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Jiang S, Lin Y, Zheng S. Development of the IMP biosensor for rapid and stable analysis of IMP concentrations in fermentation broth. Biotechnol J 2024; 19:e2400040. [PMID: 38863123 DOI: 10.1002/biot.202400040] [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: 01/17/2024] [Revised: 04/15/2024] [Accepted: 04/22/2024] [Indexed: 06/13/2024]
Abstract
IMP (inosinic acid) is a crucial intermediate in the purine metabolic pathway and is continuously synthesized in all cells. Besides its role as a precursor for DNA and RNA, IMP also plays a critical or essential role in cell growth, energy storage, conversion, and metabolism. In our study, we utilized the circularly permuted fluorescent protein (cpFP) and IMP dehydrogenase to screen and develop the IMP biosensor, IMPCP1. By introducing a mutation in the catalytically active site of IMPCP1, from Cys to Ala, we disrupted its ability to catalyze IMP while retaining its capability to bind to IMP without affecting the IMP concentration in the sample. To immobilize IMPCP1, we employed the SpyCatcher/SpyTag system and securely attached it to Magarose-Epoxy, resulting in the development of the IMP rapid test kit, referred to as IMPTK. The biosensor integrated into IMPTK offers enhanced stability, resistance to degradation activity, and specific recognition of IMP. It is also resistant to peroxides and temperature changes. IMPTK serves as a rapid and stable assay for analyzing IMP concentrations in fermentation broth. Within the linear range of IMP concentrations, it can be utilized as a substitute for HPLC. The IMPTK biosensor provides a reliable and efficient alternative for monitoring IMP levels, offering advantages such as speed, stability, and resistance to environmental factors.
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Affiliation(s)
- Shibo Jiang
- Guangdong Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, P.R. China
- Guangdong Research Center of Industrial Enzyme and Green Manufacturing Technology, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, P.R. China
| | - Ying Lin
- Guangdong Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, P.R. China
- Guangdong Research Center of Industrial Enzyme and Green Manufacturing Technology, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, P.R. China
| | - Suiping Zheng
- Guangdong Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, P.R. China
- Guangdong Research Center of Industrial Enzyme and Green Manufacturing Technology, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, P.R. China
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Zhou M, Li Y, Cai Y, Sun Y, Chen W, Wang J, Shen F, Zhan Y, Ying J, Chen S. Development of an Inosine Hyperproducer from Bacillus licheniformis by Systems Metabolic Engineering. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:20210-20221. [PMID: 38079219 DOI: 10.1021/acs.jafc.3c07715] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2023]
Abstract
Inosine is widely used in food, chemical, and medicine. This study developed Bacillus licheniformis into an inosine hyperproducer through systems metabolic engineering. First, purine metabolism was activated by deleting inhibitors PurR and YabJ and overexpressing the pur operon. Then, the 5-phosphoribosyl-1-pyrophosphate (PRPP) supply was increased by optimizing the glucose transport system and pentose phosphate pathway, increasing the inosine titer by 97% and decreasing the titers of byproducts by 36%. Next, to prevent the degradation of inosine, genes deoD and pupG coding purine nucleoside phosphorylase were deleted, accumulating 0.91 g/L inosine in the culture medium. Additionally, the downregulation of adenosine 5'-monophosphate (AMP) synthesis pathway increased the inosine titer by 409%. Importantly, enhancing the glycine and aspartate supply increased the inosine titer by 298%. Finally, the guanosine synthesis pathway was blocked, leading to strain IR-8-2 producing 27.41 g/L inosine with a 0.46 g inosine/g glucose yield and a 0.38 g/(L·h) productivity in a shake flask.
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Affiliation(s)
- Menglin Zhou
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Environmental Microbial Technology Center of Hubei Province, College of Life Sciences, Hubei University, Wuhan 430062, PR China
| | - Yi Li
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Environmental Microbial Technology Center of Hubei Province, College of Life Sciences, Hubei University, Wuhan 430062, PR China
| | - Youhua Cai
- Star Lake Bioscience Co. Inc, Zhaoging, Zhaoging, Guangdong 526000, PR China
| | - Yaqi Sun
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Environmental Microbial Technology Center of Hubei Province, College of Life Sciences, Hubei University, Wuhan 430062, PR China
| | - Wu Chen
- Star Lake Bioscience Co. Inc, Zhaoging, Zhaoging, Guangdong 526000, PR China
| | - Jin Wang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Environmental Microbial Technology Center of Hubei Province, College of Life Sciences, Hubei University, Wuhan 430062, PR China
| | - Feng Shen
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Environmental Microbial Technology Center of Hubei Province, College of Life Sciences, Hubei University, Wuhan 430062, PR China
| | - Yangyang Zhan
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Environmental Microbial Technology Center of Hubei Province, College of Life Sciences, Hubei University, Wuhan 430062, PR China
| | - Jun Ying
- Star Lake Bioscience Co. Inc, Zhaoging, Zhaoging, Guangdong 526000, PR China
| | - Shouwen Chen
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Environmental Microbial Technology Center of Hubei Province, College of Life Sciences, Hubei University, Wuhan 430062, PR China
- Key Laboratory of Green Chemical Technology of Fujian Province University, College of Ecological and Resource Engineering, Wuyi University, Wuyishan 354300, PR China
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Mengucci C, Rampelli S, Picone G, Lucchi A, Litta G, Biagi E, Candela M, Manfreda G, Brigidi P, Capozzi F, De Cesare A. Application of multi-omic features clustering and pathway enrichment to clarify the impact of vitamin B2 supplementation on broiler caeca microbiome. Front Microbiol 2023; 14:1264361. [PMID: 37840729 PMCID: PMC10568133 DOI: 10.3389/fmicb.2023.1264361] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Accepted: 09/11/2023] [Indexed: 10/17/2023] Open
Abstract
Background The results of omic methodologies are often reported as separate datasets. In this study we applied for the first time multi-omic features clustering and pathway enrichment to clarify the biological impact of vitamin B2 supplementation on broiler caeca microbiome. Methods The caeca contents of broilers fed +50 and +100 mg/kg vitamin B2 were analyzed by shotgun metagenomic and metabolomic. Latent variables extracted from NMR spectra, as well as taxonomic and functional features profiled from metagenomes, were integrated to characterize the effect of vitamin B2 in modulating caeca microbiome. A pathway-based network was obtained by mapping the observed input genes and compounds, highlighting connected strands of metabolic ways through pathway-enrichment analysis. Results At day 14, the taxonomic, functional and metabolomic features in the caeca of tested broilers showed some degree of separation between control and treated groups, becoming fully clear at 28 days and persisting up to 42 days. In the caeca of birds belonging to the control group Alistipes spp. was the signature species, while the signature species in the caeca of broilers fed +50 and +100 mg/kg vitamin B2 were Bacteroides fragilis and Lactobacillus crispatus, Lactobacillus reuteri, Ruminococcus torques, Subdoligranum spp., respectively. The pathway enrichment analysis highlighted that the specific biochemical pathways enhanced by the supplementations of vitamin B2 were N-Formyl-L-aspartate amidohydrolase, producing Aspartate and Formate; L-Alanine:2-oxoglutarate amino transferase, supporting the conversion of L-Alanine and 2-Oxoglutarate in Pyruvate and L-Glutamate; 1D-myo-inositol 1/4 phosphate phosphohydrolase, converting Inositol 1/4-phosphate and water in myo-Inositol and Orthophosphate. The results of this study demonstrated that the caeca of birds fed +50 and + 100 mg/kg were those characterized by taxonomic groups more beneficial to the host and with a higher concentration of myo-inositol, formic acid, amino acids and pyruvate involved in glycolysis and amino acid biosynthesis. Conclusion In this study we demonstrated how to perform multi-omic features integration to describe the biochemical mechanisms enhanced by the supplementation of different concentrations of vitamin B2 in the poultry diet. The relationship between vitamin B2 supplementation and myo-inositol production was highlighted in our study for the first time.
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Affiliation(s)
- Carlo Mengucci
- Department of Agricultural and Food Sciences, University of Bologna, Cesena, Italy
| | - Simone Rampelli
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Gianfranco Picone
- Department of Agricultural and Food Sciences, University of Bologna, Cesena, Italy
| | - Alex Lucchi
- Department of Agricultural and Food Sciences, University of Bologna, Cesena, Italy
| | | | - Elena Biagi
- Department of Civil, Chemical, Environmental, and Materials Engineering, University of Bologna, Bologna, Italy
| | - Marco Candela
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Gerardo Manfreda
- Department of Agricultural and Food Sciences, University of Bologna, Cesena, Italy
| | - Patrizia Brigidi
- Department of Medical and Surgical Sciences, University of Bologna, Bologna, Italy
| | - Francesco Capozzi
- Department of Agricultural and Food Sciences, University of Bologna, Cesena, Italy
| | - Alessandra De Cesare
- Department of Veterinary Medical Sciences, University of Bologna, Ozzano Emilia (BO), Italy
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Hu Y, Wang C, Fei Z, Zhou M, Yu H, Sun Z. Potential biomarkers screening of Polygonum multiflorum radix-induced liver injury based on metabonomics analysis of clinical samples. JOURNAL OF ETHNOPHARMACOLOGY 2023; 308:116217. [PMID: 36758914 DOI: 10.1016/j.jep.2023.116217] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2022] [Revised: 12/28/2022] [Accepted: 01/26/2023] [Indexed: 06/07/2023]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE Polygonum multiflorum Radix (PMR) is the dried root tuber of Polygonum multiflorum Thunb., which has been used in the clinic for a variety of pharmacological activities. However, Polygonum multiflorum Radix-induced liver injury (PMR-ILI) has been reported in recent years, which has limited its clinical use to some extent. The occurrence of PMR-ILI is not universal, so finding the different metabolic characteristics between PMR-ILI and Polygonum multiflorum Radix-tolerance group (PMR-T) is very important for the PMR rational clinical application and PMR-ILI early clinical diagnosis. METHODS In this study, 6 clinical plasma samples of PMR-ILI and 13 PMR-T were collected and analyzed by high-resolution liquid chromatography-mass spectrometry. Firstly, the differential metabolites of the two groups were screened by conventional screening methods such as multivariate statistical analysis. Secondly, the characteristic metabolites with greater contribution, correlation with liver injury and high sensitivity were screened by correlation analysis with clinical liver injury indicators, random forest analysis, and receiver operating characteristic curve (ROC). RESULTS After multivariate statistical analysis and screening analysis, 29 differential metabolites were identified. Compared with PMR-T group, the metabolism of glycerol and phospholipid, glutamine and glutamate, phenylalanine, sphingolipid and tryptophan in PMR-ILI group were disturbed. After correlation analysis with liver injury indexes and random forest screening, 8 potential biomarkers closely related to clinical liver injury were obtained. Finally, 3 potential biomarkers with high expression in PMR-ILI, hypoxanthine, LysoPC(P-16:0/0:0) and taurochenodesoxycholic acid, were screened out through the analysis of ROC, which can provide a basis for the early clinical diagnosis. CONCLUSION Based on the analysis of the PMR-ILI and PMR-T plasma samples by LC-MS, three biomarkers of clinical liver injury of Polygonum multiflorum Radix were selected: hypoxanthine, LysoPC(P-16:0/0:0) and taurochenodeoxycholic acid.
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Affiliation(s)
- Yinghuan Hu
- School of Life Sciences, Beijing University of Chinese Medicine, Beijing, 102488, China
| | - Chengyu Wang
- School of Life Sciences, Beijing University of Chinese Medicine, Beijing, 102488, China
| | - Zhanyang Fei
- School of Life Sciences, Beijing University of Chinese Medicine, Beijing, 102488, China
| | - Ming Zhou
- School of Life Sciences, Beijing University of Chinese Medicine, Beijing, 102488, China
| | - Hao Yu
- Capital Medical University Affiliated Beijing Ditan Hospital, Beijing, 100015, China.
| | - Zhenxiao Sun
- School of Life Sciences, Beijing University of Chinese Medicine, Beijing, 102488, China.
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Li M, Liu B, Li R, Yang P, Leng P, Huang Y. Exploration of the link between gut microbiota and purinergic signalling. Purinergic Signal 2023; 19:315-327. [PMID: 36121551 PMCID: PMC9984663 DOI: 10.1007/s11302-022-09891-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Accepted: 07/25/2022] [Indexed: 11/30/2022] Open
Abstract
Growing evidence reveals that microorganisms in the gut are linked to metabolic health and disease risk in human beings to a considerable extent. The focus of research at this stage must tend to focus on cause-and-effect studies. In addition to being a component of DNA and RNA, purine metabolites can be involved in purine signalling in the body as chemical messengers. Abnormalities in purinergic signalling may lead to neuropathy, rheumatic immune diseases, inflammation, tumors, and a wide range of other diseases. It has proved that gut microbes are involved in purinergic signalling. The relationship between these gut-derived purinergic signalling molecules and host metabolism may be one of the important clues to our understanding of the mechanisms by which the microbiota affects host metabolism.
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Affiliation(s)
- MingJian Li
- College of Medical Technology, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China
| | - BoWen Liu
- School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China
| | - Rong Li
- School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China
| | - Ping Yang
- School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China
| | - Ping Leng
- College of Medical Technology, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China.
| | - Yong Huang
- Innovative Institute of Chinese Medicine and Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China.
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Insights into the Metabolic Response of Lactiplantibacillus plantarum CCFM1287 upon Patulin Exposure. Int J Mol Sci 2022; 23:ijms231911652. [PMID: 36232948 PMCID: PMC9570479 DOI: 10.3390/ijms231911652] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Revised: 09/27/2022] [Accepted: 09/28/2022] [Indexed: 11/17/2022] Open
Abstract
Patulin (PAT) is a common mycotoxin in the food industry, and is found in apple products in particular. Consumption of food or feed contaminated with PAT can cause acute or chronic toxicity in humans and animals. Lactiplantibacillus plantarum CCFM1287 is a probiotic strain that effectively degrades PAT in PBS and food systems. In this study, it was found that the concentration of PAT (50 mg/L) in MRS medium decreased by 85.09% during the first stages of CCFM1287 growth, and this change was consistent with the first-order degradation kinetic model. Meanwhile, the regulation of oxidative stress by L. plantarum CCFM1287 in response to PAT exposure and metabolic changes that occur during PAT degradation were investigated. The degree of intracellular damage was attenuated after 16 h of exposure compared to 8 h. Meanwhile, metabolomic data showed that 30 and 29 significantly different metabolites were screened intracellularly in the strain after 8 h and 16 h of PAT stress at 50 mg/L, respectively. The results of pathway enrichment analysis suggested that the purine metabolic pathway was significantly enriched at both 8 h and 16 h. However, as is consistent with the performance of the antioxidant system, the changes in Lactiplantibacillus diminished with increasing time of PAT exposure. Therefore, this study helps to further explain the mechanism of PAT degradation by L. plantarum CCFM1287.
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Geissler AS, Poulsen LD, Doncheva NT, Anthon C, Seemann SE, González-Tortuero E, Breüner A, Jensen LJ, Hjort C, Vinther J, Gorodkin J. The impact of PrsA over-expression on the Bacillus subtilis transcriptome during fed-batch fermentation of alpha-amylase production. Front Microbiol 2022; 13:909493. [PMID: 35992681 PMCID: PMC9386232 DOI: 10.3389/fmicb.2022.909493] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 06/28/2022] [Indexed: 11/13/2022] Open
Abstract
The production of the alpha-amylase (AMY) enzyme in Bacillus subtilis at a high rate leads to the accumulation of unfolded AMY, which causes secretion stress. The over-expression of the PrsA chaperone aids enzyme folding and reduces stress. To identify affected pathways and potential mechanisms involved in the reduced growth, we analyzed the transcriptomic differences during fed-batch fermentation between a PrsA over-expressing strain and control in a time-series RNA-seq experiment. We observe transcription in 542 unannotated regions, of which 234 had significant changes in expression levels between the samples. Moreover, 1,791 protein-coding sequences, 80 non-coding genes, and 20 riboswitches overlapping UTR regions of coding genes had significant changes in expression. We identified putatively regulated biological processes via gene-set over-representation analysis of the differentially expressed genes; overall, the analysis suggests that the PrsA over-expression affects ATP biosynthesis activity, amino acid metabolism, and cell wall stability. The investigation of the protein interaction network points to a potential impact on cell motility signaling. We discuss the impact of these highlighted mechanisms for reducing secretion stress or detrimental aspects of PrsA over-expression during AMY production.
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Affiliation(s)
- Adrian S. Geissler
- Department of Veterinary and Animal Sciences, Center for non-coding RNA in Technology and Health, University of Copenhagen, Copenhagen, Denmark
| | - Line D. Poulsen
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Nadezhda T. Doncheva
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | - Christian Anthon
- Department of Veterinary and Animal Sciences, Center for non-coding RNA in Technology and Health, University of Copenhagen, Copenhagen, Denmark
| | - Stefan E. Seemann
- Department of Veterinary and Animal Sciences, Center for non-coding RNA in Technology and Health, University of Copenhagen, Copenhagen, Denmark
| | - Enrique González-Tortuero
- Department of Veterinary and Animal Sciences, Center for non-coding RNA in Technology and Health, University of Copenhagen, Copenhagen, Denmark
| | | | - Lars J. Jensen
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | | | - Jeppe Vinther
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Jan Gorodkin
- Department of Veterinary and Animal Sciences, Center for non-coding RNA in Technology and Health, University of Copenhagen, Copenhagen, Denmark
- *Correspondence: Jan Gorodkin,
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Aron O, Otieno FJ, Tijjani I, Yang Z, Xu H, Weng S, Guo J, Lu S, Wang Z, Tang W. De novo purine nucleotide biosynthesis mediated by MoAde4 is required for conidiation, host colonization and pathogenicity in Magnaporthe oryzae. Appl Microbiol Biotechnol 2022; 106:5587-5602. [PMID: 35918446 DOI: 10.1007/s00253-022-12100-z] [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: 11/11/2021] [Revised: 07/18/2022] [Accepted: 07/21/2022] [Indexed: 11/02/2022]
Abstract
Amidophosphoribosyltransferase catalyzes the conversion of 5-phosphoribosyl-1-pyrophosphate into 5-phosphoribosyl-1-amine in the de novo purine biosynthetic pathway. Herein, we identified and characterized the functions of MoAde4, an orthologue of yeast Ade4 in Magnaporthe oryzae. MoAde4 is a 537-amino acid protein containing GATase_6 and pribosyltran domains. MoADE4 transcripts were highly expressed during the conidiation, early-infection, and late-infection stages of the fungus. Disruption of the MoADE4 gene resulted in ΔMoade4 exhibiting adenine, adenosine, and hypoxanthine auxotrophy on minimal medium. Conidia quantification assays showed that sporulation was significantly reduced in the ΔMoade4 mutant. The conidia of ΔMoade4 could still form appressoria but mostly failed to penetrate the rice cuticle. Pathogenicity tests showed that ΔMoade4 was completely nonpathogenic on rice and barley leaves, which was attributed to restricted infectious hyphal growth within the primary cells. The ΔMoade4 mutant was defective in the induction of strong host immunity. Exogenous adenine partially rescued conidiation, infectious hyphal growth, and the pathogenicity defects of the ΔMoade4 mutant on barley and rice leaves. Taken together, our results demonstrated that purine nucleotide biosynthesis orchestrated by MoAde4 is required for fungal development and pathogenicity in M. oryzae. These findings therefore act as a suitable target for antifungal development against recalcitrant plant fungal pathogens. KEY POINTS: • MoAde4 is crucial for de novo purine nucleotide biosynthesis. • MoAde4 is pivotal for conidiogenesis and appressorium development of M. oryzae. • MoAde4 is involoved in the pathogenicity of M. oryzae.
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Affiliation(s)
- Osakina Aron
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Ministerial and Provincial Joint Innovation Centre for Safety Production of Cross-Strait Crops, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Frankine Jagero Otieno
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Ministerial and Provincial Joint Innovation Centre for Safety Production of Cross-Strait Crops, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Ibrahim Tijjani
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Ministerial and Provincial Joint Innovation Centre for Safety Production of Cross-Strait Crops, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Zifeng Yang
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Ministerial and Provincial Joint Innovation Centre for Safety Production of Cross-Strait Crops, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Huxiao Xu
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Ministerial and Provincial Joint Innovation Centre for Safety Production of Cross-Strait Crops, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Shuning Weng
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Ministerial and Provincial Joint Innovation Centre for Safety Production of Cross-Strait Crops, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Jiayuan Guo
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Ministerial and Provincial Joint Innovation Centre for Safety Production of Cross-Strait Crops, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Songmao Lu
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Ministerial and Provincial Joint Innovation Centre for Safety Production of Cross-Strait Crops, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Zonghua Wang
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Ministerial and Provincial Joint Innovation Centre for Safety Production of Cross-Strait Crops, Fujian Agriculture and Forestry University, Fuzhou, 350002, China. .,Marine and Agricultural Biotechnology Laboratory, Institute of Oceanography, Minjiang University, Fuzhou, 350108, China.
| | - Wei Tang
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Ministerial and Provincial Joint Innovation Centre for Safety Production of Cross-Strait Crops, Fujian Agriculture and Forestry University, Fuzhou, 350002, China. .,Fujian Key Laboratory for Monitoring and Integrated Management of Crop Pests, Fuzhou, 350013, China.
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Molee W, Khosinklang W, Tongduang P, Thumanu K, Yongsawatdigul J, Molee A. Biomolecules, Fatty Acids, Meat Quality, and Growth Performance of Slow-Growing Chickens in an Organic Raising System. Animals (Basel) 2022; 12:ani12050570. [PMID: 35268139 PMCID: PMC8908829 DOI: 10.3390/ani12050570] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Revised: 02/07/2022] [Accepted: 02/21/2022] [Indexed: 12/14/2022] Open
Abstract
This study was to determine the effect of the organic raising system (OR) on growth performance, meat quality, and physicochemical properties of slow-growing chickens. Three hundred and sixty (one-day-old) Korat chickens (KRC) were randomly assigned to control (CO) and OR groups. The groups comprised six replicates of thirty chickens each. The chickens were housed in indoor pens (5 birds/m2), wherein those in OR had free access to Ruzi pasture (1 bird/4 m2) from d 21 to d 84 of age. In the CO group, chickens were fed with a mixed feed derived from commercial feedstuffs, while those in the OR group were fed with mixed feed derived from organic feedstuffs. The results revealed a lower feed intake (p < 0.0001) and feed conversion ratio (p = 0.004) in the OR. The OR increased total collagen, protein, shear force, color of skin and meat, and decreased abdominal fat (p < 0.05). The OR improved fatty acid with increased DHA, n-3 PUFA, and decreased the ratio of n-6 to n-3 PUFA in KRC meat (p < 0.05). The synchrotron radiation-based Fourier transform infrared spectroscopy and correlation loading analyses confirmed these results. In conclusion, our results proved that OR could improve growth performance and meat quality and suggested the raising system be adopted commercially. In addition, the observed differences in biochemical molecules could also serve as markers for monitoring meat quality.
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Affiliation(s)
- Wittawat Molee
- School of Animal Technology and Innovation, Institute of Agricultural Technology, Suranaree University of Technology, Nakhon Ratchasima 30000, Thailand; (W.K.); (P.T.); (A.M.)
- Correspondence: ; Tel.: +66-8-9920-4970
| | - Wichuta Khosinklang
- School of Animal Technology and Innovation, Institute of Agricultural Technology, Suranaree University of Technology, Nakhon Ratchasima 30000, Thailand; (W.K.); (P.T.); (A.M.)
| | - Pramkamon Tongduang
- School of Animal Technology and Innovation, Institute of Agricultural Technology, Suranaree University of Technology, Nakhon Ratchasima 30000, Thailand; (W.K.); (P.T.); (A.M.)
| | - Kanjana Thumanu
- Research and Facility Department, Synchrotron Light Research Institute (Public Organization), Nakhon Ratchasima 30000, Thailand;
| | - Jirawat Yongsawatdigul
- School of Food Technology, Institute of Agricultural Technology, Suranaree University of Technology, Nakhon Ratchasima 30000, Thailand;
| | - Amonrat Molee
- School of Animal Technology and Innovation, Institute of Agricultural Technology, Suranaree University of Technology, Nakhon Ratchasima 30000, Thailand; (W.K.); (P.T.); (A.M.)
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Fan X, Bao T, Yi H, Zhang Z, Zhang K, Liu X, Lin X, Zhang Z, Feng Z. Ribosome Profiling and RNA Sequencing Reveal Genome-Wide Cellular Translation and Transcription Regulation Under Osmotic Stress in Lactobacillus rhamnosus ATCC 53103. Front Microbiol 2021; 12:781454. [PMID: 34899662 PMCID: PMC8656396 DOI: 10.3389/fmicb.2021.781454] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Accepted: 10/27/2021] [Indexed: 12/27/2022] Open
Abstract
To determine whether osmotic pressure affects the translation efficiency of Lactobacillus rhamnosus, the ribosome profiling assay was performed to analyze the changes in translation efficiency in L. rhamnosus ATCC 53103. Under osmotic stress, differentially expressed genes (DEGs) involved in fatty acid biosynthesis and metabolism, ribosome, and purine metabolism pathways were co-regulated with consistent expression direction at translation and transcription levels. DEGs involved in the biosynthesis of phenylalanine, tyrosine, and tryptophan, and the phosphotransferase system pathways also were co-regulated at translation and transcription levels, while they showed opposite expression direction at two levels. Moreover, DEGs involved in the two-component system, amino acid metabolism, and pyruvate metabolism pathways were only regulated at the transcription level. And DEGs involved in fructose and mannose metabolism were only regulated at the translation level. The translation efficiency of DEGs involved in the biosynthesis of amino acids was downregulated while in quorum sensing and PTS pathways was upregulated. In addition, the ribosome footprints accumulated in open reading frame regions resulted in impaired translation initiation and elongation under osmotic stress. In summary, L. rhamnosus ATCC 53103 could respond to osmotic stress by translation regulation and control the balance between survival and growth of cells by transcription and translation.
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Affiliation(s)
- Xuejing Fan
- Key Laboratory of Dairy Science, Ministry of Education, College of Food Science, Northeast Agricultural University, Harbin, China
| | - Tianyu Bao
- Key Laboratory of Dairy Science, Ministry of Education, College of Food Science, Northeast Agricultural University, Harbin, China
| | - Huaxi Yi
- College of Food Science and Engineering, Ocean University of China, Qingdao, China
| | - Zongcai Zhang
- Key Laboratory of Dairy Science, Ministry of Education, College of Food Science, Northeast Agricultural University, Harbin, China
| | - Kenan Zhang
- Key Laboratory of Dairy Science, Ministry of Education, College of Food Science, Northeast Agricultural University, Harbin, China
| | - Xin Liu
- Key Laboratory of Dairy Science, Ministry of Education, College of Food Science, Northeast Agricultural University, Harbin, China
| | - Xue Lin
- Key Laboratory of Dairy Science, Ministry of Education, College of Food Science, Northeast Agricultural University, Harbin, China
| | - Zhen Zhang
- Key Laboratory of Dairy Science, Ministry of Education, College of Food Science, Northeast Agricultural University, Harbin, China
| | - Zhen Feng
- Key Laboratory of Dairy Science, Ministry of Education, College of Food Science, Northeast Agricultural University, Harbin, China.,Spice and Beverage Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wanning, China
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11
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Jung S, Koo KM, Ryu J, Baek I, Kwon SJ, Kim JB, Ahn JW. Overexpression of Phosphoribosyl Pyrophosphate Synthase Enhances Resistance of Chlamydomonas to Ionizing Radiation. FRONTIERS IN PLANT SCIENCE 2021; 12:719846. [PMID: 34512699 PMCID: PMC8427504 DOI: 10.3389/fpls.2021.719846] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Accepted: 07/29/2021] [Indexed: 06/13/2023]
Abstract
The enzyme phosphoribosyl pyrophosphate synthase (PRPS) catalyzes the conversion of ribose 5-phosphate into phosphoribosyl diphosphate; the latter is a precursor of purine and pyrimidine nucleotides. Here, we investigated the function of PRPS from the single-celled green alga Chlamydomonas reinhardtii in its response to DNA damage from gamma radiation or the alkylating agent LiCl. CrPRPS transcripts were upregulated in cells treated with these agents. We generated CrPRPS-overexpressing transgenic lines to study the function of CrPRPS. When grown in culture with LiCl or exposed to gamma radiation, the transgenic cells grew faster and had a greater survival rate than wild-type cells. CrPRPS overexpression enhanced expression of genes associated with DNA damage response, namely RAD51, RAD1, and LIG1. We observed, from transcriptome analysis, upregulation of genes that code for key enzymes in purine metabolism, namely ribonucleoside-diphosphate pyrophosphokinase subunit M1, adenylate kinase, and nucleoside-diphosphate kinase. We conclude that CrPRPS may affect DNA repair process via regulation of de novo nucleotide synthesis.
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Affiliation(s)
- Sera Jung
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup-si, South Korea
- Advanced Process Technology and Fermentation Research Group, Research and Development Division, World Institute of Kimchi, Jeongeup-si, South Korea
| | - Kwang Min Koo
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup-si, South Korea
| | - Jaihyunk Ryu
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup-si, South Korea
| | - Inwoo Baek
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup-si, South Korea
| | - Soon-Jae Kwon
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup-si, South Korea
| | - Jin-Baek Kim
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup-si, South Korea
| | - Joon-Woo Ahn
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup-si, South Korea
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12
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Hamitouche F, Armengaud J, Dedieu L, Duport C. Cysteine Proteome Reveals Response to Endogenous Oxidative Stress in Bacillus cereus. Int J Mol Sci 2021; 22:7550. [PMID: 34299167 PMCID: PMC8305198 DOI: 10.3390/ijms22147550] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Revised: 07/08/2021] [Accepted: 07/12/2021] [Indexed: 12/30/2022] Open
Abstract
At the end of exponential growth, aerobic bacteria have to cope with the accumulation of endogenous reactive oxygen species (ROS). One of the main targets of these ROS is cysteine residues in proteins. This study uses liquid chromatography coupled to high-resolution tandem mass spectrometry to detect significant changes in protein abundance and thiol status for cysteine-containing proteins from Bacillus cereus during aerobic exponential growth. The proteomic profiles of cultures at early-, middle-, and late-exponential growth phases reveals that (i) enrichment in proteins dedicated to fighting ROS as growth progressed, (ii) a decrease in both overall proteome cysteine content and thiol proteome redox status, and (iii) changes to the reduced thiol status of some key proteins, such as the transition state transcriptional regulator AbrB. Taken together, our data indicate that growth under oxic conditions requires increased allocation of protein resources to attenuate the negative effects of ROS. Our data also provide a strong basis to understand the response mechanisms used by B. cereus to deal with endogenous oxidative stress.
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Affiliation(s)
- Fella Hamitouche
- Biology Department, Campus Jean-Henri Fabre, Avignon University, INRAE, UMR SQPOV, CEDEX 09, 84911 Avignon, France; (F.H.); (L.D.)
| | - Jean Armengaud
- Département Médicaments et Technologies pour la Santé (DMTS), Université Paris-Saclay, CEA, INRAE, SPI, 30200 Bagnols-sur-Cèze, France;
| | - Luc Dedieu
- Biology Department, Campus Jean-Henri Fabre, Avignon University, INRAE, UMR SQPOV, CEDEX 09, 84911 Avignon, France; (F.H.); (L.D.)
| | - Catherine Duport
- Biology Department, Campus Jean-Henri Fabre, Avignon University, INRAE, UMR SQPOV, CEDEX 09, 84911 Avignon, France; (F.H.); (L.D.)
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13
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Li D, Feng Y, Tian M, Ji J, Hu X, Chen F. Gut microbiota-derived inosine from dietary barley leaf supplementation attenuates colitis through PPARγ signaling activation. MICROBIOME 2021; 9:83. [PMID: 33820558 PMCID: PMC8022418 DOI: 10.1186/s40168-021-01028-7] [Citation(s) in RCA: 87] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Accepted: 02/05/2021] [Indexed: 05/12/2023]
Abstract
BACKGROUND Ulcerative colitis is a type of chronic inflammatory bowel disease closely associated with gut microbiota dysbiosis and intestinal homeostasis dysregulation. Barley leaf (BL) has a long history of use in Traditional Chinese Medicine with potential health-promoting effects on intestinal functions. However, its mechanism of action is not yet clear. Here, we explore the potential modulating roles of gut microbial metabolites of BL to protect against colitis and elucidate the underlying molecular mechanisms. RESULTS Using 16S rRNA gene-based microbiota analysis, we first found that dietary supplementation of BL ameliorated dextran sulfate sodium (DSS)-induced gut microbiota dysbiosis. The mechanisms by which BL protected against DSS-induced colitis were resulted from improved intestinal mucosal barrier functions via the activation of peroxisome proliferator-activated receptor (PPAR)γ signaling. In addition, metabolomic profiling analysis showed that the gut microbiota modulated BL-induced metabolic reprograming in the colonic tissues particularly by the enhancement of glycolysis process. Notably, dietary BL supplementation resulted in the enrichment of microbiota-derived purine metabolite inosine, which could activate PPARγ signaling in human colon epithelial cells. Furthermore, exogenous treatment of inosine reproduced similar protective effects as BL to protect against DSS-induced colitis through improving adenosine 2A receptor (A2AR)/PPARγ-dependent mucosal barrier functions. CONCLUSIONS Overall, our findings suggest that the gut microbiota-inosine-A2AR/PPARγ axis plays an important role in the maintenance of intestinal homeostasis, which may represent a novel approach for colitis prevention via manipulation of the gut microbial purine metabolite. Video Abstract.
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Affiliation(s)
- Daotong Li
- College of Food Science and Nutritional Engineering, National Engineering Research Center for Fruit and Vegetable Processing, Key Laboratory of Fruits and Vegetables Processing, Ministry of Agriculture; Engineering Research Centre for Fruits and Vegetables Processing, Ministry of Education, China Agricultural University, No.17, Qinghua East Road, Haidian District, Beijing, 100083, China
- Department of Anatomy, Histology and Embryology, Health Science Center, Peking University, Beijing, China
| | - Yu Feng
- College of Food Science and Nutritional Engineering, National Engineering Research Center for Fruit and Vegetable Processing, Key Laboratory of Fruits and Vegetables Processing, Ministry of Agriculture; Engineering Research Centre for Fruits and Vegetables Processing, Ministry of Education, China Agricultural University, No.17, Qinghua East Road, Haidian District, Beijing, 100083, China
| | - Meiling Tian
- College of Food Science and Nutritional Engineering, National Engineering Research Center for Fruit and Vegetable Processing, Key Laboratory of Fruits and Vegetables Processing, Ministry of Agriculture; Engineering Research Centre for Fruits and Vegetables Processing, Ministry of Education, China Agricultural University, No.17, Qinghua East Road, Haidian District, Beijing, 100083, China
| | - Junfu Ji
- College of Food Science and Nutritional Engineering, National Engineering Research Center for Fruit and Vegetable Processing, Key Laboratory of Fruits and Vegetables Processing, Ministry of Agriculture; Engineering Research Centre for Fruits and Vegetables Processing, Ministry of Education, China Agricultural University, No.17, Qinghua East Road, Haidian District, Beijing, 100083, China
| | - Xiaosong Hu
- College of Food Science and Nutritional Engineering, National Engineering Research Center for Fruit and Vegetable Processing, Key Laboratory of Fruits and Vegetables Processing, Ministry of Agriculture; Engineering Research Centre for Fruits and Vegetables Processing, Ministry of Education, China Agricultural University, No.17, Qinghua East Road, Haidian District, Beijing, 100083, China
| | - Fang Chen
- College of Food Science and Nutritional Engineering, National Engineering Research Center for Fruit and Vegetable Processing, Key Laboratory of Fruits and Vegetables Processing, Ministry of Agriculture; Engineering Research Centre for Fruits and Vegetables Processing, Ministry of Education, China Agricultural University, No.17, Qinghua East Road, Haidian District, Beijing, 100083, China.
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14
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Zandonadi FS, Ferreira SP, Alexandrino AV, Carnielli CM, Artier J, Barcelos MP, Nicolela NCS, Prieto EL, Goto LS, Belasque J, Novo-Mansur MTM. Periplasm-enriched fractions from Xanthomonas citri subsp. citri type A and X. fuscans subsp. aurantifolii type B present distinct proteomic profiles under in vitro pathogenicity induction. PLoS One 2020; 15:e0243867. [PMID: 33338036 PMCID: PMC7748154 DOI: 10.1371/journal.pone.0243867] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Accepted: 11/29/2020] [Indexed: 12/24/2022] Open
Abstract
The causative agent of Asiatic citrus canker, the Gram-negative bacterium Xanthomonas citri subsp. citri (XAC), produces more severe symptoms and attacks a larger number of citric hosts than Xanthomonas fuscans subsp. aurantifolii XauB and XauC, the causative agents of cancrosis, a milder form of the disease. Here we report a comparative proteomic analysis of periplasmic-enriched fractions of XAC and XauB in XAM-M, a pathogenicity- inducing culture medium, for identification of differential proteins. Proteins were resolved by two-dimensional electrophoresis combined with liquid chromatography-mass spectrometry. Among the 12 proteins identified from the 4 unique spots from XAC in XAM-M (p<0.05) were phosphoglucomutase (PGM), enolase, xylose isomerase (XI), transglycosylase, NAD(P)H-dependent glycerol 3-phosphate dehydrogenase, succinyl-CoA synthetase β subunit, 6-phosphogluconate dehydrogenase, and conserved hypothetical proteins XAC0901 and XAC0223; most of them were not detected as differential for XAC when both bacteria were grown in NB medium, a pathogenicity non-inducing medium. XauB showed a very different profile from XAC in XAM-M, presenting 29 unique spots containing proteins related to a great diversity of metabolic pathways. Preponderant expression of PGM and XI in XAC was validated by Western Blot analysis in the periplasmic-enriched fractions of both bacteria. This work shows remarkable differences between the periplasmic-enriched proteomes of XAC and XauB, bacteria that cause symptoms with distinct degrees of severity during citrus infection. The results suggest that some proteins identified in XAC can have an important role in XAC pathogenicity.
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Affiliation(s)
- Flávia S. Zandonadi
- Laboratório de Bioquímica e Biologia Molecular Aplicada, Departamento de Genética e Evolução, Universidade Federal de São Carlos, UFSCar, São Carlos, São Paulo, Brazil
| | - Sílvia P. Ferreira
- Laboratório de Bioquímica e Biologia Molecular Aplicada, Departamento de Genética e Evolução, Universidade Federal de São Carlos, UFSCar, São Carlos, São Paulo, Brazil
| | - André V. Alexandrino
- Laboratório de Bioquímica e Biologia Molecular Aplicada, Departamento de Genética e Evolução, Universidade Federal de São Carlos, UFSCar, São Carlos, São Paulo, Brazil
| | - Carolina M. Carnielli
- Laboratório de Bioquímica e Biologia Molecular Aplicada, Departamento de Genética e Evolução, Universidade Federal de São Carlos, UFSCar, São Carlos, São Paulo, Brazil
| | - Juliana Artier
- Laboratório de Bioquímica e Biologia Molecular Aplicada, Departamento de Genética e Evolução, Universidade Federal de São Carlos, UFSCar, São Carlos, São Paulo, Brazil
| | - Mariana P. Barcelos
- Laboratório de Bioquímica e Biologia Molecular Aplicada, Departamento de Genética e Evolução, Universidade Federal de São Carlos, UFSCar, São Carlos, São Paulo, Brazil
| | - Nicole C. S. Nicolela
- Laboratório de Bioquímica e Biologia Molecular Aplicada, Departamento de Genética e Evolução, Universidade Federal de São Carlos, UFSCar, São Carlos, São Paulo, Brazil
| | - Evandro L. Prieto
- Laboratório de Bioquímica e Biologia Molecular Aplicada, Departamento de Genética e Evolução, Universidade Federal de São Carlos, UFSCar, São Carlos, São Paulo, Brazil
| | - Leandro S. Goto
- Laboratório de Bioquímica e Biologia Molecular Aplicada, Departamento de Genética e Evolução, Universidade Federal de São Carlos, UFSCar, São Carlos, São Paulo, Brazil
| | - José Belasque
- Departamento de Fitopatologia e Nematologia, Escola Superior de Agricultura “Luiz de Queiroz”, Universidade de São Paulo, USP, Piracicaba, São Paulo, Brazil
| | - Maria Teresa Marques Novo-Mansur
- Laboratório de Bioquímica e Biologia Molecular Aplicada, Departamento de Genética e Evolução, Universidade Federal de São Carlos, UFSCar, São Carlos, São Paulo, Brazil
- * E-mail:
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15
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Liu M, Fu Y, Gao W, Xian M, Zhao G. Highly Efficient Biosynthesis of Hypoxanthine in Escherichia coli and Transcriptome-Based Analysis of the Purine Metabolism. ACS Synth Biol 2020; 9:525-535. [PMID: 32049513 DOI: 10.1021/acssynbio.9b00396] [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] [Indexed: 11/29/2022]
Abstract
Nucleosides and purine analogues have multiple functions in cell physiology, food additives, and pharmaceuticals, and some are produced on a large scale using different microorganisms. However, biosynthesis of purines is still lacking. In the present study, we engineered the de novo purine biosynthesis pathway, branched pathways, and a global regulator to ensure highly efficient hypoxanthine production by Escherichia coli. The engineered strain Q2973 produced 1243 mg/L hypoxanthine in fed-batch fermentation, accompanied by an extremely low accumulation of byproducts such as acetate and xanthine. We also performed global gene expression analysis to illustrate the mechanism for improving hypoxanthine production. This study demonstrated the feasibility of large-scale hypoxanthine production byan engineered E. coli strain, and provides a reference for subsequent studies on purine analogues and nucleosides.
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Affiliation(s)
- Min Liu
- CAS Key Laboratory of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Siences, Qingdao, 266101, China
| | - Yingxin Fu
- CAS Key Laboratory of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Siences, Qingdao, 266101, China
| | - Wenjie Gao
- CAS Key Laboratory of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Siences, Qingdao, 266101, China
| | - Mo Xian
- CAS Key Laboratory of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Siences, Qingdao, 266101, China
| | - Guang Zhao
- CAS Key Laboratory of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Siences, Qingdao, 266101, China
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16
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Nguyen JH, Chung JD, Lynch GS, Ryall JG. The Microenvironment Is a Critical Regulator of Muscle Stem Cell Activation and Proliferation. Front Cell Dev Biol 2019; 7:254. [PMID: 31737625 PMCID: PMC6828616 DOI: 10.3389/fcell.2019.00254] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Accepted: 10/14/2019] [Indexed: 12/21/2022] Open
Abstract
Skeletal muscle has a remarkable capacity to regenerate following injury, a property conferred by a resident population of muscle stem cells (MuSCs). In response to injury, MuSCs must double their cellular content to divide, a process requiring significant new biomass in the form of nucleotides, phospholipids, and amino acids. This new biomass is derived from a series of intracellular metabolic cycles and alternative routing of carbon. In this review, we examine the link between metabolism and skeletal muscle regeneration with particular emphasis on the role of the cellular microenvironment in supporting the production of new biomass and MuSC proliferation.
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Affiliation(s)
- John H Nguyen
- Department of Physiology, Centre for Muscle Research, The University of Melbourne, Melbourne, VIC, Australia
| | - Jin D Chung
- Department of Physiology, Centre for Muscle Research, The University of Melbourne, Melbourne, VIC, Australia
| | - Gordon S Lynch
- Department of Physiology, Centre for Muscle Research, The University of Melbourne, Melbourne, VIC, Australia
| | - James G Ryall
- Department of Physiology, Centre for Muscle Research, The University of Melbourne, Melbourne, VIC, Australia
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17
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Cheng F, Yu H, Stephanopoulos G. Engineering Corynebacterium glutamicum for high-titer biosynthesis of hyaluronic acid. Metab Eng 2019; 55:276-289. [DOI: 10.1016/j.ymben.2019.07.003] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Revised: 06/30/2019] [Accepted: 07/09/2019] [Indexed: 10/26/2022]
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18
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Zhang Y, Cai J, Shang X, Wang B, Liu S, Chai X, Tan T, Zhang Y, Wen T. A new genome-scale metabolic model of Corynebacterium glutamicum and its application. BIOTECHNOLOGY FOR BIOFUELS 2017; 10:169. [PMID: 28680478 PMCID: PMC5493880 DOI: 10.1186/s13068-017-0856-3] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2017] [Accepted: 06/22/2017] [Indexed: 05/21/2023]
Abstract
BACKGROUND Corynebacterium glutamicum is an important platform organism for industrial biotechnology to produce amino acids, organic acids, bioplastic monomers, and biofuels. The metabolic flexibility, broad substrate spectrum, and fermentative robustness of C. glutamicum make this organism an ideal cell factory to manufacture desired products. With increases in gene function, transport system, and metabolic profile information under certain conditions, developing a comprehensive genome-scale metabolic model (GEM) of C. glutamicum ATCC13032 is desired to improve prediction accuracy, elucidate cellular metabolism, and guide metabolic engineering. RESULTS Here, we constructed a new GEM for ATCC13032, iCW773, consisting of 773 genes, 950 metabolites, and 1207 reactions. Compared to the previous model, iCW773 supplemented 496 gene-protein-reaction associations, refined five lumped reactions, balanced the mass and charge, and constrained the directionality of reactions. The simulated growth rates of C. glutamicum cultivated on seven different carbon sources using iCW773 were consistent with experimental values. Pearson's correlation coefficient between the iCW773-simulated and experimental fluxes was 0.99, suggesting that iCW773 provided an accurate intracellular flux distribution of the wild-type strain growing on glucose. Furthermore, genetic interventions for overproducing l-lysine, 1,2-propanediol and isobutanol simulated using OptForceMUST were in accordance with reported experimental results, indicating the practicability of iCW773 for the design of metabolic networks to overproduce desired products. In vivo genetic modifications of iCW773-predicted targets resulted in the de novo generation of an l-proline-overproducing strain. In fed-batch culture, the engineered C. glutamicum strain produced 66.43 g/L l-proline in 60 h with a yield of 0.26 g/g (l-proline/glucose) and a productivity of 1.11 g/L/h. To our knowledge, this is the highest titer and productivity reported for l-proline production using glucose as the carbon resource in a minimal medium. CONCLUSIONS Our developed iCW773 serves as a high-quality platform for model-guided strain design to produce industrial bioproducts of interest. This new GEM will be a successful multidisciplinary tool and will make valuable contributions to metabolic engineering in academia and industry.
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Affiliation(s)
- Yu Zhang
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101 China
- University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Jingyi Cai
- Beijing University of Chemical Technology, Beijing, 100029 China
| | - Xiuling Shang
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101 China
| | - Bo Wang
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101 China
- University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Shuwen Liu
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101 China
| | - Xin Chai
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101 China
- University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Tianwei Tan
- Beijing University of Chemical Technology, Beijing, 100029 China
| | - Yun Zhang
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101 China
| | - Tingyi Wen
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101 China
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing, 100049 China
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19
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Li H, Zhang L, Guo W, Xu D. Development of a genetically engineered Escherichia coli strain for plasmid transformation in Corynebacterium glutamicum. J Microbiol Methods 2016; 131:156-160. [DOI: 10.1016/j.mimet.2016.10.019] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2016] [Revised: 10/24/2016] [Accepted: 10/24/2016] [Indexed: 10/20/2022]
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20
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Engineering a microbial platform for de novo biosynthesis of diverse methylxanthines. Metab Eng 2016; 38:191-203. [PMID: 27519552 DOI: 10.1016/j.ymben.2016.08.003] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2016] [Revised: 06/24/2016] [Accepted: 08/09/2016] [Indexed: 11/20/2022]
Abstract
Engineered microbial biosynthesis of plant natural products can support manufacturing of complex bioactive molecules and enable discovery of non-naturally occurring derivatives. Purine alkaloids, including caffeine (coffee), theophylline (antiasthma drug), theobromine (chocolate), and other methylxanthines, play a significant role in pharmacology and food chemistry. Here, we engineered the eukaryotic microbial host Saccharomyces cerevisiae for the de novo biosynthesis of methylxanthines. We constructed a xanthine-to-xanthosine conversion pathway in native yeast central metabolism to increase endogenous purine flux for the production of 7-methylxanthine, a key intermediate in caffeine biosynthesis. Yeast strains were further engineered to produce caffeine through expression of several enzymes from the coffee plant. By expressing combinations of different N-methyltransferases, we were able to demonstrate re-direction of flux to an alternate pathway and develop strains that support the production of diverse methylxanthines. We achieved production of 270μg/L, 61μg/L, and 3700μg/L of caffeine, theophylline, and 3-methylxanthine, respectively, in 0.3-L bench-scale batch fermentations. The constructed strains provide an early platform for de novo production of methylxanthines and with further development will advance the discovery and synthesis of xanthine derivatives.
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21
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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: 1.4] [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]
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22
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Ledesma-Amaro R, Buey RM, Revuelta JL. Increased production of inosine and guanosine by means of metabolic engineering of the purine pathway in Ashbya gossypii. Microb Cell Fact 2015; 14:58. [PMID: 25889888 PMCID: PMC4407346 DOI: 10.1186/s12934-015-0234-4] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2015] [Accepted: 03/25/2015] [Indexed: 11/25/2022] Open
Abstract
Background Inosine and guanosine monophosphate nucleotides are convenient sources of the umami flavor, with attributed beneficial health effects that have renewed commercial interest in nucleotide fermentations. Accordingly, several bacterial strains that excrete high levels of inosine and guanosine nucleosides are currently used in the food industry for this purpose. Results In the present study, we show that the filamentous fungus Ashbya gossypii, a natural riboflavin overproducer, excretes high amounts of inosine and guanosine nucleosides to the culture medium. Following a rational metabolic engineering approach of the de novo purine nucleotide biosynthetic pathway, we increased the excreted levels of inosine up to 27-fold. Conclusions We generated Ashbya gossypii strains with improved production titers of inosine and guanosine. Our results point to Ashbya gossypii as the first eukaryotic microorganism representing a promising candidate, susceptible to further manipulation, for industrial nucleoside fermentation. Electronic supplementary material The online version of this article (doi:10.1186/s12934-015-0234-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Rodrigo Ledesma-Amaro
- Departamento de Microbiología y Genética, Metabolic Engineering Group, Universidad de Salamanca, Laboratory 323, Edificio Departamental, Campus Miguel de Unamuno, 37007, Salamanca, Spain.
| | - Ruben M Buey
- Departamento de Microbiología y Genética, Metabolic Engineering Group, Universidad de Salamanca, Laboratory 323, Edificio Departamental, Campus Miguel de Unamuno, 37007, Salamanca, Spain.
| | - Jose Luis Revuelta
- Departamento de Microbiología y Genética, Metabolic Engineering Group, Universidad de Salamanca, Laboratory 323, Edificio Departamental, Campus Miguel de Unamuno, 37007, Salamanca, Spain.
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Shi T, Wang Y, Wang Z, Wang G, Liu D, Fu J, Chen T, Zhao X. Deregulation of purine pathway in Bacillus subtilis and its use in riboflavin biosynthesis. Microb Cell Fact 2014; 13:101. [PMID: 25023436 PMCID: PMC4223553 DOI: 10.1186/s12934-014-0101-8] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2014] [Accepted: 07/06/2014] [Indexed: 11/15/2022] Open
Abstract
Background Purine nucleotides are essential metabolites for living organisms because they are involved in many important processes, such as nucleic acid synthesis, energy supply, and biosynthesis of several amino acids and riboflavin. Owing to the pivotal roles of purines in cell physiology, the pool of intracellular purine nucleotides must be maintained under strict control, and hence the de novo purine biosynthetic pathway is tightly regulated by transcription repression and inhibition mechanism. Deregulation of purine pathway is essential for this pathway engineering in Bacillus subtilis. Results Deregulation of purine pathway was attempted to improve purine nucleotides supply, based on a riboflavin producer B. subtilis strain with modification of its rib operon. To eliminate transcription repression, the pur operon repressor PurR and the 5’-UTR of pur operon containing a guanine-sensing riboswitch were disrupted. Quantitative RT-PCR analysis revealed that the relative transcription levels of purine genes were up-regulated about 380 times. Furthermore, site-directed mutagenesis was successfully introduced into PRPP amidotransferase (encoded by purF) to remove feedback inhibition by homologous alignment and analysis. Overexpression of the novel mutant PurF (D293V, K316Q and S400W) significantly increased PRPP amidotransferase activity and triggered a strong refractory effect on purine nucleotides mediated inhibition. Intracellular metabolite target analysis indicated that the purine nucleotides supply in engineered strains was facilitated by a stepwise gene-targeted deregulation. With these genetic manipulations, we managed to enhance the metabolic flow through purine pathway and consequently increased riboflavin production 3-fold (826.52 mg/L) in the purF-VQW mutant strain. Conclusions A sequential optimization strategy was applied to deregulate the rib operon and purine pathway of B. subtilis to create genetic diversities and to improve riboflavin production. Based on the deregulation of purine pathway at transcription and metabolic levels, an extended application is recommended for the yield of products, like inosine, guanosine, adenosine and folate which are directly stemming from purine pathway in B. subtilis.
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