1
|
Tian Z, Liu L, Wu L, Yang Z, Zhang Y, Du L, Zhang D. Enhancement of vitamin B 6 production driven by omics analysis combined with fermentation optimization. Microb Cell Fact 2024; 23:137. [PMID: 38750497 PMCID: PMC11095007 DOI: 10.1186/s12934-024-02405-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Accepted: 04/24/2024] [Indexed: 05/19/2024] Open
Abstract
BACKGROUND Microbial engineering aims to enhance the ability of bacteria to produce valuable products, including vitamin B6 for various applications. Numerous microorganisms naturally produce vitamin B6, yet the metabolic pathways involved are rigorously controlled. This regulation by the accumulation of vitamin B6 poses a challenge in constructing an efficient cell factory. RESULTS In this study, we conducted transcriptome and metabolome analyses to investigate the effects of the accumulation of pyridoxine, which is the major commercial form of vitamin B6, on cellular processes in Escherichia coli. Our omics analysis revealed associations between pyridoxine and amino acids, as well as the tricarboxylic acid (TCA) cycle. Based on these findings, we identified potential targets for fermentation optimization, including succinate, amino acids, and the carbon-to-nitrogen (C/N) ratio. Through targeted modifications, we achieved pyridoxine titers of approximately 514 mg/L in shake flasks and 1.95 g/L in fed-batch fermentation. CONCLUSION Our results provide insights into pyridoxine biosynthesis within the cellular metabolic network for the first time. Our comprehensive analysis revealed that the fermentation process resulted in a remarkable final yield of 1.95 g/L pyridoxine, the highest reported yield to date. This work lays a foundation for the green industrial production of vitamin B6 in the future.
Collapse
Affiliation(s)
- Zhizhong Tian
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin, 300457, China
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
| | - Linxia Liu
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
- National Center of Technology Innovation for Synthetic Biology, Tianjin, 300308, China
- Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
| | - Lijuan Wu
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
| | - Zixuan Yang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
| | - Yahui Zhang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
| | - Liping Du
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin, 300457, China.
| | - Dawei Zhang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China.
- National Center of Technology Innovation for Synthetic Biology, Tianjin, 300308, China.
- Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
| |
Collapse
|
2
|
Li X, Zabed HM, Yun J, Zhang Y, Zhao M, Zhang C, Ouyang Z, Li J, Qi X. Sustainable bio-manufacturing of D-arabitol through combinatorial engineering of Zygosaccharomyces rouxii, bioprocess optimization and downstream separation. BIORESOURCE TECHNOLOGY 2024; 393:130162. [PMID: 38065516 DOI: 10.1016/j.biortech.2023.130162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Revised: 12/04/2023] [Accepted: 12/04/2023] [Indexed: 01/18/2024]
Abstract
Biosynthesis of D-arabitol, a high value-added platform chemical, from renewable carbon sources provides a sustainable and eco-friendly alternative to the chemical industry. Here, a robust brewing yeast, Zygosaccharomyces rouxii, capable of naturally producing D-arabitol was rewired through genome sequencing-based metabolic engineering. The recombinant Z. rouxii obtained by reinforcing the native D-xylulose pathway, improving reductive power of the rate-limiting step, and inhibiting the shunt pathway, produced 73.61% higher D-arabitol than the parent strain. Subsequently, optimization of the fermentation medium composition for the engineered strain provided 137.36 g/L D-arabitol, with a productivity of 0.64 g/L/h in a fed-batch experiment. Finally, the downstream separation of D-arabitol from the complex fermentation broth using an ethanol precipitation method provided a purity of 96.53%. This study highlights the importance of D-xylulose pathway modification in D-arabitol biosynthesis, and pave a complete and efficient way for the sustainable manufacturing of this value-added compound from biosynthesis to preparation.
Collapse
Affiliation(s)
- Xiaolan Li
- School of Pharmacy, Jiangsu University, Zhenjiang 212013, Jiangsu, PR China
| | - Hossain M Zabed
- School of Life Sciences, Guangzhou University, Guangzhou 510006, Guangdong, PR China
| | - Junhua Yun
- School of Life Sciences, Guangzhou University, Guangzhou 510006, Guangdong, PR China
| | - Yufei Zhang
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang 212013, Jiangsu, PR China
| | - Mei Zhao
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang 212013, Jiangsu, PR China
| | - Cunsheng Zhang
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang 212013, Jiangsu, PR China
| | - Zhen Ouyang
- School of Pharmacy, Jiangsu University, Zhenjiang 212013, Jiangsu, PR China
| | - Jia Li
- School of Life Sciences, Guangzhou University, Guangzhou 510006, Guangdong, PR China
| | - Xianghui Qi
- School of Life Sciences, Guangzhou University, Guangzhou 510006, Guangdong, PR China.
| |
Collapse
|
3
|
Wang ZD, Wang BT, Jin L, Ruan HH, Jin FJ. Implications of carbon catabolite repression for Aspergillus-based cell factories: A review. Biotechnol J 2024; 19:e2300551. [PMID: 38403447 DOI: 10.1002/biot.202300551] [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: 10/11/2023] [Revised: 12/19/2023] [Accepted: 12/26/2023] [Indexed: 02/27/2024]
Abstract
Carbon catabolite repression (CCR) is a global regulatory mechanism that allows organisms to preferentially utilize a preferred carbon source (usually glucose) by suppressing the expression of genes associated with the utilization of nonpreferred carbon sources. Aspergillus is a large genus of filamentous fungi, some species of which have been used as microbial cell factories for the production of organic acids, industrial enzymes, pharmaceuticals, and other fermented products due to their safety, substrate convenience, and well-established post-translational modifications. Many recent studies have verified that CCR-related genetic alterations can boost the yield of various carbohydrate-active enzymes (CAZymes), even under CCR conditions. Based on these findings, we emphasize that appropriate regulation of the CCR pathway, especially the expression of the key transcription factor CreA gene, has great potential for further expanding the application of Aspergillus cell factories to develop strains for industrial CAZymes production. Further, the genetically modified CCR strains (chassis hosts) can also be used for the production of other useful natural products and recombinant proteins, among others. We here review the regulatory mechanisms of CCR in Aspergillus and its direct application in enzyme production, as well as its potential application in organic acid and pharmaceutical production to illustrate the effects of CCR on Aspergillus cell factories.
Collapse
Affiliation(s)
- Zhen-Dong Wang
- College of Ecology and Environment, Nanjing Forestry University, Nanjing, China
| | - Bao-Teng Wang
- College of Ecology and Environment, Nanjing Forestry University, Nanjing, China
| | - Long Jin
- College of Ecology and Environment, Nanjing Forestry University, Nanjing, China
| | - Hong-Hua Ruan
- College of Ecology and Environment, Nanjing Forestry University, Nanjing, China
| | - Feng-Jie Jin
- College of Ecology and Environment, Nanjing Forestry University, Nanjing, China
| |
Collapse
|
4
|
Song K, Zhang X, Liu J, Yao Q, Li Y, Hou X, Liu S, Qiu X, Yang Y, Chen L, Hong K, Lin L. Integration of Metabolomics and Transcriptomics to Explore Dynamic Alterations in Fruit Color and Quality in 'Comte de Paris' Pineapples during Ripening Processes. Int J Mol Sci 2023; 24:16384. [PMID: 38003574 PMCID: PMC10671212 DOI: 10.3390/ijms242216384] [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: 09/26/2023] [Revised: 10/24/2023] [Accepted: 11/04/2023] [Indexed: 11/26/2023] Open
Abstract
Pineapple color yellowing and quality promotion gradually manifest as pineapple fruit ripening progresses. To understand the molecular mechanism underlying yellowing in pineapples during ripening, coupled with alterations in fruit quality, comprehensive metabolome and transcriptome investigations were carried out. These investigations were conducted using pulp samples collected at three distinct stages of maturity: young fruit (YF), mature fruit (MF), and fully mature fruit (FMF). This study revealed a noteworthy increase in the levels of total phenols and flavones, coupled with a concurrent decline in lignin and total acid contents as the fruit transitioned from YF to FMF. Furthermore, the analysis yielded 167 differentially accumulated metabolites (DAMs) and 2194 differentially expressed genes (DEGs). Integration analysis based on DAMs and DEGs revealed that the biosynthesis of plant secondary metabolites, particularly the flavonol, flavonoid, and phenypropanoid pathways, plays a pivotal role in fruit yellowing. Additionally, RNA-seq analysis showed that structural genes, such as FLS, FNS, F3H, DFR, ANR, and GST, in the flavonoid biosynthetic pathway were upregulated, whereas the COMT, CCR, and CAD genes involved in lignin metabolism were downregulated as fruit ripening progressed. APX as well as PPO, and ACO genes related to the organic acid accumulations were upregulated and downregulated, respectively. Importantly, a comprehensive regulatory network encompassing genes that contribute to the metabolism of flavones, flavonols, lignin, and organic acids was proposed. This network sheds light on the intricate processes that underlie fruit yellowing and quality alterations. These findings enhance our understanding of the regulatory pathways governing pineapple ripening and offer valuable scientific insight into the molecular breeding of pineapples.
Collapse
Affiliation(s)
- Kanghua Song
- Key Laboratory for Postharvest Physiology and Technology of Tropical Horticultural Products of Hainan Province, South Subtropical Crop Research Institute, Chinese Academy of Tropical Agricultural Sciences, Zhanjiang 524091, China; (K.S.); (X.Z.); (Q.Y.); (X.H.); (S.L.); (Y.Y.); (L.C.)
| | - Xiumei Zhang
- Key Laboratory for Postharvest Physiology and Technology of Tropical Horticultural Products of Hainan Province, South Subtropical Crop Research Institute, Chinese Academy of Tropical Agricultural Sciences, Zhanjiang 524091, China; (K.S.); (X.Z.); (Q.Y.); (X.H.); (S.L.); (Y.Y.); (L.C.)
| | - Jiameng Liu
- Hainan Key Laboratory of Storage & Processing of Fruits and Vegetables, Agricultural Products Processing Research Institute, Chinese Academy of Tropical Agricultural Sciences, Zhanjiang 524001, China; (J.L.); (X.Q.)
| | - Quansheng Yao
- Key Laboratory for Postharvest Physiology and Technology of Tropical Horticultural Products of Hainan Province, South Subtropical Crop Research Institute, Chinese Academy of Tropical Agricultural Sciences, Zhanjiang 524091, China; (K.S.); (X.Z.); (Q.Y.); (X.H.); (S.L.); (Y.Y.); (L.C.)
| | - Yixing Li
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China;
| | - Xiaowan Hou
- Key Laboratory for Postharvest Physiology and Technology of Tropical Horticultural Products of Hainan Province, South Subtropical Crop Research Institute, Chinese Academy of Tropical Agricultural Sciences, Zhanjiang 524091, China; (K.S.); (X.Z.); (Q.Y.); (X.H.); (S.L.); (Y.Y.); (L.C.)
| | - Shenghui Liu
- Key Laboratory for Postharvest Physiology and Technology of Tropical Horticultural Products of Hainan Province, South Subtropical Crop Research Institute, Chinese Academy of Tropical Agricultural Sciences, Zhanjiang 524091, China; (K.S.); (X.Z.); (Q.Y.); (X.H.); (S.L.); (Y.Y.); (L.C.)
| | - Xunxia Qiu
- Hainan Key Laboratory of Storage & Processing of Fruits and Vegetables, Agricultural Products Processing Research Institute, Chinese Academy of Tropical Agricultural Sciences, Zhanjiang 524001, China; (J.L.); (X.Q.)
| | - Yue Yang
- Key Laboratory for Postharvest Physiology and Technology of Tropical Horticultural Products of Hainan Province, South Subtropical Crop Research Institute, Chinese Academy of Tropical Agricultural Sciences, Zhanjiang 524091, China; (K.S.); (X.Z.); (Q.Y.); (X.H.); (S.L.); (Y.Y.); (L.C.)
| | - Li Chen
- Key Laboratory for Postharvest Physiology and Technology of Tropical Horticultural Products of Hainan Province, South Subtropical Crop Research Institute, Chinese Academy of Tropical Agricultural Sciences, Zhanjiang 524091, China; (K.S.); (X.Z.); (Q.Y.); (X.H.); (S.L.); (Y.Y.); (L.C.)
| | - Keqian Hong
- Key Laboratory for Postharvest Physiology and Technology of Tropical Horticultural Products of Hainan Province, South Subtropical Crop Research Institute, Chinese Academy of Tropical Agricultural Sciences, Zhanjiang 524091, China; (K.S.); (X.Z.); (Q.Y.); (X.H.); (S.L.); (Y.Y.); (L.C.)
| | - Lijing Lin
- Hainan Key Laboratory of Storage & Processing of Fruits and Vegetables, Agricultural Products Processing Research Institute, Chinese Academy of Tropical Agricultural Sciences, Zhanjiang 524001, China; (J.L.); (X.Q.)
| |
Collapse
|