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Ge HY, Zhang YH, Hu YQ, Han W, Du Y, Hu T, Zeng YX. Complete genome sequence of a novel Pseudomonas sp. IT1137 isolated from Antarctic intertidal sediment showing potential for alkane degradation at low temperatures. Mar Genomics 2024; 76:101122. [PMID: 39009495 DOI: 10.1016/j.margen.2024.101122] [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: 03/07/2024] [Revised: 05/09/2024] [Accepted: 05/09/2024] [Indexed: 07/17/2024]
Abstract
Pseudomonas species are known for their diverse metabolic abilities and broad ecological distribution. They are fundamental components of bacterial communities and perform essential ecological functions in the environment. A psychrotrophic Pseudomonas sp. IT1137 was isolated from intertidal sediment in the coastal region of the Fildes Peninsula, King George Island, Antarctica. The strain contained a circular chromosome of 5,346,697 bp with a G + C content of 61.66 mol% and one plasmid of 4481 bp with a G + C content of 64.61 mol%. A total of 4848 protein-coding genes, 65 tRNA genes and 15 rRNA genes were obtained. Genome sequence analysis revealed that strain IT1137 not only is a potentially novel species of the genus Pseudomonas but also harbors functional genes related to nitrogen, sulfur and phosphorus cycling. In addition, genes involved in alkane degradation, ectoine synthesis and cyclic lipopeptide (CLP) production were detected in the bacterial genome. The results indicate the potential of the strain Pseudomonas sp. IT1137 for biotechnological applications such as bioremediation and secondary metabolite production and are helpful for understanding bacterial adaptability and ecological function in cold coastal environments.
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Affiliation(s)
- Hui-Yan Ge
- School of Oceanography, Shanghai Jiao Tong University, Shanghai 200030, China; Key Laboratory for Polar Science, Polar Research Institute of China, Ministry of Natural Resources, Shanghai 200136, China
| | - Yi-He Zhang
- College of Science, Shantou University, Shantou 515063, China
| | - Yong-Qiang Hu
- Key Laboratory for Polar Science, Polar Research Institute of China, Ministry of Natural Resources, Shanghai 200136, China
| | - Wei Han
- Key Laboratory for Polar Science, Polar Research Institute of China, Ministry of Natural Resources, Shanghai 200136, China
| | - Yu Du
- Key Laboratory for Polar Science, Polar Research Institute of China, Ministry of Natural Resources, Shanghai 200136, China
| | - Ting Hu
- Key Laboratory for Polar Science, Polar Research Institute of China, Ministry of Natural Resources, Shanghai 200136, China
| | - Yin-Xin Zeng
- School of Oceanography, Shanghai Jiao Tong University, Shanghai 200030, China; Key Laboratory for Polar Science, Polar Research Institute of China, Ministry of Natural Resources, Shanghai 200136, China; Shanghai Key Laboratory of Polar Life and Environment Sciences, Shanghai Jiao Tong University, Shanghai 200030, China; Key Laboratory of Polar Ecosystem and Climate Change, Shanghai Jiao Tong University, Ministry of Education, Shanghai 200030, China.
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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.
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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.
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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.
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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.
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Wang Z, Li Y, Gao X, Xing J, Wang R, Zhu D, Shen G. Comparative genomic analysis of Halomonas campaniensis wild-type and ultraviolet radiation-mutated strains reveal genomic differences associated with increased ectoine production. Int Microbiol 2023; 26:1009-1020. [PMID: 37067733 PMCID: PMC10622362 DOI: 10.1007/s10123-023-00356-y] [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: 11/01/2022] [Revised: 04/01/2023] [Accepted: 04/05/2023] [Indexed: 04/18/2023]
Abstract
Ectoine is a natural amino acid derivative and one of the most widely used compatible solutes produced by Halomonas species that affects both cellular growth and osmotic equilibrium. The positive effects of UV mutagenesis on both biomass and ectoine content production in ectoine-producing strains have yet to be reported. In this study, the wild-type H. campaniensis strain XH26 (CCTCCM2019776) was subjected to UV mutagenesis to increase ectoine production. Eight rounds of mutagenesis were used to generate mutated XH26 strains with different UV-irradiation exposure times. Ectoine extract concentrations were then evaluated among all strains using high-performance liquid chromatography analysis, alongside whole genome sequencing with the PacBio RS II platform and comparison of the wild-type strain XH26 and the mutant strain G8-52 genomes. The mutant strain G8-52 (CCTCCM2019777) exhibited the highest cell growth rate and ectoine yields among mutated strains in comparison with strain XH26. Further, ectoine levels in the aforementioned strain significantly increased to 1.51 ± 0.01 g L-1 (0.65 g g-1 of cell dry weight), representing a twofold increase compared to wild-type cells (0.51 ± 0.01 g L-1) when grown in culture medium for ectoine accumulation. Concomitantly, electron microscopy revealed that mutated strain G8-52 cells were obviously shorter than wild-type strain XH26 cells. Moreover, strain G8-52 produced a relatively stable ectoine yield (1.50 g L-1) after 40 days of continuous subculture. Comparative genomics analysis suggested that strain XH26 harbored 24 mutations, including 10 nucleotide insertions, 10 nucleotide deletions, and unique single nucleotide polymorphisms. Notably, the genes orf00723 and orf02403 (lipA) of the wild-type strain mutated to davT and gabD in strain G8-52 that encoded for 4-aminobutyrate-2-oxoglutarate transaminase and NAD-dependent succinate-semialdehyde dehydrogenase, respectively. Consequently, these genes may be involved in increased ectoine yields. These results suggest that continuous multiple rounds of UV mutation represent a successful strategy for increasing ectoine production, and that the mutant strain G8-52 is suitable for large-scale fermentation applications.
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Affiliation(s)
- Zhibo Wang
- 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
| | - Xiang Gao
- 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
| | - Rong Wang
- 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.
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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.
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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.
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Quach NT, Loan TT, Nguyen TTA, Nguyen Vu TH, Pham QA, Chu HH, Phi QT, Thuoc DV. Phenotypic and genomic characterization provide new insights into adaptation to environmental stressors and biotechnological relevance of mangrove Alcaligenes faecalis D334. Res Microbiol 2023; 174:103994. [PMID: 36240959 DOI: 10.1016/j.resmic.2022.103994] [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: 05/12/2022] [Revised: 10/05/2022] [Accepted: 10/05/2022] [Indexed: 11/07/2022]
Abstract
Alcaligenes faecalis D334 was determined in this study as a salt-tolerant bacterium isolated from mangrove sediment. In response to 6% (w/v) NaCl, strain D334 produced the highest ectoines of 14.14 wt%. To understand adaptive features to mangrove environment, strain D334 was sequenced using Pacific BioScience platform, resulting in a circular chromosome of 4.23 Mb. Of note, D334 genome harbored 81 salt-responsive genes, among which two membrane-associated genes ompc and eric were absent in 3 selected A. faecalis genomes. Apart from that, a complete pathway for ectoine and 5-hydroxyectoine synthesis was predicted. To resist 40 mM H2O2, 46 genetic determinants contributing to oxidative stress response were employed. Moreover, two operons involved in polyhydroxyalkanoate (PHA) production were identified in the D334 genome, resulting in maximum PHA content of 5.03 ± 0.04 wt% and PHA concentration of 0.13 ± 0.001 g/L. A large flagellar biosynthesis operon contributing to swimming motility was found to be conserved in D334 and 8 other A. faecalis genomes. These findings shed light for the first time on the high versatility of A. faecalis D334 genome to adapt to mangrove lifestyle and the possibility to develop D334 as an industrial platform for PHA and 5-hydroxyectoine production.
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Affiliation(s)
- Ngoc Tung Quach
- Institute of Biotechnology, Vietnam Academy of Science and Technology, Hanoi 100000, Viet Nam; Graduate University of Science and Technology, Vietnam Academy of Science and Technology, Hanoi 100000, Viet Nam
| | - Tran Thi Loan
- Department of Microbiology, Faculty of Biology, University of Science, Vietnam National University, Hanoi (VNU), Hanoi 100000, Viet Nam; Department of Biotechnology and Microbiology, Faculty of Biology, Hanoi National University of Education, Hanoi 100000, Viet Nam
| | - Thi Thu An Nguyen
- Institute of Biotechnology, Vietnam Academy of Science and Technology, Hanoi 100000, Viet Nam
| | - Thi Hanh Nguyen Vu
- Institute of Biotechnology, Vietnam Academy of Science and Technology, Hanoi 100000, Viet Nam; Graduate University of Science and Technology, Vietnam Academy of Science and Technology, Hanoi 100000, Viet Nam
| | - Quynh Anh Pham
- Institute of Biotechnology, Vietnam Academy of Science and Technology, Hanoi 100000, Viet Nam
| | - Hoang Ha Chu
- Institute of Biotechnology, Vietnam Academy of Science and Technology, Hanoi 100000, Viet Nam; Graduate University of Science and Technology, Vietnam Academy of Science and Technology, Hanoi 100000, Viet Nam
| | - Quyet-Tien Phi
- Institute of Biotechnology, Vietnam Academy of Science and Technology, Hanoi 100000, Viet Nam; Graduate University of Science and Technology, Vietnam Academy of Science and Technology, Hanoi 100000, Viet Nam.
| | - Doan Van Thuoc
- Department of Biotechnology and Microbiology, Faculty of Biology, Hanoi National University of Education, Hanoi 100000, Viet Nam.
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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
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Heat, cold, acid, and bile salt induced differential proteomic responses of a novel potential probiotic Lactococcus garvieae C47 isolated from camel milk. Food Chem 2022; 397:133774. [PMID: 35905615 DOI: 10.1016/j.foodchem.2022.133774] [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: 02/19/2022] [Revised: 07/20/2022] [Accepted: 07/21/2022] [Indexed: 11/21/2022]
Abstract
Probiotics encounter various stresses during food processing and digestion. This study evaluated the differential proteomic responses of a newly identified potential probiotic lactic acid bacteria, Lactococcus garvieae, isolated from camel milk. Lc. garvieae C47 was exposed to heat, cold, acid, and bile conditions, and stress-responsive proteins were identified. The proteomic analysis was done using 2D-IEF SDS PAGE and nano-LC-MS/MS. Out of 91 differentially expressed proteins, 20 upregulated and 27 downregulated proteins were shared among the stresses. The multivariate data analysis revealed abundance of elongation factor Ts (spot C42), uridine phosphorylase, fructose-bisphosphate aldolase, peptidase T, cobalt ECF transporter T component CbiQ, UDP-N-acetylmuramate-l-alanine ligase, uncharacterized protein, aspartokinase, chaperone protein DnaK, IGP synthase cyclase subunit, probable nicotinate-nucleotide adenylyltransferase, NADH-quinone oxidoreductase, holo-[acyl-carrier-protein] synthase, l-lactate dehydrogenase, and uncharacterized protein. The maximum number of differentially expressed proteins belonged to carbohydrate and protein metabolism, which indicates Lc. garvieae shifts towards growth and energy metabolism for resistance against stress conditions.
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Li X, Yang Z, Wang Z, Li W, Zhang G, Yan H. Comparative Genomics of Pseudomonas stutzeri Complex: Taxonomic Assignments and Genetic Diversity. Front Microbiol 2022; 12:755874. [PMID: 35095786 PMCID: PMC8792951 DOI: 10.3389/fmicb.2021.755874] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Accepted: 11/29/2021] [Indexed: 11/13/2022] Open
Abstract
Pseudomonas stutzeri is a species complex with extremely broad phenotypic and genotypic diversity. However, very little is known about its diversity, taxonomy and phylogeny at the genomic scale. To address these issues, we systematically and comprehensively defined the taxonomy and nomenclature for this species complex and explored its genetic diversity using hundreds of sequenced genomes. By combining average nucleotide identity (ANI) evaluation and phylogenetic inference approaches, we identified 123 P. stutzeri complex genomes covering at least six well-defined species among all sequenced Pseudomonas genomes; of these, 25 genomes represented novel members of this species complex. ANI values of ≥∼95% and digital DNA-DNA hybridization (dDDH) values of ≥∼60% in combination with phylogenomic analysis consistently and robustly supported the division of these strains into 27 genomovars (most likely species to some extent), comprising 16 known and 11 unknown genomovars. We revealed that 12 strains had mistaken taxonomic assignments, while 16 strains without species names can be assigned to the species level within the species complex. We observed an open pan-genome of the P. stutzeri complex comprising 13,261 gene families, among which approximately 45% gene families do not match any sequence present in the COG database, and a large proportion of accessory genes. The genome contents experienced extensive genetic gain and loss events, which may be one of the major mechanisms driving diversification within this species complex. Surprisingly, we found that the ectoine biosynthesis gene cluster (ect) was present in all genomes of P. stutzeri species complex strains but distributed at very low frequency (43 out of 9548) in other Pseudomonas genomes, suggesting a possible origin of the ancestors of P. stutzeri species complex in high-osmolarity environments. Collectively, our study highlights the potential of using whole-genome sequences to re-evaluate the current definition of the P. stutzeri complex, shedding new light on its genomic diversity and evolutionary history.
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Affiliation(s)
- Xiangyang Li
- School of Sciences, Kaili University, Kaili, China
- Bacterial Genome Data Mining and Bioinformatic Analysis Center, Kaili University, Kaili, China
- *Correspondence: Xiangyang Li,
| | - Zilin Yang
- School of Sciences, Kaili University, Kaili, China
| | - Zhao Wang
- School of Life and Health Science, Kaili University, Kaili, China
| | - Weipeng Li
- School of Big Data Engineering, Kaili University, Kaili, China
| | - Guohui Zhang
- School of Life and Health Science, Kaili University, Kaili, China
| | - Hongguang Yan
- School of Life and Health Science, Kaili University, Kaili, China
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Kang MK, Park JW. Ectoine Effect on Mechanical Properties of Vesicles in Aqueous Solution. J Membr Biol 2021; 255:55-59. [PMID: 34751806 DOI: 10.1007/s00232-021-00208-8] [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: 07/27/2021] [Accepted: 10/24/2021] [Indexed: 11/29/2022]
Abstract
The mechanical properties of the vesicles incorporated with ectoine were studied using atomic force microscope (AFM). The vesicles were prepared with dipalmitoylphosphatidylcholine (DPPC) by changing only the ratio of the ectoine to DPPC. After the vesicles were adsorbed on the mica substrate and their morphology were characterized, the plot of an AFM tip displacement versus the tip deflection was acquired by monitoring the behavior of the tip into the vesicle. The breakthrough of the tip into the vesicle was observed to occur twice. Each breakthrough represented a penetration of the tip into the top and bottom portions of the vesicle, respectively. The force data between the pre-contact and the first breakthrough were comparable with the Hertzian model to estimate Young's modulus and the bending modulus of the vesicles. Both moduli decreased proportionally with the increase in the ratio of ectoine to lipid up to 0.5. However, above 0.5, the moduli were slightly changed with the increase. These results of the mechanical properties appear to be due to the osmotic and volumetric effect on the headgroup packing disruption.
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Affiliation(s)
- Min Kyeong Kang
- Department of Chemical and Biomolecular Engineering, College of Energy and Biotechnology, Seoul National University of Science and Technology, 232 Gongneung-ro, Nowon-gu, Seoul, 01811, Republic of Korea
| | - Jin-Won Park
- Department of Chemical and Biomolecular Engineering, College of Energy and Biotechnology, Seoul National University of Science and Technology, 232 Gongneung-ro, Nowon-gu, Seoul, 01811, Republic of Korea.
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Kang JY, Lee B, Kim JA, Kim MS, Kim CH. Identification and characterization of an ectoine biosynthesis gene cluster from Aestuariispira ectoiniformans sp. nov., isolated from seawater. Microbiol Res 2021; 254:126898. [PMID: 34710834 DOI: 10.1016/j.micres.2021.126898] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Revised: 09/16/2021] [Accepted: 10/19/2021] [Indexed: 11/26/2022]
Abstract
An ectoine-producing bacterium, designated SWCN16T, was isolated from seawater and could be grown in a medium containing up to 12 % NaCl. A phylogenetic analysis based on 16S rRNA gene sequences revealed that strain SWCN16T belonged to the genus Aestuariispira, class Alphaproteobacteria, and shared the highest 16S rRNA gene sequence similarity of 96.8% with Aestuariispira insulae CECT 8488T. The phenotypic, chemotaxonomic, and genotypic characteristics findings of this study suggested that strain SWCN16T represented a novel species of the genus Aestuariispira. We propose the name Aestuariispira ectoiniformans sp. nov. for this species. Whole-genome sequencing analysis of the isolate revealed a putative ectABC gene cluster for ectoine biosynthesis. These genes were found to be functional using ectoine synthesis testing and S16-ectBAC cells, which were pET21a-ectBAC-transformed E. coli BL21 cells. We found that S16-ectBAC synthesized about 1.67 g/L extracellular ectoine and about 0.59 g/L intracellular ectoine via bioconversion at optimum conditions.
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Affiliation(s)
- Ji Young Kang
- Industrial Microbiology and Bioprocess Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Jeongeup-si, 580-185, Republic of Korea.
| | - Binna Lee
- Industrial Microbiology and Bioprocess Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Jeongeup-si, 580-185, Republic of Korea.
| | - Jeong Ah Kim
- Industrial Microbiology and Bioprocess Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Jeongeup-si, 580-185, Republic of Korea.
| | - Min-Soo Kim
- Industrial Microbiology and Bioprocess Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Jeongeup-si, 580-185, Republic of Korea.
| | - Chul Ho Kim
- Industrial Microbiology and Bioprocess Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Jeongeup-si, 580-185, Republic of Korea.
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12
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Ma Q, Xia L, Wu H, Zhuo M, Yang M, Zhang Y, Tan M, Zhao K, Sun Q, Xu Q, Chen N, Xie X. Metabolic engineering of Escherichia coli for efficient osmotic stress-free production of compatible solute hydroxyectoine. Biotechnol Bioeng 2021; 119:89-101. [PMID: 34612520 DOI: 10.1002/bit.27952] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 09/22/2021] [Accepted: 09/28/2021] [Indexed: 11/08/2022]
Abstract
Compatible solutes are key for the ability of halophilic bacteria to resist high osmotic stress. They have received wide attention from researchers for their excellent osmotic protection properties. Hydroxyectoine is a particularly important compatible solute, but its production by microbes faces several challenges, including low titer/yield, the presence of the byproduct ectoine, and the requirement of high salinity. Here, we aimed to metabolically engineer Escherichia coli to efficiently produce hydroxyectoine in the absence of osmotic stress without accumulating the byproduct ectoine. First, combinatorial optimization of the expression strength of key genes in the ectoine synthesis module and hydroxyectoine synthesis module was conducted. After optimization of the expression of these genes, 12.12 g/L hydroxyectoine and 0.24 g/L ectoine were obtained at 36 h in shake-flask fermentation with the addition of the co-substrate α-ketoglutarate. Further optimization of the addition of α-ketoglutarate achieved the sole production of hydroxyectoine (i.e., no ectoine accumulation), indicating that the supply of α-ketoglutarate is critically important for sole hydroxyectoine production. Finally, quorum sensing-based auto-regulation of intracellular α-ketoglutarate pool was implemented as an alternative to α-ketoglutarate addition by coupling the expression of sucA with the esaI/esaR circuit, which led to 14.93 g/L hydroxyectoine with a unit cell yield of 1.678 g/g and no ectoine accumulation in the absence of osmotic stress. This is the highest reported titer of sole hydroxyectoine production under salinity-free fermentation to date.
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Affiliation(s)
- Qian Ma
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin University of Science and Technology, Tianjin, China.,College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China.,National and Local United Engineering Lab of Metabolic Control Fermentation Technology, Tianjin University of Science and Technology, Tianjin, China
| | - Li Xia
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin University of Science and Technology, Tianjin, China.,College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China
| | - Heyun Wu
- College of Food Science and Engineering, Tianjin University of Science and Technology, Tianjin, China
| | - Mingyang Zhuo
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin University of Science and Technology, Tianjin, China.,College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China
| | - Mengya Yang
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin University of Science and Technology, Tianjin, China.,College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China
| | - Ying Zhang
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin University of Science and Technology, Tianjin, China.,College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China
| | - Miao Tan
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin University of Science and Technology, Tianjin, China.,College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China
| | - Kexin Zhao
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin University of Science and Technology, Tianjin, China.,College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China
| | - Quanwei Sun
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin University of Science and Technology, Tianjin, China.,College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China
| | - Qingyang Xu
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin University of Science and Technology, Tianjin, China.,College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China.,National and Local United Engineering Lab of Metabolic Control Fermentation Technology, Tianjin University of Science and Technology, Tianjin, China
| | - Ning Chen
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin University of Science and Technology, Tianjin, China.,College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China.,National and Local United Engineering Lab of Metabolic Control Fermentation Technology, Tianjin University of Science and Technology, Tianjin, China
| | - Xixian Xie
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin University of Science and Technology, Tianjin, China.,College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China.,National and Local United Engineering Lab of Metabolic Control Fermentation Technology, Tianjin University of Science and Technology, Tianjin, China
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13
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Frikha-Dammak D, Ayadi H, Hakim-Rekik I, Belbahri L, Maalej S. Genome analysis of the salt-resistant Paludifilum halophilum DSM 102817 T reveals genes involved in flux-tuning of ectoines and unexplored bioactive secondary metabolites. World J Microbiol Biotechnol 2021; 37:178. [PMID: 34549358 DOI: 10.1007/s11274-021-03147-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Accepted: 09/14/2021] [Indexed: 10/20/2022]
Abstract
Paludifilum halophilum DSM 102817T is the first member of the genus Paludifilum in the Thermoactinomycetaceae family. The thermohalophilic bacterium was isolated from the solar saltern of Sfax, Tunisia and was shown to be able to produce ectoines with a relatively high-yield and to cope with salt stress conditions. In this study, the whole genome of P. halophilum was sequenced and analysed. Analysis revealed 3,789,765 base pairs with an average GC% content of 51.5%. A total of 3775 genes were predicted of which 3616 were protein-coding genes and 73 were RNA genes. The genes encoding key enzymes for ectoines (ectoine and hydroxyectoine) synthesis (ectABCD) were identified from the bacterial genome next to a gene cluster (ehuABCD) encoding a binding-protein-dependent ABC transport system responsible for ectoines mobility through the cell membrane. With the aid of KEGG analysis, we found that the central catabolic network of P. halophilum comprises the pathways of glycolysis, tricarboxylic acid cycle, and pentose phosphate. In addition, anaplerotic pathways replenishing oxaloacetate and glutamate synthesis from central metabolism needed for high ectoines biosynthetic fluxes were identified through several key enzymes. Furthermore, a total of 18 antiSMASH-predicted putative biosynthetic gene clusters for secondary metabolites with high novelty and diversity were identified in P. halophilum genome, including biosynthesis of colabomycine-A, fusaricidin-E, zwittermycin A, streptomycin, mycosubtilin and meilingmycin. Based on these data, P. halophilum emerged as a promising source for ectoines and antimicrobials with the potential to be scaled up for industrial production, which could benefit the pharmaceutical and cosmetic industries.
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Affiliation(s)
- Donyez Frikha-Dammak
- Laboratoire de Biodiversité Marine et Environnement (LR18ES30), Faculté des Sciences de Sfax, Université de Sfax, BP 1171, 3000, Sfax, Tunisia
| | - Houda Ayadi
- Laboratoire de Biodiversité Marine et Environnement (LR18ES30), Faculté des Sciences de Sfax, Université de Sfax, BP 1171, 3000, Sfax, Tunisia
| | - Imen Hakim-Rekik
- Unité de Génomique Fonctionnelle et Physiologie des Plantes, Université de Sfax, Institut Supérieur de Biotechnologie de Sfax, BP 1175, 3000, Sfax, Tunisia
| | - Lassaad Belbahri
- Laboratory of Soil Biology, University of Neuchatel, 11 Rue Emile Argand, 2000, Neuchâtel, Switzerland
| | - Sami Maalej
- Laboratoire de Biodiversité Marine et Environnement (LR18ES30), Faculté des Sciences de Sfax, Université de Sfax, BP 1171, 3000, Sfax, Tunisia.
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14
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Nowak A, Żur-Pińska J, Piński A, Pacek G, Mrozik A. Adaptation of phenol-degrading Pseudomonas putida KB3 to suboptimal growth condition: A focus on degradative rate, membrane properties and expression of xylE and cfaB genes. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2021; 221:112431. [PMID: 34146980 DOI: 10.1016/j.ecoenv.2021.112431] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2021] [Revised: 06/10/2021] [Accepted: 06/14/2021] [Indexed: 06/12/2023]
Abstract
Detailed characterization of new Pseudomonas strains that degrade toxic pollutants is required and utterly necessary before their potential use in environmental microbiology and biotechnology applications. Therefore, phenol degradation by Pseudomonas putida KB3 under suboptimal temperatures, pH, and salinity was examined in this study. Parallelly, adaptive mechanisms of bacteria to stressful growth conditions concerning changes in cell membrane properties during phenol exposure as well as the expression level of genes encoding catechol 2,3-dioxygenase (xylE) and cyclopropane fatty acid synthase (cfaB) were determined. It was found that high salinity and the low temperature had the most significant effect on the growth of bacteria and the rate of phenol utilization. Degradation of phenol (300 mg L-1) proceeded 12-fold and seven-fold longer at 10 °C and 5% NaCl compared to the optimal conditions. The ability of bacteria to degrade phenol was coupled with a relatively high activity of catechol 2,3-dioxygenase. The only factor that inhibited enzyme activity by approximately 80% compared to the control sample was salinity. Fatty acid methyl ester (FAMEs) profiling, membrane permeability measurements, and hydrophobicity tests indicated severe alterations in bacteria membrane properties during phenol degradation in suboptimal growth conditions. The highest values of pH, salinity, and temperature led to a decrease in membrane permeability. FAME analysis showed fatty acid saturation indices and cyclopropane fatty acid participation at high temperature and salinity. Genetic data showed that suboptimal growth conditions primarily resulted in down-regulation of xylE and cfaB gene expression.
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Affiliation(s)
- Agnieszka Nowak
- Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia, Jagiellońska 28, 40-032 Katowice, Poland.
| | - Joanna Żur-Pińska
- Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia, Jagiellońska 28, 40-032 Katowice, Poland
| | - Artur Piński
- Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia, Jagiellońska 28, 40-032 Katowice, Poland
| | - Gabriela Pacek
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Niezapominajek 8, 30-239 Krakow, Poland
| | - Agnieszka Mrozik
- Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia, Jagiellońska 28, 40-032 Katowice, Poland
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15
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Hermann L, Mais CN, Czech L, Smits SHJ, Bange G, Bremer E. The ups and downs of ectoine: structural enzymology of a major microbial stress protectant and versatile nutrient. Biol Chem 2021; 401:1443-1468. [PMID: 32755967 DOI: 10.1515/hsz-2020-0223] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Accepted: 07/22/2020] [Indexed: 12/13/2022]
Abstract
Ectoine and its derivative 5-hydroxyectoine are compatible solutes and chemical chaperones widely synthesized by Bacteria and some Archaea as cytoprotectants during osmotic stress and high- or low-growth temperature extremes. The function-preserving attributes of ectoines led to numerous biotechnological and biomedical applications and fostered the development of an industrial scale production process. Synthesis of ectoines requires the expenditure of considerable energetic and biosynthetic resources. Hence, microorganisms have developed ways to exploit ectoines as nutrients when they are no longer needed as stress protectants. Here, we summarize our current knowledge on the phylogenomic distribution of ectoine producing and consuming microorganisms. We emphasize the structural enzymology of the pathways underlying ectoine biosynthesis and consumption, an understanding that has been achieved only recently. The synthesis and degradation pathways critically differ in the isomeric form of the key metabolite N-acetyldiaminobutyric acid (ADABA). γ-ADABA serves as preferred substrate for the ectoine synthase, while the α-ADABA isomer is produced by the ectoine hydrolase as an intermediate in catabolism. It can serve as internal inducer for the genetic control of ectoine catabolic genes via the GabR/MocR-type regulator EnuR. Our review highlights the importance of structural enzymology to inspire the mechanistic understanding of metabolic networks at the biological scale.
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Affiliation(s)
- Lucas Hermann
- Department of Biology, Laboratory for Microbiology, Philipps-University Marburg, Karl-von Frisch Str. 8, D-35043 Marburg, Germany.,Biochemistry and Synthetic Biology of Microbial Metabolism Group, Max Planck Institute for Terrestrial Microbiology, Karl-von Frisch Str. 10, D-35043 Marburg, Germany
| | - Christopher-Nils Mais
- Center for Synthetic Microbiology (SYNMIKRO) & Faculty of Chemistry, Philipps-University Marburg, Hans-Meerwein Str. 6, D-35043 Marburg, Germany
| | - Laura Czech
- Department of Biology, Laboratory for Microbiology, Philipps-University Marburg, Karl-von Frisch Str. 8, D-35043 Marburg, Germany.,Center for Synthetic Microbiology (SYNMIKRO) & Faculty of Chemistry, Philipps-University Marburg, Hans-Meerwein Str. 6, D-35043 Marburg, Germany
| | - Sander H J Smits
- Center for Structural Studies, Heinrich Heine University Düsseldorf, Universitätsstr. 1, D-40225 Düsseldorf, Germany.,Institute of Biochemistry, Heinrich Heine University Düsseldorf, Universitätsstr. 1, D-40225 Düsseldorf, Germany
| | - Gert Bange
- Center for Synthetic Microbiology (SYNMIKRO) & Faculty of Chemistry, Philipps-University Marburg, Hans-Meerwein Str. 6, D-35043 Marburg, Germany
| | - Erhard Bremer
- Department of Biology, Laboratory for Microbiology, Philipps-University Marburg, Karl-von Frisch Str. 8, D-35043 Marburg, Germany.,Center for Synthetic Microbiology (SYNMIKRO), Philipps University Marburg, Hans-Meerwein Str. 6, D-35043 Marburg, Germany
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16
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Hwangbo M, Gill JJ, Young R, Chu KH. Dual-function oleaginous biocatalysts for non-sterile cultivation and solvent-free biolipid bioextraction to reduce biolipid-based biofuel production costs. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 758:143969. [PMID: 33333303 PMCID: PMC8061307 DOI: 10.1016/j.scitotenv.2020.143969] [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: 09/06/2020] [Revised: 10/31/2020] [Accepted: 11/14/2020] [Indexed: 06/12/2023]
Abstract
Triacylglycerols (TAGs) are starting materials for the production of biolipid-based fuels such as biodiesel and biojet fuel. While various microorganisms can produce TAGs from renewable resources, the cultivation of TAG-producing microorganisms under sterilization conditions to avoid microbial contamination and application of solvent to extract TAGs from the TAG-filled microorganisms are costly. To overcome these challenges, this study reports the feasibility of a non-sterile cultivation of an oleaginous bacterium Rhodococcus opacus PD631SpAHB under saline conditions, followed by the use of a solvent-free, phage-lysis-protein-based bioextraction approach for TAGs release. The engineered strain PD631SpAHB was developed by introducing a recombinant plasmid carrying a phage lytic gene cassette (pAHB) into Rhodococcus opacus PD631 via transformation, followed by adaptive evolution under saline conditions. This newly developed strain is a salt-tolerant strain with the inducible plasmid pAHB to enable TAGs release into the supernatant upon induction. Cell lysis of PD631SpAHB was confirmed by the decrease of the optical density of cell suspension, by the loss of cell membrane integrity, and by the detection of TAGs in the culture medium. Up to 38% of the total TAGs accumulated in PD631SpAHB was released into supernatant after the expression of the lytic genes. PD631SpAHB strain is a promising candidate to produce TAGs from non-sterile growth medium and release of its TAGs without solvent extraction - a new approach to reduce the overall cost of biolipid-based biofuel production.
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Affiliation(s)
- Myung Hwangbo
- Zachry Department of Civil and Environmental Engineering, Texas A&M University, College Station, TX 77843, United States
| | - Jason J Gill
- Department of Animal Science, Texas A&M University, College Station, TX 77843, United States; Center for Phage Technology, Texas A&M University, College Station, TX 77843, United States
| | - Ry Young
- Center for Phage Technology, Texas A&M University, College Station, TX 77843, United States; Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, United States
| | - Kung-Hui Chu
- Zachry Department of Civil and Environmental Engineering, Texas A&M University, College Station, TX 77843, United States.
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17
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Gregory GJ, Boyd EF. Stressed out: Bacterial response to high salinity using compatible solute biosynthesis and uptake systems, lessons from Vibrionaceae. Comput Struct Biotechnol J 2021; 19:1014-1027. [PMID: 33613867 PMCID: PMC7876524 DOI: 10.1016/j.csbj.2021.01.030] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 01/18/2021] [Accepted: 01/20/2021] [Indexed: 12/19/2022] Open
Abstract
Bacteria have evolved mechanisms that allow them to adapt to changes in osmolarity and some species have adapted to live optimally in high salinity environments such as in the marine ecosystem. Most bacteria that live in high salinity do so by the biosynthesis and/or uptake of compatible solutes, small organic molecules that maintain the turgor pressure of the cell. Osmotic stress response mechanisms and their regulation among marine heterotrophic bacteria are poorly understood. In this review, we discuss what is known about compatible solute metabolism and transport and new insights gained from studying marine bacteria belonging to the family Vibrionaceae.
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Affiliation(s)
| | - E. Fidelma Boyd
- Corresponding author at: Department of Biological Sciences, 341 Wolf Hall, University of Delaware, Newark, DE 19716, United States.
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18
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Imhoff JF, Rahn T, Künzel S, Keller A, Neulinger SC. Osmotic Adaptation and Compatible Solute Biosynthesis of Phototrophic Bacteria as Revealed from Genome Analyses. Microorganisms 2020; 9:E46. [PMID: 33375353 PMCID: PMC7824335 DOI: 10.3390/microorganisms9010046] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Revised: 12/21/2020] [Accepted: 12/23/2020] [Indexed: 11/21/2022] Open
Abstract
Osmotic adaptation and accumulation of compatible solutes is a key process for life at high osmotic pressure and elevated salt concentrations. Most important solutes that can protect cell structures and metabolic processes at high salt concentrations are glycine betaine and ectoine. The genome analysis of more than 130 phototrophic bacteria shows that biosynthesis of glycine betaine is common among marine and halophilic phototrophic Proteobacteria and their chemotrophic relatives, as well as in representatives of Pirellulaceae and Actinobacteria, but are also found in halophilic Cyanobacteria and Chloroherpeton thalassium. This ability correlates well with the successful toleration of extreme salt concentrations. Freshwater bacteria in general lack the possibilities to synthesize and often also to take up these compounds. The biosynthesis of ectoine is found in the phylogenetic lines of phototrophic Alpha- and Gammaproteobacteria, most prominent in the Halorhodospira species and a number of Rhodobacteraceae. It is also common among Streptomycetes and Bacilli. The phylogeny of glycine-sarcosine methyltransferase (GMT) and diaminobutyrate-pyruvate aminotransferase (EctB) sequences correlate well with otherwise established phylogenetic groups. Most significantly, GMT sequences of cyanobacteria form two major phylogenetic branches and the branch of Halorhodospira species is distinct from all other Ectothiorhodospiraceae. A variety of transport systems for osmolytes are present in the studied bacteria.
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Affiliation(s)
| | - Tanja Rahn
- GEOMAR Helmholtz Centre for Ocean Research, 24105 Kiel, Germany;
| | - Sven Künzel
- Max Planck Institute for Evolutionary Biology, 24306 Plön, Germany;
| | - Alexander Keller
- Center for Computational and Theoretical Biology, University Würzburg, 97074 Würzburg, Germany;
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19
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Asiri F, Chen CH, Hwangbo M, Shao Y, Chu KH. From Organic Wastes to Bioplastics: Feasibility of
Nonsterile Poly(3-hydroxybutyrate) Production by Zobellella
denitrificans ZD1. ACS OMEGA 2020; 5:24158-24168. [PMID: 33015431 PMCID: PMC7528165 DOI: 10.1021/acsomega.9b04002] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Accepted: 08/03/2020] [Indexed: 05/04/2023]
Abstract
![]()
Poly(3-hydroxybutyrate)
(PHB)—a renewable and biodegradable
polymer—is a promising alternative to nonbiodegradable synthetic
plastics that are derived from petrochemicals. The methods currently
employed for PHB production are costly, in part, due to the expensive
cultivation feedstocks and the need to sterilize the culture medium,
which is energy-intensive. This study investigates the feasibility
of nonsterile PHB production from several saline organic wastes using
a salt-tolerant strain, Zobellella denitrificans ZD1 (referred to as strain ZD1). Factors such as the pH, salinity,
carbon/nitrogen (C/N) ratio, nitrogen source, and electron acceptor
that might affect the growth of strain ZD1 and its PHB production
were determined. Our results showed successful nonsterile PHB production
by growing the strain ZD1 on nonsterile synthetic crude glycerol,
high-strength saline wastewater, and real municipal wastewater-activated
sludge under saline conditions. The PHB production was significantly
enhanced when the levels of salts and nitrate-nitrogen in the culture
medium were increased. This study suggested a promising low-cost nonsterile
PHB production strategy from organic wastes using strain ZD1.
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Affiliation(s)
- Fahad Asiri
- Zachry
Department of Civil and Environmental Engineering, Texas A&M University, College
Station, Texas 77843-3136, United States
| | - Chih-Hung Chen
- Zachry
Department of Civil and Environmental Engineering, Texas A&M University, College
Station, Texas 77843-3136, United States
- Department
of Environmental Engineering, National Cheng
Kung University, Tainan 70101, Taiwan
| | - Myung Hwangbo
- Zachry
Department of Civil and Environmental Engineering, Texas A&M University, College
Station, Texas 77843-3136, United States
| | - Yiru Shao
- Zachry
Department of Civil and Environmental Engineering, Texas A&M University, College
Station, Texas 77843-3136, United States
| | - Kung-Hui Chu
- Zachry
Department of Civil and Environmental Engineering, Texas A&M University, College
Station, Texas 77843-3136, United States
- . Tel: (979)-845-1403. Fax: (979)-862-1542
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20
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Mahajan SG, Nandre VS, Salunkhe RC, Shouche YS, Kulkarni MV. Chemotaxis and physiological adaptation of an indigenous abiotic stress tolerant plant growth promoting Pseudomonas stutzeri: Amelioration of salt stress to Cicer arietinum. BIOCATALYSIS AND AGRICULTURAL BIOTECHNOLOGY 2020. [DOI: 10.1016/j.bcab.2020.101652] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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21
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Bethlehem L, Moritz KD. Boosting Escherichia coli's heterologous production rate of ectoines by exploiting the non-halophilic gene cluster from Acidiphilium cryptum. Extremophiles 2020; 24:733-747. [PMID: 32699914 PMCID: PMC7445199 DOI: 10.1007/s00792-020-01188-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Accepted: 07/06/2020] [Indexed: 12/26/2022]
Abstract
The compatible solutes ectoine and hydroxyectoine are synthesized by many microorganisms as potent osmostress and desiccation protectants. Besides their successful implementation into various skincare products, they are of increasing biotechnological interest due to new applications in the healthcare sector. To meet this growing demand, efficient heterologous overproduction solutions for ectoines need to be found. This study is the first report on the utilization of the non-halophilic biosynthesis enzymes from Acidiphilium cryptum DSM 2389T for efficient heterologous production of ectoines in Escherichia coli. When grown at low salt conditions (≤ 0.5% NaCl) and utilizing the cheap carbon source glycerol, the production was characterized by the highest specific production of ectoine [2.9 g/g dry cell weight (dcw)] and hydroxyectoine (2.2 g/g dcw) reported so far and occurred at rapid specific production rates of up to 345 mg/(g dcw × h). This efficiency in production was related to an unprecedented carbon source conversion rate of approx. 60% of the theoretical maximum. These findings confirm the unique potential of the here implemented non-halophilic enzymes for ectoine production processes in E. coli and demonstrate the first efficient heterologous solution for hydroxyectoine production, as well as an extraordinary efficient low-salt ectoine production.
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Affiliation(s)
- Lukas Bethlehem
- Institute for Microbiology and Biotechnology, University Bonn, Meckenheimer Allee 168, 53115, Bonn, Germany.
| | - Katharina D Moritz
- Institute for Microbiology and Biotechnology, University Bonn, Meckenheimer Allee 168, 53115, Bonn, Germany
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22
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Richter AA, Kobus S, Czech L, Hoeppner A, Zarzycki J, Erb TJ, Lauterbach L, Dickschat JS, Bremer E, Smits SHJ. The architecture of the diaminobutyrate acetyltransferase active site provides mechanistic insight into the biosynthesis of the chemical chaperone ectoine. J Biol Chem 2020; 295:2822-2838. [PMID: 31969391 DOI: 10.1074/jbc.ra119.011277] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 01/19/2020] [Indexed: 12/17/2022] Open
Abstract
Ectoine is a solute compatible with the physiologies of both prokaryotic and eukaryotic cells and is widely synthesized by bacteria as an osmotic stress protectant. Because it preserves functional attributes of proteins and macromolecular complexes, it is considered a chemical chaperone and has found numerous practical applications. However, the mechanism of its biosynthesis is incompletely understood. The second step in ectoine biosynthesis is catalyzed by l-2,4-diaminobutyrate acetyltransferase (EctA; EC 2.3.1.178), which transfers the acetyl group from acetyl-CoA to EctB-formed l-2,4-diaminobutyrate (DAB), yielding N-γ-acetyl-l-2,4-diaminobutyrate (N-γ-ADABA), the substrate of ectoine synthase (EctC). Here, we report the biochemical and structural characterization of the EctA enzyme from the thermotolerant bacterium Paenibacillus lautus (Pl). We found that (Pl)EctA forms a homodimer whose enzyme activity is highly regiospecific by producing N-γ-ADABA but not the ectoine catabolic intermediate N-α-acetyl-l-2,4-diaminobutyric acid. High-resolution crystal structures of (Pl)EctA (at 1.2-2.2 Å resolution) (i) for its apo-form, (ii) in complex with CoA, (iii) in complex with DAB, (iv) in complex with both CoA and DAB, and (v) in the presence of the product N-γ-ADABA were obtained. To pinpoint residues involved in DAB binding, we probed the structure-function relationship of (Pl)EctA by site-directed mutagenesis. Phylogenomics shows that EctA-type proteins from both Bacteria and Archaea are evolutionarily highly conserved, including catalytically important residues. Collectively, our biochemical and structural findings yielded detailed insights into the catalytic core of the EctA enzyme that laid the foundation for unraveling its reaction mechanism.
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Affiliation(s)
- Alexandra A Richter
- Department of Biology, Laboratory for Microbiology, Philipps-University Marburg, D-35043 Marburg, Germany; SYNMIKRO Research Center, Philipps-University Marburg, D-35043 Marburg, Germany
| | - Stefanie Kobus
- Center for Structural Studies, Heinrich-Heine University Düsseldorf, D-40225 Düsseldorf, Germany
| | - Laura Czech
- Department of Biology, Laboratory for Microbiology, Philipps-University Marburg, D-35043 Marburg, Germany; SYNMIKRO Research Center, Philipps-University Marburg, D-35043 Marburg, Germany
| | - Astrid Hoeppner
- Center for Structural Studies, Heinrich-Heine University Düsseldorf, D-40225 Düsseldorf, Germany
| | - Jan Zarzycki
- Department of Biochemistry and Synthetic Metabolism, Max-Planck-Institute for Terrestrial Microbiology, D-35043 Marburg, Germany
| | - Tobias J Erb
- SYNMIKRO Research Center, Philipps-University Marburg, D-35043 Marburg, Germany; Department of Biochemistry and Synthetic Metabolism, Max-Planck-Institute for Terrestrial Microbiology, D-35043 Marburg, Germany
| | - Lukas Lauterbach
- Kekulé-Institute for Organic Chemistry and Biochemistry, Friedrich-Wilhelms-University Bonn, D-53121 Bonn, Germany
| | - Jeroen S Dickschat
- Kekulé-Institute for Organic Chemistry and Biochemistry, Friedrich-Wilhelms-University Bonn, D-53121 Bonn, Germany
| | - Erhard Bremer
- Department of Biology, Laboratory for Microbiology, Philipps-University Marburg, D-35043 Marburg, Germany; SYNMIKRO Research Center, Philipps-University Marburg, D-35043 Marburg, Germany.
| | - Sander H J Smits
- Center for Structural Studies, Heinrich-Heine University Düsseldorf, D-40225 Düsseldorf, Germany; Institute of Biochemistry, Heinrich-Heine University Düsseldorf, D-40225 Düsseldorf, Germany.
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23
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Effects of specific pathogen-free porcine platelet-rich plasma activated by the novel activator ectoine on cell proliferation and biological function. Biochem Eng J 2020. [DOI: 10.1016/j.bej.2019.107424] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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24
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Abstract
Natural nonproteinogenic amino acids vastly outnumber the well-known 22 proteinogenic amino acids. Such amino acids are generated in specialized metabolic pathways. In these pathways, diverse biosynthetic transformations, ranging from isomerizations to the stereospecific functionalization of C-H bonds, are employed to generate structural diversity. The resulting nonproteinogenic amino acids can be integrated into more complex natural products. Here we review recently discovered biosynthetic routes to freestanding nonproteinogenic α-amino acids, with an emphasis on work reported between 2013 and mid-2019.
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Affiliation(s)
- Jason B Hedges
- Department of Chemistry, University of British Columbia, Vancouver, British Columbia V6T 1Z1, Canada
| | - Katherine S Ryan
- Department of Chemistry, University of British Columbia, Vancouver, British Columbia V6T 1Z1, Canada
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25
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Richter AA, Mais CN, Czech L, Geyer K, Hoeppner A, Smits SHJ, Erb TJ, Bange G, Bremer E. Biosynthesis of the Stress-Protectant and Chemical Chaperon Ectoine: Biochemistry of the Transaminase EctB. Front Microbiol 2019; 10:2811. [PMID: 31921013 PMCID: PMC6915088 DOI: 10.3389/fmicb.2019.02811] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Accepted: 11/20/2019] [Indexed: 12/20/2022] Open
Abstract
Bacteria frequently adapt to high osmolarity surroundings through the accumulation of compatible solutes. Ectoine is a prominent member of these types of stress protectants and is produced via an evolutionarily conserved biosynthetic pathway beginning with the L-2,4-diaminobutyrate (DAB) transaminase (TA) EctB. Here, we studied EctB from the thermo-tolerant Gram-positive bacterium Paenibacillus lautus (Pl) and show that this tetrameric enzyme is highly tolerant to salt, pH, and temperature. During ectoine biosynthesis, EctB converts L-glutamate and L-aspartate-beta-semialdehyde into 2-oxoglutarate and DAB, but it also catalyzes the reverse reaction. Our analysis unravels that EctB enzymes are mechanistically identical to the PLP-dependent gamma-aminobutyrate TAs (GABA-TAs) and only differ with respect to substrate binding. Inspection of the genomic context of the ectB gene in P. lautus identifies an unusual arrangement of juxtapositioned genes for ectoine biosynthesis and import via an Ehu-type binding-protein-dependent ABC transporter. This operon-like structure suggests the operation of a highly coordinated system for ectoine synthesis and import to maintain physiologically adequate cellular ectoine pools under osmotic stress conditions in a resource-efficient manner. Taken together, our study provides an in-depth mechanistic and physiological description of EctB, the first enzyme of the ectoine biosynthetic pathway.
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Affiliation(s)
- Alexandra A Richter
- Laboratory for Microbiology, Department of Biology, Philipps-University Marburg, Marburg, Germany.,SYNMIKRO Research Center, Philipps-University Marburg, Marburg, Germany
| | - Christopher-Nils Mais
- SYNMIKRO Research Center, Philipps-University Marburg, Marburg, Germany.,Department of Chemistry, Philipps-University Marburg, Marburg, Germany
| | - Laura Czech
- Laboratory for Microbiology, Department of Biology, Philipps-University Marburg, Marburg, Germany.,SYNMIKRO Research Center, Philipps-University Marburg, Marburg, Germany
| | - Kyra Geyer
- Department of Biochemistry and Synthetic Metabolism, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Astrid Hoeppner
- Center for Structural Studies, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Sander H J Smits
- Center for Structural Studies, Heinrich Heine University Düsseldorf, Düsseldorf, Germany.,Institute of Biochemistry, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Tobias J Erb
- SYNMIKRO Research Center, Philipps-University Marburg, Marburg, Germany.,Department of Biochemistry and Synthetic Metabolism, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Gert Bange
- SYNMIKRO Research Center, Philipps-University Marburg, Marburg, Germany.,Department of Chemistry, Philipps-University Marburg, Marburg, Germany
| | - Erhard Bremer
- Laboratory for Microbiology, Department of Biology, Philipps-University Marburg, Marburg, Germany.,SYNMIKRO Research Center, Philipps-University Marburg, Marburg, Germany
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26
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Mustakhimov II, Reshetnikov AS, But SY, Rozova ON, Khmelenina VN, Trotsenko YA. Engineering of Hydroxyectoine Production based on the Methylomicrobium alcaliphilum. APPL BIOCHEM MICRO+ 2019. [DOI: 10.1134/s0003683819130015] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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27
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Czech L, Wilcken S, Czech O, Linne U, Brauner J, Smits SHJ, Galinski EA, Bremer E. Exploiting Substrate Promiscuity of Ectoine Hydroxylase for Regio- and Stereoselective Modification of Homoectoine. Front Microbiol 2019; 10:2745. [PMID: 31827466 PMCID: PMC6890836 DOI: 10.3389/fmicb.2019.02745] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Accepted: 11/12/2019] [Indexed: 11/13/2022] Open
Abstract
Extant enzymes are not only highly efficient biocatalysts for a single, or a group of chemically closely related substrates but often have retained, as a mark of their evolutionary history, a certain degree of substrate ambiguity. We have exploited the substrate ambiguity of the ectoine hydroxylase (EctD), a member of the non-heme Fe(II)-containing and 2-oxoglutarate-dependent dioxygenase superfamily, for such a task. Naturally, the EctD enzyme performs a precise regio- and stereoselective hydroxylation of the ubiquitous stress protectant and chemical chaperone ectoine (possessing a six-membered pyrimidine ring structure) to yield trans-5-hydroxyectoine. Using a synthetic ectoine derivative, homoectoine, which possesses an expanded seven-membered diazepine ring structure, we were able to selectively generate, both in vitro and in vivo, trans-5-hydroxyhomoectoine. For this transformation, we specifically used the EctD enzyme from Pseudomonas stutzeri in a whole cell biocatalyst approach, as this enzyme exhibits high catalytic efficiency not only for its natural substrate ectoine but also for homoectoine. Molecular docking approaches with the crystal structure of the Sphingopyxis alaskensis EctD protein predicted the formation of trans-5-hydroxyhomoectoine, a stereochemical configuration that we experimentally verified by nuclear-magnetic resonance spectroscopy. An Escherichia coli cell factory expressing the P. stutzeri ectD gene from a synthetic promoter imported homoectoine via the ProU and ProP compatible solute transporters, hydroxylated it, and secreted the formed trans-5-hydroxyhomoectoine, independent from all currently known mechanosensitive channels, into the growth medium from which it could be purified by high-pressure liquid chromatography.
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Affiliation(s)
- Laura Czech
- Laboratory for Microbiology, Department of Biology, Philipps-Universität Marburg, Marburg, Germany
| | - Sarah Wilcken
- Laboratory for Microbiology, Department of Biology, Philipps-Universität Marburg, Marburg, Germany
| | - Oliver Czech
- Department of Chemistry, Philipps-Universität Marburg, Marburg, Germany
| | - Uwe Linne
- Department of Chemistry, Philipps-Universität Marburg, Marburg, Germany
| | - Jarryd Brauner
- Institute of Microbiology and Biotechnology, Rheinische Friedrich-Wilhelms-Universität, Bonn, Germany
| | - Sander H J Smits
- Institute of Biochemistry, Heinrich-Heine Universität Düsseldorf, Düsseldorf, Germany.,Center for Structural Studies, Heinrich-Heine Universität Düsseldorf, Düsseldorf, Germany
| | - Erwin A Galinski
- Institute of Microbiology and Biotechnology, Rheinische Friedrich-Wilhelms-Universität, Bonn, Germany
| | - Erhard Bremer
- Laboratory for Microbiology, Department of Biology, Philipps-Universität Marburg, Marburg, Germany.,SYNMIKRO Research Center, Philipps-Universität Marburg, Marburg, Germany
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28
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Chen WC, Yuan FW, Wang LF, Chien CC, Wei YH. Ectoine production with indigenous Marinococcus sp. MAR2 isolated from the marine environment. Prep Biochem Biotechnol 2019; 50:74-81. [PMID: 31517565 DOI: 10.1080/10826068.2019.1663534] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Ectoine has fostered the development of products for skin care and cosmetics. In this study, we employed the marine bacterial strain Marinococcus sp. MAR2 to increase ectoine production by optimizing medium constituents using Response Surface Methodology (RSM) and a fed-batch strategy. The results from the steepest ascent and central composite design indicated that 54 g/L of yeast extract, 14.0 g/L of ammonium acetate, 74.4 g/L of sodium glutamate, and 6.2 g/L of sodium citrate constituted the optimal medium with maximum ectoine production (3.5 g/L). In addition, we performed fed-batch culture in the bioreactor, combining pH and dissolved oxygen to produce ectoine by Marinococcus sp. MAR2. The ectoine production, content, and productivity of 5.6 g/L, 10%, and 3.9 g/L/day were further reached by a fed-batch culture. Thus, the ectoine production by Marinococcus sp. MAR2 using RSM and fed-batch strategy shows its potential for industrial production.
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Affiliation(s)
- Wei-Chuan Chen
- Graduate School of Biotechnology and Bioengineering, Yuan Ze University, Taoyuan, Taiwan (R.O.C.)
| | - Fang-Wei Yuan
- Graduate School of Biotechnology and Bioengineering, Yuan Ze University, Taoyuan, Taiwan (R.O.C.)
| | - Li-Fen Wang
- Department of Applied Chemistry and Materials Science, Fooyin University, Kaohsiung, Taiwan (R.O.C.)
| | - Chih-Ching Chien
- Graduate School of Biotechnology and Bioengineering, Yuan Ze University, Taoyuan, Taiwan (R.O.C.)
| | - Yu-Hong Wei
- Graduate School of Biotechnology and Bioengineering, Yuan Ze University, Taoyuan, Taiwan (R.O.C.)
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29
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Fructose metabolism in Chromohalobacter salexigens: interplay between the Embden-Meyerhof-Parnas and Entner-Doudoroff pathways. Microb Cell Fact 2019; 18:134. [PMID: 31409414 PMCID: PMC6692947 DOI: 10.1186/s12934-019-1178-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Accepted: 07/30/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The halophilic bacterium Chromohalobacter salexigens metabolizes glucose exclusively through the Entner-Doudoroff (ED) pathway, an adaptation which results in inefficient growth, with significant carbon overflow, especially at low salinity. Preliminary analysis of C. salexigens genome suggests that fructose metabolism could proceed through the Entner-Doudoroff and Embden-Meyerhof-Parnas (EMP) pathways. In order to thrive at high salinity, this bacterium relies on the biosynthesis and accumulation of ectoines as major compatible solutes. This metabolic pathway imposes a high metabolic burden due to the consumption of a relevant proportion of cellular resources, including both energy molecules (NADPH and ATP) and carbon building blocks. Therefore, the existence of more than one glycolytic pathway with different stoichiometries may be an advantage for C. salexigens. The aim of this work is to experimentally characterize the metabolism of fructose in C. salexigens. RESULTS Fructose metabolism was analyzed using in silico genome analysis, RT-PCR, isotopic labeling, and genetic approaches. During growth on fructose as the sole carbon source, carbon overflow was not observed in a wide range of salt concentrations, and higher biomass yields were reached. We unveiled the initial steps of the two pathways for fructose incorporation and their links to central metabolism. While glucose is metabolized exclusively through the Entner-Doudoroff (ED) pathway, fructose is also partially metabolized by the Embden-Meyerhof-Parnas (EMP) route. Tracking isotopic label from [1-13C] fructose to ectoines revealed that 81% and 19% of the fructose were metabolized through ED and EMP-like routes, respectively. Activities of enzymes from both routes were demonstrated in vitro by 31P-NMR. Genes encoding predicted fructokinase and 1-phosphofructokinase were cloned and the activities of their protein products were confirmed. Importantly, the protein encoded by csal1534 gene functions as fructose bisphosphatase, although it had been annotated previously as pyrophosphate-dependent phosphofructokinase. The gluconeogenic rather than glycolytic role of this enzyme in vivo is in agreement with the lack of 6-phosphofructokinase activity previously described. CONCLUSIONS Overall, this study shows that C. salexigens possesses a greater metabolic flexibility for fructose catabolism, the ED and EMP pathways contributing to a fine balancing of energy and biosynthetic demands and, subsequently, to a more efficient metabolism.
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30
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Gießelmann G, Dietrich D, Jungmann L, Kohlstedt M, Jeon EJ, Yim SS, Sommer F, Zimmer D, Mühlhaus T, Schroda M, Jeong KJ, Becker J, Wittmann C. Metabolic Engineering of
Corynebacterium glutamicum
for High‐Level Ectoine Production: Design, Combinatorial Assembly, and Implementation of a Transcriptionally Balanced Heterologous Ectoine Pathway. Biotechnol J 2019; 14:e1800417. [DOI: 10.1002/biot.201800417] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2018] [Revised: 05/03/2019] [Indexed: 12/27/2022]
Affiliation(s)
- Gideon Gießelmann
- Institute of Systems BiotechnologySaarland University 66123 Saarbrücken Germany
| | - Demian Dietrich
- Institute of Systems BiotechnologySaarland University 66123 Saarbrücken Germany
| | - Lukas Jungmann
- Institute of Systems BiotechnologySaarland University 66123 Saarbrücken Germany
| | - Michael Kohlstedt
- Institute of Systems BiotechnologySaarland University 66123 Saarbrücken Germany
| | - Eun J. Jeon
- Department of Chemical and Biomolecular EngineeringKAIST 335 Gwahagno Yuseong‐gu Daejeon 305‐701 Republic of Korea
| | - Sung S. Yim
- Department of Chemical and Biomolecular EngineeringKAIST 335 Gwahagno Yuseong‐gu Daejeon 305‐701 Republic of Korea
| | - Frederik Sommer
- Department of Molecular Biotechnology and Systems BiologyTU Kaiserslautern Kaiserslautern 67663 Germany
| | - David Zimmer
- Department of Molecular Biotechnology and Systems BiologyTU Kaiserslautern Kaiserslautern 67663 Germany
| | - Timo Mühlhaus
- Department of Molecular Biotechnology and Systems BiologyTU Kaiserslautern Kaiserslautern 67663 Germany
| | - Michael Schroda
- Department of Molecular Biotechnology and Systems BiologyTU Kaiserslautern Kaiserslautern 67663 Germany
| | - Ki J. Jeong
- Department of Chemical and Biomolecular EngineeringKAIST 335 Gwahagno Yuseong‐gu Daejeon 305‐701 Republic of Korea
| | - Judith Becker
- Institute of Systems BiotechnologySaarland University 66123 Saarbrücken Germany
| | - Christoph Wittmann
- Institute of Systems BiotechnologySaarland University 66123 Saarbrücken Germany
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31
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Heterologous Ectoine Production in Escherichia coli: Optimization Using Response Surface Methodology. Int J Microbiol 2019; 2019:5475361. [PMID: 31354830 PMCID: PMC6636453 DOI: 10.1155/2019/5475361] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Revised: 05/10/2019] [Accepted: 06/03/2019] [Indexed: 01/20/2023] Open
Abstract
Introduction A halophilic bacterium of the Halomonas elongata BK-AG25 has successfully produced ectoine with high productivity. To overcome the drawbacks of high levels of salt in the production process, a nonhalophilic bacteria of Escherichia coli (E. coli) was used to express the ectoine gene cluster of the halophilic bacteria, and the production of ectoine by the recombinant cell was optimized. Methods The ectoine gene cluster from the halophilic bacterium was isolated and inserted into an expression plasmid of pET30(a) and subsequently transformed into E. coli BL21 (DE3). Production of ectoine from the recombinant E. coli was investigated and then maximized by optimizing the level of nutrients in the medium, as well as the bioprocess conditions using response surface methodology. The experimental designs were performed using a central composite design. Results The recombinant E. coli successfully expressed the ectoine gene cluster of Halomonas elongata BK-AG25 under the control of the T7 promoter. The recombinant cell was able to produce ectoine, of which most were excreted into the medium. The optimization of ectoine production with the response surface methodology showed that the level of salt in the medium, the incubation temperature, the optical density of the bacteria before induction, and the final concentration of the inducer gave a significant effect on ectoine production by the recombinant E. coli. Interestingly, the level of salt in the medium and the incubation temperature showed an inverse effect on the production of intracellular and extracellular ectoine by the recombinant cell. At the optimum conditions, the production yield was about 418 mg ectoine/g cdw (cell dry weight) after 12 hours of incubation. Conclusion This study is the first report on the expression of an ectoine gene cluster of Halomonas elongata BK-AG25 in E. coli BL21, under the control of the T7 promoter. Optimization of the level of nutrients in the medium, as well as the bioprocess condition using response surface methodology, has successfully increased the production of ectoine by the recombinant bacteria.
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32
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Illuminating the catalytic core of ectoine synthase through structural and biochemical analysis. Sci Rep 2019; 9:364. [PMID: 30674920 PMCID: PMC6344544 DOI: 10.1038/s41598-018-36247-w] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Accepted: 11/16/2018] [Indexed: 11/26/2022] Open
Abstract
Ectoine synthase (EctC) is the signature enzyme for the production of ectoine, a compatible solute and chemical chaperone widely synthesized by bacteria as a cellular defense against the detrimental effects of osmotic stress. EctC catalyzes the last step in ectoine synthesis through cyclo-condensation of the EctA-formed substrate N-gamma-acetyl-L-2,4-diaminobutyric acid via a water elimination reaction. We have biochemically and structurally characterized the EctC enzyme from the thermo-tolerant bacterium Paenibacillus lautus (Pl). EctC is a member of the cupin superfamily and forms dimers, both in solution and in crystals. We obtained high-resolution crystal structures of the (Pl)EctC protein in forms that contain (i) the catalytically important iron, (ii) iron and the substrate N-gamma-acetyl-L-2,4-diaminobutyric acid, and (iii) iron and the enzyme reaction product ectoine. These crystal structures lay the framework for a proposal for the EctC-mediated water-elimination reaction mechanism. Residues involved in coordinating the metal, the substrate, or the product within the active site of ectoine synthase are highly conserved among a large group of EctC-type proteins. Collectively, the biochemical, mutational, and structural data reported here yielded detailed insight into the structure-function relationship of the (Pl)EctC enzyme and are relevant for a deeper understanding of the ectoine synthase family as a whole.
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33
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Czech L, Hermann L, Stöveken N, Richter AA, Höppner A, Smits SHJ, Heider J, Bremer E. Role of the Extremolytes Ectoine and Hydroxyectoine as Stress Protectants and Nutrients: Genetics, Phylogenomics, Biochemistry, and Structural Analysis. Genes (Basel) 2018; 9:genes9040177. [PMID: 29565833 PMCID: PMC5924519 DOI: 10.3390/genes9040177] [Citation(s) in RCA: 130] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2018] [Revised: 03/13/2018] [Accepted: 03/15/2018] [Indexed: 01/26/2023] Open
Abstract
Fluctuations in environmental osmolarity are ubiquitous stress factors in many natural habitats of microorganisms, as they inevitably trigger osmotically instigated fluxes of water across the semi-permeable cytoplasmic membrane. Under hyperosmotic conditions, many microorganisms fend off the detrimental effects of water efflux and the ensuing dehydration of the cytoplasm and drop in turgor through the accumulation of a restricted class of organic osmolytes, the compatible solutes. Ectoine and its derivative 5-hydroxyectoine are prominent members of these compounds and are synthesized widely by members of the Bacteria and a few Archaea and Eukarya in response to high salinity/osmolarity and/or growth temperature extremes. Ectoines have excellent function-preserving properties, attributes that have led to their description as chemical chaperones and fostered the development of an industrial-scale biotechnological production process for their exploitation in biotechnology, skin care, and medicine. We review, here, the current knowledge on the biochemistry of the ectoine/hydroxyectoine biosynthetic enzymes and the available crystal structures of some of them, explore the genetics of the underlying biosynthetic genes and their transcriptional regulation, and present an extensive phylogenomic analysis of the ectoine/hydroxyectoine biosynthetic genes. In addition, we address the biochemistry, phylogenomics, and genetic regulation for the alternative use of ectoines as nutrients.
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Affiliation(s)
- Laura Czech
- Laboratory for Microbiology, Department of Biology, Philipps-University Marburg, Karl-von-Frisch Str. 8, D-35043 Marburg, Germany.
| | - Lucas Hermann
- Laboratory for Microbiology, Department of Biology, Philipps-University Marburg, Karl-von-Frisch Str. 8, D-35043 Marburg, Germany.
| | - Nadine Stöveken
- Laboratory for Microbiology, Department of Biology, Philipps-University Marburg, Karl-von-Frisch Str. 8, D-35043 Marburg, Germany.
- LOEWE-Center for Synthetic Microbiology, Philipps-University Marburg, Hans-Meerwein Str. 6, D-35043 Marburg, Germany.
| | - Alexandra A Richter
- Laboratory for Microbiology, Department of Biology, Philipps-University Marburg, Karl-von-Frisch Str. 8, D-35043 Marburg, Germany.
| | - Astrid Höppner
- Center for Structural Studies, Heinrich-Heine University Düsseldorf, Universitäts Str. 1, D-40225 Düsseldorf, Germany.
| | - Sander H J Smits
- Center for Structural Studies, Heinrich-Heine University Düsseldorf, Universitäts Str. 1, D-40225 Düsseldorf, Germany.
- Institute of Biochemistry, Heinrich-Heine University Düsseldorf, Universitäts Str. 1, D-40225 Düsseldorf, Germany.
| | - Johann Heider
- Laboratory for Microbiology, Department of Biology, Philipps-University Marburg, Karl-von-Frisch Str. 8, D-35043 Marburg, Germany.
- LOEWE-Center for Synthetic Microbiology, Philipps-University Marburg, Hans-Meerwein Str. 6, D-35043 Marburg, Germany.
| | - Erhard Bremer
- Laboratory for Microbiology, Department of Biology, Philipps-University Marburg, Karl-von-Frisch Str. 8, D-35043 Marburg, Germany.
- LOEWE-Center for Synthetic Microbiology, Philipps-University Marburg, Hans-Meerwein Str. 6, D-35043 Marburg, Germany.
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34
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Mechanistic insights into the allosteric regulation of Pseudomonas aeruginosa aspartate kinase. Biochem J 2018; 475:1107-1119. [PMID: 29382741 DOI: 10.1042/bcj20170829] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2017] [Revised: 01/18/2018] [Accepted: 01/24/2018] [Indexed: 02/05/2023]
Abstract
In plants and microorganisms, aspartate kinase (AK) catalyzes an initial commitment step of the aspartate family amino acid biosynthesis. Owing to various structural organizations, AKs from different species show tremendous diversity and complex allosteric controls. We report the crystal structure of AK from Pseudomonas aeruginosa (PaAK), a typical α2β2 hetero-tetrameric enzyme, in complex with inhibitory effectors. Distinctive features of PaAK are revealed by structural and biochemical analyses. Essentially, the open conformation of Lys-/Thr-bound PaAK structure clarifies the inhibitory mechanism of α2β2-type AK. Moreover, the various inhibitory effectors of PaAK have been identified and a general amino acid effector motif of AK family is described.
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35
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León MJ, Hoffmann T, Sánchez-Porro C, Heider J, Ventosa A, Bremer E. Compatible Solute Synthesis and Import by the Moderate Halophile Spiribacter salinus: Physiology and Genomics. Front Microbiol 2018; 9:108. [PMID: 29497403 PMCID: PMC5818414 DOI: 10.3389/fmicb.2018.00108] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Accepted: 01/17/2018] [Indexed: 11/13/2022] Open
Abstract
Members of the genus Spiribacter are found worldwide and are abundant in ecosystems possessing intermediate salinities between seawater and saturated salt concentrations. Spiribacter salinus M19-40 is the type species of this genus and its first cultivated representative. In the habitats of S. salinus M19-40, high salinity is a key determinant for growth and we therefore focused on the cellular adjustment strategy to this persistent environmental challenge. We coupled these experimental studies to the in silico mining of the genome sequence of this moderate halophile with respect to systems allowing this bacterium to control its potassium and sodium pools, and its ability to import and synthesize compatible solutes. S. salinus M19-40 produces enhanced levels of the compatible solute ectoine, both under optimal and growth-challenging salt concentrations, but the genes encoding the corresponding biosynthetic enzymes are not organized in a canonical ectABC operon. Instead, they are scrambled (ectAC; ectB) and are physically separated from each other on the S. salinus M19-40 genome. Genomes of many phylogenetically related bacteria also exhibit a non-canonical organization of the ect genes. S. salinus M19-40 also synthesizes trehalose, but this compatible solute seems to make only a minor contribution to the cytoplasmic solute pool under osmotic stress conditions. However, its cellular levels increase substantially in stationary phase cells grown under optimal salt concentrations. In silico genome mining revealed that S. salinus M19-40 possesses different types of uptake systems for compatible solutes. Among the set of compatible solutes tested in an osmostress protection growth assay, glycine betaine and arsenobetaine were the most effective. Transport studies with radiolabeled glycine betaine showed that S. salinus M19-40 increases the pool size of this osmolyte in a fashion that is sensitively tied to the prevalent salinity of the growth medium. It was amassed in salt-stressed cells in unmodified form and suppressed the synthesis of ectoine. In conclusion, the data presented here allow us to derive a genome-scale picture of the cellular adjustment strategy of a species that represents an environmentally abundant group of ecophysiologically important halophilic microorganisms.
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Affiliation(s)
- María J León
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Seville, Seville, Spain
| | - Tamara Hoffmann
- Laboratory for Microbiology, Department of Biology, Philipps University of Marburg, Marburg, Germany
| | - Cristina Sánchez-Porro
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Seville, Seville, Spain
| | - Johann Heider
- Laboratory for Microbiology, Department of Biology, Philipps University of Marburg, Marburg, Germany.,LOEWE-Center for Synthetic Microbiology, Philipps University of Marburg, Marburg, Germany
| | - Antonio Ventosa
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Seville, Seville, Spain
| | - Erhard Bremer
- Laboratory for Microbiology, Department of Biology, Philipps University of Marburg, Marburg, Germany.,LOEWE-Center for Synthetic Microbiology, Philipps University of Marburg, Marburg, Germany
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Tinkering with Osmotically Controlled Transcription Allows Enhanced Production and Excretion of Ectoine and Hydroxyectoine from a Microbial Cell Factory. Appl Environ Microbiol 2018; 84:AEM.01772-17. [PMID: 29101191 DOI: 10.1128/aem.01772-17] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2017] [Accepted: 10/28/2017] [Indexed: 12/21/2022] Open
Abstract
Ectoine and hydroxyectoine are widely synthesized by members of the Bacteria and a few members of the Archaea as potent osmostress protectants. We have studied the salient features of the osmostress-responsive promoter directing the transcription of the ectoine/hydroxyectoine biosynthetic gene cluster from the plant-root-associated bacterium Pseudomonas stutzeri by transferring it into Escherichia coli, an enterobacterium that does not produce ectoines naturally. Using ect-lacZ reporter fusions, we found that the heterologous ect promoter reacted with exquisite sensitivity in its transcriptional profile to graded increases in sustained high salinity, responded to a true osmotic signal, and required the buildup of an osmotically effective gradient across the cytoplasmic membrane for its induction. The involvement of the -10, -35, and spacer regions of the sigma-70-type ect promoter in setting promoter strength and response to osmotic stress was assessed through site-directed mutagenesis. Moderate changes in the ect promoter sequence that increase its resemblance to housekeeping sigma-70-type promoters of E. coli afforded substantially enhanced expression, both in the absence and in the presence of osmotic stress. Building on this set of ect promoter mutants, we engineered an E. coli chassis strain for the heterologous production of ectoines. This synthetic cell factory lacks the genes for the osmostress-responsive synthesis of trehalose and the compatible solute importers ProP and ProU, and it continuously excretes ectoines into the growth medium. By combining appropriate host strains and different plasmid variants, excretion of ectoine, hydroxyectoine, or a mixture of both compounds was achieved under mild osmotic stress conditions.IMPORTANCE Ectoines are compatible solutes, organic osmolytes that are used by microorganisms to fend off the negative consequences of high environmental osmolarity on cellular physiology. An understanding of the salient features of osmostress-responsive promoters directing the expression of the ectoine/hydroxyectoine biosynthetic gene clusters is lacking. We exploited the ect promoter from an ectoine/hydroxyectoine-producing soil bacterium for such a study by transferring it into a surrogate bacterial host. Despite the fact that E. coli does not synthesize ectoines naturally, the ect promoter retained its exquisitely sensitive osmotic control, indicating that osmoregulation of ect transcription is an inherent feature of the promoter and its flanking sequences. These sequences were narrowed to a 116-bp DNA fragment. Ectoines have interesting commercial applications. Building on data from a site-directed mutagenesis study of the ect promoter, we designed a synthetic cell factory that secretes ectoine, hydroxyectoine, or a mixture of both compounds into the growth medium.
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Nunn PB, Codd GA. Metabolic solutions to the biosynthesis of some diaminomonocarboxylic acids in nature: Formation in cyanobacteria of the neurotoxins 3-N-methyl-2,3-diaminopropanoic acid (BMAA) and 2,4-diaminobutanoic acid (2,4-DAB). PHYTOCHEMISTRY 2017; 144:253-270. [PMID: 29059579 DOI: 10.1016/j.phytochem.2017.09.015] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2017] [Revised: 09/18/2017] [Accepted: 09/20/2017] [Indexed: 06/07/2023]
Abstract
The non-encoded diaminomonocarboxylic acids, 3-N-methyl-2,3-diaminopropanoic acid (syn: α-amino-β-methylaminopropionic acid, MeDAP; β-N-methylaminoalanine, BMAA) and 2,4-diaminobutanoic acid (2,4-DAB), are distributed widely in cyanobacterial species in free and bound forms. Both amino acids are neurotoxic in whole animal and cell-based bioassays. The biosynthetic pathway to 2,4-DAB is well documented in bacteria and in one higher plant species, but has not been confirmed in cyanobacteria. The biosynthetic pathway to BMAA is unknown. This review considers possible metabolic routes, by analogy with reactions used in other species, by which these amino acids might be biosynthesised by cyanobacteria, which are a widespread potential environmental source of these neurotoxins. Where possible, the gene expression that might be implicated in these biosyntheses is discussed.
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Affiliation(s)
- Peter B Nunn
- School of Pharmacy and Biomedical Sciences, University of Portsmouth, PO1 2DT, UK.
| | - Geoffrey A Codd
- School of Life Sciences, University of Dundee, DD1 5EH, UK; School of Natural Sciences, University of Stirling, FK9 4LA, UK.
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Schulz A, Hermann L, Freibert SA, Bönig T, Hoffmann T, Riclea R, Dickschat JS, Heider J, Bremer E. Transcriptional regulation of ectoine catabolism in response to multiple metabolic and environmental cues. Environ Microbiol 2017; 19:4599-4619. [PMID: 28892254 DOI: 10.1111/1462-2920.13924] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2017] [Revised: 08/29/2017] [Accepted: 08/31/2017] [Indexed: 01/04/2023]
Abstract
Ectoine and hydroxyectoine are effective microbial osmostress protectants, but can also serve as versatile nutrients for bacteria. We have studied the genetic regulation of ectoine and hydroxyectoine import and catabolism in the marine Roseobacter species Ruegeria pomeroyi and identified three transcriptional regulators involved in these processes: the GabR/MocR-type repressor EnuR, the feast and famine-type regulator AsnC and the two-component system NtrYX. The corresponding genes are widely associated with ectoine and hydroxyectoine uptake and catabolic gene clusters (enuR, asnC), and with microorganisms predicted to consume ectoines (ntrYX). EnuR contains a covalently bound pyridoxal-5'-phosphate as a co-factor and the chemistry underlying the functioning of MocR/GabR-type regulators typically requires a system-specific low molecular mass effector molecule. Through ligand binding studies with purified EnuR, we identified N-(alpha)-L-acetyl-2,4-diaminobutyric acid and L-2,4-diaminobutyric acid as inducers for EnuR that are generated through ectoine catabolism. AsnC/Lrp-type proteins can wrap DNA into nucleosome-like structures, and we found that the asnC gene was essential for use of ectoines as nutrients. Furthermore, we discovered through transposon mutagenesis that the NtrYX two-component system is required for their catabolism. Database searches suggest that our findings have important ramifications for an understanding of the molecular biology of most microbial consumers of ectoines.
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Affiliation(s)
- Annina Schulz
- Department of Biology, Laboratory for Microbiology, Philipps-University Marburg, Karl-von-Frisch-Str. 8, D-35043 Marburg, Germany
| | - Lucas Hermann
- Department of Biology, Laboratory for Microbiology, Philipps-University Marburg, Karl-von-Frisch-Str. 8, D-35043 Marburg, Germany
| | - Sven-Andreas Freibert
- Department of Medicine, Institute for Cytobiology and Cytopathology, Philipps-University Marburg, Robert-Koch Str. 6, D-35032 Marburg, Germany
| | - Tobias Bönig
- Department of Biology, Laboratory for Microbiology, Philipps-University Marburg, Karl-von-Frisch-Str. 8, D-35043 Marburg, Germany
| | - Tamara Hoffmann
- Department of Biology, Laboratory for Microbiology, Philipps-University Marburg, Karl-von-Frisch-Str. 8, D-35043 Marburg, Germany
| | - Ramona Riclea
- Institute of Organic Chemistry, Technical University Braunschweig, D-38106 Braunschweig, Germany.,Kekulé-Institute for Organic Chemistry and Biochemistry, Friedrich-Wilhelms-Universität Bonn, D-53121 Bonn, Germany
| | - Jeroen S Dickschat
- Institute of Organic Chemistry, Technical University Braunschweig, D-38106 Braunschweig, Germany.,Kekulé-Institute for Organic Chemistry and Biochemistry, Friedrich-Wilhelms-Universität Bonn, D-53121 Bonn, Germany
| | - Johann Heider
- Department of Biology, Laboratory for Microbiology, Philipps-University Marburg, Karl-von-Frisch-Str. 8, D-35043 Marburg, Germany.,LOEWE-Center for Synthetic Microbiology, Philipps-University Marburg, Hans-Meerwein Str. 6, D-35043 Marburg, Germany
| | - Erhard Bremer
- Department of Biology, Laboratory for Microbiology, Philipps-University Marburg, Karl-von-Frisch-Str. 8, D-35043 Marburg, Germany.,LOEWE-Center for Synthetic Microbiology, Philipps-University Marburg, Hans-Meerwein Str. 6, D-35043 Marburg, Germany
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Improved fermentative production of the compatible solute ectoine by Corynebacterium glutamicum from glucose and alternative carbon sources. J Biotechnol 2017; 258:59-68. [DOI: 10.1016/j.jbiotec.2017.04.039] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2016] [Revised: 04/30/2017] [Accepted: 04/30/2017] [Indexed: 11/23/2022]
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Osmoregulation in the Halophilic Bacterium Halomonas elongata: A Case Study for Integrative Systems Biology. PLoS One 2017; 12:e0168818. [PMID: 28081159 PMCID: PMC5231179 DOI: 10.1371/journal.pone.0168818] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Accepted: 11/17/2016] [Indexed: 12/02/2022] Open
Abstract
Halophilic bacteria use a variety of osmoregulatory methods, such as the accumulation of one or more compatible solutes. The wide diversity of compounds that can act as compatible solute complicates the task of understanding the different strategies that halophilic bacteria use to cope with salt. This is specially challenging when attempting to go beyond the pathway that produces a certain compatible solute towards an understanding of how the metabolic network as a whole addresses the problem. Metabolic reconstruction based on genomic data together with Flux Balance Analysis (FBA) is a promising tool to gain insight into this problem. However, as more of these reconstructions become available, it becomes clear that processes predicted by genome annotation may not reflect the processes that are active in vivo. As a case in point, E. coli is unable to grow aerobically on citrate in spite of having all the necessary genes to do it. It has also been shown that the realization of this genetic potential into an actual capability to metabolize citrate is an extremely unlikely event under normal evolutionary conditions. Moreover, many marine bacteria seem to have the same pathways to metabolize glucose but each species uses a different one. In this work, a metabolic network inferred from genomic annotation of the halophilic bacterium Halomonas elongata and proteomic profiling experiments are used as a starting point to motivate targeted experiments in order to find out some of the defining features of the osmoregulatory strategies of this bacterium. This new information is then used to refine the network in order to describe the actual capabilities of H. elongata, rather than its genetic potential.
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Schulz A, Stöveken N, Binzen IM, Hoffmann T, Heider J, Bremer E. Feeding on compatible solutes: A substrate-induced pathway for uptake and catabolism of ectoines and its genetic control by EnuR. Environ Microbiol 2016; 19:926-946. [PMID: 27318028 DOI: 10.1111/1462-2920.13414] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2016] [Accepted: 06/19/2016] [Indexed: 01/19/2023]
Abstract
Ectoine and 5-hydroxyectoine are widely synthesized microbial osmostress protectants. They are also versatile nutrients but their catabolism and the genetic regulation of the corresponding genes are incompletely understood. Using the marine bacterium Ruegeria pomeroyi DSS-3, we investigated the utilization of ectoines and propose a seven steps comprising catabolic route that entails an initial conversion of 5-hydroxyectoine to ectoine, the opening of the ectoine ring, and the subsequent degradation of this intermediate to l-aspartate. The catabolic genes are co-transcribed with three genes encoding a 5-hydroxyectoine/ectoine-specific TRAP transporter. A chromosomal deletion of this entire gene cluster abolishes the utilization of ectoines as carbon and nitrogen sources. The presence of ectoines in the growth medium triggers enhanced expression of the importer and catabolic operon, a process dependent on a substrate-inducible promoter that precedes this gene cluster. EnuR, a member of the MocR/GabR-type transcriptional regulators, controls the activity of this promoter and functions as a repressor. EnuR contains a covalently bound pyridoxal-5'-phosphate, and we suggest that this co-factor is critical for the substrate-mediated induction of the 5-hydroxyectoine/ectoine import and catabolic genes. Bioinformatics showed that ectoine consumers are restricted to the Proteobacteria and that EnuR is likely a central regulator for most ectoine/5-hydroxyectoine catabolic genes.
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Affiliation(s)
- Annina Schulz
- Department of Biology, Laboratory for Microbiology, Philipps-University Marburg, Karl-von-Frisch-Str. 8, Marburg, D-35043, Germany
| | - Nadine Stöveken
- Department of Biology, Laboratory for Microbiology, Philipps-University Marburg, Karl-von-Frisch-Str. 8, Marburg, D-35043, Germany.,Philipps-University Marburg, LOEWE-Center for Synthetic Microbiology, Hans-Meerwein Str. 6, Marburg, D-35043, Germany
| | - Ina M Binzen
- Department of Biology, Laboratory for Microbiology, Philipps-University Marburg, Karl-von-Frisch-Str. 8, Marburg, D-35043, Germany
| | - Tamara Hoffmann
- Department of Biology, Laboratory for Microbiology, Philipps-University Marburg, Karl-von-Frisch-Str. 8, Marburg, D-35043, Germany
| | - Johann Heider
- Department of Biology, Laboratory for Microbiology, Philipps-University Marburg, Karl-von-Frisch-Str. 8, Marburg, D-35043, Germany.,Philipps-University Marburg, LOEWE-Center for Synthetic Microbiology, Hans-Meerwein Str. 6, Marburg, D-35043, Germany
| | - Erhard Bremer
- Department of Biology, Laboratory for Microbiology, Philipps-University Marburg, Karl-von-Frisch-Str. 8, Marburg, D-35043, Germany.,Philipps-University Marburg, LOEWE-Center for Synthetic Microbiology, Hans-Meerwein Str. 6, Marburg, D-35043, Germany
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Harding T, Brown MW, Simpson AGB, Roger AJ. Osmoadaptative Strategy and Its Molecular Signature in Obligately Halophilic Heterotrophic Protists. Genome Biol Evol 2016; 8:2241-58. [PMID: 27412608 PMCID: PMC4987115 DOI: 10.1093/gbe/evw152] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/22/2016] [Indexed: 01/17/2023] Open
Abstract
Halophilic microbes living in hypersaline environments must counteract the detrimental effects of low water activity and salt interference. Some halophilic prokaryotes equilibrate their intracellular osmotic strength with the extracellular milieu by importing inorganic solutes, mainly potassium. These "salt-in" organisms characteristically have proteins that are highly enriched with acidic and hydrophilic residues. In contrast, "salt-out" halophiles accumulate large amounts of organic solutes like amino acids, sugars and polyols, and lack a strong signature of halophilicity in the amino acid composition of cytoplasmic proteins. Studies to date have examined halophilic prokaryotes, yeasts, or algae, thus virtually nothing is known about the molecular adaptations of the other eukaryotic microbes, that is, heterotrophic protists (protozoa), that also thrive in hypersaline habitats. We conducted transcriptomic investigations to unravel the molecular adaptations of two obligately halophilic protists, Halocafeteria seosinensis and Pharyngomonas kirbyi Their predicted cytoplasmic proteomes showed increased hydrophilicity compared with marine protists. Furthermore, analysis of reconstructed ancestral sequences suggested that, relative to mesophiles, proteins in halophilic protists have undergone fewer substitutions from hydrophilic to hydrophobic residues since divergence from their closest relatives. These results suggest that these halophilic protists have a higher intracellular salt content than marine protists. However, absence of the acidic signature of salt-in microbes suggests that Haloc. seosinensis and P. kirbyi utilize organic osmolytes to maintain osmotic equilibrium. We detected increased expression of enzymes involved in synthesis and transport of organic osmolytes, namely hydroxyectoine and myo-inositol, at maximal salt concentration for growth in Haloc. seosinensis, suggesting possible candidates for these inferred organic osmolytes.
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Affiliation(s)
- Tommy Harding
- Department of Biochemistry and Molecular Biology, Centre for Comparative Genomics and Evolutionary Bioinformatics, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Matthew W Brown
- Department of Biological Sciences, Mississippi State University
| | - Alastair G B Simpson
- Department of Biology, Centre for Comparative Genomics and Evolutionary Bioinformatics, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Andrew J Roger
- Department of Biochemistry and Molecular Biology, Centre for Comparative Genomics and Evolutionary Bioinformatics, Dalhousie University, Halifax, Nova Scotia, Canada
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Tsujimoto M, Yoshida A, Shimizu T, Tomita T, Ohnishi Y, Kuzuyama T, Nishiyama M. Aspartate kinase involved in 4-hydroxy-3-nitrosobenzamide biosynthesis in Streptomyces murayamaensis. Biosci Biotechnol Biochem 2016; 80:2255-2263. [PMID: 27485103 DOI: 10.1080/09168451.2016.1214534] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Streptomyces murayamensis carries two aspartate kinase (AK) genes: one for the biosynthesis of lysine, threonine, and methionine, and the other (nspJ) contained in the biosynthetic gene cluster for the secondary metabolite, 4-hydroxy-3-nitrosobenzamide, for catalyzing the first reaction. AKs involved in the biosynthesis of amino acids are often regulated allosterically by the end products. In the present study, we characterized NspJ to investigate whether AKs involved in secondary metabolism were also allosterically regulated. NspJ was in α2β2 and (α2β2)2 heterooligomeric forms, and was insensitive to all the compounds tested including lysine, threonine, and methionine. The reduction in the activity following the removal of ammonium sulfate, which induced subunit dissociation, suggests that the β subunit may be involved in stabilizing the structure of the α subunit in order to exhibit its activity. This study has provided the first example of a feedback-insensitive α2β2-type AK, which is involved in the secondary metabolism.
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Affiliation(s)
- Mai Tsujimoto
- a Biotechnology Research Center , The University of Tokyo , Tokyo , Japan
| | - Ayako Yoshida
- a Biotechnology Research Center , The University of Tokyo , Tokyo , Japan
| | - Tetsu Shimizu
- a Biotechnology Research Center , The University of Tokyo , Tokyo , Japan
| | - Takeo Tomita
- a Biotechnology Research Center , The University of Tokyo , Tokyo , Japan
| | - Yasuo Ohnishi
- b Department of Biotechnology , Graduate School of Agricultural and Life Sciences, The University of Tokyo , Tokyo , Japan
| | - Tomohisa Kuzuyama
- a Biotechnology Research Center , The University of Tokyo , Tokyo , Japan
| | - Makoto Nishiyama
- a Biotechnology Research Center , The University of Tokyo , Tokyo , Japan
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Czech L, Stöveken N, Bremer E. EctD-mediated biotransformation of the chemical chaperone ectoine into hydroxyectoine and its mechanosensitive channel-independent excretion. Microb Cell Fact 2016; 15:126. [PMID: 27439307 PMCID: PMC4955205 DOI: 10.1186/s12934-016-0525-4] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2016] [Accepted: 07/12/2016] [Indexed: 11/26/2022] Open
Abstract
Background Ectoine and its derivative 5-hydroxyectoine are cytoprotectants widely synthesized by microorganisms as a defense against the detrimental effects of high osmolarity on cellular physiology and growth. Both ectoines possess the ability to preserve the functionality of proteins, macromolecular complexes, and even entire cells, attributes that led to their description as chemical chaperones. As a consequence, there is growing interest in using ectoines for biotechnological purposes, in skin care, and in medical applications. 5-Hydroxyectoine is synthesized from ectoine through a region- and stereo-specific hydroxylation reaction mediated by the EctD enzyme, a member of the non-heme-containing iron(II) and 2-oxoglutarate-dependent dioxygenases. This chemical modification endows the newly formed 5-hydroxyectoine with either superior or different stress- protecting and stabilizing properties. Microorganisms producing 5-hydroxyectoine typically contain a mixture of both ectoines. We aimed to establish a recombinant microbial cell factory where 5-hydroxyectoine is (i) produced in highly purified form, and (ii) secreted into the growth medium. Results We used an Escherichia coli strain (FF4169) defective in the synthesis of the osmostress protectant trehalose as the chassis for our recombinant cell factory. We expressed in this strain a plasmid-encoded ectD gene from Pseudomonas stutzeri A1501 under the control of the anhydrotetracycline-inducible tet promoter. We chose the ectoine hydroxylase from P. stutzeri A1501 for our cell factory after a careful comparison of the in vivo performance of seven different EctD proteins. In the final set-up of the cell factory, ectoine was provided to salt-stressed cultures of strain FF4169 (pMP41; ectD+). Ectoine was imported into the cells via the osmotically inducible ProP and ProU transport systems, intracellularly converted to 5-hydroxyectoine, which was then almost quantitatively secreted into the growth medium. Experiments with an E. coli mutant lacking all currently known mechanosensitive channels (MscL, MscS, MscK, MscM) revealed that the release of 5-hydroxyectoine under osmotic steady-state conditions occurred independently of these microbial safety valves. In shake-flask experiments, 2.13 g l−1 ectoine (15 mM) was completely converted into 5-hydroxyectoine within 24 h. Conclusions We describe here a recombinant E. coli cell factory for the production and secretion of the chemical chaperone 5-hydroxyectoine free from contaminating ectoine. Electronic supplementary material The online version of this article (doi:10.1186/s12934-016-0525-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Laura Czech
- Laboratory for Microbiology, Department of Biology, Philipps-University at Marburg, 35043, Marburg, Germany
| | - Nadine Stöveken
- Laboratory for Microbiology, Department of Biology, Philipps-University at Marburg, 35043, Marburg, Germany.,LOEWE Center for Synthetic Microbiology, Philipps-University Marburg at Marburg, 35043, Marburg, Germany
| | - Erhard Bremer
- Laboratory for Microbiology, Department of Biology, Philipps-University at Marburg, 35043, Marburg, Germany. .,LOEWE Center for Synthetic Microbiology, Philipps-University Marburg at Marburg, 35043, Marburg, Germany. .,Laboratory for Microbiology, Department of Biology, Philipps-University at Marburg, Karl-von-Frisch-Str. 8, 35043, Marburg, Germany.
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45
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Ericsson AC, Personett AR, Grobman ME, Rindt H, Reinero CR. Composition and Predicted Metabolic Capacity of Upper and Lower Airway Microbiota of Healthy Dogs in Relation to the Fecal Microbiota. PLoS One 2016; 11:e0154646. [PMID: 27136381 PMCID: PMC4852910 DOI: 10.1371/journal.pone.0154646] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2016] [Accepted: 04/15/2016] [Indexed: 02/06/2023] Open
Abstract
The upper and lower airways of healthy humans are reported to harbor stable and consistent bacterial populations, and the composition of these communities is altered in individuals affected with several respiratory diseases. Data regarding the presence of airway microbiota in other animals are scant and a better understanding of the composition and metabolic function of such bacterial populations is essential for the development of novel therapeutic and diagnostic modalities for use in both veterinary and human medicine. Based on targeted next-generation sequencing of feces and samples collected at multiple levels of the airways from 16 healthy female dogs, we demonstrate that canine airways harbor a topographically continuous microbiota with increasing relative abundance of proteobacterial species from the upper to lower airways. The lung-associated microbiota, as assessed via bronchoalveolar lavage fluid (BALF), was the most consistent between dogs and was dominated by three distinct taxa, two of which were resolved to the species level and one to the level of family. The gene content of the nasal, oropharyngeal, and lung-associated microbiota, predicted using the Phylogenetic Investigations into Communities by Reconstruction of Unobserved States (PICRUSt) software, provided information regarding the glyoxylate and citrate cycle metabolic pathways utilized by these bacterial populations to colonize such nutrient-poor, low-throughput environments. These data generated in healthy subjects provide context for future analysis of diseased canine airways. Moreover, as dogs have similar respiratory anatomy, physiology, and immune systems as humans, are exposed to many of the same environmental stimuli, and spontaneously develop similar respiratory diseases, these data support the use of dogs as a model species for prospective studies of the airway microbiota, with findings translatable to the human condition.
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Affiliation(s)
- Aaron C. Ericsson
- University of Missouri Metagenomics Center, University of Missouri, Columbia, Missouri, United States of America
- College of Veterinary Medicine, University of Missouri, Columbia, Missouri, United States of America
- Department of Veterinary Pathobiology, College of Veterinary Medicine, University of Missouri, Columbia, Missouri, United States of America
- * E-mail: (ACE); (CRR)
| | - Alexa R. Personett
- College of Veterinary Medicine, University of Missouri, Columbia, Missouri, United States of America
| | - Megan E. Grobman
- College of Veterinary Medicine, University of Missouri, Columbia, Missouri, United States of America
- Department of Veterinary Medicine and Surgery, College of Veterinary Medicine, University of Missouri, Columbia, Missouri, United States of America
- Comparative Internal Medicine Laboratory, University of Missouri, Columbia, Missouri, United States of America
| | - Hansjorg Rindt
- College of Veterinary Medicine, University of Missouri, Columbia, Missouri, United States of America
- Comparative Internal Medicine Laboratory, University of Missouri, Columbia, Missouri, United States of America
| | - Carol R. Reinero
- College of Veterinary Medicine, University of Missouri, Columbia, Missouri, United States of America
- Department of Veterinary Medicine and Surgery, College of Veterinary Medicine, University of Missouri, Columbia, Missouri, United States of America
- Comparative Internal Medicine Laboratory, University of Missouri, Columbia, Missouri, United States of America
- * E-mail: (ACE); (CRR)
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46
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Widderich N, Kobus S, Höppner A, Riclea R, Seubert A, Dickschat JS, Heider J, Smits SHJ, Bremer E. Biochemistry and Crystal Structure of Ectoine Synthase: A Metal-Containing Member of the Cupin Superfamily. PLoS One 2016; 11:e0151285. [PMID: 26986827 PMCID: PMC4795551 DOI: 10.1371/journal.pone.0151285] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2015] [Accepted: 02/25/2016] [Indexed: 01/24/2023] Open
Abstract
Ectoine is a compatible solute and chemical chaperone widely used by members of the Bacteria and a few Archaea to fend-off the detrimental effects of high external osmolarity on cellular physiology and growth. Ectoine synthase (EctC) catalyzes the last step in ectoine production and mediates the ring closure of the substrate N-gamma-acetyl-L-2,4-diaminobutyric acid through a water elimination reaction. However, the crystal structure of ectoine synthase is not known and a clear understanding of how its fold contributes to enzyme activity is thus lacking. Using the ectoine synthase from the cold-adapted marine bacterium Sphingopyxis alaskensis (Sa), we report here both a detailed biochemical characterization of the EctC enzyme and the high-resolution crystal structure of its apo-form. Structural analysis classified the (Sa)EctC protein as a member of the cupin superfamily. EctC forms a dimer with a head-to-tail arrangement, both in solution and in the crystal structure. The interface of the dimer assembly is shaped through backbone-contacts and weak hydrophobic interactions mediated by two beta-sheets within each monomer. We show for the first time that ectoine synthase harbors a catalytically important metal co-factor; metal depletion and reconstitution experiments suggest that EctC is probably an iron-dependent enzyme. We found that EctC not only effectively converts its natural substrate N-gamma-acetyl-L-2,4-diaminobutyric acid into ectoine through a cyclocondensation reaction, but that it can also use the isomer N-alpha-acetyl-L-2,4-diaminobutyric acid as its substrate, albeit with substantially reduced catalytic efficiency. Structure-guided site-directed mutagenesis experiments targeting amino acid residues that are evolutionarily highly conserved among the extended EctC protein family, including those forming the presumptive iron-binding site, were conducted to functionally analyze the properties of the resulting EctC variants. An assessment of enzyme activity and iron content of these mutants give important clues for understanding the architecture of the active site positioned within the core of the EctC cupin barrel.
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Affiliation(s)
- Nils Widderich
- Department of Biology, Laboratory for Microbiology, Philipps-Universität Marburg, Marburg, Germany
| | - Stefanie Kobus
- X-ray Facility and Crystal Farm, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany
| | - Astrid Höppner
- X-ray Facility and Crystal Farm, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany
| | - Ramona Riclea
- Kekulé-Institute for Organic Chemistry and Biochemistry, Friedrich-Wilhelms-Universität Bonn, Bonn, Germany
- Institute of Organic Chemistry, TU Braunschweig, Braunschweig, Germany
| | - Andreas Seubert
- Department of Chemistry, Analytical Chemistry, Philipps-Universität Marburg, Marburg, Germany
| | - Jeroen S. Dickschat
- Kekulé-Institute for Organic Chemistry and Biochemistry, Friedrich-Wilhelms-Universität Bonn, Bonn, Germany
- Institute of Organic Chemistry, TU Braunschweig, Braunschweig, Germany
| | - Johann Heider
- Department of Biology, Laboratory for Microbiology, Philipps-Universität Marburg, Marburg, Germany
- LOEWE Center for Synthetic Microbiology, Philipps-University Marburg, D-35043 Marburg, Germany
| | - Sander H. J. Smits
- Institute of Biochemistry, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany
- * E-mail: (SS); (EB)
| | - Erhard Bremer
- Department of Biology, Laboratory for Microbiology, Philipps-Universität Marburg, Marburg, Germany
- LOEWE Center for Synthetic Microbiology, Philipps-University Marburg, D-35043 Marburg, Germany
- * E-mail: (SS); (EB)
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Widderich N, Czech L, Elling FJ, Könneke M, Stöveken N, Pittelkow M, Riclea R, Dickschat JS, Heider J, Bremer E. Strangers in the archaeal world: osmostress-responsive biosynthesis of ectoine and hydroxyectoine by the marine thaumarchaeon Nitrosopumilus maritimus. Environ Microbiol 2016; 18:1227-48. [PMID: 26636559 DOI: 10.1111/1462-2920.13156] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2015] [Revised: 11/19/2015] [Accepted: 11/27/2015] [Indexed: 11/29/2022]
Abstract
Ectoine and hydroxyectoine are compatible solutes widely synthesized by members of the Bacteria to cope with high osmolarity surroundings. Inspection of 557 archaeal genomes revealed that only 12 strains affiliated with the Nitrosopumilus, Methanothrix or Methanobacterium genera harbour ectoine/hydroxyectoine gene clusters. Phylogenetic considerations suggest that these Archaea have acquired these genes through horizontal gene transfer events. Using the Thaumarchaeon 'Candidatus Nitrosopumilus maritimus' as an example, we demonstrate that the transcription of its ectABCD genes is osmotically induced and functional since it leads to the production of both ectoine and hydroxyectoine. The ectoine synthase and the ectoine hydroxylase were biochemically characterized, and their properties resemble those of their counterparts from Bacteria. Transcriptional analysis of osmotically stressed 'Ca. N. maritimus' cells demonstrated that they possess an ectoine/hydroxyectoine gene cluster (hyp-ectABCD-mscS) different from those recognized previously since it contains a gene for an MscS-type mechanosensitive channel. Complementation experiments with an Escherichia coli mutant lacking all known mechanosensitive channel proteins demonstrated that the (Nm)MscS protein is functional. Hence, 'Ca. N. maritimus' cells cope with high salinity not only through enhanced synthesis of osmostress-protective ectoines but they already prepare themselves simultaneously for an eventually occurring osmotic down-shock by enhancing the production of a safety-valve (NmMscS).
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Affiliation(s)
- Nils Widderich
- Laboratory for Molecular Microbiology, Department of Biology, Philipps-University, Karl-von-Frisch Str. 8, D-35043, Marburg, Germany
| | - Laura Czech
- Laboratory for Molecular Microbiology, Department of Biology, Philipps-University, Karl-von-Frisch Str. 8, D-35043, Marburg, Germany
| | - Felix J Elling
- Organic Geochemistry Group, MARUM - Center for Marine Environmental Sciences, University of Bremen, PO Box 330 440, D-28334, Bremen, Germany
| | - Martin Könneke
- Organic Geochemistry Group, MARUM - Center for Marine Environmental Sciences, University of Bremen, PO Box 330 440, D-28334, Bremen, Germany
| | - Nadine Stöveken
- Laboratory for Molecular Microbiology, Department of Biology, Philipps-University, Karl-von-Frisch Str. 8, D-35043, Marburg, Germany.,LOEWE-Center for Synthetic Microbiology, Philipps-University Marburg, Hans-Meerwein-Str. 6, D-35043, Marburg, Germany
| | - Marco Pittelkow
- Laboratory for Molecular Microbiology, Department of Biology, Philipps-University, Karl-von-Frisch Str. 8, D-35043, Marburg, Germany
| | - Ramona Riclea
- Kekulé-Institut for Organic Chemistry and Biochemistry, Friedrich-Wilhelms-University Bonn, Gerhard-Domagk Str. 1, D-53121, Bonn, Germany.,Institute of Organic Chemistry, TU Braunschweig, Hagenring 30, D-38106, Braunschweig, Germany
| | - Jeroen S Dickschat
- Kekulé-Institut for Organic Chemistry and Biochemistry, Friedrich-Wilhelms-University Bonn, Gerhard-Domagk Str. 1, D-53121, Bonn, Germany.,Institute of Organic Chemistry, TU Braunschweig, Hagenring 30, D-38106, Braunschweig, Germany
| | - Johann Heider
- Laboratory for Molecular Microbiology, Department of Biology, Philipps-University, Karl-von-Frisch Str. 8, D-35043, Marburg, Germany.,LOEWE-Center for Synthetic Microbiology, Philipps-University Marburg, Hans-Meerwein-Str. 6, D-35043, Marburg, Germany
| | - Erhard Bremer
- Laboratory for Molecular Microbiology, Department of Biology, Philipps-University, Karl-von-Frisch Str. 8, D-35043, Marburg, Germany.,LOEWE-Center for Synthetic Microbiology, Philipps-University Marburg, Hans-Meerwein-Str. 6, D-35043, Marburg, Germany
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Becker J, Gießelmann G, Hoffmann SL, Wittmann C. Corynebacterium glutamicum for Sustainable Bioproduction: From Metabolic Physiology to Systems Metabolic Engineering. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2016; 162:217-263. [DOI: 10.1007/10_2016_21] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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Chen W, Zhang S, Jiang P, Yao J, He Y, Chen L, Gui X, Dong Z, Tang SY. Design of an ectoine-responsive AraC mutant and its application in metabolic engineering of ectoine biosynthesis. Metab Eng 2015; 30:149-155. [PMID: 26051748 DOI: 10.1016/j.ymben.2015.05.004] [Citation(s) in RCA: 67] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2015] [Revised: 05/22/2015] [Accepted: 05/26/2015] [Indexed: 01/27/2023]
Abstract
Advanced high-throughput screening methods for small molecules may have important applications in the metabolic engineering of the biosynthetic pathways of these molecules. Ectoine is an excellent osmoprotectant that has been widely used in cosmetics. In this study, the Escherichia coli regulatory protein AraC was engineered to recognize ectoine as its non-natural effector and to activate transcription upon ectoine binding. As an endogenous reporter of ectoine, the mutated AraC protein was successfully incorporated into high-throughput screening of ectoine hyper-producing strains. The ectoine biosynthetic cluster from Halomonas elongata was cloned into E. coli. By engineering the rate-limiting enzyme L-2,4-diaminobutyric acid (DABA) aminotransferase (EctB), ectoine production and the specific activity of the EctB mutant were increased. Thus, these results demonstrated the effectiveness of engineering regulatory proteins into sensitive and rapid screening tools for small molecules and highlighted the importance and efficacy of directed evolution strategies applied to the engineering of genetic components for yield improvement in the biosynthesis of small molecules.
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Affiliation(s)
- Wei Chen
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Shan Zhang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Peixia Jiang
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Jun Yao
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yongzhi He
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Lincai Chen
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Xiwu Gui
- College of Animal Science and Veterinary Medicine, Shanxi Agricultural University, Taigu 030801, China
| | - Zhiyang Dong
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China.
| | - Shuang-Yan Tang
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China.
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He YZ, Gong J, Yu HY, Tao Y, Zhang S, Dong ZY. High production of ectoine from aspartate and glycerol by use of whole-cell biocatalysis in recombinant Escherichia coli. Microb Cell Fact 2015; 14:55. [PMID: 25886618 PMCID: PMC4405841 DOI: 10.1186/s12934-015-0238-0] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2015] [Accepted: 04/01/2015] [Indexed: 01/14/2023] Open
Abstract
Background Recently, the compatible solute 1, 4, 5, 6-tetrahydro-2-methyl-4-pyrimidinecarboxylic acid (ectoine) has attracted considerable interest due to its great potential as a protecting agent. To overcome the drawbacks of high salinity in the traditional bioprocess of ectoine using halophilic bacteria, various attempts have been made to engineer ectoine biosynthesis in nonhalophilic bacteria. Unfortunately, the yields of ectoine in these producers are still low and hardly meet the demands of large scale production. In this paper, the whole-cell biocatalytic process using aspartate and glycerol as substrates was tried for high production of ectoine in nonhalophilic bacteria. Results The ectoine genes ectABC from the halophilic bacterium Halomonas elongata were successfully introduced into Escherichia coli K-12 strain BW25113 under the arabinose-inducible promoter. To our delight, a large amount of ectoine was synthesized and excreted into the medium during the course of whole-cell biocatalysis, when using aspartate and glycerol as the direct substrates. At the low cell density of 5 OD/mL in flask, under the optimal conditions (100 mM sodium phosphate buffer (pH 7.0), 100 mM sodium aspartate, 100 mM KCl and 100 mM glycerol), the concentration of extracellular ectoine was increased to 2.67 mg/mL. At the high cell density of 20 OD/mL in fermentor, a maximum titre of 25.1 g/L ectoine was achieved in 24 h. Meanwhile, the biomass productivity of ectoine is as high as 4048 mg per gram dry cell weight (g DCW)−1, which is the highest value ever reported. Furthermore, it was demonstrated that the same batch of cells could be used for at least three rounds. Finally, a total yield of 63.4 g ectoine was obtained using one litre cells. Conclusion Using aspartate and glycerol as the direct substrates, high production of ectoine was achieved by the whole-cell biocatalysis in recombinant E. coli. Multiple rounds of whole-cell biocatalysis were established to further improve the production of ectoine. Our study herein provided a feasible biosynthesis process of ectoine with potential applications in large-scale industrial production.
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Affiliation(s)
- Yong-Zhi He
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China. .,University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Jiao Gong
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Hai-Ying Yu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Yong Tao
- Department of Industrial Microbiology and Biotechnology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Shan Zhang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Zhi-Yang Dong
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China.
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