1
|
Xiao X, Fu Y, Zhang D, Gao S. Enhancement of FK520 production in Streptomyces hygroscopicus var. ascomyceticus ATCC 14891 by overexpressing the regulatory gene fkbR2. Bioprocess Biosyst Eng 2025:10.1007/s00449-024-03124-y. [PMID: 39775883 DOI: 10.1007/s00449-024-03124-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2024] [Accepted: 12/20/2024] [Indexed: 01/11/2025]
Abstract
Ascomycin (FK520) is a 23-membered macrolide antibiotic primarily produced by the Streptomyces hygroscopicus var. ascomyceticus. Structurally similar to tacrolimus and rapamycin, it serves as an effective immunosuppressant widely used in the treatment of rejection reactions after organ transplantation and certain autoimmune diseases. Currently, FK520 is mainly produced through microbial fermentation, but its yield remains low. Since the gene fkbR2 is a regulatory gene within the FK520 biosynthesis gene cluster that has not been studied, this paper focuses on the overexpression of the gene fkbR2 in Streptomyces hygroscopicus var. ascomyceticus ATCC 14891 (WT). By constructing a strain with overexpressed fkbR2 gene, we initially obtained a high-yield strain R2-17 through shake flask fermentation, with a 28% increase in yield compared to WT. In the process of further improving the stability of the high-yield strain, this paper defines two indices: high-yield index and stability index. After two consecutive rounds of natural breeding, strain R2-17 achieved a high-yield index of 100% and a stability index of 80%. Finally, the high-yield strain R2-17-3-10 was successfully screened, and the yield was increased by 34% compared with the strain WT, reaching 686.47 mg/L. A comparative analysis between the high-yield strain R2-17-3-10 and the original strain WT revealed differences in fermentation process parameters such as FK520 synthesis rate, pH, bacterial growth, glycerol consumption rate, ammonia nitrogen level, and ammonium ion concentration. In addition, the transcription levels of genes involved in the synthesis of precursors 4,5-dihydroxycyclohex-1-enecarboxylic acid (fkbO), ethylmalonyl-CoA (fkbE, fkbU, fkbS), and pipecolic acid (fkbL), as well as pathway-specific regulatory genes (fkbN, fkbR1), were significantly increased at different time points in the high-yield strain R2-17-3-10. EMSAs analysis showed that the FkbR2 protein could not bind to the promoter region of above genes. This suggests that the gene fkbR2 may enhance the supply of FK520 synthetic precursors by indirectly regulating the transcription levels of these genes, thereby promoting an increase in FK520 production. These results demonstrate that modifying genes within the biosynthetic gene clusters of natural products can be successfully applied to increase the yields of industrially and clinically important compounds. However, it is found that fkbR2 gene is a regulatory gene that has not been fully studied, and it is worth further studying its regulatory mechanism.
Collapse
Affiliation(s)
- Xue Xiao
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, China
| | - Yu Fu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, China
| | - Daojing Zhang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, China
| | - Shuhong Gao
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, China.
| |
Collapse
|
2
|
Neal M, Brakewood W, Betenbaugh M, Zengler K. Pan-genome-scale metabolic modeling of Bacillus subtilis reveals functionally distinct groups. mSystems 2024; 9:e0092324. [PMID: 39365060 PMCID: PMC11575223 DOI: 10.1128/msystems.00923-24] [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: 07/10/2024] [Accepted: 08/20/2024] [Indexed: 10/05/2024] Open
Abstract
Bacillus subtilis is an important industrial and environmental microorganism known to occupy many niches and produce many compounds of interest. Although it is one of the best-studied organisms, much of this focus including the reconstruction of genome-scale metabolic models has been placed on a few key laboratory strains. Here, we substantially expand these prior models to pan-genome-scale, representing 481 genomes of B. subtilis with 2,315 orthologous gene clusters, 1,874 metabolites, and 2,239 reactions. Furthermore, we incorporate data from carbon utilization experiments for eight strains to refine and validate its metabolic predictions. This comprehensive pan-genome model enables the assessment of strain-to-strain differences related to nutrient utilization, fermentation outputs, robustness, and other metabolic aspects. Using the model and phenotypic predictions, we divide B. subtilis strains into five groups with distinct patterns of behavior that correlate across these features. The pan-genome model offers deep insights into B. subtilis' metabolism as it varies across environments and provides an understanding as to how different strains have adapted to dynamic habitats. IMPORTANCE As the volume of genomic data and computational power have increased, so has the number of genome-scale metabolic models. These models encapsulate the totality of metabolic functions for a given organism. Bacillus subtilis strain 168 is one of the first bacteria for which a metabolic network was reconstructed. Since then, several updated reconstructions have been generated for this model microorganism. Here, we expand the metabolic model for a single strain into a pan-genome-scale model, which consists of individual models for 481 B. subtilis strains. By evaluating differences between these strains, we identified five distinct groups of strains, allowing for the rapid classification of any particular strain. Furthermore, this classification into five groups aids the rapid identification of suitable strains for any application.
Collapse
Affiliation(s)
- Maxwell Neal
- Department of Bioengineering, University of California, San Diego, California, USA
| | - William Brakewood
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland, USA
| | - Michael Betenbaugh
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland, USA
| | - Karsten Zengler
- Department of Bioengineering, University of California, San Diego, California, USA
- Department of Pediatrics, University of California, San Diego, California, USA
- Center for Microbiome Innovation, University of California, San Diego, California, USA
- Program in Materials Science and Engineering, University of California, San Diego, La Jolla, California, USA
| |
Collapse
|
3
|
Wang J, Wang W, Chen Y, Liu Z, Ji X, Pan G, Li Z, Fan K. Development of a xylose-inducible and glucose-insensitive expression system for Parageobacillus thermoglucosidasius. Appl Microbiol Biotechnol 2024; 108:493. [PMID: 39441395 PMCID: PMC11499391 DOI: 10.1007/s00253-024-13333-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: 01/25/2024] [Revised: 09/06/2024] [Accepted: 10/15/2024] [Indexed: 10/25/2024]
Abstract
Inducible expression systems are pivotal for governing gene expression in strain engineering and synthetic biotechnological applications. Therefore, a critical need persists for the development of versatile and efficient inducible expression mechanisms. In this study, the xylose-responsive promoter xylA5p and its transcriptional regulator XylR were identified in Parageobacillus thermoglucosidasius DSM 2542. By combining promoter xylA5p with its regulator XylR, fine-tuning the expression strength of XylR, and reducing the glucose catabolite repression on xylose uptake, we successfully devised a xylose-inducible and glucose-insensitive expression system, denoted as IExyl*. This system exhibited diverse promoter strengths upon induction with xylose at varying concentrations and remained unhindered in the presence of glucose. Moreover, we showed the applicability of IExyl* in P. thermoglucosidasius by redirecting metabolic flux towards riboflavin biosynthesis, culminating in a 2.8-fold increase in riboflavin production compared to that of the starting strain. This glucose-insensitive and xylose-responsive expression system provides valuable tools for designing optimized biosynthetic pathways for high-value products and facilitates future synthetic biology investigations in Parageobacillus. KEY POINTS: • A xylose-inducible and glucose-insensitive expression system IExyl* was developed. • IExyl* was applied to enhance the riboflavin production in P. thermoglucosidasius • A tool for metabolic engineering and synthetic biology research in Parageobacillus strains.
Collapse
Affiliation(s)
- Junyang Wang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
- College of Life Science and Technology, Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Weishan Wang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yihua Chen
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zihe Liu
- College of Life Science and Technology, Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Xu Ji
- College of Life Science and Technology, Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Guohui Pan
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zilong Li
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Keqiang Fan
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China.
| |
Collapse
|
4
|
Pérez-García F, Brito LF, Bakken TI, Brautaset T. Riboflavin overproduction from diverse feedstocks with engineered Corynebacterium glutamicum. Biofabrication 2024; 16:045012. [PMID: 38996414 DOI: 10.1088/1758-5090/ad628e] [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: 03/19/2024] [Accepted: 07/12/2024] [Indexed: 07/14/2024]
Abstract
Riboflavin overproduction byCorynebacterium glutamicumwas achieved by screening synthetic operons, enabling fine-tuned expression of the riboflavin biosynthetic genesribGCAH.The synthetic operons were designed by means of predicted translational initiation rates of each open reading frame, with the best-performing selection enabling riboflavin overproduction without negatively affecting cell growth. Overexpression of the fructose-1,6-bisphosphatase (fbp) and 5-phosphoribosyl 1-pyrophosphate aminotransferase (purF) encoding genes was then done to redirect the metabolic flux towards the riboflavin precursors. The resulting strain produced 8.3 g l-1of riboflavin in glucose-based fed-batch fermentations, which is the highest reported riboflavin titer withC. glutamicum. Further genetic engineering enabled both xylose and mannitol utilization byC. glutamicum, and we demonstrated riboflavin overproduction with the xylose-rich feedstocks rice husk hydrolysate and spent sulfite liquor, and the mannitol-rich feedstock brown seaweed hydrolysate. Remarkably, rice husk hydrolysate provided 30% higher riboflavin yields compared to glucose in the bioreactors.
Collapse
Affiliation(s)
- Fernando Pérez-García
- Department of Biotechnology and Food Science, Faculty of Natural Sciences, Norwegian University of Science and Technology, Trondheim, Norway
| | - Luciana Fernandes Brito
- Department of Biotechnology and Food Science, Faculty of Natural Sciences, Norwegian University of Science and Technology, Trondheim, Norway
| | - Thea Isabel Bakken
- Department of Biotechnology and Food Science, Faculty of Natural Sciences, Norwegian University of Science and Technology, Trondheim, Norway
| | - Trygve Brautaset
- Department of Biotechnology and Food Science, Faculty of Natural Sciences, Norwegian University of Science and Technology, Trondheim, Norway
| |
Collapse
|
5
|
Maslanka R, Przywara M, Janeczko A, Zadrag-Tecza R. Microbial cell autofluorescence as a method for measuring the intracellular content of B2 and B6 vitamins. INT J VITAM NUTR RES 2024; 94:334-341. [PMID: 37859397 DOI: 10.1024/0300-9831/a000796] [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: 10/21/2023]
Abstract
Vitamins are important organic compound required for the proper functioning of cells and organisms. Vitamins of special industrial and pharmaceutical interests include riboflavin (vitamin B2) and pyridoxine (vitamin B6). Commercial production of those biological compounds has increasingly relied on microorganisms and requires simple methods for detecting and estimating their level of synthesis during the biotechnological process. In the case of yeast, methods based on autofluorescence, i.e. natural fluorescence emitted by several cellular compounds, including vitamins, may be useful. Considering that the intensity of emitted light is proportional to the intracellular concentration of riboflavin and pyridoxine, autofluorescence may be a convenient method for their quantification. In this report, we demonstrate a simple, rapid, and sufficiently trustworthy spectrofluorimetric method for determining the content of vitamins B2 and B6 in yeast cells which consists of cells growing, harvesting, washing, and resuspending in a buffer, and then measuring the emitted visible light using specific wavelength of excitation (λex=340 nm and λem=385 nm for pyridoxine; λex=460 nm and λem=535 nm for riboflavin). The limits of detection (LOD) and quantification (LOQ) estimated through measurements of vitamin fluorescence were below 0.005 μg/ml for riboflavin and below 0.05 μg/ml for pyridoxine, respectively. In turn, the smallest credible cell density for measuring autofluorescence was set at 1×108 yeast cells/ml. The relative level of the cell's autofluorescence can be expressed in mass units by applying proper calculation formulas. A comparison of the autofluorescence-based method with the reference HPLC-UV method shows that autofluorescence measurement can be used in the screening analysis of vitamin content (especially riboflavin) in microbial cells.
Collapse
Affiliation(s)
- Roman Maslanka
- Institute of Biology, College of Natural Sciences, University of Rzeszow, Poland
| | - Michał Przywara
- Institute of Biology, College of Natural Sciences, University of Rzeszow, Poland
| | - Agnieszka Janeczko
- Institute of Biology, College of Natural Sciences, University of Rzeszow, Poland
| | - Renata Zadrag-Tecza
- Institute of Biology, College of Natural Sciences, University of Rzeszow, Poland
| |
Collapse
|
6
|
Walgraeve J, Ferrero-Bordera B, Maaß S, Becher D, Schwerdtfeger R, van Dijl JM, Seefried M. Diamide-based screening method for the isolation of improved oxidative stress tolerance phenotypes in Bacillus mutant libraries. Microbiol Spectr 2023; 11:e0160823. [PMID: 37819171 PMCID: PMC10714788 DOI: 10.1128/spectrum.01608-23] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Accepted: 08/30/2023] [Indexed: 10/13/2023] Open
Abstract
IMPORTANCE During their life cycle, bacteria are exposed to a range of different stresses that need to be managed appropriately in order to ensure their growth and viability. This applies not only to bacteria in their natural habitats but also to bacteria employed in biotechnological production processes. Oxidative stress is one of these stresses that may originate either from bacterial metabolism or external factors. In biotechnological settings, it is of critical importance that production strains are resistant to oxidative stresses. Accordingly, this also applies to the major industrial cell factory Bacillus subtilis. In the present study, we, therefore, developed a screen for B. subtilis strains with enhanced oxidative stress tolerance. The results show that our approach is feasible and time-, space-, and resource-efficient. We, therefore, anticipate that it will enhance the development of more robust industrial production strains with improved robustness under conditions of oxidative stress.
Collapse
Affiliation(s)
| | | | - Sandra Maaß
- Department of Microbial Proteomics, University of Greifswald, Greifswald, Germany
| | - Dörte Becher
- Department of Microbial Proteomics, University of Greifswald, Greifswald, Germany
| | | | - Jan Maarten van Dijl
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | | |
Collapse
|
7
|
Lin H, Li P, Ma L, Lai S, Sun S, Hu K, Zhang L. Analysis and modification of central carbon metabolism in Hypsizygus marmoreus for improving mycelial growth performance and fruiting body yield. Front Microbiol 2023; 14:1233512. [PMID: 37560516 PMCID: PMC10407233 DOI: 10.3389/fmicb.2023.1233512] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Accepted: 07/03/2023] [Indexed: 08/11/2023] Open
Abstract
Hypsizygus marmoreus is one of the main industrially cultivated varieties of edible fungi, with a delicious taste and high nutritional value. However, the long harvest period of 130-150 days greatly limits its large-scale expansion. This study aimed to investigate the effects of central carbon metabolism (CCM) on the mycelial growth performance and fruiting body formation of H. marmoreus. Nine edible fungi with different harvest periods were collected and used to evaluate their intracellular carbon metabolic differences in the CCM, which revealed that the imbalanced distribution of intracellular carbon metabolic levels in the CCM of H. marmoreus might be one of the key factors resulting in a slow mycelial growth rate and a long harvest period. Further analysis by three strategies, including metabolomics, adaptation of different carbon sources, and chemical interference, confirmed that low carbon flux into the pentose phosphate pathway (PPP) limited the supply of raw materials, reduced power, and thus influenced the mycelial growth of H. marmoreus. Furthermore, four transformants with increased expression levels of glucose-6-phosphate dehydrogenase (G6PDH), a key rate-limiting enzyme in the PPP of H. marmoreus, were developed and showed more extracellular soluble protein secretion and higher sugar assimilation rates, as well as improved mycelial growth rates in bottle substrate mixtures. Finally, cultivation experiments indicated that the maturation periods of the fruiting body with ~4-5 days in advance and the maximum fruiting body yield of 574.8 g per bag with an increase of 7.4% were achieved by improving the G6PDH expression level of the PPP in H. marmoreus. This study showed that CCM played an important role in the mycelial growth and development of H. marmoreus, which provided new insights for future advancements in cultivating and breeding edible fungi.
Collapse
Affiliation(s)
- Hui Lin
- Department of Bioengineering, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
- Institute of Edible Fungi, Fujian Academy of Agricultural Sciences, Fuzhou, Fujian, China
| | - Pengfei Li
- Department of Bioengineering, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Lu Ma
- Institute of Edible Fungi, Fujian Academy of Agricultural Sciences, Fuzhou, Fujian, China
| | - Shufang Lai
- Fujian Edible Fungus Technology Promotion General Station, Fuzhou, Fujian, China
| | - Shujing Sun
- Department of Bioengineering, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Kaihui Hu
- Department of Bioengineering, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Liaoyuan Zhang
- Department of Bioengineering, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| |
Collapse
|
8
|
Liu Y, Zhang Q, Qi X, Gao H, Wang M, Guan H, Yu B. Metabolic Engineering of Bacillus subtilis for Riboflavin Production: A Review. Microorganisms 2023; 11:microorganisms11010164. [PMID: 36677456 PMCID: PMC9863419 DOI: 10.3390/microorganisms11010164] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 12/30/2022] [Accepted: 01/02/2023] [Indexed: 01/11/2023] Open
Abstract
Riboflavin (vitamin B2) is one of the essential vitamins that the human body needs to maintain normal metabolism. Its biosynthesis has become one of the successful models for gradual replacement of traditional chemical production routes. B. subtilis is characterized by its short fermentation time and high yield, which shows a huge competitive advantage in microbial fermentation for production of riboflavin. This review summarized the advancements of regulation on riboflavin production as well as the synthesis of two precursors of ribulose-5-phosphate riboflavin (Ru5P) and guanosine 5'-triphosphate (GTP) in B. subtilis. The different strategies to improve production of riboflavin by metabolic engineering were also reviewed.
Collapse
Affiliation(s)
- Yang Liu
- Key Laboratory of Biofuels and Biochemical Engineering, SINOPEC (Dalian) Research Institute of Petroleum and Petro-Chemicals Co., Ltd., Dalian 116045, China
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Quan Zhang
- Key Laboratory of Biofuels and Biochemical Engineering, SINOPEC (Dalian) Research Institute of Petroleum and Petro-Chemicals Co., Ltd., Dalian 116045, China
- Correspondence: (Q.Z.); (B.Y.)
| | - Xiaoxiao Qi
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- School of Life Science, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Huipeng Gao
- Key Laboratory of Biofuels and Biochemical Engineering, SINOPEC (Dalian) Research Institute of Petroleum and Petro-Chemicals Co., Ltd., Dalian 116045, China
| | - Meng Wang
- Key Laboratory of Biofuels and Biochemical Engineering, SINOPEC (Dalian) Research Institute of Petroleum and Petro-Chemicals Co., Ltd., Dalian 116045, China
| | - Hao Guan
- Key Laboratory of Biofuels and Biochemical Engineering, SINOPEC (Dalian) Research Institute of Petroleum and Petro-Chemicals Co., Ltd., Dalian 116045, China
| | - Bo Yu
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- Correspondence: (Q.Z.); (B.Y.)
| |
Collapse
|
9
|
Li Y, Li Y, Chen Y, Cheng M, Yu H, Song H, Cao Y. Coupling riboflavin de novo biosynthesis and cytochrome expression for improving extracellular electron transfer efficiency in Shewanella oneidensis. Biotechnol Bioeng 2022; 119:2806-2818. [PMID: 35798677 DOI: 10.1002/bit.28172] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 07/01/2022] [Accepted: 07/06/2022] [Indexed: 11/06/2022]
Abstract
Shewanella oneidensis MR-1, as a model exoelectrogen with divergent extracellular electron transfer (EET) pathways, has been widely used in microbial fuel cells (MFCs). The electron transfer rate is largely determined by riboflavin (RF) and c-type cytochromes (c-Cyts). However, relatively low RF production and inappropriate amount of c-Cyts substantially impedes the capacity of improving the EET rate. In this work, coupling of riboflavin de novo biosynthesis and c-Cyts expression was implemented to enhance the efficiency of EET in S. oneidensis. Firstly, the upstream pathway of RF de novo biosynthesis was divided into four modules, and the expression level of 22 genes in above four modules was fine-tuned by employing promoters with different strength. Among them, genes zwf*, glyA, ybjU which exhibited the optimal RF production were combinatorially overexpressed, leading to enhancement of maximum output power density by 166%. Secondly, the diverse c-Cyts genes were overexpressed to match high RF production, and omcA was selected for further combination. Thirdly, RF de novo biosynthesis and c-Cyts expression were combined, resulting in 2.34-fold higher power output than the parent strain. This modular and combinatorial manipulation strategy provides a generalized reference to advance versatile practical applications of electroactive microorganisms. This article is protected by copyright. All rights reserved.
Collapse
Affiliation(s)
- Yan Li
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, China.,Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, 300072, China
| | - Yuanyuan Li
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, China.,Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, 300072, China
| | - Yaru Chen
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, China.,Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, 300072, China
| | - Meijie Cheng
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, China.,Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, 300072, China
| | - Huan Yu
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, China.,Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, 300072, China
| | - Hao Song
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, China.,Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, 300072, China
| | - Yingxiu Cao
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, China.,Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, 300072, China
| |
Collapse
|
10
|
You J, Du Y, Pan X, Zhang X, Yang T, Rao Z. Increased Production of Riboflavin by Coordinated Expression of Multiple Genes in Operons in Bacillus subtilis. ACS Synth Biol 2022; 11:1801-1810. [PMID: 35467340 DOI: 10.1021/acssynbio.1c00640] [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] [Indexed: 11/28/2022]
Abstract
Riboflavin is an essential vitamin widely used in the food, pharmaceutical, and feed industries. However, the insufficient supply of precursors caused by the imbalance of intracellular metabolic flow limits the riboflavin synthesis by industrial strains. Here, we increase riboflavin production by tuning multiple gene expression to balance intracellular metabolic flow. First, we tuned the expression of mCherry and egfp genes within operons by generating libraries of tunable intergenic regions (TIGRs) and confirmed the relative expression of the two reporter genes. The TIGR library can coordinate the expression ratio of reporter genes more than 180 times in Escherichia coli and more than 70 times in Bacillus subtilis. Next, we used this strategy to tune the expression of zwf, ribBA, and ywlf genes within operons through the TIGR library to increase the intracellular precursor pool for riboflavin biosynthesis. Based on the fluorescence characteristics of riboflavin, 96-well plates were used to screen the optimal combination mutants quickly. The best-engineered strain was selected from the library, which produced 2.7 g/L riboflavin, increasing by 64.35% in the shake flask. Finally, the riboflavin titer increased by 59.27% to 11.77 g/L in fed-batch fermentation. The strategy described here will contribute to the industrial production of riboflavin and related products by B. subtilis.
Collapse
Affiliation(s)
- Jiajia You
- Key Laboratory of Industrial Biotechnology of the Ministry of Education, Laboratory of Applied Microorganisms and Metabolic Engineering, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Yuxuan Du
- Key Laboratory of Industrial Biotechnology of the Ministry of Education, Laboratory of Applied Microorganisms and Metabolic Engineering, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Xuewei Pan
- Key Laboratory of Industrial Biotechnology of the Ministry of Education, Laboratory of Applied Microorganisms and Metabolic Engineering, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Xian Zhang
- Key Laboratory of Industrial Biotechnology of the Ministry of Education, Laboratory of Applied Microorganisms and Metabolic Engineering, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Taowei Yang
- Key Laboratory of Industrial Biotechnology of the Ministry of Education, Laboratory of Applied Microorganisms and Metabolic Engineering, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Zhiming Rao
- Key Laboratory of Industrial Biotechnology of the Ministry of Education, Laboratory of Applied Microorganisms and Metabolic Engineering, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| |
Collapse
|
11
|
Co-Overexpression of RIB1 and RIB6 Increases Riboflavin Production in the Yeast Candida famata. FERMENTATION 2022. [DOI: 10.3390/fermentation8040141] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Riboflavin or vitamin B2 is a water-soluble vitamin and a precursor of flavin coenzymes, flavin mononucleotide, and flavin adenine dinucleotide, which play a key role as enzyme cofactors in energy metabolism. Candida famata yeast is a promising producer of riboflavin, as it belongs to the group of so-called flavinogenic yeasts, capable of riboflavin oversynthesis under conditions of iron starvation. The role of the particular structural genes in the limitation of riboflavin oversynthesis is not known. To study the impact of overexpression of the structural genes of riboflavin synthesis on riboflavin production, a set of plasmids containing genes RIB1, RIB6, and RIB7 in different combinations was constructed. The transformants of the wild-type strain of C. famata, as well as riboflavin overproducer, were obtained, and the synthesis of riboflavin was studied. It was found that overexpression of RIB1 and RIB6 genes coding for enzymes GTP cyclohydrolase II and 3,4-dihydroxy-2-butanone-4-phosphate synthase, which catalase the initial steps of riboflavin synthesis, elevated riboflavin production by 13–28% relative to the parental riboflavin-overproducing strains.
Collapse
|
12
|
Xu J, Wang C, Ban R. Improving riboflavin production by modifying related metabolic pathways in Bacillus subtilis. Lett Appl Microbiol 2021; 74:78-83. [PMID: 34704264 DOI: 10.1111/lam.13584] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 09/07/2021] [Accepted: 09/25/2021] [Indexed: 12/01/2022]
Abstract
Riboflavin is a feed additive, food additive and clinical drug, with a significant annual demand of nearly 8000 t. Fermentation using recombinant Bacillus subtilis is currently one of the most important industrial production method for riboflavin. First, a suitable medium was selected and the expression of the ureABC operon was modified. The ykgB gene was overexpressed in B. subtilis RX10, the production of the derivative strain RX20 was increased to 4·61 g l-1 riboflavin, and the yield was increased to 52 mg riboflavin g-1 glucose. The relative transcription level of pyr operon in RX20 was reduced to 71%, the production of the derivative strain RX21 was increased to 5·82 g l-1 riboflavin, and the yield was 76 mg riboflavin g-1 glucose. The start codon of the pyrE gene in RX21 was modified to 'TTG', the production of the derivative strain RX22 was increased to 7·01 g l-1 riboflavin, and the yield was 89 mg riboflavin g-1 glucose. These results indicated that overexpression of the ykgB gene and reduction of the metabolic flux of de novo synthesis of pyrimidine nucleotides were beneficial to the synthesis of riboflavin.
Collapse
Affiliation(s)
- J Xu
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, People's Republic of China
| | - C Wang
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, People's Republic of China
| | - R Ban
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, People's Republic of China
| |
Collapse
|
13
|
Liu S, Hu W, Wang Z, Chen T. Rational Engineering of Escherichia coli for High-Level Production of Riboflavin. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2021; 69:12241-12249. [PMID: 34623820 DOI: 10.1021/acs.jafc.1c04471] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Riboflavin is widely used as a food additive. Here, multiple strategies were used to increase riboflavin production in Escherichia coli LS31T. First, purR deletion and co-overexpression of fbp, purF, prs, gmk, and ndk genes resulted in an increase of 18.6% in riboflavin titer (reaching 729.7 mg/L). Second, optimization of reduced nicotinamide adenine dinucleotide phosphate/nicotinamide adenine dinucleotide ratio and respiratory chain activity in LS31T increased the titer up to 1020.2 mg/L. Third, the expression level of the guaC gene in LS31T was downregulated by ribosome binding site replacement, and the riboflavin production was increased by 10.6% to 658.5 mg/L. Then, all the favorable modifications were integrated together, and the resulting strain LS72T produced 1339 mg/L of riboflavin. Moreover, the riboflavin titer of LS72T reached 21 g/L in fed-batch cultivation, with a yield of 110 mg riboflavin/g glucose. To our knowledge, both the riboflavin titer and yield obtained in fed-batch fermentation are the highest ones among all the rationally engineered strains.
Collapse
Affiliation(s)
- Shuang Liu
- School of Chemical Engineering and Technology, Tianjin University, Tianjin 300350, China
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin 300072, China
- SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering, Tianjin 300072, China
| | - Wenya Hu
- School of Chemical Engineering and Technology, Tianjin University, Tianjin 300350, China
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin 300072, China
- SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering, Tianjin 300072, China
| | - Zhiwen Wang
- School of Chemical Engineering and Technology, Tianjin University, Tianjin 300350, China
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin 300072, China
- SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering, Tianjin 300072, China
| | - Tao Chen
- School of Chemical Engineering and Technology, Tianjin University, Tianjin 300350, China
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin 300072, China
- SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering, Tianjin 300072, China
| |
Collapse
|
14
|
You J, Pan X, Yang C, Du Y, Osire T, Yang T, Zhang X, Xu M, Xu G, Rao Z. Microbial production of riboflavin: Biotechnological advances and perspectives. Metab Eng 2021; 68:46-58. [PMID: 34481976 DOI: 10.1016/j.ymben.2021.08.009] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 08/19/2021] [Accepted: 08/31/2021] [Indexed: 10/24/2022]
Abstract
Riboflavin is an essential nutrient for humans and animals, and its derivatives flavin mononucleotide (FMN) and flavin adenine dinucleotide (FAD) are cofactors in the cells. Therefore, riboflavin and its derivatives are widely used in the food, pharmaceutical, nutraceutical and cosmetic industries. Advances in biotechnology have led to a complete shift in the commercial production of riboflavin from chemical synthesis to microbial fermentation. In this review, we provide a comprehensive review of biotechnologies that enhance riboflavin production in microorganisms, as well as representative examples. Firstly, the synthesis pathways and metabolic regulatory processes of riboflavin in microorganisms; and the current strategies and methods of metabolic engineering for riboflavin production are systematically summarized and compared. Secondly, the using of systematic metabolic engineering strategies to enhance riboflavin production is discussed, including laboratory evolution, histological analysis and high-throughput screening. Finally, the challenges for efficient microbial production of riboflavin and the strategies to overcome these challenges are prospected.
Collapse
Affiliation(s)
- Jiajia You
- Key Laboratory of Industrial Biotechnology of the Ministry of Education, Laboratory of Applied Microorganisms and Metabolic Engineering, School of Biotechnology, Jiangnan University, Wuxi, 214122, China
| | - Xuewei Pan
- Key Laboratory of Industrial Biotechnology of the Ministry of Education, Laboratory of Applied Microorganisms and Metabolic Engineering, School of Biotechnology, Jiangnan University, Wuxi, 214122, China
| | - Chen Yang
- Key Laboratory of Industrial Biotechnology of the Ministry of Education, Laboratory of Applied Microorganisms and Metabolic Engineering, School of Biotechnology, Jiangnan University, Wuxi, 214122, China
| | - Yuxuan Du
- Key Laboratory of Industrial Biotechnology of the Ministry of Education, Laboratory of Applied Microorganisms and Metabolic Engineering, School of Biotechnology, Jiangnan University, Wuxi, 214122, China
| | - Tolbert Osire
- Key Laboratory of Industrial Biotechnology of the Ministry of Education, Laboratory of Applied Microorganisms and Metabolic Engineering, School of Biotechnology, Jiangnan University, Wuxi, 214122, China
| | - Taowei Yang
- Key Laboratory of Industrial Biotechnology of the Ministry of Education, Laboratory of Applied Microorganisms and Metabolic Engineering, School of Biotechnology, Jiangnan University, Wuxi, 214122, China
| | - Xian Zhang
- Key Laboratory of Industrial Biotechnology of the Ministry of Education, Laboratory of Applied Microorganisms and Metabolic Engineering, School of Biotechnology, Jiangnan University, Wuxi, 214122, China
| | - Meijuan Xu
- Key Laboratory of Industrial Biotechnology of the Ministry of Education, Laboratory of Applied Microorganisms and Metabolic Engineering, School of Biotechnology, Jiangnan University, Wuxi, 214122, China
| | - Guoqiang Xu
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi, Jiangsu, 214122, China; National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi, Jiangsu, 214122, China; Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY, 12180, United States; Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, Wuxi, 214122, China
| | - Zhiming Rao
- Key Laboratory of Industrial Biotechnology of the Ministry of Education, Laboratory of Applied Microorganisms and Metabolic Engineering, School of Biotechnology, Jiangnan University, Wuxi, 214122, China.
| |
Collapse
|
15
|
You J, Yang C, Pan X, Hu M, Du Y, Osire T, Yang T, Rao Z. Metabolic engineering of Bacillus subtilis for enhancing riboflavin production by alleviating dissolved oxygen limitation. BIORESOURCE TECHNOLOGY 2021; 333:125228. [PMID: 33957462 DOI: 10.1016/j.biortech.2021.125228] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 04/23/2021] [Accepted: 04/25/2021] [Indexed: 06/12/2023]
Abstract
Riboflavin, an essential vitamin for animals, is used widely in the pharmaceutical industry and as a food and feed additive. The microbial synthesis of riboflavin requires a large amount of oxygen, which limits the industrial-scale production of the vitamin. In this study, a metabolic engineering strategy based on transcriptome analysis was identified as effective in increasing riboflavin production. First, transcriptional profiling revealed that hypoxia affects purine, and nitrogen metabolism. Next, the precursor supply pool was increased by purR knockout and tnrA and glnR knockdown to balance intracellular nitrogen metabolism. Finally, increased oxygen utilization was achieved by dynamically regulating vgb. Fed-batch fermentation of the engineered strain in a 5-liter bioreactor produced 10.71 g/l riboflavin, a 45.51% higher yield than that obtained with Bacillus subtilis RF1. The metabolic engineering strategy described herein is useful for alleviating the oxygen limitation of bacterial strains used for the industrial production of riboflavin and related products.
Collapse
Affiliation(s)
- Jiajia You
- Key Laboratory of Industrial Biotechnology of the Ministry of Education, Laboratory of Applied Microorganisms and Metabolic Engineering, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Chen Yang
- Key Laboratory of Industrial Biotechnology of the Ministry of Education, Laboratory of Applied Microorganisms and Metabolic Engineering, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Xuewei Pan
- Key Laboratory of Industrial Biotechnology of the Ministry of Education, Laboratory of Applied Microorganisms and Metabolic Engineering, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Mengkai Hu
- Key Laboratory of Industrial Biotechnology of the Ministry of Education, Laboratory of Applied Microorganisms and Metabolic Engineering, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Yuxuan Du
- Key Laboratory of Industrial Biotechnology of the Ministry of Education, Laboratory of Applied Microorganisms and Metabolic Engineering, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Tolbert Osire
- Key Laboratory of Industrial Biotechnology of the Ministry of Education, Laboratory of Applied Microorganisms and Metabolic Engineering, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Taowei Yang
- Key Laboratory of Industrial Biotechnology of the Ministry of Education, Laboratory of Applied Microorganisms and Metabolic Engineering, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Zhiming Rao
- Key Laboratory of Industrial Biotechnology of the Ministry of Education, Laboratory of Applied Microorganisms and Metabolic Engineering, School of Biotechnology, Jiangnan University, Wuxi 214122, China.
| |
Collapse
|
16
|
Yang B, Sun Y, Fu S, Xia M, Su Y, Liu C, Zhang C, Zhang D. Improving the Production of Riboflavin by Introducing a Mutant Ribulose 5-Phosphate 3-Epimerase Gene in Bacillus subtilis. Front Bioeng Biotechnol 2021; 9:704650. [PMID: 34395408 PMCID: PMC8359813 DOI: 10.3389/fbioe.2021.704650] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Accepted: 05/25/2021] [Indexed: 11/17/2022] Open
Abstract
Ribulose 5-phosphate (Ru5P) and guanosine 5′-triphosphate (GTP) are two key precursors of riboflavin, whereby Ru5P is also a precursor of GTP. Ribulose 5-phosphate 3-epimerase (Rpe) catalyzes the conversion of ribulose 5-phosphate into xylulose 5-phosphate. Inactivation of Rpe can reduce the consumption of Ru5P, enhancing the carbon flux toward riboflavin biosynthesis. Here we investigated the effect of mutation of rpe and other related genes on riboflavin production, physiological and metabolic phenotypes in Bacillus subtilis LY (BSLY). Introducing single nucleotide deletion (generated BSR) or nonsense mutation (generated BSRN) on the genomic copy of rpe, resulting in more than fivefold increase of riboflavin production over the parental strain. BSR process 62% Rpe activity, while BSRN lost the entire Rpe activity and had a growth defect compared with the parent strain. BSR and BSRN exhibited increases of the inosine and guanine titers, in addition, BSRN exhibited an increase of inosine 5′-monophosphate titer in fermentation. The transcription levels of most oxidative pentose phosphate pathway and purine synthesis genes were unchanged in BSR, except for the levels of zwf and ndk, which were higher than in BSLY. The production of riboflavin was increased to 479.90 ± 33.21 mg/L when ribA was overexpressed in BSR. The overexpression of zwf, gntZ, prs, and purF also enhanced the riboflavin production. Finally, overexpression of the rib operon by the pMX45 plasmid and mutant gnd by pHP03 plasmid in BSR led to a 3.05-fold increase of the riboflavin production (977.29 ± 63.44 mg/L), showing the potential for further engineering of this strain.
Collapse
Affiliation(s)
- Bin Yang
- School of Biological Engineering, Dalian Polytechnic University, Dalian, China.,Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Yiwen Sun
- School of Biological Engineering, Dalian Polytechnic University, Dalian, China.,Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Shouying Fu
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China.,College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China
| | - Miaomiao Xia
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China.,Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Yuan Su
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China.,College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China
| | - Chuan Liu
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China.,Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Chunzhi Zhang
- School of Biological Engineering, Dalian Polytechnic University, Dalian, China
| | - Dawei Zhang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China.,Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, China.,University of Chinese Academy of Sciences, Beijing, China
| |
Collapse
|
17
|
Ryhan Bashandy S, Hemida Abd-Alla M, Mahmoud GAE. Using fermentation waste of ethanol-producing yeast for bacterial riboflavin production and recycling of spent bacterial mass for enhancing the growth of oily plants. J Appl Microbiol 2021; 132:2020-2033. [PMID: 34265162 DOI: 10.1111/jam.15221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Revised: 03/24/2021] [Accepted: 07/12/2021] [Indexed: 11/29/2022]
Abstract
AIM This study aims to use fermentation waste of ethanol production (solid and liquid) for riboflavin and recycling of bacterial biomass as biofertilizers to enhance the growth of some oily crop plants. METHODS AND RESULTS Out of ten yeast isolates from fresh milk, Clavispora lusitaniae ASU 33 (MN583181) was able to ferment different concentrations of glucose (2.5, 5, 7.5, 10, 15, and 20 %) into ethanol with high efficiency at 10%. Among seven non-Lactobacillus bacterial isolates recovered from cheese samples, two bacterial isolates Bacillus subtlis-SR2 (MT002768) and Novosphingobium panipatense-SR3 (MT002778) were selected for their high riboflavin production. Different media (control medium, fermentation waste medium, and a mixture of the fermentation waste medium and control medium (1:1)) were used for riboflavin production. These media were inoculated by a single or mixture of B. subtlis-SR2, N. panipatense-SR3. The addition of the waste medium of ethanol production to the control medium (1:1) had a stimulatory effect on riboflavin production whether inoculated either with a single strain or mixture of B. subtlis-SR2, N. panipatense-SR3. A mixture of fermentation waste and control media inoculated with N. panipatense produced a high riboflavin yield in comparison with other media. Inoculation of Zea mays and Ocimum basilicum plants either with the bacterial biomass waste of riboflavin production (B. subtlis or N. panipatense or a mixture of B. subtlis and N. panipatense) shows a stimulatory effect on the plant growth in comparison with control (uninoculated plants). CONCLUSIONS These results demonstrate the possibility of minimizing the cost of riboflavin and biofertilizer manufacturing via interlinking ethanol and riboflavin with the biofertilizer production technology. SIGNIFICANCE AND IMPACT OF STUDY This study outlines methods of evaluating the strength of spent media by applying procedures developed in the vitamins production industries. Furthermore, bacterial biomass waste can act as an environmentally friendly alternative for agrochemicals.
Collapse
Affiliation(s)
- Shymaa Ryhan Bashandy
- Botany and Microbiology Department, Faculty of Science, Assiut University, Assiut, 71516, Egypt
| | - Mohamed Hemida Abd-Alla
- Botany and Microbiology Department, Faculty of Science, Assiut University, Assiut, 71516, Egypt
| | | |
Collapse
|
18
|
Hoff B, Plassmeier J, Blankschien M, Letzel AC, Kourtz L, Schröder H, Koch W, Zelder O. Unlocking Nature's Biosynthetic Power-Metabolic Engineering for the Fermentative Production of Chemicals. Angew Chem Int Ed Engl 2021; 60:2258-2278. [PMID: 33026132 DOI: 10.1002/anie.202004248] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Revised: 07/08/2020] [Indexed: 01/03/2023]
Abstract
Fermentation as a production method for chemicals is especially attractive, as it is based on cheap renewable raw materials and often exhibits advantages in terms of costs and sustainability. The tremendous development of technology in bioscience has resulted in an exponentially increasing knowledge about biological systems and has become the main driver for innovations in the field of metabolic engineering. Progress in recombinant DNA technology, genomics, and computational methods open new, cheaper, and faster ways to metabolically engineer microorganisms. Existing biosynthetic pathways for natural products, such as vitamins, organic acids, amino acids, or secondary metabolites, can be discovered and optimized efficiently, thereby enabling competitive commercial production processes. Novel biosynthetic routes can now be designed by the rearrangement of nature's unlimited number of enzymes and metabolic pathways in microbial strains. This expands the range of chemicals accessible by biotechnology and has yielded the first commercial products, while new fermentation technologies targeting novel active ingredients, commodity chemicals, and CO2 -fixation methods are on the horizon.
Collapse
Affiliation(s)
- Birgit Hoff
- RBW, White Biotechnology Research, BASF SE, building: A30, Carl-Bosch-Strasse 38, 67056, Ludwigshafen am Rhein, Germany
| | - Jens Plassmeier
- Biomaterials, Conagen, Inc., 15 DeAngelo Drive, 01730, Bedford, MA, USA
| | - Matthew Blankschien
- James R. Randall Research Center, ADM, 1001 North Brush College Road, 62521, Decatur, Il, USA
| | - Anne-Catrin Letzel
- RBW, White Biotechnology Research, BASF SE, building: A30, Carl-Bosch-Strasse 38, 67056, Ludwigshafen am Rhein, Germany
| | - Lauralynn Kourtz
- R&D, Allied Microbiota, 1345 Ave of Americas, 10105, New York, NY, USA
| | - Hartwig Schröder
- RBW, White Biotechnology Research, BASF SE, building: A30, Carl-Bosch-Strasse 38, 67056, Ludwigshafen am Rhein, Germany
| | - Walter Koch
- RBW, White Biotechnology Research, BASF SE, building: A30, Carl-Bosch-Strasse 38, 67056, Ludwigshafen am Rhein, Germany
| | - Oskar Zelder
- RBW, White Biotechnology Research, BASF SE, building: A30, Carl-Bosch-Strasse 38, 67056, Ludwigshafen am Rhein, Germany
| |
Collapse
|
19
|
Pramastya H, Song Y, Elfahmi EY, Sukrasno S, Quax WJ. Positioning Bacillus subtilis as terpenoid cell factory. J Appl Microbiol 2020; 130:1839-1856. [PMID: 33098223 PMCID: PMC8247319 DOI: 10.1111/jam.14904] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Revised: 09/29/2020] [Accepted: 10/09/2020] [Indexed: 12/16/2022]
Abstract
Increasing demands for bioactive compounds have motivated researchers to employ micro‐organisms to produce complex natural products. Currently, Bacillus subtilis has been attracting lots of attention to be developed into terpenoids cell factories due to its generally recognized safe status and high isoprene precursor biosynthesis capacity by endogenous methylerythritol phosphate (MEP) pathway. In this review, we describe the up‐to‐date knowledge of each enzyme in MEP pathway and the subsequent steps of isomerization and condensation of C5 isoprene precursors. In addition, several representative terpene synthases expressed in B. subtilis and the engineering steps to improve corresponding terpenoids production are systematically discussed. Furthermore, the current available genetic tools are mentioned as along with promising strategies to improve terpenoids in B. subtilis, hoping to inspire future directions in metabolic engineering of B. subtilis for further terpenoid cell factory development.
Collapse
Affiliation(s)
- H Pramastya
- University of Groningen, Groningen, The Netherlands.,Pharmaceutical Biology Research Group, School of Pharmacy, Institut Teknologi Bandung, Bandung, Indonesia
| | - Y Song
- University of Groningen, Groningen, The Netherlands
| | - E Y Elfahmi
- Pharmaceutical Biology Research Group, School of Pharmacy, Institut Teknologi Bandung, Bandung, Indonesia
| | - S Sukrasno
- Pharmaceutical Biology Research Group, School of Pharmacy, Institut Teknologi Bandung, Bandung, Indonesia
| | - W J Quax
- University of Groningen, Groningen, The Netherlands
| |
Collapse
|
20
|
Sun Y, Liu C, Tang W, Zhang D. Manipulation of Purine Metabolic Networks for Riboflavin Production in Bacillus subtilis. ACS OMEGA 2020; 5:29140-29146. [PMID: 33225145 PMCID: PMC7675574 DOI: 10.1021/acsomega.0c03867] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Accepted: 10/06/2020] [Indexed: 06/11/2023]
Abstract
Guanosine monophosphate, the precursor for riboflavin biosynthesis, can be converted to or generated from other purine compounds in purine metabolic networks. In this study, genes in these networks were manipulated in a riboflavin producer, Bacillus subtilis R, to test their contribution to riboflavin biosynthesis. Knocking out adenine phosphoribosyltransferase (apt), xanthine phosphoribosyltransferase (xpt), and adenine deaminase (adeC) increased the riboflavin production by 14.02, 6.78, and 41.50%, respectively, while other deletions in the salvage pathway, interconversion pathway, and nucleoside decomposition genes have no positive effects. The enhancement of riboflavin production in apt and adeC deletion mutants is dependent on the purine biosynthesis regulator PurR. Repression of ribonucleotide reductases (RNRs) led to a 13.12% increase of riboflavin production, which also increased in two RNR regulator mutants PerR and NrdR by 37.52 and 8.09%, respectively. The generation of deoxyribonucleoside competed for precursors with riboflavin biosynthesis, while other pathways do not contribute to the supply of precursors; nevertheless, they have regulatory effects.
Collapse
Affiliation(s)
- Yiwen Sun
- Department
of Biological Sciences, School of Biological Engineering, Dalian Polytechnic University, Dalian 116034, People’s Republic of China
- Tianjin
Institute of Industrial Biotechnology, Chinese
Academy of Sciences, Tianjin 300308, People’s Republic
of China
| | - Chuan Liu
- Tianjin
Institute of Industrial Biotechnology, Chinese
Academy of Sciences, Tianjin 300308, People’s Republic
of China
- Key
Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, People’s Republic
of China
- University
of Chinese Academy of Sciences, Beijing 100049, People’s
Republic of China
| | - Wenzhu Tang
- Department
of Biological Sciences, School of Biological Engineering, Dalian Polytechnic University, Dalian 116034, People’s Republic of China
| | - Dawei Zhang
- Tianjin
Institute of Industrial Biotechnology, Chinese
Academy of Sciences, Tianjin 300308, People’s Republic
of China
- Key
Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, People’s Republic
of China
- University
of Chinese Academy of Sciences, Beijing 100049, People’s
Republic of China
| |
Collapse
|
21
|
Averianova LA, Balabanova LA, Son OM, Podvolotskaya AB, Tekutyeva LA. Production of Vitamin B2 (Riboflavin) by Microorganisms: An Overview. Front Bioeng Biotechnol 2020; 8:570828. [PMID: 33304888 PMCID: PMC7693651 DOI: 10.3389/fbioe.2020.570828] [Citation(s) in RCA: 80] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Accepted: 09/15/2020] [Indexed: 12/30/2022] Open
Abstract
Riboflavin is a crucial micronutrient that is a precursor to coenzymes flavin mononucleotide and flavin adenine dinucleotide, and it is required for biochemical reactions in all living cells. For decades, one of the most important applications of riboflavin has been its global use as an animal and human nutritional supplement. Being well-informed of the latest research on riboflavin production via the fermentation process is necessary for the development of new and improved microbial strains using biotechnology and metabolic engineering techniques to increase vitamin B2 yield. In this review, we describe well-known industrial microbial producers, namely, Ashbya gossypii, Bacillus subtilis, and Candida spp. and summarize their biosynthetic pathway optimizations through genetic and metabolic engineering, combined with random chemical mutagenesis and rational medium components to increase riboflavin production.
Collapse
Affiliation(s)
- Liudmila A. Averianova
- Department of Bioeconomy and Food Security, School of Economics and Management, Far Eastern Federal University, Vladivostok, Russia
| | - Larissa A. Balabanova
- Department of Bioeconomy and Food Security, School of Economics and Management, Far Eastern Federal University, Vladivostok, Russia
- Laboratory of Marine Biochemistry, G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch, Russian Academy of Sciences, Vladivostok, Russia
| | - Oksana M. Son
- Department of Bioeconomy and Food Security, School of Economics and Management, Far Eastern Federal University, Vladivostok, Russia
- ARNIKA, Territory of PDA Nadezhdinskaya, Primorsky Krai, Russia
| | - Anna B. Podvolotskaya
- Department of Bioeconomy and Food Security, School of Economics and Management, Far Eastern Federal University, Vladivostok, Russia
- ARNIKA, Territory of PDA Nadezhdinskaya, Primorsky Krai, Russia
| | - Liudmila A. Tekutyeva
- Department of Bioeconomy and Food Security, School of Economics and Management, Far Eastern Federal University, Vladivostok, Russia
- ARNIKA, Territory of PDA Nadezhdinskaya, Primorsky Krai, Russia
| |
Collapse
|
22
|
Hoff B, Plassmeier J, Blankschien M, Letzel A, Kourtz L, Schröder H, Koch W, Zelder O. Unlocking Nature's Biosynthetic Power—Metabolic Engineering for the Fermentative Production of Chemicals. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202004248] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Birgit Hoff
- RBW, White Biotechnology Research BASF SE building: A30, Carl-Bosch-Strasse 38 67056 Ludwigshafen am Rhein Germany
| | - Jens Plassmeier
- Biomaterials Conagen, Inc. 15 DeAngelo Drive 01730 Bedford, MA USA
| | - Matthew Blankschien
- James R. Randall Research Center ADM 1001 North Brush College Road 62521 Decatur, Il USA
| | - Anne‐Catrin Letzel
- RBW, White Biotechnology Research BASF SE building: A30, Carl-Bosch-Strasse 38 67056 Ludwigshafen am Rhein Germany
| | - Lauralynn Kourtz
- R&D Allied Microbiota 1345 Ave of Americas 10105 New York, NY USA
| | - Hartwig Schröder
- RBW, White Biotechnology Research BASF SE building: A30, Carl-Bosch-Strasse 38 67056 Ludwigshafen am Rhein Germany
| | - Walter Koch
- RBW, White Biotechnology Research BASF SE building: A30, Carl-Bosch-Strasse 38 67056 Ludwigshafen am Rhein Germany
| | - Oskar Zelder
- RBW, White Biotechnology Research BASF SE building: A30, Carl-Bosch-Strasse 38 67056 Ludwigshafen am Rhein Germany
| |
Collapse
|
23
|
Peng Z, Mao X, Zhang J, Du G, Chen J. Biotransformation of keratin waste to amino acids and active peptides based on cell-free catalysis. BIOTECHNOLOGY FOR BIOFUELS 2020; 13:61. [PMID: 32266007 PMCID: PMC7110813 DOI: 10.1186/s13068-020-01700-4] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Accepted: 03/24/2020] [Indexed: 06/11/2023]
Abstract
BACKGROUND Keratin is the primary constituent of the vertebrate epidermis and epidermal appendages, as well as the main waste product generated during poultry processing from feathers, hair, scales, nails, etc. Keratin is generally hard, stubborn and difficult to hydrolyze; however, it is also inexpensive and contains more than 85% protein. Currently, tens of millions of tons of keratin waste are produced each year worldwide; however, no effective methods for the recovery of keratin waste have been reported thus far, making such research urgent. Keratinase has been reported to be useful for keratin waste recovery; however, nearly all keratinases are unable to hydrolyze keratin after they are detached from living cell systems. This may be due to low keratinase activity and lack of synergistic factors. RESULTS Herein, the keratinase gene from Bacillus licheniformis BBE11-1 was successfully expressed in Bacillus subtilis WB600, allowing for improved activity of the recombinant keratinase KerZ1 to 45.14 KU/mL via promoter substitution and screening of the ribosome-binding sites. Further, real-time control of temperature, pH, dissolved oxygen, and feed strategy allowed the activity of KerZ1 to reach 426.60 KU/mL in a 15-L fermenter, accounting for a 3552-fold increase compared to the wild-type keratinase (120.1 U/mL). Most importantly, we proposed a method based on the synergistic action of keratinase KerZ1 and sodium sulfite, to hydrolyze feathers into amino acids. In specific, 100 g/L of feather waste can be successfully converted into 56.6% amino acids within 12 h, while supporting the production of dozens of bioactive peptides. CONCLUSIONS The activity of recombinant keratinase can be greatly enhanced via transcription and translational regulation in Bacillus subtilis. The synergistic action of keratinase and sulfite can rapidly degrade feather waste and produce amino acids and polypeptides.
Collapse
Affiliation(s)
- Zheng Peng
- School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122 China
- Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, 1800 Lihu Road, Wuxi, 214122 China
| | - Xinzhe Mao
- School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122 China
- Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, 1800 Lihu Road, Wuxi, 214122 China
| | - Juan Zhang
- School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122 China
- Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, 1800 Lihu Road, Wuxi, 214122 China
| | - Guocheng Du
- School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122 China
- Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, 1800 Lihu Road, Wuxi, 214122 China
| | - Jian Chen
- School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122 China
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122 China
| |
Collapse
|
24
|
Liu S, Hu W, Wang Z, Chen T. Production of riboflavin and related cofactors by biotechnological processes. Microb Cell Fact 2020; 19:31. [PMID: 32054466 PMCID: PMC7017516 DOI: 10.1186/s12934-020-01302-7] [Citation(s) in RCA: 65] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2019] [Accepted: 02/05/2020] [Indexed: 12/15/2022] Open
Abstract
Riboflavin (RF) and its active forms, the cofactors flavin mononucleotide (FMN) and flavin adenine dinucleotide (FAD), have been extensively used in the food, feed and pharmaceutical industries. Modern commercial production of riboflavin is based on microbial fermentation, but the established genetically engineered production strains are facing new challenges due to safety concerns in the food and feed additives industry. High yields of flavin mononucleotide and flavin adenine dinucleotide have been obtained using whole-cell biocatalysis processes. However, the necessity of adding expensive precursors results in high production costs. Consequently, developing microbial cell factories that are capable of efficiently producing flavin nucleotides at low cost is an increasingly attractive approach. The biotechnological processes for the production of RF and its cognate cofactors are reviewed in this article.
Collapse
Affiliation(s)
- Shuang Liu
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072 People’s Republic of China
| | - Wenya Hu
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072 People’s Republic of China
| | - Zhiwen Wang
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072 People’s Republic of China
| | - Tao Chen
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072 People’s Republic of China
| |
Collapse
|
25
|
Advances and prospects of Bacillus subtilis cellular factories: From rational design to industrial applications. Metab Eng 2018; 50:109-121. [DOI: 10.1016/j.ymben.2018.05.006] [Citation(s) in RCA: 115] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2017] [Revised: 05/02/2018] [Accepted: 05/10/2018] [Indexed: 01/29/2023]
|
26
|
Enhancement of Bacitracin Production by NADPH Generation via Overexpressing Glucose-6-Phosphate Dehydrogenase Zwf in Bacillus licheniformis. Appl Biochem Biotechnol 2018; 187:1502-1514. [PMID: 30267286 DOI: 10.1007/s12010-018-2894-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Accepted: 09/10/2018] [Indexed: 12/14/2022]
Abstract
Bacitracin, a kind of cyclic peptide antibiotic mainly produced by Bacillus, has wide ranges of applications. NADPH generation plays an important role in amino acid synthesis, which might influence precursor amino acid supply for bacitracin production. In this study, we want to improve bacitracin yield by enhancing intracellular precursor amino acids via strengthening NAPDH generation pathways in the bacitracin industrial production strain Bacillus licheniformis DW2. Based on our results, strengthening of NADPH pathway genes (zwf, gnd, ppnk, pntAB, and udhA) could all improve bacitracin yields in DW2, and the glucose-6-phosphate dehydrogenase Zwf overexpression strain DW2::Zwf displayed the best performance, the yield of which (886.43 U/mL) was increased by 12.43% compared to DW2 (788.40 U/mL). Then, the zwf transcriptional level and Zwf activity of DW2::Zwf were increased by 12.24-fold and 1.57-fold; NADPH and NADPH/NADH were enhanced by 61.24% and 90.63%, compared with those of DW2, respectively. Moreover, the concentrations of intracellular precursor amino acids (isoleucine, leucine, cysteine, ornithine, lysine, glutamic acid) were all enhanced obviously for bacitracin production in DW2::Zwf. Collectively, this research constructed a promising B. licheniformis strain for industrial production of bacitracin, more importantly, which revealed that strengthening of NADPH generation is an efficient strategy to improve precursor amino acid supplies for bacitracin production.
Collapse
|
27
|
Fan X, Wu H, Jia Z, Li G, Li Q, Chen N, Xie X. Metabolic engineering of Bacillus subtilis for the co-production of uridine and acetoin. Appl Microbiol Biotechnol 2018; 102:8753-8762. [DOI: 10.1007/s00253-018-9316-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Revised: 07/31/2018] [Accepted: 08/08/2018] [Indexed: 01/19/2023]
|
28
|
Integrated whole-genome and transcriptome sequence analysis reveals the genetic characteristics of a riboflavin-overproducing Bacillus subtilis. Metab Eng 2018; 48:138-149. [DOI: 10.1016/j.ymben.2018.05.022] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2018] [Revised: 05/17/2018] [Accepted: 05/31/2018] [Indexed: 11/23/2022]
|
29
|
Autofluorescence of yeast Saccharomyces cerevisiae cells caused by glucose metabolism products and its methodological implications. J Microbiol Methods 2018; 146:55-60. [DOI: 10.1016/j.mimet.2018.01.017] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2017] [Revised: 01/26/2018] [Accepted: 01/26/2018] [Indexed: 11/23/2022]
|
30
|
Yan S, Wu G. Bottleneck in secretion of α-amylase in Bacillus subtilis. Microb Cell Fact 2017; 16:124. [PMID: 28724440 PMCID: PMC5518135 DOI: 10.1186/s12934-017-0738-1] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2017] [Accepted: 07/10/2017] [Indexed: 11/10/2022] Open
Abstract
Amylase plays an important role in biotechnology industries, and Gram-positive bacterium Bacillus subtilis is a major host to produce heterogeneous α-amylases. However, the secretion stress limits the high yield of α-amylase in B. subtilis although huge efforts have been made to address this secretion bottleneck. In this question-oriented review, every effort is made to answer the following questions, which look simple but are long-standing, through reviewing of literature: (1) Does α-amylase need a specific and dedicated chaperone? (2) What signal sequence does CsaA recognize? (3) Does CsaA require ATP for its operation? (4) Does an unfolded α-amylase is less soluble than a folded one? (5) Does α-amylase aggregate before transporting through Sec secretion system? (6) Is α-amylase sufficient stable to prevent itself from misfolding? (7) Does α-amylase need more disulfide bonds to be stabilized? (8) Which secretion system does PrsA pass through? (9) Is PrsA ATP-dependent? (10) Is PrsA reused after folding of α-amylase? (11) What is the fate of PrsA? (12) Is trigger factor (TF) ATP-dependent? The literature review suggests that not only the most of those questions are still open to answers but also it is necessary to calculate ATP budget in order to better understand how B. subtilis uses its energy for production and secretion.
Collapse
Affiliation(s)
- Shaomin Yan
- National Engineering Research Center for Non-food Biorefinery, Guangxi Academy of Sciences, 98 Daling Road, Nanning, 530007, Guangxi, China
| | - Guang Wu
- National Engineering Research Center for Non-food Biorefinery, Guangxi Academy of Sciences, 98 Daling Road, Nanning, 530007, Guangxi, China.
| |
Collapse
|
31
|
Liu L, Xu QM, Chen T, Cheng JS, Yuan YJ. Artificial consortium that produces riboflavin regulates distribution of acetoin and 2,3-butanediol by Paenibacillus polymyxa CJX518. Eng Life Sci 2017; 17:1039-1049. [PMID: 32624854 DOI: 10.1002/elsc.201600239] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2016] [Revised: 05/23/2017] [Accepted: 05/29/2017] [Indexed: 11/09/2022] Open
Abstract
The introduction of an NADH/NAD+ regeneration system can regulate the distribution between acetoin and 2,3-butanediol. NADH regeneration can also enhance butanol production in coculture fermentation. In this work, a novel artificial consortium of Paenibacillus polymyxa CJX518 and recombinant Escherichia coli LS02T that produces riboflavin (VB2) was used to regulate the NADH/NAD+ ratio and, consequently, the distribution of acetoin and 2,3-butanediol by P. polymyxa. Compared with a pure culture of P. polymyxa, the level of acetoin was increased 76.7% in the P. polymyxa and recombinant E. coli coculture. Meanwhile, the maximum production and yield of acetoin in an artificial consortium with fed-batch fermentation were 57.2 g/L and 0.4 g/g glucose, respectively. Additionally, the VB2 production of recombinant E. coli could maintain a relatively low NADH/NAD+ ratio by changing NADH dehydrogenase activity. It was also found that 2,3-butanediol dehydrogenase activity was enhanced and improved acetoin production by the addition of exogenous VB2 or by being in the artificial consortium that produces VB2. These results illustrate that the coculture of P. polymyxa and recombinant E. coli has enormous potential to improve acetoin production. It was also a novel strategy to regulate the NADH/NAD+ ratio to improve the acetoin production of P. polymyxa.
Collapse
Affiliation(s)
- Lei Liu
- Key Laboratory of Systems Bioengineering (Ministry of Education) School of Chemical Engineering and Technology Tianjin University Tianjin People's Republic of China.,SynBio Research Platform Collaborative Innovation Centre of Chemical Science and Engineering (Tianjin) School of Chemical Engineering and Technology Tianjin University Tianjin People's Republic of China
| | - Qiu-Man Xu
- College of Life Science Tianjin Normal University Tianjin People's Republic of China
| | - Tao Chen
- Key Laboratory of Systems Bioengineering (Ministry of Education) School of Chemical Engineering and Technology Tianjin University Tianjin People's Republic of China.,SynBio Research Platform Collaborative Innovation Centre of Chemical Science and Engineering (Tianjin) School of Chemical Engineering and Technology Tianjin University Tianjin People's Republic of China
| | - Jing-Sheng Cheng
- Key Laboratory of Systems Bioengineering (Ministry of Education) School of Chemical Engineering and Technology Tianjin University Tianjin People's Republic of China.,SynBio Research Platform Collaborative Innovation Centre of Chemical Science and Engineering (Tianjin) School of Chemical Engineering and Technology Tianjin University Tianjin People's Republic of China
| | - Ying-Jin Yuan
- Key Laboratory of Systems Bioengineering (Ministry of Education) School of Chemical Engineering and Technology Tianjin University Tianjin People's Republic of China.,SynBio Research Platform Collaborative Innovation Centre of Chemical Science and Engineering (Tianjin) School of Chemical Engineering and Technology Tianjin University Tianjin People's Republic of China
| |
Collapse
|
32
|
Hohmann HP, van Dijl JM, Krishnappa L, Prágai Z. Host Organisms:Bacillus subtilis. Ind Biotechnol (New Rochelle N Y) 2016. [DOI: 10.1002/9783527807796.ch7] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Affiliation(s)
- Hans-Peter Hohmann
- Nutrition Innovation Center R&D Biotechnology; DSM Nutritional Products Ltd; Wurmisweg 576 CH-4303 Kaiseraugst Switzerland
| | - Jan M. van Dijl
- University of Groningen, University Medical Center Groningen; Department of Medical Microbiology; Hanzeplein 1 9700 RB Groningen The Netherlands
| | - Laxmi Krishnappa
- University of Groningen, University Medical Center Groningen; Department of Medical Microbiology; Hanzeplein 1 9700 RB Groningen The Netherlands
| | - Zoltán Prágai
- Nutrition Innovation Center R&D Biotechnology; DSM Nutritional Products Ltd; Wurmisweg 576 CH-4303 Kaiseraugst Switzerland
| |
Collapse
|
33
|
Bioproduction of riboflavin: a bright yellow history. J Ind Microbiol Biotechnol 2016; 44:659-665. [PMID: 27696023 DOI: 10.1007/s10295-016-1842-7] [Citation(s) in RCA: 79] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2016] [Accepted: 09/23/2016] [Indexed: 10/20/2022]
Abstract
Riboflavin (vitamin B2) is an essential nutrient for humans and animals that must be obtained from the diet. To ensure an optimal supply, riboflavin is used on a large scale as additive in the food and feed industries. Here, we describe a historical overview of the industrial process of riboflavin production starting from its discovery and the need to produce the vitamin in bulk at prices that would allow for their use in human and animal nutrition. Riboflavin was produced industrially by chemical synthesis for many decades. At present, the development of economical and eco-efficient fermentation processes, which are mainly based on Bacillus subtilis and Ashbya gossypii strains, has replaced the synthetic process at industrial scale. A detailed account is given of the development of the riboflavin overproducer strains as well as future prospects for its improvement.
Collapse
|
34
|
Wang X, Wang G, Li X, Fu J, Chen T, Wang Z, Zhao X. Directed evolution of adenylosuccinate synthetase from Bacillus subtilis and its application in metabolic engineering. J Biotechnol 2016; 231:115-121. [DOI: 10.1016/j.jbiotec.2016.05.032] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2016] [Revised: 04/18/2016] [Accepted: 05/23/2016] [Indexed: 11/16/2022]
|
35
|
Song Y, Nikoloff JM, Fu G, Chen J, Li Q, Xie N, Zheng P, Sun J, Zhang D. Promoter Screening from Bacillus subtilis in Various Conditions Hunting for Synthetic Biology and Industrial Applications. PLoS One 2016; 11:e0158447. [PMID: 27380260 PMCID: PMC4933340 DOI: 10.1371/journal.pone.0158447] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2016] [Accepted: 06/16/2016] [Indexed: 11/24/2022] Open
Abstract
The use of Bacillus subtilis in synthetic biology and metabolic engineering is highly desirable to take advantage of the unique metabolic pathways present in this organism. To do this, an evaluation of B. subtilis’ intrinsic biological parts is required to determine the best strategies to accurately regulate metabolic circuits and expression of target proteins. The strengths of promoter candidates were evaluated by measuring relative fluorescence units of a green fluorescent protein reporter, integrated into B. subtilis’ chromosome. A total of 84 predicted promoter sequences located upstream of different classes of proteins including heat shock proteins, cell-envelope proteins, and proteins resistant against toxic metals (based on similarity) and other kinds of genes were tested. The expression levels measured ranged from 0.0023 to 4.53-fold of the activity of the well-characterized strong promoter P43. No significant shifts were observed when strains, carrying different promoter candidates, were cultured at high temperature or in media with ethanol, but some strains showed increased activity when cultured under high osmotic pressure. Randomly selected promoter candidates were tested and found to activate transcription of thermostable β-galactosidase (bgaB) at a similar level, implying the ability of these sequences to function as promoter elements in multiple genetic contexts. In addition, selected promoters elevated the final production of both cytoplasmic bgaB and secreted protein α-amylase to about fourfold and twofold, respectively. The generated data allows a deeper understanding of B. subtilis’ metabolism and will facilitate future work to develop this organism for synthetic biology.
Collapse
Affiliation(s)
- Yafeng Song
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, P. R. China
- Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, P. R. China
| | - Jonas M Nikoloff
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, P. R. China
| | - Gang Fu
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, P. R. China
- Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, P. R. China
| | - Jingqi Chen
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, P. R. China
- Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, P. R. China
| | - Qinggang Li
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, P. R. China
- Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, P. R. China
| | - Nengzhong Xie
- National Engineering Research Center for Non-food Biorefinery, State Key Laboratory of Non-food Biomass Energy and Enzyme Technology, Nanning 5300074, P. R. China
- Guangxi Biomass Industrialization Engineering Institute, Guangxi Academy of Sciences, Nanning 530007, P. R. China
| | - Ping Zheng
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, P. R. China
- Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, P. R. China
| | - Jibin Sun
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, P. R. China
- Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, P. R. China
| | - Dawei Zhang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, P. R. China
- Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, P. R. China
| |
Collapse
|
36
|
Liu S, Kang P, Cui Z, Wang Z, Chen T. Increased riboflavin production by knockout of 6-phosphofructokinase I and blocking the Entner-Doudoroff pathway in Escherichia coli. Biotechnol Lett 2016; 38:1307-14. [PMID: 27071937 DOI: 10.1007/s10529-016-2104-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2016] [Accepted: 04/06/2016] [Indexed: 01/30/2023]
Abstract
OBJECTIVES To construct an Escherichia coli strain capable of producing riboflavin with high titer and yield. RESULTS A low copy number plasmid pLS01 containing a riboflavin operon under the control of a constitutive promoter was constructed and introduced into Escherichia coli MG1655. Subsequently, the pfkA, edd and ead genes were disrupted, and the resulting strain LS02T produced 667 mg riboflavin/l in MSY medium supplied with 10 g glucose/l in flask cultivation. In a fed-batch process, riboflavin production of the strain reached 10.4 g/l with a yield of 56.8 mg riboflavin/g glucose. CONCLUSION To our knowledge, this is the first report of engineered E. coli strains that can produce more than 10 g riboflavin/l in fed-batch cultivation, indicating that E. coli has potential for riboflavin production.
Collapse
Affiliation(s)
- Shuang Liu
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, People's Republic of China
| | - Pei Kang
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, People's Republic of China
| | - Zhenzhen Cui
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, People's Republic of China
| | - Zhiwen Wang
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, People's Republic of China
| | - Tao Chen
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, People's Republic of China. .,Key Laboratory of System Bioengineering, Ministry of Education, Tianjin University, Tianjin, 300072, People's Republic of China.
| |
Collapse
|
37
|
Biotechnology of riboflavin. Appl Microbiol Biotechnol 2016; 100:2107-19. [DOI: 10.1007/s00253-015-7256-z] [Citation(s) in RCA: 81] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2015] [Revised: 12/14/2015] [Accepted: 12/17/2015] [Indexed: 10/22/2022]
|
38
|
Qiu Y, Xiao F, Wei X, Wen Z, Chen S. Improvement of lichenysin production in Bacillus licheniformis by replacement of native promoter of lichenysin biosynthesis operon and medium optimization. Appl Microbiol Biotechnol 2014; 98:8895-903. [PMID: 25085615 DOI: 10.1007/s00253-014-5978-y] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2014] [Revised: 07/21/2014] [Accepted: 07/27/2014] [Indexed: 11/29/2022]
Abstract
Lichenysin is a biodegradable surfactant with huge potential for recovering crude oil from the oil reservoir. The current production of lichenysin is made through fermentation from wild strain of Bacillus licheniformis, which is limited by low yield. The aim of this work was to improve lichenysin-producing capability of a wide strain B. licheniformis WX-02. Lichenysin produced from WX-02 was first extracted, purified, and identified. Through the substitution of the promoter of lichenysin biosynthesis operon, the mutants B. licheniformis WX02-P43lch, WX02-Pxyllch, and WX02-Psrflch were constructed with the constitutive promoter (P43), the xylose-inducible promoter (P xyl ), and the surfactin operon promoter (P srf ), respectively. A consistent change trend was observed between lichenysin production and lchAA gene transcription, confirming the strength of the promoters as an important factor for lichenysin synthesis. Among the three mutants, WX02-Psrflch produced the highest lichenysin yield. The production by the mutant WX02-Psrflch was further improved with the optimization of the major medium components including glucose, NH4NO3, and Na2HPO4/KH2PO4. Under 30 g/L glucose, 5 g/L NH4NO3, and 80 mM/60 mM Na2HPO4/KH2PO4, the strain WX02-Psrflch produced 2,149 mg/L lichenysin, a 16.8-fold improvement compared to that of wild strain WX-02.
Collapse
Affiliation(s)
- Yimin Qiu
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | | | | | | | | |
Collapse
|
39
|
Lin Z, Xu Z, Li Y, Wang Z, Chen T, Zhao X. Metabolic engineering of Escherichia coli for the production of riboflavin. Microb Cell Fact 2014; 13:104. [PMID: 25027702 PMCID: PMC4223517 DOI: 10.1186/s12934-014-0104-5] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2014] [Accepted: 07/09/2014] [Indexed: 01/05/2023] Open
Abstract
BACKGROUND Riboflavin (vitamin B2), the precursor of the flavin cofactors flavin mononucleotide (FMN) and flavin adenine dinucleotide (FAD), is used commercially as an animal feed supplement and food colorant. E. coli is a robust host for various genetic manipulations and has been employed for efficient production of biofuels, polymers, amino acids, and bulk chemicals. Thus, the aim of this study was to understand the metabolic capacity of E. coli for the riboflavin production by modification of central metabolism, riboflavin biosynthesis pathway and optimization of the fermentation conditions. RESULTS The basic producer RF01S, in which the riboflavin biosynthesis genes ribABDEC from E. coli were overexpressed under the control of the inducible trc promoter, could accumulate 229.1 mg/L of riboflavin. Further engineering was performed by examining the impact of expression of zwf (encodes glucose 6-phosphate dehydrogenase) and gnd (encodes 6-phosphogluconate dehydrogenase) from Corynebacterium glutamicum and pgl (encodes 6-phosphogluconolactonase) from E. coli on riboflavin production. Deleting pgi (encodes glucose-6-phosphate isomerase) and genes of Entner-Doudoroff (ED) pathway successfully redirected the carbon flux into the oxidative pentose phosphate pathway, and overexpressing the acs (encodes acetyl-CoA synthetase) reduced the acetate accumulation. These modifications increased riboflavin production to 585.2 mg/L. By further modulating the expression of ribF (encodes riboflavin kinase) for reducing the conversion of riboflavin to FMN in RF05S, the final engineering strain RF05S-M40 could produce 1036.1 mg/L riboflavin in LB medium at 37°C. After optimizing the fermentation conditions, strain RF05S-M40 produced 2702.8 mg/L riboflavin in the optimized semi-defined medium, which was a value nearly 12-fold higher than that of RF01S, with a yield of 137.5 mg riboflavin/g glucose. CONCLUSIONS The engineered strain RF05S-M40 has the highest yield among all reported riboflavin production strains in shake flask culture. This work collectively demonstrates that E. coli has a potential to be a microbial cell factory for riboflavin bioproduction.
Collapse
Affiliation(s)
- Zhenquan Lin
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, People’s Republic of China
- Key Laboratory of Systems Bioengineering, Ministry of Education, Tianjin University, Tianjin 300072, People’s Republic of China
- Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin University, Tianjin 300072, People’s Republic of China
| | - Zhibo Xu
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, People’s Republic of China
- Key Laboratory of Systems Bioengineering, Ministry of Education, Tianjin University, Tianjin 300072, People’s Republic of China
- Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin University, Tianjin 300072, People’s Republic of China
| | - Yifan Li
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, People’s Republic of China
- Key Laboratory of Systems Bioengineering, Ministry of Education, Tianjin University, Tianjin 300072, People’s Republic of China
- Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin University, Tianjin 300072, People’s Republic of China
| | - Zhiwen Wang
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, People’s Republic of China
- Key Laboratory of Systems Bioengineering, Ministry of Education, Tianjin University, Tianjin 300072, People’s Republic of China
- Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin University, Tianjin 300072, People’s Republic of China
| | - Tao Chen
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, People’s Republic of China
- Key Laboratory of Systems Bioengineering, Ministry of Education, Tianjin University, Tianjin 300072, People’s Republic of China
- Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin University, Tianjin 300072, People’s Republic of China
| | - Xueming Zhao
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, People’s Republic of China
- Key Laboratory of Systems Bioengineering, Ministry of Education, Tianjin University, Tianjin 300072, People’s Republic of China
- Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin University, Tianjin 300072, People’s Republic of China
| |
Collapse
|
40
|
Enhancement of riboflavin production by deregulating gluconeogenesis in Bacillus subtilis. World J Microbiol Biotechnol 2014; 30:1893-900. [DOI: 10.1007/s11274-014-1611-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2013] [Accepted: 01/19/2014] [Indexed: 10/25/2022]
|
41
|
Man ZW, Rao ZM, Cheng YP, Yang TW, Zhang X, Xu MJ, Xu ZH. Enhanced riboflavin production by recombinant Bacillus subtilis RF1 through the optimization of agitation speed. World J Microbiol Biotechnol 2013; 30:661-7. [PMID: 24068533 DOI: 10.1007/s11274-013-1492-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2012] [Accepted: 09/16/2013] [Indexed: 11/30/2022]
Abstract
Dissolved oxygen is one of the most important bioprocess parameters that could affect cell growth and product formation, and it is easy to control by changing agitation speed. In this work, the effects of agitation speed on the performance of riboflavin production by recombinant Bacillus subtilis RF1 was investigated in fed-batch fermentation. The lower agitation speed (600 rpm) was beneficial for cell growth and riboflavin biosynthesis in the initial phase of fermentation process. While, during the later phase, higher agitation speed (900 rpm) was favor for cell growth and riboflavin biosynthesis. Thus, a two-stage agitation speed control strategy was proposed based on kinetic analysis, in which the agitation speed was controlled at 600 rpm in the first 26 h and then switched to 900 rpm to maintain high μ for cell growth and high q(p) for riboflavin production during the entire fermentation process. However, it was observed that a sharp increase of agitation speed resulted in an adverse effect on cell growth and riboflavin synthesis within a short time. To avoid this phenomenon, a multi-stage agitation speed control strategy was set up based on the two-stage control strategy, the maximum concentration of riboflavin reached 9.4 g l(-1) in 48 h with the yield of 0.051 g g(-1) by applying this strategy, which were 20.5 and 21.4% over the best results controlled by constant agitation speeds.
Collapse
Affiliation(s)
- Zai-wei Man
- The Key Laboratory of Industrial Biotechnology of Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, Jiangsu, People's Republic of China
| | | | | | | | | | | | | |
Collapse
|
42
|
Enhancement of FK506 production by engineering secondary pathways of Streptomyces tsukubaensis and exogenous feeding strategies. J Ind Microbiol Biotechnol 2013; 40:1023-37. [PMID: 23779221 DOI: 10.1007/s10295-013-1301-7] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2013] [Accepted: 05/29/2013] [Indexed: 01/13/2023]
Abstract
FK506 is a clinically important macrocyclic polyketide with immunosuppressive activity produced by Streptomyces tsukubaensis. However, the low titer at which it is produced is a bottleneck to its application and use in industrial processes. We have overexpressed five potential targets associated with FK506 production (fkbO, fkbL, fkbP, fkbM, fkbD) which were identified in our previous study, with the aim to improve FK506 production. The results of the analysis showed that the constructed strains with an additional copy of each gene increased FK506 production by approximately 10-40 % compared with the wild-type strain D852. The results of the gene expression analysis indicated that each gene was upregulated. Combinatorial overexpression of the five genes resulted in a 146 % increase in the FK506 titer to 353.2 mg/L, in comparison with the titer produced by D852. To further improve the production of FK506 by the engineered strain HT-FKBOPLMD, we supplemented the medium with various nutrients, including soybean oil, lactate, succinate, shikimate, chorismate, lysine, pipecolate, isoleucine and valine. Optimization of feeding concentrations and times resulted in HT-FKBOPLMD being able to produce approximately 70 % more FK506, thereby reaching the maximal titer of 457.5 mg/L, with lower amounts of by-products (FK520 and 37,38-dihydro-FK506). These results demonstrate that the combination of the metabolically engineered secondary pathways and the exogenous feeding strategies developed here was able to be successfully applied to improve the production of industrially and clinically important compounds.
Collapse
|
43
|
Liu L, Liu Y, Shin HD, Chen RR, Wang NS, Li J, Du G, Chen J. Developing Bacillus spp. as a cell factory for production of microbial enzymes and industrially important biochemicals in the context of systems and synthetic biology. Appl Microbiol Biotechnol 2013; 97:6113-27. [DOI: 10.1007/s00253-013-4960-4] [Citation(s) in RCA: 91] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2013] [Revised: 04/25/2013] [Accepted: 04/27/2013] [Indexed: 01/29/2023]
|
44
|
Huang D, Li S, Xia M, Wen J, Jia X. Genome-scale metabolic network guided engineering of Streptomyces tsukubaensis for FK506 production improvement. Microb Cell Fact 2013; 12:52. [PMID: 23705993 PMCID: PMC3680238 DOI: 10.1186/1475-2859-12-52] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2013] [Accepted: 05/21/2013] [Indexed: 01/31/2023] Open
Abstract
Background FK506 is an important immunosuppressant, which can be produced by Streptomyces tsukubaensis. However, the production capacity of the strain is very low. Hereby, a computational guided engineering approach was proposed in order to improve the intracellular precursor and cofactor availability of FK506 in S. tsukubaensis. Results First, a genome-scale metabolic model of S. tsukubaensis was constructed based on its annotated genome and biochemical information. Subsequently, several potential genetic targets (knockout or overexpression) that guaranteed an improved yield of FK506 were identified by the recently developed methodology. To validate the model predictions, each target gene was manipulated in the parent strain D852, respectively. All the engineered strains showed a higher FK506 production, compared with D852. Furthermore, the combined effect of the genetic modifications was evaluated. Results showed that the strain HT-ΔGDH-DAZ with gdhA-deletion and dahp-, accA2-, zwf2-overexpression enhanced FK506 concentration up to 398.9 mg/L, compared with 143.5 mg/L of the parent strain D852. Finally, fed-batch fermentations of HT-ΔGDH-DAZ were carried out, which led to the FK506 production of 435.9 mg/L, 1.47-fold higher than the parent strain D852 (158.7 mg/L). Conclusions Results confirmed that the promising targets led to an increase in FK506 titer. The present work is the first attempt to engineer the primary precursor pathways to improve FK506 production in S. tsukubaensis with genome-scale metabolic network guided metabolic engineering. The relationship between model prediction and experimental results demonstrates the rationality and validity of this approach for target identification. This strategy can also be applied to the improvement of other important secondary metabolites.
Collapse
Affiliation(s)
- Di Huang
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, PR China
| | | | | | | | | |
Collapse
|
45
|
Chen X, Zhang C, Cheng J, Shi X, Li L, Zhang Z, Bai J, Chen Y, li S, Ying H. Enhancement of adenosine production by Bacillus subtilis CGMCC 4484 through metabolic flux analysis and simplified feeding strategies. Bioprocess Biosyst Eng 2013; 36:1851-9. [DOI: 10.1007/s00449-013-0959-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2012] [Accepted: 04/14/2013] [Indexed: 10/26/2022]
|
46
|
Recent advances in engineering the central carbon metabolism of industrially important bacteria. Microb Cell Fact 2012; 11:50. [PMID: 22545791 PMCID: PMC3461431 DOI: 10.1186/1475-2859-11-50] [Citation(s) in RCA: 86] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2012] [Accepted: 04/30/2012] [Indexed: 01/19/2023] Open
Abstract
This paper gives an overview of the recent advances in engineering the central carbon metabolism of the industrially important bacteria Escherichia coli, Bacillus subtilis, Corynobacterium glutamicum, Streptomyces spp., Lactococcus lactis and other lactic acid bacteria. All of them are established producers of important classes of products, e.g. proteins, amino acids, organic acids, antibiotics, high-value metabolites for the food industry and also, promising producers of a large number of industrially or therapeutically important chemicals. Optimization of existing or introduction of new cellular processes in these microorganisms is often achieved through manipulation of targets that reside at major points of central metabolic pathways, such as glycolysis, gluconeogenesis, the pentose phosphate pathway and the tricarboxylic acid cycle with the glyoxylate shunt. Based on the huge progress made in recent years in biochemical, genetic and regulatory studies, new fascinating engineering approaches aim at ensuring an optimal carbon and energy flow within central metabolism in order to achieve optimized metabolite production.
Collapse
|
47
|
Huang D, Wen J, Wang G, Yu G, Jia X, Chen Y. In silico aided metabolic engineering of Streptomyces roseosporus for daptomycin yield improvement. Appl Microbiol Biotechnol 2012; 94:637-49. [PMID: 22406858 DOI: 10.1007/s00253-011-3773-6] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2011] [Revised: 09/18/2011] [Accepted: 11/21/2011] [Indexed: 11/25/2022]
Abstract
In silico metabolic network models are valuable tools for strain improvement with desired properties. In this work, based on the comparisons of each pathway flux under two different objective functions for the reconstructed metabolic network of Streptomyces roseosporus, three potential targets of zwf2 (code for glucose-6-phosphate hydrogenase), dptI (code for α-ketoglutarate methyltransferase), and dptJ (code for tryptophan oxygenase) were identified and selected for the genetic modifications. Overexpression of zwf2, dptI, and dptJ genes increased the daptomycin concentration up to 473.2, 452.5, and 489.1 mg/L, respectively. Furthermore, co-overexpression of three genes in series resulted in a 34.4% higher daptomycin concentration compared with the parental strain, which ascribed to the synergistic effect of the enzymes responsible for daptomycin biosynthesis. Finally, the engineered strain enhanced the yield of daptomycin up to 581.5 mg/L in the fed-batch culture, which was approximately 43.2% higher than that of the parental strain. These results demonstrated that the metabolic network based on in silico prediction would be accurate, reasonable, and practical for target gene identification and strain improvement.
Collapse
Affiliation(s)
- Di Huang
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, People's Republic of China
| | | | | | | | | | | |
Collapse
|
48
|
Riboflavin production by Ashbya gossypii. Biotechnol Lett 2011; 34:611-8. [DOI: 10.1007/s10529-011-0833-z] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2011] [Accepted: 12/09/2011] [Indexed: 10/14/2022]
|
49
|
Abbas CA, Sibirny AA. Genetic control of biosynthesis and transport of riboflavin and flavin nucleotides and construction of robust biotechnological producers. Microbiol Mol Biol Rev 2011; 75:321-60. [PMID: 21646432 PMCID: PMC3122625 DOI: 10.1128/mmbr.00030-10] [Citation(s) in RCA: 251] [Impact Index Per Article: 17.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Riboflavin [7,8-dimethyl-10-(1'-d-ribityl)isoalloxazine, vitamin B₂] is an obligatory component of human and animal diets, as it serves as the precursor of flavin coenzymes, flavin mononucleotide, and flavin adenine dinucleotide, which are involved in oxidative metabolism and other processes. Commercially produced riboflavin is used in agriculture, medicine, and the food industry. Riboflavin synthesis starts from GTP and ribulose-5-phosphate and proceeds through pyrimidine and pteridine intermediates. Flavin nucleotides are synthesized in two consecutive reactions from riboflavin. Some microorganisms and all animal cells are capable of riboflavin uptake, whereas many microorganisms have distinct systems for riboflavin excretion to the medium. Regulation of riboflavin synthesis in bacteria occurs by repression at the transcriptional level by flavin mononucleotide, which binds to nascent noncoding mRNA and blocks further transcription (named the riboswitch). In flavinogenic molds, riboflavin overproduction starts at the stationary phase and is accompanied by derepression of enzymes involved in riboflavin synthesis, sporulation, and mycelial lysis. In flavinogenic yeasts, transcriptional repression of riboflavin synthesis is exerted by iron ions and not by flavins. The putative transcription factor encoded by SEF1 is somehow involved in this regulation. Most commercial riboflavin is currently produced or was produced earlier by microbial synthesis using special selected strains of Bacillus subtilis, Ashbya gossypii, and Candida famata. Whereas earlier RF overproducers were isolated by classical selection, current producers of riboflavin and flavin nucleotides have been developed using modern approaches of metabolic engineering that involve overexpression of structural and regulatory genes of the RF biosynthetic pathway as well as genes involved in the overproduction of the purine precursor of riboflavin, GTP.
Collapse
Affiliation(s)
| | - Andriy A. Sibirny
- Institute of Cell Biology, NAS of Ukraine, Lviv 79005, Ukraine
- University of Rzeszow, Rzeszow 35-601, Poland
| |
Collapse
|
50
|
Lee WH, Chin YW, Han NS, Kim MD, Seo JH. Enhanced production of GDP-L-fucose by overexpression of NADPH regenerator in recombinant Escherichia coli. Appl Microbiol Biotechnol 2011; 91:967-76. [PMID: 21538115 DOI: 10.1007/s00253-011-3271-x] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2011] [Revised: 03/19/2011] [Accepted: 03/23/2011] [Indexed: 11/29/2022]
Abstract
Biosynthesis of guanosine 5'-diphosphate-L-fucose (GDP-L-fucose) requires NADPH as a reducing cofactor. In this study, endogenous NADPH regenerating enzymes such as glucose-6-phosphate dehydrogenase (G6PDH), isocitrate dehydrogenase (Icd), and NADP(+)-dependent malate dehydrogenase (MaeB) were overexpressed to increase GDP-L-fucose production in recombinant Escherichia coli. The effects of overexpression of each NADPH regenerating enzyme on GDP-L-fucose production were investigated in a series of batch and fed-batch fermentations. Batch fermentations showed that overexpression of G6PDH was the most effective for GDP-L-fucose production. However, GDP-L-fucose production was not enhanced by overexpression of G6PDH in the glucose-limited fed-batch fermentation. Hence, a glucose feeding strategy was optimized to enhance GDP-L-fucose production. Fed-batch fermentation with a pH-stat feeding mode for sufficient supply of glucose significantly enhanced GDP-L-fucose production compared with glucose-limited fed-batch fermentation. A maximum GDP-L-fucose concentration of 235.2 ± 3.3 mg l(-1), corresponding to a 21% enhancement in the GDP-L-fucose production compared with the control strain overexpressing GDP-L-fucose biosynthetic enzymes only, was achieved in the pH-stat fed-batch fermentation of the recombinant E. coli overexpressing G6PDH. It was concluded that sufficient glucose supply and efficient NADPH regeneration are crucial for NADPH-dependent GDP-L-fucose production in recombinant E. coli.
Collapse
Affiliation(s)
- Won-Heong Lee
- Department of Agricultural Biotechnology and Center for Agricultural Biomaterials, Seoul National University, Seoul 151-921, South Korea
| | | | | | | | | |
Collapse
|