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Zhang H, Guo L, Su Y, Wang R, Yang W, Mu W, Xuan L, Huang L, Wang J, Gao W. Hosts engineering and in vitro enzymatic synthesis for the discovery of novel natural products and their derivatives. Crit Rev Biotechnol 2024; 44:1121-1139. [PMID: 37574211 DOI: 10.1080/07388551.2023.2236787] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Revised: 05/23/2023] [Accepted: 06/17/2023] [Indexed: 08/15/2023]
Abstract
Novel natural products (NPs) and their derivatives are important sources for drug discovery, which have been broadly applied in the fields of agriculture, livestock, and medicine, making the synthesis of NPs and their derivatives necessarily important. In recent years, biosynthesis technology has received increasing attention due to its high efficiency in the synthesis of high value-added novel products and its advantages of green, environmental protection, and controllability. In this review, the technological advances of biosynthesis strategies in the discovery of novel NPs and their derivatives are outlined, with an emphasis on two areas of host engineering and in vitro enzymatic synthesis. In terms of hosts engineering, multiple microorganisms, including Streptomyces, Aspergillus, and Penicillium, have been used as the biosynthetic gene clusters (BGCs) provider and host strain for the expression of BGCs to discover new compounds over the past years. In addition, the use of in vitro enzymatic synthesis strategy to generate novel compounds such as triterpenoid saponins and flavonoids is also hereby described.
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Affiliation(s)
- Huanyu Zhang
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, P.R. China
- Key Laboratory of Systems Bioengineering, Ministry of Education, Tianjin University, Tianjin, P.R. China
| | - Lanping Guo
- National Resource Center for Chinese Meteria Medica, China Academy of Chinese Medical Sciences, Beijing, P.R. China
| | - Yaowu Su
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, P.R. China
- Key Laboratory of Systems Bioengineering, Ministry of Education, Tianjin University, Tianjin, P.R. China
| | - Rubing Wang
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, P.R. China
- Key Laboratory of Systems Bioengineering, Ministry of Education, Tianjin University, Tianjin, P.R. China
| | - Wenqi Yang
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, P.R. China
- Key Laboratory of Systems Bioengineering, Ministry of Education, Tianjin University, Tianjin, P.R. China
| | - Wenrong Mu
- College of Pharmacy, Henan University of Chinese Medicine, Zhengzhou, P.R. China
| | - Liangshuang Xuan
- College of Pharmacy, Henan University of Chinese Medicine, Zhengzhou, P.R. China
| | - Luqi Huang
- National Resource Center for Chinese Meteria Medica, China Academy of Chinese Medical Sciences, Beijing, P.R. China
| | - Juan Wang
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, P.R. China
- Key Laboratory of Systems Bioengineering, Ministry of Education, Tianjin University, Tianjin, P.R. China
| | - Wenyuan Gao
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, P.R. China
- Key Laboratory of Systems Bioengineering, Ministry of Education, Tianjin University, Tianjin, P.R. China
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da Silva S, Guedes FADF, Amaral JRV, Ribeiro JRDA, de Souza YPA, de Freitas-Almeida ÂC, Thompson FL, Ramos RTJ, Whiteley AS, Macrae A, de Oliveira SS. Aeromonas allosaccharophila Strain AE59-TE2 Is Highly Antagonistic towards Multidrug-Resistant Human Pathogens, What Does Its Genome Tell Us? Life (Basel) 2022; 12:1492. [PMID: 36294926 PMCID: PMC9605075 DOI: 10.3390/life12101492] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 09/15/2022] [Accepted: 09/19/2022] [Indexed: 11/16/2022] Open
Abstract
Multidrug-resistant bacteria are of critical importance and a problem for human health and food preservation; the discovery of new antimicrobial substances to control their proliferation is part of the solution. This work reports on 57 antagonistic Aeromonas strains, of which 38 strains were antagonistic towards problematic human pathogens. The genome of the most antagonistic strain was sequenced and identified as Aeromonas allosaccharophila. Its genome was fully annotated and mined for genes that might explain that activity. Strain AE59-TE was antagonistic toward clinically relevant gram-negative and gram-positive multidrug-resistant bacteria, including Klebsiella pneumoniae KPC, Escherichia coli ESBL, Salmonella typhimurium, and Staphylococcus aureus MRSA. Strain AE59-TE2 was identified by multilocus sequence analysis. Genome mining identified four genes homologous to the bacteriocin, zoocin A from Streptococcus equi and a gene 98% similar to cvpA linked to colicin V production. A. allosaccharophila strain AE59-TE2 produced antimicrobial activity against a broad range of bacteria, including important gram-negative bacteria, not typically targeted by bacteriocins. Herewere described novel zoocin genes that are promising for industrial applications in the food and health sectors. Interesting and important antagonistic activity is described combined with the first detailed genomic analysis of the species Aeromonas allosaccharophila.
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Affiliation(s)
- Sheila da Silva
- Programa Pós-Graduação de Biotecnologia Vegetal e Bioprocessos da Universidade Federal do Rio de Janeiro, Av. Prof. Rodolpho Paulo Rocco, s/n-Prédio do CCS-Bloco K, 2° Andar-Sala 032, Rio de Janeiro 21941-902, Brazil
| | - Fernanda Alves de Freitas Guedes
- Programa Pós-Graduação de Biotecnologia Vegetal e Bioprocessos da Universidade Federal do Rio de Janeiro, Av. Prof. Rodolpho Paulo Rocco, s/n-Prédio do CCS-Bloco K, 2° Andar-Sala 032, Rio de Janeiro 21941-902, Brazil
| | - João Ricardo Vidal Amaral
- Programa Pós-Graduação de Biotecnologia Vegetal e Bioprocessos da Universidade Federal do Rio de Janeiro, Av. Prof. Rodolpho Paulo Rocco, s/n-Prédio do CCS-Bloco K, 2° Andar-Sala 032, Rio de Janeiro 21941-902, Brazil
| | - José Roberto de Assis Ribeiro
- Programa Pós-Graduação de Biotecnologia Vegetal e Bioprocessos da Universidade Federal do Rio de Janeiro, Av. Prof. Rodolpho Paulo Rocco, s/n-Prédio do CCS-Bloco K, 2° Andar-Sala 032, Rio de Janeiro 21941-902, Brazil
| | | | - Ângela Correa de Freitas-Almeida
- Departamento de Microbiologia, Imunologia e Parasitologia, Centro Biomédico, Faculdade de Ciências Médicas, Universidade do Estado do Rio de Janeiro (UERJ), Av. 28 de Setembro, 87, 3° Andar, Fundos, Vila Isabel, Rio de Janeiro 20550-170, Brazil
| | - Fabiano Lopes Thompson
- Departamento de Genética, Instituto de Biologia, Universidade Federal do Rio de Janeiro, Av. Prof. Rodolpho Paulo Rocco, s/n-Prédio do CCS-Instituto de Biologia, 2° Andar-Sala 93, Rio de Janeiro 219410-970, Brazil
| | - Rommel Thiago Jucá Ramos
- Instituto de Ciências Biológicas, Centro de Genômica e Biologia de Sistemas da Universidade Federal do Pará (UFPA), Rua Augusto Corrêa, 01 Guamá, Belém 66075-970, Brazil
| | - Andrew Steven Whiteley
- Commonwealth Scientific and Industrial Research Organization (CSIRO), Canberra, ACT 2601, Australia
| | - Andrew Macrae
- Programa Pós-Graduação de Biotecnologia Vegetal e Bioprocessos da Universidade Federal do Rio de Janeiro, Av. Prof. Rodolpho Paulo Rocco, s/n-Prédio do CCS-Bloco K, 2° Andar-Sala 032, Rio de Janeiro 21941-902, Brazil
- Instituto de Microbiologia Paulo de Góes da Universidade Federal do Rio de Janeiro, Av. Prof. Rodolpho Paulo Rocco, s/n-Prédio do CCS-Bloco I, 1° Andar-Sala 047, Rio de Janeiro 21941-902, Brazil
| | - Selma Soares de Oliveira
- Programa Pós-Graduação de Biotecnologia Vegetal e Bioprocessos da Universidade Federal do Rio de Janeiro, Av. Prof. Rodolpho Paulo Rocco, s/n-Prédio do CCS-Bloco K, 2° Andar-Sala 032, Rio de Janeiro 21941-902, Brazil
- Instituto de Microbiologia Paulo de Góes da Universidade Federal do Rio de Janeiro, Av. Prof. Rodolpho Paulo Rocco, s/n-Prédio do CCS-Bloco I, 1° Andar-Sala 047, Rio de Janeiro 21941-902, Brazil
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Yun K, Zhang Y, Li S, Wang Y, Tu R, Liu H, Wang M. Droplet-Microfluidic-Based Promoter Engineering and Expression Fine-Tuning for Improved Erythromycin Production in Saccharopolyspora erythraea NRRL 23338. Front Bioeng Biotechnol 2022; 10:864977. [PMID: 35445005 PMCID: PMC9013967 DOI: 10.3389/fbioe.2022.864977] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Accepted: 03/18/2022] [Indexed: 11/23/2022] Open
Abstract
Erythromycin is a clinically important drug produced by the rare actinomycete Saccharopolyspora erythraea. In the wide-type erythromycin producer S. erythraea NRRL 23338, there is a lack of systematical method for promoter engineering as well as a well-characterized promoter panel for comprehensive metabolic engineering. Here we demonstrated a systematical promoter acquiring process including promoter characterization, engineering and high-throughput screening by the droplet-microfluidic based platform in S. erythraea NRRL 23338, and rapidly obtained a panel of promoters with 21.5-fold strength variation for expression fine-tuning in the native host. By comparative qRT-PCR of S. erythraea NRRL 23338 and a high-producing strain S0, potential limiting enzymes were identified and overexpressed individually using two screened synthetic promoters. As a result, erythromycin production in the native host was improved by as high as 137.24 folds by combinational gene overexpression. This work enriches the accessible regulatory elements in the important erythromycin-producing strain S. erythraea NRRL 23338, and also provides a rapid and systematic research paradigm of promoter engineering and expression fine-tuning in the similar filamentous actinomycete hosts.
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Affiliation(s)
- Kaiyue Yun
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China
- Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, China
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Yue Zhang
- Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, China
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Shixin Li
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China
- Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, China
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Yan Wang
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China
- Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, China
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Ran Tu
- Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, China
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Hao Liu
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China
- *Correspondence: Hao Liu, ; Meng Wang,
| | - Meng Wang
- Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, China
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
- *Correspondence: Hao Liu, ; Meng Wang,
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Verma VA, Wang L, Labadie SS, Liang J, Sellers BD, Wang J, Dong L, Wang Q, Zhang S, Xu Z, Zhang Y, Niu Y, Wang X, Wai J, Koehler MFT, Hu H, Alexander MK, Nishiyama M, Miu A, Xu Y, Pang J, Katakam AK, Reichelt M, Austin CD, Ho H, Payandeh J, Koth CM. Discovery of Inhibitors of the Lipopolysaccharide Transporter MsbA: From a Screening Hit to Potent Wild-Type Gram-Negative Activity. J Med Chem 2022; 65:4085-4120. [DOI: 10.1021/acs.jmedchem.1c01909] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Vishal A. Verma
- Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Lan Wang
- Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Sharada S. Labadie
- Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Jun Liang
- Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Benjamin D. Sellers
- Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Jian Wang
- WuXi AppTec Co., Ltd., 288 Fute Zhong Road, Waigaoqiao Free Trade Zone, Shanghai 200131, People’s Republic of China
| | - Liting Dong
- WuXi AppTec Co., Ltd., 288 Fute Zhong Road, Waigaoqiao Free Trade Zone, Shanghai 200131, People’s Republic of China
| | - Qiuyue Wang
- WuXi AppTec Co., Ltd., 288 Fute Zhong Road, Waigaoqiao Free Trade Zone, Shanghai 200131, People’s Republic of China
| | - Shuang Zhang
- WuXi AppTec Co., Ltd., 288 Fute Zhong Road, Waigaoqiao Free Trade Zone, Shanghai 200131, People’s Republic of China
| | - Zhongya Xu
- WuXi AppTec Co., Ltd., 288 Fute Zhong Road, Waigaoqiao Free Trade Zone, Shanghai 200131, People’s Republic of China
| | - Yexia Zhang
- WuXi AppTec Co., Ltd., 288 Fute Zhong Road, Waigaoqiao Free Trade Zone, Shanghai 200131, People’s Republic of China
| | - Yanan Niu
- WuXi AppTec Co., Ltd., 288 Fute Zhong Road, Waigaoqiao Free Trade Zone, Shanghai 200131, People’s Republic of China
| | - Xinxin Wang
- WuXi AppTec Co., Ltd., 288 Fute Zhong Road, Waigaoqiao Free Trade Zone, Shanghai 200131, People’s Republic of China
| | - John Wai
- WuXi AppTec Co., Ltd., 288 Fute Zhong Road, Waigaoqiao Free Trade Zone, Shanghai 200131, People’s Republic of China
| | | | - Huiyong Hu
- Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Mary Kate Alexander
- Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Mireille Nishiyama
- Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Anh Miu
- Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Yiming Xu
- Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Jodie Pang
- Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Anand K. Katakam
- Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Michael Reichelt
- Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Cary D. Austin
- Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Hoangdung Ho
- Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Jian Payandeh
- Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Christopher M. Koth
- Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
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In Silico/In Vitro Strategies Leading to the Discovery of New Nonribosomal Peptide and Polyketide Antibiotics Active against Human Pathogens. Microorganisms 2021; 9:microorganisms9112297. [PMID: 34835423 PMCID: PMC8625390 DOI: 10.3390/microorganisms9112297] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Revised: 10/29/2021] [Accepted: 11/01/2021] [Indexed: 12/12/2022] Open
Abstract
Antibiotics are majorly important molecules for human health. Following the golden age of antibiotic discovery, a period of decline ensued, characterised by the rediscovery of the same molecules. At the same time, new culture techniques and high-throughput sequencing enabled the discovery of new microorganisms that represent a potential source of interesting new antimicrobial substances to explore. The aim of this review is to present recently discovered nonribosomal peptide (NRP) and polyketide (PK) molecules with antimicrobial activity against human pathogens. We highlight the different in silico/in vitro strategies and approaches that led to their discovery. As a result of technological progress and a better understanding of the NRP and PK synthesis mechanisms, these new antibiotic compounds provide an additional option in human medical treatment and a potential way out of the impasse of antibiotic resistance.
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Kumar K, Bruheim P. A comparative study at bioprocess and metabolite levels of superhost strain Streptomyces coelicolor M1152 and its derivative M1581 heterologously expressing chloramphenicol biosynthetic gene cluster. Biotechnol Bioeng 2021; 119:145-161. [PMID: 34636422 DOI: 10.1002/bit.27958] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 09/20/2021] [Accepted: 10/03/2021] [Indexed: 11/09/2022]
Abstract
Microbial superhost strains should provide an ideal platform for the efficient homologous or heterologous phenotypic expression of biosynthetic gene clusters (BGCs) of new and novel bioactive molecules. Our aim in the current study was to perform a comparative study at the bioprocess and metabolite levels of the previously designed superhost strain Streptomyces coelicolor M1152 and its derivative strain S. coelicolor M1581 heterologously expressing chloramphenicol BGC. Parent strain M1152 was characterized by a higher specific growth rate, specific CO2 evolution rate, and a higher specific l-glutamate consumption rate as compared with M1581. Intracellular primary central metabolites (nucleoside/sugar phosphates, amino acids, organic acids, and CoAs) were quantified using four targeted LC-MS/MS-based methods. The metabolite pathways in the nonantibiotic producing S. coelicolor host strain were flooded with carbon from both carbon sources, whereas in antibiotic-producing strain, the carbon of l-glutamate seems to be draining out through excreting synthesized antibiotic. The 13 C-isotope-labeling experiments revealed the bidirectionality in the glycolytic pathway and reversibility in the non-oxidative part of PPP even with continuous uptake of d-glucose. The change in the primary metabolites due to the insertion of BGC disclosed a clear linkage between the primary and secondary metabolites.
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Affiliation(s)
- Kanhaiya Kumar
- Department of Biotechnology and Food Science, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Per Bruheim
- Department of Biotechnology and Food Science, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
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