101
|
Recent advances in genetic modification systems for Actinobacteria. Appl Microbiol Biotechnol 2017; 101:2217-2226. [PMID: 28184986 DOI: 10.1007/s00253-017-8156-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2016] [Revised: 01/19/2017] [Accepted: 01/24/2017] [Indexed: 01/08/2023]
Abstract
Actinobacteria are extremely important to human health, agriculture, and forests. Because of the vast differences of the characteristics of Actinobacteria, a lot of genetic tools have been developed for efficiently manipulating the genetics. Although there are a lot of successful examples of engineering Actinobacteria, they are still more difficult to be genetically manipulated than other model microorganisms such as Saccharomyces cerevisiae, Escherichia coli, and Bacillus subtilis etc. due to the diverse genomics and biochemical machinery. Here, we review the methods to introduce heterologous DNA into Actinobacteria and the available genetic modification tools. The trends and problems existing in engineering Actinobacteria are also covered.
Collapse
|
102
|
Richardson-Sanchez T, Tieu W, Codd R. Reverse Biosynthesis: Generating Combinatorial Pools of Drug Leads from Enzyme-Mediated Fragmentation of Natural Products. Chembiochem 2017; 18:368-373. [DOI: 10.1002/cbic.201600636] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2016] [Indexed: 11/06/2022]
Affiliation(s)
- Tomas Richardson-Sanchez
- School of Medical Sciences (Pharmacology); The University of Sydney; Camperdown NSW 2006 Australia
| | - William Tieu
- School of Medical Sciences (Pharmacology); The University of Sydney; Camperdown NSW 2006 Australia
| | - Rachel Codd
- School of Medical Sciences (Pharmacology); The University of Sydney; Camperdown NSW 2006 Australia
| |
Collapse
|
103
|
KURT KIZILDOĞAN A, VANLI JACCARD G, MUTLU A, SERTDEMİR İ, ÖZCENGİZ G. Genetic engineering of an industrial strain of Streptomyces clavuligerusfor further enhancement of clavulanic acid production. Turk J Biol 2017. [DOI: 10.3906/biy-1608-17] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
|
104
|
Rey T, Dumas B. Plenty Is No Plague: Streptomyces Symbiosis with Crops. TRENDS IN PLANT SCIENCE 2017; 22:30-37. [PMID: 27916552 DOI: 10.1016/j.tplants.2016.10.008] [Citation(s) in RCA: 67] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2016] [Revised: 09/28/2016] [Accepted: 10/13/2016] [Indexed: 05/19/2023]
Abstract
Streptomyces spp. constitute a major clade of the phylum Actinobacteria. These Gram-positive, filamentous prokaryotes are ubiquitous in soils and marine sediments, and are commonly found in the rhizosphere or inside plant roots. Plant-interacting Streptomyces have received limited attention, in contrast to Streptomyces spp. extensively investigated for decades in medicine given their rich potential for secondary metabolite biosynthesis. Recent genomic, metabolomic, and biotechnological advances have produced key insights into Streptomyces spp., paving the way to the use of their metabolites in agriculture. In this Opinion article we propose how Streptomyces spp. could dominate future aspects of crop nutrition and protection. Risks and benefits of the use of these microorganisms in agriculture are also discussed.
Collapse
Affiliation(s)
- Thomas Rey
- De Sangosse, Bonnel, 47480 Pont-Du-Casse, France; Laboratoire de Recherche en Sciences Végétales, Université de Toulouse, CNRS, UPS, 24 Chemin de Borde Rouge, Auzeville, BP42617, 31326 Castanet Tolosan, France.
| | - Bernard Dumas
- Laboratoire de Recherche en Sciences Végétales, Université de Toulouse, CNRS, UPS, 24 Chemin de Borde Rouge, Auzeville, BP42617, 31326 Castanet Tolosan, France
| |
Collapse
|
105
|
Bilyk O, Luzhetskyy A. Metabolic engineering of natural product biosynthesis in actinobacteria. Curr Opin Biotechnol 2016; 42:98-107. [DOI: 10.1016/j.copbio.2016.03.008] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2016] [Revised: 03/03/2016] [Accepted: 03/11/2016] [Indexed: 11/25/2022]
|
106
|
Ünsaldı E, Kurt-Kızıldoğan A, Voigt B, Becher D, Özcengiz G. Proteome-wide alterations in an industrial clavulanic acid producing strain of Streptomyces clavuligerus. Synth Syst Biotechnol 2016; 2:39-48. [PMID: 29062960 PMCID: PMC5625738 DOI: 10.1016/j.synbio.2016.10.003] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2016] [Revised: 10/17/2016] [Accepted: 10/23/2016] [Indexed: 11/26/2022] Open
Abstract
The usefulness of genetic/metabolic engineering for further improvement of industrial strains is subject of discussion because of the general lack of knowledge on genetic alterations introduced by iterative cycles of random mutagenesis in such strains. An industrial clavulanic acid (CA)-overproducer Streptomyces clavuligerus DEPA was assessed to understand proteome-wide changes that have occurred in a local industrial CA overproducer developed through succesive mutagenesis programs. The proteins that could be identified corresponded to 33 distinct ORFs for underrepresented ones and 60 ORFs for overrepresented ones. Three CA biosynthetic enzymes were overrepresented in S. clavuligerus DEPA; carboxyethylarginine synthase (Ceas2), clavaldehyde dehydrogenase (Car) and carboxyethyl-arginine beta-lactam-synthase (Bls2) whereas the enzymes of two other secondary metabolites were underrepresented along with two important global regulators [two-component system (TCS) response regulator (SCLAV_2102) and TetR-family transcriptional regulator (SCLAV_3146)] that might be related with CA production and/or differentiation. γ-butyrolactone biosynthetic protein AvaA2 was 2.6 fold underrepresented in S. clavuligerus DEPA. The levels of two glycolytic enzymes, 2,3-bisphosphoglycerate-dependent phosphoglycerate mutase and phosophoglycerate kinase were found decreased while those of dihydrolipoyl dehydrogenase (E3) and isocitrate dehydrogenase, with two isoforms were found as significantly increased. A decrease of amino acid metabolism, methionine biosynthesis in particular, as well as S-adenosylmethionine synthetase appeared as one of the prominent mechanisms of success of S. clavuligerus DEPA strain as a prolific producer of CA. The levels of two enzymes of shikimate pathway that leads to the production of aromatic amino acids and aromatic secondary metabolites were also underrepresented. Some of the overrepresented stress proteins in S. clavuligerus DEPA included polynucleotide phosphorylase/polyadenylase (PNPase), ATP-dependent DNA helicase, two isoforms of an anti-sigma factor and thioredoxin reductase. Downregulation of important proteins of cell wall synthesis and division was recorded and a protein with β-lactamase domain (SCLAV_p1007) appeared in 12 isoforms, 5 of which were drastically overrepresented in DEPA strain. These results described herein provide useful information for rational engineering to improve CA production in Streptomyces clavuligerus.
Collapse
Affiliation(s)
- Eser Ünsaldı
- Department of Biological Sciences, Middle East Technical University, 06800, Ankara, Turkey
| | - Aslıhan Kurt-Kızıldoğan
- Department of Biological Sciences, Middle East Technical University, 06800, Ankara, Turkey.,Department of Agricultural Biotechnology, Ondokuz Mayıs University, 55139, Samsun, Turkey
| | - Birgit Voigt
- Institute of Microbiology, Ernst-Moritz-Arndt-University of Greifswald, D-17487, Greifswald, Germany
| | - Dörte Becher
- Institute of Microbiology, Ernst-Moritz-Arndt-University of Greifswald, D-17487, Greifswald, Germany
| | - Gülay Özcengiz
- Department of Biological Sciences, Middle East Technical University, 06800, Ankara, Turkey
| |
Collapse
|
107
|
Beckers V, Dersch LM, Lotz K, Melzer G, Bläsing OE, Fuchs R, Ehrhardt T, Wittmann C. In silico metabolic network analysis of Arabidopsis leaves. BMC SYSTEMS BIOLOGY 2016; 10:102. [PMID: 27793154 PMCID: PMC5086045 DOI: 10.1186/s12918-016-0347-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/25/2016] [Accepted: 10/21/2016] [Indexed: 12/23/2022]
Abstract
Background During the last decades, we face an increasing interest in superior plants to supply growing demands for human and animal nutrition and for the developing bio-based economy. Presently, our limited understanding of their metabolism and its regulation hampers the targeted development of desired plant phenotypes. In this regard, systems biology, in particular the integration of metabolic and regulatory networks, is promising to broaden our knowledge and to further explore the biotechnological potential of plants. Results The thale cress Arabidopsis thaliana provides an ideal model to understand plant primary metabolism. To obtain insight into its functional properties, we constructed a large-scale metabolic network of the leaf of A. thaliana. It represented 511 reactions with spatial separation into compartments. Systematic analysis of this network, utilizing elementary flux modes, investigates metabolic capabilities of the plant and predicts relevant properties on the systems level: optimum pathway use for maximum growth and flux re-arrangement in response to environmental perturbation. Our computational model indicates that the A. thaliana leaf operates near its theoretical optimum flux state in the light, however, only in a narrow range of photon usage. The simulations further demonstrate that the natural day-night shift requires substantial re-arrangement of pathway flux between compartments: 89 reactions, involving redox and energy metabolism, substantially change the extent of flux, whereas 19 reactions even invert flux direction. The optimum set of anabolic pathways differs between day and night and is partly shifted between compartments. The integration with experimental transcriptome data pinpoints selected transcriptional changes that mediate the diurnal adaptation of the plant and superimpose the flux response. Conclusions The successful application of predictive modelling in Arabidopsis thaliana can bring systems-biological interpretation of plant systems forward. Using the gained knowledge, metabolic engineering strategies to engage plants as biotechnological factories can be developed. Electronic supplementary material The online version of this article (doi:10.1186/s12918-016-0347-3) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Veronique Beckers
- Institute for Systems Biotechnology, Saarland University, Campus A1.5, 66123, Saarbrücken, Germany
| | - Lisa Maria Dersch
- Institute for Systems Biotechnology, Saarland University, Campus A1.5, 66123, Saarbrücken, Germany
| | | | - Guido Melzer
- Institute of Biochemical Engineering, Technical University Braunschweig, Braunschweig, Germany
| | | | | | | | - Christoph Wittmann
- Institute for Systems Biotechnology, Saarland University, Campus A1.5, 66123, Saarbrücken, Germany.
| |
Collapse
|
108
|
Long-Term Warming Alters Carbohydrate Degradation Potential in Temperate Forest Soils. Appl Environ Microbiol 2016; 82:6518-6530. [PMID: 27590813 PMCID: PMC5086546 DOI: 10.1128/aem.02012-16] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2016] [Accepted: 08/19/2016] [Indexed: 11/20/2022] Open
Abstract
As Earth's climate warms, soil carbon pools and the microbial communities that process them may change, altering the way in which carbon is recycled in soil. In this study, we used a combination of metagenomics and bacterial cultivation to evaluate the hypothesis that experimentally raising soil temperatures by 5°C for 5, 8, or 20 years increased the potential for temperate forest soil microbial communities to degrade carbohydrates. Warming decreased the proportion of carbohydrate-degrading genes in the organic horizon derived from eukaryotes and increased the fraction of genes in the mineral soil associated with Actinobacteria in all studies. Genes associated with carbohydrate degradation increased in the organic horizon after 5 years of warming but had decreased in the organic horizon after warming the soil continuously for 20 years. However, a greater proportion of the 295 bacteria from 6 phyla (10 classes, 14 orders, and 34 families) isolated from heated plots in the 20-year experiment were able to depolymerize cellulose and xylan than bacterial isolates from control soils. Together, these findings indicate that the enrichment of bacteria capable of degrading carbohydrates could be important for accelerated carbon cycling in a warmer world.
IMPORTANCE The massive carbon stocks currently held in soils have been built up over millennia, and while numerous lines of evidence indicate that climate change will accelerate the processing of this carbon, it is unclear whether the genetic repertoire of the microbes responsible for this elevated activity will also change. In this study, we showed that bacteria isolated from plots subject to 20 years of 5°C of warming were more likely to depolymerize the plant polymers xylan and cellulose, but that carbohydrate degradation capacity is not uniformly enriched by warming treatment in the metagenomes of soil microbial communities. This study illustrates the utility of combining culture-dependent and culture-independent surveys of microbial communities to improve our understanding of the role changing microbial communities may play in soil carbon cycling under climate change.
Collapse
|
109
|
Yoo YJ, Kim H, Park SR, Yoon YJ. An overview of rapamycin: from discovery to future perspectives. J Ind Microbiol Biotechnol 2016; 44:537-553. [PMID: 27613310 DOI: 10.1007/s10295-016-1834-7] [Citation(s) in RCA: 65] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2016] [Accepted: 08/22/2016] [Indexed: 12/17/2022]
Abstract
Rapamycin is an immunosuppressive metabolite produced from several actinomycete species. Besides its immunosuppressive activity, rapamycin and its analogs have additional therapeutic potentials, including antifungal, antitumor, neuroprotective/neuroregenerative, and lifespan extension activities. The core structure of rapamycin is derived from (4R,5R)-4,5-dihydrocyclohex-1-ene-carboxylic acid that is extended by polyketide synthase. The resulting linear polyketide chain is cyclized by incorporating pipecolate and further decorated by post-PKS modification enzymes. Herein, we review the discovery and biological activities of rapamycin as well as its mechanism of action, mechanistic target, biosynthesis, and regulation. In addition, we introduce the many efforts directed at enhancing the production of rapamycin and generating diverse analogs and also explore future perspectives in rapamycin research. This review will also emphasize the remarkable pilot studies on the biosynthesis and production improvement of rapamycin by Dr. Demain, one of the world's distinguished scientists in industrial microbiology and biotechnology.
Collapse
Affiliation(s)
- Young Ji Yoo
- Department of Chemistry and Nanoscience, Ewha Womans University, Seoul, 120-750, Republic of Korea
| | - Hanseong Kim
- Department of Biological Chemistry, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Sung Ryeol Park
- Natural Products Discovery Institute, The Baruch S. Blumberg Institute, Hepatitis B Foundation, Doylestown, PA, 18902, USA.
| | - Yeo Joon Yoon
- Department of Chemistry and Nanoscience, Ewha Womans University, Seoul, 120-750, Republic of Korea.
| |
Collapse
|
110
|
Aguda AH, Lavallee V, Cheng P, Bott TM, Meimetis LG, Law S, Nguyen NT, Williams DE, Kaleta J, Villanueva I, Davies J, Andersen RJ, Brayer GD, Brömme D. Affinity Crystallography: A New Approach to Extracting High-Affinity Enzyme Inhibitors from Natural Extracts. JOURNAL OF NATURAL PRODUCTS 2016; 79:1962-1970. [PMID: 27498895 DOI: 10.1021/acs.jnatprod.6b00215] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Natural products are an important source of novel drug scaffolds. The highly variable and unpredictable timelines associated with isolating novel compounds and elucidating their structures have led to the demise of exploring natural product extract libraries in drug discovery programs. Here we introduce affinity crystallography as a new methodology that significantly shortens the time of the hit to active structure cycle in bioactive natural product discovery research. This affinity crystallography approach is illustrated by using semipure fractions of an actinomycetes culture extract to isolate and identify a cathepsin K inhibitor and to compare the outcome with the traditional assay-guided purification/structural analysis approach. The traditional approach resulted in the identification of the known inhibitor antipain (1) and its new but lower potency dehydration product 2, while the affinity crystallography approach led to the identification of a new high-affinity inhibitor named lichostatinal (3). The structure and potency of lichostatinal (3) was verified by total synthesis and kinetic characterization. To the best of our knowledge, this is the first example of isolating and characterizing a potent enzyme inhibitor from a partially purified crude natural product extract using a protein crystallographic approach.
Collapse
Affiliation(s)
- Adeleke H Aguda
- Department of Oral Biological and Medical Sciences, Faculty of Dentistry, ‡Department of Biochemistry and Molecular Biology, Faculty of Medicine, §Department of Chemistry and Earth, Ocean & Atmospheric Sciences, Faculty of Science, ⊥Department of Microbiology, Faculty of Science, and ∥Centre for Blood Research, University of British Columbia , Vancouver, BC Canada , V6T 1Z3
| | - Vincent Lavallee
- Department of Oral Biological and Medical Sciences, Faculty of Dentistry, ‡Department of Biochemistry and Molecular Biology, Faculty of Medicine, §Department of Chemistry and Earth, Ocean & Atmospheric Sciences, Faculty of Science, ⊥Department of Microbiology, Faculty of Science, and ∥Centre for Blood Research, University of British Columbia , Vancouver, BC Canada , V6T 1Z3
| | - Ping Cheng
- Department of Oral Biological and Medical Sciences, Faculty of Dentistry, ‡Department of Biochemistry and Molecular Biology, Faculty of Medicine, §Department of Chemistry and Earth, Ocean & Atmospheric Sciences, Faculty of Science, ⊥Department of Microbiology, Faculty of Science, and ∥Centre for Blood Research, University of British Columbia , Vancouver, BC Canada , V6T 1Z3
| | - Tina M Bott
- Department of Oral Biological and Medical Sciences, Faculty of Dentistry, ‡Department of Biochemistry and Molecular Biology, Faculty of Medicine, §Department of Chemistry and Earth, Ocean & Atmospheric Sciences, Faculty of Science, ⊥Department of Microbiology, Faculty of Science, and ∥Centre for Blood Research, University of British Columbia , Vancouver, BC Canada , V6T 1Z3
| | - Labros G Meimetis
- Department of Oral Biological and Medical Sciences, Faculty of Dentistry, ‡Department of Biochemistry and Molecular Biology, Faculty of Medicine, §Department of Chemistry and Earth, Ocean & Atmospheric Sciences, Faculty of Science, ⊥Department of Microbiology, Faculty of Science, and ∥Centre for Blood Research, University of British Columbia , Vancouver, BC Canada , V6T 1Z3
| | - Simon Law
- Department of Oral Biological and Medical Sciences, Faculty of Dentistry, ‡Department of Biochemistry and Molecular Biology, Faculty of Medicine, §Department of Chemistry and Earth, Ocean & Atmospheric Sciences, Faculty of Science, ⊥Department of Microbiology, Faculty of Science, and ∥Centre for Blood Research, University of British Columbia , Vancouver, BC Canada , V6T 1Z3
| | - Nham T Nguyen
- Department of Oral Biological and Medical Sciences, Faculty of Dentistry, ‡Department of Biochemistry and Molecular Biology, Faculty of Medicine, §Department of Chemistry and Earth, Ocean & Atmospheric Sciences, Faculty of Science, ⊥Department of Microbiology, Faculty of Science, and ∥Centre for Blood Research, University of British Columbia , Vancouver, BC Canada , V6T 1Z3
| | - David E Williams
- Department of Oral Biological and Medical Sciences, Faculty of Dentistry, ‡Department of Biochemistry and Molecular Biology, Faculty of Medicine, §Department of Chemistry and Earth, Ocean & Atmospheric Sciences, Faculty of Science, ⊥Department of Microbiology, Faculty of Science, and ∥Centre for Blood Research, University of British Columbia , Vancouver, BC Canada , V6T 1Z3
| | - Jadwiga Kaleta
- Department of Oral Biological and Medical Sciences, Faculty of Dentistry, ‡Department of Biochemistry and Molecular Biology, Faculty of Medicine, §Department of Chemistry and Earth, Ocean & Atmospheric Sciences, Faculty of Science, ⊥Department of Microbiology, Faculty of Science, and ∥Centre for Blood Research, University of British Columbia , Vancouver, BC Canada , V6T 1Z3
| | - Ivan Villanueva
- Department of Oral Biological and Medical Sciences, Faculty of Dentistry, ‡Department of Biochemistry and Molecular Biology, Faculty of Medicine, §Department of Chemistry and Earth, Ocean & Atmospheric Sciences, Faculty of Science, ⊥Department of Microbiology, Faculty of Science, and ∥Centre for Blood Research, University of British Columbia , Vancouver, BC Canada , V6T 1Z3
| | - Julian Davies
- Department of Oral Biological and Medical Sciences, Faculty of Dentistry, ‡Department of Biochemistry and Molecular Biology, Faculty of Medicine, §Department of Chemistry and Earth, Ocean & Atmospheric Sciences, Faculty of Science, ⊥Department of Microbiology, Faculty of Science, and ∥Centre for Blood Research, University of British Columbia , Vancouver, BC Canada , V6T 1Z3
| | - Raymond J Andersen
- Department of Oral Biological and Medical Sciences, Faculty of Dentistry, ‡Department of Biochemistry and Molecular Biology, Faculty of Medicine, §Department of Chemistry and Earth, Ocean & Atmospheric Sciences, Faculty of Science, ⊥Department of Microbiology, Faculty of Science, and ∥Centre for Blood Research, University of British Columbia , Vancouver, BC Canada , V6T 1Z3
| | - Gary D Brayer
- Department of Oral Biological and Medical Sciences, Faculty of Dentistry, ‡Department of Biochemistry and Molecular Biology, Faculty of Medicine, §Department of Chemistry and Earth, Ocean & Atmospheric Sciences, Faculty of Science, ⊥Department of Microbiology, Faculty of Science, and ∥Centre for Blood Research, University of British Columbia , Vancouver, BC Canada , V6T 1Z3
| | - Dieter Brömme
- Department of Oral Biological and Medical Sciences, Faculty of Dentistry, ‡Department of Biochemistry and Molecular Biology, Faculty of Medicine, §Department of Chemistry and Earth, Ocean & Atmospheric Sciences, Faculty of Science, ⊥Department of Microbiology, Faculty of Science, and ∥Centre for Blood Research, University of British Columbia , Vancouver, BC Canada , V6T 1Z3
| |
Collapse
|
111
|
A Novel Insecticidal Peptide SLP1 Produced by Streptomyces laindensis H008 against Lipaphis erysimi. Molecules 2016; 21:molecules21081101. [PMID: 27556442 PMCID: PMC6273262 DOI: 10.3390/molecules21081101] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2016] [Revised: 08/15/2016] [Accepted: 08/18/2016] [Indexed: 11/17/2022] Open
Abstract
Aphids are major insect pests for crops, causing damage by direct feeding and transmission of plant diseases. This paper was completed to discover and characterize a novel insecticidal metabolite against aphids from soil actinobacteria. An insecticidal activity assay was used to screen 180 bacterial strains from soil samples against mustard aphid, Lipaphis erysimi. The bacterial strain H008 showed the strongest activity, and it was identified by the phylogenetic analysis of the 16S rRNA gene and physiological traits as a novel species of genus Streptomyces (named S. laindensis H008). With the bioassay-guided method, the insecticidal extract from S. laindensis H008 was subjected to chromatographic separations. Finally, a novel insecticidal peptide was purified from Streptomyces laindensis H008 against L. erysimi, and it was determined to be S-E-P-A-Q-I-V-I-V-D-G-V-D-Y-W by TOF-MS and amino acid analysis.
Collapse
|
112
|
Wang W, Yang T, Li Y, Li S, Yin S, Styles K, Corre C, Yang K. Development of a Synthetic Oxytetracycline-Inducible Expression System for Streptomycetes Using de Novo Characterized Genetic Parts. ACS Synth Biol 2016; 5:765-73. [PMID: 27100123 DOI: 10.1021/acssynbio.6b00087] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Precise control of gene expression using exogenous factors is of great significance. To develop ideal inducible expression systems for streptomycetes, new genetic parts, oxytetracycline responsive repressor OtrR, operator otrO, and promoter otrBp from Streptomyces rimosus, were selected de novo and characterized in vivo and in vitro. OtrR showed strong affinity to otrO (KD = 1.7 × 10(-10) M) and oxytetracycline induced dissociation of the OtrR/DNA complex in a concentration-dependent manner. On the basis of these genetic parts, a synthetic inducible expression system Potr* was optimized. Induction of Potr* with 0.01-4 μM of oxytetracycline triggered a wide-range expression level of gfp reporter gene in different Streptomyces species. Benchmarking Potr* against the widely used constitutive promoters ermE* and kasOp* revealed greatly enhanced levels of expression when Potr* was fully induced. Finally, Potr* was used as a tool to activate and optimize the expression of the silent jadomycin biosynthetic gene cluster in Streptomyces venezuelae. Altogether, the synthetic Potr* presents a new versatile tool for fine-tuning gene expression in streptomycetes.
Collapse
Affiliation(s)
- Weishan Wang
- State
Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, No.1 West Beichen Road, Chaoyang District, Beijing 100101, People’s Republic of China
| | - Tongjian Yang
- State
Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, No.1 West Beichen Road, Chaoyang District, Beijing 100101, People’s Republic of China
- University of Chinese Academy of Sciences, No.19A Yuquan Road, Beijing 100049, People’s Republic of China
| | - Yihong Li
- State
Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, No.1 West Beichen Road, Chaoyang District, Beijing 100101, People’s Republic of China
| | - Shanshan Li
- State
Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, No.1 West Beichen Road, Chaoyang District, Beijing 100101, People’s Republic of China
| | - Shouliang Yin
- State
Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, No.1 West Beichen Road, Chaoyang District, Beijing 100101, People’s Republic of China
| | - Kathryn Styles
- School
of Life Sciences and Department of Chemistry, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Christophe Corre
- School
of Life Sciences and Department of Chemistry, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Keqian Yang
- State
Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, No.1 West Beichen Road, Chaoyang District, Beijing 100101, People’s Republic of China
| |
Collapse
|
113
|
Complete genome sequence of the Streptomyces sp. strain CdTB01, a bacterium tolerant to cadmium. J Biotechnol 2016; 229:42-3. [PMID: 27165503 DOI: 10.1016/j.jbiotec.2016.04.040] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2016] [Accepted: 04/20/2016] [Indexed: 11/24/2022]
|
114
|
King JR, Edgar S, Qiao K, Stephanopoulos G. Accessing Nature's diversity through metabolic engineering and synthetic biology. F1000Res 2016; 5. [PMID: 27081481 PMCID: PMC4813638 DOI: 10.12688/f1000research.7311.1] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 03/21/2016] [Indexed: 12/31/2022] Open
Abstract
In this perspective, we highlight recent examples and trends in metabolic engineering and synthetic biology that demonstrate the synthetic potential of enzyme and pathway engineering for natural product discovery. In doing so, we introduce natural paradigms of secondary metabolism whereby simple carbon substrates are combined into complex molecules through “scaffold diversification”, and subsequent “derivatization” of these scaffolds is used to synthesize distinct complex natural products. We provide examples in which modern pathway engineering efforts including combinatorial biosynthesis and biological retrosynthesis can be coupled to directed enzyme evolution and rational enzyme engineering to allow access to the “privileged” chemical space of natural products in industry-proven microbes. Finally, we forecast the potential to produce natural product-like discovery platforms in biological systems that are amenable to single-step discovery, validation, and synthesis for streamlined discovery and production of biologically active agents.
Collapse
Affiliation(s)
- Jason R King
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Steven Edgar
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Kangjian Qiao
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Gregory Stephanopoulos
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| |
Collapse
|
115
|
Dersch LM, Beckers V, Wittmann C. Green pathways: Metabolic network analysis of plant systems. Metab Eng 2016; 34:1-24. [DOI: 10.1016/j.ymben.2015.12.001] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Revised: 11/30/2015] [Accepted: 12/01/2015] [Indexed: 12/18/2022]
|
116
|
|
117
|
Deciphering the streamlined genome of Streptomyces xiamenensis 318 as the producer of the anti-fibrotic drug candidate xiamenmycin. Sci Rep 2016; 6:18977. [PMID: 26744183 PMCID: PMC4705527 DOI: 10.1038/srep18977] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2015] [Accepted: 12/01/2015] [Indexed: 12/13/2022] Open
Abstract
Streptomyces xiamenensis 318, a moderate halophile isolated from a mangrove sediment, produces the anti-fibrotic compound xiamenmycin. The whole genome sequence of strain 318 was obtained through long-read single-molecule real-time (SMRT) sequencing, high-throughput Illumina HiSeq and 454 pyrosequencing technologies. The assembled genome comprises a linear chromosome as a single contig of 5,961,401-bp, which is considerably smaller than other reported complete genomes of the genus Streptomyces. Based on the antiSMASH pipeline, a total of 21 gene clusters were predicted to be involved in secondary metabolism. The gene cluster responsible for the biosynthesis of xiamenmycin resides in a strain-specific 61,387-bp genomic island belonging to the left-arm region. A core metabolic network consisting of 104 reactions that supports xiamenmycin biosynthesis was constructed to illustrate the necessary precursors derived from the central metabolic pathway. In accordance with the finding of a putative ikarugamycin gene cluster in the genome, the targeted chemical profiling of polycyclic tetramate macrolactams (PTMs) resulted in the identification of ikarugamycin. A successful genome mining for bioactive molecules with different skeletons suggests that the naturally minimized genome of S. xiamenensis 318 could be used as a blueprint for constructing a chassis cell with versatile biosynthetic capabilities for the production of secondary metabolites.
Collapse
|
118
|
Kim HU, Charusanti P, Lee SY, Weber T. Metabolic engineering with systems biology tools to optimize production of prokaryotic secondary metabolites. Nat Prod Rep 2016; 33:933-41. [DOI: 10.1039/c6np00019c] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
This Highlight examines current status of metabolic engineering and systems biology tools deployed for the optimal production of prokaryotic secondary metabolites.
Collapse
Affiliation(s)
- Hyun Uk Kim
- BioInformatics Research Center
- Korea Advanced Institute of Science and Technology (KAIST)
- Daejeon
- Republic of Korea
- The Novo Nordisk Foundation Center for Biosustainability
| | - Pep Charusanti
- The Novo Nordisk Foundation Center for Biosustainability
- Technical University of Denmark
- Hørsholm
- Denmark
| | - Sang Yup Lee
- BioInformatics Research Center
- Korea Advanced Institute of Science and Technology (KAIST)
- Daejeon
- Republic of Korea
- The Novo Nordisk Foundation Center for Biosustainability
| | - Tilmann Weber
- The Novo Nordisk Foundation Center for Biosustainability
- Technical University of Denmark
- Hørsholm
- Denmark
| |
Collapse
|
119
|
Improvement of chloramphenicol production in Streptomyces venezuelae ATCC 10712 by overexpression of the aroB and aroK genes catalysing steps in the shikimate pathway. Antonie van Leeuwenhoek 2015; 109:379-88. [DOI: 10.1007/s10482-015-0640-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2015] [Accepted: 12/18/2015] [Indexed: 01/13/2023]
|
120
|
Song JY, Yoo YJ, Lim SK, Cha SH, Kim JE, Roe JH, Kim JF, Yoon YJ. Complete genome sequence of Streptomyces venezuelae ATCC 15439, a promising cell factory for production of secondary metabolites. J Biotechnol 2015; 219:57-8. [PMID: 26718561 DOI: 10.1016/j.jbiotec.2015.12.028] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2015] [Accepted: 12/15/2015] [Indexed: 11/17/2022]
Abstract
Streptomyces venezuelae ATCC 15439, which produces 12- and 14-membered ring macrolide antibiotics, is a platform strain for heterologous expression of secondary metabolites. Its 9.05-Mb genome sequence revealed an abundance of genes involved in the biosynthesis of secondary metabolites and their precursors, which should be useful for the production of bioactive compounds.
Collapse
Affiliation(s)
- Ju Yeon Song
- Department of Systems Biology and Division of Life Sciences, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul 03722, Republic of Korea
| | - Young Ji Yoo
- Department of Chemistry and Nanoscience, Ewha Womans University, 52 Ewhayeodae-gil, Seodaemun-gu, Seoul 03760, Republic of Korea
| | - Si-Kyu Lim
- GenoTech Corporation, 26-69 Gajeongbuk-ro, Daejeon 34113, Republic of Korea
| | - Sun Ho Cha
- GenoTech Corporation, 26-69 Gajeongbuk-ro, Daejeon 34113, Republic of Korea
| | - Ji-Eun Kim
- School of Biological Sciences and Institute of Microbiology, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Republic of Korea
| | - Jung-Hye Roe
- School of Biological Sciences and Institute of Microbiology, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Republic of Korea
| | - Jihyun F Kim
- Department of Systems Biology and Division of Life Sciences, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul 03722, Republic of Korea; Strategic Initiative for Microbiomes in Agriculture and Food, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul 03722, Republic of Korea.
| | - Yeo Joon Yoon
- Department of Chemistry and Nanoscience, Ewha Womans University, 52 Ewhayeodae-gil, Seodaemun-gu, Seoul 03760, Republic of Korea.
| |
Collapse
|
121
|
Xu Z, Sun Z, Li S, Xu Z, Cao C, Xu Z, Feng X, Xu H. Systematic unravelling of the biosynthesis of poly (L-diaminopropionic acid) in Streptomyces albulus PD-1. Sci Rep 2015; 5:17400. [PMID: 26632244 PMCID: PMC4668381 DOI: 10.1038/srep17400] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2015] [Accepted: 10/27/2015] [Indexed: 12/20/2022] Open
Abstract
Poly(L-diaminopropionic acid) (PDAP) is one of the four homopoly(amino acid)s that have been discovered in nature. However, the molecular mechanism of PDAP biosynthesis has yet to be described. In this work, the general layout of the PDAP biosynthetic pathway is characterised in Streptomyces albulus PD-1 by genome mining, gene disruption, heterologous expression and in vitro feeding experiments. As a result, L-diaminopropionic acid (L-DAP), which is the monomer of PDAP, is shown to be jointly synthesised by two protein homologues of cysteine synthetase and ornithine cyclodeaminase. Then, L-DAP is assembled into PDAP by a novel nonribosomal peptide synthetase (NRPS) with classical adenylation and peptidyl carrier protein domains. However, instead of the traditional condensation or thioesterase domain of NRPSs, this NRPS has seven transmembrane domains surrounding three tandem soluble domains at the C-terminus. As far as we know, this novel single-module NRPS structure has only been reported in poly(ε-L-lysine) synthetase. The similar NRPS structure of PDAP synthetase and poly(ε-L-lysine) synthetase may be a common characteristic of homopoly(amino acid)s synthetases. In this case, we may discover and/or design more homopoly(amino acid)s by mining this kind of novel NRPS structure in the future.
Collapse
Affiliation(s)
- Zhaoxian Xu
- State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing, 211816, China.,College of Food Science and Light Industry, Nanjing Tech University, Nanjing, 211816, China
| | - Zhuzhen Sun
- State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing, 211816, China.,College of Food Science and Light Industry, Nanjing Tech University, Nanjing, 211816, China
| | - Sha Li
- State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing, 211816, China.,College of Food Science and Light Industry, Nanjing Tech University, Nanjing, 211816, China
| | - Zheng Xu
- State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing, 211816, China.,College of Food Science and Light Industry, Nanjing Tech University, Nanjing, 211816, China
| | - Changhong Cao
- State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing, 211816, China.,College of Food Science and Light Industry, Nanjing Tech University, Nanjing, 211816, China
| | - Zongqi Xu
- State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing, 211816, China.,College of Food Science and Light Industry, Nanjing Tech University, Nanjing, 211816, China
| | - Xiaohai Feng
- State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing, 211816, China.,College of Food Science and Light Industry, Nanjing Tech University, Nanjing, 211816, China
| | - Hong Xu
- State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing, 211816, China.,College of Food Science and Light Industry, Nanjing Tech University, Nanjing, 211816, China
| |
Collapse
|
122
|
Affiliation(s)
- Sarah E. O'Connor
- The John Innes Centre, Norwich Research Park, Norwich NR4 7UH, United Kingdom;
| |
Collapse
|
123
|
Sakai K, Komaki H, Gonoi T. Identification and Functional Analysis of the Nocardithiocin Gene Cluster in Nocardia pseudobrasiliensis. PLoS One 2015; 10:e0143264. [PMID: 26588225 PMCID: PMC4654471 DOI: 10.1371/journal.pone.0143264] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2015] [Accepted: 11/01/2015] [Indexed: 11/19/2022] Open
Abstract
Nocardithiocin is a thiopeptide compound isolated from the opportunistic pathogen Nocardia pseudobrasiliensis. It shows a strong activity against acid-fast bacteria and is also active against rifampicin-resistant Mycobacterium tuberculosis. Here, we report the identification of the nocardithiocin gene cluster in N. pseudobrasiliensis IFM 0761 based on conserved thiopeptide biosynthesis gene sequence and the whole genome sequence. The predicted gene cluster was confirmed by gene disruption and complementation. As expected, strains containing the disrupted gene did not produce nocardithiocin while gene complementation restored nocardithiocin production in these strains. The predicted cluster was further analyzed using RNA-seq which showed that the nocardithiocin gene cluster contains 12 genes within a 15.2-kb region. This finding will promote the improvement of nocardithiocin productivity and its derivatives production.
Collapse
Affiliation(s)
- Kanae Sakai
- Medical Mycology Research Center, Chiba University, Chiba, Japan
- * E-mail:
| | - Hisayuki Komaki
- Biological Resource Center, National Institute of Technology and Evaluation, Chiba, Japan
| | - Tohru Gonoi
- Medical Mycology Research Center, Chiba University, Chiba, Japan
| |
Collapse
|
124
|
Zhu C, Kang Q, Bai L, Cheng L, Deng Z. Identification and engineering of regulation-related genes toward improved kasugamycin production. Appl Microbiol Biotechnol 2015; 100:1811-1821. [PMID: 26521251 DOI: 10.1007/s00253-015-7082-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2015] [Revised: 10/06/2015] [Accepted: 10/12/2015] [Indexed: 10/22/2022]
Abstract
Kasugamycin, produced by Streptomyces kasugaensis and Streptomyces microaureus, is an important amino-glycoside family antibiotic and widely used for veterinary and agricultural applications. In the left flanking region of the previously reported kasugamycin gene cluster, four additional genes (two-component system kasW and kasX, MerR-family kasV, and isoprenylcysteine carboxyl methyltransferase kasS) were identified both in the low-yielding S. kasugaensis BCRC12349 and high-yielding S. microaureus XM301. Deletion of regulatory gene kasT abolished kasugamycin production, and its overexpression in BCRC12349 resulted in an increased titer by 186 %. Deletion of kasW, kasX, kasV, and kasS improved kasugamycin production by 12, 19, 194, and 22 %, respectively. qRT-PCR analysis demonstrated that the transcription of kas genes was significantly increased in all the four mutants. Similar gene inactivation was performed in the high-yielding strain S. microaureus XM301. As expected, the deletion of kasW/X resulted in a 58 % increase of the yield from 6 to 9.5 g/L. However, the deletion of kasV and over-expression of kasT had no obvious effect, and the disruption of kasS surprisingly decreased kasugamycin production. In addition, trans-complementation of the kasS mutant with a TTA codon-mutated kasS increased the kasugamycin yield by 20 %. A much higher transcription of kas genes was detected in the high-yielding XM301 than in the low-yielding BCRC12349, which may partially account for the discrepancy of gene inactivation effects between them. Our work not only generated engineered strains with improved kasugamycin yield, but also pointed out that different strategies on manipulating regulatory-related genes should be considered for low-yielding or high-yielding strains.
Collapse
Affiliation(s)
- Chenchen Zhu
- State Key Laboratory of Microbial Metabolism, and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, People's Republic of China
| | - Qianjin Kang
- State Key Laboratory of Microbial Metabolism, and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, People's Republic of China
| | - Linquan Bai
- State Key Laboratory of Microbial Metabolism, and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, People's Republic of China.
| | - Lin Cheng
- School of Pharmaceutical Sciences, Wuhan University, Wuhan, 430071, People's Republic of China.
| | - Zixin Deng
- State Key Laboratory of Microbial Metabolism, and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, People's Republic of China.,School of Pharmaceutical Sciences, Wuhan University, Wuhan, 430071, People's Republic of China
| |
Collapse
|
125
|
Li S, Wang J, Li X, Yin S, Wang W, Yang K. Genome-wide identification and evaluation of constitutive promoters in streptomycetes. Microb Cell Fact 2015; 14:172. [PMID: 26515616 PMCID: PMC4625935 DOI: 10.1186/s12934-015-0351-0] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2015] [Accepted: 10/01/2015] [Indexed: 01/24/2023] Open
Abstract
Background Streptomycetes attract a lot of attention in metabolic engineering and synthetic biology because of their well-known ability to produce secondary metabolites. However, the available constitutive promoters are rather limited in this genus. Results In this work, constitutive promoters were selected from a pool of promoters whose downstream genes maintained constant expression profiles in various conditions. A total of 941 qualified genes were selected based on systematic analysis of five sets of time-series transcriptome microarray data of Streptomyces coelicolor M145 cultivated under different conditions. Then, 166 putative constitutive promoters were selected by following a rational selection workflow containing disturbance analysis, function analysis, genetic loci analysis, and transcript abundance analysis. Further, eight promoters with different strengths were chosen and subjected to experimental validation by green fluorescent protein reporter and real-time reverse-transcription quantitative polymerase chain reaction in S. coelicolor, Streptomyces venezuelae and Streptomyces albus. The eight promoters drove the stable expression of downstream genes in different conditions, implying that the 166 promoters that we identified might be constitutive under the genus Streptomyces. Four promoters were used in a plug-and-play platform to control the expression of the cryptic cluster of jadomycin B in S. venezuelae ISP5230 and resulted in different levels of the production of jadomycin B that corresponded to promoter strength. Conclusions This work identified and evaluated a set of constitutive promoters with different strengths in streptomycetes, and it enriched the presently available promoter toolkit in this genus. These promoters should be valuable in current platforms of metabolic engineering and synthetic biology for the activation of cryptic biosynthetic clusters and the optimization of pathways for the biosynthesis of important natural products in Streptomyces species. Electronic supplementary material The online version of this article (doi:10.1186/s12934-015-0351-0) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Shanshan Li
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, People's Republic of China.
| | - Junyang Wang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, People's Republic of China.
| | - Xiao Li
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, People's Republic of China.
| | - Shouliang Yin
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, People's Republic of China.
| | - Weishan Wang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, People's Republic of China.
| | - Keqian Yang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, People's Republic of China.
| |
Collapse
|
126
|
Muhamadali H, Xu Y, Ellis DI, Trivedi DK, Rattray NJW, Bernaerts K, Goodacre R. Metabolomics investigation of recombinant mTNFα production in Streptomyces lividans. Microb Cell Fact 2015; 14:157. [PMID: 26449894 PMCID: PMC4598958 DOI: 10.1186/s12934-015-0350-1] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2015] [Accepted: 09/29/2015] [Indexed: 02/02/2023] Open
Abstract
BACKGROUND Whilst undergoing differentiation, Streptomyces produce a large quantity of hydrolytic enzymes and secondary metabolites, and it is this very ability that has focussed increasing interest on the use of these bacteria as hosts for the production of various heterologous proteins. However, within this genus, the exploration and understanding of the metabolic burden associated with such bio-products has only just begun. In this study our overall aim was to apply metabolomics approaches as tools to get a glimpse of the metabolic alterations within S. lividans TK24 when this industrially relevant microbe is producing recombinant murine tumour necrosis factor alpha (mTNFα), in comparison to wild type and empty (non-recombinant protein containing) plasmid-carrying strains as controls. RESULTS Whilst growth profiles of all strains demonstrated comparable trends, principal component-discriminant function analysis of Fourier transform infrared (FT-IR) spectral data, showed clear separation of wild type from empty plasmid and mTNFα-producing strains, throughout the time course of incubation. Analysis of intra- and extra-cellular metabolic profiles using gas chromatography-mass spectrometry (GC-MS) displayed similar trends to the FT-IR data. Although the strain carrying the empty plasmid demonstrated metabolic changes due to the maintenance of the plasmid, the metabolic behaviour of the recombinant mTNFα-producing strain appeared to be the most significantly affected. GC-MS results also demonstrated a significant overflow of several organic acids (pyruvate, 2-ketoglutarate and propanoate) and sugars (xylitol, mannose and fructose) in the mTNFα-producing strain. CONCLUSION The results obtained in this study have clearly demonstrated the metabolic impacts of producing mTNFα in S. lividans TK24, while displaying profound metabolic effects of harbouring the empty PIJ486 plasmid. In addition, the level of mTNFα produced in this study, further highlights the key role of media composition towards the efficiency of a bioprocess and metabolic behaviour of the host cells, which directly influences the yield of the recombinant product.
Collapse
Affiliation(s)
- Howbeer Muhamadali
- School of Chemistry, Manchester Institute of Biotechnology, University of Manchester, Manchester, UK.
| | - Yun Xu
- School of Chemistry, Manchester Institute of Biotechnology, University of Manchester, Manchester, UK.
| | - David I Ellis
- School of Chemistry, Manchester Institute of Biotechnology, University of Manchester, Manchester, UK.
| | - Drupad K Trivedi
- School of Chemistry, Manchester Institute of Biotechnology, University of Manchester, Manchester, UK.
| | - Nicholas J W Rattray
- School of Chemistry, Manchester Institute of Biotechnology, University of Manchester, Manchester, UK.
| | - Kristel Bernaerts
- Bio- and Chemical Systems Technology, Reactor Engineering and Safety, Department of Chemical Engineering, KU Leuven (University of Leuven), Leuven Chem&Tech, Celestijnenlaan 200F (bus 2424), 3001, Leuven, Belgium.
| | - Royston Goodacre
- School of Chemistry, Manchester Institute of Biotechnology, University of Manchester, Manchester, UK.
| |
Collapse
|
127
|
Kim M, Yi JS, Lakshmanan M, Lee DY, Kim BG. Transcriptomics-based strain optimization tool for designing secondary metabolite overproducing strains of Streptomyces coelicolor. Biotechnol Bioeng 2015; 113:651-60. [PMID: 26369755 DOI: 10.1002/bit.25830] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2015] [Revised: 08/26/2015] [Accepted: 09/07/2015] [Indexed: 12/23/2022]
Abstract
In silico model-driven analysis using genome-scale model of metabolism (GEM) has been recognized as a promising method for microbial strain improvement. However, most of the current GEM-based strain design algorithms based on flux balance analysis (FBA) heavily rely on the steady-state and optimality assumptions without considering any regulatory information. Thus, their practical usage is quite limited, especially in its application to secondary metabolites overproduction. In this study, we developed a transcriptomics-based strain optimization tool (tSOT) in order to overcome such limitations by integrating transcriptomic data into GEM. Initially, we evaluated existing algorithms for integrating transcriptomic data into GEM using Streptomyces coelicolor dataset, and identified iMAT algorithm as the only and the best algorithm for characterizing the secondary metabolism of S. coelicolor. Subsequently, we developed tSOT platform where iMAT is adopted to predict the reaction states, and successfully demonstrated its applicability to secondary metabolites overproduction by designing actinorhodin (ACT), a polyketide antibiotic, overproducing strain of S. coelicolor. Mutants overexpressing tSOT targets such as ribulose 5-phosphate 3-epimerase and NADP-dependent malic enzyme showed 2 and 1.8-fold increase in ACT production, thereby validating the tSOT prediction. It is expected that tSOT can be used for solving other metabolic engineering problems which could not be addressed by current strain design algorithms, especially for the secondary metabolite overproductions.
Collapse
Affiliation(s)
- Minsuk Kim
- School of Chemical and Biological Engineering, Institute of Molecular Biology and Genetics, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, Republic of Korea.,Bioengineering Institute, Seoul National University, Seoul, Republic of Korea
| | - Jeong Sang Yi
- School of Chemical and Biological Engineering, Institute of Molecular Biology and Genetics, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, Republic of Korea.,Bioengineering Institute, Seoul National University, Seoul, Republic of Korea
| | - Meiyappan Lakshmanan
- Bioprocessing Technology Institute, A*STAR (Agency for Science, Technology and Research), Centros, Singapore
| | - Dong-Yup Lee
- Bioprocessing Technology Institute, A*STAR (Agency for Science, Technology and Research), Centros, Singapore. .,Department of Chemical and Biomolecular Engineering, National University of Singapore, Singapore. .,NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), Life Sciences Institute, National University of Singapore, Singapore.
| | - Byung-Gee Kim
- School of Chemical and Biological Engineering, Institute of Molecular Biology and Genetics, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, Republic of Korea. .,Bioengineering Institute, Seoul National University, Seoul, Republic of Korea. .,Interdisciplinary Program for Biochemical Engineering and Biotechnology, Seoul National University, Seoul, Republic of Korea.
| |
Collapse
|
128
|
Tong Y, Charusanti P, Zhang L, Weber T, Lee SY. CRISPR-Cas9 Based Engineering of Actinomycetal Genomes. ACS Synth Biol 2015; 4:1020-9. [PMID: 25806970 DOI: 10.1021/acssynbio.5b00038] [Citation(s) in RCA: 296] [Impact Index Per Article: 32.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Bacteria of the order Actinomycetales are one of the most important sources of pharmacologically active and industrially relevant secondary metabolites. Unfortunately, many of them are still recalcitrant to genetic manipulation, which is a bottleneck for systematic metabolic engineering. To facilitate the genetic manipulation of actinomycetes, we developed a highly efficient CRISPR-Cas9 system to delete gene(s) or gene cluster(s), implement precise gene replacements, and reversibly control gene expression in actinomycetes. We demonstrate our system by targeting two genes, actIORF1 (SCO5087) and actVB (SCO5092), from the actinorhodin biosynthetic gene cluster in Streptomyces coelicolor A3(2). Our CRISPR-Cas9 system successfully inactivated the targeted genes. When no templates for homology-directed repair (HDR) were present, the site-specific DNA double-strand breaks (DSBs) introduced by Cas9 were repaired through the error-prone nonhomologous end joining (NHEJ) pathway, resulting in a library of deletions with variable sizes around the targeted sequence. If templates for HDR were provided at the same time, precise deletions of the targeted gene were observed with near 100% frequency. Moreover, we developed a system to efficiently and reversibly control expression of target genes, deemed CRISPRi, based on a catalytically dead variant of Cas9 (dCas9). The CRISPR-Cas9 based system described here comprises a powerful and broadly applicable set of tools to manipulate actinomycetal genomes.
Collapse
Affiliation(s)
- Yaojun Tong
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kogle Alle 6, Hørsholm 2970, Denmark
| | - Pep Charusanti
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kogle Alle 6, Hørsholm 2970, Denmark
- Department
of Bioengineering, University of California, San Diego, La Jolla, California 92093, United States
| | - Lixin Zhang
- Chinese Academy of Sciences,
Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Beijing 100190, China
| | - Tilmann Weber
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kogle Alle 6, Hørsholm 2970, Denmark
| | - Sang Yup Lee
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kogle Alle 6, Hørsholm 2970, Denmark
- Metabolic and Biomolecular Engineering
National Research Laboratory, Department of Chemical and Biomolecular
Engineering (BK21 Plus Program), Center for Systems and Synthetic
Biotechnology, Institute for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 305-701, Republic of Korea
| |
Collapse
|
129
|
Ban YH, Park SR, Yoon YJ. The biosynthetic pathway of FK506 and its engineering: from past achievements to future prospects. J Ind Microbiol Biotechnol 2015; 43:389-400. [PMID: 26342319 DOI: 10.1007/s10295-015-1677-7] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2015] [Accepted: 08/19/2015] [Indexed: 11/28/2022]
Abstract
FK506, a 23-membered macrolide produced by several Streptomyces species, is an immunosuppressant widely used to prevent the rejection of transplanted organs. In addition, FK506 and its analogs possess numerous promising therapeutic potentials including antifungal, neuroprotective, and neuroregenerative activities. Herein, we introduce the biological activities and mechanisms of action of FK506 and discuss recent progress made in understanding its biosynthetic pathway, improving production, and in the mutasynthesis of diverse analogs. Perspectives highlighting further strain improvement and structural diversification aimed at generating more analogs with improved pharmaceutical properties will be emphasized.
Collapse
Affiliation(s)
- Yeon Hee Ban
- Department of Chemistry and Nano Science, Ewha Womans University, Seoul, 120-750, Republic of Korea
| | - Sung Ryeol Park
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Yeo Joon Yoon
- Department of Chemistry and Nano Science, Ewha Womans University, Seoul, 120-750, Republic of Korea.
| |
Collapse
|
130
|
Herboxidiene biosynthesis, production, and structural modifications: prospect for hybrids with related polyketide. Appl Microbiol Biotechnol 2015; 99:8351-62. [DOI: 10.1007/s00253-015-6860-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2015] [Revised: 07/13/2015] [Accepted: 07/16/2015] [Indexed: 01/06/2023]
|
131
|
Fedorenko V, Genilloud O, Horbal L, Marcone GL, Marinelli F, Paitan Y, Ron EZ. Antibacterial Discovery and Development: From Gene to Product and Back. BIOMED RESEARCH INTERNATIONAL 2015; 2015:591349. [PMID: 26339625 PMCID: PMC4538407 DOI: 10.1155/2015/591349] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/30/2014] [Revised: 12/30/2014] [Accepted: 01/13/2015] [Indexed: 12/23/2022]
Abstract
Concern over the reports of antibiotic-resistant bacterial infections in hospitals and in the community has been publicized in the media, accompanied by comments on the risk that we may soon run out of antibiotics as a way to control infectious disease. Infections caused by Enterococcus faecium, Staphylococcus aureus, Klebsiella species, Clostridium difficile, Acinetobacter baumannii, Pseudomonas aeruginosa, Escherichia coli, and other Enterobacteriaceae species represent a major public health burden. Despite the pharmaceutical sector's lack of interest in the topic in the last decade, microbial natural products continue to represent one of the most interesting sources for discovering and developing novel antibacterials. Research in microbial natural product screening and development is currently benefiting from progress that has been made in other related fields (microbial ecology, analytical chemistry, genomics, molecular biology, and synthetic biology). In this paper, we review how novel and classical approaches can be integrated in the current processes for microbial product screening, fermentation, and strain improvement.
Collapse
Affiliation(s)
- Victor Fedorenko
- Department of Genetics and Biotechnology, Ivan Franko National University of Lviv, Lviv 79005, Ukraine
| | - Olga Genilloud
- Fundación MEDINA, Health Sciences Technology Park, 18016 Granada, Spain
| | - Liliya Horbal
- Department of Genetics and Biotechnology, Ivan Franko National University of Lviv, Lviv 79005, Ukraine
| | - Giorgia Letizia Marcone
- Department of Biotechnology and Life Sciences, University of Insubria, 21100 Varese, Italy
- The Protein Factory, Interuniversity Centre Politecnico di Milano, ICRM CNR Milano, and University of Insubria, 21100 Varese, Italy
| | - Flavia Marinelli
- Department of Biotechnology and Life Sciences, University of Insubria, 21100 Varese, Italy
- The Protein Factory, Interuniversity Centre Politecnico di Milano, ICRM CNR Milano, and University of Insubria, 21100 Varese, Italy
| | - Yossi Paitan
- Clinical Microbiology Laboratory, Meir Medical Center, 44281 Kfar Saba, Israel
| | - Eliora Z. Ron
- Department of Molecular Microbiology and Biotechnology, Tel Aviv University, 6997801 Tel Aviv, Israel
- Galilee Research Institute (MIGAL), 11016 Kiryat Shmona, Israel
| |
Collapse
|
132
|
Dhakal D, Sohng JK. Commentary: Toward a new focus in antibiotic and drug discovery from the Streptomyces arsenal. Front Microbiol 2015; 6:727. [PMID: 26236304 PMCID: PMC4503920 DOI: 10.3389/fmicb.2015.00727] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2015] [Accepted: 07/02/2015] [Indexed: 12/16/2022] Open
Affiliation(s)
- Dipesh Dhakal
- Institute of Biomolecule Reconstruction (iBR), Department of BT-Convergent Pharmaceutical Engineering, Sun Moon University Asan, South Korea
| | - Jae Kyung Sohng
- Institute of Biomolecule Reconstruction (iBR), Department of BT-Convergent Pharmaceutical Engineering, Sun Moon University Asan, South Korea
| |
Collapse
|
133
|
Ahmad MS, Yasser MM, Sholkamy EN, Ali AM, Mehanni MM. Anticancer activity of biostabilized selenium nanorods synthesized by Streptomyces bikiniensis strain Ess_amA-1. Int J Nanomedicine 2015; 10:3389-401. [PMID: 26005349 PMCID: PMC4428361 DOI: 10.2147/ijn.s82707] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Selenium is an important component of human diet and a number of studies have declared its chemopreventive and therapeutic properties against cancer. However, very limited studies have been conducted about the properties of selenium nanostructured materials in comparison to other well-studied selenospecies. Here, we have shown that the anticancer property of biostabilized selenium nanorods (SeNrs) synthesized by applying a novel strain Ess_amA-1 of Streptomyces bikiniensis. The strain was grown aerobically with selenium dioxide and produced stable SeNrs with average particle size of 17 nm. The optical, structural, morphological, elemental, and functional characterizations of the SeNrs were carried out using techniques such as UV-vis spectrophotometry, transmission electron microscopy, energy dispersive X-ray spectrometry, and Fourier transform infrared spectrophotometry, respectively. The MTT (3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide) assay revealed that the biosynthesized SeNrs induces cell death of Hep-G2 and MCF-7 human cancer cells. The lethal dose (LD50%) of SeNrs on Hep-G2 and MCF-7 cells was recorded at 75.96 μg/mL and 61.86 μg/mL, respectively. It can be concluded that S. bikiniensis strain Ess_amA-1 could be used as renewable bioresources of biosynthesis of anticancer SeNrs. A hypothetical mechanism for anticancer activity of SeNrs is also proposed.
Collapse
Affiliation(s)
- Maged Sayed Ahmad
- Department of Botany, Faculty of Science, University of Beni-Suef, Beni-Suef, Egypt
| | - Manal Mohamed Yasser
- Department of Botany, Faculty of Science, University of Beni-Suef, Beni-Suef, Egypt
| | - Essam Nageh Sholkamy
- Department of Botany, Faculty of Science, University of Beni-Suef, Beni-Suef, Egypt
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Ali Mohamed Ali
- Department of Botany and Microbiology, College of Science, Minia University, El-Minia, Egypt
- Department of Biological Sciences, College of Science, King Faisal University, Saudi Arabia
| | - Magda Mohamed Mehanni
- Department of Botany and Microbiology, College of Science, Minia University, El-Minia, Egypt
| |
Collapse
|
134
|
Involvement of the TetR-Type Regulator PaaR in the Regulation of Pristinamycin I Biosynthesis through an Effect on Precursor Supply in Streptomyces pristinaespiralis. J Bacteriol 2015; 197:2062-71. [PMID: 25868645 DOI: 10.1128/jb.00045-15] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2015] [Accepted: 03/30/2015] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED Pristinamycin I (PI), produced by Streptomyces pristinaespiralis, is a streptogramin type B antibiotic, which contains two proteinogenic and five aproteinogenic amino acid precursors. PI is coproduced with pristinamycin II (PII), a member of streptogramin type A antibiotics. The PI biosynthetic gene cluster has been cloned and characterized. However, thus far little is understood about the regulation of PI biosynthesis. In this study, a TetR family regulator (encoded by SSDG_03033) was identified as playing a positive role in PI biosynthesis. Its homologue, PaaR, from Corynebacterium glutamicum serves as a transcriptional repressor of the paa genes involved in phenylacetic acid (PAA) catabolism. Herein, we also designated the identified regulator as PaaR. Deletion of paaR led to an approximately 70% decrease in PI production but had little effect on PII biosynthesis. Identical to the function of its homologue from C. glutamicum, PaaR is also involved in the suppression of paa expression. Given that phenylacetyl coenzyme A (PA-CoA) is the common intermediate of the PAA catabolic pathway and the biosynthetic pathway of L-phenylglycine (L-Phg), the last amino acid precursor for PI biosynthesis, we proposed that derepression of the transcription of paa genes in a ΔpaaR mutant possibly diverts more PA-CoA to the PAA catabolic pathway, thereby with less PA-CoA metabolic flux toward L-Phg formation, thus resulting in lower PI titers. This hypothesis was verified by the observations that PI production of a ΔpaaR mutant was restored by L-Phg supplementation as well as by deletion of the paaABCDE operon in the ΔpaaR mutant. Altogether, this study provides new insights into the regulation of PI biosynthesis by S. pristinaespiralis. IMPORTANCE A better understanding of the regulation mechanisms for antibiotic biosynthesis will provide valuable clues for Streptomyces strain improvement. Herein, a TetR family regulator PaaR, which serves as the repressor of the transcription of paa genes involved in phenylacetic acid (PAA) catabolism, was identified as playing a positive role in the regulation of pristinamycin I (PI) by affecting the supply of one of seven amino acid precursors, L-phenylglycine, in Streptomyces pristinaespiralis. To our knowledge, this is the first report describing the interplay between PAA catabolism and antibiotic biosynthesis in Streptomyces strains. Considering that the PAA catabolic pathway and its regulation by PaaR are widespread in antibiotic-producing actinomycetes, it could be suggested that PaaR-dependent regulation of antibiotic biosynthesis might commonly exist.
Collapse
|
135
|
Plants and endophytes: equal partners in secondary metabolite production? Biotechnol Lett 2015; 37:1325-34. [PMID: 25792513 DOI: 10.1007/s10529-015-1814-4] [Citation(s) in RCA: 141] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2015] [Accepted: 03/12/2015] [Indexed: 01/24/2023]
Abstract
Well known plant production systems should be re-evaluated due to findings that the interesting metabolite might actually be produced by microbes intimately associated with the plant, so-called endophytes. Endophytes can be bacteria or fungi and they are characterized usually by the feature that they do not cause any harm to the host. Indeed, in some cases, such as mycorrhizal fungi or other growth promoting endophytes, they can be beneficial for the plant. Here some examples are reviewed where the host plant and/or endophyte metabolism can be induced by the other partner. Also, partial or complete biosynthesis pathways for plant secondary metabolites can be attributed to such endophytes. In other cases the host plant is able to metabolize substances from fungal origin. The question of the natural role of such metabolic changes for the endophyte will be briefly touched. Finally, the consequences for the use of plant cultures for secondary metabolite production is discussed.
Collapse
|
136
|
Guo F, Xiang S, Li L, Wang B, Rajasärkkä J, Gröndahl-Yli-Hannuksela K, Ai G, Metsä-Ketelä M, Yang K. Targeted activation of silent natural product biosynthesis pathways by reporter-guided mutant selection. Metab Eng 2014; 28:134-142. [PMID: 25554073 DOI: 10.1016/j.ymben.2014.12.006] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2014] [Revised: 12/12/2014] [Accepted: 12/18/2014] [Indexed: 11/27/2022]
Abstract
The continuously increasing genome sequencing data has revealed numerous cryptic pathways, which might encode novel secondary metabolites with interesting biological activities. However, utilization of this hidden potential has been hindered by the observation that many of these gene clusters remain silent (or poorly expressed) under laboratory conditions. Here we present reporter-guided mutant selection (RGMS) as an effective and widely applicable method for targeted activation of silent gene clusters in the native producers. The strategy takes advantage of genome-scale random mutagenesis for generation of genetic diversity and a reporter-guided selection system for the identification of the desired target-activated mutants. It was first validated in the re-activation of jadomycin biosynthesis in Streptomyces venezuelae ISP5230, where high efficiency of activation was achieved. The same strategy was then applied to a hitherto unactivable pga gene cluster in Streptomyces sp. PGA64 leading to the identification of two new anthraquinone aminoglycosides, gaudimycin D and E.
Collapse
Affiliation(s)
- Fang Guo
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, No. 1 West Beichen Road, Chaoyang District, Beijing 100101, People׳s Republic of China; University of Chinese Academy of Sciences, Beijing 100049, People׳s Republic of China
| | - Sihai Xiang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, No. 1 West Beichen Road, Chaoyang District, Beijing 100101, People׳s Republic of China
| | - Liyuan Li
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, No. 1 West Beichen Road, Chaoyang District, Beijing 100101, People׳s Republic of China
| | - Bin Wang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, No. 1 West Beichen Road, Chaoyang District, Beijing 100101, People׳s Republic of China; University of Chinese Academy of Sciences, Beijing 100049, People׳s Republic of China
| | - Johanna Rajasärkkä
- Department of Biochemistry, University of Turku, Vatselankatu 2, FIN-20014 Turku, Finland
| | | | - Guomin Ai
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, No. 1 West Beichen Road, Chaoyang District, Beijing 100101, People׳s Republic of China
| | - Mikko Metsä-Ketelä
- Department of Biochemistry, University of Turku, Vatselankatu 2, FIN-20014 Turku, Finland
| | - Keqian Yang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, No. 1 West Beichen Road, Chaoyang District, Beijing 100101, People׳s Republic of China.
| |
Collapse
|
137
|
Weber T, Charusanti P, Musiol-Kroll EM, Jiang X, Tong Y, Kim HU, Lee SY. Metabolic engineering of antibiotic factories: new tools for antibiotic production in actinomycetes. Trends Biotechnol 2014; 33:15-26. [PMID: 25497361 DOI: 10.1016/j.tibtech.2014.10.009] [Citation(s) in RCA: 120] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2014] [Revised: 10/21/2014] [Accepted: 10/31/2014] [Indexed: 12/15/2022]
Abstract
Actinomycetes are excellent sources for novel bioactive compounds, which serve as potential drug candidates for antibiotics development. While industrial efforts to find and develop novel antimicrobials have been severely reduced during the past two decades, the increasing threat of multidrug-resistant pathogens and the development of new technologies to find and produce such compounds have again attracted interest in this field. Based on improvements in whole-genome sequencing, novel methods have been developed to identify the secondary metabolite biosynthetic gene clusters by genome mining, to clone them, and to express them in heterologous hosts in much higher throughput than before. These technologies now enable metabolic engineering approaches to optimize production yields and to directly manipulate the pathways to generate modified products.
Collapse
Affiliation(s)
- Tilmann Weber
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kogle Alle 6, Hørsholm, Denmark
| | - Pep Charusanti
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kogle Alle 6, Hørsholm, Denmark; Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
| | - Ewa Maria Musiol-Kroll
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kogle Alle 6, Hørsholm, Denmark
| | - Xinglin Jiang
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kogle Alle 6, Hørsholm, Denmark
| | - Yaojun Tong
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kogle Alle 6, Hørsholm, Denmark
| | - Hyun Uk Kim
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kogle Alle 6, Hørsholm, Denmark; Metabolic and Biomolecular Engineering National Research Laboratory, Department of Chemical and Biomolecular Engineering (BK21 Plus Program), Center for Systems and Synthetic Biotechnology, Institute for the BioCentury, BioInformatics Research Center, and BioProcess Engineering Research Center, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 305-701, Republic of Korea
| | - Sang Yup Lee
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kogle Alle 6, Hørsholm, Denmark; Metabolic and Biomolecular Engineering National Research Laboratory, Department of Chemical and Biomolecular Engineering (BK21 Plus Program), Center for Systems and Synthetic Biotechnology, Institute for the BioCentury, BioInformatics Research Center, and BioProcess Engineering Research Center, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 305-701, Republic of Korea.
| |
Collapse
|
138
|
Enhanced production of validamycin A in Streptomyces hygroscopicus 5008 by engineering validamycin biosynthetic gene cluster. Appl Microbiol Biotechnol 2014; 98:7911-22. [DOI: 10.1007/s00253-014-5943-9] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2014] [Revised: 06/24/2014] [Accepted: 07/07/2014] [Indexed: 10/25/2022]
|
139
|
Yu L, Trujillo ME, Miyanaga S, Saiki I, Igarashi Y. Campechic acids A and B: anti-invasive polyether polyketides from a soil-derived Streptomyces. JOURNAL OF NATURAL PRODUCTS 2014; 77:976-982. [PMID: 24592993 DOI: 10.1021/np401071x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Campechic acids A (1) and B (2), two new polyketides, were isolated from the culture extract of Streptomyces sp., and their structures were determined by NMR and MS spectroscopic analysis. Campechic acids are polyether-polyketides functionalized by two tetrahydrofuran rings, an enolized 1,3-diketone, and multiple methyl substitutions. Absolute configuration of nine stereogenic centers in 1, except for four chiral centers in the cyclic ether moieties, was determined by the 1H NMR anisotropy method in combination with chemical degradation. Campechic acids exhibited potent inhibitory effects on tumor cell invasion with IC50 values in the nanomolar to submicromolar range.
Collapse
Affiliation(s)
- Linkai Yu
- Biotechnology Research Center and Department of Biotechnology, Toyama Prefectural University , 5180 Kurokawa, Imizu, Toyama 939-0398, Japan
| | | | | | | | | |
Collapse
|
140
|
Kim M, Sang Yi J, Kim J, Kim JN, Kim MW, Kim BG. Reconstruction of a high-quality metabolic model enables the identification of gene overexpression targets for enhanced antibiotic production inStreptomyces coelicolorA3(2). Biotechnol J 2014; 9:1185-94. [DOI: 10.1002/biot.201300539] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2013] [Revised: 02/13/2014] [Accepted: 03/11/2014] [Indexed: 12/22/2022]
|