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Wilbanks L, Hennigan HE, Martinez-Brokaw CD, Lakkis H, Thormann S, Eggly AS, Buechel G, Parkinson EI. Synthesis of Gamma-Butyrolactone Hormones Enables Understanding of Natural Product Induction. ACS Chem Biol 2023; 18:1624-1631. [PMID: 37338162 PMCID: PMC10368014 DOI: 10.1021/acschembio.3c00241] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Accepted: 06/05/2023] [Indexed: 06/21/2023]
Abstract
Bacteria produce natural products (NPs) via biosynthetic gene clusters. Unfortunately, many biosynthetic gene clusters are silent under traditional laboratory conditions. To access novel NPs, a better understanding of their regulation is needed. γ-Butyrolactones, including the A-factor and Streptomyces coelicolor butanolides, SCBs, are a major class of Streptomyces' hormones. Study of these hormones has been limited due to challenges in accessing them in stereochemically pure forms. Herein, we describe an efficient route to (R)-paraconyl alcohol, a key intermediate for these molecules, as well as a biocatalytic method to access the exocyclic hydroxyl group that differentiates A-factor-type from SCB-type hormones. Utilizing these methods, a library of hormones have been synthesized and tested in a green fluorescent protein reporter assay for their ability to relieve repression by the repressor ScbR. This allowed the most quantitative structure-activity relationship of γ-butyrolactones and a cognate repressor to date. Bioinformatics analysis strongly suggests that many other repressors of NP biosynthesis likely bind similar molecules. This efficient, diversifiable synthesis will enable further investigation of the regulation of NP biosynthesis.
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Affiliation(s)
- Lauren
E. Wilbanks
- Department
of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
| | - Haylie E. Hennigan
- Department
of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
| | | | - Hani Lakkis
- Department
of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
| | - Sarah Thormann
- Department
of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
| | - Alyssa S. Eggly
- Department
of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
| | - Grace Buechel
- Department
of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
| | - Elizabeth I. Parkinson
- Department
of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
- Department
of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, Indiana 47907, United States
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2
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Alwali AY, Parkinson EI. Small molecule inducers of actinobacteria natural product biosynthesis. J Ind Microbiol Biotechnol 2023; 50:kuad019. [PMID: 37587009 PMCID: PMC10549211 DOI: 10.1093/jimb/kuad019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Accepted: 08/14/2023] [Indexed: 08/18/2023]
Abstract
Actinobacteria are a large and diverse group of bacteria that are known to produce a wide range of secondary metabolites, many of which have important biological activities, including antibiotics, anti-cancer agents, and immunosuppressants. The biosynthesis of these compounds is often highly regulated with many natural products (NPs) being produced at very low levels in laboratory settings. Environmental factors, such as small molecule elicitors, can induce the production of secondary metabolites. Specifically, they can increase titers of known NPs as well as enabling discovery of novel NPs typically produced at undetectable levels. These elicitors can be NPs, including antibiotics or hormones, or synthetic compounds. In recent years, there has been a growing interest in the use of small molecule elicitors to induce the production of secondary metabolites from actinobacteria, especially for the discovery of NPs from "silent" biosynthetic gene clusters. This review aims to highlight classes of molecules that induce secondary metabolite production in actinobacteria and to describe the potential mechanisms of induction. ONE-SENTENCE SUMMARY This review describes chemical elicitors of actinobacteria natural products described to date and the proposed mechanisms of induction.
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Affiliation(s)
- Amir Y Alwali
- Department of Chemistry, Purdue University, West Lafayette, IN 47907, USA
| | - Elizabeth I Parkinson
- Department of Chemistry, Purdue University, West Lafayette, IN 47907, USA
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN 47907, USA
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3
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Chen D, Nie M, Tang W, Zhang Y, Wang J, Lan Y, Chen Y, Du W. Whole lifecycle observation of single-spore germinated Streptomyces using a nanogap-stabilized microfluidic chip. MLIFE 2022; 1:341-349. [PMID: 38818224 PMCID: PMC10989842 DOI: 10.1002/mlf2.12039] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/02/2022] [Revised: 08/01/2022] [Accepted: 08/12/2022] [Indexed: 06/01/2024]
Abstract
Streptomyces is a model bacterium to study multicellular differentiation and the major reservoir for antibiotics discovery. However, the cellular-level lifecycle of Streptomyces has not been well studied due to its complexity and lack of research tools that can mimic their natural conditions. In this study, we developed a simple microfluidic chip for the cultivation and observation of the entire lifecycle of Streptomyces development from the single-cell perspective. The chip consists of channels for loading samples and supplying nutrients, microwell arrays for the seeding and growth of single spores, and air chambers beside the microwells that facilitate the development of aerial hyphae and spores. A unique feature of this chip is that each microwell is surrounded by a 1.5 µm nanogap connected to an air chamber, which provides a stabilized water-air interface. We used this chip to observe the lifecycle development of Streptomyces coelicolor and Streptomyces griseus germinated from single spores, which revealed differentiation of aerial hyphae with progeny spores at micron-scale water-air interfaces and air chambers. Finally, we demonstrated the applicability of this chip in phenotypic assays by showing that the microbial hormone A-Factor is involved in the regulatory pathways of aerial hyphae and spore formation. The microfluidic chip could become a robust tool for studying multicellular differentiation, single-spore heterogeneity, and secondary metabolism of single-spore germinated Streptomyces.
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Affiliation(s)
- Dongwei Chen
- State Key Laboratory of Microbial Resources, Institute of MicrobiologyChinese Academy of SciencesBeijingChina
| | - Mengyue Nie
- State Key Laboratory of Microbial Resources, Institute of MicrobiologyChinese Academy of SciencesBeijingChina
- College of Life SciencesUniversity of the Chinese Academy of SciencesBeijingChina
| | - Wei Tang
- State Key Laboratory of Microbial Resources, Institute of MicrobiologyChinese Academy of SciencesBeijingChina
| | - Yuwei Zhang
- State Key Laboratory of Microbial Resources, Institute of MicrobiologyChinese Academy of SciencesBeijingChina
| | - Jian Wang
- State Key Laboratory of Microbial Resources, Institute of MicrobiologyChinese Academy of SciencesBeijingChina
| | - Ying Lan
- State Key Laboratory of Microbial Resources, Institute of MicrobiologyChinese Academy of SciencesBeijingChina
| | - Yihua Chen
- State Key Laboratory of Microbial Resources, Institute of MicrobiologyChinese Academy of SciencesBeijingChina
- College of Life SciencesUniversity of the Chinese Academy of SciencesBeijingChina
| | - Wenbin Du
- State Key Laboratory of Microbial Resources, Institute of MicrobiologyChinese Academy of SciencesBeijingChina
- Savaid Medical SchoolUniversity of the Chinese Academy of SciencesBeijingChina
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Connolly JA, Harcombe WR, Smanski MJ, Kinkel LL, Takano E, Breitling R. Harnessing intercellular signals to engineer the soil microbiome. Nat Prod Rep 2021; 39:311-324. [PMID: 34850800 DOI: 10.1039/d1np00034a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Covering: Focus on 2015 to 2020Plant and soil microbiomes consist of diverse communities of organisms from across kingdoms and can profoundly affect plant growth and health. Natural product-based intercellular signals govern important interactions between microbiome members that ultimately regulate their beneficial or harmful impacts on the plant. Exploiting these evolved signalling circuits to engineer microbiomes towards beneficial interactions with crops is an attractive goal. There are few reports thus far of engineering the intercellular signalling of microbiomes, but this article argues that it represents a tremendous opportunity for advancing the field of microbiome engineering. This could be achieved through the selection of synergistic consortia in combination with genetic engineering of signal pathways to realise an optimised microbiome.
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Affiliation(s)
- Jack A Connolly
- Manchester Institute of Biotechnology, Manchester Synthetic Biology Research Centre SYNBIOCHEM, Faculty of Science and Engineering, School of Natural Sciences, Department of Chemistry, The University of Manchester, Manchester, M1 7DN, UK.
| | - William R Harcombe
- BioTechnology Institute, University of Minnesota, Twin-Cities, Saint Paul, MN55108, USA.,Department of Evolution, and Behaviour, University of Minnesota, Twin-Cities Saint Paul, MN55108, USA
| | - Michael J Smanski
- BioTechnology Institute, University of Minnesota, Twin-Cities, Saint Paul, MN55108, USA.,Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Twin-Cities, Saint Paul, MN55108, USA
| | - Linda L Kinkel
- BioTechnology Institute, University of Minnesota, Twin-Cities, Saint Paul, MN55108, USA.,Department of Plant Pathology, University of Minnesota, Twin-Cities, Saint Paul, MN 55108, USA
| | - Eriko Takano
- Manchester Institute of Biotechnology, Manchester Synthetic Biology Research Centre SYNBIOCHEM, Faculty of Science and Engineering, School of Natural Sciences, Department of Chemistry, The University of Manchester, Manchester, M1 7DN, UK.
| | - Rainer Breitling
- Manchester Institute of Biotechnology, Manchester Synthetic Biology Research Centre SYNBIOCHEM, Faculty of Science and Engineering, School of Natural Sciences, Department of Chemistry, The University of Manchester, Manchester, M1 7DN, UK.
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Siupka P, Hansen FT, Schier A, Rocco S, Sørensen T, Piotrowska-Seget Z. Antifungal Activity and Biosynthetic Potential of New Streptomyces sp. MW-W600-10 Strain Isolated from Coal Mine Water. Int J Mol Sci 2021; 22:ijms22147441. [PMID: 34299061 PMCID: PMC8303363 DOI: 10.3390/ijms22147441] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Revised: 06/30/2021] [Accepted: 07/08/2021] [Indexed: 12/20/2022] Open
Abstract
Crop infections by fungi lead to severe losses in food production and pose risks for human health. The increasing resistance of pathogens to fungicides has led to the higher usage of these chemicals, which burdens the environment and highlights the need to find novel natural biocontrol agents. Members of the genus Streptomyces are known to produce a plethora of bioactive compounds. Recently, researchers have turned to extreme and previously unexplored niches in the search for new strains with antimicrobial activities. One such niche are underground coal mine environments. We isolated the new Streptomyces sp. MW-W600-10 strain from coal mine water samples collected at 665 m below ground level. We examined the antifungal activity of the strain against plant pathogens Fusarium culmorum DSM62188 and Nigrospora oryzae roseF7. Furthermore, we analyzed the strain’s biosynthetic potential with the antiSMASH tool. The strain showed inhibitory activity against both fungi strains. Genome mining revealed that it has 39 BGCs, among which 13 did not show similarity to those in databases. Additionally, we examined the activity of the Streptomyces sp. S-2 strain isolated from black soot against F. culmorum DSM62188. These results show that coal-related strains could be a source of novel bioactive compounds. Future studies will elucidate their full biotechnological potential.
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Affiliation(s)
- Piotr Siupka
- Faculty of Natural Sciences, Institute of Biology, Biotechnology and Environmental Protection, University of Silesia in Katowice, 40032 Katowice, Poland; (A.S.); (S.R.); (Z.P.-S.)
- Correspondence:
| | - Frederik Teilfeldt Hansen
- Faculty of Engineering and Science, Department of Chemistry and Biosciences, University of Aalborg, 9220 Aalborg, Denmark; (F.T.H.); (T.S.)
| | - Aleksandra Schier
- Faculty of Natural Sciences, Institute of Biology, Biotechnology and Environmental Protection, University of Silesia in Katowice, 40032 Katowice, Poland; (A.S.); (S.R.); (Z.P.-S.)
| | - Simone Rocco
- Faculty of Natural Sciences, Institute of Biology, Biotechnology and Environmental Protection, University of Silesia in Katowice, 40032 Katowice, Poland; (A.S.); (S.R.); (Z.P.-S.)
| | - Trine Sørensen
- Faculty of Engineering and Science, Department of Chemistry and Biosciences, University of Aalborg, 9220 Aalborg, Denmark; (F.T.H.); (T.S.)
| | - Zofia Piotrowska-Seget
- Faculty of Natural Sciences, Institute of Biology, Biotechnology and Environmental Protection, University of Silesia in Katowice, 40032 Katowice, Poland; (A.S.); (S.R.); (Z.P.-S.)
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6
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Rational engineering strategies for achieving high-yield, high-quality and high-stability of natural product production in actinomycetes. Metab Eng 2021; 67:198-215. [PMID: 34166765 DOI: 10.1016/j.ymben.2021.06.003] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Revised: 05/30/2021] [Accepted: 06/19/2021] [Indexed: 12/11/2022]
Abstract
Actinomycetes are recognized as excellent producers of microbial natural products, which have a wide range of applications, especially in medicine, agriculture and stockbreeding. The three main indexes of industrialization (titer, purity and stability) must be taken into overall consideration in the manufacturing process of natural products. Over the past decades, synthetic biology techniques have expedited the development of industrially competitive strains with excellent performances. Here, we summarize various rational engineering strategies for upgrading the performance of industrial actinomycetes, which include enhancing the yield of natural products, eliminating the by-products and improving the genetic stability of engineered strains. Furthermore, the current challenges and future perspectives for optimizing the industrial strains more systematically through combinatorial engineering strategies are also discussed.
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Zhou Q, Ning S, Luo Y. Coordinated regulation for nature products discovery and overproduction in Streptomyces. Synth Syst Biotechnol 2020; 5:49-58. [PMID: 32346621 PMCID: PMC7176746 DOI: 10.1016/j.synbio.2020.04.002] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Revised: 04/04/2020] [Accepted: 04/08/2020] [Indexed: 12/19/2022] Open
Abstract
Streptomyces is an important treasure trove for natural products discovery. In recent years, many scientists focused on the genetic modification and metabolic regulation of Streptomyces to obtain diverse bioactive compounds with high yields. This review summarized the commonly used regulatory strategies for natural products discovery and overproduction in Streptomyces from three main aspects, including regulator-related strategies, promoter engineering, as well as other strategies employing transposons, signal factors, or feedback regulations. It is expected that the metabolic regulation network of Streptomyces will be elucidated more comprehensively to shed light on natural products research in the future.
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Affiliation(s)
- Qun Zhou
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China
| | - Shuqing Ning
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China
| | - Yunzi Luo
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China
- Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin University, Tianjin, 300072, China
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