1
|
Yue X, Tian T, Duan W, Zhao Y, Shi J, Ran J, Zhang Y, Yuan S, Xu X, Zuo J, Feng B, Wang Q. Ectoine maintains the flavor and nutritional quality of broccoli during postharvest storage. Food Chem 2024; 458:140204. [PMID: 38964092 DOI: 10.1016/j.foodchem.2024.140204] [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: 04/04/2024] [Revised: 06/13/2024] [Accepted: 06/22/2024] [Indexed: 07/06/2024]
Abstract
The bacterial derived osmolyte ectoine has been shown to stabilize cell structure and function, a property that may help to extend the shelf life of broccoli. The impact of ectoine on broccoli stored for 4 d at 20 °C and 90% relative humidity was investigated. Results indicated that 0.20% ectoine treatment maintained the quality of broccoli, by reducing rate of respiration and ethylene generation, while increasing the levels of total phenolics, flavonoids, TSS, soluble protein, and vitamin C, relative to control. Headspace-gas chromatography-mass spectrometry, transcriptomic and metabolomic analyses revealed that ectoine stabilized aroma components in broccoli by maintaining level of volatile compounds and altered the expression of genes and metabolites associated with sulfur metabolism, as well as fatty acid and amino acid biosynthesis pathways. These findings provide a greater insight into how ectoine preserves the flavor and nutritional quality of broccoli, thus, extending its shelf life.
Collapse
Affiliation(s)
- Xiaozhen Yue
- Key Laboratory of Vegetable Postharvest Processing, Ministry of Agriculture and Rural Affairs, Beijing Key Laboratory of Fruits and Vegetable Storage and Processing, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China) of Ministry of Agriculture, Key Laboratory of Urban Agriculture (North) of Ministry of Agriculture, Institute of Agri-food Processing and Nutrition, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Tian Tian
- Key Laboratory of Vegetable Postharvest Processing, Ministry of Agriculture and Rural Affairs, Beijing Key Laboratory of Fruits and Vegetable Storage and Processing, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China) of Ministry of Agriculture, Key Laboratory of Urban Agriculture (North) of Ministry of Agriculture, Institute of Agri-food Processing and Nutrition, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China; College of Agricultural, Guangxi University, Nanning 530004, China
| | - Wenhui Duan
- Key Laboratory of Food Nutrition and Functional Food of Hainan Province, School of Food Science and Engineering, Hainan University, Haikou 570228, China
| | - Yaqi Zhao
- Key Laboratory of Vegetable Postharvest Processing, Ministry of Agriculture and Rural Affairs, Beijing Key Laboratory of Fruits and Vegetable Storage and Processing, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China) of Ministry of Agriculture, Key Laboratory of Urban Agriculture (North) of Ministry of Agriculture, Institute of Agri-food Processing and Nutrition, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Junyan Shi
- Key Laboratory of Vegetable Postharvest Processing, Ministry of Agriculture and Rural Affairs, Beijing Key Laboratory of Fruits and Vegetable Storage and Processing, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China) of Ministry of Agriculture, Key Laboratory of Urban Agriculture (North) of Ministry of Agriculture, Institute of Agri-food Processing and Nutrition, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Jie Ran
- Key Laboratory of Vegetable Postharvest Processing, Ministry of Agriculture and Rural Affairs, Beijing Key Laboratory of Fruits and Vegetable Storage and Processing, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China) of Ministry of Agriculture, Key Laboratory of Urban Agriculture (North) of Ministry of Agriculture, Institute of Agri-food Processing and Nutrition, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | | | - Shuzhi Yuan
- Key Laboratory of Vegetable Postharvest Processing, Ministry of Agriculture and Rural Affairs, Beijing Key Laboratory of Fruits and Vegetable Storage and Processing, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China) of Ministry of Agriculture, Key Laboratory of Urban Agriculture (North) of Ministry of Agriculture, Institute of Agri-food Processing and Nutrition, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Xiaodi Xu
- Key Laboratory of Vegetable Postharvest Processing, Ministry of Agriculture and Rural Affairs, Beijing Key Laboratory of Fruits and Vegetable Storage and Processing, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China) of Ministry of Agriculture, Key Laboratory of Urban Agriculture (North) of Ministry of Agriculture, Institute of Agri-food Processing and Nutrition, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Jinhua Zuo
- Key Laboratory of Vegetable Postharvest Processing, Ministry of Agriculture and Rural Affairs, Beijing Key Laboratory of Fruits and Vegetable Storage and Processing, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China) of Ministry of Agriculture, Key Laboratory of Urban Agriculture (North) of Ministry of Agriculture, Institute of Agri-food Processing and Nutrition, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China.
| | - Bihong Feng
- College of Agricultural, Guangxi University, Nanning 530004, China.
| | - Qing Wang
- Key Laboratory of Vegetable Postharvest Processing, Ministry of Agriculture and Rural Affairs, Beijing Key Laboratory of Fruits and Vegetable Storage and Processing, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China) of Ministry of Agriculture, Key Laboratory of Urban Agriculture (North) of Ministry of Agriculture, Institute of Agri-food Processing and Nutrition, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China.
| |
Collapse
|
2
|
Qin Z, Li L, Zeng W, Li H, Zhou J, Xu S. High efficiency production of 5-hydroxyectoine Zusing metabolically engineered Escherichia coli. BIORESOURCE TECHNOLOGY 2024; 413:131493. [PMID: 39284374 DOI: 10.1016/j.biortech.2024.131493] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2024] [Revised: 09/11/2024] [Accepted: 09/12/2024] [Indexed: 09/21/2024]
Abstract
The 5-hydroxyectoine is a natural protective agent with long-lasting moisturising and radiation resistance properties. It can be naturally synthesized by some extremophiles using the "bacterial milking" process, but this can corrode bioreactors and downstream purification may cause environmental pollution. In this study, an engineered Escherichia coli (E. coli) strain was constructed for the 5-hydroxyectoine production. First, three ectoine hydroxylases were characterised and the enzyme from Halomonas elongata was the most effective. The L-2,4-diaminobutyrate transaminase mutant was introduced into the engineered strain, which could accumulate 2.8 g/L 5-hydroxyectoine in shake flasks. By activating the glyoxylate cycle and balancing the α-ketoglutarate distribution, the 5-hydroxyectoine titer was further increased to 3.4 g/L. Finally, the optimized strain synthesized 58 g/L 5-hydroxyectoine via a semi-continuous feeding process in a NaCl-free medium. Overall, this study reported the highest titer of 5-hydroxyectoine synthesized by E. coli and established a low-salt fermentation process through the aforementioned efforts.
Collapse
Affiliation(s)
- Zhijie Qin
- National Engineering Research Center of Cereal Fermentation and Food Biomanufacturing, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; Science Center for Future Foods, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Lihong Li
- National Engineering Research Center of Cereal Fermentation and Food Biomanufacturing, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; Science Center for Future Foods, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Weizhu Zeng
- National Engineering Research Center of Cereal Fermentation and Food Biomanufacturing, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; Science Center for Future Foods, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Hongbiao Li
- National Engineering Research Center of Cereal Fermentation and Food Biomanufacturing, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; Science Center for Future Foods, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Jingwen Zhou
- National Engineering Research Center of Cereal Fermentation and Food Biomanufacturing, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; Science Center for Future Foods, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; School of Food Science and Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Sha Xu
- National Engineering Research Center of Cereal Fermentation and Food Biomanufacturing, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; School of Food Science and Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China.
| |
Collapse
|
3
|
Chen Y, Liu Y, Meng Y, Jiang Y, Xiong W, Wang S, Yang C, Liu R. Elucidating the salt-tolerant mechanism of Halomonas cupida J9 and unsterile ectoine production from lignocellulosic biomass. Microb Cell Fact 2024; 23:237. [PMID: 39217338 PMCID: PMC11365141 DOI: 10.1186/s12934-024-02515-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2024] [Accepted: 08/24/2024] [Indexed: 09/04/2024] Open
Abstract
BACKGROUND Ectoine as an amino acid derivative is widely applied in many fields, such as the food industry, cosmetic manufacturing, biologics, and therapeutic agent. Large-scale production of ectoine is mainly restricted by the cost of fermentation substrates (e.g., carbon sources) and sterilization. RESULTS In this study, Halomonas cupida J9 was shown to be capable of synthesizing ectoine using xylose as the sole carbon source. A pathway was proposed in H. cupida J9 that synergistically utilizes both WBG xylose metabolism and EMP glucose metabolism for the synthesis of ectoine. Transcriptome analysis indicated that expression of ectoine biosynthesis module was enhanced under salt stress. Ectoine production by H. cupida J9 was enhanced by improving the expression of ectoine biosynthesis module, increasing the intracellular supply of the precursor oxaloacetate, and utilizing urea as the nitrogen source. The constructed J9U-P8EC achieved a record ectoine production of 4.12 g/L after 60 h of xylose fermentation. Finally, unsterile production of ectoine by J9U-P8EC from either a glucose-xylose mixture or corn straw hydrolysate was demonstrated, with an output of 8.55 g/L and 1.30 g/L of ectoine, respectively. CONCLUSIONS This study created a promising H. cupida J9-based cell factory for low-cost production of ectoine. Our results highlight the potential of J9U-P8EC to utilize lignocellulose-rich agriculture waste for open production of ectoine.
Collapse
Affiliation(s)
- Yaping Chen
- Key Laboratory of Molecular Microbiology and Technology for Ministry of Education, College of Life Sciences, Nankai University, Tianjin, 300071, China
| | - Yujie Liu
- Key Laboratory of Molecular Microbiology and Technology for Ministry of Education, College of Life Sciences, Nankai University, Tianjin, 300071, China
| | - Yan Meng
- Key Laboratory of Molecular Microbiology and Technology for Ministry of Education, College of Life Sciences, Nankai University, Tianjin, 300071, China
| | - Yuting Jiang
- Key Laboratory of Molecular Microbiology and Technology for Ministry of Education, College of Life Sciences, Nankai University, Tianjin, 300071, China
| | - Weini Xiong
- Key Laboratory of Molecular Microbiology and Technology for Ministry of Education, College of Life Sciences, Nankai University, Tianjin, 300071, China
| | - Shufang Wang
- Key Laboratory of Bioactive Materials for Ministry of Education, College of Life Sciences, Nankai University, Tianjin, 300071, China.
| | - Chao Yang
- Key Laboratory of Molecular Microbiology and Technology for Ministry of Education, College of Life Sciences, Nankai University, Tianjin, 300071, China.
| | - Ruihua Liu
- Tianjin Key Laboratory of Protein Science, College of Life Sciences, Nankai University, Tianjin, 300071, China.
| |
Collapse
|
4
|
Ma Z, Chang R, Zhu L, Zhu D, Deng Y, Guo X, Cheng Z, Chen X. Metabolic Engineering of Corynebacterium glutamicum for Highly Efficient Production of Ectoine. ACS Synth Biol 2024; 13:2081-2090. [PMID: 38607270 DOI: 10.1021/acssynbio.4c00019] [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: 04/13/2024]
Abstract
Ectoine is a compatible solute that functions as a cell protector from various stresses, protecting cells and stabilizing biomolecules, and is widely used in medicine, cosmetics, and biotechnology. Microbial fermentation has been widely used for the large-scale production of ectoine, and a number of fermentation strategies have been developed to increase the ectoine yield, reduce production costs, and simplify the production process. Here, Corynebacterium glutamicum was engineered for ectoine production by heterologous expression of the ectoine biosynthesis operon ectBAC gene from Halomonas elongata, and a series of genetic modifications were implemented. This included introducing the de3 gene from Escherichia coli BL21 (DE3) to express the T7 promoter, eliminating the lysine transporter protein lysE to limit lysine production, and performing a targeted mutation lysCS301Y on aspartate kinase to alleviate feedback inhibition of lysine. The new engineered strain Ect10 obtained an ectoine titer of 115.87 g/L in an optimized fed-batch fermentation, representing the highest ectoine production level in C. glutamicum and achieving the efficient production of ectoine in a low-salt environment.
Collapse
Affiliation(s)
- Zhi Ma
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, PR China
| | - Renjie Chang
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, PR China
| | - Linjiang Zhu
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, PR China
| | - Dianhao Zhu
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, PR China
| | - Yanfeng Deng
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, PR China
| | - Xinying Guo
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, PR China
| | - Ziyi Cheng
- Department of Mechanical & Industrial Engineering, University of Toronto, 5 King's College Road, Toronto, Ontario M5S 3G8, Canada
| | - Xiaolong Chen
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, PR China
- Quzhou Eco-Industrial Innovation Institute, Zhejiang University of Technology, Quzhou 324003, PR China
| |
Collapse
|
5
|
Raimundo I, Rosado PM, Barno AR, Antony CP, Peixoto RS. Unlocking the genomic potential of Red Sea coral probiotics. Sci Rep 2024; 14:14514. [PMID: 38914624 PMCID: PMC11196684 DOI: 10.1038/s41598-024-65152-8] [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: 03/10/2024] [Accepted: 06/17/2024] [Indexed: 06/26/2024] Open
Abstract
The application of beneficial microorganisms for corals (BMC) decreases the bleaching susceptibility and mortality rate of corals. BMC selection is typically performed via molecular and biochemical assays, followed by genomic screening for BMC traits. Herein, we present a comprehensive in silico framework to explore a set of six putative BMC strains. We extracted high-quality DNA from coral samples collected from the Red Sea and performed PacBio sequencing. We identified BMC traits and mechanisms associated with each strain as well as proposed new traits and mechanisms, such as chemotaxis and the presence of phages and bioactive secondary metabolites. The presence of prophages in two of the six studied BMC strains suggests their possible distribution within beneficial bacteria. We also detected various secondary metabolites, such as terpenes, ectoines, lanthipeptides, and lasso peptides. These metabolites possess antimicrobial, antifungal, antiviral, anti-inflammatory, and antioxidant activities and play key roles in coral health by reducing the effects of heat stress, high salinity, reactive oxygen species, and radiation. Corals are currently facing unprecedented challenges, and our revised framework can help select more efficient BMC for use in studies on coral microbiome rehabilitation, coral resilience, and coral restoration.
Collapse
Affiliation(s)
- Inês Raimundo
- Biological and Environmental Science and Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology, Biological and Environmental Science and Engineering Division, Thuwal, Saudi Arabia
| | - Phillipe M Rosado
- Biological and Environmental Science and Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology, Biological and Environmental Science and Engineering Division, Thuwal, Saudi Arabia
| | - Adam R Barno
- Biological and Environmental Science and Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology, Biological and Environmental Science and Engineering Division, Thuwal, Saudi Arabia
| | - Chakkiath P Antony
- Biological and Environmental Science and Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology, Biological and Environmental Science and Engineering Division, Thuwal, Saudi Arabia
| | - Raquel S Peixoto
- Biological and Environmental Science and Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology, Biological and Environmental Science and Engineering Division, Thuwal, Saudi Arabia.
| |
Collapse
|
6
|
Orhan F, Akıncıoğlu A, Ceyran E. Ectoine production from a novel bacterial strain and high-purity purification with a cost-effective and single-step method. J Biotechnol 2024; 388:24-34. [PMID: 38599284 DOI: 10.1016/j.jbiotec.2024.04.003] [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: 11/24/2023] [Revised: 03/08/2024] [Accepted: 04/05/2024] [Indexed: 04/12/2024]
Abstract
This study marks the exploration into the production of ectoine, a valuable compound with significant potential as an antioxidant, osmoprotectant, anti-inflammatory agent, and stabilizer of cell membranes, proteins, and DNA integrity. Our focus centred on investigating the presence of ectoine and optimizing its production by the novel ectoine producer bacterial strain, Piscibacillus halophilus. For the optimization of ectoine production the effects of carbon and nitrogen sources, salt, pH, agitation and incubation period were optimized by one-factor-at-a-time. We started with an initial ectoine content of 46.92 mg/L, and through a series of optimization processes, we achieved a remarkable increase, resulting in an ectoine content of 1498.2 mg/L. The bacterial species P. halophilus achieved its highest ectoine production after 48 h of incubation, with conditions set at 10 % (w/v) salinity, pH of 7.50, and an agitation speed of 160 rpm. These precise conditions were found to be the most favourable for maximizing ectoine production by this strain. Besides, we have achieved successful purification of ectoine from the crude extract through a streamlined single-step process. This purification method has delivered an exceptional level of purity, surpassing 99.15 %, and an impressive yield of over 99 %. Importantly, we accomplished this using readily available and cost-effective strong acids (HCl) and strong bases (NaOH) to arrange pH gradients. The use of acid and base in the purification process of ectoine reflects an innovative and sustainable methodology.
Collapse
Affiliation(s)
- Furkan Orhan
- Agri Ibrahim Cecen University, Art and Science Faculty, Department of Molecular Biology and Genetics, Agri 4100, Turkey; Central Research and Application Laboratory, Agri Ibrahim Cecen University, Agri, Turkey.
| | - Akın Akıncıoğlu
- Central Research and Application Laboratory, Agri Ibrahim Cecen University, Agri, Turkey; Vocational School, Agri Ibrahim Cecen University, Agri, Turkey
| | - Ertuğrul Ceyran
- Central Research and Application Laboratory, Agri Ibrahim Cecen University, Agri, Turkey
| |
Collapse
|
7
|
Yang N, Liu M, Han J, Jiang M, Zeng Y, Liu Y, Xiang H, Zheng Y. Rational engineering of Halomonas salifodinae to enhance hydroxyectoine production under lower-salt conditions. Appl Microbiol Biotechnol 2024; 108:353. [PMID: 38819481 PMCID: PMC11142988 DOI: 10.1007/s00253-024-13197-0] [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: 12/28/2023] [Revised: 05/01/2024] [Accepted: 05/21/2024] [Indexed: 06/01/2024]
Abstract
Hydroxyectoine is an important compatible solute that holds potential for development into a high-value chemical with broad applications. However, the traditional high-salt fermentation for hydroxyectoine production presents challenges in treating the high-salt wastewater. Here, we report the rational engineering of Halomonas salifodinae to improve the bioproduction of hydroxyectoine under lower-salt conditions. The comparative transcriptomic analysis suggested that the increased expression of ectD gene encoding ectoine hydroxylase (EctD) and the decreased expressions of genes responsible for tricarboxylic acid (TCA) cycle contributed to the increased hydroxyectoine production in H. salifodinae IM328 grown under high-salt conditions. By blocking the degradation pathway of ectoine and hydroxyectoine, enhancing the expression of ectD, and increasing the supply of 2-oxoglutarate, the engineered H. salifodinae strain HS328-YNP15 (ΔdoeA::PUP119-ectD p-gdh) produced 8.3-fold higher hydroxyectoine production than the wild-type strain and finally achieved a hydroxyectoine titer of 4.9 g/L in fed-batch fermentation without any detailed process optimization. This study shows the potential to integrate hydroxyectoine production into open unsterile fermentation process that operates under low-salinity and high-alkalinity conditions, paving the way for next-generation industrial biotechnology. KEY POINTS: • Hydroxyectoine production in H. salifodinae correlates with the salinity of medium • Transcriptomic analysis reveals the limiting factors for hydroxyectoine production • The engineered strain produced 8.3-fold more hydroxyectoine than the wild type.
Collapse
Affiliation(s)
- Niping Yang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, No.1 Beichen West Road, Chaoyang District, Beijing, 100101, China
- School of Life Sciences, Hebei University, Baoding, 071002, China
| | - Mengshuang Liu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, No.1 Beichen West Road, Chaoyang District, Beijing, 100101, China
- College of Life Science, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jing Han
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, No.1 Beichen West Road, Chaoyang District, Beijing, 100101, China
| | - Mingyue Jiang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, No.1 Beichen West Road, Chaoyang District, Beijing, 100101, China
- College of Life Science, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yan Zeng
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, No.1 Beichen West Road, Chaoyang District, Beijing, 100101, China
| | - Ying Liu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, No.1 Beichen West Road, Chaoyang District, Beijing, 100101, China
| | - Hua Xiang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, No.1 Beichen West Road, Chaoyang District, Beijing, 100101, China
- College of Life Science, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yanning Zheng
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, No.1 Beichen West Road, Chaoyang District, Beijing, 100101, China.
| |
Collapse
|
8
|
Yadav S, Koenen M, Bale NJ, Reitsma W, Engelmann JC, Stefanova K, Damsté JSS, Villanueva L. Organic matter degradation in the deep, sulfidic waters of the Black Sea: insights into the ecophysiology of novel anaerobic bacteria. MICROBIOME 2024; 12:98. [PMID: 38797849 PMCID: PMC11129491 DOI: 10.1186/s40168-024-01816-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Accepted: 04/15/2024] [Indexed: 05/29/2024]
Abstract
BACKGROUND Recent studies have reported the identity and functions of key anaerobes involved in the degradation of organic matter (OM) in deep (> 1000 m) sulfidic marine habitats. However, due to the lack of available isolates, detailed investigation of their physiology has been precluded. In this study, we cultivated and characterized the ecophysiology of a wide range of novel anaerobes potentially involved in OM degradation in deep (2000 m depth) sulfidic waters of the Black Sea. RESULTS We have successfully cultivated a diverse group of novel anaerobes belonging to various phyla, including Fusobacteriota (strain S5), Bacillota (strains A1T and A2), Spirochaetota (strains M1T, M2, and S2), Bacteroidota (strains B1T, B2, S6, L6, SYP, and M2P), Cloacimonadota (Cloa-SY6), Planctomycetota (Plnct-SY6), Mycoplasmatota (Izemo-BS), Chloroflexota (Chflx-SY6), and Desulfobacterota (strains S3T and S3-i). These microorganisms were able to grow at an elevated hydrostatic pressure of up to 50 MPa. Moreover, this study revealed that different anaerobes were specialized in degrading specific types of OM. Strains affiliated with the phyla Fusobacteriota, Bacillota, Planctomycetota, and Mycoplasmatota were found to be specialized in the degradation of cellulose, cellobiose, chitin, and DNA, respectively, while strains affiliated with Spirochaetota, Bacteroidota, Cloacimonadota, and Chloroflexota preferred to ferment less complex forms of OM. We also identified members of the phylum Desulfobacterota as terminal oxidizers, potentially involved in the consumption of hydrogen produced during fermentation. These results were supported by the identification of genes in the (meta)genomes of the cultivated microbial taxa which encode proteins of specific metabolic pathways. Additionally, we analyzed the composition of membrane lipids of selected taxa, which could be critical for their survival in the harsh environment of the deep sulfidic waters and could potentially be used as biosignatures for these strains in the sulfidic waters of the Black Sea. CONCLUSIONS This is the first report that demonstrates the cultivation and ecophysiology of such a diverse group of microorganisms from any sulfidic marine habitat. Collectively, this study provides a step forward in our understanding of the microbes thriving in the extreme conditions of the deep sulfidic waters of the Black Sea. Video Abstract.
Collapse
Affiliation(s)
- Subhash Yadav
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, 1797AB Den Burg, P.O. Box 59, Texel, The Netherlands
- Department of Microbiology, Radboud Institute for Biological and Environmental Sciences, Radboud University, Nijmegen, The Netherlands
| | - Michel Koenen
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, 1797AB Den Burg, P.O. Box 59, Texel, The Netherlands
| | - Nicole J Bale
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, 1797AB Den Burg, P.O. Box 59, Texel, The Netherlands
| | - Wietse Reitsma
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, 1797AB Den Burg, P.O. Box 59, Texel, The Netherlands
| | - Julia C Engelmann
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, 1797AB Den Burg, P.O. Box 59, Texel, The Netherlands
| | - Kremena Stefanova
- Institute of Oceanology "Fridtjof Nansen", Bulgarian Academy of Sciences, Varna, Bulgaria
| | - Jaap S Sinninghe Damsté
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, 1797AB Den Burg, P.O. Box 59, Texel, The Netherlands
- Faculty of Geosciences, Department of Earth Sciences, Utrecht University, P.O. Box 80.021, 3508 TA, Utrecht, The Netherlands
| | - Laura Villanueva
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, 1797AB Den Burg, P.O. Box 59, Texel, The Netherlands.
- Faculty of Geosciences, Department of Earth Sciences, Utrecht University, P.O. Box 80.021, 3508 TA, Utrecht, The Netherlands.
| |
Collapse
|
9
|
Lim SE, Cho S, Choi Y, Na JG, Lee J. High production of ectoine from methane in genetically engineered Methylomicrobium alcaliphilum 20Z by preventing ectoine degradation. Microb Cell Fact 2024; 23:127. [PMID: 38698430 PMCID: PMC11067125 DOI: 10.1186/s12934-024-02404-2] [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: 03/19/2024] [Accepted: 04/24/2024] [Indexed: 05/05/2024] Open
Abstract
BACKGROUND Methane is a greenhouse gas with a significant potential to contribute to global warming. The biological conversion of methane to ectoine using methanotrophs represents an environmentally and economically beneficial technology, combining the reduction of methane that would otherwise be combusted and released into the atmosphere with the production of value-added products. RESULTS In this study, high ectoine production was achieved using genetically engineered Methylomicrobium alcaliphilum 20Z, a methanotrophic ectoine-producing bacterium, by knocking out doeA, which encodes a putative ectoine hydrolase, resulting in complete inhibition of ectoine degradation. Ectoine was confirmed to be degraded by doeA to N-α-acetyl-L-2,4-diaminobutyrate under nitrogen depletion conditions. Optimal copper and nitrogen concentrations enhanced biomass and ectoine production, respectively. Under optimal fed-batch fermentation conditions, ectoine production proportionate with biomass production was achieved, resulting in 1.0 g/L of ectoine with 16 g/L of biomass. Upon applying a hyperosmotic shock after high-cell-density culture, 1.5 g/L of ectoine was obtained without further cell growth from methane. CONCLUSIONS This study suggests the optimization of a method for the high production of ectoine from methane by preventing ectoine degradation. To our knowledge, the final titer of ectoine obtained by M. alcaliphilum 20ZDP3 was the highest in the ectoine production from methane to date. This is the first study to propose ectoine production from methane applying high cell density culture by preventing ectoine degradation.
Collapse
Affiliation(s)
- Sang Eun Lim
- Department of Chemical and Biomolecular Engineering, Sogang University, Seoul, Republic of Korea
| | - Sukhyeong Cho
- C1 Gas Refinery R&D Center, Sogang University, Seoul, Republic of Korea
| | - Yejin Choi
- Department of Chemical and Biomolecular Engineering, Sogang University, Seoul, Republic of Korea
| | - Jeong-Geol Na
- Department of Chemical and Biomolecular Engineering, Sogang University, Seoul, Republic of Korea
| | - Jinwon Lee
- Department of Chemical and Biomolecular Engineering, Sogang University, Seoul, Republic of Korea.
- C1 Gas Refinery R&D Center, Sogang University, Seoul, Republic of Korea.
| |
Collapse
|
10
|
Andrys-Olek J, Kluza A, Tataruch M, Heider J, Korecki J, Borowski T. Bacteria at Work - Experimental and Theoretical Studies Reveal the Catalytic Mechanism of Ectoine Synthase. Chemistry 2024; 30:e202304163. [PMID: 38258332 DOI: 10.1002/chem.202304163] [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: 12/13/2023] [Revised: 01/21/2024] [Accepted: 01/22/2024] [Indexed: 01/24/2024]
Abstract
Ectoine synthase (EctC) catalyses the ultimate step of ectoine biosynthesis, a kosmotropic compound produced as compatible solute by many bacteria and some archaea or eukaryotes. EctC is an Fe2+-dependent homodimeric cytoplasmic protein. Using Mössbauer spectroscopy, molecular dynamics simulations and QM/MM calculations, we determined the most likely coordination number and geometry of the Fe2+ ion and proposed a mechanism of the EctC-catalysed reaction. Most notably, we show that apart from the three amino acids binding to the iron ion (Glu57, Tyr84 and His92), one water molecule and one hydroxide ion are required as additional ligands for the reaction to occur. They fill the first coordination sphere of the Fe2+-cofactor and act as critical proton donors and acceptors during the cyclization reaction.
Collapse
Affiliation(s)
- Justyna Andrys-Olek
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, 30-239, Kraków, Poland
| | - Anna Kluza
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, 30-239, Kraków, Poland
| | - Mateusz Tataruch
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, 30-239, Kraków, Poland
| | - Johann Heider
- Department of Biology, Philipps-Universität Marburg, 35043, Marburg, Germany
| | - Józef Korecki
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, 30-239, Kraków, Poland
| | - Tomasz Borowski
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, 30-239, Kraków, Poland
| |
Collapse
|
11
|
Chen J, Qiao D, Yuan T, Feng Y, Zhang P, Wang X, Zhang L. Biotechnological production of ectoine: current status and prospects. Folia Microbiol (Praha) 2024; 69:247-258. [PMID: 37962826 DOI: 10.1007/s12223-023-01105-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2023] [Accepted: 11/05/2023] [Indexed: 11/15/2023]
Abstract
Ectoine is an important natural secondary metabolite in halophilic microorganisms. It protects cells against environmental stressors, such as salinity, freezing, drying, and high temperatures. Ectoine is widely used in medical, cosmetic, and other industries. Due to the commercial market demand of ectoine, halophilic microorganisms are the primary method for producing ectoine, which is produced using the industrial fermentation process "bacterial milking." The method has some limitations, such as the high salt concentration fermentation, which is highly corrosive to the equipment, and this also increases the difficulty of downstream purification and causes high production costs. The ectoine synthesis gene cluster has been successfully heterologously expressed in industrial microorganisms, and the yield of ectoine was significantly increased and the cost was reduced. This review aims to summarize and update microbial production of ectoine using different microorganisms, environments, and metabolic engineering and fermentation strategies and provides important reference for the development and application of ectoine.
Collapse
Affiliation(s)
- Jun Chen
- College of Biotechnology and Pharmaceutical Engineering, West Anhui University, Lu'an, 237012, China
- Anhui Engineering Research Center for Eco-Agriculture of Traditional Chinese Medicine, West Anhui University, Lu'an, 23702, China
- Key Laboratory of Marine Ecosystem and Biogeochemistry, Ministry of Natural Resources, State Oceanic Administration & Second Institute of Oceanography, Hangzhou, 310012, China
| | - Deliang Qiao
- College of Biotechnology and Pharmaceutical Engineering, West Anhui University, Lu'an, 237012, China
- Anhui Province Key Laboratory for Quality Evaluationand, Improvement of Traditional Chinese Medicine, West Anhui University, Lu, 237012, China
| | - Tao Yuan
- College of Biotechnology and Pharmaceutical Engineering, West Anhui University, Lu'an, 237012, China
| | - Yeyuan Feng
- College of Biotechnology and Pharmaceutical Engineering, West Anhui University, Lu'an, 237012, China
| | - Pengjun Zhang
- College of Biotechnology and Pharmaceutical Engineering, West Anhui University, Lu'an, 237012, China
| | - Xuejun Wang
- College of Biotechnology and Pharmaceutical Engineering, West Anhui University, Lu'an, 237012, China
| | - Li Zhang
- College of Biotechnology and Pharmaceutical Engineering, West Anhui University, Lu'an, 237012, China.
- Anhui Province Key Laboratory for Quality Evaluationand, Improvement of Traditional Chinese Medicine, West Anhui University, Lu, 237012, China.
| |
Collapse
|
12
|
Suárez‐Moo P, Prieto‐Davó A. Biosynthetic potential of the sediment microbial subcommunities of an unexplored karst ecosystem and its ecological implications. Microbiologyopen 2024; 13:e1407. [PMID: 38593340 PMCID: PMC11003711 DOI: 10.1002/mbo3.1407] [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: 11/06/2023] [Revised: 03/13/2024] [Accepted: 03/16/2024] [Indexed: 04/11/2024] Open
Abstract
Microbial communities from various environments have been studied in the quest for new natural products with a broad range of applications in medicine and biotechnology. We employed an enrichment method and genome mining tools to examine the biosynthetic potential of microbial communities in the sediments of a coastal sinkhole within the karst ecosystem of the Yucatán Peninsula, Mexico. Our investigation led to the detection of 203 biosynthetic gene clusters (BGCs) and 55 secondary metabolites (SMs) within 35 high-quality metagenome-assembled genomes (MAGs) derived from these subcommunities. The most abundant types of BGCs were Terpene, Nonribosomal peptide-synthetase, and Type III polyketide synthase. Some of the in silico identified BGCs and SMs have been previously reported to exhibit biological activities against pathogenic bacteria and fungi. Others could play significant roles in the sinkhole ecosystem, such as iron solubilization and osmotic stress protection. Interestingly, 75% of the BGCs showed no sequence homology with bacterial BGCs previously reported in the MiBIG database. This suggests that the microbial communities in this environment could be an untapped source of genes encoding novel specialized compounds. The majority of the BGCs were identified in pathways found in the genus Virgibacillus, followed by Sporosarcina, Siminovitchia, Rhodococcus, and Halomonas. The latter, along with Paraclostridium and Lysinibacillus, had the highest number of identified BGC types. This study offers fresh insights into the potential ecological role of SMs from sediment microbial communities in an unexplored environment, underscoring their value as a source of novel natural products.
Collapse
Affiliation(s)
- Pablo Suárez‐Moo
- Unidad de Química‐Sisal, Facultad de QuímicaUniversidad Nacional Autónoma de MéxicoSisalYucatánMéxico
| | - Alejandra Prieto‐Davó
- Unidad de Química‐Sisal, Facultad de QuímicaUniversidad Nacional Autónoma de MéxicoSisalYucatánMéxico
| |
Collapse
|
13
|
Kadam P, Khisti M, Ravishankar V, Barvkar V, Dhotre D, Sharma A, Shouche Y, Zinjarde S. Recent advances in production and applications of ectoine, a compatible solute of industrial relevance. BIORESOURCE TECHNOLOGY 2024; 393:130016. [PMID: 37979886 DOI: 10.1016/j.biortech.2023.130016] [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: 10/17/2023] [Revised: 11/10/2023] [Accepted: 11/10/2023] [Indexed: 11/20/2023]
Abstract
Extremophilic bacteria growing in saline ecosystems are potential producers of biotechnologically important products including compatible solutes. Ectoine/hydroxyectoine are two such solutes that protect cells and associated macromolecules from osmotic, heat, cold and UV stress without interfering with cellular functions. Since ectoine is a high value product, overviewing strategies for improving yields become relevant. Screening of natural isolates, use of inexpensive substrates and response surface methodology approaches have been used to improve bioprocess parameters. In addition, genome mining exercises can aid in identifying hitherto unreported microorganisms with a potential to produce ectoine that can be exploited in the future. Application wise, ectoine has various biotechnological (protein protectant, membrane modulator, DNA protectant, cryoprotective agent, wastewater treatment) and biomedical (dermatoprotectant and in overcoming respiratory and hypersensitivity diseases) uses. The review summarizes current updates on the potential of microorganisms in the production of this industrially relevant metabolite and its varied applications.
Collapse
Affiliation(s)
- Pratik Kadam
- Department of Biotechnology (with jointly merged Institute of Bioinformatics and Biotechnology), Savitribai Phule Pune University, Pune,411007, India
| | - Mitesh Khisti
- Department of Biotechnology (with jointly merged Institute of Bioinformatics and Biotechnology), Savitribai Phule Pune University, Pune,411007, India
| | - Varun Ravishankar
- Department of Biotechnology (with jointly merged Institute of Bioinformatics and Biotechnology), Savitribai Phule Pune University, Pune,411007, India
| | - Vitthal Barvkar
- Department of Botany, Savitribai Phule Pune University, Pune,411007, India
| | - Dhiraj Dhotre
- National Center for Microbial Resource (NCMR), National Center for Cell Science (NCCS), Pune,411007, India
| | - Avinash Sharma
- National Center for Microbial Resource (NCMR), National Center for Cell Science (NCCS), Pune,411007, India; School of Agriculture, Graphic Era Hill University, Dehradun, India
| | - Yogesh Shouche
- National Center for Microbial Resource (NCMR), National Center for Cell Science (NCCS), Pune,411007, India; SKAN Research Center, Bengaluru, India
| | - Smita Zinjarde
- Department of Biotechnology (with jointly merged Institute of Bioinformatics and Biotechnology), Savitribai Phule Pune University, Pune,411007, India.
| |
Collapse
|
14
|
Zhang JT, Wang JX, Liu Y, Zhang Y, Wang JH, Chi ZY, Kong FT. Microalgal-bacterial biofilms for wastewater treatment: Operations, performances, mechanisms, and uncertainties. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 907:167974. [PMID: 37884155 DOI: 10.1016/j.scitotenv.2023.167974] [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: 07/18/2023] [Revised: 09/28/2023] [Accepted: 10/18/2023] [Indexed: 10/28/2023]
Abstract
Microalgal-bacterial biofilms have been increasingly considered of great potential in wastewater treatment due to the advantages of microalgal-bacterial synergistic pollutants removal/recovery, CO2 sequestration, and cost-effective biomass-water separation. However, such advantages may vary widely among different types of microalgal-bacterial biofilms, as the biofilms could be formed on different shapes and structures of attachment substratum, generating "false hope" for certain systems in large-scale wastewater treatment if the operating conditions and pollutants removal properties are evaluated based on the general term "microalgal-bacterial biofilm". This study, therefore, classified microalgal-bacterial biofilms into biofilms formed on 2D substratum, biofilms formed on 3D substratum, and biofilms formed without substratum (i.e. microalgal-bacterial granular sludge, MBGS). Biofilms formed on 2D substratum display higher microalgae fractions and nutrients removal efficiencies, while the adopted long hydraulic retention times were unacceptable for large-scale wastewater treatment. MBGS are featured with much lower microalgae fractions, most efficient pollutants removal, and acceptable retention times for realistic application, yet the feasibility of using natural sunlight should be further explored. 3D substratum systems display wide variations in operating conditions and pollutants removal properties because of diversified substratum shapes and structures. 2D and 3D substratum biofilms share more common in eukaryotic and prokaryotic microbial community structures, while MGBS biofilms are more enriched with microorganisms favoring EPS production, biofilm formation, and denitrification. The specific roles of stratified extracellular polymeric substances (EPS) in nutrients adsorption and condensation still require in-depth exploration. Nutrients removal uncertainties caused by microalgal-bacterial synergy decoupling under insufficient illumination, limited microbial community control, and possible greenhouse gas emission exacerbation arising from microalgal N2O generation were also indicated. This review is helpful for revealing the true potential of applying various microalgal-bacterial biofilms in large-scale wastewater treatment, and will provoke some insights on the challenges to the ideal state of synergistic pollutants reclamation and carbon neutrality via microalgal-bacterial interactions.
Collapse
Affiliation(s)
- Jing-Tian Zhang
- School of Bioengineering, Dalian University of Technology, Dalian 116024, PR China
| | - Jian-Xia Wang
- School of Bioengineering, Dalian University of Technology, Dalian 116024, PR China
| | - Yang Liu
- School of Bioengineering, Dalian University of Technology, Dalian 116024, PR China
| | - Ying Zhang
- School of Bioengineering, Dalian University of Technology, Dalian 116024, PR China
| | - Jing-Han Wang
- School of Bioengineering, Dalian University of Technology, Dalian 116024, PR China; Key Laboratory of Environment Controlled Aquaculture, Dalian Ocean University, Dalian 116023, PR China.
| | - Zhan-You Chi
- School of Bioengineering, Dalian University of Technology, Dalian 116024, PR China
| | - Fan-Tao Kong
- School of Bioengineering, Dalian University of Technology, Dalian 116024, PR China
| |
Collapse
|
15
|
Feng Y, Qiu M, Shao L, Jiang Y, Zhang W, Jiang W, Xin F, Jiang M. Strategies for the biological production of ectoine by using different chassis strains. Biotechnol Adv 2024; 70:108306. [PMID: 38157997 DOI: 10.1016/j.biotechadv.2023.108306] [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: 09/27/2023] [Revised: 11/27/2023] [Accepted: 12/23/2023] [Indexed: 01/03/2024]
Abstract
As an amino acid derivative and a typical compatible solute, ectoine can assist microorganisms in resisting high osmotic pressure. Own to its long-term moisturizing effects, ectoine shows extensive applications in cosmetics, medicine and other fields. With the rapid development of synthetic biology and fermentation engineering, many biological strategies have been developed to improve the ectoine production and simplify the production process. Currently, the microbial fermentation has been widely used for large scaling ectoine production. Accordingly, this review will introduce the metabolic pathway for ectoine synthesis and also comprehensively evaluate both wild-type and genetically modified strains for ectoine production. Furthermore, process parameters affecting the ectoine production efficiency and adoption of low cost substrates will be evaluated. Lastly, future prospects on the improvement of ectoine production will be proposed.
Collapse
Affiliation(s)
- Yifan Feng
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211816, PR China
| | - Min Qiu
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211816, PR China
| | - Lei Shao
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211816, PR China
| | - Yujia Jiang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211816, PR China; Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing Tech University, Nanjing 211816, PR China
| | - Wenming Zhang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211816, PR China; Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing Tech University, Nanjing 211816, PR China
| | - Wankui Jiang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211816, PR China.
| | - Fengxue Xin
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211816, PR China; Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing Tech University, Nanjing 211816, PR China.
| | - Min Jiang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211816, PR China; Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing Tech University, Nanjing 211816, PR China
| |
Collapse
|
16
|
Liu C, Wang L, Chen X, Li J, Wang X, Chu Y. Pseudonocardia lacus sp. nov., An Actinomycete Isolated from a Lake Sediment Sample. Curr Microbiol 2023; 81:7. [PMID: 37962701 DOI: 10.1007/s00284-023-03520-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Accepted: 10/11/2023] [Indexed: 11/15/2023]
Abstract
A novel actinomycete strain, designated H11425T, was isolated from a sediment sample collected from Baihua Lake, Guizhou Province, PR China, and a polyphasic approach was employed to determine its taxonomic position. 16S rRNA gene sequence comparisons showed that strain H11425T is most closely related to Pseudonocardia sulfidoxydans JCM 10411T (97.9%) and Pseudonocardia kunmingensis JCM 32122T (97.8%). Both of phylogenetic analysis based on 16S rRNA gene sequence and phylogenomic analysis based on whole-genome sequence showed that strain H11425T formed a separate clade within the genus Pseudonocardia. The draft genome had a length of 8,059,576 bp with a G + C content of 74.5%. The average nucleotide identity, average amino acid identity, and digital DNA-DNA hybridization values between strain H11425T and its closely related Pseudonocardia species were 76.8-79.0%, 64.8-69.9% and 21.7-23.3%, respectively, which were significantly lower than the widely accepted species-defined threshold. Strain H11425T contained meso-diaminopimelic acid, arabinose, galactose, glucose and ribose in its whole-cell hydrolysates. Mycolic acids were absent. The menaquinone was identifed as MK-8(H4). The phospholipid profile consisted of diphosphatidylglycerol, phosphatidylethanolamine, hydroxy-phosphatidylethanolamine, phosphatidylglycerol, phosphatidylinositol, phosphatidylcholine, an unknown phospholipid and four unidentified aminophospholipids. The major fatty acids were iso-C16:0, iso-C14:0, iso H-C16:1 and iso-C16:0 2OH. On the basis of the taxonomic evidence, strain H11425T represents a novel species of the genus Pseudonocardia, for which the name Pseudonocardia lacus sp. nov. is proposed. The type strain is H11425T (= JCM 34851T = CICC 25118T).
Collapse
Affiliation(s)
- Chaolan Liu
- Antibiotics Research and Re-evaluation Key Laboratory of Sichuan Province, School of Pharmacy, Chengdu University, Chengdu, 610106, People's Republic of China
| | - Limei Wang
- Antibiotics Research and Re-evaluation Key Laboratory of Sichuan Province, School of Pharmacy, Chengdu University, Chengdu, 610106, People's Republic of China
| | - Xue Chen
- Antibiotics Research and Re-evaluation Key Laboratory of Sichuan Province, School of Pharmacy, Chengdu University, Chengdu, 610106, People's Republic of China
| | - Jianghua Li
- Antibiotics Research and Re-evaluation Key Laboratory of Sichuan Province, School of Pharmacy, Chengdu University, Chengdu, 610106, People's Republic of China
| | - Xingrong Wang
- Antibiotics Research and Re-evaluation Key Laboratory of Sichuan Province, School of Pharmacy, Chengdu University, Chengdu, 610106, People's Republic of China
| | - Yiwen Chu
- Antibiotics Research and Re-evaluation Key Laboratory of Sichuan Province, School of Pharmacy, Chengdu University, Chengdu, 610106, People's Republic of China.
| |
Collapse
|
17
|
Bohl S, Le Mignon M, Kilian T, Zimmer A. Sodium chloride impacts glycosylation and N- and O-glycan site occupancy of an Fc-fusion protein. Biotechnol Bioeng 2023; 120:3163-3176. [PMID: 37489835 DOI: 10.1002/bit.28512] [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: 05/07/2023] [Revised: 07/11/2023] [Accepted: 07/16/2023] [Indexed: 07/26/2023]
Abstract
Fc-fusion proteins are highly complex molecules, difficult to manufacture at scale. In this work, undesired proteoforms were detected during the manufacture of a therapeutic fusion protein produced in CHO cells. These species were characterized using gel electrophoresis, size exclusion chromatography and liquid chromatography-mass spectrometry leading to the identification of low molecular weight proteoforms presenting low N- and O-glycan site occupancy, as well as a low sialylation content. Upstream process parameters were investigated, and fusion protein quality was shown to be linked to the sodium chloride content of the medium. A mitigation strategy was developed to avoid formation of unwanted glyco-variants, resulting in an increased yield of highly glycosylated Fc-fusion protein. The effect of sodium chloride was shown to be independent of the osmolality increase and was hypothesized to be linked to a modulation of Golgi acidity, which is required for the correct localization and function of glycosyltransferases. Altogether, this study highlights the importance of the salt balance in cell culture media used to produce highly sialylated and occupied glycoproteins, helping to maximize the yield and increase robustness of processes aiming at producing biopharmaceutical complex therapeutic molecules.
Collapse
Affiliation(s)
- Susanne Bohl
- Upstream R&D, Merck Life Science KGaA, Darmstadt, Germany
| | | | - Thomas Kilian
- Biomolecule Analytics & Proteomics, Merck KGaA, Darmstadt, Germany
| | - Aline Zimmer
- Upstream R&D, Merck Life Science KGaA, Darmstadt, Germany
| |
Collapse
|
18
|
Rodero MDR, Carmona-Martínez AA, Martínez-Fraile C, Herrero-Lobo R, Rodríguez E, García-Encina PA, Peña M, Muñoz R. Ectoines production from biogas in pilot bubble column bioreactors and their subsequent extraction via bio-milking. WATER RESEARCH 2023; 245:120665. [PMID: 37801795 DOI: 10.1016/j.watres.2023.120665] [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: 04/11/2023] [Revised: 09/17/2023] [Accepted: 09/22/2023] [Indexed: 10/08/2023]
Abstract
Despite the potential of biogas from waste/wastewater treatment as a renewable energy source, the presence of pollutants and the rapid decrease in the levelized cost of solar and wind power constrain the use of biogas for energy generation. Biogas conversion into ectoine, one of the most valuable bioproducts (1000 €/kg), constitutes a new strategy to promote a competitive biogas market. The potential for a stand-alone 20 L bubble column bioreactor operating at 6% NaCl and two 10 L interconnected bioreactors (at 0 and 6% NaCl, respectively) for ectoine production from biogas was comparatively assessed. The stand-alone reactor supported the best process performance due to its highest robustness and efficiency for ectoine accumulation (20-52 mgectoine/gVSS) and CH4 degradation (up to 84%). The increase in N availability and internal gas recirculation did not enhance ectoine synthesis. However, a 2-fold increase in the internal gas recirculation resulted in an approximately 1.3-fold increase in CH4 removal efficiency. Finally, the recovery of ectoine through bacterial bio-milking resulted in efficiencies of >70% without any negative impact of methanotrophic cell recycling to the bioreactors on CH4 biodegradation or ectoine synthesis.
Collapse
Affiliation(s)
- María Del Rosario Rodero
- Institute of Sustainable Processes, University of Valladolid, Valladolid 47011, Spain; Department of Chemical Engineering and Environmental Technology, University of Valladolid, Dr. Mergelina s/n., Valladolid 47011, Spain
| | - Alessandro A Carmona-Martínez
- Institute of Sustainable Processes, University of Valladolid, Valladolid 47011, Spain; Department of Chemical Engineering and Environmental Technology, University of Valladolid, Dr. Mergelina s/n., Valladolid 47011, Spain
| | - Cristina Martínez-Fraile
- Institute of Sustainable Processes, University of Valladolid, Valladolid 47011, Spain; Department of Chemical Engineering and Environmental Technology, University of Valladolid, Dr. Mergelina s/n., Valladolid 47011, Spain
| | - Raquel Herrero-Lobo
- Institute of Sustainable Processes, University of Valladolid, Valladolid 47011, Spain; Department of Chemical Engineering and Environmental Technology, University of Valladolid, Dr. Mergelina s/n., Valladolid 47011, Spain
| | - Elisa Rodríguez
- Institute of Sustainable Processes, University of Valladolid, Valladolid 47011, Spain; Department of Chemical Engineering and Environmental Technology, University of Valladolid, Dr. Mergelina s/n., Valladolid 47011, Spain
| | - Pedro A García-Encina
- Institute of Sustainable Processes, University of Valladolid, Valladolid 47011, Spain; Department of Chemical Engineering and Environmental Technology, University of Valladolid, Dr. Mergelina s/n., Valladolid 47011, Spain
| | - Mar Peña
- Institute of Sustainable Processes, University of Valladolid, Valladolid 47011, Spain; Department of Chemical Engineering and Environmental Technology, University of Valladolid, Dr. Mergelina s/n., Valladolid 47011, Spain
| | - Raúl Muñoz
- Institute of Sustainable Processes, University of Valladolid, Valladolid 47011, Spain; Department of Chemical Engineering and Environmental Technology, University of Valladolid, Dr. Mergelina s/n., Valladolid 47011, Spain.
| |
Collapse
|
19
|
de França P, Costa JH, Fill TP, Lancellotti M, Ruiz ALTG, Fantinatti-Garboggini F. Genome mining reveals secondary metabolites of Antarctic bacterium Streptomyces albidoflavus related to antimicrobial and antiproliferative activities. Arch Microbiol 2023; 205:354. [PMID: 37828121 DOI: 10.1007/s00203-023-03691-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Revised: 09/10/2023] [Accepted: 09/26/2023] [Indexed: 10/14/2023]
Abstract
The urgent need for new antimicrobials arises from antimicrobial resistance. Actinobacteria, especially Streptomyces genus, are responsible for production of numerous clinical antibiotics and anticancer agents. Genome mining reveals the biosynthetic gene clusters (BGCs) related to secondary metabolites and the genetic potential of a strain to produce natural products. However, this potential may not be expressed under laboratory conditions. In the present study, the Antarctic bacterium was taxonomically affiliated as Streptomyces albidoflavus ANT_B131 (CBMAI 1855). The crude extracts showed antimicrobial activity against both fungi, Gram-positive and Gram-negative bacteria and antiproliferative activity against five human tumor cell lines. Whole-genome sequencing reveals a genome size of 6.96 Mb, and the genome mining identified 24 BGCs, representing 13.3% of the genome. The use of three culture media and three extraction methods reveals the expression and recovery of 20.8% of the BGCs. The natural products identified included compounds, such as surugamide A, surugamide D, desferrioxamine B + Al, desferrioxamine E, and ectoine. This study reveals the potential of S. albidoflavus ANT_B131 as a natural product producer. Yet, the diversity of culture media and extraction methods could enhance the BGCs expression and recovery of natural products, and could be a strategy to intensify the BGC expression of natural products.
Collapse
Affiliation(s)
- Paula de França
- Division of Microbial Resources, Pluridisciplinary Center for Chemical, Biological and Agricultural Research, University of Campinas, Paulínia, SP, Brazil.
- Graduate Program in Genetics and Molecular Biology, Institute of Biology, University of Campinas, Campinas, SP, Brazil.
| | - Jonas Henrique Costa
- Institute of Chemistry, University of Campinas, CP 6154, Campinas, SP, 13083-970, Brazil
| | - Taícia Pacheco Fill
- Institute of Chemistry, University of Campinas, CP 6154, Campinas, SP, 13083-970, Brazil
| | - Marcelo Lancellotti
- Faculty of Pharmaceutical Sciences, University of Campinas, Campinas, SP, Brazil
| | | | - Fabiana Fantinatti-Garboggini
- Division of Microbial Resources, Pluridisciplinary Center for Chemical, Biological and Agricultural Research, University of Campinas, Paulínia, SP, Brazil.
| |
Collapse
|
20
|
Kiledal EA, Shaw M, Polson SW, Maresca JA. Metagenomic Analysis of a Concrete Bridge Reveals a Microbial Community Dominated by Halophilic Bacteria and Archaea. Microbiol Spectr 2023; 11:e0511222. [PMID: 37404173 PMCID: PMC10434110 DOI: 10.1128/spectrum.05112-22] [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: 12/13/2022] [Accepted: 06/15/2023] [Indexed: 07/06/2023] Open
Abstract
Concrete hosts a small but diverse microbiome that changes over time. Shotgun metagenomic sequencing would enable assessment of both the diversity and function of the microbial community in concrete, but a number of unique challenges make this difficult for concrete samples. The high concentration of divalent cations in concrete interferes with nucleic acid extraction, and the extremely low biomass in concrete means that DNA from laboratory contamination may be a large fraction of the sequence data. Here, we develop an improved method for DNA extraction from concrete, with higher yield and lower laboratory contamination. To show that this method provides DNA of sufficient quality and quantity to do shotgun metagenomic sequencing, DNA was extracted from a sample of concrete obtained from a road bridge and sequenced with an Illumina MiSeq system. This microbial community was dominated by halophilic Bacteria and Archaea, with enriched functional pathways related to osmotic stress responses. Although this was a pilot-scale effort, we demonstrate that metagenomic sequencing can be used to characterize microbial communities in concrete and that older concrete structures may host different microbes than recently poured concrete. IMPORTANCE Prior work on the microbial communities of concrete focused on the surfaces of concrete structures such as sewage pipes or bridge pilings, where thick biofilms were easy to observe and sample. Because the biomass inside concrete is so low, more recent analyses of the microbial communities inside concrete used amplicon sequencing methods to describe those communities. However, to understand the activity and physiology of microbes in concrete, or to develop living infrastructure, we must develop more direct methods of community analysis. The method developed here for DNA extraction and metagenomic sequencing can be used for analysis of microbial communities inside concrete and can likely be adapted for other cementitious materials.
Collapse
Affiliation(s)
- E. Anders Kiledal
- Department of Biological Sciences, University of Delaware, Newark, Delaware, USA
| | - Mark Shaw
- Sequencing and Genotyping Center, University of Delaware, Newark, Delaware, USA
| | - Shawn W. Polson
- Center for Bioinformatics and Computational Biology, University of Delaware, Newark, Delaware, USA
| | - Julia A. Maresca
- Department of Civil and Environmental Engineering, University of Delaware, Newark, Delaware, USA
| |
Collapse
|
21
|
Shu Z, Zhang X, Wang R, Xing J, Li Y, Zhu D, Shen G. Metabolic engineering of Halomonas campaniensis strain XH26 to remove competing pathways to enhance ectoine production. Sci Rep 2023; 13:9732. [PMID: 37322079 PMCID: PMC10272175 DOI: 10.1038/s41598-023-36975-8] [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: 02/01/2023] [Accepted: 06/13/2023] [Indexed: 06/17/2023] Open
Abstract
Ectoine has gained considerable attention as a high-value chemical with significant application potential and market demand. This study aimed to increase ectoine yields by blocking the metabolic shunt pathway of L-aspartate-4-semialdehyde, the precursor substrate in ectoine synthesis. The homoserine dehydrogenase encoded by hom in H. campaniensis strain XH26 is responsible for the metabolic shunt of L-aspartate-4-semialdehyde to glycine. CRISPR/Cas9 technology was used to seamlessly knockout hom, blocking the metabolic shunt pathway to increase ectoine yields. The ectoine yield of XH26/Δhom was 351.13 mg (g CDW)-1 after 48 h of incubation in 500 mL shake flasks using optimal medium with 1.5 mol L-1 NaCl, which was significantly higher than the 239.18 mg (g CDW)-1 of the wild-type strain. Additionally, the absence of the ectoine metabolic shunt pathway affects betaine synthesis, and thus the betaine yields of XH26/Δhom was 19.98 mg (g CDW)-1, considerably lower than the 69.58 mg (g CDW)-1 of the wild-type strain. Batch fermentation parameters were optimized, and the wild-type strain and XH26/Δhom were fermented in 3 L fermenters, resulting in a high ectoine yield of 587.09 mg (g CDW)-1 for the defective strain, which was significantly greater than the ectoine yield of 385.03 mg (g CDW)-1 of the wild-type strain. This study showed that blocking the metabolic shunt of synthetic substrates effectively increases ectoine production, and a reduction in the competitively compatible solute betaine appears to promote increased ectoine synthesis.
Collapse
Affiliation(s)
- Zhiwan Shu
- Research Center of Basic Medical Science, Medical College of Qinghai University, Xining, 810016, China
| | - Xin Zhang
- Research Center of Basic Medical Science, Medical College of Qinghai University, Xining, 810016, China
| | - Rong Wang
- Research Center of Basic Medical Science, Medical College of Qinghai University, Xining, 810016, China
| | - Jiangwa Xing
- Research Center of Basic Medical Science, Medical College of Qinghai University, Xining, 810016, China
| | - Yongzhen Li
- Research Center of Basic Medical Science, Medical College of Qinghai University, Xining, 810016, China
| | - Derui Zhu
- Research Center of Basic Medical Science, Medical College of Qinghai University, Xining, 810016, China
| | - Guoping Shen
- Research Center of Basic Medical Science, Medical College of Qinghai University, Xining, 810016, China.
| |
Collapse
|
22
|
Rong JC, Sheng L, Jiang LH, Yi ML, Wu JY, Zhao Q. Genomic insights into secondary metabolites of pharmaceutical utility for Hyphococcus flavus MCCC 1K03223 T, isolated from bathypelagic seawater. Mar Genomics 2023; 69:101031. [PMID: 37100527 DOI: 10.1016/j.margen.2023.101031] [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: 03/09/2023] [Revised: 04/03/2023] [Accepted: 04/04/2023] [Indexed: 04/28/2023]
Abstract
During an attempt to screen secondary metabolites of pharmaceutical utility, we sequenced the complete genome of type strain of a novel marine bacterial genus, named genus Hyphococcus. The type strain, Hyphococcus flavus MCCC 1K03223T, was isolated from bathypelagic seawater of South China Sea at a depth of 2500 m. The complete genome of strain MCCC 1K03223T is composed of a circular chromosome of 3,472,649 bp with a mean G + C content of 54.8%. Functional genomic analysis showed that this genome encodes five biosynthetic gene clusters, which were annotated to synthesize medicinally important secondary metabolites. Secondary metabolites annotated include ectoine which acts cytoprotection, ravidomycin which is an antitumor antibiotic and three other different metabolites of terpene type. The secondary metabolic potentials of H. flavus revealed in this study provide more evidences on mining bioactive substances from marine bathypelagic microorganisms.
Collapse
Affiliation(s)
- Jin-Cheng Rong
- Department of Medical Laboratory, Yantai Yuhuangding Hospital, Qingdao University, Yantai 264000, China
| | - Li Sheng
- Department of Medical Laboratory, Yantai Yuhuangding Hospital, Qingdao University, Yantai 264000, China
| | - Li-Hua Jiang
- Department of Medical Laboratory, Yantai Yuhuangding Hospital, Qingdao University, Yantai 264000, China
| | - Mao-Li Yi
- Department of Medical Laboratory, Yantai Yuhuangding Hospital, Qingdao University, Yantai 264000, China
| | - Jin-Ying Wu
- Department of Medical Laboratory, Yantai Yuhuangding Hospital, Qingdao University, Yantai 264000, China
| | - Qi Zhao
- Department of Medical Laboratory, Yantai Yuhuangding Hospital, Qingdao University, Yantai 264000, China.
| |
Collapse
|
23
|
Palmieri O, Castellana S, Latiano A, Latiano T, Gentile A, Panza A, Nardella M, Ciardiello D, Latiano TP, Corritore G, Mazza T, Perri F, Biscaglia G. Mucosal Microbiota from Colorectal Cancer, Adenoma and Normal Epithelium Reveals the Imprint of Fusobacterium nucleatum in Cancerogenesis. Microorganisms 2023; 11:1147. [PMID: 37317121 DOI: 10.3390/microorganisms11051147] [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: 03/15/2023] [Revised: 04/17/2023] [Accepted: 04/25/2023] [Indexed: 06/16/2023] Open
Abstract
An increasing amount of evidence suggests the emerging role of the gut microbiota in the development of colorectal cancer (CRC). This study aimed to elucidate the architecture of microbial communities within normal and neoplastic colonic mucosa. METHODS Microbiota were analyzed by NGS and by an ensemble of metagenomics analysis tools in a total of 69 tissues from 9 patients with synchronous colorectal neoplasia and adenomas (27 specimens: 9 from normal tissues, 9 adenomas, and 9 tumours), 16 patients with only colonic adenomas (32 specimens: 16 from normal tissues and 16 adenomas), and from healthy subjects (10 specimens of normal mucosa). RESULTS Weak differences were observed in alpha and beta metrics among the synchronous tissues from CRC and controls. Through pairwise differential abundance analyses of sample groups, an increasing trend of Rikenellaceae, Pseudomonas and Fusobacterium, and decreasing trends of Staphylococcus, Actinobacillus and Gemmiger were observed in CRC, while Staphylococcus and Bifidobacterium were decreased in patients with only adenomas. At RT-qPCR analysis, Fusobacterium nucleatum was significantly enriched in all the tissues of subjects with synchronous colorectal neoplasia. CONCLUSION Our findings provide a comprehensive view of the human mucosa-associated gut microbiota, emphasizing global microbial diversity mostly in synchronous lesions and proving the constant presence of Fusobacterium nucleatum, with its ability to drive carcinogenesis.
Collapse
Affiliation(s)
- Orazio Palmieri
- Division of Gastroenterology and Endoscopy, Fondazione IRCCS "Casa Sollievo della Sofferenza", 71013 San Giovanni Rotondo, Italy
| | - Stefano Castellana
- Unit of Bioinformatics, Fondazione IRCCS "Casa Sollievo della Sofferenza", 71013 San Giovanni Rotondo, Italy
| | - Anna Latiano
- Division of Gastroenterology and Endoscopy, Fondazione IRCCS "Casa Sollievo della Sofferenza", 71013 San Giovanni Rotondo, Italy
| | - Tiziana Latiano
- Division of Gastroenterology and Endoscopy, Fondazione IRCCS "Casa Sollievo della Sofferenza", 71013 San Giovanni Rotondo, Italy
| | - Annamaria Gentile
- Division of Gastroenterology and Endoscopy, Fondazione IRCCS "Casa Sollievo della Sofferenza", 71013 San Giovanni Rotondo, Italy
| | - Anna Panza
- Division of Gastroenterology and Endoscopy, Fondazione IRCCS "Casa Sollievo della Sofferenza", 71013 San Giovanni Rotondo, Italy
| | - Marianna Nardella
- Division of Gastroenterology and Endoscopy, Fondazione IRCCS "Casa Sollievo della Sofferenza", 71013 San Giovanni Rotondo, Italy
| | - Davide Ciardiello
- Division of Oncology, Fondazione IRCCS "Casa Sollievo della Sofferenza", 71013 San Giovanni Rotondo, Italy
- Division of Medical Oncology, Department of Precision Medicine, University of Campania Luigi Vanvitelli, 80131 Naples, Italy
| | - Tiziana Pia Latiano
- Division of Oncology, Fondazione IRCCS "Casa Sollievo della Sofferenza", 71013 San Giovanni Rotondo, Italy
| | - Giuseppe Corritore
- Division of Gastroenterology and Endoscopy, Fondazione IRCCS "Casa Sollievo della Sofferenza", 71013 San Giovanni Rotondo, Italy
| | - Tommaso Mazza
- Unit of Bioinformatics, Fondazione IRCCS "Casa Sollievo della Sofferenza", 71013 San Giovanni Rotondo, Italy
| | - Francesco Perri
- Division of Gastroenterology and Endoscopy, Fondazione IRCCS "Casa Sollievo della Sofferenza", 71013 San Giovanni Rotondo, Italy
| | - Giuseppe Biscaglia
- Division of Gastroenterology and Endoscopy, Fondazione IRCCS "Casa Sollievo della Sofferenza", 71013 San Giovanni Rotondo, Italy
| |
Collapse
|
24
|
Benítez-Mateos AI, Paradisi F. Halomonas elongata: a microbial source of highly stable enzymes for applied biotechnology. Appl Microbiol Biotechnol 2023; 107:3183-3190. [PMID: 37052635 PMCID: PMC10160191 DOI: 10.1007/s00253-023-12510-7] [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: 02/15/2023] [Revised: 03/27/2023] [Accepted: 03/29/2023] [Indexed: 04/14/2023]
Abstract
Extremophilic microorganisms, which are resistant to extreme levels of temperature, salinity, pH, etc., have become popular tools for biotechnological applications. Due to their availability and cost-efficacy, enzymes from extremophiles are getting the attention of researchers and industries in the field of biocatalysis to catalyze diverse chemical reactions in a selective and sustainable manner. In this mini-review, we discuss the advantages of Halomonas elongata as moderate halophilic bacteria to provide suitable enzymes for biotechnology. While enzymes from H. elongata are more resistant to the presence of salt compared to their mesophilic counterparts, they are also easier to produce in heterologous hosts compared with more extremophilic microorganisms. Herein, a set of different enzymes (hydrolases, transferases, and oxidoreductases) from H. elongata are showcased, highlighting their interesting properties as more efficient and sustainable biocatalysts. With this, we aim to improve the visibility of halotolerant enzymes and their uncommon properties to integrate biocatalysis in industrial set-ups. KEYPOINTS: • Production and use of halotolerant enzymes can be easier than strong halophilic ones. • Enzymes from halotolerant organisms are robust catalysts under harsh conditions. • Halomonas elongata has shown a broad enzyme toolbox with biotechnology applications.
Collapse
Affiliation(s)
- Ana I Benítez-Mateos
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Bern, Switzerland.
| | - Francesca Paradisi
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Bern, Switzerland.
| |
Collapse
|
25
|
Bhowmick S, Shenouda ML, Tschowri N. Osmotic stress responses and the biology of the second messenger c-di-AMP in Streptomyces. MICROLIFE 2023; 4:uqad020. [PMID: 37223731 PMCID: PMC10117811 DOI: 10.1093/femsml/uqad020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Revised: 03/02/2023] [Accepted: 04/10/2023] [Indexed: 05/25/2023]
Abstract
Streptomyces are prolific antibiotic producers that thrive in soil, where they encounter diverse environmental cues, including osmotic challenges caused by rainfall and drought. Despite their enormous value in the biotechnology sector, which often relies on ideal growth conditions, how Streptomyces react and adapt to osmotic stress is heavily understudied. This is likely due to their complex developmental biology and an exceptionally broad number of signal transduction systems. With this review, we provide an overview of Streptomyces' responses to osmotic stress signals and draw attention to open questions in this research area. We discuss putative osmolyte transport systems that are likely involved in ion balance control and osmoadaptation and the role of alternative sigma factors and two-component systems (TCS) in osmoregulation. Finally, we highlight the current view on the role of the second messenger c-di-AMP in cell differentiation and the osmotic stress responses with specific emphasis on the two models, S. coelicolor and S. venezuelae.
Collapse
Affiliation(s)
- Sukanya Bhowmick
- Institute of Microbiology, Leibniz Universität Hannover, 30419 Hannover, Germany
| | - Mary L Shenouda
- Institute of Microbiology, Leibniz Universität Hannover, 30419 Hannover, Germany
| | - Natalia Tschowri
- Corresponding author. Institute of Microbiology, Leibniz Universität Hannover, 30419 Hannover, Germany. E-mail:
| |
Collapse
|
26
|
Bird LJ, Mickol RL, Eddie BJ, Thakur M, Yates MD, Glaven SM. Marinobacter: A case study in bioelectrochemical chassis evaluation. Microb Biotechnol 2023; 16:494-506. [PMID: 36464922 PMCID: PMC9948230 DOI: 10.1111/1751-7915.14170] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 10/28/2022] [Accepted: 11/03/2022] [Indexed: 12/08/2022] Open
Abstract
The junction of bioelectrochemical systems and synthetic biology opens the door to many potentially groundbreaking technologies. When developing these possibilities, choosing the correct chassis organism can save a great deal of engineering effort and, indeed, can mean the difference between success and failure. Choosing the correct chassis for a specific application requires a knowledge of the metabolic potential of the candidate organisms, as well as a clear delineation of the traits, required in the application. In this review, we will explore the metabolic and electrochemical potential of a single genus, Marinobacter. We will cover its strengths, (salt tolerance, biofilm formation and electrochemical potential) and weaknesses (insufficient characterization of many strains and a less developed toolbox for genetic manipulation) in potential synthetic electromicrobiology applications. In doing so, we will provide a roadmap for choosing a chassis organism for bioelectrochemical systems.
Collapse
Affiliation(s)
- Lina J. Bird
- Center for Bio/Molecular Science and Engineering, Naval Research LaboratoryWashingtonDistrict of ColumbiaUSA
| | - Rebecca L. Mickol
- Center for Bio/Molecular Science and Engineering, Naval Research LaboratoryWashingtonDistrict of ColumbiaUSA
| | - Brian J. Eddie
- Center for Bio/Molecular Science and Engineering, Naval Research LaboratoryWashingtonDistrict of ColumbiaUSA
| | - Meghna Thakur
- Center for Bio/Molecular Science and Engineering, Naval Research LaboratoryWashingtonDistrict of ColumbiaUSA
- College of Science, George Mason UniversityFairfaxVirginiaUSA
| | - Matthew D. Yates
- Center for Bio/Molecular Science and Engineering, Naval Research LaboratoryWashingtonDistrict of ColumbiaUSA
| | - Sarah M. Glaven
- Center for Bio/Molecular Science and Engineering, Naval Research LaboratoryWashingtonDistrict of ColumbiaUSA
| |
Collapse
|
27
|
Production and Recovery of Ectoine: A Review of Current State and Future Prospects. Processes (Basel) 2023. [DOI: 10.3390/pr11020339] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Ectoine (1,4,5,6-tetrahydro-2-methyl-4-pyrimidinecarboxylic acid) is a revolutionizing substance with vast applications in the cosmetic and food industries. Ectoine is often sourced from halobacteria. The increasing market demand for ectoine has urged the development of cost-effective and sustainable large-scale production of ectoine from microbial sources. This review describes the existing and potential microbial sources of ectoine and its derivatives, as well as microbial production and fermentation approaches for ectoine recovery. In addition, conventional methods and emerging technologies for enhanced production and recovery of ectoine from microbial fermentation with a focus on the aqueous biphasic system (ABS) are discussed. The ABS is a practically feasible approach for the integration of fermentation, cell disruption, bioconversion, and clarification of various biomolecules in a single-step operation. Nonetheless, the implementation of the ABS on an industrial-scale basis for the enhanced production and recovery of ectoine is yet to be exploited. Therefore, the feasibility of the ABS to integrate the production and direct recovery of ectoine from microbial sources is also highlighted in this review.
Collapse
|
28
|
Zhang X, Arbour T, Zhang D, Wei S, Rabaey K. Microbial electrosynthesis of acetate from CO 2 under hypersaline conditions. ENVIRONMENTAL SCIENCE AND ECOTECHNOLOGY 2023; 13:100211. [PMID: 36419905 PMCID: PMC9676218 DOI: 10.1016/j.ese.2022.100211] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2022] [Revised: 10/25/2022] [Accepted: 10/25/2022] [Indexed: 05/19/2023]
Abstract
Microbial electrosynthesis (MES) enables the bioproduction of multicarbon compounds from CO2 using electricity as the driver. Although high salinity can improve the energetic performance of bioelectrochemical systems, acetogenic processes under elevated salinity are poorly known. Here MES under 35-60 g L-1 salinity was evaluated. Acetate production in two-chamber MES systems at 35 g L-1 salinity (seawater composition) gradually decreased within 60 days, both under -1.2 V cathode potential (vs. Ag/AgCl) and -1.56 A m-2 reductive current. Carbonate precipitation on cathodes (mostly CaCO3) likely declined the production through inhibiting CO2 supply, the direct electrode contact for acetogens and H2 production. Upon decreasing Ca2+ and Mg2+ levels in three-chamber reactors, acetate was stably produced over 137 days along with a low cathode apparent resistance at 1.9 ± 0.6 mΩ m2 and an average production rate at 3.80 ± 0.21 g m-2 d-1. Increasing the salinity step-wise from 35 to 60 g L-1 gave the most efficient acetate production at 40 g L-1 salinity with average rates of acetate production and CO2 consumption at 4.56 ± 3.09 and 7.02 ± 4.75 g m-2 d-1, respectively. The instantaneous coulombic efficiency for VFA averaged 55.1 ± 31.4%. Acetate production dropped at higher salinity likely due to the inhibited CO2 dissolution and acetogenic metabolism. Acetobacterium up to 78% was enriched on cathodes as the main acetogen at 35 g L-1. Under high-salinity selection, 96.5% Acetobacterium dominated on the cathode along with 34.0% Sphaerochaeta in catholyte. This research provides a first proof of concept that MES starting from CO2 reduction can be achieved at elevated salinity.
Collapse
Affiliation(s)
- Xiaoting Zhang
- College of Resources and Environment, Southwest University, Chongqing, 400715, China
- Center for Microbial Ecology and Technology (CMET), Ghent University, Coupure Links 653, 9000, Ghent, Belgium
| | - Tyler Arbour
- Center for Microbial Ecology and Technology (CMET), Ghent University, Coupure Links 653, 9000, Ghent, Belgium
| | - Daijun Zhang
- State Key Laboratory of Coal Mine Disaster Dynamics and Control, Chongqing University, Chongqing, 400044, China
| | - Shiqiang Wei
- College of Resources and Environment, Southwest University, Chongqing, 400715, China
| | - Korneel Rabaey
- Center for Microbial Ecology and Technology (CMET), Ghent University, Coupure Links 653, 9000, Ghent, Belgium
- Center for Advanced Process Technology for Urban Resource Recovery (CAPTURE), Frieda Saeysstraat 1, 9052, Ghent, Belgium
- Corresponding author. Center for Microbial Ecology and Technology - FBE - Ghent University, Belgium.
| |
Collapse
|
29
|
Jungmann L, Hoffmann SL, Lang C, De Agazio R, Becker J, Kohlstedt M, Wittmann C. High-efficiency production of 5-hydroxyectoine using metabolically engineered Corynebacterium glutamicum. Microb Cell Fact 2022; 21:274. [PMID: 36578077 PMCID: PMC9798599 DOI: 10.1186/s12934-022-02003-z] [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: 09/27/2022] [Accepted: 12/17/2022] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND Extremolytes enable microbes to withstand even the most extreme conditions in nature. Due to their unique protective properties, the small organic molecules, more and more, become high-value active ingredients for the cosmetics and the pharmaceutical industries. While ectoine, the industrial extremolyte flagship, has been successfully commercialized before, an economically viable route to its highly interesting derivative 5-hydroxyectoine (hydroxyectoine) is not existing. RESULTS Here, we demonstrate high-level hydroxyectoine production, using metabolically engineered strains of C. glutamicum that express a codon-optimized, heterologous ectD gene, encoding for ectoine hydroxylase, to convert supplemented ectoine in the presence of sucrose as growth substrate into the desired derivative. Fourteen out of sixteen codon-optimized ectD variants from phylogenetically diverse bacterial and archaeal donors enabled hydroxyectoine production, showing the strategy to work almost regardless of the origin of the gene. The genes from Pseudomonas stutzeri (PST) and Mycobacterium smegmatis (MSM) worked best and enabled hydroxyectoine production up to 97% yield. Metabolic analyses revealed high enrichment of the ectoines inside the cells, which, inter alia, reduced the synthesis of other compatible solutes, including proline and trehalose. After further optimization, C. glutamicum Ptuf ectDPST achieved a titre of 74 g L-1 hydroxyectoine at 70% selectivity within 12 h, using a simple batch process. In a two-step procedure, hydroxyectoine production from ectoine, previously synthesized fermentatively with C. glutamicum ectABCopt, was successfully achieved without intermediate purification. CONCLUSIONS C. glutamicum is a well-known and industrially proven host, allowing the synthesis of commercial products with granted GRAS status, a great benefit for a safe production of hydroxyectoine as active ingredient for cosmetic and pharmaceutical applications. Because ectoine is already available at commercial scale, its use as precursor appears straightforward. In the future, two-step processes might provide hydroxyectoine de novo from sugar.
Collapse
Affiliation(s)
- Lukas Jungmann
- grid.11749.3a0000 0001 2167 7588Institute of Systems Biotechnology, Saarland University, Campus A1.5, Saarbrücken, Germany
| | - Sarah Lisa Hoffmann
- grid.11749.3a0000 0001 2167 7588Institute of Systems Biotechnology, Saarland University, Campus A1.5, Saarbrücken, Germany
| | - Caroline Lang
- grid.11749.3a0000 0001 2167 7588Institute of Systems Biotechnology, Saarland University, Campus A1.5, Saarbrücken, Germany
| | - Raphaela De Agazio
- grid.11749.3a0000 0001 2167 7588Institute of Systems Biotechnology, Saarland University, Campus A1.5, Saarbrücken, Germany
| | - Judith Becker
- grid.11749.3a0000 0001 2167 7588Institute of Systems Biotechnology, Saarland University, Campus A1.5, Saarbrücken, Germany
| | - Michael Kohlstedt
- grid.11749.3a0000 0001 2167 7588Institute of Systems Biotechnology, Saarland University, Campus A1.5, Saarbrücken, Germany
| | - Christoph Wittmann
- grid.11749.3a0000 0001 2167 7588Institute of Systems Biotechnology, Saarland University, Campus A1.5, Saarbrücken, Germany
| |
Collapse
|
30
|
Ma Z, Wu C, Zhu L, Chang R, Ma W, Deng Y, Chen X. Bioactivity profiling of the extremolyte ectoine as a promising protectant and its heterologous production. 3 Biotech 2022; 12:331. [PMID: 36311375 PMCID: PMC9606177 DOI: 10.1007/s13205-022-03370-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Accepted: 09/20/2022] [Indexed: 11/28/2022] Open
Abstract
Ectoine is a compatible solutes that is diffusely dispersed in bacteria and archaea. It plays a significant role as protectant against various external pressures, such as high temperature, high osmolarity, dryness and radiation, in cells. Ectoine can be utilized in cosmetics due to its properties of moisturizing and antiultraviolet. It can also be used in the pharmaceutical industry for treating various diseases. Therefore, strong protection of ectoine creates a high commercial value. Its current market value is approximately US$1000 kg-1. However, traditional ectoine production in high-salinity media causes high costs of equipment loss and wastewater treatment. There is a growing attention to reduce the salinity of the fermentation broth without sacrificing the production of ectoine. Thus, heterologous production of ectoine in nonhalophilic microorganisms may represent the new generation of the industrial production of ectoine. In this review, we summarized and discussed the biological activities of ectoine on cell and human health protection and its heterologous production.
Collapse
Affiliation(s)
- Zhi Ma
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014 People’s Republic of China
| | - Chutian Wu
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014 People’s Republic of China
| | - Linjiang Zhu
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014 People’s Republic of China
| | - Renjie Chang
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014 People’s Republic of China
| | - Weilin Ma
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014 People’s Republic of China
| | - Yanfeng Deng
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014 People’s Republic of China
| | - Xiaolong Chen
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014 People’s Republic of China
| |
Collapse
|
31
|
Cho S, Lee YS, Chai H, Lim SE, Na JG, Lee J. Enhanced production of ectoine from methane using metabolically engineered Methylomicrobium alcaliphilum 20Z. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2022; 15:5. [PMID: 35418141 PMCID: PMC8759281 DOI: 10.1186/s13068-022-02104-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Accepted: 01/04/2022] [Indexed: 11/22/2022]
Abstract
Background Ectoine (1,3,4,5-tetrahydro-2-methyl-4-pyrimidinecarboxylic acid) is an attractive compatible solute because of its wide industrial applications. Previous studies on the microbial production of ectoine have focused on sugar fermentation. Alternatively, methane can be used as an inexpensive and abundant resource for ectoine production by using the halophilic methanotroph, Methylomicrobium alcaliphilum 20Z. However, there are some limitations, including the low production of ectoine from methane and the limited tools for the genetic manipulation of methanotrophs to facilitate their use as industrial strains. Results We constructed M. alcaliphilum 20ZDP with a high conjugation efficiency and stability of the episomal plasmid by the removal of its native plasmid. To improve the ectoine production in M. alcaliphilum 20Z from methane, the ectD (encoding ectoine hydroxylase) and ectR (transcription repressor of the ectABC-ask operon) were deleted to reduce the formation of by-products (such as hydroxyectoine) and induce ectoine production. When the double mutant was batch cultured with methane, ectoine production was enhanced 1.6-fold compared to that obtained with M. alcaliphilum 20ZDP (45.58 mg/L vs. 27.26 mg/L) without growth inhibition. Notably, a maximum titer of 142.32 mg/L was reached by the use of an optimized medium for ectoine production containing 6% NaCl and 0.05 μM of tungsten without hydroxyectoine production. This result demonstrates the highest ectoine production from methane to date. Conclusions Ectoine production was significantly enhanced by the disruption of the ectD and ectR genes in M. alcaliphilum 20Z under optimized conditions favoring ectoine accumulation. We demonstrated effective genetic engineering in a methanotrophic bacterium, with enhanced production of ectoine from methane as the sole carbon source. This study suggests a potentially transformational path to commercial sugar-based ectoine production. Graphical Abstract ![]()
Supplementary Information The online version contains supplementary material available at 10.1186/s13068-022-02104-2.
Collapse
|
32
|
Biswas J, Jana SK, Mandal S. Biotechnological impacts of Halomonas: a promising cell factory for industrially relevant biomolecules. Biotechnol Genet Eng Rev 2022:1-30. [PMID: 36253947 DOI: 10.1080/02648725.2022.2131961] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Accepted: 09/27/2022] [Indexed: 11/02/2022]
Abstract
Extremophiles are the most fascinating life forms for their special adaptations and ability to offer unique extremozymes or bioactive molecules. Halophiles, the natural inhabitants of hypersaline environments, are one among them. Halomonas are the common genus of halophilic bacteria. To support growth in unusual environments, Halomonas produces various hydrolytic enzymes, compatible solutes, biopolymers like extracellular polysaccharides (EPS) and polyhydroxy alkaloates (PHA), antibiotics, biosurfactants, pigments, etc. Many of such molecules are being produced in large-scale bioreactors for commercial use. However, the prospect of the remaining bioactive molecules with industrial relevance is far from their application. Furthermore, the genetic engineering of the respective gene clusters could open up a new path to bio-prospect these molecules by overproducing their products through heterologous expression. The present survey on Halomonas highlights their ecological diversity, application potential of the their various industrially relevant biomolecules and impact of these biomolecules on respective fields.
Collapse
Affiliation(s)
- Jhuma Biswas
- Laboratory of Molecular Bacteriology, Department of Microbiology, University of Calcutta, Kolkata, India
| | - Santosh Kumar Jana
- Laboratory of Molecular Bacteriology, Department of Microbiology, University of Calcutta, Kolkata, India
| | - Sukhendu Mandal
- Laboratory of Molecular Bacteriology, Department of Microbiology, University of Calcutta, Kolkata, India
| |
Collapse
|
33
|
Phithakrotchanakoon C, Mayteeworakoon S, Siriarchawatana P, Kitikhun S, Harnpicharnchai P, Wansom S, Eurwilaichitr L, Ingsriswang S. Beneficial bacterial- Auricularia cornea interactions fostering growth enhancement identified from microbiota present in spent mushroom substrate. Front Microbiol 2022; 13:1006446. [PMID: 36299733 PMCID: PMC9589457 DOI: 10.3389/fmicb.2022.1006446] [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: 07/29/2022] [Accepted: 09/26/2022] [Indexed: 11/13/2022] Open
Abstract
Complex dynamic bacterial-fungal interactions play key roles during mushroom growth, ranging from mutualism to antagonism. These interactions convey a large influence on mushroom's mycelial and fruiting body formation during mushroom cultivation. In this study, high-throughput amplicon sequencing was conducted to investigate the structure of bacterial communities in spent mushroom substrates obtained from cultivation of two different groups of Auricularia cornea with (A) high yield and (B) low yield of fruiting body production. It was found that species richness and diversity of microbiota in group (A) samples were significantly higher than in group (B) samples. Among the identified 765 bacterial OTUs, 5 bacterial species found to exhibit high differential abundance between group (A) and group (B) were Pseudonocardia mangrovi, Luteimonas composti, Paracoccus pantotrophus, Sphingobium jiangsuense, and Microvirga massiliensis. The co-cultivation with selected bacterial strains showed that A. cornea TBRC 12900 co-cultivated with P. mangrovi TBRC-BCC 42794 promoted a high level of mycelial growth. Proteomics analysis was performed to elucidate the biological activities involved in the mutualistic association between A. cornea TBRC 12900 and P. mangrovi TBRC-BCC 42794. After co-cultivation of A. cornea TBRC 12900 and P. mangrovi TBRC-BCC 42794, 1,616 proteins were detected including 578 proteins of A. cornea origin and 1,038 proteins of P. mangrovi origin. Functional analysis and PPI network construction revealed that the high level of mycelial growth in the co-culture condition most likely resulted from concerted actions of (a) carbohydrate-active enzymes including hydrolases, glycosyltransferases, and carbohydrate esterases important for carbohydrate metabolism and cell wall generation/remodeling, (b) peptidases including cysteine-, metallo-, and serine-peptidases, (c) transporters including the ABC-type transporter superfamily, the FAT transporter family, and the VGP family, and (d) proteins with proposed roles in formation of metabolites that can act as growth-promoting molecules or those normally contain antimicrobial activity (e.g., indoles, terpenes, β-lactones, lanthipeptides, iturins, and ectoines). The findings will provide novel insights into bacterial-fungal interactions during mycelial growth and fruiting body formation. Our results can be utilized for the selection of growth-promoting bacteria to improve the cultivation process of A. cornea with a high production yield, thus conveying potentially high socio-economic impact to mushroom agriculture.
Collapse
Affiliation(s)
- Chitwadee Phithakrotchanakoon
- Microbial Systems and Computational Biology Research Team, Thailand Bioresource Research Center, National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Pathum Thani, Thailand
| | - Sermsiri Mayteeworakoon
- Microbial Systems and Computational Biology Research Team, Thailand Bioresource Research Center, National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Pathum Thani, Thailand
| | - Paopit Siriarchawatana
- Microbial Systems and Computational Biology Research Team, Thailand Bioresource Research Center, National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Pathum Thani, Thailand
| | - Supattra Kitikhun
- Microbial Systems and Computational Biology Research Team, Thailand Bioresource Research Center, National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Pathum Thani, Thailand
| | - Piyanun Harnpicharnchai
- Microbial Systems and Computational Biology Research Team, Thailand Bioresource Research Center, National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Pathum Thani, Thailand
| | - Supaporn Wansom
- National Energy Technology Center, National Science and Technology Development Agency, Pathum Thani, Thailand
| | - Lily Eurwilaichitr
- National Energy Technology Center, National Science and Technology Development Agency, Pathum Thani, Thailand
| | - Supawadee Ingsriswang
- Microbial Systems and Computational Biology Research Team, Thailand Bioresource Research Center, National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Pathum Thani, Thailand
| |
Collapse
|
34
|
Ma D, Liu S, Han X, Nan M, Xu Y, Qian B, Wang L, Mao J. Complete genome sequence, metabolic model construction, and huangjiu application of Saccharopolyspora rosea A22, a thermophilic, high amylase and glucoamylase actinomycetes. Front Microbiol 2022; 13:995978. [PMID: 36246298 PMCID: PMC9554608 DOI: 10.3389/fmicb.2022.995978] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2022] [Accepted: 08/26/2022] [Indexed: 11/13/2022] Open
Abstract
Saccharopolyspora is an important microorganism in the fermentation process of wheat qu and huangjiu, yet the mechanisms by which it performs specific functions in huangjiu remain unclear. A strain with high amylase and glucoamylase activities was isolated from wheat qu and identified as Saccharopolyspora rosea (S. rosea) A22. We initially reported the whole genome sequence of S. rosea A22, which comprised a circular chromosome 6,562,638 bp in size with a GC content of 71.71%, and 6,118 protein-coding genes. A functional genomic analysis highlighted regulatory genes involved in adaptive mechanisms to harsh conditions, and in vitro experiments revealed that the growth of S. rosea A22 could be regulated in response to the stress condition. Based on whole-genome sequencing, the first genome-scale metabolic model of S. rosea A22 named iSR1310 was constructed to predict the growth ability on different media with 91% accuracy. Finally, S. rosea A22 was applied to huangjiu fermentation by inoculating raw wheat qu, and the results showed that the total higher alcohol content was reduced by 12.64% compared with the control group. This study has elucidated the tolerance mechanisms and enzyme-producing properties of S. rosea A22 at the genetic level, providing new insights into its application to huangjiu.
Collapse
Affiliation(s)
- Donglin Ma
- State Key Laboratory of Food Science and Technology, National Engineering Research Center of Cereal Fermentation and Food Biomanufacturing, School of Food Science and Technology, Jiangnan University, Wuxi, China
| | - Shuangping Liu
- State Key Laboratory of Food Science and Technology, National Engineering Research Center of Cereal Fermentation and Food Biomanufacturing, School of Food Science and Technology, Jiangnan University, Wuxi, China
- Shaoxing Key Laboratory of Traditional Fermentation Food and Human Health, Jiangnan University (Shaoxing) Industrial Technology Research Institute, Shaoxing, China
- National Engineering Research Center of Huangjiu, Zhejiang Guyuelongshan Shaoxing Wine Co., Ltd., Shaoxing Huangjiu Industry Innovation Service Complex, Shaoxing, China
- *Correspondence: Shuangping Liu,
| | - Xiao Han
- State Key Laboratory of Food Science and Technology, National Engineering Research Center of Cereal Fermentation and Food Biomanufacturing, School of Food Science and Technology, Jiangnan University, Wuxi, China
- Shaoxing Key Laboratory of Traditional Fermentation Food and Human Health, Jiangnan University (Shaoxing) Industrial Technology Research Institute, Shaoxing, China
- National Engineering Research Center of Huangjiu, Zhejiang Guyuelongshan Shaoxing Wine Co., Ltd., Shaoxing Huangjiu Industry Innovation Service Complex, Shaoxing, China
| | - Mujia Nan
- Basic Department, University of Tibetan Medicine, Lhasa, China
| | - Yuezheng Xu
- National Engineering Research Center of Huangjiu, Zhejiang Guyuelongshan Shaoxing Wine Co., Ltd., Shaoxing Huangjiu Industry Innovation Service Complex, Shaoxing, China
| | - Bin Qian
- National Engineering Research Center of Huangjiu, Zhejiang Guyuelongshan Shaoxing Wine Co., Ltd., Shaoxing Huangjiu Industry Innovation Service Complex, Shaoxing, China
| | - Lan Wang
- National Engineering Research Center of Huangjiu, Zhejiang Guyuelongshan Shaoxing Wine Co., Ltd., Shaoxing Huangjiu Industry Innovation Service Complex, Shaoxing, China
| | - Jian Mao
- State Key Laboratory of Food Science and Technology, National Engineering Research Center of Cereal Fermentation and Food Biomanufacturing, School of Food Science and Technology, Jiangnan University, Wuxi, China
- Shaoxing Key Laboratory of Traditional Fermentation Food and Human Health, Jiangnan University (Shaoxing) Industrial Technology Research Institute, Shaoxing, China
- National Engineering Research Center of Huangjiu, Zhejiang Guyuelongshan Shaoxing Wine Co., Ltd., Shaoxing Huangjiu Industry Innovation Service Complex, Shaoxing, China
- Jian Mao,
| |
Collapse
|
35
|
Whole-Genome Sequencing of the Tropical Marine Bacterium Nocardiopsis dassonvillei NCIM 5124, Containing the Ectoine Biosynthesis Gene Cluster
ectABC. Microbiol Resour Announc 2022; 11:e0043522. [PMID: 36154194 PMCID: PMC9584341 DOI: 10.1128/mra.00435-22] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The genome sequence (7,057,619 bp; GC content, 72.07%) of a tropical marine isolate, Nocardiopsis dassonvillei NCIM 5124, containing the biomedically and biotechnologically important gene cluster ectABC is reported here.
Collapse
|
36
|
Wang S, Sun L, Narsing Rao MP, Fang B, Li W. Comparative Genome Analysis of a Novel Alkaliphilic Actinobacterial Species Nesterenkonia haasae. Pol J Microbiol 2022; 71:453-461. [PMID: 36185029 PMCID: PMC9608169 DOI: 10.33073/pjm-2022-040] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Accepted: 07/31/2022] [Indexed: 11/24/2022] Open
Abstract
In the present study, a comparative genome analysis of the novel alkaliphilic actinobacterial Nesterenkonia haasae with other members of the genus Nesterenkonia was performed. The genome size of Nesterenkonia members ranged from 2,188,008 to 3,676,111 bp. N. haasae and Nesterenkonia members of the present study encode the essential glycolysis and pentose phosphate pathway genes. In addition, some Nesterenkonia members encode the crucial genes for Entner-Doudoroff pathways. Some Nesterenkonia members possess the genes responsible for sulfate/thiosulfate transport system permease protein/ ATP-binding protein and conversion of sulfate to sulfite. Nesterenkonia members also encode the genes for assimilatory nitrate reduction, nitrite reductase, and the urea cycle. All Nesterenkonia members have the genes to overcome environmental stress and produce secondary metabolites. The present study helps to understand N. haasae and Nesterenkonia members' environmental adaptation and niches specificity based on their specific metabolic properties. Further, based on genome analysis, we propose reclassifying Nesterenkonia jeotgali as a later heterotypic synonym of Nesterenkonia sandarakina.
Collapse
Affiliation(s)
- Shuang Wang
- Heilongjiang Academy of Black Soil Conservation and Utilization, BeijingPeople’s Republic of China,State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, BeijingPeople’s Republic of China, S. Wang, Heilongjiang Academy of Black Soil Conservation and Utilization, Heilongjiang Academy of Agricultural Sciences, People’s Republic of China; State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, People’s Republic of China
| | - Lei Sun
- Heilongjiang Academy of Black Soil Conservation and Utilization, BeijingPeople’s Republic of China
| | - Manik Prabhu Narsing Rao
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, GuangzhouPeople’s Republic of China
| | - Bao‑zhu Fang
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, BeijingPeople’s Republic of China,State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, GuangzhouPeople’s Republic of China
| | - Wen‑jun Li
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, BeijingPeople’s Republic of China,State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, GuangzhouPeople’s Republic of China
| |
Collapse
|
37
|
Czech L, Gertzen C, Smits SHJ, Bremer E. Guilty by association: importers, exporters and
MscS
‐type mechanosensitive channels encoded in biosynthetic gene clusters for the stress‐protectant ectoine. Environ Microbiol 2022; 24:5306-5331. [DOI: 10.1111/1462-2920.16203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Accepted: 09/07/2022] [Indexed: 11/28/2022]
Affiliation(s)
- Laura Czech
- Department of Biology, Laboratory for Microbiology and Center for Synthetic Microbiology (SYNMIKRO) Philipps‐University Marburg Marburg Germany
- Department of Chemistry and Center for Synthetic Microbiology (SYNMIKRO) Philipps‐University Marburg Marburg Germany
| | - Christoph Gertzen
- Center for Structural Studies (CSS) Heinrich‐Heine‐University Düsseldorf Düsseldorf Germany
- Institute of Pharmaceutical and Medicinal Chemistry Heinrich‐Heine‐University Düsseldorf Düsseldorf Germany
| | - Sander H. J. Smits
- Center for Structural Studies (CSS) Heinrich‐Heine‐University Düsseldorf Düsseldorf Germany
- Institute of Biochemistry Heinrich Heine University Düsseldorf Düsseldorf Germany
| | - Erhard Bremer
- Department of Biology, Laboratory for Microbiology and Center for Synthetic Microbiology (SYNMIKRO) Philipps‐University Marburg Marburg Germany
| |
Collapse
|
38
|
Yu J, Wang Z, Wang J, Mohisn A, Liu H, Zhang Y, Zhuang Y, Guo M. Physiological metabolic topology analysis of Halomonas elongata DSM 2581 T in response to sodium chloride stress. Biotechnol Bioeng 2022; 119:3509-3525. [PMID: 36062959 DOI: 10.1002/bit.28222] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Revised: 08/25/2022] [Accepted: 08/30/2022] [Indexed: 11/06/2022]
Abstract
The halophilic bacterium Halomonas elongata DSM 2581T generally adapts well to high level of salinity by biosynthesizing ectoine, which functions as an important compatible solute protecting the cell against external salinity environment. Halophilic bacteria have specific metabolic activities under high-salt conditions and are gradually applied in various industries. The present study focuses on investigating the physiological and metabolic mechanism of Halomonas elongata DSM 2581T driven by the external salinity environment. The physiological metabolic dynamics under salt stress were investigated to evaluate the effect of NaCl stress on the metabolism of H. elongata. The obtained results demonstrated that ectoine biosynthesis transited from a non-growth-related process to a growth-related process when the NaCl concentration varied from 1% to 13% (w/v). The maximum biomass (Xm =41.37 g/L), and highest ectoine production (Pm =12.91 g/L) were achieved under 8% NaCl. Moreover, the maximum biomass (Xm ) and the maximum specific growth rates (μm ) showed a first rising and then declining trend with the increased NaCl stress. Furthermore, the transcriptome analysis of H. elongata under different NaCl concentrations demonstrated that both 8% and 13% NaCl conditions resulted in increased expressions of genes involved in the pentose phosphate pathway (PPP), Entner-Doudoroff (ED) pathway, Flagellar assembly pathway and ectoine metabolism, but negatively affected the tricarboxylic acid (TCA) cycle and Fatty acid metabolism. At last, the proposed possible adaptation mechanism under the optimum NaCl concentration in H. elongata was described. This article is protected by copyright. All rights reserved.
Collapse
Affiliation(s)
- Junxiong Yu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Rd, Shanghai, 200237, China
| | - Zejian Wang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Rd, Shanghai, 200237, China
| | - Jing Wang
- Department of Chemical Engineering for Energy Resources, East China University of Science and Technology, 130 Meilong Rd, Shanghai, 200237, China
| | - Ali Mohisn
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Rd, Shanghai, 200237, China
| | - Hao Liu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Rd, Shanghai, 200237, China
| | - Yue Zhang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Rd, Shanghai, 200237, China
| | - Yingping Zhuang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Rd, Shanghai, 200237, China
| | - Meijin Guo
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Rd, Shanghai, 200237, China
| |
Collapse
|
39
|
Modulatory effect of Gracilaria gracilis on European seabass gut microbiota community and its functionality. Sci Rep 2022; 12:14836. [PMID: 36050345 PMCID: PMC9437047 DOI: 10.1038/s41598-022-17891-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Accepted: 08/02/2022] [Indexed: 12/02/2022] Open
Abstract
Seaweeds are an important source of nutrients and bioactive compounds and have a high potential as health boosters in aquaculture. This study evaluated the effect of dietary inclusion of Gracilaria gracilis biomass or its extract on the European seabass (Dicentrarchus labrax) gut microbial community. Juvenile fish were fed a commercial-like diet with 2.5% or 5% seaweed biomass or 0.35% seaweed extract for 47 days. The gut microbiome was assessed by 16S rRNA amplicon sequencing, and its diversity was not altered by the seaweed supplementation. However, a reduction in Proteobacteria abundance was observed. Random forest analysis highlighted the genera Photobacterium, Staphylococcus, Acinetobacter, Micrococcus and Sphingomonas, and their abundances were reduced when fish were fed diets with algae. SparCC correlation network analysis suggested several mutualistic and other antagonistic relationships that could be related to the predicted altered functions. These pathways were mainly related to the metabolism and biosynthesis of protective compounds such as ectoine and were upregulated in fish fed diets supplemented with algae. This study shows the beneficial potential of Gracilaria as a functional ingredient through the modulation of the complex microbial network towards fish health improvement.
Collapse
|
40
|
Hobmeier K, Oppermann M, Stasinski N, Kremling A, Pflüger-Grau K, Kunte HJ, Marin-Sanguino A. Metabolic engineering of Halomonas elongata: Ectoine secretion is increased by demand and supply driven approaches. Front Microbiol 2022; 13:968983. [PMID: 36090101 PMCID: PMC9453808 DOI: 10.3389/fmicb.2022.968983] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Accepted: 07/29/2022] [Indexed: 11/30/2022] Open
Abstract
The application of naturally-derived biomolecules in everyday products, replacing conventional synthetic manufacturing, is an ever-increasing market. An example of this is the compatible solute ectoine, which is contained in a plethora of treatment formulations for medicinal products and cosmetics. As of today, ectoine is produced in a scale of tons each year by the natural producer Halomonas elongata. In this work, we explore two complementary approaches to obtain genetically improved producer strains for ectoine production. We explore the effect of increased precursor supply (oxaloacetate) on ectoine production, as well as an implementation of increased ectoine demand through the overexpression of a transporter. Both approaches were implemented on an already genetically modified ectoine-excreting strain H. elongata KB2.13 (ΔteaABC ΔdoeA) and both led to new strains with higher ectoine excretion. The supply driven approach led to a 45% increase in ectoine titers in two different strains. This increase was attributed to the removal of phosphoenolpyruvate carboxykinase (PEPCK), which allowed the conversion of 17.9% of the glucose substrate to ectoine. For the demand driven approach, we investigated the potential of the TeaBC transmembrane proteins from the ectoine-specific Tripartite ATP-Independent Periplasmic (TRAP) transporter as export channels to improve ectoine excretion. In the absence of the substrate-binding protein TeaA, an overexpression of both subunits TeaBC facilitated a three-fold increased excretion rate of ectoine. Individually, the large subunit TeaC showed an approximately five times higher extracellular ectoine concentration per dry weight compared to TeaBC shortly after its expression was induced. However, the detrimental effect on growth and ectoine titer at the end of the process hints toward a negative impact of TeaC overexpression on membrane integrity and possibly leads to cell lysis. By using either strategy, the ectoine synthesis and excretion in H. elongata could be boosted drastically. The inherent complementary nature of these approaches point at a coordinated implementation of both as a promising strategy for future projects in Metabolic Engineering. Moreover, a wide variation of intracelllular ectoine levels was observed between the strains, which points at a major disruption of mechanisms responsible for ectoine regulation in strain KB2.13.
Collapse
Affiliation(s)
- Karina Hobmeier
- Professorship for Systems Biotechnology, Technical University of Munich, Garching, Germany
| | - Martin Oppermann
- Professorship for Systems Biotechnology, Technical University of Munich, Garching, Germany
| | - Natalie Stasinski
- Professorship for Systems Biotechnology, Technical University of Munich, Garching, Germany
| | - Andreas Kremling
- Professorship for Systems Biotechnology, Technical University of Munich, Garching, Germany
| | - Katharina Pflüger-Grau
- Professorship for Systems Biotechnology, Technical University of Munich, Garching, Germany
| | - Hans Jörg Kunte
- Division Biodeterioration and Reference Organisms, Bundesanstalt für Materialforschung und-prüfung (BAM), Berlin, Germany
| | - Alberto Marin-Sanguino
- Professorship for Systems Biotechnology, Technical University of Munich, Garching, Germany
- Departament de Ciències Mèdiques Bàsiques, Universitat de Lleida, Lleida, Spain
| |
Collapse
|
41
|
Merckx C, Zschüntzsch J, Meyer S, Raedt R, Verschuere H, Schmidt J, De Paepe B, De Bleecker JL. Exploring the Therapeutic Potential of Ectoine in Duchenne Muscular Dystrophy: Comparison with Taurine, a Supplement with Known Beneficial Effects in the mdx Mouse. Int J Mol Sci 2022; 23:ijms23179567. [PMID: 36076964 PMCID: PMC9455265 DOI: 10.3390/ijms23179567] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 08/17/2022] [Accepted: 08/22/2022] [Indexed: 11/17/2022] Open
Abstract
Duchenne Muscular Dystrophy (DMD) is a debilitating muscle disorder that condemns patients to year-long dependency on glucocorticoids. Chronic glucocorticoid use elicits many unfavourable side-effects without offering satisfying clinical improvement, thus, the search for alternative treatments to alleviate muscle inflammation persists. Taurine, an osmolyte with anti-inflammatory effects, mitigated pathological features in the mdx mouse model for DMD but interfered with murine development. In this study, ectoine is evaluated as an alternative for taurine in vitro in CCL-136 cells and in vivo in the mdx mouse. Pre-treating CCL-136 cells with 0.1 mM taurine and 0.1 mM ectoine prior to exposure with 300 U/mL IFN-γ and 20 ng/mL IL-1β partially attenuated cell death, whilst 100 mM taurine reduced MHC-I protein levels. In vivo, histopathological features of the tibialis anterior in mdx mice were mitigated by ectoine, but not by taurine. Osmolyte treatment significantly reduced mRNA levels of inflammatory disease biomarkers, respectively, CCL2 and SPP1 in ectoine-treated mdx mice, and CCL2, HSPA1A, TNF-α and IL-1β in taurine-treated mdx mice. Functional performance was not improved by osmolyte treatment. Furthermore, ectoine-treated mdx mice exhibited reduced body weight. Our results confirmed beneficial effects of taurine in mdx mice and, for the first time, demonstrated similar and differential effects of ectoine.
Collapse
Affiliation(s)
- Caroline Merckx
- Department of Neurology, Ghent University and Ghent University Hospital, 9000 Ghent, Belgium
| | - Jana Zschüntzsch
- Department of Neurology, University Medical Center Göttingen, 37075 Göttingen, Germany
| | - Stefanie Meyer
- Department of Neurology, University Medical Center Göttingen, 37075 Göttingen, Germany
| | - Robrecht Raedt
- 4BRAIN, Department Head and Skin, Ghent University, 9000 Ghent, Belgium
| | - Hanne Verschuere
- Unit of Molecular Signaling and Cell Death, Center for Inflammation Research, Flemish Institute for Biotechnology, 9052 Ghent, Belgium
| | - Jens Schmidt
- Department of Neurology, University Medical Center Göttingen, 37075 Göttingen, Germany
- Department of Neurology and Pain Treatment, Immanuel Klinik Rüdersdorf, University Hospital of the Brandenburg Medical School Theodor Fontane, 15562 Rüdersdorf bei Berlin, Germany
- Faculty of Health Sciences Brandenburg, Brandenburg Medical School Theodor Fontane, 15562 Rüdersdorf bei Berlin, Germany
| | - Boel De Paepe
- Department of Neurology, Ghent University and Ghent University Hospital, 9000 Ghent, Belgium
- Correspondence:
| | - Jan L. De Bleecker
- Department of Neurology, Ghent University and Ghent University Hospital, 9000 Ghent, Belgium
| |
Collapse
|
42
|
Rodero MDR, Herrero-Lobo R, Pérez V, Muñoz R. Influence of operational conditions on the performance of biogas bioconversion into ectoines in pilot bubble column bioreactors. BIORESOURCE TECHNOLOGY 2022; 358:127398. [PMID: 35640813 DOI: 10.1016/j.biortech.2022.127398] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Revised: 05/26/2022] [Accepted: 05/27/2022] [Indexed: 06/15/2023]
Abstract
The application of biogas as a low-priced substrate for the production of ectoines constitutes an opportunity to decrease their production costs and to enhance the viability of anaerobic digestion. The influence of operational conditions on CH4-biogas biodegradation and on ectoines production yields was assessed in continuous pilot bubble column bioreactors. The rise in biomass concentration from 1 to 3 g L-1 resulted in a decrease in the specific ectoine content from 42 ± 8 to 30 ± 4 mgectoine gVSS-1. The concentration of Cu2+ and Mg2+ did not impact process performance, while the use of ammonium as N source resulted in low CH4 biodegradation and ectoine yields (13 ± 7 mgectoine gVSS-1). The increase in CH4 content from 4.5 to 9 %v·v-1 enhanced CH4 removal efficiency. Process operation at NaCl concentrations of 3 %w·w-1 instead of 6 %w·w-1 decreased the ectoine yield to 17 mgectoine gVSS-1. Finally, Methylomicrobiumburyatense was identified as the dominant species.
Collapse
Affiliation(s)
- María Del Rosario Rodero
- Institute of Sustainable Processes, University of Valladolid, 47011, Valladolid, Spain; Department of Chemical Engineering and Environmental Technology, School of Industrial Engineerings. University of Valladolid, Dr. Mergelina s/n., 47011, Valladolid, Spain
| | - Raquel Herrero-Lobo
- Institute of Sustainable Processes, University of Valladolid, 47011, Valladolid, Spain; Department of Chemical Engineering and Environmental Technology, School of Industrial Engineerings. University of Valladolid, Dr. Mergelina s/n., 47011, Valladolid, Spain
| | - Víctor Pérez
- Institute of Sustainable Processes, University of Valladolid, 47011, Valladolid, Spain; Department of Chemical Engineering and Environmental Technology, School of Industrial Engineerings. University of Valladolid, Dr. Mergelina s/n., 47011, Valladolid, Spain
| | - Raúl Muñoz
- Institute of Sustainable Processes, University of Valladolid, 47011, Valladolid, Spain; Department of Chemical Engineering and Environmental Technology, School of Industrial Engineerings. University of Valladolid, Dr. Mergelina s/n., 47011, Valladolid, Spain.
| |
Collapse
|
43
|
Cantera S, Sousa DZ, Sánchez-Andrea I. Enhanced ectoines production by carbon dioxide capture: A step further towards circular economy. J CO2 UTIL 2022. [DOI: 10.1016/j.jcou.2022.102009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
|
44
|
Chen SY, Peng TC, Huang SZ, Chien CC. Isolation of an ectoine-producing Sinobaca sp. and identification of genes that are involved in ectoine biosynthesis. FEMS Microbiol Lett 2022; 369:6596284. [PMID: 35641156 DOI: 10.1093/femsle/fnac046] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2022] [Revised: 04/07/2022] [Accepted: 05/26/2022] [Indexed: 11/13/2022] Open
Abstract
A moderate halophilic bacterium that could accumulate ectoine and hydroxyectoine was isolated from soil near a salt mine and was identified as a Sinobaca sp. (designed strain H24) according to 16S rRNA gene sequence analysis. The bacterium grew well in the presence of 1 to 2 M NaCl, while growth in a medium that contained 2 M NaCl led to higher accumulation of ectoines. The yields of ectoine and hydroxyectoine by Sinobaca sp. H24 reached 11.27 mg/L and 1.34 mg/L, respectively, when cultured in the following medium: NaCl (2 M), peptone (5 g/L), yeast extract (1 g/L), NH4Cl (0.02 M), KH2PO4 (1 M), K2HPO4 (0.1 M) and glycerol (1% w/v). Genes that are involved in ectoine biosynthesis of Sinobaca sp. H24 were also identified, and their sequences were determined by a metagenomics approach. The results demonstrated that Sinobaca sp. H24 possesses ectoine metabolism genes for both ectoine biosynthesis (ectA, ectB, ectC and ectD) and ectoine degradation (doeA). Genes that are related to ectoine biosynthesis, such as lysC and asd, were also characterized. The identification and characterization results for ectoine/hydroxyectoine biosynthesis genes are in agreement with the physiology of Sinobaca sp. H24 as a potential candidate for ectoine production for industrial applications. This report established for the first time the accumulation of ectoine/hydroxyectoine in Sinobaca sp. and characterized the genes that are involved in ectoine/hydroxyectoine biosynthesis in Sinobaca sp. H24.
Collapse
Affiliation(s)
- Shan-Yu Chen
- Graduate School of Biotechnology and Bioengineering, Yuan Ze University, Taoyuan, Taiwan
| | - Tzu-Chia Peng
- Graduate School of Biotechnology and Bioengineering, Yuan Ze University, Taoyuan, Taiwan
| | - Shan-Ze Huang
- Graduate School of Biotechnology and Bioengineering, Yuan Ze University, Taoyuan, Taiwan
| | - Chih-Ching Chien
- Graduate School of Biotechnology and Bioengineering, Yuan Ze University, Taoyuan, Taiwan
| |
Collapse
|
45
|
Abosamaha A, Williamson MP, Gilmour DJ. Utilization and accumulation of compatible solutes in Halomonas pacifica: a species of moderately halophilic bacteria isolated from a saline lake in South Libya. Access Microbiol 2022; 4:acmi000359. [PMID: 36003353 PMCID: PMC9394535 DOI: 10.1099/acmi.0.000359] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Accepted: 04/12/2022] [Indexed: 11/23/2022] Open
Abstract
When grown in high salt concentrations, halophilic bacteria often accumulate compatible solutes, which have major applications in biotechnology because they stabilize cells and proteins. Four Gram-negative bacterial strains, belonging to the family Halomonadaceae, were isolated from Qaberoun and Um-Alma lakes in South Libya using high-salinity medium. The strains were identified using 16S rRNA gene sequencing as belonging to Halomonas pacifica (strain ABQ1), Halomonas venusta (ABQ2), Halomonas elongata (ABU1) and Halomonas salifodinae (ABU2). H. pacifica ABQ1 is a moderate halophile (salinity range 0.05 to 2.5 M NaCl), with a broad tolerance to pH (7 to 9) and temperature (25–37 °C). Addition of the compatible solutes glycine betaine (betaine) and ectoine (1,4,5,6-tetrahydro-2-methyl-4-pyrimidine carboxylic acid) to the medium had a positive effect on growth of H. pacifica at 2 M NaCl. In rich LB medium, betaine was the major compatible solute accumulated, with ectoine only being accumulated at salinities in excess of 1 M NaCl. In minimal M9 medium, betaine was not produced, but increasing amounts of ectoine were synthesized with increasing salinity, and hydroxyectoine [(4S,5S)−5-hydroxy-2-methyl-1,4,5,6-tetrahydropyrimidine-4-carboxylic acid] was also synthesized when the cells were grown in very high salt. We have thus identified H. pacifica as a producer of ectoine and hydroxyectoine, with more being produced at higher salinities. As industrial demand for these compatible solutes continues to increase, this system has biotechnological potential.
Collapse
Affiliation(s)
- Abdolkader Abosamaha
- School of Science and Technology, Nottingham Trent University, Nottingham NG11 8NS, UK
| | - Mike P. Williamson
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield S10 2TN, UK
| | - D. James Gilmour
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield S10 2TN, UK
| |
Collapse
|
46
|
Zhang T, Cui T, Cao Y, Li Y, Li F, Zhu D, Xing J. Whole genome sequencing of the halophilic Halomonas qaidamensis XH36, a novel species strain with high ectoine production. Antonie Van Leeuwenhoek 2022; 115:545-559. [PMID: 35243586 DOI: 10.1007/s10482-022-01709-9] [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: 10/23/2021] [Accepted: 01/18/2022] [Indexed: 10/18/2022]
Abstract
Here, we report the whole genome of a novel halophilic Halomonas species strain XH36 with high ectoine production potential. The genome was 3,818,310 bp in size with a GC content of 51.97%, and contained 3533 genes, 61 tRNAs and 18 rRNAs. The phylogenetic analysis using the 16s rRNA genes, the UBCGs and the TYGS database indicated that XH36 belongs to a novel Halomonas species, which we named as Halomonas qaidamensis. Osmoadaptation related genes including Na(+) and K(+) transport and compatible solute accumulation were both present in the XH36 genome, the latter of which mainly contained ectoine, 5-hydroxyectoine and betaine. HPLC validation studies showed that H. qaidamensis XH36 accumulated ectoine to cope with salt stress, and the content of ectoine could be as high as 315 mg/g CDW under 3 mol/l NaCl. Our results show that XH36 is a new promising industrial strain for ectoine production, and the genomic analysis will guide us to better understand its salt-induced osmoadaptation mechanisms, and provide theoretical references for future application research of ectoine.
Collapse
Affiliation(s)
- Tiantian Zhang
- Research Centre of Basic Medical Sciences, Medical College, Qinghai University, Xining, 810016, China
| | - Tianqi Cui
- Research Centre of Basic Medical Sciences, Medical College, Qinghai University, Xining, 810016, China
| | - Yaning Cao
- Research Centre of Basic Medical Sciences, Medical College, Qinghai University, Xining, 810016, China
| | - Yongzhen Li
- Research Centre of Basic Medical Sciences, Medical College, Qinghai University, Xining, 810016, China
| | - Fenghui Li
- Research Centre of Basic Medical Sciences, Medical College, Qinghai University, Xining, 810016, China
| | - Derui Zhu
- Research Centre of Basic Medical Sciences, Medical College, Qinghai University, Xining, 810016, China
| | - Jiangwa Xing
- Research Centre of Basic Medical Sciences, Medical College, Qinghai University, Xining, 810016, China.
| |
Collapse
|
47
|
Systematic studies on stabilization of AAV vector formulations by lyophilization. J Pharm Sci 2022; 111:2288-2298. [DOI: 10.1016/j.xphs.2022.03.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2022] [Revised: 03/02/2022] [Accepted: 03/02/2022] [Indexed: 01/31/2023]
|
48
|
Plasma Metabolite Profiles of Red Meat, Poultry, and Fish Consumption, and Their Associations with Colorectal Cancer Risk. Nutrients 2022; 14:nu14050978. [PMID: 35267954 PMCID: PMC8912563 DOI: 10.3390/nu14050978] [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: 01/18/2022] [Revised: 02/17/2022] [Accepted: 02/22/2022] [Indexed: 01/22/2023] Open
Abstract
BACKGROUND Red and processed meat consumption has been consistently associated with increased risk of colorectal cancer (CRC), but the association for fish intake is unclear. Evidence using objective dietary assessment approaches to evaluate these associations is sparse. OBJECTIVES We aim to investigate the plasma metabolite profiles related to red meat, poultry, and fish consumption and examine their associations with CRC risk. METHODS We measured plasma metabolites among 5269 participants from the Nurses' Health Study (NHS), NHSII, and Health Professionals Follow-Up study (HPFS). We calculated partial Spearman correlations between each metabolite and self-reported intake of seven red meat, poultry, and fish groups. Metabolite profile scores correlated to self-reported dietary intakes were developed using elastic net regression. Associations between self-reported intakes, metabolite profile scores, and subsequent CRC risk were further evaluated using conditional logistic regression among 559 matched (1:1) case-control pairs in NHS/HPFS and replicated among 266 pairs in Women's Health Study. RESULTS Plasma metabolites, especially highly unsaturated lipids, were differentially associated with red meat and fish groups. Metabolite profile scores for each food group were significantly correlated with the corresponding self-reported dietary intake. A higher dietary intake of processed red meat was associated with a higher risk of CRC (pooled OR per 1 SD, 1.15; 95% CI: 1.03, 1.29). In contrast, higher metabolite profile scores for all fish groups, not dietary intakes, were consistently associated with a lower CRC risk: the pooled OR per 1 SD was 0.86 (95% CI: 0.78, 0.96) for total fish, 0.86 (95% CI: 0.77, 0.96) for dark meat fish, and 0.87 (95% CI: 0.78, 0.97) for canned tuna fish. No significant associations were found for other food groups. CONCLUSIONS Red meat and fish intake exhibited systematically different plasma metabolite profiles. Plasma metabolite profile of fish intake was inversely associated with CRC risk.
Collapse
|
49
|
Zan ZY, Ge XF, Huang RR, Liu WZ. Pseudonocardia humida sp. nov., an Actinomycete Isolated from Mangrove Soil Showing Distinct Distribution Pattern of Biosynthetic Gene Clusters. Curr Microbiol 2022; 79:87. [PMID: 35129703 DOI: 10.1007/s00284-022-02784-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 01/24/2022] [Indexed: 11/03/2022]
Abstract
A novel actinomycete strain, designated S2-4T, was isolated from a mangrove soil sample, and a polyphasic approach was employed to determine its taxonomic position. Phylogenetic analysis based on 16S rRNA gene indicated that strain S2-4T formed a unique clade next to that harboring Pseudonocardia dioxanivorans CB1190T, which shared the highest sequence similarity (98.20%) with the new isolate. Phylogenetic analysis based on core genes of genomic sequences displayed a different scenario, exhibiting closer phylogenetic relationship of strain S2-4T with several species with 16S rRNA gene sequence similarities ranging from 96.95 to 98.06%, which was confirmed by the phylogenetic tree reconstructed based on genomic sequences. Further, substantial differences between the genotypic properties of strain S2-4T and its closest neighbors, including digital DNA-DNA hybridization, average nucleotide identity, and distribution patterns of biosynthetic gene clusters (BGC), indicated the taxonomic position of strain S2-4T as a novel species of the genus Pseudonocardia. Accordingly, strain S2-4T was observed to show a different distribution pattern of a predicted BGC encoding ectoine by comparative genomic analysis, which could be strongly linked to its unique habitat distinct from where its close neighbors were isolated. The major cellular fatty acids were iso-C15:0, C21:0, and iso-C16:0. The predominant menaquinone was MK-8(H4). The polar lipids were composed of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidyl-N-monomethylethanolamine, phosphatidylcholine, phosphatidylinositol, phosphatidylinositol mannosides, and two unidentified glycolipids. Here, we propose a novel species of the genus Pseudonocardia: Pseudonocardia humida sp. nov. with the type strain S2-4T (= JCM 34291T = CGMCC 4.7706T).
Collapse
Affiliation(s)
- Zhen-Yu Zan
- School of Food and Pharmaceutical Engineering, Nanjing Normal University, Xuelin Road No. 2, Nanjing, 210023, People's Republic of China
| | - Xian-Feng Ge
- School of Food and Pharmaceutical Engineering, Nanjing Normal University, Xuelin Road No. 2, Nanjing, 210023, People's Republic of China
| | - Rui-Rui Huang
- School of Food and Pharmaceutical Engineering, Nanjing Normal University, Xuelin Road No. 2, Nanjing, 210023, People's Republic of China
| | - Wen-Zheng Liu
- School of Food and Pharmaceutical Engineering, Nanjing Normal University, Xuelin Road No. 2, Nanjing, 210023, People's Republic of China.
| |
Collapse
|
50
|
Sattar OIA, Abuseada HH, Emara MS, Rabee M. Green Electrochemical and Chromatographic Quantifications of the Extremolyte Ectoine in Halophilic Bacterial Cultures and Related Pharmaceutical Preparations. J Pharm Biomed Anal 2022; 213:114680. [DOI: 10.1016/j.jpba.2022.114680] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 02/15/2022] [Accepted: 02/16/2022] [Indexed: 11/27/2022]
|