moreover, regulator gene nanR was deleted, 1-DNJ yield was further increased to 267.37 mg/L by 2.41-fold. Subsequently, promoter of 1-DNJ synthetase cluster was optimized, as well as 5'-UTRs of downstream genes in synthetase cluster, and 1-DNJ produced by the final strain reached 478.62 mg/L. Last but not the least, 1-DNJ yield of 1632.50 mg/L was attained in 3 L fermenter, which was the highest yield of 1-DNJ reported to date. Taken together, our results demonstrated that metabolic engineering was an effective strategy for 1-DNJ synthesis, this research laid a foundation for industrialization of functional food and drugs based on 1-DNJ.
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Affiliation(s)
- Xujie Li
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Environmental Microbial Technology Center of Hubei Province, College of Life Sciences, Hubei University, Wuhan, 430062, China
| | - Meng Zhang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Environmental Microbial Technology Center of Hubei Province, College of Life Sciences, Hubei University, Wuhan, 430062, China
| | - Yu Lu
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Ningyang Wu
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Environmental Microbial Technology Center of Hubei Province, College of Life Sciences, Hubei University, Wuhan, 430062, China
| | - Jian'gang Chen
- Wuhan Jun'an Biotechnology Co., Ltd., Wuhan, 430070, China
| | - Zhixia Ji
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Yangyang Zhan
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Environmental Microbial Technology Center of Hubei Province, College of Life Sciences, Hubei University, Wuhan, 430062, China
| | - Xin Ma
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Environmental Microbial Technology Center of Hubei Province, College of Life Sciences, Hubei University, Wuhan, 430062, China
| | - Junyong Chen
- Department of Urology, Zhuhai People's Hospital (Zhuhai Hospital Affiliated to Jinan University), Zhuhai, 519000, China
| | - Dongbo Cai
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Environmental Microbial Technology Center of Hubei Province, College of Life Sciences, Hubei University, Wuhan, 430062, China
| | - Shouwen Chen
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Environmental Microbial Technology Center of Hubei Province, College of Life Sciences, Hubei University, Wuhan, 430062, China
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Biosynthesis of (±)-Differolide, an Antioxidant Isolate from Streptomyces qaidamensis S10T. APPLIED SCIENCES-BASEL 2022. [DOI: 10.3390/app12083741] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Streptomyces from unexplored or underexplored environments may be an essential source of discoveries of bioactive molecules. One such example is Streptomyces qaidamensis S10T, which was isolated from a sand sample collected in Qaidam Basin, Qinghai Province, China. Here, we report on (±)-differolide, an antioxidant isolated from S. qaidamensis, and verified with scavenging experiments on 2,2-diphenyl-1-picrylhydrazyl (DPPH). The biosynthetic gene cluster responsible for synthesizing the compound was also identified using comparative genomic methods. These results provide a basis for further study of the biological activities of (±)-differolide, which also make it possible to develop as an antioxidant medicine.
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Liu L, Ji Z, Zhao K, Zhao Y, Zhang Y, Huang S. Validation of housekeeping genes as internal controls for gene expression studies on biofilm formation in Bacillus velezensis. Appl Microbiol Biotechnol 2022; 106:2079-2089. [PMID: 35171340 DOI: 10.1007/s00253-022-11831-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Revised: 01/19/2022] [Accepted: 02/10/2022] [Indexed: 11/02/2022]
Abstract
Bacillus velezensis is an important bacterium widely applied in agriculture and industry, and biofilms play critical roles in its environmental tolerance. The appropriate choice of reference genes is essential for key gene expression studies. Multiple internal control genes were selected and validated from the 21 housekeeping genes of B. velezensis by expression stability evaluation during biofilm formation and were used to study the expression of key genes involved in the process. The results showed that pyk, gyrA, recA, and gyrB were stably expressed, and the expression of pyk was the most stable during biofilm formation. A pair of two genes, pyk and gyrA, provided high-quality data when used as internal controls, and the combination of three genes, pyk, gyrA, and recA, was even better. The expression levels of pyk, gyrA, and recA approximated those of five key genes, abrB, epsD, kinC, sinR, and tasA, in biofilm formation, meeting the requirements of ideal internal control genes. The expression patterns of 5 key genes were studied with 16S, pyk, the pair of 2 genes, pyk and gyrA, and the combination of 3 genes, pyk, gyrA, and recA, as internal controls during the biofilm formation process. The results proved that pyk was a suitable internal control, as were the pair of 2 genes, pyk and gyrA, and the combination of 3 genes, pyk, gyrA, and recA. This study provided genes and gene combinations which were validated as suitable internal controls for gene expression studies, especially those on the mechanism of biofilm formation in B. velezensis or even other Bacillus spp. KEY POINTS: • Reference genes is necessary for gene expression study in biofilm formation of Bacillus velezensis • Pyk and 2 gene combinations were selected and validated from 21 common used genes • Expression of key genes in biofilm formation was normalized with the selected internal controls.
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Affiliation(s)
- Lianmeng Liu
- State Key Laboratory of Rice Biology, China National Rice Research Institute, 311400, Hangzhou, China.
| | - Zhiming Ji
- College of Biological and Food Engineering, Huaihua University, Huaihua, 418000, China
| | - Kehan Zhao
- State Key Laboratory of Rice Biology, China National Rice Research Institute, 311400, Hangzhou, China
| | - Yuan Zhao
- State Key Laboratory of Rice Biology, China National Rice Research Institute, 311400, Hangzhou, China
| | - Yilin Zhang
- State Key Laboratory of Rice Biology, China National Rice Research Institute, 311400, Hangzhou, China
| | - Shiwen Huang
- State Key Laboratory of Rice Biology, China National Rice Research Institute, 311400, Hangzhou, China. .,College of Agriculture, Guangxi University, 530003, Nanning, China.
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OUP accepted manuscript. FEMS Microbiol Lett 2022; 369:6528915. [DOI: 10.1093/femsle/fnac017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Revised: 01/26/2022] [Accepted: 02/12/2022] [Indexed: 11/12/2022] Open
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Park JS, Kim DE, Hong SC, Kim SY, Kwon HC, Hyun CG, Choi J. Genome Analysis of Streptomyces nojiriensis JCM 3382 and Distribution of Gene Clusters for Three Antibiotics and an Azasugar across the Genus Streptomyces. Microorganisms 2021; 9:microorganisms9091802. [PMID: 34576698 PMCID: PMC8466323 DOI: 10.3390/microorganisms9091802] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Revised: 08/15/2021] [Accepted: 08/18/2021] [Indexed: 11/29/2022] Open
Abstract
Streptomyces spp. have been major contributors of novel natural products that are used in many application areas. We found that the nojirimycin (NJ) producer JCM 3382 has antimicrobial activity against Staphylococcus aureus via cellular degradation. Genome analysis revealed 30 biosynthetic gene clusters, including those responsible for producing antibiotics, including an azasugar NJ. In-depth MS/MS analysis confirmed the production of 1-deoxynojirimycin (DNJ) along with NJ. In addition, the production of tambromycins, setomimycin, and linearmycins was verified by spectroscopic analyses, including LC-MS and NMR. The distribution of the clusters of genes coding for antibiotics in 2061 Streptomyces genomes suggested potential producers of tambromycin, setomimycin, and linearmycin. For a DNJ gene cluster, homologs of gabT1 and gutB1 were commonly found; however, yktC1 was identified in only 112 genomes. The presence of several types of clusters suggests that different strains may produce different types of azasugars. Chemical-profile-inspired comparative genome analysis may facilitate a more accurate assessment of the biosynthetic potential to produce secondary metabolites.
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Affiliation(s)
- Jin-Soo Park
- Natural Product Informatics Research Center, Korea Institute of Science and Technology, Gangneung 25451, Korea; (J.-S.P.); (D.-E.K.); (S.-C.H.); (H.C.K.)
| | - Da-Eun Kim
- Natural Product Informatics Research Center, Korea Institute of Science and Technology, Gangneung 25451, Korea; (J.-S.P.); (D.-E.K.); (S.-C.H.); (H.C.K.)
| | - Sung-Chul Hong
- Natural Product Informatics Research Center, Korea Institute of Science and Technology, Gangneung 25451, Korea; (J.-S.P.); (D.-E.K.); (S.-C.H.); (H.C.K.)
| | - Seung-Young Kim
- Department of Pharmaceutical Engineering & Biotechnology, Sunmoon University, Chungnam 31460, Korea;
| | - Hak Cheol Kwon
- Natural Product Informatics Research Center, Korea Institute of Science and Technology, Gangneung 25451, Korea; (J.-S.P.); (D.-E.K.); (S.-C.H.); (H.C.K.)
| | - Chang-Gu Hyun
- Department of Chemistry and Cosmetics, Jeju National University, Jeju 63243, Korea
- Correspondence: (C.-G.H.); (J.C.)
| | - Jaeyoung Choi
- Smart Farm Research Center, Korea Institute of Science and Technology, Gangneung 25451, Korea
- Correspondence: (C.-G.H.); (J.C.)
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Beal HE, Horenstein NA. Comparative genomic analysis of azasugar biosynthesis. AMB Express 2021; 11:120. [PMID: 34424396 PMCID: PMC8382821 DOI: 10.1186/s13568-021-01279-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Accepted: 08/13/2021] [Indexed: 11/13/2022] Open
Abstract
Azasugars are monosaccharide analogs in which the ring oxygen is replaced with a nitrogen atom. These well-known glycosidase inhibitors are of interest as therapeutics, yet several aspects of azasugars remain unknown including their distribution, structural diversity, and chemical ecology. The hallmark signature of bacterial azasugar biosynthesis is a three gene cluster (3GC) coding for aminotransferase, phosphatase, and dehydrogenase enzymes. Using the bioinformatics platform Enzyme Similarity Tool (EST), we identified hundreds of putative three gene clusters coding for azasugar production in microbial species. In the course of this work, we also report a consensus sequence for the aminotransferase involved in azasugar biosynthesis as being: SGNXFRXXXFPNXXXXXXXLXVPXPYCXRC. Most clusters are found in Bacillus and Streptomyces species which typically inhabit soil and the rhizosphere, but some clusters are found with diverse species representation such as Photorhabdus and Xenorhabdus which are symbiotic with entomopathogenic nematodes; the human skin commensal Cutibacterium acnes, and the marine Bacillus rugosus SPB7, a symbiont to the sea sponge Spongia officinalis. This pan-taxonomic survey of the azasugar 3GC signature may lead to the identification of new azasugar producers, facilitate studies of their natural functions, and lead to new potential therapeutics.
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Xu P, Xie S, Liu W, Jin P, Wei D, Yaseen DG, Wang Y, Miao W. Comparative Genomics Analysis Provides New Strategies for Bacteriostatic Ability of Bacillus velezensis HAB-2. Front Microbiol 2020; 11:594079. [PMID: 33281792 PMCID: PMC7705179 DOI: 10.3389/fmicb.2020.594079] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Accepted: 10/29/2020] [Indexed: 01/29/2023] Open
Abstract
Biocontrol formulations prepared from biocontrol bacteria are increasingly applied in sustainable agriculture. Notably, inoculants prepared from Bacillus strains have been proven efficient and environmentally friendly alternatives to chemical bactericides. The bacterium Bacillus velezensis HAB-2 (formerly classified as B. amyloliquefaciens HAB-2) is used as a biological control agent in agricultural fields. In this study, we reported a high-quality genome sequence of HAB-2 using third-generation sequencing technology (PacBio RS II). The 3.89 Mb genome encoded 3,820 predicted genes. Comparative analysis among the genome sequences of reference strains B. velezensis FZB42, B. amyloliquefaciens DSM7 and B. subtilis 168 with the HAB-2 genome revealed obvious differences in the variable part of the genomes, while the core genome shared by FZB42 and HAB-2 was similar (96.14%). However, there were differences in the prophage region among the four strains. The numbers of prophage regions and coding genes in HAB-2 and FZB42 were smaller than the other two strains. The HAB-2 genome showed superior ability to produce secondary metabolites and harbored 13 gene clusters involved in synthesis of antifungal and antibacterial acting secondary metabolites. Furthermore, there were two unique clusters: one cluster which encoded lanthipeptide was involved in mersacidin synthesis and another cluster which encoded ladderane was shown to direct an unknown compound. Multidomain enzymes, such as non-ribosomal peptide synthetase and polyketide synthase, control the biosynthesis of secondary metabolites and rely on 4'-phosphopantetheinyl transferases (PPTases). Key genes lpaH2 and a encoded PPTases in HAB-2 encoded 224 and 120 amino acids, respectively. The genomic features revealed that HAB-2 possesses immense potential to synthesize antimicrobial acting secondary metabolites by regulating and controlling gene clusters. The prophage regions and genes encoding PPTases may provide novel insight for the bacteriostatic mechanism of Bacillus in the biological control of plant diseases.
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Affiliation(s)
- Peidong Xu
- Key Laboratory of Green Prevention and Control of Tropical Plant Diseases and Pests, Ministry of Education, College of Plant Protection, Hainan University, Haikou, China.,School of Life and Pharmaceutical Sciences, Hainan University, Haikou, China
| | - Shangqian Xie
- Key Laboratory of Green Prevention and Control of Tropical Plant Diseases and Pests, Ministry of Education, College of Plant Protection, Hainan University, Haikou, China.,College of Forestry, Hainan University, Haikou, China
| | - Wenbo Liu
- Key Laboratory of Green Prevention and Control of Tropical Plant Diseases and Pests, Ministry of Education, College of Plant Protection, Hainan University, Haikou, China
| | - Pengfei Jin
- Key Laboratory of Green Prevention and Control of Tropical Plant Diseases and Pests, Ministry of Education, College of Plant Protection, Hainan University, Haikou, China
| | - Dandan Wei
- Key Laboratory of Green Prevention and Control of Tropical Plant Diseases and Pests, Ministry of Education, College of Plant Protection, Hainan University, Haikou, China
| | - Dahar Ghulam Yaseen
- Key Laboratory of Green Prevention and Control of Tropical Plant Diseases and Pests, Ministry of Education, College of Plant Protection, Hainan University, Haikou, China
| | - Yu Wang
- Key Laboratory of Green Prevention and Control of Tropical Plant Diseases and Pests, Ministry of Education, College of Plant Protection, Hainan University, Haikou, China
| | - Weiguo Miao
- Key Laboratory of Green Prevention and Control of Tropical Plant Diseases and Pests, Ministry of Education, College of Plant Protection, Hainan University, Haikou, China
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