1
|
Zhao X, Hussain MH, Mohsin A, Liu Z, Xu Z, Li Z, Guo W, Guo M. Mechanistic insight for improving butenyl-spinosyn production through combined ARTP/UV mutagenesis and ribosome engineering in Saccharopolyspora pogona. Front Bioeng Biotechnol 2024; 11:1329859. [PMID: 38292303 PMCID: PMC10825966 DOI: 10.3389/fbioe.2023.1329859] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Accepted: 12/22/2023] [Indexed: 02/01/2024] Open
Abstract
Butenyl-spinosyn is a highly effective, wide-spectrum and environmentally-friendly biological insecticide produced by Saccharopolyspora pogona. However, its scale-up is impeded due to its lower titer in wild-type strains. In this work, ARTP/UV mutagenesis and ribosome engineering were employed to enhance the butenyl-spinosyn production, and a stable mutant Saccharopolyspora pogona aG6 with high butenyl-spinosyn yield was successfully obtained. For the first time, the fermentation results in the 5 L bioreactor demonstrated that the butenyl-spinosyn produced by mutant Saccharopolyspora pogona aG6 reached the maximum value of 130 mg/L, almost 4-fold increase over the wild-type strain WT. Furthermore, comparative genomic, transcriptome and target metabolomic analysis revealed that the accumulation of butenyl-spinosyn was promoted by alterations in ribosomal proteins, branched-chain amino acid degradation and oxidative phosphorylation. Conclusively, the proposed model of ribosome engineering combined with ARTP/UV showed the improved biosynthesis regulation of butenyl-spinosyn in S. pogona.
Collapse
Affiliation(s)
- Xueli Zhao
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
| | - Muhammad Hammad Hussain
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
| | - Ali Mohsin
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
| | - Zebo Liu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
| | - Zhixian Xu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
| | - Zhanxia Li
- Department of Respiratory Medicine, Shanghai Sixth People’s Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Weiqun Guo
- Academy of National Food and Strategic Reserves Administration, Beijing, China
| | - Meijin Guo
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
| |
Collapse
|
2
|
Wang Z, Zhang Z, Shi Q, Liu S, Wu Q, Wang Z, Saiding E, Han J, Zhou J, Wang R, Su X. Comparison of Lactiplantibacillus plantarum isolates from the gut of mice supplemented with different types of nutrients: a genomic and metabolomic study. Front Microbiol 2023; 14:1295058. [PMID: 38033563 PMCID: PMC10684713 DOI: 10.3389/fmicb.2023.1295058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Accepted: 10/30/2023] [Indexed: 12/02/2023] Open
Abstract
Many studies have focused on the influence of dietary supplements on gut microbiota composition, but limited research have reported their effects on specific bacterial species in the gut. Lactiplantibacillus plantarum is one of the most widely studied probiotics, with a wide range of sources and good environmental adaptability. In this study, in order to elucidate the adaptation strategies of L. plantarum to the gut of mice supplemented with carbohydrates, peptides and minerals, whole genome resequencing and intracellular metabolites detection were performed, and high-frequency mutant genes and differential metabolites were screened. The results suggested different types of dietary supplements do have different effects on L. plantarum from the gut of mice. Additionally, KEGG annotation unveiled that the effects of these dietary supplements on the gene level of L. plantarum primarily pertained to environmental information processing, while the differential metabolites were predominantly associated with metabolism. This study provided new perspectives on the adaptive mechanism of L. plantarum in response to the host's gut environment, suggesting that the diversity of the genome and metabolome of L. plantarum was correlated with dietary supplements. Furthermore, this study offered useful guidance in the effective utilization of dietary supplements.
Collapse
Affiliation(s)
- Ziyan Wang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agroproducts, Ningbo, China
- Key Laboratory of Aquacultural Biotechnology Ministry of Education, Ningbo University, Ningbo, China
- School of Marine Sciences, Ningbo University, Ningbo, China
| | - Zhixuan Zhang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agroproducts, Ningbo, China
- Key Laboratory of Aquacultural Biotechnology Ministry of Education, Ningbo University, Ningbo, China
- School of Marine Sciences, Ningbo University, Ningbo, China
| | - Qiuyue Shi
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agroproducts, Ningbo, China
- Key Laboratory of Aquacultural Biotechnology Ministry of Education, Ningbo University, Ningbo, China
- School of Marine Sciences, Ningbo University, Ningbo, China
| | - Songyi Liu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agroproducts, Ningbo, China
- Key Laboratory of Aquacultural Biotechnology Ministry of Education, Ningbo University, Ningbo, China
- School of Marine Sciences, Ningbo University, Ningbo, China
| | - Qiaoli Wu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agroproducts, Ningbo, China
- Key Laboratory of Aquacultural Biotechnology Ministry of Education, Ningbo University, Ningbo, China
- School of Marine Sciences, Ningbo University, Ningbo, China
| | - Ze Wang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agroproducts, Ningbo, China
- Key Laboratory of Aquacultural Biotechnology Ministry of Education, Ningbo University, Ningbo, China
- School of Marine Sciences, Ningbo University, Ningbo, China
| | - Emilaguli Saiding
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agroproducts, Ningbo, China
- Key Laboratory of Aquacultural Biotechnology Ministry of Education, Ningbo University, Ningbo, China
- School of Marine Sciences, Ningbo University, Ningbo, China
| | - Jiaojiao Han
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agroproducts, Ningbo, China
- Key Laboratory of Aquacultural Biotechnology Ministry of Education, Ningbo University, Ningbo, China
- School of Marine Sciences, Ningbo University, Ningbo, China
| | - Jun Zhou
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agroproducts, Ningbo, China
- Key Laboratory of Aquacultural Biotechnology Ministry of Education, Ningbo University, Ningbo, China
- School of Marine Sciences, Ningbo University, Ningbo, China
| | - Rixin Wang
- Key Laboratory of Aquacultural Biotechnology Ministry of Education, Ningbo University, Ningbo, China
- School of Marine Sciences, Ningbo University, Ningbo, China
| | - Xiurong Su
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agroproducts, Ningbo, China
- Key Laboratory of Aquacultural Biotechnology Ministry of Education, Ningbo University, Ningbo, China
- School of Marine Sciences, Ningbo University, Ningbo, China
| |
Collapse
|
3
|
Patil RS, Sharma S, Bhaskarwar AV, Nambiar S, Bhat NA, Koppolu MK, Bhukya H. TetR and OmpR family regulators in natural product biosynthesis and resistance. Proteins 2023. [PMID: 37874037 DOI: 10.1002/prot.26621] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2023] [Revised: 08/30/2023] [Accepted: 10/06/2023] [Indexed: 10/25/2023]
Abstract
This article provides a comprehensive review and sequence-structure analysis of transcription regulator (TR) families, TetR and OmpR/PhoB, involved in specialized secondary metabolite (SSM) biosynthesis and resistance. Transcription regulation is a fundamental process, playing a crucial role in orchestrating gene expression to confer a survival advantage in response to frequent environmental stress conditions. This process, coupled with signal sensing, enables bacteria to respond to a diverse range of intra and extracellular signals. Thus, major bacterial signaling systems use a receptor domain to sense chemical stimuli along with an output domain responsible for transcription regulation through DNA-binding. Sensory and output domains on a single polypeptide chain (one component system, OCS) allow response to stimuli by allostery, that is, DNA-binding affinity modulation upon signal presence/absence. On the other hand, two component systems (TCSs) allow cross-talk between the sensory and output domains as they are disjoint and transmit information by phosphorelay to mount a response. In both cases, however, TRs play a central role. Biosynthesis of SSMs, which includes antibiotics, is heavily regulated by TRs as it diverts the cell's resources towards the production of these expendable compounds, which also have clinical applications. These TRs have evolved to relay information across specific signals and target genes, thus providing a rich source of unique mechanisms to explore towards addressing the rapid escalation in antimicrobial resistance (AMR). Here, we focus on the TetR and OmpR family TRs, which belong to OCS and TCS, respectively. These TR families are well-known examples of regulators in secondary metabolism and are ubiquitous across different bacteria, as they also participate in a myriad of cellular processes apart from SSM biosynthesis and resistance. As a result, these families exhibit higher sequence divergence, which is also evident from our bioinformatic analysis of 158 389 and 77 437 sequences from TetR and OmpR family TRs, respectively. The analysis of both sequence and structure allowed us to identify novel motifs in addition to the known motifs responsible for TR function and its structural integrity. Understanding the diverse mechanisms employed by these TRs is essential for unraveling the biosynthesis of SSMs. This can also help exploit their regulatory role in biosynthesis for significant pharmaceutical, agricultural, and industrial applications.
Collapse
Affiliation(s)
- Rachit S Patil
- Department of Biology, Indian Institute of Science Education and Research, Tirupati, India
| | - Siddhant Sharma
- Department of Biology, Indian Institute of Science Education and Research, Tirupati, India
| | - Aditya V Bhaskarwar
- Department of Biology, Indian Institute of Science Education and Research, Tirupati, India
| | - Souparnika Nambiar
- Department of Biology, Indian Institute of Science Education and Research, Tirupati, India
| | - Niharika A Bhat
- Department of Biology, Indian Institute of Science Education and Research, Tirupati, India
| | - Mani Kanta Koppolu
- Department of Biology, Indian Institute of Science Education and Research, Tirupati, India
| | - Hussain Bhukya
- Department of Biology, Indian Institute of Science Education and Research, Tirupati, India
| |
Collapse
|
4
|
Cao L, Zhu Z, Qin H, Xia Z, Xie J, Li X, Rang J, Hu S, Sun Y, Xia L. Effects of a Pirin-like protein on strain growth and spinosad biosynthesis in Saccharopolyspora spinosa. Appl Microbiol Biotechnol 2023; 107:5439-5451. [PMID: 37428187 DOI: 10.1007/s00253-023-12636-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2023] [Revised: 06/01/2023] [Accepted: 06/11/2023] [Indexed: 07/11/2023]
Abstract
Pirin family proteins perform a variety of biological functions and widely exist in all living organisms. A few studies have shown that Pirin family proteins may be involved in the biosynthesis of antibiotics in actinomycetes. However, the function of Pirin-like proteins in S. spinosa is still unclear. In this study, the inactivation of the sspirin gene led to serious growth defects and the accumulation of H2O2. Surprisingly, the overexpression and knockout of sspirin slightly accelerated the consumption and utilization of glucose, weakened the TCA cycle, delayed sporulation, and enhanced sporulation in the later stage. In addition, the overexpression of sspirin can enhance the β-oxidation pathway and increase the yield of spinosad by 0.88 times, while the inactivation of sspirin hardly produced spinosad. After adding MnCl2, the spinosad yield of the sspirin overexpression strain was further increased to 2.5 times that of the wild-type strain. This study preliminarily revealed the effects of Pirin-like proteins on the growth development and metabolism of S. spinosa and further expanded knowledge of Pirin-like proteins in actinomycetes. KEY POINTS: • Overexpression of the sspirin gene possibly triggers carbon catabolite repression (CCR) • Overexpression of the sspirin gene can promote the synthesis of spinosad • Knockout of the sspirin gene leads to serious growth and spinosad production defects.
Collapse
Affiliation(s)
- Li Cao
- Hunan Provincial Key Laboratory of Microbial Molecular Biology, State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, 410081, Hunan, China
| | - Zirong Zhu
- Hunan Provincial Key Laboratory of Microbial Molecular Biology, State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, 410081, Hunan, China
| | - Hao Qin
- Hunan Provincial Key Laboratory of Microbial Molecular Biology, State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, 410081, Hunan, China
| | - Ziyuan Xia
- Hunan Provincial Key Laboratory of Microbial Molecular Biology, State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, 410081, Hunan, China
| | - Jiao Xie
- Hunan Provincial Key Laboratory of Microbial Molecular Biology, State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, 410081, Hunan, China
| | - Xiaomin Li
- Hunan Provincial Key Laboratory of Microbial Molecular Biology, State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, 410081, Hunan, China
| | - Jie Rang
- Hunan Provincial Key Laboratory of Microbial Molecular Biology, State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, 410081, Hunan, China
| | - Shengbiao Hu
- Hunan Provincial Key Laboratory of Microbial Molecular Biology, State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, 410081, Hunan, China
| | - Yunjun Sun
- Hunan Provincial Key Laboratory of Microbial Molecular Biology, State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, 410081, Hunan, China.
| | - Liqiu Xia
- Hunan Provincial Key Laboratory of Microbial Molecular Biology, State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, 410081, Hunan, China.
| |
Collapse
|
5
|
Toopaang W, Bunnak W, Srisuksam C, Wattananukit W, Tanticharoen M, Yang YL, Amnuaykanjanasin A. Microbial polyketides and their roles in insect virulence: from genomics to biological functions. Nat Prod Rep 2022; 39:2008-2029. [PMID: 35822627 DOI: 10.1039/d1np00058f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Covering: May 1966 up to January 2022Entomopathogenic microorganisms have potential for biological control of insect pests. Their main secondary metabolites include polyketides, nonribosomal peptides, and polyketide-nonribosomal peptide (PK-NRP) hybrids. Among these secondary metabolites, polyketides have mainly been studied for structural identification, pathway engineering, and for their contributions to medicine. However, little is known about the function of polyketides in insect virulence. This review focuses on the role of bacterial and fungal polyketides, as well as PK-NRP hybrids in insect infection and killing. We also discuss gene distribution and evolutional relationships among different microbial species. Further, the role of microbial polyketides and the hybrids in modulating insect-microbial symbiosis is also explored. Understanding the mechanisms of polyketides in insect pathogenesis, how compounds moderate the host-fungus interaction, and the distribution of PKS genes across different fungi and bacteria will facilitate the discovery and development of novel polyketide-derived bio-insecticides.
Collapse
Affiliation(s)
- Wachiraporn Toopaang
- National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, 113 Thailand Science Park, Phahonyothin Rd., Khlong Nueng, Amphoe Khlong Luang, Pathum Thani 12120, Thailand. .,Molecular and Biological Agricultural Sciences, Taiwan International Graduate Program, Academia Sinica and National Chung Hsing University, Taiwan.,Agricultural Biotechnology Research Center, Academia Sinica, Taipei 11529, Taiwan.
| | - Warapon Bunnak
- National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, 113 Thailand Science Park, Phahonyothin Rd., Khlong Nueng, Amphoe Khlong Luang, Pathum Thani 12120, Thailand.
| | - Chettida Srisuksam
- National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, 113 Thailand Science Park, Phahonyothin Rd., Khlong Nueng, Amphoe Khlong Luang, Pathum Thani 12120, Thailand.
| | - Wilawan Wattananukit
- National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, 113 Thailand Science Park, Phahonyothin Rd., Khlong Nueng, Amphoe Khlong Luang, Pathum Thani 12120, Thailand.
| | - Morakot Tanticharoen
- School of Bioresources and Technology, King Mongkut's University of Technology Thonburi, Bangkok 10140, Thailand
| | - Yu-Liang Yang
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei 11529, Taiwan. .,Biotechnology Center in Southern Taiwan, Academia Sinica, Tainan 711010, Taiwan
| | - Alongkorn Amnuaykanjanasin
- National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, 113 Thailand Science Park, Phahonyothin Rd., Khlong Nueng, Amphoe Khlong Luang, Pathum Thani 12120, Thailand.
| |
Collapse
|
6
|
Tang J, Chen J, Liu Y, Hu J, Xia Z, Li X, He H, Rang J, Sun Y, Yu Z, Cui J, Xia L. The Global Regulator PhoU Positively Controls Growth and Butenyl-Spinosyn Biosynthesis in Saccharopolyspora pogona. Front Microbiol 2022; 13:904627. [PMID: 35756073 PMCID: PMC9218956 DOI: 10.3389/fmicb.2022.904627] [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: 03/25/2022] [Accepted: 05/23/2022] [Indexed: 11/13/2022] Open
Abstract
Butenyl-spinosyn, a highly effective biological insecticide, is produced by Saccharopolyspora pogona. However, its application has been severely hampered by its low yield. Recent studies have shown that PhoU plays a pivotal role in regulating cell growth, secondary metabolite biosynthesis and intracellular phosphate levels. Nevertheless, the function of PhoU remains ambiguous in S. pogona. In this study, we investigated the effects of PhoU on the growth and the butenyl-spinosyn biosynthesis of S. pogona by constructing the mutants. Overexpression of phoU increased the production of butenyl-spinosyn to 2.2-fold that of the wild-type strain. However, the phoU deletion resulted in a severe imbalance of intracellular phosphate levels, and suppression of the growth and butenyl-spinosyn biosynthesis. Quantitative Real-time PCR (qRT-PCR) analysis, distinctive protein detection and mass spectrometry revealed that PhoU widely regulated primary metabolism, energy metabolism and DNA repair, which implied that PhoU influences the growth and butenyl-spinosyn biosynthesis of S. pogona as a global regulator.
Collapse
Affiliation(s)
- Jianli Tang
- Hunan Provincial Key Laboratory for Microbial Molecular Biology, State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, China
| | - Jianming Chen
- Hunan Provincial Key Laboratory for Microbial Molecular Biology, State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, China
| | - Yang Liu
- Hunan Provincial Key Laboratory for Microbial Molecular Biology, State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, China
| | - Jinjuan Hu
- Hunan Provincial Key Laboratory for Microbial Molecular Biology, State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, China
| | - Ziyuan Xia
- Hunan Provincial Key Laboratory for Microbial Molecular Biology, State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, China
| | - Xiaomin Li
- Hunan Provincial Key Laboratory for Microbial Molecular Biology, State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, China
| | - Haocheng He
- Hunan Provincial Key Laboratory for Microbial Molecular Biology, State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, China
| | - Jie Rang
- Hunan Provincial Key Laboratory for Microbial Molecular Biology, State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, China
| | - Yunjun Sun
- Hunan Provincial Key Laboratory for Microbial Molecular Biology, State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, China
| | - Ziquan Yu
- Hunan Provincial Key Laboratory for Microbial Molecular Biology, State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, China
| | - Jun Cui
- Hunan Provincial Key Laboratory for Microbial Molecular Biology, State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, China
| | - Liqiu Xia
- Hunan Provincial Key Laboratory for Microbial Molecular Biology, State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, China
| |
Collapse
|
7
|
Rang J, Xia Z, Shuai L, Cao L, Liu Y, Li X, Xie J, Li Y, Hu S, Xie Q, Xia L. A TetR family transcriptional regulator, SP_2854 can affect the butenyl-spinosyn biosynthesis by regulating glucose metabolism in Saccharopolyspora pogona. Microb Cell Fact 2022; 21:83. [PMID: 35568948 PMCID: PMC9107242 DOI: 10.1186/s12934-022-01808-2] [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: 01/14/2022] [Accepted: 04/27/2022] [Indexed: 11/10/2022] Open
Abstract
Background Butenyl-spinosyn produced by Saccharopolyspora pogona exhibits strong insecticidal activity and a broad pesticidal spectrum. Currently, important functional genes involve in butenyl-spinosyn biosynthesis remain unknown, which leads to difficulty in efficiently understanding its regulatory mechanism, and improving its production by metabolic engineering. Results Here, we identified a TetR family transcriptional regulator, SP_2854, that can positively regulate butenyl-spinosyn biosynthesis and affect strain growth, glucose consumption, and mycelial morphology in S. pogona. Using targeted metabolomic analyses, we found that SP_2854 overexpression enhanced glucose metabolism, while SP_2854 deletion had the opposite effect. To decipher the overproduction mechanism in detail, comparative proteomic analysis was carried out in the SP-2854 overexpressing mutant and the original strain, and we found that SP_2854 overexpression promoted the expression of proteins involved in glucose metabolism. Conclusion Our findings suggest that SP_2854 can affect strain growth and development and butenyl-spinosyn biosynthesis in S. pogona by controlling glucose metabolism. The strategy reported here will be valuable in paving the way for genetic engineering of regulatory elements in actinomycetes to improve important natural products production. Supplementary Information The online version contains supplementary material available at 10.1186/s12934-022-01808-2.
Collapse
Affiliation(s)
- Jie Rang
- Hunan Provincial Key Laboratory for Microbial Molecular Biology, State Key Laboratory of Development Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, 410081, China.,Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research (MOE of China), National & Local Joint Engineering Laboratory for New Petro-Chemical Materials and Fine Utilization of Resources, College of Chemistry and Chemical Engineering, Hunan Normal University, Changsha, 410081, China
| | - Ziyuan Xia
- Hunan Provincial Key Laboratory for Microbial Molecular Biology, State Key Laboratory of Development Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, 410081, China
| | - Ling Shuai
- Hunan Provincial Key Laboratory for Microbial Molecular Biology, State Key Laboratory of Development Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, 410081, China
| | - Li Cao
- Hunan Provincial Key Laboratory for Microbial Molecular Biology, State Key Laboratory of Development Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, 410081, China
| | - Yang Liu
- Hunan Provincial Key Laboratory for Microbial Molecular Biology, State Key Laboratory of Development Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, 410081, China
| | - Xiaomin Li
- Hunan Provincial Key Laboratory for Microbial Molecular Biology, State Key Laboratory of Development Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, 410081, China
| | - Jiao Xie
- Hunan Provincial Key Laboratory for Microbial Molecular Biology, State Key Laboratory of Development Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, 410081, China
| | - Yunlong Li
- Hunan Provincial Key Laboratory for Microbial Molecular Biology, State Key Laboratory of Development Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, 410081, China
| | - Shengbiao Hu
- Hunan Provincial Key Laboratory for Microbial Molecular Biology, State Key Laboratory of Development Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, 410081, China
| | - Qingji Xie
- Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research (MOE of China), National & Local Joint Engineering Laboratory for New Petro-Chemical Materials and Fine Utilization of Resources, College of Chemistry and Chemical Engineering, Hunan Normal University, Changsha, 410081, China.
| | - Liqiu Xia
- Hunan Provincial Key Laboratory for Microbial Molecular Biology, State Key Laboratory of Development Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, 410081, China.
| |
Collapse
|
8
|
Rang J, Cao L, Shuai L, Liu Y, Zhu Z, Xia Z, Jin D, Sun Y, Yu Z, Hu S, Xie Q, Xia L. Promoting Butenyl-spinosyn Production Based on Omics Research and Metabolic Network Construction in Saccharopolyspora pogona. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:3557-3567. [PMID: 35245059 DOI: 10.1021/acs.jafc.2c00285] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Understanding the metabolism of Saccharopolyspora pogona on a global scale is essential for manipulating its metabolic capabilities to improve butenyl-spinosyn biosynthesis. Here, we combined multiomics analysis to parse S. pogona genomic information, construct a metabolic network, and mine important functional genes that affect the butenyl-spinosyn biosynthesis. This research not only elucidated the relationship between butenyl-spinosyn biosynthesis and the primary metabolic pathway but also showed that the low expression level and continuous downregulation of the bus cluster and the competitive utilization of acetyl-CoA were the main reasons for reduced butenyl-spinosyn production. Our framework identified 148 genes related to butenyl-spinosyn biosynthesis that were significantly differentially expressed, confirming that butenyl-spinosyn polyketide synthase (PKS) and succinic semialdehyde dehydrogenase (GabD) play an important role in regulating butenyl-spinosyn biosynthesis. Combined modification of these genes increased overall butenyl-spinosyn production by 6.38-fold to 154.1 ± 10.98 mg/L. Our results provide an important strategy for further promoting the butenyl-spinosyn titer.
Collapse
Affiliation(s)
- Jie Rang
- Hunan Provincial Key Laboratory for Microbial Molecular Biology, State Key Laboratory of Development Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, Hunan 410081, People's Republic of China
- Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research (MOE of China), National & Local Joint Engineering Laboratory for New Petro-chemical Materials and Fine Utilization of Resources, College of Chemistry and Chemical Engineering, Hunan Normal University, Changsha, Hunan 410081, People's Republic of China
| | - Li Cao
- Hunan Provincial Key Laboratory for Microbial Molecular Biology, State Key Laboratory of Development Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, Hunan 410081, People's Republic of China
| | - Ling Shuai
- Hunan Provincial Key Laboratory for Microbial Molecular Biology, State Key Laboratory of Development Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, Hunan 410081, People's Republic of China
| | - Yang Liu
- Hunan Provincial Key Laboratory for Microbial Molecular Biology, State Key Laboratory of Development Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, Hunan 410081, People's Republic of China
| | - Zirong Zhu
- Hunan Provincial Key Laboratory for Microbial Molecular Biology, State Key Laboratory of Development Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, Hunan 410081, People's Republic of China
| | - Ziyuan Xia
- Hunan Provincial Key Laboratory for Microbial Molecular Biology, State Key Laboratory of Development Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, Hunan 410081, People's Republic of China
| | - Duo Jin
- Hunan Provincial Key Laboratory for Microbial Molecular Biology, State Key Laboratory of Development Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, Hunan 410081, People's Republic of China
| | - Yunjun Sun
- Hunan Provincial Key Laboratory for Microbial Molecular Biology, State Key Laboratory of Development Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, Hunan 410081, People's Republic of China
| | - Ziquan Yu
- Hunan Provincial Key Laboratory for Microbial Molecular Biology, State Key Laboratory of Development Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, Hunan 410081, People's Republic of China
| | - Shengbiao Hu
- Hunan Provincial Key Laboratory for Microbial Molecular Biology, State Key Laboratory of Development Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, Hunan 410081, People's Republic of China
| | - Qingji Xie
- Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research (MOE of China), National & Local Joint Engineering Laboratory for New Petro-chemical Materials and Fine Utilization of Resources, College of Chemistry and Chemical Engineering, Hunan Normal University, Changsha, Hunan 410081, People's Republic of China
| | - Liqiu Xia
- Hunan Provincial Key Laboratory for Microbial Molecular Biology, State Key Laboratory of Development Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, Hunan 410081, People's Republic of China
| |
Collapse
|
9
|
Nag A, Mehra S. Involvement of the SCO3366 efflux pump from S. coelicolor in rifampicin resistance and its regulation by a TetR regulator. Appl Microbiol Biotechnol 2022; 106:2175-2190. [PMID: 35194656 DOI: 10.1007/s00253-022-11837-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Revised: 02/05/2022] [Accepted: 02/12/2022] [Indexed: 11/26/2022]
Abstract
Overexpression of efflux pumps represents a key mechanism of resistance in bacteria. Soil bacteria such as Streptomyces harbour a vast array of efflux genes that are transcriptionally silent under laboratory conditions. However, dissemination of many of these genes into clinical pathogens via horizontal gene transfer results in conferring resistance to multiple drugs. In this study, we have identified the role of a MFS transporter, SCO3366 from Streptomyces coelicolor, in governing multidrug resistance. Overexpression and knockout studies revealed that SCO3366 provides resistance to several structurally unrelated drugs including ciprofloxacin, chloramphenicol, rifampicin and EtBr, with rifampicin being the major substrate. Beyond multidrug resistance, SCO3366 was efficient in providing tolerance towards oxidative stress. A combinatorial mechanism of increased oxidative stress tolerance decreased intracellular drug levels and decreased permeability act synergistically to provide resistance towards rifampicin. Shedding light on the regulation of SCO3366, we find the pump to be directly regulated by the TetR regulator SCO3367 in a negative manner and the repression was found to be relieved in presence of different compounds recognized as substrates of SCO3366. KEY POINTS: • First reported rifampicin efflux pump in Streptomyces coelicolor • Resistance to rifampicin is the result of a synergistic action of increased efflux with increased oxidative stress tolerance and decreased permeability, which can potentially arise in clinically relevant bacteria • SCO3366-SCO3367 to be a novel system that operates to protect the bacteria under varied environmental stress conditions.
Collapse
Affiliation(s)
- Ankita Nag
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Mumbai, 400076, India
| | - Sarika Mehra
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Mumbai, 400076, India.
| |
Collapse
|
10
|
Rang J, Li Y, Cao L, Shuai L, Liu Y, He H, Wan Q, Luo Y, Yu Z, Zhang Y, Sun Y, Ding X, Hu S, Xie Q, Xia L. Deletion of a hybrid NRPS-T1PKS biosynthetic gene cluster via Latour gene knockout system in Saccharopolyspora pogona and its effect on butenyl-spinosyn biosynthesis and growth development. Microb Biotechnol 2021; 14:2369-2384. [PMID: 33128503 PMCID: PMC8601190 DOI: 10.1111/1751-7915.13694] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Revised: 10/04/2020] [Accepted: 10/11/2020] [Indexed: 12/22/2022] Open
Abstract
Butenyl-spinosyn, a promising biopesticide produced by Saccharopolyspora pogona, exhibits stronger insecticidal activity and a broader pesticidal spectrum. However, its titre in the wild-type S. pogona strain is too low to meet the industrial production requirements. Deletion of non-target natural product biosynthetic gene clusters resident in the genome of S. pogona could reduce the consumption of synthetic precursors, thereby promoting the biosynthesis of butenyl-spinosyn. However, it has always been a challenge for scientists to genetically engineer S. pogona. In this study, the Latour gene knockout system (linear DNA fragment recombineering system) was established in S. pogona. Using the Latour system, a hybrid NRPS-T1PKS cluster (˜20 kb) which was responsible for phthoxazolin biosynthesis was efficiently deleted in S. pogona. The resultant mutant S. pogona-Δura4-Δc14 exhibited an extended logarithmic phase, increased biomass and a lower glucose consumption rate. Importantly, the production of butenyl-spinosyn in S. pogona-Δura4-Δc14 was increased by 4.72-fold compared with that in the wild-type strain. qRT-PCR analysis revealed that phthoxazolin biosynthetic gene cluster deletion could promote the expression of the butenyl-spinosyn biosynthetic gene cluster. Furthermore, a TetR family transcriptional regulatory gene that could regulate the butenyl-spinosyn biosynthesis has been identified from the phthoxazolin biosynthetic gene cluster. Because dozens of natural product biosynthetic gene clusters exist in the genome of S. pogona, the strategy reported here will be used to further promote the production of butenyl-spinosyn by deleting other secondary metabolite synthetic gene clusters.
Collapse
Affiliation(s)
- Jie Rang
- Hunan Provincial Key Laboratory for Microbial Molecular BiologyState Key Laboratory of Development Biology of Freshwater FishCollege of Life ScienceHunan Normal UniversityChangsha410081China
- Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research (MOE of China)National & Local Joint Engineering Laboratory for New Petro‐chemical Materials and Fine Utilization of ResourcesCollege of Chemistry and Chemical EngineeringHunan Normal UniversityChangsha410081China
| | - Yunlong Li
- Hunan Provincial Key Laboratory for Microbial Molecular BiologyState Key Laboratory of Development Biology of Freshwater FishCollege of Life ScienceHunan Normal UniversityChangsha410081China
| | - Li Cao
- Hunan Provincial Key Laboratory for Microbial Molecular BiologyState Key Laboratory of Development Biology of Freshwater FishCollege of Life ScienceHunan Normal UniversityChangsha410081China
| | - Ling Shuai
- Hunan Provincial Key Laboratory for Microbial Molecular BiologyState Key Laboratory of Development Biology of Freshwater FishCollege of Life ScienceHunan Normal UniversityChangsha410081China
| | - Yang Liu
- Hunan Provincial Key Laboratory for Microbial Molecular BiologyState Key Laboratory of Development Biology of Freshwater FishCollege of Life ScienceHunan Normal UniversityChangsha410081China
| | - Haocheng He
- Hunan Provincial Key Laboratory for Microbial Molecular BiologyState Key Laboratory of Development Biology of Freshwater FishCollege of Life ScienceHunan Normal UniversityChangsha410081China
| | - Qianqian Wan
- Hunan Provincial Key Laboratory for Microbial Molecular BiologyState Key Laboratory of Development Biology of Freshwater FishCollege of Life ScienceHunan Normal UniversityChangsha410081China
| | - Yuewen Luo
- Hunan Provincial Key Laboratory for Microbial Molecular BiologyState Key Laboratory of Development Biology of Freshwater FishCollege of Life ScienceHunan Normal UniversityChangsha410081China
| | - Ziquan Yu
- Hunan Provincial Key Laboratory for Microbial Molecular BiologyState Key Laboratory of Development Biology of Freshwater FishCollege of Life ScienceHunan Normal UniversityChangsha410081China
| | - Youming Zhang
- Hunan Provincial Key Laboratory for Microbial Molecular BiologyState Key Laboratory of Development Biology of Freshwater FishCollege of Life ScienceHunan Normal UniversityChangsha410081China
| | - Yunjun Sun
- Hunan Provincial Key Laboratory for Microbial Molecular BiologyState Key Laboratory of Development Biology of Freshwater FishCollege of Life ScienceHunan Normal UniversityChangsha410081China
| | - Xuezhi Ding
- Hunan Provincial Key Laboratory for Microbial Molecular BiologyState Key Laboratory of Development Biology of Freshwater FishCollege of Life ScienceHunan Normal UniversityChangsha410081China
| | - Shengbiao Hu
- Hunan Provincial Key Laboratory for Microbial Molecular BiologyState Key Laboratory of Development Biology of Freshwater FishCollege of Life ScienceHunan Normal UniversityChangsha410081China
| | - Qingji Xie
- Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research (MOE of China)National & Local Joint Engineering Laboratory for New Petro‐chemical Materials and Fine Utilization of ResourcesCollege of Chemistry and Chemical EngineeringHunan Normal UniversityChangsha410081China
| | - Liqiu Xia
- Hunan Provincial Key Laboratory for Microbial Molecular BiologyState Key Laboratory of Development Biology of Freshwater FishCollege of Life ScienceHunan Normal UniversityChangsha410081China
| |
Collapse
|
11
|
Tang J, He H, Li Y, Liu Z, Xia Z, Cao L, Zhu Z, Shuai L, Liu Y, Wan Q, Luo Y, Zhang Y, Rang J, Xia L. Comparative Proteomics Reveals the Effect of the Transcriptional Regulator Sp13016 on Butenyl-Spinosyn Biosynthesis in Saccharopolyspora pogona. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2021; 69:12554-12565. [PMID: 34657420 DOI: 10.1021/acs.jafc.1c03654] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Butenyl-spinosyn is a highly effective and broad-spectrum biopesticide produced by Saccharopolyspora pogona. However, the yield of this compound is difficult to increase because the regulatory mechanism of secondary metabolism is still unknown. Here, the transcriptional regulator Sp13016 was discovered to be highly associated with butenyl-spinosyn synthesis and bacterial growth. Overexpression of sp13016 improved butenyl-spinosyn production to a level that was 2.84-fold that of the original strain, while deletion of sp13016 resulted in a significant decrease in yield and growth inhibition. Comparative proteomics revealed that these phenotypic changes were attributed to the influence of Sp13016 on the central carbon metabolism pathway to regulate the supply of precursors. Our research helps to reveal the regulatory mechanism of butenyl-spinosyn biosynthesis and provides a reference for increasing the yield of natural products of Actinomycetes.
Collapse
Affiliation(s)
- Jianli Tang
- Hunan Provincial Key Laboratory for Microbial Molecular Biology, State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Lushan Road 36, Changsha 410081, China
| | - Haocheng He
- Hunan Provincial Key Laboratory for Microbial Molecular Biology, State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Lushan Road 36, Changsha 410081, China
| | - Yunlong Li
- Hunan Provincial Key Laboratory for Microbial Molecular Biology, State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Lushan Road 36, Changsha 410081, China
| | - Zhudong Liu
- Hunan Provincial Key Laboratory for Microbial Molecular Biology, State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Lushan Road 36, Changsha 410081, China
| | - Ziyuan Xia
- Hunan Provincial Key Laboratory for Microbial Molecular Biology, State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Lushan Road 36, Changsha 410081, China
| | - Li Cao
- Hunan Provincial Key Laboratory for Microbial Molecular Biology, State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Lushan Road 36, Changsha 410081, China
| | - Zirong Zhu
- Hunan Provincial Key Laboratory for Microbial Molecular Biology, State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Lushan Road 36, Changsha 410081, China
| | - Ling Shuai
- Hunan Provincial Key Laboratory for Microbial Molecular Biology, State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Lushan Road 36, Changsha 410081, China
| | - Yang Liu
- Hunan Provincial Key Laboratory for Microbial Molecular Biology, State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Lushan Road 36, Changsha 410081, China
| | - Qianqian Wan
- Hunan Provincial Key Laboratory for Microbial Molecular Biology, State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Lushan Road 36, Changsha 410081, China
| | - Yuewen Luo
- Hunan Provincial Key Laboratory for Microbial Molecular Biology, State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Lushan Road 36, Changsha 410081, China
| | - Youming Zhang
- Hunan Provincial Key Laboratory for Microbial Molecular Biology, State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Lushan Road 36, Changsha 410081, China
| | - Jie Rang
- Hunan Provincial Key Laboratory for Microbial Molecular Biology, State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Lushan Road 36, Changsha 410081, China
| | - Liqiu Xia
- Hunan Provincial Key Laboratory for Microbial Molecular Biology, State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Lushan Road 36, Changsha 410081, China
| |
Collapse
|
12
|
Inactivation of Nitrite-Dependent Nitric Oxide Biosynthesis Is Responsible for Overlapped Antibiotic Resistance between Naturally and Artificially Evolved Pseudomonas aeruginosa. mSystems 2021; 6:e0073221. [PMID: 34546070 PMCID: PMC8547483 DOI: 10.1128/msystems.00732-21] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Metabolic flexibility of Pseudomonas aeruginosa could lead to new strategies to combat bacterial infection. The present study used gas chromatography-mass spectrometry (GC-MS)-based metabolomics to investigate global metabolism in naturally and artificially evolved strains with cefoperazone-sulbactam (SCF) resistance (AP-RCLIN-EVO and AP-RLAB-EVO, respectively) from the same parent strain (AP-RCLIN). Inactivation of the pyruvate cycle and nitric oxide (NO) biosynthesis was identified as characteristic features of SCF resistance in both evolved strains. Nitrite-dependent NO biosynthesis instead of an arginine-dependent NO pathway is responsible for the reduced NO, which is attributed to lower nitrite and electrons from the oxidation of NADH to NAD+ provided by the pyruvate cycle. Exogenous fumarate, NADH, nitrate, and nitrite promoted the NO level and thereby potentiated SCF-mediated killing. Unexpectedly, fumarate caused the elevation of nitrite, while nitrite/nitrate resulted in the increase of Cyt bc1 complex (providing electrons). These interesting findings indicate that the nitrite-dependent NO biosynthesis and the pyruvate cycle are mutual to promote NO metabolism. In addition, the NO-potentiated sensitivity to SCF was validated by NO donor sodium nitroprusside. These results reveal an endogenous NO-mediated SCF resistance and develop its reversion by metabolites in P. aeruginosa. IMPORTANCE Infections with Pseudomonas aeruginosa have become a real concern among hospital-acquired infections, especially in cystic fibrosis patients and immunocompromised individuals. Control of the pathogen is challenging due to antibiotic resistance. Since bacterial metabolic state impacts sensitivity and resistance to antibiotics, exploring and disclosing bacterial metabolic mechanisms can be used to develop a metabolome-reprogramming approach to elevate bacterial sensitivity to antibiotics. Therefore, GC-MS-based metabolomics is used to explore the similarities and differences of metabolomes between naturally and artificially evolved cefoperazone-sulbactam (SCF)-resistant P. aeruginosa (AP-RCLIN-EVO and AP-RLAB-EVO, respectively) from the same parent strain (AP-RCLIN). It identifies the depressed nitrite-dependent nitric oxide (NO) biosynthesis as the most overlapping characteristic feature between AP-RCLIN-EVO and AP-RLAB-EVO. This is because the pyruvate cycle fluctuates, thereby generating fewer NADH and providing fewer electrons for nitrite-dependent NO biosynthesis than the control. Interestingly, exogenous fumarate, NADH, nitrate, and nitrite as well as NO donor sodium nitroprusside promote NO generation to elevate sensitivity to SCF. These results highlight the way to understand metabolic mechanisms of antibiotic resistance and explore metabolic modulation to combat the bacterial pathogen.
Collapse
|
13
|
He H, Tang J, Chen J, Hu J, Zhu Z, Liu Y, Shuai L, Cao L, Liu Z, Xia Z, Ding X, Hu S, Zhang Y, Rang J, Xia L. Flaviolin-Like Gene Cluster Deletion Optimized the Butenyl-Spinosyn Biosynthesis Route in Saccharopolyspora pogona. ACS Synth Biol 2021; 10:2740-2752. [PMID: 34601869 DOI: 10.1021/acssynbio.1c00344] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Reduction and optimization of the microbial genome is an important strategy for constructing synthetic biological chassis cells and overcoming obstacles in natural product discovery and production. However, it is of great challenge to discover target genes that can be deleted and optimized due to the complicated genome of actinomycetes. Saccharopolyspora pogona can produce butenyl-spinosyn during aerobic fermentation, and its genome contains 32 different gene clusters. This suggests that there is a large amount of potential competitive metabolism in S. pogona, which affects the biosynthesis of butenyl-spinosyn. By analyzing the genome of S. pogona, six polyketide gene clusters were identified. From those, the complete deletion of clu13, a flaviolin-like gene cluster, generated a high butenyl-spinosyn-producing strain. Production of this strain was 4.06-fold higher than that of the wildtype strain. Transcriptome profiling revealed that butenyl-spinosyn biosynthesis was not primarily induced by the polyketide synthase RppA-like but was related to hypothetical protein Sp1764. However, the repression of sp1764 was not enough to explain the enormous enhancement of butenyl-spinosyn yields in S. pogona-Δclu13. After the comparative proteomic analysis of S. pogona-Δclu13 and S. pogona, two proteins, biotin carboxyl carrier protein (BccA) and response regulator (Reg), were investigated, whose overexpression led to great advantages of butenyl-spinosyn biosynthesis. In this way, we successfully discovered three key genes that obviously optimize the biosynthesis of butenyl-spinosyn. Gene cluster simplification performed in conjunction with multiomics analysis is of great practical significance for screening dominant chassis strains and optimizing secondary metabolism. This work provided an idea about screening key factors and efficient construction of production strains.
Collapse
Affiliation(s)
- Haocheng He
- Hunan Provincial Key Laboratory for Microbial Molecular Biology, State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha 410083, China
| | - Jianli Tang
- Hunan Provincial Key Laboratory for Microbial Molecular Biology, State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha 410083, China
| | - Jianming Chen
- Hunan Provincial Key Laboratory for Microbial Molecular Biology, State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha 410083, China
| | - Jinjuan Hu
- Hunan Provincial Key Laboratory for Microbial Molecular Biology, State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha 410083, China
| | - Zirong Zhu
- Hunan Provincial Key Laboratory for Microbial Molecular Biology, State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha 410083, China
| | - Yang Liu
- Hunan Provincial Key Laboratory for Microbial Molecular Biology, State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha 410083, China
| | - Ling Shuai
- Hunan Provincial Key Laboratory for Microbial Molecular Biology, State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha 410083, China
| | - Li Cao
- Hunan Provincial Key Laboratory for Microbial Molecular Biology, State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha 410083, China
| | - Zhudong Liu
- Hunan Provincial Key Laboratory for Microbial Molecular Biology, State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha 410083, China
| | - Ziyuan Xia
- Hunan Provincial Key Laboratory for Microbial Molecular Biology, State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha 410083, China
| | - Xuezhi Ding
- Hunan Provincial Key Laboratory for Microbial Molecular Biology, State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha 410083, China
| | - Shengbiao Hu
- Hunan Provincial Key Laboratory for Microbial Molecular Biology, State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha 410083, China
| | - Youming Zhang
- Hunan Provincial Key Laboratory for Microbial Molecular Biology, State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha 410083, China
| | - Jie Rang
- Hunan Provincial Key Laboratory for Microbial Molecular Biology, State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha 410083, China
| | - Liqiu Xia
- Hunan Provincial Key Laboratory for Microbial Molecular Biology, State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha 410083, China
| |
Collapse
|
14
|
Tang J, Zhu Z, He H, Liu Z, Xia Z, Chen J, Hu J, Cao L, Rang J, Shuai L, Liu Y, Sun Y, Ding X, Hu S, Xia L. Bacterioferritin: a key iron storage modulator that affects strain growth and butenyl-spinosyn biosynthesis in Saccharopolyspora pogona. Microb Cell Fact 2021; 20:157. [PMID: 34391414 PMCID: PMC8364703 DOI: 10.1186/s12934-021-01651-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Accepted: 08/06/2021] [Indexed: 12/02/2022] Open
Abstract
Background Butenyl-spinosyn, produced by Saccharopolyspora pogona, is a promising biopesticide due to excellent insecticidal activity and broad pesticidal spectrum. Bacterioferritin (Bfr, encoded by bfr) regulates the storage and utilization of iron, which is essential for the growth and metabolism of microorganisms. However, the effect of Bfr on the growth and butenyl-spinosyn biosynthesis in S. pogona has not been explored. Results Here, we found that the storage of intracellular iron influenced butenyl-spinosyn biosynthesis and the stress resistance of S. pogona, which was regulated by Bfr. The overexpression of bfr increased the production of butenyl-spinosyn by 3.14-fold and enhanced the tolerance of S. pogona to iron toxicity and oxidative damage, while the knockout of bfr had the opposite effects. Based on the quantitative proteomics analysis and experimental verification, the inner mechanism of these phenomena was explored. Overexpression of bfr enhanced the iron storage capacity of the strain, which activated polyketide synthase genes and enhanced the supply of acyl-CoA precursors to improve butenyl-spinosyn biosynthesis. In addition, it induced the oxidative stress response to improve the stress resistance of S. pogona. Conclusion Our work reveals the role of Bfr in increasing the yield of butenyl-spinosyn and enhancing the stress resistance of S. pogona, and provides insights into its enhancement on secondary metabolism, which provides a reference for optimizing the production of secondary metabolites in actinomycetes. Supplementary Information The online version contains supplementary material available at 10.1186/s12934-021-01651-x.
Collapse
Affiliation(s)
- Jianli Tang
- Hunan Provincial Key Laboratory for Microbial Molecular Biology, State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, 410081, China
| | - Zirong Zhu
- Hunan Provincial Key Laboratory for Microbial Molecular Biology, State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, 410081, China
| | - Haocheng He
- Hunan Provincial Key Laboratory for Microbial Molecular Biology, State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, 410081, China
| | - Zhudong Liu
- Hunan Provincial Key Laboratory for Microbial Molecular Biology, State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, 410081, China
| | - Ziyuan Xia
- Hunan Provincial Key Laboratory for Microbial Molecular Biology, State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, 410081, China
| | - Jianming Chen
- Hunan Provincial Key Laboratory for Microbial Molecular Biology, State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, 410081, China
| | - Jinjuan Hu
- Hunan Provincial Key Laboratory for Microbial Molecular Biology, State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, 410081, China
| | - Li Cao
- Hunan Provincial Key Laboratory for Microbial Molecular Biology, State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, 410081, China
| | - Jie Rang
- Hunan Provincial Key Laboratory for Microbial Molecular Biology, State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, 410081, China.
| | - Ling Shuai
- Hunan Provincial Key Laboratory for Microbial Molecular Biology, State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, 410081, China
| | - Yang Liu
- Hunan Provincial Key Laboratory for Microbial Molecular Biology, State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, 410081, China
| | - Yunjun Sun
- Hunan Provincial Key Laboratory for Microbial Molecular Biology, State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, 410081, China
| | - Xuezhi Ding
- Hunan Provincial Key Laboratory for Microbial Molecular Biology, State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, 410081, China
| | - Shengbiao Hu
- Hunan Provincial Key Laboratory for Microbial Molecular Biology, State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, 410081, China
| | - Liqiu Xia
- Hunan Provincial Key Laboratory for Microbial Molecular Biology, State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, 410081, China.
| |
Collapse
|
15
|
Liu Z, Zhu Z, Tang J, He H, Wan Q, Luo Y, Huang W, Yu Z, Hu Y, Ding X, Xia L. RNA-Seq-Based Transcriptomic Analysis of Saccharopolyspora spinosa Revealed the Critical Function of PEP Phosphonomutase in the Replenishment Pathway. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2020; 68:14660-14669. [PMID: 33258371 DOI: 10.1021/acs.jafc.0c04443] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Spinosyns, the secondary metabolites produced by Saccharopolyspora spinosa, are the active ingredients in a family of novel biological insecticides. Although the complete genome sequence of S. spinosa has been published, the transcriptome of S. spinosa remains poorly characterized. In this study, high-throughput RNA sequencing (RNA-seq) technology was applied to dissect the transcriptome of S. spinosa. Through transcriptomic analysis of different periods of S. spinosa growth, we found large numbers of differentially expressed genes and classified them according to their different functions. Based on the RNA-seq data, the CRISPR-Cas9 method was used to knock out the PEP phosphonomutase gene (orf 06952-4171). The yield of spinosyns A and D in S. spinosa-ΔPEP was 178.91 mg/L and 42.72 mg/L, which was 2.14-fold and 1.76-fold higher than that in the wild type (83.51 and 24.34 mg/L), respectively. The analysis of the mutant strains also verified the validity of the transcriptome data. The deletion of the PEP phosphonomutase gene leads to an increase in pyruvate content and affects the biosynthesis of spinosad. The replenishment of phosphoenol pyruvate in S. spinosa provides the substrate for the production of spinosad. We envision that these transcriptomic analysis results will contribute to the further study of secondary metabolites in actinomycetes.
Collapse
Affiliation(s)
- Zhudong Liu
- State Key Laboratory of Development Biology of Freshwater Fish, Hunan Provincial Key Laboratory for Microbial Molecular Biology, College of Life Science, Hunan Normal University, Changsha 410081, China
| | - Zirong Zhu
- State Key Laboratory of Development Biology of Freshwater Fish, Hunan Provincial Key Laboratory for Microbial Molecular Biology, College of Life Science, Hunan Normal University, Changsha 410081, China
| | - Jianli Tang
- State Key Laboratory of Development Biology of Freshwater Fish, Hunan Provincial Key Laboratory for Microbial Molecular Biology, College of Life Science, Hunan Normal University, Changsha 410081, China
| | - Haocheng He
- State Key Laboratory of Development Biology of Freshwater Fish, Hunan Provincial Key Laboratory for Microbial Molecular Biology, College of Life Science, Hunan Normal University, Changsha 410081, China
| | - Qianqian Wan
- State Key Laboratory of Development Biology of Freshwater Fish, Hunan Provincial Key Laboratory for Microbial Molecular Biology, College of Life Science, Hunan Normal University, Changsha 410081, China
| | - Yuewen Luo
- State Key Laboratory of Development Biology of Freshwater Fish, Hunan Provincial Key Laboratory for Microbial Molecular Biology, College of Life Science, Hunan Normal University, Changsha 410081, China
| | - Weitao Huang
- State Key Laboratory of Development Biology of Freshwater Fish, Hunan Provincial Key Laboratory for Microbial Molecular Biology, College of Life Science, Hunan Normal University, Changsha 410081, China
| | - Ziquan Yu
- State Key Laboratory of Development Biology of Freshwater Fish, Hunan Provincial Key Laboratory for Microbial Molecular Biology, College of Life Science, Hunan Normal University, Changsha 410081, China
| | - Yibo Hu
- State Key Laboratory of Development Biology of Freshwater Fish, Hunan Provincial Key Laboratory for Microbial Molecular Biology, College of Life Science, Hunan Normal University, Changsha 410081, China
| | - Xuezhi Ding
- State Key Laboratory of Development Biology of Freshwater Fish, Hunan Provincial Key Laboratory for Microbial Molecular Biology, College of Life Science, Hunan Normal University, Changsha 410081, China
| | - Liqiu Xia
- State Key Laboratory of Development Biology of Freshwater Fish, Hunan Provincial Key Laboratory for Microbial Molecular Biology, College of Life Science, Hunan Normal University, Changsha 410081, China
| |
Collapse
|
16
|
He H, Peng S, Yuan S, Tang J, Liu Z, Rang J, Xia Z, Hu J, Chen J, Ding X, Hu S, Sun Y, Xia L. Effects of lytS-L on the primary metabolism and butenyl-spinosyn biosynthesis in Saccharopolyspora pogona. Gene 2020; 766:145130. [PMID: 32911030 DOI: 10.1016/j.gene.2020.145130] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2019] [Revised: 07/31/2020] [Accepted: 09/01/2020] [Indexed: 12/11/2022]
Abstract
The LytTR family two-component system widely exists in bacterial cells and plays an important role in metabolic regulation. The lytS-L gene that encodes for a LytTR family sensor kinase was knocked out to study its influence on the growth, phenotype, and the biosynthesis of the insecticidal polyketide butenyl-spinosyn in Saccharopolyspora pogona NRRL 30141 (S. pogona). High performance liquid chromatography (HPLC) results showed that the butenyl-spinosyn yield of the lytS-L knockout mutant decreased by 58.9% compared with that of the parental strain. This is manifested by a weak toxicity of the mutant against the insect Helicoverpa assulta (H. armigera). Comparative proteomic analysis revealed the expression characteristics of the proteins in S. pogona and S. pogona-ΔlytS-L: a total of 14 proteins involved in energy metabolism were down-regulated, 9 proteins related to carbon metabolism such as glycolysis, and tricarboxylic acid cycle (TCA) were up-regulated, while 13 proteins involved in the biosynthesis of butenyl-spinosyn were down-regulated (fold change >1.2 or< 0.83). The qRT-PCR (Quantitative Real-time PCR) analysis illustrated that the changes in the expression levels of transcription and translation of the identified genes were consistent. This study explores the function of the two-component system of the LytTR family in S. pogona and shows that the lytS-L gene has an important influence on regulating primary metabolism and butenyl-spinosyn biosynthesis of S. pogona.
Collapse
Affiliation(s)
- Haocheng He
- Hunan Provincial Key Laboratory for Microbial Molecular Biology, State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, China
| | - Shengnan Peng
- Hunan Provincial Key Laboratory for Microbial Molecular Biology, State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, China
| | - Shuangqin Yuan
- Hunan Provincial Key Laboratory for Microbial Molecular Biology, State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, China
| | - Jianli Tang
- Hunan Provincial Key Laboratory for Microbial Molecular Biology, State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, China
| | - Zhudong Liu
- Hunan Provincial Key Laboratory for Microbial Molecular Biology, State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, China
| | - Jie Rang
- Hunan Provincial Key Laboratory for Microbial Molecular Biology, State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, China
| | - Ziyuan Xia
- Hunan Provincial Key Laboratory for Microbial Molecular Biology, State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, China
| | - Jinjuan Hu
- Hunan Provincial Key Laboratory for Microbial Molecular Biology, State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, China
| | - Jianming Chen
- Hunan Provincial Key Laboratory for Microbial Molecular Biology, State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, China
| | - Xuezhi Ding
- Hunan Provincial Key Laboratory for Microbial Molecular Biology, State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, China
| | - Shengbiao Hu
- Hunan Provincial Key Laboratory for Microbial Molecular Biology, State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, China
| | - Yunjun Sun
- Hunan Provincial Key Laboratory for Microbial Molecular Biology, State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, China.
| | - Liqiu Xia
- Hunan Provincial Key Laboratory for Microbial Molecular Biology, State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, China.
| |
Collapse
|