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Xu J, Shen S, Hu Z, Xu G, Li H, Xu Z, Shi J. Enhanced Production of Sisomicin in Micromonospora inyoensis by Protoplast Mutagenesis and Fermentation Optimization. Appl Biochem Biotechnol 2024:10.1007/s12010-024-04889-4. [PMID: 38381313 DOI: 10.1007/s12010-024-04889-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/12/2024] [Indexed: 02/22/2024]
Abstract
Sisomicin is a broad-spectrum aminoglycoside antibiotic and is the precursor of netilmicin and plazomicin. However, the fermentation level of sisomicin is still low compared with other antibiotics, which restricts the application of sisomicin and its derivatives. In this study, to improve sisomicin production, breeding of high-yielding sisomicin strains was conducted with chemical mutagenesis using Micromonospora inyoensis OG-1 (titer, 1042 U·mL-1) as the starting strain. Protoplast preparation was conducted under optimal conditions, and protoplast mutagenesis was performed with a suitable concentration of diethyl sulfate. Subsequently, a high-yielding and genetically stable strain (H6-32) was obtained by screening, with a sisomicin titer of 1486 U·mL-1 (an increase of 42.6%). Finally, carbon and nitrogen sources were optimized to further improve sisomicin production, and a sisomicin titer of 1780 U·mL-1 was ultimately obtained by controlling the dissolved oxygen level at 30% in a 5-L fermenter, which to the best of our knowledge is the highest reported titer ever achieved by fermentation. Comparative genome analysis showed that a total of 13 genes in the genome of the mutant strain H6-32 were mutated compared to the original strain. This study not only provides a reference for further breeding of high-yielding strains and fermentation optimization, but also enhances our understanding of sisomicin production.
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Affiliation(s)
- Jianguo Xu
- Laboratory of Pharmaceutical Engineering, School of Life Science and Health Engineering, Jiangnan University, Wuxi, 214122, China
- Wuxi Fortune Pharmaceutical Co., Ltd, Wuxi, 214041, China
| | - Shulin Shen
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China
- National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi, 214122, China
| | - Zhehua Hu
- Laboratory of Pharmaceutical Engineering, School of Life Science and Health Engineering, Jiangnan University, Wuxi, 214122, China
| | - Guoqiang Xu
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China
- National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi, 214122, China
| | - Hui Li
- Laboratory of Pharmaceutical Engineering, School of Life Science and Health Engineering, Jiangnan University, Wuxi, 214122, China
| | - Zhenghong Xu
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China
- National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi, 214122, China
| | - Jinsong Shi
- Laboratory of Pharmaceutical Engineering, School of Life Science and Health Engineering, Jiangnan University, Wuxi, 214122, China.
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China.
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Melkonian TR, Vuksanovic N, Silvaggi NR. Probing mechanistic questions in the PLP- and O 2-dependent l-Arg oxidases. Methods Enzymol 2023; 685:493-529. [PMID: 37245913 DOI: 10.1016/bs.mie.2023.03.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
The pyridoxal-5'-phosphate-dependent l-Arg oxidases are unusual in that they are able to catalyze 4-electron oxidations of arginine using only the PLP cofactor. No metals or other accessory cosubstrates are involved; only arginine, dioxygen, and PLP. The catalytic cycles of these enzymes are replete with colored intermediates whose accumulation and decay can be monitored spectrophotometrically. This makes the l-Arg oxidases excellent subjects for detailed mechanistic investigations. They are worth studying, because they can teach us much about how PLP-dependent enzymes modulate the cofactor (structure-function-dynamics) and how new activities can arise from existing enzyme scaffolds. Herein we describe a series of experiments that can be used to probe the mechanisms of l-Arg oxidases. These methods by no means originated in our lab but were learned from talented researchers in other enzyme fields (flavoenzymes and Fe(II)-dependent oxygenases) and have been adapted to fit the requirements of our system. We present practical information for expressing and purifying the l-Arg oxidases, protocols for running stopped-flow experiments to examine the reactions with l-Arg and with dioxygen, and a tandem mass spectrometry-based quench-flow assay to follow the accumulation of the products of the hydroxylating l-Arg oxidases.
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Affiliation(s)
- Trevor R Melkonian
- Department of Chemistry and Biochemistry, University of Wisconsin-Milwaukee, Milwaukee, WI, United States
| | | | - Nicholas R Silvaggi
- Department of Chemistry and Biochemistry, University of Wisconsin-Milwaukee, Milwaukee, WI, United States.
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Banihani SA, Aljabali SM. Men with oligozoospermia had lower level of seminal plasma pyridoxine compared to normozoospermic men. Heliyon 2022; 8:e11983. [DOI: 10.1016/j.heliyon.2022.e11983] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Revised: 09/22/2021] [Accepted: 11/22/2022] [Indexed: 12/03/2022] Open
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(Meta)Genomic Analysis Reveals Diverse Energy Conservation Strategies Employed by Globally Distributed Gemmatimonadota. mSystems 2022; 7:e0022822. [PMID: 35913193 PMCID: PMC9426454 DOI: 10.1128/msystems.00228-22] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Gemmatimonadota is a phylum-level lineage distributed widely but rarely reported. Only six representatives of Gemmatimonadota have so far been isolated and cultured in laboratory. The physiology, ecology, and evolutionary history of this phylum remain unknown. The 16S rRNA gene survey of our salt lake and deep-sea sediments, and Earth Microbiome Project (EMP) samples, reveals that Gemmatimonadota exist in diverse environments globally. In this study, we retrieved 17 metagenome-assembled genomes (MAGs) from salt lake sediments (12 MAGs) and deep-sea sediments (5 MAGs). Analysis of these MAGs and the nonredundant MAGs or genomes from public databases reveals Gemmatimonadota can degrade various complex organic substrates, and mainly employ heterotrophic pathways (e.g., glycolysis and tricarboxylic acid [TCA] cycle) for growth via aerobic respiration. And the processes of sufficient energy being stored in glucose through gluconeogenesis, followed by the synthesis of more complex compounds, are prevalent in Gemmatimonadota. A highly expandable pangenome for Gemmatimonadota has been observed, which presumably results from their adaptation to thriving in diverse environments. The enrichment of the Na+/H+ antiporter in the SG8-23 order represents their adaptation to salty habitats. Notably, we identified a novel lineage of the SG8-23 order, which is potentially anoxygenic phototrophic. This lineage is not closely related to the phototrophs in the order of Gemmatimonadales. The two orders differ distinctly in the gene organization and phylogenetic relationship of their photosynthesis gene clusters, indicating photosystems in Gemmatimonadota have evolved in two independent routes. IMPORTANCE The phylum Gemmatimonadota is widely distributed in various environments. However, their physiology, ecology and evolutionary history remain unknown, primary due to the limited cultured isolates and available genomes. We were intrigued to find out how widespread this phylum is, and how it can thrive under diverse conditions. Our results here expand the knowledge of the genetic and metabolic diversity of Gemmatimonadota, and shed light on the diverse energy conservation strategies (i.e., oxidative phosphorylation, substrate phosphorylation, and photosynthetic phosphorylation) responsible for their global distribution. Moreover, gene organization and phylogenetic analysis of photosynthesis gene clusters in Gemmatimonadota provide a valuable insight into the evolutionary history of photosynthesis.
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Kudo F, Eguchi T. Biosynthesis of cyclitols. Nat Prod Rep 2022; 39:1622-1642. [PMID: 35726901 DOI: 10.1039/d2np00024e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Review covering up to 2021Cyclitols derived from carbohydrates are naturally stable hydrophilic substances under ordinary physiological conditions, increasing the water solubility of whole molecules in cells. The stability of cyclitols is derived from their carbocyclic structures bearing no acetal groups, in contrast to sugar molecules. Therefore, carbocycle-forming reactions are critical for the biosynthesis of cyclitols. Herein, we review naturally occurring cyclitols that have been identified to date and categorize them according to the type of carbocycle-forming enzymatic reaction. Furthermore, the cyclitol-forming enzymatic reaction mechanisms and modification pathways of the initially generated cyclitols are reviewed.
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Affiliation(s)
- Fumitaka Kudo
- Department of Chemistry, Tokyo Institute of Technology, 2-12-1 O-Okayama, Meguro-ku, Tokyo, Japan.
| | - Tadashi Eguchi
- Department of Chemistry, Tokyo Institute of Technology, 2-12-1 O-Okayama, Meguro-ku, Tokyo, Japan.
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Li S, Santos Bury PD, Huang F, Guo J, Sun G, Reva A, Huang C, Jian X, Li Y, Zhou J, Deng Z, Leeper FJ, Leadlay PF, Dias MVB, Sun Y. Mechanistic Insights into Dideoxygenation in Gentamicin Biosynthesis. ACS Catal 2021. [DOI: 10.1021/acscatal.1c03508] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Sicong Li
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Ministry of Education), and School of Pharmaceutical Sciences, Wuhan University, Wuhan 430071, China
| | - Priscila Dos Santos Bury
- Department of Microbiology, Institute of Biomedical Science, University of São Paulo, São Paulo 05508-000, Brazil
| | - Fanglu Huang
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, United Kingdom
| | - Junhong Guo
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Ministry of Education), and School of Pharmaceutical Sciences, Wuhan University, Wuhan 430071, China
| | - Guo Sun
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Ministry of Education), and School of Pharmaceutical Sciences, Wuhan University, Wuhan 430071, China
| | - Anna Reva
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, United Kingdom
| | - Chuan Huang
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Ministry of Education), and School of Pharmaceutical Sciences, Wuhan University, Wuhan 430071, China
| | - Xinyun Jian
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Ministry of Education), and School of Pharmaceutical Sciences, Wuhan University, Wuhan 430071, China
| | - Yuan Li
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Ministry of Education), and School of Pharmaceutical Sciences, Wuhan University, Wuhan 430071, China
| | - Jiahai Zhou
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Zixin Deng
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Ministry of Education), and School of Pharmaceutical Sciences, Wuhan University, Wuhan 430071, China
| | - Finian J. Leeper
- Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom
| | - Peter F. Leadlay
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, United Kingdom
| | - Marcio V. B. Dias
- Department of Microbiology, Institute of Biomedical Science, University of São Paulo, São Paulo 05508-000, Brazil
- Department of Chemistry, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Yuhui Sun
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Ministry of Education), and School of Pharmaceutical Sciences, Wuhan University, Wuhan 430071, China
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