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Boukouvala S, Kontomina E, Olbasalis I, Patriarcheas D, Tzimotoudis D, Arvaniti K, Manolias A, Tsatiri MA, Basdani D, Zekkas S. Insights into the genomic and functional divergence of NAT gene family to serve microbial secondary metabolism. Sci Rep 2024; 14:14905. [PMID: 38942826 PMCID: PMC11213898 DOI: 10.1038/s41598-024-65342-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2024] [Accepted: 06/19/2024] [Indexed: 06/30/2024] Open
Abstract
Microbial NAT enzymes, which employ acyl-CoA to acylate aromatic amines and hydrazines, have been well-studied for their role in xenobiotic metabolism. Some homologues have also been linked to secondary metabolism, but this function of NAT enzymes is not as well-known. For this comparative study, we surveyed sequenced microbial genomes to update the list of formally annotated NAT genes, adding over 4000 new sequences (mainly bacterial, but also archaeal, fungal and protist) and portraying a broad but not universal distribution of NATs in the microbiocosmos. Localization of NAT sequences within microbial gene clusters was not a rare finding, and this association was evident across all main types of biosynthetic gene clusters (BGCs) implicated in secondary metabolism. Interrogation of the MIBiG database for experimentally characterized clusters with NAT genes further supports that secondary metabolism must be a major function for microbial NAT enzymes and should not be overlooked by researchers in the field. We also show that NAT sequences can be associated with bacterial plasmids potentially involved in horizontal gene transfer. Combined, our computational predictions and MIBiG literature findings reveal the extraordinary functional diversification of microbial NAT genes, prompting further research into their role in predicted BGCs with as yet uncharacterized function.
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Affiliation(s)
- Sotiria Boukouvala
- Department of Molecular Biology and Genetics, Democritus University of Thrace, 68100, Alexandroupolis, Greece.
| | - Evanthia Kontomina
- Department of Molecular Biology and Genetics, Democritus University of Thrace, 68100, Alexandroupolis, Greece
| | - Ioannis Olbasalis
- Department of Molecular Biology and Genetics, Democritus University of Thrace, 68100, Alexandroupolis, Greece
| | - Dionysios Patriarcheas
- Department of Molecular Biology and Genetics, Democritus University of Thrace, 68100, Alexandroupolis, Greece
| | - Dimosthenis Tzimotoudis
- Department of Molecular Biology and Genetics, Democritus University of Thrace, 68100, Alexandroupolis, Greece
| | - Konstantina Arvaniti
- Department of Molecular Biology and Genetics, Democritus University of Thrace, 68100, Alexandroupolis, Greece
| | - Aggelos Manolias
- Department of Molecular Biology and Genetics, Democritus University of Thrace, 68100, Alexandroupolis, Greece
| | - Maria-Aggeliki Tsatiri
- Department of Molecular Biology and Genetics, Democritus University of Thrace, 68100, Alexandroupolis, Greece
| | - Dimitra Basdani
- Department of Molecular Biology and Genetics, Democritus University of Thrace, 68100, Alexandroupolis, Greece
| | - Sokratis Zekkas
- Department of Molecular Biology and Genetics, Democritus University of Thrace, 68100, Alexandroupolis, Greece
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2
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Liu Q, Wang Y, Xia X, Li Z, Li Y, Shen Y, Wang H. Combinatorial Biosynthesis of 3- O-Carbamoylmaytansinol by Rational Engineering of the Tailoring Steps of Ansamitocins. ACS Synth Biol 2024; 13:721-727. [PMID: 38377312 DOI: 10.1021/acssynbio.3c00575] [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] [Indexed: 02/22/2024]
Abstract
Currently, most maytansine-containing antibody-drug conjugates (ADCs) in clinical trials are prepared with DM1 or DM4, which in turn is synthesized mainly from ansamitocin P-3 (AP-3), a bacterial maytansinoid, isolated from Actinosynnema pretiosum. However, due to the high self-toxicity of AP-3 to A. pretiosum, the yield of AP-3 has been difficult to improve. Herein, a new maytansinoid with much lower self-toxicity to A. pretiosum, 3-O-carbamoylmaytansinol (CAM, 3), was designed and generated by introducing the 3-O-carbamoyltransferase gene asc21b together with the N-methyltransferase genes from exogenous maytansinoid gene clusters into the 3-O-acyltransferase gene (asm19) deleted mutant HGF052. Meanwhile, two new shunt products, 20-O-demethyl-19-dechloro-N-demethyl-4,5-desepoxy-CAM (4) and 20-O-demethyl-N-demethyl-4,5-desepoxy-CAM (5) were identified from the recombinant strain. Furthermore, by screening of liquid fermentation media, overexpression of bottleneck tailoring enzymes and the pathway-specific activator, the titer of CAM reached 498 mg/L in the engineered strain. Since the 3-O-carbamoyl group of CAM can be removed by chemical cleavage as AP-3 to produce maytansinol, our work suggests that CAM may be a promising alternative to AP-3 in the future development of ADCs.
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Affiliation(s)
- Qingqing Liu
- State Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Yu Wang
- State Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Xin Xia
- Key Laboratory of Chemical Biology of Ministry of Education, School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan 250012, China
| | - Zhongyue Li
- Key Laboratory of Chemical Biology of Ministry of Education, School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan 250012, China
| | - Yaoyao Li
- Key Laboratory of Chemical Biology of Ministry of Education, School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan 250012, China
| | - Yuemao Shen
- Key Laboratory of Chemical Biology of Ministry of Education, School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan 250012, China
| | - Haoxin Wang
- State Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao 266237, China
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3
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Dai P, Qin Y, Li L, Li H, Lv L, Xu D, Song Y, Huang T, Lin S, Deng Z, Tao M. Enhancing tylosin production by combinatorial overexpression of efflux, SAM biosynthesis, and regulatory genes in hyperproducing Streptomyces xinghaiensis strain. Synth Syst Biotechnol 2023; 8:486-497. [PMID: 37519989 PMCID: PMC10372049 DOI: 10.1016/j.synbio.2023.07.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 06/29/2023] [Accepted: 07/06/2023] [Indexed: 08/01/2023] Open
Abstract
Tylosin is a 16-membered macrolide antibiotic widely used in veterinary medicine to control infections caused by Gram-positive pathogens and mycoplasmas. To improve the fermentation titer of tylosin in the hyperproducing Streptomyces xinghaiensis strain TL01, we sequenced its whole genome and identified the biosynthetic gene cluster therein. Overexpression of the tylosin efflux gene tlrC, the cluster-situated S-adenosyl methionine (SAM) synthetase gene metKcs, the SAM biosynthetic genes adoKcs-metFcs, or the pathway-specific activator gene tylR enhanced tylosin production by 18%, 12%, 11%, and 11% in the respective engineered strains TLPH08-2, TLPH09, TLPH10, and TLPH12. Co-overexpression of metKcs and adoKcs-metFcs as two transcripts increased tylosin production by 22% in the resultant strain TLPH11 compared to that in TL01. Furthermore, combinational overexpression of tlrC, metKcs, adoKcs-metFcs, and tylR as four transcripts increased tylosin production by 23% (10.93g/L) in the resultant strain TLPH17 compared to that in TL01. However, a negligible additive effect was displayed upon combinational overexpression in TLPH17 as suggested by the limited increment of fermentation titer compared to that in TLPH08-2. Transcription analyses indicated that the expression of tlrC and three SAM biosynthetic genes in TLPH17 was considerably lower than that of TLPH08-2 and TLPH11. Based on this observation, the five genes were rearranged into one or two operons to coordinate their overexpression, yielding two engineered strains TLPH23 and TLPH24, and leading to further enhancement of tylosin production over TLPH17. In particular, the production of TLPH23 reached 11.35 g/L. These findings indicated that the combinatorial strategy is a promising approach for enhancing tylosin production in high-yielding industrial strains.
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Affiliation(s)
- Penghui Dai
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Yuyao Qin
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Luyuan Li
- Zhejiang Apeloa Biotechnology Co., Ltd., Jinhua, 322109, China
| | - Haidi Li
- Zhejiang Apeloa Jiayuan Pharmaceutical Co., Ltd., Jinhua, 322118, China
| | - Lihuo Lv
- Zhejiang Apeloa Jiayuan Pharmaceutical Co., Ltd., Jinhua, 322118, China
| | - Danying Xu
- Zhejiang Apeloa Jiayuan Pharmaceutical Co., Ltd., Jinhua, 322118, China
| | - Yuqing Song
- Zhejiang Apeloa Jiayuan Pharmaceutical Co., Ltd., Jinhua, 322118, China
| | - Tingting Huang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Shuangjun Lin
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
- Haihe Laboratory of Synthetic Biology, Tianjin, 300308, China
| | - Zixin Deng
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
- Haihe Laboratory of Synthetic Biology, Tianjin, 300308, China
| | - Meifeng Tao
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
- Haihe Laboratory of Synthetic Biology, Tianjin, 300308, China
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Huang Q, Zhang X, Guo Z, Fu X, Zhao Y, Kang Q, Bai L. Biosynthesis of ansamitocin P-3 incurs stress on the producing strain Actinosynnema pretiosum at multiple targets. Commun Biol 2023; 6:860. [PMID: 37596387 PMCID: PMC10439133 DOI: 10.1038/s42003-023-05227-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Accepted: 08/07/2023] [Indexed: 08/20/2023] Open
Abstract
Microbial bioactive natural products mediate ecologically beneficial functions to the producing strains, and have been widely used in clinic and agriculture with clearly defined targets and underlying mechanisms. However, the physiological effects of their biosynthesis on the producing strains remain largely unknown. The antitumor ansamitocin P-3 (AP-3), produced by Actinosynnema pretiosum ATCC 31280, was found to repress the growth of the producing strain at high concentration and target the FtsZ protein involved in cell division. Previous work suggested the presence of additional cryptic targets of AP-3 in ATCC 31280. Herein we use chemoproteomic approach with an AP-3-derived photoaffinity probe to profile the proteome-wide interactions of AP-3. AP-3 exhibits specific bindings to the seemingly unrelated deoxythymidine diphosphate glucose-4,6-dehydratase, aldehyde dehydrogenase, and flavin-dependent thymidylate synthase, which are involved in cell wall assembly, central carbon metabolism and nucleotide biosynthesis, respectively. AP-3 functions as a non-competitive inhibitor of all three above target proteins, generating physiological stress on the producing strain through interfering diverse metabolic pathways. Overexpression of these target proteins increases strain biomass and markedly boosts AP-3 titers. This finding demonstrates that identification and engineering of cryptic targets of bioactive natural products can lead to in-depth understanding of microbial physiology and improved product titers.
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Affiliation(s)
- Qungang Huang
- State Key Laboratory of Microbial Metabolism, Shanghai-Islamabad-Belgrade Joint Innovation Center on Antibacterial Resistances, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
- Joint International Research Laboratory of Metabolic and Developmental Sciences, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Xin Zhang
- State Key Laboratory of Microbial Metabolism, Shanghai-Islamabad-Belgrade Joint Innovation Center on Antibacterial Resistances, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
- Joint International Research Laboratory of Metabolic and Developmental Sciences, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Ziyue Guo
- State Key Laboratory of Microbial Metabolism, Shanghai-Islamabad-Belgrade Joint Innovation Center on Antibacterial Resistances, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
- Joint International Research Laboratory of Metabolic and Developmental Sciences, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Xinnan Fu
- State Key Laboratory of Microbial Metabolism, Shanghai-Islamabad-Belgrade Joint Innovation Center on Antibacterial Resistances, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
- Joint International Research Laboratory of Metabolic and Developmental Sciences, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Yilei Zhao
- State Key Laboratory of Microbial Metabolism, Shanghai-Islamabad-Belgrade Joint Innovation Center on Antibacterial Resistances, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
- Joint International Research Laboratory of Metabolic and Developmental Sciences, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Qianjin Kang
- State Key Laboratory of Microbial Metabolism, Shanghai-Islamabad-Belgrade Joint Innovation Center on Antibacterial Resistances, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China.
- Joint International Research Laboratory of Metabolic and Developmental Sciences, Shanghai Jiao Tong University, Shanghai, 200240, China.
| | - Linquan Bai
- State Key Laboratory of Microbial Metabolism, Shanghai-Islamabad-Belgrade Joint Innovation Center on Antibacterial Resistances, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China.
- Joint International Research Laboratory of Metabolic and Developmental Sciences, Shanghai Jiao Tong University, Shanghai, 200240, China.
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Global Regulator AdpA_1075 Regulates Morphological Differentiation and Ansamitocin Production in Actinosynnema pretiosum subsp. auranticum. Bioengineering (Basel) 2022; 9:bioengineering9110719. [DOI: 10.3390/bioengineering9110719] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2022] [Revised: 11/16/2022] [Accepted: 11/17/2022] [Indexed: 11/23/2022] Open
Abstract
Actinosynnema pretiosum is a well-known producer of maytansinoid antibiotic ansamitocin P-3 (AP-3). Growth of A. pretiosum in submerged culture was characterized by the formation of complex mycelial particles strongly affecting AP-3 production. However, the genetic determinants involved in mycelial morphology are poorly understood in this genus. Herein a continuum of morphological types of a morphologically stable variant was observed during submerged cultures. Expression analysis revealed that the ssgA_6663 and ftsZ_5883 genes are involved in mycelial aggregation and entanglement. Combing morphology observation and morphology engineering, ssgA_6663 was identified to be responsible for the mycelial intertwining during liquid culture. However, down-regulation of ssgA_6663 transcription was caused by inactivation of adpA_1075, gene coding for an AdpA-like protein. Additionally, the overexpression of adpA_1075 led to an 85% increase in AP-3 production. Electrophoretic mobility shift assays (EMSA) revealed that AdpA_1075 may bind the promoter regions of asm28 gene in asm gene cluster as well as the promoter regions of ssgA_6663. These results confirm that adpA_1075 plays a positive role in AP-3 biosynthesis and morphological differentiation.
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Endowing homodimeric carbamoyltransferase GdmN with iterative functions through structural characterization and mechanistic studies. Nat Commun 2022; 13:6617. [PMID: 36329057 PMCID: PMC9633730 DOI: 10.1038/s41467-022-34387-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Accepted: 10/24/2022] [Indexed: 11/06/2022] Open
Abstract
Iterative enzymes, which catalyze sequential reactions, have the potential to improve the atom economy and diversity of industrial enzymatic processes. Redesigning one-step enzymes to be iterative biocatalysts could further enhance these processes. Carbamoyltransferases (CTases) catalyze carbamoylation, an important modification for the bioactivity of many secondary metabolites with pharmaceutical applications. To generate an iterative CTase, we determine the X-ray structure of GdmN, a one-step CTase involved in ansamycin biosynthesis. GdmN forms a face-to-face homodimer through unusual C-terminal domains, a previously unknown functional form for CTases. Structural determination of GdmN complexed with multiple intermediates elucidates the carbamoylation process and identifies key binding residues within a spacious substrate-binding pocket. Further structural and computational analyses enable multi-site enzyme engineering, resulting in an iterative CTase with the capacity for successive 7-O and 3-O carbamoylations. Our findings reveal a subclade of the CTase family and exemplify the potential of protein engineering for generating iterative enzymes.
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Guo S, Sun X, Li R, Zhang T, Hu F, Liu F, Hua Q. Two strategies to improve the supply of PKS extender units for ansamitocin P-3 biosynthesis by CRISPR-Cas9. BIORESOUR BIOPROCESS 2022; 9:90. [PMID: 38647752 PMCID: PMC10991131 DOI: 10.1186/s40643-022-00583-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Accepted: 08/15/2022] [Indexed: 11/10/2022] Open
Abstract
Ansamitocin P-3 (AP-3) produced by Actinosynnema pretiosum is a potent antitumor agent. However, lack of efficient genome editing tools greatly hinders the AP-3 overproduction in A. pretiosum. To solve this problem, a tailor-made pCRISPR-Cas9apre system was developed from pCRISPR-Cas9 for increasing the accessibility of A. pretiosum to genetic engineering, by optimizing cas9 for the host codon preference and replacing pSG5 with pIJ101 replicon. Using pCRISPR-Cas9apre, five large-size gene clusters for putative competition pathway were individually deleted with homology-directed repair (HDR) and their effects on AP-3 yield were investigated. Especially, inactivation of T1PKS-15 increased AP-3 production by 27%, which was most likely due to the improved intracellular triacylglycerol (TAG) pool for essential precursor supply of AP-3 biosynthesis. To enhance a "glycolate" extender unit, two combined bidirectional promoters (BDPs) ermEp-kasOp and j23119p-kasOp were knocked into asm12-asm13 spacer in the center region of gene cluster, respectively, by pCRISPR-Cas9apre. It is shown that in the two engineered strains BDP-ek and BDP-jk, the gene transcription levels of asm13-17 were significantly upregulated to improve the methoxymalonyl-acyl carrier protein (MM-ACP) biosynthetic pathway and part of the post-PKS pathway. The AP-3 yields of BDP-ek and BDP-jk were finally increased by 30% and 50% compared to the parent strain L40. Both CRISPR-Cas9-mediated engineering strategies employed in this study contributed to the availability of AP-3 PKS extender units and paved the way for further metabolic engineering of ansamitocin overproduction.
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Affiliation(s)
- Siyu Guo
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, China
| | - Xueyuan Sun
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, China
| | - Ruihua Li
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, China
| | - Tianyao Zhang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, China
| | - Fengxian Hu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, China
| | - Feng Liu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, China.
| | - Qiang Hua
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, China.
- Shanghai Collaborative Innovation Center for Biomanufacturing Technology, 130 Meilong Road, Shanghai, 200237, China.
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Improvement of Biosynthetic Ansamitocin P-3 Production Based on Oxygen-Vector Screening and Metabonomics Analysis. EVIDENCE-BASED COMPLEMENTARY AND ALTERNATIVE MEDICINE 2022; 2022:3564185. [PMID: 35692578 PMCID: PMC9184225 DOI: 10.1155/2022/3564185] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Revised: 04/23/2022] [Accepted: 05/06/2022] [Indexed: 11/18/2022]
Abstract
A novel approach involving exogenous oxygen vectors was developed for improving the production of biosynthetic Ansamitocin P-3 (AP-3). Four types of oxygen vectors including soybean oil, n-dodecane, n-hexadecane, and Tween-80 were applied to explore the effect of exogenous oxygen vectors on AP-3 yield. It was observed that soybean oil exhibited a better ability for promoting AP-3 generation than the other three oxygen vectors. Based on the results of the single-factor experiment, response surface methodology was employed to obtain the optimal soybean oil addition method. The optimum soybean oil concentration was 0.52%, and the addition time was 50 h. Under this condition, the yield of AP-3 reached 106.04 mg/L, which was 49.48% higher than that of the control group without adding oxygen vectors. To further investigate the influence of dissolved oxygen on precious orange tufts actinomycetes variety A. pretiosum strain metabolism and AP-3 yield, metabolomics analysis was carried out by detecting strain intermediate metabolites at various stages under different dissolved oxygen levels. Moreover, differential metabolite screening and metabolic pathway enrichment analysis were combined to exploit the effect mechanism of soybean oil on AP-3 production. Results suggested that primary metabolic levels of the TCA cycle and amino acid metabolism increased with the increase in dissolved oxygen level, which was beneficial to the life activities of bacteria and the synthesis of secondary metabolic precursors, thus increasing the production of AP-3.
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Vu MT, Geraldi A, Do HDK, Luqman A, Nguyen HD, Fauzia FN, Amalludin FI, Sadila AY, Wijaya NH, Santoso H, Manuhara YSW, Bui LM, Hariyanto S, Wibowo AT. Soil Mineral Composition and Salinity Are the Main Factors Regulating the Bacterial Community Associated with the Roots of Coastal Sand Dune Halophytes. BIOLOGY 2022; 11:biology11050695. [PMID: 35625422 PMCID: PMC9138652 DOI: 10.3390/biology11050695] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 04/15/2022] [Accepted: 04/27/2022] [Indexed: 11/16/2022]
Abstract
Soil salinity and mineral deficiency are major problems in agriculture. Many studies have reported that plant-associated microbiota, particularly rhizosphere and root microbiota, play a crucial role in tolerance against salinity and mineral deficiency. Nevertheless, there are still many unknown parts of plant–microbe interaction, especially regarding their role in halophyte adaptation to coastal ecosystems. Here, we report the bacterial community associated with the roots of coastal sand dune halophytes Spinifex littoreus and Calotropis gigantea, and the soil properties that affect their composition. Strong correlations were observed between root bacterial diversity and soil mineral composition, especially with soil Calcium (Ca), Titanium (Ti), Cuprum (Cu), and Zinc (Zn) content. Soil Ti and Zn content showed a positive correlation with bacterial diversity, while soil Ca and Cu had a negative effect on bacterial diversity. A strong correlation was also found between the abundance of several bacterial species with soil salinity and mineral content, suggesting that some bacteria are responsive to changes in soil salinity and mineral content. Some of the identified bacteria, such as Bacillus idriensis and Kibdelosporangium aridum, are known to have growth-promoting effects on plants. Together, the findings of this work provided valuable information regarding bacterial communities associated with the roots of sand dune halophytes and their interactions with soil properties. Furthermore, we also identified several bacterial species that might be involved in tolerance against stresses. Further work will be focused on isolation and transplantation of these potential microbes, to validate their role in plant tolerance against stresses, not only in their native hosts but also in crops.
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Affiliation(s)
- Minh Thiet Vu
- NTT Hi-Tech Institute, Nguyen Tat Thanh University, Ho Chi Minh City 70000, Vietnam; (M.T.V.); (H.D.K.D.); (H.D.N.)
| | - Almando Geraldi
- Departement of Biology, Faculty of Science and Technology, Airlangga University, Surabaya 60115, Indonesia; (A.G.); (F.N.F.); (F.I.A.); (A.Y.S.); (N.H.W.); (Y.S.W.M.); (L.M.B.)
- Biotechnology of Tropical Medicinal Plants Research Group, Airlangga University, Surabaya 60115, Indonesia
| | - Hoang Dang Khoa Do
- NTT Hi-Tech Institute, Nguyen Tat Thanh University, Ho Chi Minh City 70000, Vietnam; (M.T.V.); (H.D.K.D.); (H.D.N.)
| | - Arif Luqman
- Biology Department, Institut Teknologi Sepuluh Nopember, Surabaya 60111, Indonesia;
| | - Hoang Danh Nguyen
- NTT Hi-Tech Institute, Nguyen Tat Thanh University, Ho Chi Minh City 70000, Vietnam; (M.T.V.); (H.D.K.D.); (H.D.N.)
| | - Faiza Nur Fauzia
- Departement of Biology, Faculty of Science and Technology, Airlangga University, Surabaya 60115, Indonesia; (A.G.); (F.N.F.); (F.I.A.); (A.Y.S.); (N.H.W.); (Y.S.W.M.); (L.M.B.)
| | - Fahmi Ikhlasul Amalludin
- Departement of Biology, Faculty of Science and Technology, Airlangga University, Surabaya 60115, Indonesia; (A.G.); (F.N.F.); (F.I.A.); (A.Y.S.); (N.H.W.); (Y.S.W.M.); (L.M.B.)
| | - Aliffa Yusti Sadila
- Departement of Biology, Faculty of Science and Technology, Airlangga University, Surabaya 60115, Indonesia; (A.G.); (F.N.F.); (F.I.A.); (A.Y.S.); (N.H.W.); (Y.S.W.M.); (L.M.B.)
| | - Nabilla Hapsari Wijaya
- Departement of Biology, Faculty of Science and Technology, Airlangga University, Surabaya 60115, Indonesia; (A.G.); (F.N.F.); (F.I.A.); (A.Y.S.); (N.H.W.); (Y.S.W.M.); (L.M.B.)
| | - Heri Santoso
- Generasi Biologi Indonesia (Genbinesia) Foundation, Gresik 61171, Indonesia;
| | - Yosephine Sri Wulan Manuhara
- Departement of Biology, Faculty of Science and Technology, Airlangga University, Surabaya 60115, Indonesia; (A.G.); (F.N.F.); (F.I.A.); (A.Y.S.); (N.H.W.); (Y.S.W.M.); (L.M.B.)
- Biotechnology of Tropical Medicinal Plants Research Group, Airlangga University, Surabaya 60115, Indonesia
| | - Le Minh Bui
- Departement of Biology, Faculty of Science and Technology, Airlangga University, Surabaya 60115, Indonesia; (A.G.); (F.N.F.); (F.I.A.); (A.Y.S.); (N.H.W.); (Y.S.W.M.); (L.M.B.)
- Department of Biotechnology, NTT Hi-tech Institute, Nguyen Tat Thanh University, Ho Chi Minh City 70000, Vietnam
| | - Sucipto Hariyanto
- Departement of Biology, Faculty of Science and Technology, Airlangga University, Surabaya 60115, Indonesia; (A.G.); (F.N.F.); (F.I.A.); (A.Y.S.); (N.H.W.); (Y.S.W.M.); (L.M.B.)
- Correspondence: (S.H.); (A.T.W.)
| | - Anjar Tri Wibowo
- Departement of Biology, Faculty of Science and Technology, Airlangga University, Surabaya 60115, Indonesia; (A.G.); (F.N.F.); (F.I.A.); (A.Y.S.); (N.H.W.); (Y.S.W.M.); (L.M.B.)
- Biotechnology of Tropical Medicinal Plants Research Group, Airlangga University, Surabaya 60115, Indonesia
- Correspondence: (S.H.); (A.T.W.)
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Wang X, Luo X. Precursor Quantitation Methods for Next Generation Food Production. Front Bioeng Biotechnol 2022; 10:849177. [PMID: 35360389 PMCID: PMC8960114 DOI: 10.3389/fbioe.2022.849177] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Accepted: 02/22/2022] [Indexed: 11/21/2022] Open
Abstract
Food is essential for human survival. Nowadays, traditional agriculture faces challenges in balancing the need of sustainable environmental development and the rising food demand caused by an increasing population. In addition, in the emerging of consumers' awareness of health related issues bring a growing trend towards novel nature-based food additives. Synthetic biology, using engineered microbial cell factories for production of various molecules, shows great advantages for generating food alternatives and additives, which not only relieve the pressure laid on tradition agriculture, but also create a new stage in healthy and sustainable food supplement. The biosynthesis of food components (protein, fats, carbohydrates or vitamins) in engineered microbial cells often involves cellular central metabolic pathways, where common precursors are processed into different proteins and products. Quantitation of the precursors provides information of the metabolic flux and intracellular metabolic state, giving guidance for precise pathway engineering. In this review, we summarized the quantitation methods for most cellular biosynthetic precursors, including energy molecules and co-factors involved in redox-reactions. It will also be useful for studies worked on pathway engineering of other microbial-derived metabolites. Finally, advantages and limitations of each method are discussed.
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Affiliation(s)
- Xinran Wang
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Xiaozhou Luo
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
- Shenzhen Institute of Advanced Technology, Shenzhen, China
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11
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Pitakbut T, Spiteller M, Kayser O. Genome Mining and Gene Expression Reveal Maytansine Biosynthetic Genes from Endophytic Communities Living inside Gymnosporia heterophylla (Eckl. and Zeyh.) Loes. and the Relationship with the Plant Biosynthetic Gene, Friedelin Synthase. PLANTS (BASEL, SWITZERLAND) 2022; 11:321. [PMID: 35161302 PMCID: PMC8840412 DOI: 10.3390/plants11030321] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 01/09/2022] [Accepted: 01/22/2022] [Indexed: 06/14/2023]
Abstract
Even though maytansine was first discovered from Celastraceae plants, it was later proven to be an endophytic bacterial metabolite. However, a pure bacterial culture cannot synthesize maytansine. Therefore, an exclusive interaction between plant and endophytes is required for maytansine production. Unfortunately, our understanding of plant-endophyte interaction is minimal, and critical questions remain. For example: how do endophytes synthesize maytansine inside their plant host, and what is the impact of maytansine production in plant secondary metabolites? Our study aimed to address these questions. We selected Gymnosporia heterophylla as our model and used amino-hydroxybenzoic acid (AHBA) synthase and halogenase genes as biomarkers, as these two genes respond to biosynthesize maytansine. As a result, we found a consortium of seven endophytes involved in maytansine production in G. heterophylla, based on genome mining and gene expression experiments. Subsequently, we evaluated the friedelin synthase (FRS) gene's expression level in response to biosynthesized 20-hydroxymaytenin in the plant. We found that the FRS expression level was elevated and linked with the expression of the maytansine biosynthetic genes. Thus, we achieved our goals and provided new evidence on endophyte-endophyte and plant-endophyte interactions, focusing on maytansine production and its impact on plant metabolite biosynthesis in G. heterophylla.
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Affiliation(s)
- Thanet Pitakbut
- Technical Biochemistry, Department of Biochemical and Chemical Engineering, TU Dortmund University, 44227 Dortmund, Germany;
| | - Michael Spiteller
- Department of Chemistry and Chemical Biology, Institute of Environmental Research (INFU), TU Dortmund University, 44227 Dortmund, Germany;
| | - Oliver Kayser
- Technical Biochemistry, Department of Biochemical and Chemical Engineering, TU Dortmund University, 44227 Dortmund, Germany;
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12
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Zhou Z, Tang H, Wang W, Zhang L, Su F, Wu Y, Bai L, Li S, Sun Y, Tao F, Xu P. A cold shock protein promotes high-temperature microbial growth through binding to diverse RNA species. Cell Discov 2021; 7:15. [PMID: 33727528 PMCID: PMC7966797 DOI: 10.1038/s41421-021-00246-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2020] [Accepted: 01/27/2021] [Indexed: 01/18/2023] Open
Abstract
Endowing mesophilic microorganisms with high-temperature resistance is highly desirable for industrial microbial fermentation. Here, we report a cold-shock protein (CspL) that is an RNA chaperone protein from a lactate producing thermophile strain (Bacillus coagulans 2–6), which is able to recombinantly confer strong high-temperature resistance to other microorganisms. Transgenic cspL expression massively enhanced high-temperature growth of Escherichia coli (a 2.4-fold biomass increase at 45 °C) and eukaryote Saccharomyces cerevisiae (a 2.6-fold biomass increase at 36 °C). Importantly, we also found that CspL promotes growth rates at normal temperatures. Mechanistically, bio-layer interferometry characterized CspL’s nucleotide-binding functions in vitro, while in vivo we used RNA-Seq and RIP-Seq to reveal CspL’s global effects on mRNA accumulation and CspL’s direct RNA binding targets, respectively. Thus, beyond establishing how a cold-shock protein chaperone provides high-temperature resistance, our study introduces a strategy that may facilitate industrial thermal fermentation.
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Affiliation(s)
- Zikang Zhou
- State Key Laboratory of Microbial Metabolism, and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, People's Republic of China
| | - Hongzhi Tang
- State Key Laboratory of Microbial Metabolism, and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, People's Republic of China.
| | - Weiwei Wang
- State Key Laboratory of Microbial Metabolism, and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, People's Republic of China
| | - Lige Zhang
- State Key Laboratory of Microbial Metabolism, and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, People's Republic of China
| | - Fei Su
- State Key Laboratory of Microbial Metabolism, and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, People's Republic of China
| | - Yuanting Wu
- 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
| | - Sicong Li
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Wuhan University), Ministry of Education, and Wuhan University School of Pharmaceutical Sciences, Wuhan, Hubei, 430071, People's Republic of China
| | - Yuhui Sun
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Wuhan University), Ministry of Education, and Wuhan University School of Pharmaceutical Sciences, Wuhan, Hubei, 430071, People's Republic of China
| | - Fei Tao
- State Key Laboratory of Microbial Metabolism, and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, People's Republic of China
| | - Ping Xu
- State Key Laboratory of Microbial Metabolism, and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, People's Republic of China.
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13
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Wang X, Wei J, Xiao Y, Luan S, Ning X, Bai L. Efflux identification and engineering for ansamitocin P-3 production in Actinosynnema pretiosum. Appl Microbiol Biotechnol 2021; 105:695-706. [PMID: 33394151 DOI: 10.1007/s00253-020-11044-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 11/25/2020] [Accepted: 12/06/2020] [Indexed: 12/31/2022]
Abstract
Ansamitocin P-3 (AP-3) exhibits potent biological activities against various tumor cells. As an important drug precursor, reliable supply of AP-3 is limited by low fermentation yield. Although different strategies have been implemented to improve AP-3 yield, few have investigated the impact of efflux on AP-3 production. In this study, AP-3 efflux genes were identified through combined analysis of two sets of transcriptomes. The production-based transcriptome was implemented to search for efflux genes highly expressed in response to AP-3 accumulation during the fermentation process, while the resistance-based transcriptome was designed to screen for genes actively expressed in response to the exogenous supplementation of AP-3. After comprehensive analysis of two transcriptomes, six efflux genes outside the ansamitocin BGC were identified. Among the six genes, individual deletion of APASM_2704, APASM_6861, APASM_3193, and APASM_2805 resulted in decreased AP-3 production, and alternative overexpression led to AP-3 yield increase from 264.6 to 302.4, 320.4, 330.6, and 320.6 mg/L, respectively. Surprisingly, APASM_2704 was found to be responsible for exportation of AP-3 and another macro-lactam antibiotic pretilactam. Furthermore, growth of APASM_2704, APASM_3193, or APASM_2805 overexpression mutants was obviously improved under 300 mg/L AP-3 supplementation. In summary, our study has identified AP-3 efflux genes outside the ansamitocin BGC by comparative transcriptomic analysis, and has shown that enhancing the transcription of transporter genes can improve AP-3 production, shedding light on strategies used for exporter screening and antibiotic production improvement. KEY POINTS: • AP-3-related efflux genes were identified by transcriptomic analysis. • Deletion of the identified efflux genes led in AP-3 yield decrease. • Overexpression of the efflux genes resulted in increased AP-3 production.
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Affiliation(s)
- Xinran Wang
- Center for Synthetic Biochemistry, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes for Advanced Technology, Chinese Academy of Sciences, Shenzhen, China. .,State Key Laboratory of Microbial Metabolism, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, China.
| | - Jianhua Wei
- State Key Laboratory of Microbial Metabolism, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Yifan Xiao
- State Key Laboratory of Microbial Metabolism, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Shuhui Luan
- State Key Laboratory of Microbial Metabolism, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Xinjuan Ning
- State Key Laboratory of Microbial Metabolism, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Linquan Bai
- State Key Laboratory of Microbial Metabolism, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, China.
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p-Aminophenylalanine Involved in the Biosynthesis of Antitumor Dnacin B1 for Quinone Moiety Formation. Molecules 2020; 25:molecules25184186. [PMID: 32932689 PMCID: PMC7570522 DOI: 10.3390/molecules25184186] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Revised: 09/08/2020] [Accepted: 09/10/2020] [Indexed: 12/04/2022] Open
Abstract
Actinosynnema species produce diverse natural products with important biological activities, which represent an important resource of antibiotic discovery. Advances in genome sequencing and bioinformatics tools have accelerated the exploration of the biosynthetic gene clusters (BGCs) encoding natural products. Herein, the completed BGCs of dnacin B1 were first discovered in two Actinosynnema pretiosum subsp. auranticum strains DSM 44131T (hereafter abbreviated as strain DSM 44131T) and X47 by comparative genome mining strategy. The BGC for dnacin B1 contains 41 ORFs and spans a 66.9 kb DNA region in strain DSM 44131T. Its involvement in dnacin B1 biosynthesis was identified through the deletion of a 9.7 kb region. Based on the functional gene analysis, we proposed the biosynthetic pathway for dnacin B1. Moreover, p-amino-phenylalanine (PAPA) unit was found to be the dnacin B1 precursor for the quinone moiety formation, and this was confirmed by heterologous expression of dinV, dinE and dinF in Escherichia coli. Furthermore, nine potential PAPA aminotransferases (APAT) from the genome of strain DSM 44131T were explored and expressed. Biochemical evaluation of their amino group transformation ability was carried out with p-amino-phenylpyruvic acid (PAPP) or PAPA as the substrate for the final product formation. Two of those, APAT4 and APAT9, displayed intriguing aminotransferase ability for the formation of PAPA. The proposed dnacin B1 biosynthetic machinery and PAPA biosynthetic investigations not only enriched the knowledge of tetrahydroisoquinoline (THIQ) biosynthesis, but also provided PAPA building blocks to generate their structurally unique homologues.
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15
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Wu Y, Kang Q, Zhang LL, Bai L. Subtilisin-Involved Morphology Engineering for Improved Antibiotic Production in Actinomycetes. Biomolecules 2020; 10:biom10060851. [PMID: 32503302 PMCID: PMC7356834 DOI: 10.3390/biom10060851] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2020] [Revised: 05/27/2020] [Accepted: 05/30/2020] [Indexed: 12/27/2022] Open
Abstract
In the submerged cultivation of filamentous microbes, including actinomycetes, complex morphology is one of the critical process features for the production of secondary metabolites. Ansamitocin P-3 (AP-3), an antitumor agent, is a secondary metabolite produced by Actinosynnema pretiosum ATCC 31280. An excessive mycelial fragmentation of A. pretiosum ATCC 31280 was observed during the early stage of fermentation. Through comparative transcriptomic analysis, a subtilisin-like serine peptidase encoded gene APASM_4178 was identified to be responsible for the mycelial fragmentation. Mutant WYT-5 with the APASM_4178 deletion showed increased biomass and improved AP-3 yield by 43.65%. We also found that the expression of APASM_4178 is specifically regulated by an AdpA-like protein APASM_1021. Moreover, the mycelial fragmentation was alternatively alleviated by the overexpression of subtilisin inhibitor encoded genes, which also led to a 46.50 ± 0.79% yield increase of AP-3. Furthermore, APASM_4178 was overexpressed in salinomycin-producing Streptomyces albus BK 3-25 and validamycin-producing S. hygroscopicus TL01, which resulted in not only dispersed mycelia in both strains, but also a 33.80% yield improvement of salinomycin to 24.07 g/L and a 14.94% yield improvement of validamycin to 21.46 g/L. In conclusion, our work elucidates the involvement of a novel subtilisin-like serine peptidase in morphological differentiation, and modulation of its expression could be an effective strategy for morphology engineering and antibiotic yield improvement in actinomycetes.
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Affiliation(s)
- Yuanting Wu
- State Key Laboratory of Microbial Metabolism, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai 200204, China; (Y.W.); (Q.K.)
- Joint International Research Laboratory of Metabolic & Developmental Sciences, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Qianjin Kang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai 200204, China; (Y.W.); (Q.K.)
- Joint International Research Laboratory of Metabolic & Developmental Sciences, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Li-Li Zhang
- College of Life Science, Tarim University, Alar 843300, China;
| | - Linquan Bai
- State Key Laboratory of Microbial Metabolism, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai 200204, China; (Y.W.); (Q.K.)
- Joint International Research Laboratory of Metabolic & Developmental Sciences, Shanghai Jiao Tong University, Shanghai 200240, China
- College of Life Science, Tarim University, Alar 843300, China;
- Correspondence:
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16
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The Antitumor Agent Ansamitocin P-3 Binds to Cell Division Protein FtsZ in Actinosynnema pretiosum. Biomolecules 2020; 10:biom10050699. [PMID: 32365857 PMCID: PMC7277737 DOI: 10.3390/biom10050699] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Revised: 04/25/2020] [Accepted: 04/28/2020] [Indexed: 02/02/2023] Open
Abstract
Ansamitocin P-3 (AP-3) is an important antitumor agent. The antitumor activity of AP-3 is a result of its affinity towards β-tubulin in eukaryotic cells. In this study, in order to improve AP-3 production, the reason for severe growth inhibition of the AP-3 producing strain Actinosynnema pretiosum WXR-24 under high concentrations of exogenous AP-3 was investigated. The cell division protein FtsZ, which is the analogue of β-tubulin in bacteria, was discovered to be the AP-3 target through structural comparison followed by a SPR biosensor assay. AP-3 was trapped into a less hydrophilic groove near the GTPase pocket on FtsZ by hydrogen bounding and hydrophobic interactions, as revealed by docking analysis. After overexpression of the APASM_5716 gene coding for FtsZ in WXR-30, the resistance to AP-3 was significantly improved. Moreover, AP-3 yield was increased from 250.66 mg/L to 327.37 mg/L. After increasing the concentration of supplemented yeast extract, the final yield of AP-3 reached 371.16 mg/L. In summary, we demonstrate that the cell division protein FtsZ is newly identified as the bacterial target of AP-3, and improving resistance is an effective strategy to enhance AP-3 production.
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17
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Liu T, Jin Z, Wang Z, Chen J, Wei LJ, Hua Q. Metabolomics analysis of Actinosynnema pretiosum with improved AP-3 production by enhancing UDP-glucose biosynthesis. J Biosci Bioeng 2020; 130:36-47. [PMID: 32179024 DOI: 10.1016/j.jbiosc.2020.02.013] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Revised: 02/08/2020] [Accepted: 02/13/2020] [Indexed: 02/08/2023]
Abstract
Ansamitocin P-3 (AP-3) shows strong anticancer effects and has used as a payload for antibody-drug conjugates. Our previous study have shown that although genetically engineered Actinosynnema pretiosum strains with enhanced UDP-glucose (UDPG) biosynthesis displayed improved AP-3 production compared to the wild-type strain, the increase in yield was far from meeting the industrial demand. In this study, comparative metabolomics analysis complemented with quantitative real-time PCR analysis was performed for the wild-type strain and two mutants (OpgmOugp, ΔzwfΔgnd) to identify possible metabolic bottlenecks and non-intuitive targets for further enhancement of AP-3 production. We observed that enhancing intracellular UDPG availability facilitated the accumulation of intracellular N-demethyl-AP-3 and AP-3, where the transporting of them outside the cell still needs to be developed. We also found that the UDPG biosynthesis was closely associated with the availability of fructose in the medium and a suitable fructose feeding strategy could promote the further improvement of AP-3 titer. In addition, pathway abundance analysis revealed that undesired fatty acid accumulation and down-regulation of amino acid metabolism may be unfavorable for ansamitocin biosynthesis in later stage of production. These results indicate that genetic modification of the UDPG biosynthetic pathways may have pleiotropic effects on AP-3 production. Efforts must be made to eliminate these newly identified metabolic bottlenecks to boost AP-3 production in A. pretiosum.
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Affiliation(s)
- Ting Liu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, PR China
| | - Ziwen Jin
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, PR China
| | - Ziwei Wang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, PR China
| | - Jun Chen
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, PR China
| | - Liu-Jing Wei
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, PR China
| | - Qiang Hua
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, PR China; Shanghai Collaborative Innovation Center for Biomanufacturing Technology, 130 Meilong Road, Shanghai 200237, PR China.
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18
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Metabolomic change and pathway profiling reveal enhanced ansamitocin P-3 production in Actinosynnema pretiosum with low organic nitrogen availability in culture medium. Appl Microbiol Biotechnol 2020; 104:3555-3568. [PMID: 32114676 DOI: 10.1007/s00253-020-10463-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Revised: 12/07/2019] [Accepted: 02/12/2020] [Indexed: 10/24/2022]
Abstract
Ansamitocin P-3 (AP-3), a 19-membered polyketide macrocyclic lactam, has potent antitumor activity. Our previous study showed that a relatively low organic nitrogen concentration in culture medium could significantly improve AP-3 production of Actinosynnema pretiosum. In the present study, we aimed to reveal the possible reasons for this improvement through metabolomic and gene transcriptional analytical methods. At the same time, a metabolic pathway profile based on metabolome data and pathway correlation information was performed to obtain a systematic view of the metabolic network modulations of A. pretiosum. Orthogonal partial least squares discriminant analysis showed that nine and eleven key metabolites directly associated with AP-3 production at growth phase and ansamitocin production phase, respectively. In-depth pathway analysis results highlighted that low organic nitrogen availability had significant impacts on central carbon metabolism and amino acid metabolic pathways of A. pretiosum and these metabolic responses were found to be beneficial to precursor supply and ansamitocin biosynthesis. Furthermore, real-time PCR results showed that the transcription of genes involved in precursor and ansamitocin biosynthetic pathways were remarkably upregulated under low organic nitrogen condition thus directing increased carbon flux toward ansamitocin biosynthesis. More importantly, the metabolic pathway analysis demonstrated a competitive relationship between fatty acid and AP-3 biosynthesis could significantly affect the accumulation of AP-3. Our findings provided new knowledge on the organic nitrogen metabolism and ansamitocin biosynthetic precursor in A. pretiosum and identified several important rate-limiting steps involved in ansamitocin biosynthesis thus providing a theoretical basis of further improvement in AP-3 production.
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Zhang F, Ji H, Ali I, Deng Z, Bai L, Zheng J. Structural and Biochemical Insight into the Recruitment of Acyl Carrier Protein-Linked Extender Units in Ansamitocin Biosynthesis. Chembiochem 2020; 21:1309-1314. [PMID: 31777147 DOI: 10.1002/cbic.201900628] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Indexed: 01/17/2023]
Abstract
A few acyltransferase (AT) domains of modular polyketide synthases (PKSs) recruit acyl carrier protein (ACP)-linked extender units with unusual C2 substituents to confer functionalities that are not available in coenzyme A (CoA)-linked ones. In this study, an AT specific for methoxymalonyl (MOM)-ACP in the third module of the ansamitocin PKS was structurally and biochemically characterized. The AT uses a conserved tryptophan residue at the entrance of the substrate binding tunnel to discriminate between different carriers. A W275R mutation switches its carrier specificity from the ACP to the CoA molecule. The acyl-AT complex structures clearly show that the MOM-ACP accepted by the AT has the 2S instead of the opposite 2R stereochemistry that is predicted according to the biosynthetic derivation from a d-glycolytic intermediate. Together, these results reveal the structural basis of ATs recognizing ACP-linked extender units in polyketide biosynthesis.
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Affiliation(s)
- Fa Zhang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Minhang District, 200240, Shanghai, P. R. China
| | - Huining Ji
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Minhang District, 200240, Shanghai, P. R. China
| | - Imtiaz Ali
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Minhang District, 200240, Shanghai, P. R. China
| | - Zixin Deng
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Minhang District, 200240, Shanghai, P. R. China
| | - Linquan Bai
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Minhang District, 200240, Shanghai, P. R. China
| | - Jianting Zheng
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Minhang District, 200240, Shanghai, P. R. China
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Liu T, Bessembayeva L, Chen J, Wei LJ, Hua Q. Development of an economical fermentation platform for enhanced ansamitocin P-3 production in Actinosynnema pretiosum. BIORESOUR BIOPROCESS 2019. [DOI: 10.1186/s40643-018-0235-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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21
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Li J, Sun R, Ning X, Wang X, Wang Z. Genome-Scale Metabolic Model of Actinosynnema pretiosum ATCC 31280 and Its Application for Ansamitocin P-3 Production Improvement. Genes (Basel) 2018; 9:E364. [PMID: 30036981 PMCID: PMC6070911 DOI: 10.3390/genes9070364] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2018] [Revised: 07/06/2018] [Accepted: 07/09/2018] [Indexed: 01/12/2023] Open
Abstract
Actinosynnema pretiosum ATCC 31280 is the producer of antitumor agent ansamitocin P-3 (AP-3). Understanding of the AP-3 biosynthetic pathway and the whole metabolic network in A. pretiosum is important for the improvement of AP-3 titer. In this study, we reconstructed the first complete Genome-Scale Metabolic Model (GSMM) Aspm1282 for A. pretiosum ATCC 31280 based on the newly sequenced genome, with 87% reactions having definite functional annotation. The model has been validated by effectively predicting growth and the key genes for AP-3 biosynthesis. Then we built condition-specific models for an AP-3 high-yield mutant NXJ-24 by integrating Aspm1282 model with time-course transcriptome data. The changes of flux distribution reflect the metabolic shift from growth-related pathway to secondary metabolism pathway since the second day of cultivation. The AP-3 and methionine metabolisms were both enriched in active flux for the last two days, which uncovered the relationships among cell growth, activation of methionine metabolism, and the biosynthesis of AP-3. Furthermore, we identified four combinatorial gene modifications for overproducing AP-3 by in silico strain design, which improved the theoretical flux of AP-3 biosynthesis from 0.201 to 0.372 mmol/gDW/h. Upregulation of methionine metabolic pathway is a potential strategy to improve the production of AP-3.
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Affiliation(s)
- Jian Li
- Bio-X Institutes, Key laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, Shanghai 200030, China.
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200040, China.
| | - Renliang Sun
- Bio-X Institutes, Key laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, Shanghai 200030, China.
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200040, China.
| | - Xinjuan Ning
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200040, China.
- State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai 200040, China.
| | - Xinran Wang
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200040, China.
- State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai 200040, China.
| | - Zhuo Wang
- Bio-X Institutes, Key laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, Shanghai 200030, China.
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200040, China.
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22
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Du Z, Zhong J. Rational approach to improve ansamitocin P‐3 production by integrating pathway engineering and substrate feeding in
Actinosynnema pretiosum. Biotechnol Bioeng 2018; 115:2456-2466. [DOI: 10.1002/bit.26775] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2018] [Revised: 06/19/2018] [Accepted: 06/22/2018] [Indexed: 12/15/2022]
Affiliation(s)
- Zhi‐Qiang Du
- State Key Laboratory of Microbial MetabolismSchool of Life Sciences and Biotechnology, Shanghai Jiao Tong UniversityShanghai China
- Joint International Research Laboratory of Metabolic and Developmental SciencesSchool of Life Sciences and Biotechnology, Shanghai Jiao Tong UniversityShanghai China
- Laboratory of Molecular Biochemical Engineering and Advanced Fermentation TechnologySchool of Life Sciences and Biotechnology, Shanghai Jiao Tong UniversityShanghai China
| | - Jian‐Jiang Zhong
- State Key Laboratory of Microbial MetabolismSchool of Life Sciences and Biotechnology, Shanghai Jiao Tong UniversityShanghai China
- Joint International Research Laboratory of Metabolic and Developmental SciencesSchool of Life Sciences and Biotechnology, Shanghai Jiao Tong UniversityShanghai China
- Laboratory of Molecular Biochemical Engineering and Advanced Fermentation TechnologySchool of Life Sciences and Biotechnology, Shanghai Jiao Tong UniversityShanghai China
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23
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Tao H, Zhang Y, Deng Z, Liu T. Strategies for Enhancing the Yield of the Potent Insecticide Spinosad in Actinomycetes. Biotechnol J 2018; 14:e1700769. [DOI: 10.1002/biot.201700769] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Revised: 05/19/2018] [Indexed: 01/20/2023]
Affiliation(s)
- Hui Tao
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery; Ministry of Education and Wuhan University School of Pharmaceutical Sciences; Wuhan 430071 P. R. China
| | - Yuchen Zhang
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery; Ministry of Education and Wuhan University School of Pharmaceutical Sciences; Wuhan 430071 P. R. China
| | - Zixin Deng
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery; Ministry of Education and Wuhan University School of Pharmaceutical Sciences; Wuhan 430071 P. R. China
- Hubei Engineering Laboratory for Synthetic Microbiology; Wuhan Institute of Biotechnology; Wuhan 430075 P. R. China
- State Key Laboratory of Microbial Metabolism, and School of Life Sciences and Biotechnology; Shanghai Jiao Tong University; Shanghai 200240 P. R. China
| | - Tiangang Liu
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery; Ministry of Education and Wuhan University School of Pharmaceutical Sciences; Wuhan 430071 P. R. China
- Hubei Engineering Laboratory for Synthetic Microbiology; Wuhan Institute of Biotechnology; Wuhan 430075 P. R. China
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