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Al-Rooqi MM, Ullah Mughal E, Raja QA, Obaid RJ, Sadiq A, Naeem N, Qurban J, Asghar BH, Moussa Z, Ahmed SA. Recent advancements on the synthesis and biological significance of pipecolic acid and its derivatives. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2022.133719] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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2
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Vallejo-Zamora JA, Vega-Cantu YI, Rodriguez C, Cordell GA, Rodriguez-Garcia A. Drug-Eluting, Bioresorbable Cardiovascular Stents─Challenges and Perspectives. ACS APPLIED BIO MATERIALS 2022; 5:4701-4717. [PMID: 36150217 DOI: 10.1021/acsabm.2c00551] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Globally, the leading causes of natural death are attributed to coronary heart disease and type 1 and type 2 diabetes. High blood pressure levels, high cholesterol levels, smoking, and poor eating habits lead to the agglomeration of plaque in the arteries, reducing the blood flow. The implantation of devices used to unclog vessels, known as stents, sometimes results in a lack of irrigation due to the excessive proliferation of endothelial tissue within the blood vessels and is known as restenosis. The use of drug-eluting stents (DESs) to deliver antiproliferative drugs has led to the development of different encapsulation techniques. However, due to the potency of the drugs used in the initial stent designs, a chronic inflammatory reaction of the arterial wall known as thrombosis can cause a myocardial infarction (MI). One of the most promising drugs to reduce this risk is everolimus, which can be encapsulated in lipid systems for controlled release directly into the artery. This review aims to discuss the current status of stent design, fabrication, and functionalization. Variables such as the mechanical properties, metals and their alloys, drug encapsulation and controlled elution, and stent degradation are also addressed. Additionally, this review covers the use of polymeric surface coatings on stents and the recent advances in layer-by-layer coating and drug delivery. The advances in nanoencapsulation techniques such as liposomes and micro- and nanoemulsions and their functionalization in bioresorbable, drug-eluting stents are also highlighted.
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Affiliation(s)
- Julio A Vallejo-Zamora
- Tecnologico de Monterrey, Escuela de Ingeniería y Ciencias, Ave. Eugenio Garza Sada 2501, Monterrey, Nuevo León64849, Mexico
| | - Yadira I Vega-Cantu
- Tecnologico de Monterrey, Escuela de Ingeniería y Ciencias, Ave. Eugenio Garza Sada 2501, Monterrey, Nuevo León64849, Mexico
| | - Ciro Rodriguez
- Tecnologico de Monterrey, Escuela de Ingeniería y Ciencias, Ave. Eugenio Garza Sada 2501, Monterrey, Nuevo León64849, Mexico
- Laboratorio Nacional de Manufactura Aditiva y Digital (MADIT), Apodaca, Nuevo León66629, Mexico
| | - Geoffrey A Cordell
- Natural Products, Inc., Evanston, Illinois60201, United States
- College of Pharmacy, University of Florida, Gainesville, Florida32610, United States
| | - Aida Rodriguez-Garcia
- Tecnologico de Monterrey, Escuela de Ingeniería y Ciencias, Ave. Eugenio Garza Sada 2501, Monterrey, Nuevo León64849, Mexico
- Universidad Autónoma de Nuevo León, Facultad de Ciencias Biológicas, Instituto de Biotecnología, Ciudad Universitaria, Ave. Pedro de Alba S/N, San Nicolás de los Garza, Nuevo León66455, Mexico
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Enhanced Triacylglycerol Metabolism Contributes to Efficient Oil Utilization and High-Level Production of Salinomycin in Streptomyces albus ZD11. Appl Environ Microbiol 2020; 86:AEM.00763-20. [PMID: 32532869 DOI: 10.1128/aem.00763-20] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Accepted: 05/31/2020] [Indexed: 11/20/2022] Open
Abstract
Streptomyces is well known for biosynthesis of secondary metabolites with diverse bioactivities. Although oils have been employed as carbon sources to produce polyketide antibiotics for several industrial Streptomyces strains, the intrinsic correlation between oil utilization and high production of antibiotics still remains unclear. In this study, we investigated the correlation between oil metabolism and salinomycin biosynthesis in Streptomyces albus ZD11, which employs soybean oil as the main carbon source. Comparative genomic analysis revealed the enrichment of genes related to triacylglycerol (TAG) metabolism in S. albus ZD11. Transcriptomic profiling further confirmed the enhancement of TAG metabolism and acyl coenzyme A biosynthesis in S. albus ZD11. Multiple secreted lipases, which catalyze TAG hydrolysis, were seen to be working in a synergistic and complementary manner in aiding the efficient and stable hydrolyzation of TAGs. Together, our results suggest that enhanced TAG hydrolysis and fatty acid degradation contribute to the high efficiency of oil utilization in S. albus ZD11 in order to provide abundant carbon precursors for cell growth and salinomycin biosynthesis.IMPORTANCE In order to obtain high-level production of antibiotics, oils have been used as the main carbon source for some Streptomyces strains. Based on multiomics analysis, this study provides insight into the relationship between triacylglycerol (TAG) metabolism and antibiotic biosynthesis in S. albus ZD11, an oil-preferring industrial Streptomyces strain. Our investigation into TAG hydrolysis yielded further evidence that this strain utilizes complicated strategies enabling an efficient TAG metabolism. In addition, a novel secreted lipase was identified that exhibited highly hydrolytic activity for medium- and long-chain TAGs. Our findings represent a good start toward clarifying the complicated relationship between TAG catabolism and high-level antibiotic production in the industrial strains.
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Zhang B, Zhang YH, Chen Y, Chen K, Jiang SX, Huang K, Liu ZQ, Zheng YG. Enhanced AmB Production in Streptomyces nodosus by Fermentation Regulation and Rational Combined Feeding Strategy. Front Bioeng Biotechnol 2020; 8:597. [PMID: 32760700 PMCID: PMC7373727 DOI: 10.3389/fbioe.2020.00597] [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: 03/02/2020] [Accepted: 05/15/2020] [Indexed: 12/12/2022] Open
Abstract
Amphotericin B is a clinically important polyene macrolide antibiotic with a broad-spectrum antifungal activity. In this work, the addition of key precursors and differential metabolites, combined with staged fermentation process control strategies, was carried out to improve AmB production. Rationally designed addition strategies were proposed as follows: 4 mg/L isopropanol, 1 mM alanine, 1 g/L pyruvate, and 0.025 g/L nicotinamide were supplemented at 24 h. The AmB titer was ultimately enhanced to 6.63 g/L, with 28.5% increase in shake flasks fermentation. To further promote the biosynthesis of AmB, different glucose feeding strategies were investigated and the highest AmB titer (15.78 g/L) was obtained by constant speed fed-batch fermentation in a 5-L fermentor. Subsequently, compared with the batch fermentation (9.89 g/L), a novel combined feeding strategy was ultimately developed to improve the production of AmB by 85.9%, reaching 18.39 g/L that is the highest titer of AmB ever reported so far, in which the optimized components were fed at 24 h and the staged fermentation regulation strategies were used simultaneously. Moreover, the ratio of co-metabolite AmA decreased by 32.3%, from 3.1 to 2.1%. Through the detection of extracellular organic acids, the changes in α-ketoglutaric acid, pyruvate, and citric acid concentrations were identified as the most flexible metabolite nodes to further clarify the potential mechanism under different fermentation regulation strategies. These results demonstrated that the strategies above may provide new guidance for the industrial-scale production of AmB.
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Affiliation(s)
- Bo Zhang
- The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, China.,Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China
| | - Yu-Han Zhang
- The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, China.,Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China
| | - Yu Chen
- The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, China.,Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China
| | - Kai Chen
- The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, China.,Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China
| | - Sheng-Xian Jiang
- The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, China.,Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China
| | - Kai Huang
- The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, China.,Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China
| | - Zhi-Qiang Liu
- The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, China.,Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China
| | - Yu-Guo Zheng
- The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, China.,Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China
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Zhang Y, Chen H, Wang P, Wen J. Identification of the regulon FkbN for ascomycin biosynthesis and its interspecies conservation analysis as LAL family regulator. Biochem Eng J 2019. [DOI: 10.1016/j.bej.2019.107349] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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6
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Si Y, Chu H, Zhu W, Xiao T, Shen X, Fu Y, Xu R, Jiang H. Concentration-dependent effects of rapamycin on proliferation, migration and apoptosis of endothelial cells in human venous malformation. Exp Ther Med 2018; 16:4595-4601. [PMID: 30542410 PMCID: PMC6257489 DOI: 10.3892/etm.2018.6782] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Accepted: 07/27/2018] [Indexed: 01/21/2023] Open
Abstract
Rapamycin has been reported to be immunosuppressive and anti-proliferative towards vascular endothelial and smooth muscle cells. The purpose of the present study was to investigate the effects of rapamycin on the biological behaviors of endothelial cells that have been separated from the deformed vein in human venous malformation (VM). Cellular morphology was observed using inverted microscopy. An MTT assay was performed to measure the cell viability at different concentrations of rapamycin and different time points. Cell apoptosis and migration were detected using a terminal deoxynucleotidyl-transferase-mediated dUTP nick end labeling assay and a wound-healing assay, respectively. At 48 and 72 h, rapamycin inhibited proliferation of human VM endothelial cells, with the effects becoming more pronounced with increasing concentration. Only rapamycin at a concentration of 1,000 ng/ml had a significant effect at 24 h in repressing proliferation. At 48 h, compared with the blank group, the majority of cells maintained a clear nuclear boundary and a regular shape following treatment with 1 ng/ml rapamycin; 10 and 100 ng/ml rapamycin caused desquamation and rounded shape; and 1,000 ng/ml rapamycin caused even more marked desquamation, rounded shape and necrosis. Rapamycin at concentrations of 1, 10, 100 and 1,000 ng/ml reduced cell viability, increased the number of apoptotic cells and suppressed the migration capacity of human VM endothelial cells, and the effects became more pronounced with increasing concentration, when compared with the blank group. These findings provide evidence that rapamycin induces apoptosis and inhibits proliferation and migration of human VM endothelial cells in a concentration-dependent manner.
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Affiliation(s)
- Yameng Si
- Jiangsu Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, Jiangsu 210029, P.R. China.,Department of Oral and Maxillofacial Surgery, Xuzhou Central Hospital, Xuzhou, Jiangsu 221009, P.R. China
| | - Hanchen Chu
- College of Stomatology, Xuzhou Medical University, Xuzhou, Jiangsu 221004, P.R. China
| | - Weiwen Zhu
- Jiangsu Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, Jiangsu 210029, P.R. China
| | - Tao Xiao
- Jiangsu Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, Jiangsu 210029, P.R. China
| | - Xiang Shen
- Jiangsu Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, Jiangsu 210029, P.R. China
| | - Yu Fu
- Jiangsu Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, Jiangsu 210029, P.R. China
| | - Rongyao Xu
- Jiangsu Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, Jiangsu 210029, P.R. China
| | - Hongbing Jiang
- Jiangsu Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, Jiangsu 210029, P.R. China.,Department of Oral and Maxillofacial Surgery, Affiliated Stomatological Hospital of Nanjing Medical University, Nanjing, Jiangsu 210029, P.R. China
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Lyu X, Ng KR, Mark R, Lee JL, Chen WN. Comparative metabolic profiling of engineered Saccharomyces cerevisiae with enhanced flavonoids production. J Funct Foods 2018. [DOI: 10.1016/j.jff.2018.03.012] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
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8
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Combining metabolomics and network analysis to improve tacrolimus production in Streptomyces tsukubaensis using different exogenous feedings. ACTA ACUST UNITED AC 2017; 44:1527-1540. [DOI: 10.1007/s10295-017-1974-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Accepted: 07/31/2017] [Indexed: 02/07/2023]
Abstract
Abstract
Tacrolimus is widely used as an immunosuppressant in the treatment of various autoimmune diseases. However, the low fermentation yield of tacrolimus has thus far restricted its industrial applications. To solve this problem, the time-series response mechanisms of the intracellular metabolism that were highly correlated with tacrolimus biosynthesis were investigated using different exogenous feeding strategies in S. tsukubaensis. The metabolomic datasets, which contained 93 metabolites, were subjected to weighted correlation network analysis (WGCNA), and eight distinct metabolic modules and seven hub metabolites were identified to be specifically associated with tacrolimus biosynthesis. The analysis of metabolites within each metabolic module suggested that the pentose phosphate pathway (PPP), shikimate and aspartate pathway might be the main limiting factors in the rapid synthesis phase of tacrolimus accumulation. Subsequently, all possible key-limiting steps in the above metabolic pathways were further screened using a genome-scale metabolic network model (GSMM) of S. tsukubaensis. Based on the prediction results, two newly identified targets (aroC and dapA) were overexpressed experimentally, and both of the engineered strains showed higher tacrolimus production. Moreover, the best strain, HT-aroC/dapA, that was engineered to simultaneously enhanced chorismate and lysine biosynthesis was able to produce 128.19 mg/L tacrolimus, 1.64-fold higher than control (78.26 mg/L). These findings represent a valuable addition to our understanding of tacrolimus accumulation in S. tsukubaensis, and pave the way to further production improvements.
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Insights into the metabolic mechanism of rapamycin overproduction in the shikimate-resistant Streptomyces hygroscopicus strain UV-II using comparative metabolomics. World J Microbiol Biotechnol 2017; 33:101. [DOI: 10.1007/s11274-017-2266-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Accepted: 04/12/2017] [Indexed: 01/27/2023]
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10
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Wang J, Liu H, Huang D, Jin L, Wang C, Wen J. Comparative proteomic and metabolomic analysis of Streptomyces tsukubaensis reveals the metabolic mechanism of FK506 overproduction by feeding soybean oil. Appl Microbiol Biotechnol 2017; 101:2447-2465. [DOI: 10.1007/s00253-017-8136-5] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2016] [Revised: 01/11/2017] [Accepted: 01/16/2017] [Indexed: 11/29/2022]
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11
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Dang L, Liu J, Wang C, Liu H, Wen J. Enhancement of rapamycin production by metabolic engineering in Streptomyces hygroscopicus based on genome-scale metabolic model. ACTA ACUST UNITED AC 2017; 44:259-270. [DOI: 10.1007/s10295-016-1880-1] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2016] [Accepted: 11/26/2016] [Indexed: 12/18/2022]
Abstract
Abstract
Rapamycin, as a macrocyclic polyketide with immunosuppressive, antifungal, and anti-tumor activity produced by Streptomyces hygroscopicus, is receiving considerable attention for its significant contribution in medical field. However, the production capacity of the wild strain is very low. Hereby, a computational guided engineering approach was proposed to improve the capability of rapamycin production. First, a genome-scale metabolic model of Streptomyces hygroscopicus ATCC 29253 was constructed based on its annotated genome and biochemical information. The model consists of 1003 reactions, 711 metabolites after manual refinement. Subsequently, several potential genetic targets that likely guaranteed an improved yield of rapamycin were identified by flux balance analysis and minimization of metabolic adjustment algorithm. Furthermore, according to the results of model prediction, target gene pfk (encoding 6-phosphofructokinase) was knocked out, and target genes dahP (encoding 3-deoxy-d-arabino-heptulosonate-7-phosphate synthase) and rapK (encoding chorismatase) were overexpressed in the parent strain ATCC 29253. The yield of rapamycin increased by 30.8% by knocking out gene pfk and increased by 36.2 and 44.8% by overexpression of rapK and dahP, respectively, compared with parent strain. Finally, the combined effect of the genetic modifications was evaluated. The titer of rapamycin reached 250.8 mg/l by knockout of pfk and co-expression of genes dahP and rapK, corresponding to a 142.3% increase relative to that of the parent strain. The relationship between model prediction and experimental results demonstrates the validity and rationality of this approach for target identification and rapamycin production improvement.
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Affiliation(s)
- Lanqing Dang
- grid.419897.a 0000 0004 0369 313X Key Laboratory of System Bioengineering (Tianjin University), Ministry of Education 300072 Tianjin People’s Republic of China
- grid.33763.32 0000000417612484 School of Chemical Engineering and Technology Tianjin University 300072 Tianjin People’s Republic of China
- grid.33763.32 0000000417612484 SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin) 300072 Tianjin People’s Republic of China
| | - Jiao Liu
- grid.419897.a 0000 0004 0369 313X Key Laboratory of System Bioengineering (Tianjin University), Ministry of Education 300072 Tianjin People’s Republic of China
- grid.33763.32 0000000417612484 School of Chemical Engineering and Technology Tianjin University 300072 Tianjin People’s Republic of China
- grid.33763.32 0000000417612484 SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin) 300072 Tianjin People’s Republic of China
| | - Cheng Wang
- grid.419897.a 0000 0004 0369 313X Key Laboratory of System Bioengineering (Tianjin University), Ministry of Education 300072 Tianjin People’s Republic of China
- grid.33763.32 0000000417612484 School of Chemical Engineering and Technology Tianjin University 300072 Tianjin People’s Republic of China
- grid.33763.32 0000000417612484 SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin) 300072 Tianjin People’s Republic of China
| | - Huanhuan Liu
- grid.419897.a 0000 0004 0369 313X Key Laboratory of System Bioengineering (Tianjin University), Ministry of Education 300072 Tianjin People’s Republic of China
- grid.33763.32 0000000417612484 School of Chemical Engineering and Technology Tianjin University 300072 Tianjin People’s Republic of China
- grid.33763.32 0000000417612484 SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin) 300072 Tianjin People’s Republic of China
| | - Jianping Wen
- grid.419897.a 0000 0004 0369 313X Key Laboratory of System Bioengineering (Tianjin University), Ministry of Education 300072 Tianjin People’s Republic of China
- grid.33763.32 0000000417612484 School of Chemical Engineering and Technology Tianjin University 300072 Tianjin People’s Republic of China
- grid.33763.32 0000000417612484 SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin) 300072 Tianjin People’s Republic of China
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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.
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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.
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Bekiesch P, Forchhammer K, Apel AK. Characterization of DNA Binding Sites of RokB, a ROK-Family Regulator from Streptomyces coelicolor Reveals the RokB Regulon. PLoS One 2016; 11:e0153249. [PMID: 27145180 PMCID: PMC4856308 DOI: 10.1371/journal.pone.0153249] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2016] [Accepted: 03/27/2016] [Indexed: 12/27/2022] Open
Abstract
ROK-family proteins have been described to act either as sugar kinases or as transcriptional regulators. Few ROK-family regulators have been characterized so far and most of them are involved in carbon catabolite repression. RokB (Sco6115) has originally been identified in a DNA-affinity capturing approach as a possible regulator of the heterologously expressed novobiocin biosynthetic gene cluster in Streptomyces coelicolor M512. Interestingly, both, the rokB deletion mutants as well as its overexpressing mutants showed significantly reduced novobiocin production in the host strain S.coelicolor M512. We identified the DNA-binding site for RokB in the promoter region of the novobiocin biosynthetic genes novH-novW. It overlaps with the novH start codon which may explain the reduction of novobiocin production caused by overexpression of rokB. Bioinformatic screening coupled with surface plasmon resonance based interaction studies resulted in the discovery of five RokB binding sites within the genome of S. coelicolor. Using the genomic binding sites, a consensus motif for RokB was calculated, which differs slightly from previously determined binding motifs for ROK-family regulators. The annotations of the possible members of the so defined RokB regulon gave hints that RokB might be involved in amino acid metabolism and transport. This hypothesis was supported by feeding experiments with casamino acids and L-tyrosine, which could also explain the reduced novobiocin production in the deletion mutants.
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Affiliation(s)
- Paulina Bekiesch
- Pharmaceutical Biology, Pharmaceutical Institute, Eberhard-Karls-Universität Tübingen, Auf der Morgenstelle 8, 72076, Tübingen, Germany
- German Centre for Infection Research (DZIF), Partner site Tübingen, 72076, Tübingen, Germany
| | - Karl Forchhammer
- Microbiology/Department of Organismic Interactions, Interfaculty Institute of Microbiology and Infection, Eberhard-Karls-Universität Tübingen, Auf der Morgenstelle 28, 72076, Tübingen, Germany
| | - Alexander Kristian Apel
- Pharmaceutical Biology, Pharmaceutical Institute, Eberhard-Karls-Universität Tübingen, Auf der Morgenstelle 8, 72076, Tübingen, Germany
- German Centre for Infection Research (DZIF), Partner site Tübingen, 72076, Tübingen, Germany
- * E-mail:
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Liu H, Huang D, Wen J. Integrated intracellular metabolic profiling and pathway analysis approaches reveal complex metabolic regulation by Clostridium acetobutylicum. Microb Cell Fact 2016; 15:36. [PMID: 26879529 PMCID: PMC4753663 DOI: 10.1186/s12934-016-0436-4] [Citation(s) in RCA: 15] [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: 10/17/2015] [Accepted: 02/01/2016] [Indexed: 01/27/2023] Open
Abstract
BACKGROUND Clostridium acetobutylicum is one of the most important butanol producing strains. However, environmental stress in the fermentation process usually leads to a lower yield, seriously hampering its industrialization. In order to systematically investigate the key intracellular metabolites that influence the strain growth and butanol production, and find out the critical regulation nodes, an integrated analysis approach has been carried out in this study. RESULTS Based on the gas chromatography-mass spectrometry technology, the partial least square discriminant analysis and the pathway analysis, 40 metabolic pathways linked with 43 key metabolic nodes were identified. In-depth analysis showed that lots of amino acids metabolism promoted cell growth but exerted slight influence on butanol production, while sugar metabolism was favorable for cell growth but unfavorable for butanol synthesis. Besides, both lysine and succinic acid metabolism generated a complex effect on the whole metabolic network. Dicarboxylate metabolism exerted an indispensable role on cell growth and butanol production. Subsequently, rational feeding strategies were proposed to verify these conclusions and facilitate the butanol biosynthesis. Feeding amino acids, especially glycine and serine, could obviously improve cell growth while yeast extract, citric acid and ethylene glycol could significantly enhance both growth and butanol production. CONCLUSIONS The feeding experiment confirmed that metabolic profiling combined with pathway analysis provided an accurate, reasonable and practical approach to explore the cellular metabolic activity and supplied a basis for improving butanol production. These strategies can also be extended for the production of other important bio-chemical compounds.
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Affiliation(s)
- Huanhuan Liu
- Key Laboratory of System Bioengineering (Tianjin University), Ministry of Education, Tianjin, 300072, People's Republic of China.
- SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, People's Republic of China.
| | - Di Huang
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, TEDA, Tianjin, 300457, People's Republic of China.
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Tianjin, 300071, People's Republic of China.
- Tianjin Key Laboratory of Microbial Functional Genomics, Tianjin, 300457, People's Republic of China.
| | - Jianping Wen
- Key Laboratory of System Bioengineering (Tianjin University), Ministry of Education, Tianjin, 300072, People's Republic of China.
- SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, People's Republic of China.
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Xia ML, Wang L, Yang ZX, Chen HZ. Periodic-peristole agitation for process enhancement of butanol fermentation. BIOTECHNOLOGY FOR BIOFUELS 2015; 8:225. [PMID: 26702300 PMCID: PMC4689062 DOI: 10.1186/s13068-015-0409-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/02/2015] [Accepted: 12/04/2015] [Indexed: 06/05/2023]
Abstract
BACKGROUND Mass transfer plays an important role in determining the efficiency of the biofuel conversion. However, adverse effect of shear stress from traditional agitation inhibits the cell growth and production of biofuels. How to enhance the mass transfer with less adverse effect is considered as one of the important bioengineering issues. RESULTS In this study, a novel agitation type, named periodic-peristole was applied to butanol fermentation with Clostridium acetobutylicum ATCC 824. Meanwhile, the enhancement mechanism was studied. Initially, the fermentation performance of periodic-peristole agitation was compared with the traditional Rushton impeller and stationary cultivation. Result showed that the biomass, butanol and total solvent in periodic-peristole group (PPG) was enhanced to 1.92-, 2.06-, and 2.4-fold of those in the traditional Rushton impeller group (TIG), as well as 1.64-, 1.19- and 1.41-fold of those in the stationary group (SG). Subsequently, to get in-depth insight into enhancement mechanism, hydromechanics analysis and metabolic flux analysis (MFA) were carried out. The periodic-peristole agitation exhibits significant difference on velocity distribution, shear force, and mixing efficiency from the traditional Rushton impeller agitation. And the shear force in PPG is only 74 % of that in TIG. According to MFA result, fructose 6-phosphate, pyruvate, acetyl-CoA, oxaloacetate and α-ketoglutarate were determined the key nodes of cells in response to hydrodynamic mechanical stress. Based on such key information, rational enhancement strategies were proposed and butanol production was further improved. CONCLUSION The agitation associated with three issues which resulted in significant changes in cell metabolic behaviors: first, a rebalanced redox status; second, the energy (ATP) acquirement and consumption; third, the tolerance mechanism of the cell for survival of solvent. Periodic-peristole agitation provides an answer to address a long-standing problem of biofuel engineering. Key information derived from current study deepens the understanding of agitation, which can guide the designment of new bioreactors and development of enhancement strategies for biofuel refinery.
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Affiliation(s)
- Meng-lei Xia
- />State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, No. 1 Beiertiao, Zhongguancun, Haidian District, Beijing, 100190 China
- />University of Chinese Academy of Sciences, No. 80 Zhongguancun East Road, Haidian District, Beijing, 100039 China
| | - Lan Wang
- />State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, No. 1 Beiertiao, Zhongguancun, Haidian District, Beijing, 100190 China
| | - Zhi-xia Yang
- />College of Mathematics and System Science, Xinjiang University, No. 14 Shengli Road, Urumchi, 830046 China
| | - Hong-zhang Chen
- />State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, No. 1 Beiertiao, Zhongguancun, Haidian District, Beijing, 100190 China
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Comparative metabolic profiling reveals the key role of amino acids metabolism in the rapamycin overproduction by Streptomyces hygroscopicus. ACTA ACUST UNITED AC 2015; 42:949-63. [DOI: 10.1007/s10295-015-1611-z] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2015] [Accepted: 03/23/2015] [Indexed: 01/06/2023]
Abstract
Abstract
Rapamycin is an important natural macrolide antibiotic with antifungal, immunosuppressive and anticancer activity produced by Streptomyces hygroscopicus. In this study, a mutant strain obtained by ultraviolet mutagenesis displayed higher rapamycin production capacity compared to the wild-type S. hygroscopicus ATCC 29253. To gain insights into the mechanism of rapamycin overproduction, comparative metabolic profiling between the wild-type and mutant strain was performed. A total of 86 metabolites were identified by gas chromatography–mass spectrometry. Pattern recognition methods, including principal component analysis, partial least squares and partial least squares discriminant analysis, were employed to determine the key biomarkers. The results showed that 22 potential biomarkers were closely associated with the increase of rapamycin production and the tremendous metabolic difference was observed between the two strains. Furthermore, metabolic pathway analysis revealed that amino acids metabolism played an important role in the synthesis of rapamycin, especially lysine, valine, tryptophan, isoleucine, glutamate, arginine and ornithine. The inadequate supply of amino acids, or namely “nitrogen starvation” occurred in the mutant strain. Subsequently, the exogenous addition of amino acids into the fermentation medium of the mutant strain confirmed the above conclusion, and rapamycin production of the mutant strain increased to 426.7 mg/L after adding lysine, approximately 5.8-fold of that in the wild-type strain. Finally, the results of real-time PCR and enzyme activity assays demonstrated that dihydrodipicolinate synthase involved with lysine metabolism played vital role in the biosynthesis of rapamycin. These findings will provide a theoretical basis for further improving production of rapamycin.
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Qi H, Zhao S, Fu H, Wen J, Jia X. Coupled cell morphology investigation and metabolomics analysis improves rapamycin production in Streptomyces hygroscopicus. Biochem Eng J 2014. [DOI: 10.1016/j.bej.2014.08.015] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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Enhancement of ascomycin production in Streptomyces hygroscopicus var. ascomyceticus by combining resin HP20 addition and metabolic profiling analysis. ACTA ACUST UNITED AC 2014; 41:1365-74. [DOI: 10.1007/s10295-014-1473-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2014] [Accepted: 06/09/2014] [Indexed: 10/25/2022]
Abstract
Abstract
Combinatorial approach of adsorbent resin HP20 addition and metabolic profiling analysis were carried out to enhance ascomycin production. Under the optimal condition of 5 % m/v HP20 added at 24 h, ascomycin production was increased to 380 from 300 mg/L. To further rationally guide the improvement of ascomycin production, metabolic profiling analysis was employed to investigate the intracellular metabolite changes of Streptomyces hygroscopicus var. ascomyceticus FS35 in response to HP20 addition. A correlation between the metabolic profiles and ascomycin accumulation was revealed by partial least-squares to latent structures discriminant analysis, and 11 key metabolites that most contributed to metabolism differences and ascomycin biosynthesis were identified. Based on the analysis of metabolite changes together with their pathways, the potential key factors associated with ascomycin overproduction were determined. Finally, rationally designed fermentation strategies based on HP20 addition were performed as follows: 2 % v/v n-hexadecane was added at 24 h; 1.0 g/L valine was supplemented at 48 h; 1.0 g/L lysine was added at 72 h. The ascomycin production was ultimately improved to 460 mg/L, a 53.3 % enhancement compared with that obtained in initial condition. These results demonstrated that the combination of HP20 addition and metabolic profiling analysis could be successfully applied to the rational guidance of production improvement of ascomycin, as well as other clinically important compounds.
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Qi H, Zhao S, Wen J, Chen Y, Jia X. Analysis of ascomycin production enhanced by shikimic acid resistance and addition in Streptomyces hygroscopicus var. ascomyceticus. Biochem Eng J 2014. [DOI: 10.1016/j.bej.2013.11.006] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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