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The Structural Diversity of Marine Microbial Secondary Metabolites Based on Co-Culture Strategy: 2009-2019. Mar Drugs 2020; 18:md18090449. [PMID: 32867339 PMCID: PMC7551240 DOI: 10.3390/md18090449] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Revised: 08/25/2020] [Accepted: 08/25/2020] [Indexed: 12/15/2022] Open
Abstract
Marine microorganisms have drawn great attention as novel bioactive natural product sources, particularly in the drug discovery area. Using different strategies, marine microbes have the ability to produce a wide variety of molecules. One of these strategies is the co-culturing of marine microbes; if two or more microorganisms are aseptically cultured together in a solid or liquid medium in a certain environment, their competition or synergetic relationship can activate the silent biosynthetic genes to produce cryptic natural products which do not exist in monocultures of the partner microbes. In recent years, the co-cultivation strategy of marine microbes has made more novel natural products with various biological activities. This review focuses on the significant and excellent examples covering sources, types, structures and bioactivities of secondary metabolites based on co-cultures of marine-derived microorganisms from 2009 to 2019. A detailed discussion on future prospects and current challenges in the field of co-culture is also provided on behalf of the authors’ own views of development tendencies.
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Xie Y, Chen J, Wang B, Chen T, Chen J, Zhang Y, Liu X, Chen Q. Activation and enhancement of caerulomycin A biosynthesis in marine-derived Actinoalloteichus sp. AHMU CJ021 by combinatorial genome mining strategies. Microb Cell Fact 2020; 19:159. [PMID: 32762690 PMCID: PMC7412835 DOI: 10.1186/s12934-020-01418-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2020] [Accepted: 07/30/2020] [Indexed: 12/17/2022] Open
Abstract
Background Activation of silent biosynthetic gene clusters (BGCs) in marine-derived actinomycete strains is a feasible strategy to discover bioactive natural products. Actinoalloteichus sp. AHMU CJ021, isolated from the seashore, was shown to contain an intact but silent caerulomycin A (CRM A) BGC-cam in its genome. Thus, a genome mining work was preformed to activate the strain’s production of CRM A, an immunosuppressive drug lead with diverse bioactivities. Results To well activate the expression of cam, ribosome engineering was adopted to treat the wild type Actinoalloteichus sp. AHMU CJ021. The initial mutant strain XC-11G with gentamycin resistance and CRM A production titer of 42.51 ± 4.22 mg/L was selected from all generated mutant strains by gene expression comparison of the essential biosynthetic gene-camE. The titer of CRM A production was then improved by two strain breeding methods via UV mutagenesis and cofactor engineering-directed increase of intracellular riboflavin, which finally generated the optimal mutant strain XC-11GUR with a CRM A production titer of 113.91 ± 7.58 mg/L. Subsequently, this titer of strain XC-11GUR was improved to 618.61 ± 16.29 mg/L through medium optimization together with further adjustment derived from response surface methodology. In terms of this 14.6 folds increase in the titer of CRM A compared to the initial value, strain XC-GUR could be a well alternative strain for CRM A development. Conclusions Our results had constructed an ideal CRM A producer. More importantly, our efforts also had demonstrated the effectiveness of abovementioned combinatorial strategies, which is applicable to the genome mining of bioactive natural products from abundant actinomycetes strains.
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Affiliation(s)
- Yunchang Xie
- Key Laboratory of Functional Small Organic Molecule Ministry of Education and Jiangxi's Key Laboratory of Green Chemistry, Key Laboratory of Protection and Utilization of Subtropic Plant Resources of Jiangxi Province, College of Life Sciences, Jiangxi Normal University, Nanchang, 330022, China
| | - Jiawen Chen
- Key Laboratory of Functional Small Organic Molecule Ministry of Education and Jiangxi's Key Laboratory of Green Chemistry, Key Laboratory of Protection and Utilization of Subtropic Plant Resources of Jiangxi Province, College of Life Sciences, Jiangxi Normal University, Nanchang, 330022, China
| | - Bo Wang
- Guangdong Provincial Key Laboratory of Genome Read and Write, Shenzhen Engineering Laboratory for Innovative Molecular Diagnostics, Guangdong Provincial Academician Workstation of BGI Synthetic Genomics, BGI-Shenzhen, Beishan Industrial Zone, Shenzhen, 518083, China.,China National GeneBank, BGI-Shenzhen, Jinsha Road, Shenzhen, 518120, China
| | - Tai Chen
- Guangdong Provincial Key Laboratory of Genome Read and Write, Shenzhen Engineering Laboratory for Innovative Molecular Diagnostics, Guangdong Provincial Academician Workstation of BGI Synthetic Genomics, BGI-Shenzhen, Beishan Industrial Zone, Shenzhen, 518083, China.,China National GeneBank, BGI-Shenzhen, Jinsha Road, Shenzhen, 518120, China
| | - Junyu Chen
- Key Laboratory of Functional Small Organic Molecule Ministry of Education and Jiangxi's Key Laboratory of Green Chemistry, Key Laboratory of Protection and Utilization of Subtropic Plant Resources of Jiangxi Province, College of Life Sciences, Jiangxi Normal University, Nanchang, 330022, China
| | - Yuan Zhang
- School of Life Sciences, Anhui Medical University, Hefei, 230032, China
| | - Xiaoying Liu
- School of Life Sciences, Anhui Medical University, Hefei, 230032, China.
| | - Qi Chen
- School of Life Sciences, Anhui Medical University, Hefei, 230032, China.
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Mao D, Yoshimura A, Wang R, Seyedsayamdost MR. Reporter-Guided Transposon Mutant Selection for Activation of Silent Gene Clusters in Burkholderia thailandensis. Chembiochem 2020; 21:1826-1831. [PMID: 31984619 DOI: 10.1002/cbic.201900748] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Indexed: 01/01/2023]
Abstract
Most natural product biosynthetic gene clusters that can be observed bioinformatically are silent. This insight has prompted the development of several methodologies for inducing their expression. One of the more recent methods, termed reporter-guided mutant selection (RGMS), entails creation of a library of mutants that is then screened for the desired phenotype via reporter gene expression. Herein, we apply a similar approach to Burkholderia thailandensis and, using transposon mutagenesis, mutagenize three strains, each carrying a fluorescent reporter in the malleilactone (mal), capistruin (cap), or an unidentified ribosomal peptide (tomm) gene cluster. We show that even a small library of <500 mutants can be used to induce expression of each cluster. We also explore the mechanism of activation and find that inhibition of pyrimidine biosynthesis is linked to the induction of the mal cluster. Both a transposon insertion into pyrF as well as small-molecule-mediated inhibition of PyrF trigger malleilactone biosynthesis. Our results pave the way toward the broad application of RGMS and related approaches to Burkholderia spp.
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Affiliation(s)
- Dainan Mao
- Department of Chemistry, Princeton University, Princeton, NJ, 08544, USA
| | - Aya Yoshimura
- Department of Chemistry, Princeton University, Princeton, NJ, 08544, USA
| | - Rurun Wang
- Department of Chemistry, Princeton University, Princeton, NJ, 08544, USA
| | - Mohammad R Seyedsayamdost
- Department of Chemistry, Princeton University, Princeton, NJ, 08544, USA.,Department of Molecular Biology, Princeton University, Princeton, NJ, 08544, USA
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54
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Peng F, Zhang MY, Hou SY, Chen J, Wu YY, Zhang YX. Insights into Streptomyces spp. isolated from the rhizospheric soil of Panax notoginseng: isolation, antimicrobial activity and biosynthetic potential for polyketides and non-ribosomal peptides. BMC Microbiol 2020; 20:143. [PMID: 32493249 PMCID: PMC7271549 DOI: 10.1186/s12866-020-01832-5] [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: 07/02/2019] [Accepted: 05/25/2020] [Indexed: 12/17/2022] Open
Abstract
Background Streptomycetes from the rhizospheric soils are a rich resource of novel secondary metabolites with various biological activities. However, there is still little information related to the isolation, antimicrobial activity and biosynthetic potential for polyketide and non-ribosomal peptide discovery associated with the rhizospheric streptomycetes of Panax notoginseng. Thus, the aims of the present study are to (i) identify culturable streptomycetes from the rhizospheric soil of P. notoginseng by 16S rRNA gene, (ii) evaluate the antimicrobial activities of isolates and analyze the biosynthetic gene encoding polyketide synthases (PKSs) and nonribosomal peptide synthetases (NRPSs) of isolates, (iii) detect the bioactive secondary metabolites from selected streptomycetes, (iv) study the influence of the selected isolate on the growth of P. notoginseng in the continuous cropping field. This study would provide a preliminary basis for the further discovery of the secondary metabolites from streptomycetes isolated from the rhizospheric soil of P. notoginseng and their further utilization for biocontrol of plants. Results A total of 42 strains representing 42 species of the genus Streptomyces were isolated from 12 rhizospheric soil samples in the cultivation field of P. notoginseng and were analyzed by 16S rRNA gene sequencing. Overall, 40 crude cell extracts out of 42 under two culture conditions showed antibacterial and antifungal activities. Also, the presence of biosynthesis genes encoding type I and II polyketide synthase (PKS I and PKS II) and nonribosomal peptide synthetases (NRPSs) in 42 strains were established. Based on characteristic chemical profiles screening by High Performance Liquid Chromatography-Diode Array Detector (HPLC-DAD), the secondary metabolite profiles of strain SYP-A7257 were evaluated by High Performance Liquid Chromatography-High Resolution Mass Spectrometry (HPLC-HRMS). Finally, four compounds actinomycin X2 (F1), fungichromin (F2), thailandin B (F7) and antifungalmycin (F8) were isolated from strain SYP-A7257 by using chromatography techniques, UV, HR-ESI-MS and NMR, and their antimicrobial activities against the test bacteria and fungus were also evaluated. In the farm experiments, Streptomyces sp. SYP-A7257 showed healthy growth promotion and survival rate improvement of P. notoginseng in the continuous cropping field. Conclusions We demonstrated the P. notoginseng rhizospheric soil-derived Streptomyces spp. distribution and diversity with respect to their metabolic potential for polyketides and non-ribosomal peptides, as well as the presence of biosynthesis genes PKS I, PKS II and NRPSs. Our results showed that cultivatable Streptomyces isolates from the rhizospheric soils of P. notoginseng have the ability to produce bioactive secondary metabolites. The farm experiments suggested that the rhizospheric soil Streptomyces sp. SYP-A7257 may be a potential biological control agent for healthy growth promotion and survival rate improvement of P. notoginseng in the continuous cropping field.
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Affiliation(s)
- Fei Peng
- School of Life Science and Biopharmaceutics, Shenyang Pharmaceutical University, Shenyang, 110016, People's Republic of China.,Quanzhou Medical College, Quanzhou, People's Republic of China
| | - Meng-Yue Zhang
- School of Life Science and Biopharmaceutics, Shenyang Pharmaceutical University, Shenyang, 110016, People's Republic of China
| | - Shao-Yang Hou
- School of Life Science and Biopharmaceutics, Shenyang Pharmaceutical University, Shenyang, 110016, People's Republic of China
| | - Juan Chen
- School of Life Science and Biopharmaceutics, Shenyang Pharmaceutical University, Shenyang, 110016, People's Republic of China
| | - Ying-Ying Wu
- School of Life Science and Biopharmaceutics, Shenyang Pharmaceutical University, Shenyang, 110016, People's Republic of China
| | - Yi-Xuan Zhang
- School of Life Science and Biopharmaceutics, Shenyang Pharmaceutical University, Shenyang, 110016, People's Republic of China.
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55
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Park JD, Moon K, Miller C, Rose J, Xu F, Ebmeier CC, Jacobsen JR, Mao D, Old WM, DeShazer D, Seyedsayamdost MR. Thailandenes, Cryptic Polyene Natural Products Isolated from Burkholderia thailandensis Using Phenotype-Guided Transposon Mutagenesis. ACS Chem Biol 2020; 15:1195-1203. [PMID: 31816232 DOI: 10.1021/acschembio.9b00883] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Burkholderia thailandensis has emerged as a model organism for investigating the production and regulation of diverse secondary metabolites. Most of the biosynthetic gene clusters encoded in B. thailandensis are silent, motivating the development of new methods for accessing their products. In the current work, we add to the canon of available approaches using phenotype-guided transposon mutagenesis to characterize a silent biosynthetic gene cluster. Because secondary metabolite biosynthesis is often associated with phenotypic changes, we carried out random transposon mutagenesis followed by phenotypic inspection of the resulting colonies. Several mutants exhibited intense pigmentation and enhanced expression of an iterative type I polyketide synthase cluster that we term org. Disruptions of orgA, orgB, and orgC abolished the biosynthesis of the diffusible pigment, thus linking it to the org operon. Isolation and structural elucidation by HR-MS and 1D/2D NMR spectroscopy revealed three novel, cryptic metabolites, thailandene A-C. Thailandenes are linear formylated or acidic polyenes containing a combination of cis and trans double bonds. Variants A and B exhibited potent antibiotic activity against Staphylococcus aureus and Saccharomyces cerevisiae but not against Escherichia coli. One of the transposon mutants that exhibited an enhanced expression of org contained an insertion upstream of a σ54-dependent transcription factor. Closer inspection of the org operon uncovered a σ54 promoter consensus sequence upstream of orgA, providing clues regarding its regulation. Our results showcase the utility of phenotype-guided transposon mutagenesis in uncovering cryptic metabolites encoded in bacterial genomes.
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Affiliation(s)
- Jong-Duk Park
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
| | - Kyuho Moon
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
| | - Cheryl Miller
- Molecular and Translational Science Division, U.S. Army Medical Research Institute of Infectious Diseases, Frederick, Maryland 21702, United States
| | - Jessica Rose
- Biotechnology Program, Hagerstown Community College, Hagerstown, Maryland 21742, United States
| | - Fei Xu
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
| | - Christopher C. Ebmeier
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, Colorado 80309, United States
| | - Jeremy R. Jacobsen
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, Colorado 80309, United States
| | - Dainan Mao
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
| | - William M. Old
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, Colorado 80309, United States
| | - David DeShazer
- Bacteriology Division, U.S. Army Medical Research Institute of Infectious Diseases, Frederick, Maryland 21702, United States
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56
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Núñez-Montero K, Quezada-Solís D, Khalil ZG, Capon RJ, Andreote FD, Barrientos L. Genomic and Metabolomic Analysis of Antarctic Bacteria Revealed Culture and Elicitation Conditions for the Production of Antimicrobial Compounds. Biomolecules 2020; 10:E673. [PMID: 32349314 PMCID: PMC7277857 DOI: 10.3390/biom10050673] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Revised: 04/15/2020] [Accepted: 04/21/2020] [Indexed: 01/08/2023] Open
Abstract
Concern about finding new antibiotics against drug-resistant pathogens is increasing every year. Antarctic bacteria have been proposed as an unexplored source of bioactive metabolites; however, most biosynthetic gene clusters (BGCs) producing secondary metabolites remain silent under common culture conditions. Our work aimed to characterize elicitation conditions for the production of antibacterial secondary metabolites from 34 Antarctic bacterial strains based on MS/MS metabolomics and genome mining approaches. Bacterial strains were cultivated under different nutrient and elicitation conditions, including the addition of lipopolysaccharide (LPS), sodium nitroprusside (SNP), and coculture. Metabolomes were obtained by HPLC-QTOF-MS/MS and analyzed through molecular networking. Antibacterial activity was determined, and seven strains were selected for genome sequencing and analysis. Biosynthesis pathways were activated by all the elicitation treatments, which varies among strains and dependents of culture media. Increased antibacterial activity was observed for a few strains and addition of LPS was related with inhibition of Gram-negative pathogens. Antibiotic BGCs were found for all selected strains and the expressions of putative actinomycin, carotenoids, and bacillibactin were characterized by comparison of genomic and metabolomic data. This work established the use of promising new elicitors for bioprospection of Antarctic bacteria and highlights the importance of new "-omics" comparative approaches for drug discovery.
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Affiliation(s)
- Kattia Núñez-Montero
- Laboratory of Molecular Applied Biology, Center of Excellence in Translational Medicine, Universidad de La Frontera, Avenida Alemania 0458, Temuco 4810296, Chile; (K.N.-M.); (D.Q.-S.)
- Scientific and Technological Bioresource Nucleus (BIOREN), Universidad de La Frontera, Temuco 4811230, Chile
- Biotechnology Investigation Center, Department of Biology, Instituto Tecnológico de Costa Rica, Cartago 159-7050, Costa Rica
| | - Damián Quezada-Solís
- Laboratory of Molecular Applied Biology, Center of Excellence in Translational Medicine, Universidad de La Frontera, Avenida Alemania 0458, Temuco 4810296, Chile; (K.N.-M.); (D.Q.-S.)
| | - Zeinab G. Khalil
- Institute for Molecular Bioscience, The University of Queensland, St Lucia, QLD 4072, Australia; (Z.G.K.); (R.J.C.)
| | - Robert J. Capon
- Institute for Molecular Bioscience, The University of Queensland, St Lucia, QLD 4072, Australia; (Z.G.K.); (R.J.C.)
| | - Fernando D. Andreote
- Department of Soil Science, “Luiz de Queiroz” College of Agriculture, University of São Paulo, Piracicaba, SP 13418-900, Brazil;
| | - Leticia Barrientos
- Laboratory of Molecular Applied Biology, Center of Excellence in Translational Medicine, Universidad de La Frontera, Avenida Alemania 0458, Temuco 4810296, Chile; (K.N.-M.); (D.Q.-S.)
- Scientific and Technological Bioresource Nucleus (BIOREN), Universidad de La Frontera, Temuco 4811230, Chile
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57
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Zhang C, Seyedsayamdost MR. CanE, an Iron/2-Oxoglutarate-Dependent Lasso Peptide Hydroxylase from Streptomyces canus. ACS Chem Biol 2020; 15:890-894. [PMID: 32191027 DOI: 10.1021/acschembio.0c00109] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Lasso peptides are a class of ribosomally synthesized and post-translationally modified peptides (RiPPs) that feature a unique lariat-knot topology. Canucin A, a post-translationally hydroxylated lasso peptide, was recently discovered via activation of its otherwise silent biosynthetic gene cluster in Streptomyces canus. The biosynthesis of canucin A, notably the introduction of a hydroxyl group at the β-carbon of the terminal aspartate residue, is the topic of the current report. We combine genetic and biochemical experiments to show that an iron/2-oxoglutarate-dependent enzyme, CanE, installs the hydroxyl group onto the precursor peptide in vivo and in vitro. Moreover, we show that hydroxylation occurs prior to macrocyclization and that the RiPP recognition element (RRE), encoded within the gene cluster to facilitate the initial proteolytic reaction, also increases the yield of hydroxylation, hinting at a dual role for the RRE. Our results have implications for the combinatorial biosynthesis of lasso peptides.
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Affiliation(s)
- Chen Zhang
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
| | - Mohammad R. Seyedsayamdost
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
- Department of Molecular Biology, Princeton University, Princeton, New Jersey 08544, United States
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58
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Kim C, Gatsios A, Cuesta S, Lam YC, Wei Z, Chen H, Russell RM, Shine EE, Wang R, Wyche TP, Piizzi G, Flavell RA, Palm NW, Sperandio V, Crawford JM. Characterization of Autoinducer-3 Structure and Biosynthesis in E. coli. ACS CENTRAL SCIENCE 2020; 6:197-206. [PMID: 32123737 PMCID: PMC7047286 DOI: 10.1021/acscentsci.9b01076] [Citation(s) in RCA: 70] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Indexed: 05/09/2023]
Abstract
Escherichia coli is a common inhabitant of the human microbiota and a beacon model organism in biology. However, an understanding of its signaling systems that regulate population-level phenotypes known as quorum sensing remain incomplete. Here, we define the structure and biosynthesis of autoinducer-3 (AI-3), a metabolite of previously unknown structure involved in the pathogenesis of enterohemorrhagic E. coli (EHEC). We demonstrate that novel AI-3 analogs are derived from threonine dehydrogenase (Tdh) products and "abortive" tRNA synthetase reactions, and they are distributed across a variety of Gram-negative and Gram-positive bacterial pathogens. In addition to regulating virulence genes in EHEC, we show that the metabolites exert diverse immunological effects on primary human tissues. The discovery of AI-3 metabolites and their biochemical origins now provides a molecular foundation for investigating the diverse biological roles of these elusive yet widely distributed bacterial signaling molecules.
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Affiliation(s)
- Chung
Sub Kim
- Department
of Chemistry, Yale University, New Haven, Connecticut 06520, United States
- Chemical
Biology Institute, Yale University, West Haven, Connecticut 06516, United States
| | - Alexandra Gatsios
- Department
of Chemistry, Yale University, New Haven, Connecticut 06520, United States
- Chemical
Biology Institute, Yale University, West Haven, Connecticut 06516, United States
| | - Santiago Cuesta
- Department
of Microbiology, University of Texas Southwestern
Medical Center, Dallas, Texas 75390, United States
- Department
of Biochemistry, University of Texas Southwestern
Medical Center, Dallas, Texas 75390, United States
| | - Yick Chong Lam
- Department
of Chemistry, Yale University, New Haven, Connecticut 06520, United States
- Chemical
Biology Institute, Yale University, West Haven, Connecticut 06516, United States
| | - Zheng Wei
- Chemical
Biology Institute, Yale University, West Haven, Connecticut 06516, United States
- Department
of Immunobiology, Yale University School
of Medicine, New Haven, Connecticut 06520, United States
| | - Haiwei Chen
- Department
of Immunobiology, Yale University School
of Medicine, New Haven, Connecticut 06520, United States
| | - Regan M. Russell
- Department
of Microbiology, University of Texas Southwestern
Medical Center, Dallas, Texas 75390, United States
- Department
of Biochemistry, University of Texas Southwestern
Medical Center, Dallas, Texas 75390, United States
| | - Emilee E. Shine
- Chemical
Biology Institute, Yale University, West Haven, Connecticut 06516, United States
- Department
of Microbial Pathogenesis, Yale University
School of Medicine, New Haven, Connecticut 06536, United States
| | - Rurun Wang
- Merck Exploratory
Science Center, Merck & Co., Inc., Cambridge, Massachusetts 02141, United States
| | - Thomas P. Wyche
- Merck Exploratory
Science Center, Merck & Co., Inc., Cambridge, Massachusetts 02141, United States
| | - Grazia Piizzi
- Merck Exploratory
Science Center, Merck & Co., Inc., Cambridge, Massachusetts 02141, United States
| | - Richard A. Flavell
- Department
of Immunobiology, Yale University School
of Medicine, New Haven, Connecticut 06520, United States
- Howard
Hughes
Medical Institute, Yale University School
of Medicine, New Haven, Connecticut 06519, United States
| | - Noah W. Palm
- Department
of Immunobiology, Yale University School
of Medicine, New Haven, Connecticut 06520, United States
| | - Vanessa Sperandio
- Department
of Microbiology, University of Texas Southwestern
Medical Center, Dallas, Texas 75390, United States
- Department
of Biochemistry, University of Texas Southwestern
Medical Center, Dallas, Texas 75390, United States
| | - Jason M. Crawford
- Department
of Chemistry, Yale University, New Haven, Connecticut 06520, United States
- Chemical
Biology Institute, Yale University, West Haven, Connecticut 06516, United States
- Department
of Microbial Pathogenesis, Yale University
School of Medicine, New Haven, Connecticut 06536, United States
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Multi-Omic Analyses Provide Links between Low-Dose Antibiotic Treatment and Induction of Secondary Metabolism in Burkholderia thailandensis. mBio 2020; 11:mBio.03210-19. [PMID: 32098820 PMCID: PMC7042699 DOI: 10.1128/mbio.03210-19] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Low doses of antibiotics can trigger secondary metabolite biosynthesis in bacteria, but the underlying mechanisms are generally unknown. We sought to better understand this phenomenon by studying how the antibiotic trimethoprim activates the synthesis of the virulence factor malleilactone in Burkholderia thailandensis Using transcriptomics, quantitative multiplexed proteomics, and primary metabolomics, we systematically mapped the changes induced by trimethoprim. Surprisingly, even subinhibitory doses of the antibiotic resulted in broad transcriptional and translational alterations, with ∼8.5% of the transcriptome and ∼5% of the proteome up- or downregulated >4-fold. Follow-up studies with genetic-biochemical experiments showed that the induction of malleilactone synthesis can be sufficiently explained by the accumulation of methionine biosynthetic precursors, notably homoserine, as a result of inhibition of the folate pathway. Homoserine activated the malleilactone gene cluster via the transcriptional regulator MalR and gave rise to a secondary metabolome which was very similar to that generated by trimethoprim. Our work highlights the expansive changes that low-dose trimethoprim induces on bacterial physiology and provides insights into its stimulatory effect on secondary metabolism.IMPORTANCE The discovery of antibiotics ranks among the most significant accomplishments of the last century. Although the targets of nearly all clinical antibiotics are known, our understanding regarding their natural functions and the effects of subinhibitory concentrations is in its infancy. Stimulatory rather than inhibitory functions have been attributed to low-dose antibiotics. Among these, we previously found that antibiotics activate silent biosynthetic genes and thereby enhance the metabolic output of bacteria. The regulatory circuits underlying this phenomenon are unknown. We take a first step toward elucidating these circuits and show that low doses of trimethoprim (Tmp) have cell-wide effects on the saprophyte Burkholderia thailandensis Most importantly, inhibition of one-carbon metabolic processes by Tmp leads to an accumulation of homoserine, which induces the production of an otherwise silent cytotoxin via a LuxR-type transcriptional regulator. These results provide a starting point for uncovering the molecular basis of the hormetic effects of antibiotics.
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Ganley JG, Derbyshire ER. Linking Genes to Molecules in Eukaryotic Sources: An Endeavor to Expand Our Biosynthetic Repertoire. Molecules 2020; 25:E625. [PMID: 32023950 PMCID: PMC7036892 DOI: 10.3390/molecules25030625] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Revised: 01/23/2020] [Accepted: 01/30/2020] [Indexed: 02/06/2023] Open
Abstract
The discovery of natural products continues to interest chemists and biologists for their utility in medicine as well as facilitating our understanding of signaling, pathogenesis, and evolution. Despite an attenuation in the discovery rate of new molecules, the current genomics and transcriptomics revolution has illuminated the untapped biosynthetic potential of many diverse organisms. Today, natural product discovery can be driven by biosynthetic gene cluster (BGC) analysis, which is capable of predicting enzymes that catalyze novel reactions and organisms that synthesize new chemical structures. This approach has been particularly effective in mining bacterial and fungal genomes where it has facilitated the discovery of new molecules, increased the understanding of metabolite assembly, and in some instances uncovered enzymes with intriguing synthetic utility. While relatively less is known about the biosynthetic potential of non-fungal eukaryotes, there is compelling evidence to suggest many encode biosynthetic enzymes that produce molecules with unique bioactivities. In this review, we highlight how the advances in genomics and transcriptomics have aided natural product discovery in sources from eukaryotic lineages. We summarize work that has successfully connected genes to previously identified molecules and how advancing these techniques can lead to genetics-guided discovery of novel chemical structures and reactions distributed throughout the tree of life. Ultimately, we discuss the advantage of increasing the known biosynthetic space to ease access to complex natural and non-natural small molecules.
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Affiliation(s)
- Jack G Ganley
- Department of Chemistry, Duke University, 124 Science Drive, Durham, NC 27708-0346, USA
| | - Emily R Derbyshire
- Department of Chemistry, Duke University, 124 Science Drive, Durham, NC 27708-0346, USA
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, 213 Research Drive, Durham, NC 27710, USA
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61
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Kong D, Wang X, Nie J, Niu G. Regulation of Antibiotic Production by Signaling Molecules in Streptomyces. Front Microbiol 2019; 10:2927. [PMID: 31921086 PMCID: PMC6930871 DOI: 10.3389/fmicb.2019.02927] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Accepted: 12/05/2019] [Indexed: 11/22/2022] Open
Abstract
The genus Streptomyces is a unique subgroup of actinomycetes bacteria that are well-known as prolific producers of antibiotics and many other bioactive secondary metabolites. Various environmental and physiological signals affect the onset and level of production of each antibiotic. Here we highlight recent findings on the regulation of antibiotic biosynthesis in Streptomyces by signaling molecules, with special focus on autoregulators such as hormone-like signaling molecules and antibiotics themselves. Hormone-like signaling molecules are a group of small diffusible signaling molecules that interact with specific receptor proteins to initiate complex regulatory cascades of antibiotic biosynthesis. Antibiotics and their biosynthetic intermediates can also serve as autoregulators to fine-tune their own biosynthesis or cross-regulators of disparate biosynthetic pathways. Advances in understanding of signaling molecules-mediated regulation of antibiotic production in Streptomyces may aid the discovery of new signaling molecules and their use in eliciting silent antibiotic biosynthetic pathways in a wide range of actinomycetes.
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Affiliation(s)
- Dekun Kong
- Biotechnology Research Center, Southwest University, Chongqing, China.,State Cultivation Base of Crop Stress Biology for Southern Mountainous Land, Academy of Agricultural Sciences, Southwest University, Chongqing, China
| | - Xia Wang
- Biotechnology Research Center, Southwest University, Chongqing, China.,State Cultivation Base of Crop Stress Biology for Southern Mountainous Land, Academy of Agricultural Sciences, Southwest University, Chongqing, China
| | - Ju Nie
- Biotechnology Research Center, Southwest University, Chongqing, China.,College of Horticulture and Landscape Architecture, Southwest University, Chongqing, China
| | - Guoqing Niu
- Biotechnology Research Center, Southwest University, Chongqing, China.,State Cultivation Base of Crop Stress Biology for Southern Mountainous Land, Academy of Agricultural Sciences, Southwest University, Chongqing, China
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62
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Timmermans ML, Ross AC. Unearthing Hidden Chemical Potential from Discarded Actinobacterial Libraries. Trends Biotechnol 2019; 38:7-9. [PMID: 31785780 DOI: 10.1016/j.tibtech.2019.11.003] [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: 11/08/2019] [Accepted: 11/12/2019] [Indexed: 11/25/2022]
Abstract
The redundancy of natural product biosynthesis in microbes poses a practical challenge for discovering new antimicrobial compounds from bacteria. The recent application of clustered regularly interspaced short palindromic repeats (CRISPR) technology by Culp et al. to inactivate the production of abundant antibiotics generates a metabolic clean slate for the detection and/or isolation of new and less plentiful antibiotics activated in mutant strains.
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Affiliation(s)
| | - Avena C Ross
- Department of Chemistry, Queen's University, Kingston, ONT, Canada.
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63
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Advances in microbial culturing conditions to activate silent biosynthetic gene clusters for novel metabolite production. ACTA ACUST UNITED AC 2019; 46:1381-1400. [DOI: 10.1007/s10295-019-02198-y] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Accepted: 05/24/2019] [Indexed: 02/08/2023]
Abstract
Abstract
Natural products (NPs) produced by bacteria and fungi are often used as therapeutic agents due to their complex structures and wide range of bioactivities. Enzymes that build NPs are encoded by co-localized biosynthetic gene clusters (BGCs), and genome sequencing has recently revealed that many BGCs are “silent” under standard laboratory conditions. There are numerous methods used to activate “silent” BGCs that rely either upon altering culture conditions or genetic modification. In this review, we discuss several recent microbial cultivation methods that have been used to expand the scope of NPs accessible in the laboratory. These approaches are divided into three categories: addition of a physical scaffold, addition of small molecule elicitors, and co-cultivation with another microbe.
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64
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Hidden antibiotics in actinomycetes can be identified by inactivation of gene clusters for common antibiotics. Nat Biotechnol 2019; 37:1149-1154. [PMID: 31501558 DOI: 10.1038/s41587-019-0241-9] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Accepted: 07/25/2019] [Indexed: 12/30/2022]
Abstract
Actinobacteria, which are one of the largest bacterial phyla and comprise between 13 and 30% of the soil microbiota, are the main source of antibiotic classes in clinical use1. During screens for antimicrobials, as many as 50% of actinomycete strains are discarded because they produce a known antibiotic (Supplementary Fig. 1) (ref. 2). Despite each strain likely having the capacity to produce many compounds, strains are abandoned because the already characterized antibiotic could interfere with screening for, or purification of, newly discovered compounds3. We applied CRISPR-Cas9 genome engineering to knockout genes encoding two of the most frequently rediscovered antibiotics, streptothricin or streptomycin, in 11 actinomycete strains. We report that this simple approach led to production of different antibiotics that were otherwise masked. We were able to rapidly discover rare and previously unknown variants of antibiotics including thiolactomycin, amicetin, phenanthroviridin and 5-chloro-3-formylindole. This strategy could be applied to existing strain collections to realize their biosynthetic potential.
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65
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Okada BK, Li A, Seyedsayamdost MR. Identification of the Hypertension Drug Guanfacine as an Antivirulence Agent in Pseudomonas aeruginosa. Chembiochem 2019; 20:2005-2011. [PMID: 30927315 PMCID: PMC6814388 DOI: 10.1002/cbic.201900129] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Indexed: 12/11/2022]
Abstract
An alternative solution to the cyclical development of new antibiotics is the concept of disarming pathogens without affecting their growth, thereby eliminating the selective pressures that lead to resistant phenotypes. Here, we have employed our previously developed HiTES methodology to identify one such compound against the ESKAPE pathogen Pseudomonas aeruginosa. Rather than induce silent biosynthetic gene clusters, we used HiTES to suppress actively expressed virulence genes. By screening a library of 770 FDA-approved drugs, we identified guanfacine, a clinical hypertension drug, as an antivirulence agent in P. aeruginosa. Follow-up studies showed that guanfacine reduces biofilm formation and pyocycanin production without altering growth. Moreover, we identified a homologue of QseC, a sensor His kinase used by multiple pathogens to turn on virulence, as a target of guanfacine. Our studies suggest that guanfacine might be an attractive antivirulence lead in P. aeruginosa and provide a template for uncovering such molecules by screening for downregulators of actively expressed biosynthetic genes.
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Affiliation(s)
- Bethany K Okada
- Department of Chemistry, Princeton University, Princeton, NJ, 08544, USA
| | - Anran Li
- Department of Molecular Biology, Princeton University, Princeton, NJ, 08544, USA
| | - Mohammad R Seyedsayamdost
- Department of Chemistry, Princeton University, Princeton, NJ, 08544, USA
- Department of Molecular Biology, Princeton University, Princeton, NJ, 08544, USA
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66
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Niu G, Li W. Next-Generation Drug Discovery to Combat Antimicrobial Resistance. Trends Biochem Sci 2019; 44:961-972. [PMID: 31256981 DOI: 10.1016/j.tibs.2019.05.005] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Revised: 05/30/2019] [Accepted: 05/31/2019] [Indexed: 12/16/2022]
Abstract
The widespread emergence of antibiotic-resistant pathogens poses a severe threat to public health. This problem becomes even worse with a coincident decline in the supply of new antibiotics. Conventional bioactivity-guided natural product discovery has failed to meet the urgent need for new antibiotics, largely due to limited resources and high rediscovery rates. Recent advances in cultivation techniques, analytical technologies, and genomics-based approaches have greatly expanded our access to previously underexploited microbial sources. These strategies will enable us to access new reservoirs of microorganisms and unleash their chemical potentials, thus opening new opportunities for the discovery of next-generation drugs to address the growing concerns of antimicrobial resistance.
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Affiliation(s)
- Guoqing Niu
- Biotechnology Research Center, Southwest University, Chongqing 400715, China; Chongqing Key Laboratory of Plant Resource Conservation and Germplasm Innovation, Southwest University, Chongqing 400715, China; State Cultivation Base of Crop Stress Biology for Southern Mountainous Land, Academy of Agricultural Sciences, Southwest University, Chongqing 400715, China.
| | - Wenli Li
- Key Laboratory of Marine Drugs, Ministry of Education of China, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China; Laboratory for Marine Drugs and Bioproducts, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China.
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67
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Gregory K, Salvador LA, Akbar S, Adaikpoh BI, Stevens DC. Survey of Biosynthetic Gene Clusters from Sequenced Myxobacteria Reveals Unexplored Biosynthetic Potential. Microorganisms 2019; 7:E181. [PMID: 31238501 PMCID: PMC6616573 DOI: 10.3390/microorganisms7060181] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Revised: 06/20/2019] [Accepted: 06/21/2019] [Indexed: 01/31/2023] Open
Abstract
Coinciding with the increase in sequenced bacteria, mining of bacterial genomes for biosynthetic gene clusters (BGCs) has become a critical component of natural product discovery. The order Myxococcales, a reputable source of biologically active secondary metabolites, spans three suborders which all include natural product producing representatives. Utilizing the BiG-SCAPE-CORASON platform to generate a sequence similarity network that contains 994 BGCs from 36 sequenced myxobacteria deposited in the antiSMASH database, a total of 843 BGCs with lower than 75% similarity scores to characterized clusters within the MIBiG database are presented. This survey provides the biosynthetic diversity of these BGCs and an assessment of the predicted chemical space yet to be discovered. Considering the mere snapshot of myxobacteria included in this analysis, these untapped BGCs exemplify the potential for natural product discovery from myxobacteria.
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Affiliation(s)
- Katherine Gregory
- Department of BioMolecular Sciences, School of Pharmacy, University of Mississippi, University, MS 38677, USA.
| | - Laura A Salvador
- Department of BioMolecular Sciences, School of Pharmacy, University of Mississippi, University, MS 38677, USA.
| | - Shukria Akbar
- Department of BioMolecular Sciences, School of Pharmacy, University of Mississippi, University, MS 38677, USA.
| | - Barbara I Adaikpoh
- Department of BioMolecular Sciences, School of Pharmacy, University of Mississippi, University, MS 38677, USA.
| | - D Cole Stevens
- Department of BioMolecular Sciences, School of Pharmacy, University of Mississippi, University, MS 38677, USA.
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68
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Moon K, Xu F, Seyedsayamdost MR. Cebulantin, a Cryptic Lanthipeptide Antibiotic Uncovered Using Bioactivity‐Coupled HiTES. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201901342] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Kyuho Moon
- Department of ChemistryPrinceton University Princeton NJ 08544 USA
| | - Fei Xu
- Department of ChemistryPrinceton University Princeton NJ 08544 USA
| | - Mohammad R. Seyedsayamdost
- Department of ChemistryPrinceton University Princeton NJ 08544 USA
- Department of Molecular BiologyPrinceton University USA
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69
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Moon K, Xu F, Zhang C, Seyedsayamdost MR. Bioactivity-HiTES Unveils Cryptic Antibiotics Encoded in Actinomycete Bacteria. ACS Chem Biol 2019; 14:767-774. [PMID: 30830740 DOI: 10.1021/acschembio.9b00049] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Bacteria harbor an immense reservoir of potentially new and therapeutic small molecules in the form of "silent" biosynthetic gene clusters (BGCs). These BGCs can be identified bioinformatically but are sparingly expressed under normal laboratory growth conditions, or not at all, and therefore do not produce significant levels of the corresponding small molecule product. Several methods have been developed for activating silent BGCs. A major limitation for nearly all methods is that they require genetic procedures and/or do not report on the bioactivity of the cryptic metabolite. We herein report "Bioactivty-HiTES", an approach that links the bioactivity of cryptic metabolites to their induction while at the same time obviating the need for genetic manipulations. Using this method, we detected induction of cryptic antibiotics in three actinomycete strains that were tested. Follow-up studies in one case allowed us to structurally elucidate two cryptic metabolites, elicited by the β-blocker atenolol in Streptomyces hiroshimensis, with selective growth-inhibitory activity against Gram-negative bacteria, notably Escherichia coli and Acinetobacter baumannii. Atenolol turned out to be a global elicitor of secondary metabolism, and characterization of additional cryptic metabolites led to the discovery of a novel naphthoquinone epoxide. Bioactivity-HiTES is a general, widely applicable procedure that will be useful in identifying cryptic bioactive metabolites in the future.
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Affiliation(s)
- Kyuho Moon
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
| | - Fei Xu
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
| | - Chen Zhang
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
| | - Mohammad R. Seyedsayamdost
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
- Department of Molecular Biology, Princeton University, Princeton, New Jersey 08544, United States
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70
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Moon K, Xu F, Seyedsayamdost MR. Cebulantin, a Cryptic Lanthipeptide Antibiotic Uncovered Using Bioactivity-Coupled HiTES. Angew Chem Int Ed Engl 2019; 58:5973-5977. [PMID: 30843641 DOI: 10.1002/anie.201901342] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Indexed: 01/22/2023]
Abstract
The majority of natural product biosynthetic gene clusters in bacteria are silent under standard laboratory growth conditions, making it challenging to uncover any antibiotics that they may encode. Herein, bioactivity assays are combined with high-throughput elicitor screening (HiTES) to access cryptic, bioactive metabolites. Application of this strategy in Saccharopolyspora cebuensis, with inhibition of Escherichia coli growth as a read-out, led to the identification of a novel lanthipeptide, cebulantin. Extensive NMR spectroscopic analysis allowed the elucidation of the structure of cebulantin. Subsequent bioactivity assays revealed it to be an antibiotic selective for Gram-negative bacteria, especially against Vibrio species. This approach, referred to as bioactivity-HiTES, has the potential to uncover cryptic metabolites with desired biological activities that are hidden in microbial genomes.
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Affiliation(s)
- Kyuho Moon
- Department of Chemistry, Princeton University, Princeton, NJ, 08544, USA
| | - Fei Xu
- Department of Chemistry, Princeton University, Princeton, NJ, 08544, USA
| | - Mohammad R Seyedsayamdost
- Department of Chemistry, Princeton University, Princeton, NJ, 08544, USA.,Department of Molecular Biology, Princeton University, USA
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71
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Zhou C, Liu H, Yuan F, Chai H, Wang H, Liu F, Li Y, Zhang H, Lu F. Development and application of a CRISPR/Cas9 system for Bacillus licheniformis genome editing. Int J Biol Macromol 2019; 122:329-337. [PMID: 30401651 DOI: 10.1016/j.ijbiomac.2018.10.170] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Revised: 10/24/2018] [Accepted: 10/25/2018] [Indexed: 10/28/2022]
Abstract
A highly efficient genome editing system for Bacillus licheniformis was developed based on single-plasmid CRISPR/Cas9. For highly efficient genome editing the shuttle vector pWH1520 was selected to construct the knockout plasmids. A construct harboring a pS promoter driving cas9 endonuclease expression, a strong pLY-2 promoter driving the transcription of a single guide RNA was demonstrated as being the most effective. To verify the feasibility of the method the uprT gene coding uracil phosphoribosyltransferase was selected as the reporter gene. The efficiency of introducing nucleotide point mutations and single gene deletion reached an editing efficiency of up to 99.2% and 97.3%, respectively. After a upp-deficient strain was engineered, the system and strain were applied to introduce genomic deletions of another two genes, amyL and chiA (encoding amylase and chitinase, respectively) with about 90% deletion efficiency. As two native extracellular proteins with relatively high secretion in the host, amylase and chitinase can hamper the secretion and expression of alkaline protease. It was demonstrated that the mutant with deletions of the two genes effectively improved the alkaline protease yield by 24.8%. The results illustrated that the establishment of a CRISPR/Cas9 system for Bacillus licheniformis is of significance, and confirmed the system's high efficiency. The system provides support for effective molecular modification and metabolic regulation of Bacillus licheniformis, and offers promise for applications in genetic modification of other industrially relevant Bacillus species.
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Affiliation(s)
- Cuixia Zhou
- State Key Laboratory of Food Nutrition and Safety, College of Biotechnology, Tianjin University of Science &Technology, Tianjin 022, PR China
| | - Huan Liu
- State Key Laboratory of Food Nutrition and Safety, College of Biotechnology, Tianjin University of Science &Technology, Tianjin 022, PR China
| | - Feiyan Yuan
- State Key Laboratory of Food Nutrition and Safety, College of Biotechnology, Tianjin University of Science &Technology, Tianjin 022, PR China
| | - Haonan Chai
- State Key Laboratory of Food Nutrition and Safety, College of Biotechnology, Tianjin University of Science &Technology, Tianjin 022, PR China
| | - Haikuan Wang
- State Key Laboratory of Food Nutrition and Safety, College of Biotechnology, Tianjin University of Science &Technology, Tianjin 022, PR China
| | - Fufeng Liu
- State Key Laboratory of Food Nutrition and Safety, College of Biotechnology, Tianjin University of Science &Technology, Tianjin 022, PR China
| | - Yu Li
- State Key Laboratory of Food Nutrition and Safety, College of Biotechnology, Tianjin University of Science &Technology, Tianjin 022, PR China
| | - Huitu Zhang
- State Key Laboratory of Food Nutrition and Safety, College of Biotechnology, Tianjin University of Science &Technology, Tianjin 022, PR China.
| | - Fuping Lu
- State Key Laboratory of Food Nutrition and Safety, College of Biotechnology, Tianjin University of Science &Technology, Tianjin 022, PR China.
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72
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Seyedsayamdost MR. Toward a global picture of bacterial secondary metabolism. J Ind Microbiol Biotechnol 2019; 46:301-311. [PMID: 30684124 DOI: 10.1007/s10295-019-02136-y] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Accepted: 01/02/2019] [Indexed: 12/20/2022]
Abstract
Bacterial metabolism is comprised of primary metabolites, the intracellular molecules of life that enable growth and proliferation, and secondary metabolites, predominantly extracellular molecules that facilitate a microbe's interaction with its environment. While our knowledge of primary metabolism and its web of interconnected intermediates is quantitative and holistic, significant knowledge gaps remain in our understanding of the secondary metabolomes of bacteria. In this Perspective, I discuss the main challenges involved in obtaining a global, comprehensive picture of bacterial secondary metabolomes, specifically in biosynthetically "gifted" microbes. Recent methodological advances that can meet these challenges will be reviewed. Applications of these methods combined with ongoing innovations will enable a detailed picture of global secondary metabolomes, which will in turn shed light onto the biology, chemistry, and enzymology underlying natural products and simultaneously aid drug discovery.
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Affiliation(s)
- Mohammad R Seyedsayamdost
- Department of Chemistry, Princeton University, Princeton, NJ, 08544, USA.
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA.
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73
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Buijs Y, Bech PK, Vazquez-Albacete D, Bentzon-Tilia M, Sonnenschein EC, Gram L, Zhang SD. Marine Proteobacteria as a source of natural products: advances in molecular tools and strategies. Nat Prod Rep 2019; 36:1333-1350. [DOI: 10.1039/c9np00020h] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
This review covers the recent advances in molecular tools and strategies for studies and use of natural products from marine Proteobacteria.
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Affiliation(s)
- Yannick Buijs
- Department of Biotechnology and Biomedicine
- Technical University of Denmark
- DK-2800 Kgs Lyngby
- Denmark
| | - Pernille Kjersgaard Bech
- Department of Biotechnology and Biomedicine
- Technical University of Denmark
- DK-2800 Kgs Lyngby
- Denmark
| | - Dario Vazquez-Albacete
- Department of Biotechnology and Biomedicine
- Technical University of Denmark
- DK-2800 Kgs Lyngby
- Denmark
| | - Mikkel Bentzon-Tilia
- Department of Biotechnology and Biomedicine
- Technical University of Denmark
- DK-2800 Kgs Lyngby
- Denmark
| | - Eva C. Sonnenschein
- Department of Biotechnology and Biomedicine
- Technical University of Denmark
- DK-2800 Kgs Lyngby
- Denmark
| | - Lone Gram
- Department of Biotechnology and Biomedicine
- Technical University of Denmark
- DK-2800 Kgs Lyngby
- Denmark
| | - Sheng-Da Zhang
- Department of Biotechnology and Biomedicine
- Technical University of Denmark
- DK-2800 Kgs Lyngby
- Denmark
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