151
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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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152
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Oprzeska-Zingrebe EA, Meyer S, Roloff A, Kunte HJ, Smiatek J. Influence of compatible solute ectoine on distinct DNA structures: thermodynamic insights into molecular binding mechanisms and destabilization effects. Phys Chem Chem Phys 2018; 20:25861-25874. [DOI: 10.1039/c8cp03543a] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We study ectoine-induced destabilization effects on DNA hairpins by a combination of atomistic molecular dynamics simulations, experiments, and theoretical approaches.
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Affiliation(s)
| | - Susann Meyer
- Federal Institute for Materials Research and Testing (BAM)
- D-12205 Berlin
- Germany
- Institute of Biochemistry and Biology
- University of Potsdam
| | - Alexander Roloff
- Federal Institute for Materials Research and Testing (BAM)
- D-12489 Berlin
- Germany
| | - Hans-Jörg Kunte
- Federal Institute for Materials Research and Testing (BAM)
- D-12205 Berlin
- Germany
| | - Jens Smiatek
- Institute for Computational Physics
- University of Stuttgart
- D-70569 Stuttgart
- Germany
- Helmholtz Institute Münster: Ionics in Energy Storage (HI MS IEK-12)
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153
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Wan PK, Lan JCW, Chen PW, Tan JS, Ng HS. Recovery of intracellular ectoine from Halomonas salina cells with poly(propylene) glycol/salt aqueous biphasic system. J Taiwan Inst Chem Eng 2018. [DOI: 10.1016/j.jtice.2017.11.003] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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154
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Sahle CJ, Schroer MA, Jeffries CM, Niskanen J. Hydration in aqueous solutions of ectoine and hydroxyectoine. Phys Chem Chem Phys 2018; 20:27917-27923. [DOI: 10.1039/c8cp05308a] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
We explore the influence of the two osmolytes ectoine and hydroxyectoine on the structure of pure water and aqueous NaCl solutions using non-resonant X-ray Raman scattering spectroscopy at the oxygen K-edge.
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Affiliation(s)
- Christoph J. Sahle
- European Synchrotron Radiation Facility, 71 Avenue des Martyrs
- 38000 Grenoble
- France
| | - Martin A. Schroer
- European Molecular Biology Laboratory (EMBL)
- Hamburg Outstation c/o DESY
- 22607 Hamburg
- Germany
| | - Cy M. Jeffries
- European Molecular Biology Laboratory (EMBL)
- Hamburg Outstation c/o DESY
- 22607 Hamburg
- Germany
| | - Johannes Niskanen
- University of Turku
- Department of Physics and Astronomy
- FI-20014 Turun yliopisto
- Finland
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155
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Remali J, Sarmin N'IM, Ng CL, Tiong JJL, Aizat WM, Keong LK, Zin NM. Genomic characterization of a new endophytic Streptomyces kebangsaanensis identifies biosynthetic pathway gene clusters for novel phenazine antibiotic production. PeerJ 2017; 5:e3738. [PMID: 29201559 PMCID: PMC5712208 DOI: 10.7717/peerj.3738] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2017] [Accepted: 08/04/2017] [Indexed: 11/20/2022] Open
Abstract
Background Streptomyces are well known for their capability to produce many bioactive secondary metabolites with medical and industrial importance. Here we report a novel bioactive phenazine compound, 6-((2-hydroxy-4-methoxyphenoxy) carbonyl) phenazine-1-carboxylic acid (HCPCA) extracted from Streptomyces kebangsaanensis, an endophyte isolated from the ethnomedicinal Portulaca oleracea. Methods The HCPCA chemical structure was determined using nuclear magnetic resonance spectroscopy. We conducted whole genome sequencing for the identification of the gene cluster(s) believed to be responsible for phenazine biosynthesis in order to map its corresponding pathway, in addition to bioinformatics analysis to assess the potential of S. kebangsaanensis in producing other useful secondary metabolites. Results The S. kebangsaanensis genome comprises an 8,328,719 bp linear chromosome with high GC content (71.35%) consisting of 12 rRNA operons, 81 tRNA, and 7,558 protein coding genes. We identified 24 gene clusters involved in polyketide, nonribosomal peptide, terpene, bacteriocin, and siderophore biosynthesis, as well as a gene cluster predicted to be responsible for phenazine biosynthesis. Discussion The HCPCA phenazine structure was hypothesized to derive from the combination of two biosynthetic pathways, phenazine-1,6-dicarboxylic acid and 4-methoxybenzene-1,2-diol, originated from the shikimic acid pathway. The identification of a biosynthesis pathway gene cluster for phenazine antibiotics might facilitate future genetic engineering design of new synthetic phenazine antibiotics. Additionally, these findings confirm the potential of S. kebangsaanensis for producing various antibiotics and secondary metabolites.
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Affiliation(s)
- Juwairiah Remali
- School of Diagnostic and Applied Health Sciences, Faculty of Health Sciences, Universiti Kebangsaan Malaysia, Kuala Lumpur, Malaysia
| | - Nurul 'Izzah Mohd Sarmin
- Centre of PreClinical Science Studies, Faculty of Dentistry, Universiti Teknologi MARA Sungai Buloh Campus, Sungai Buloh, Selangor, Malaysia
| | - Chyan Leong Ng
- Institute of Systems Biology (INBIOSIS), Universiti Kebangsaan Malaysia, Bangi, Selangor, Malaysia
| | - John J L Tiong
- School of Pharmacy, Taylor's University, Subang Jaya, Selangor, Malaysia
| | - Wan M Aizat
- Institute of Systems Biology (INBIOSIS), Universiti Kebangsaan Malaysia, Bangi, Selangor, Malaysia
| | - Loke Kok Keong
- Institute of Systems Biology (INBIOSIS), Universiti Kebangsaan Malaysia, Bangi, Selangor, Malaysia
| | - Noraziah Mohamad Zin
- School of Diagnostic and Applied Health Sciences, Faculty of Health Sciences, Universiti Kebangsaan Malaysia, Kuala Lumpur, Malaysia
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156
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Yun JH, Bae JW. Complete genome sequence of the halophile bacterium Kushneria marisflavi KCCM 80003 T, isolated from seawater in Korea. Mar Genomics 2017; 37:35-38. [PMID: 33250124 DOI: 10.1016/j.margen.2017.11.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2017] [Revised: 11/01/2017] [Accepted: 11/13/2017] [Indexed: 12/01/2022]
Abstract
We present the genome sequence of Kushneria marisflavi KCCM 80003T isolated from Yellow Sea in Korea. The complete genome of KCCM 80003T consisted of a single, circular chromosome of 3,667,185bp, with an average G+C content of 59.05%, and 3287 coding sequences, 12 rRNAs, and 66 tRNAs. Kushneria marisflavi KCCM 80003T, belonging to the family Halomonadaceae, exhibited resistance to high salt concentrations and possessed potassium metabolism- or osmotic stress-related coding sequences, including potassium homeostasis, ectoine biosynthesis and regulation, choline and betaine uptake, and betaine biosynthesis features in the genome. These results provide a basis for understanding resistance strategies to osmotic stress at the genetic level and accordingly have implications for genetic engineering and biotechnology.
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Affiliation(s)
- Ji-Hyun Yun
- Department of Life and Nanopharmaceutical Sciences, Kyung Hee University, Hoegi-dong, Dongdaemun-gu, Seoul 130-701, Republic of Korea; Department of Biology, Kyung Hee University, Hoegi-dong, Dongdaemun-gu, Seoul 130-701, Republic of Korea
| | - Jin-Woo Bae
- Department of Life and Nanopharmaceutical Sciences, Kyung Hee University, Hoegi-dong, Dongdaemun-gu, Seoul 130-701, Republic of Korea; Department of Biology, Kyung Hee University, Hoegi-dong, Dongdaemun-gu, Seoul 130-701, Republic of Korea.
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157
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Ren M, Zhang G, Ye Z, Qiao Z, Xie M, Lin Y, Li T, Zhao J. Metagenomic analysis reveals potential interactions in an artificial coculture. AMB Express 2017; 7:193. [PMID: 29098480 PMCID: PMC5668215 DOI: 10.1186/s13568-017-0490-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2017] [Accepted: 10/14/2017] [Indexed: 01/23/2023] Open
Abstract
Disentangling the interactions between cyanobacteria and associated bacterial community is important for understanding the mechanisms that mediate the formation of cyanobacterial blooms in freshwater ecosystems. Despite the fact that a metagenomic approach enables researchers to profile the structure of microbial communities associated with cyanobacteria, reconstructing genome sequences for all members remains inefficient, due to the inherent enormous microbial diversity. Here, we have established a stable coculture system under high salinity, originally from a mixture of an axenic cyanobacterium Synechococcus sp. PCC 7002 and a non-axenic bloom-forming cyanobacterium Microcystis colony. Metagenomic analysis showed that the coculture consists of S. sp. PCC 7002 and two heterotrophic bacteria, designated as Pseudomonas stutzeri TAIHU and Mesorhizobium sp. TAIHU, respectively. And near-complete genome sequences of both bacteria were reconstructed from the metagenomic dataset with an average completeness of 99.8%. Genome-wide pathway analysis revealed that M. sp. TAIHU carried all the genes involved in the de novo biosynthesis of cobalamin, which is required by S. sp. PCC 7002 for growth. To cope with the high salinity in the coculture, experimental evidence demonstrated that S. sp. PCC 7002 would synthesize the compatible solutes including sucrose and glucosylglycerol, which are supposed to be exploited by both heterotrophic bacteria as potential carbon and/or nitrogen sources. Furthermore, the genes encoding for the biosynthesis of the ectoine, another common osmolyte are found exclusively in P. stutzeri TAIHU, while the genes responsible for the catabolism of ectoine and its derives are present only in M. sp. TAIHU. These genomic evidence indicates beneficial interaction between three members in the coculture. Establishment of the coculture system with relative simplicity provides a useful model system for investigating the interspecies interactions, and genome sequences of both bacteria associated with Microcystis bloom described here will facilitate the researcher to elucidate the role of these heterotrophic bacteria in the formation and maintenance of cyanobacterial bloom in freshwater ecosystem.
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158
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Weiss TL, Young EJ, Ducat DC. A synthetic, light-driven consortium of cyanobacteria and heterotrophic bacteria enables stable polyhydroxybutyrate production. Metab Eng 2017; 44:236-245. [DOI: 10.1016/j.ymben.2017.10.009] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Revised: 09/28/2017] [Accepted: 10/16/2017] [Indexed: 10/18/2022]
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159
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Jain P, Hung HC, Lin X, Ma J, Zhang P, Sun F, Wu K, Jiang S. Poly(ectoine) Hydrogels Resist Nonspecific Protein Adsorption. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2017; 33:11264-11269. [PMID: 28850239 DOI: 10.1021/acs.langmuir.7b02434] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
The development of nonfouling zwitterionic materials has a wide range of biomedical and engineering applications. This work delineates the design and synthesis of a new zwitterionic material based on a naturally occurring compatible solute, ectoine, which is known to possess additional protective properties that stabilize even whole cells against ultraviolet radiation or cytotoxins. These properties and applications of ectoine inspire us to design a functional monomer containing the natural zwitterion moiety of ectoine imparting nonfouling properties and the methacrylate moiety for polymerization. The synthesis route designed for the ectoine methacrylate monomer is simple with a high yield, which is characterized by nuclear magnetic resonance spectroscopy and mass spectrometry. After monomer synthesis, we have prepared a poly(ectoine) hydrogel via thermal polymerization. The equilibrium water content, degree of cross-linking, mechanical strength, and nonfouling properties are determined for polyectoine hydrogels with different cross-linking conditions. Poly(ectoine) hydrogels are shown to have highly hydrated and excellent nonfouling properties and can be considered to be a promising biomaterial.
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Affiliation(s)
- Priyesh Jain
- Department of Chemical Engineering, University of Washington , Seattle, Washington 98195, United States
| | - Hsiang-Chieh Hung
- Department of Chemical Engineering, University of Washington , Seattle, Washington 98195, United States
| | - Xiaojie Lin
- Department of Chemical Engineering, University of Washington , Seattle, Washington 98195, United States
| | - Jinrong Ma
- Department of Chemical Engineering, University of Washington , Seattle, Washington 98195, United States
| | - Peng Zhang
- Department of Chemical Engineering, University of Washington , Seattle, Washington 98195, United States
| | - Fang Sun
- Department of Chemical Engineering, University of Washington , Seattle, Washington 98195, United States
| | - Kan Wu
- Department of Chemical Engineering, University of Washington , Seattle, Washington 98195, United States
| | - Shaoyi Jiang
- Department of Chemical Engineering, University of Washington , Seattle, Washington 98195, United States
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160
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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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161
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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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162
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Ma Y, Wang Q, Xu W, Liu X, Gao X, Zhang Y. Stationary phase-dependent accumulation of ectoine is an efficient adaptation strategy in Vibrio anguillarum against cold stress. Microbiol Res 2017; 205:8-18. [PMID: 28942848 DOI: 10.1016/j.micres.2017.08.005] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Revised: 07/28/2017] [Accepted: 08/09/2017] [Indexed: 10/19/2022]
Abstract
The capability of cold-adaptation is a prerequisite of microorganisms that survive in an environment with frequent fluctuations in temperature. As a global causative agent of vibriosis in marine fish farming, Vibrio anguillarum can efficiently grow and proliferate under cold-stress conditions, which is 15°C lower than the optimal growth temperatures (25-30°C). Our data showed that V. anguillarum was able to synthesize ectoine de novo and that ectoine was essential for its growth under cold stress. Using 1H nuclear magnetic resonance spectroscopy and mutants lacking ectABC and proVWX (ectoine synthesis and transporter system genes, respectively), we confirmed that accumulation of this compatible solute occurs strictly at low temperatures and that the expression of ectA and proV is highly activated in the stationary growth phase. However, the synthesis of ectoine was repressed by exogenous choline (precursor of glycine betaine), suggesting that ectoine is an alternative compatible solute as a cold-stress protectant in V. anguillarum. Based on these results, we present possible scenarios of the synthesis and uptake of ectoine, which will facilitate the understanding of the molecular mechanism of V. anguillarum adaptation to cold environments and help improve freezing-dry processes for the V. anguillarum live vaccine.
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Affiliation(s)
- Yue Ma
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China; Shanghai Engineering Research Center of Maricultured Animal Vaccines, Shanghai 200237, China
| | - Qiyao Wang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China; Shanghai Engineering Research Center of Maricultured Animal Vaccines, Shanghai 200237, China; Shanghai Collaborative Innovation Center for Biomanufacturing, Shanghai 200237, China.
| | - Wensheng Xu
- Food Science and Engineering College, Beijing University of Agriculture, Beijing 102206, China
| | - Xiaohong Liu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China; Shanghai Engineering Research Center of Maricultured Animal Vaccines, Shanghai 200237, China; Shanghai Collaborative Innovation Center for Biomanufacturing, Shanghai 200237, China
| | - Xiating Gao
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Yuanxing Zhang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China; Shanghai Engineering Research Center of Maricultured Animal Vaccines, Shanghai 200237, China; Shanghai Collaborative Innovation Center for Biomanufacturing, Shanghai 200237, China.
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163
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Meyer S, Schröter MA, Hahn MB, Solomun T, Sturm H, Kunte HJ. Ectoine can enhance structural changes in DNA in vitro. Sci Rep 2017; 7:7170. [PMID: 28775267 PMCID: PMC5543045 DOI: 10.1038/s41598-017-07441-z] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2017] [Accepted: 06/26/2017] [Indexed: 11/20/2022] Open
Abstract
Strand breaks and conformational changes of DNA have consequences for the physiological role of DNA. The natural protecting molecule ectoine is beneficial to entire bacterial cells and biomolecules such as proteins by mitigating detrimental effects of environmental stresses. It was postulated that ectoine-like molecules bind to negatively charged spheres that mimic DNA surfaces. We investigated the effect of ectoine on DNA and whether ectoine is able to protect DNA from damages caused by ultraviolet radiation (UV-A). In order to determine different isoforms of DNA, agarose gel electrophoresis and atomic force microscopy experiments were carried out with plasmid pUC19 DNA. Our quantitative results revealed that a prolonged incubation of DNA with ectoine leads to an increase in transitions from supercoiled (undamaged) to open circular (single-strand break) conformation at pH 6.6. The effect is pH dependent and no significant changes were observed at physiological pH of 7.5. After UV-A irradiation in ectoine solution, changes in DNA conformation were even more pronounced and this effect was pH dependent. We hypothesize that ectoine is attracted to the negatively charge surface of DNA at lower pH and therefore fails to act as a stabilizing agent for DNA in our in vitro experiments.
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Affiliation(s)
- S Meyer
- Federal Institute for Materials Research and Testing, D-12205, Berlin, Germany. .,Institute of Biochemistry and Biology, University of Potsdam, D-14476, Potsdam, Germany.
| | - M-A Schröter
- Federal Institute for Materials Research and Testing, D-12205, Berlin, Germany
| | - M B Hahn
- Federal Institute for Materials Research and Testing, D-12205, Berlin, Germany.,Institute of Experimental Physics, Free University Berlin, Department of Physics, D-14195, Berlin, Germany
| | - T Solomun
- Federal Institute for Materials Research and Testing, D-12205, Berlin, Germany
| | - H Sturm
- Federal Institute for Materials Research and Testing, D-12205, Berlin, Germany.,Technical University Berlin, D-10587, Berlin, Germany
| | - H J Kunte
- Federal Institute for Materials Research and Testing, D-12205, Berlin, Germany
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164
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Wang T, Li J, Zhang LH, Yu Y, Zhu YM. Simultaneous heterotrophic nitrification and aerobic denitrification at high concentrations of NaCl and ammonia nitrogen by Halomonas bacteria. WATER SCIENCE AND TECHNOLOGY : A JOURNAL OF THE INTERNATIONAL ASSOCIATION ON WATER POLLUTION RESEARCH 2017; 76:386-395. [PMID: 28726704 DOI: 10.2166/wst.2017.214] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
To improve the efficiency of simultaneous heterotrophic nitrification and aerobic denitrification (SND) at high concentrations of NaCl and ammonia nitrogen (NH4+-N), we investigated the SND characteristics of Halomonas bacteria with the ability to synthesize the compatible solute ectoine. Halomonas sp. strain B01, which was isolated, screened and identified in this study, could simultaneously remove nitrogen (N) by SND and synthesize ectoine under high NaCl conditions. Gene cloning and sequencing analysis indicated that this bacterial genome contains ammonia monooxygenase (amoA) and nitrate reductase (narH) genes. Optimal conditions for N removal in a solution containing 600 mg/L NH4+-N were as follows: sodium succinate supplied as organic carbon (C) source at a C/N ratio of 5, pH 8 and shaking culture at 90 rpm. The N removal rate was 96.0% under these conditions. The SND by Halomonas sp. strain B01 was performed in N removal medium containing 60 g/L NaCl and 4,000 mg/L NH4+-N; after 180 h the residual total inorganic N concentration was 21.7 mg/L and the N removal rate was 99.2%. Halomonas sp. strain B01, with the ability to synthesize the compatible solute ectoine, could simultaneously tolerate high concentrations of NaCl and NH4+-N and efficiently perform N removal by SND.
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Affiliation(s)
- Te Wang
- Environmental Science and Engineering College, Dalian Maritime University, Dalian 116026, China E-mail:
| | - Jian Li
- Environmental Science and Engineering College, Dalian Maritime University, Dalian 116026, China E-mail:
| | - Ling Hua Zhang
- Environmental Science and Engineering College, Dalian Maritime University, Dalian 116026, China E-mail:
| | - Ying Yu
- Environmental Science and Engineering College, Dalian Maritime University, Dalian 116026, China E-mail:
| | - Yi Min Zhu
- Environmental Science and Engineering College, Dalian Maritime University, Dalian 116026, China E-mail:
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165
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Properties of alternative microbial hosts used in synthetic biology: towards the design of a modular chassis. Essays Biochem 2017; 60:303-313. [PMID: 27903818 PMCID: PMC5264504 DOI: 10.1042/ebc20160015] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2016] [Revised: 07/24/2016] [Accepted: 08/05/2016] [Indexed: 12/14/2022]
Abstract
The chassis is the cellular host used as a recipient of engineered biological systems in synthetic biology. They are required to propagate the genetic information and to express the genes encoded in it. Despite being an essential element for the appropriate function of genetic circuits, the chassis is rarely considered in their design phase. Consequently, the circuits are transferred to model organisms commonly used in the laboratory, such as Escherichia coli, that may be suboptimal for a required function. In this review, we discuss some of the properties desirable in a versatile chassis and summarize some examples of alternative hosts for synthetic biology amenable for engineering. These properties include a suitable life style, a robust cell wall, good knowledge of its regulatory network as well as of the interplay of the host components with the exogenous circuits, and the possibility of developing whole-cell models and tuneable metabolic fluxes that could allow a better distribution of cellular resources (metabolites, ATP, nucleotides, amino acids, transcriptional and translational machinery). We highlight Pseudomonas putida, widely used in many different biotechnological applications as a prominent organism for synthetic biology due to its metabolic diversity, robustness and ease of manipulation.
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Chen R, Zhu L, Lv L, Yao S, Li B, Qian J. Optimization of the extraction and purification of the compatible solute ectoine from Halomonas elongate in the laboratory experiment of a commercial production project. World J Microbiol Biotechnol 2017; 33:116. [DOI: 10.1007/s11274-017-2281-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2016] [Accepted: 04/30/2017] [Indexed: 11/24/2022]
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167
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Chakravorty D, Khan MF, Patra S. Multifactorial level of extremostability of proteins: can they be exploited for protein engineering? Extremophiles 2017; 21:419-444. [PMID: 28283770 DOI: 10.1007/s00792-016-0908-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2016] [Accepted: 12/19/2016] [Indexed: 12/20/2022]
Abstract
Research on extremostable proteins has seen immense growth in the past decade owing to their industrial importance. Basic research of attributes related to extreme-stability requires further exploration. Modern mechanistic approaches to engineer such proteins in vitro will have more impact in industrial biotechnology economy. Developing a priori knowledge about the mechanism behind extreme-stability will nurture better understanding of pathways leading to protein molecular evolution and folding. This review is a vivid compilation about all classes of extremostable proteins and the attributes that lead to myriad of adaptations divulged after an extensive study of 6495 articles belonging to extremostable proteins. Along with detailing on the rationale behind extreme-stability of proteins, emphasis has been put on modern approaches that have been utilized to render proteins extremostable by protein engineering. It was understood that each protein shows different approaches to extreme-stability governed by minute differences in their biophysical properties and the milieu in which they exist. Any general rule has not yet been drawn regarding adaptive mechanisms in extreme environments. This review was further instrumental to understand the drawback of the available 14 stabilizing mutation prediction algorithms. Thus, this review lays the foundation to further explore the biophysical pleiotropy of extreme-stable proteins to deduce a global prediction model for predicting the effect of mutations on protein stability.
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Affiliation(s)
- Debamitra Chakravorty
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, 781039, Assam, India
| | - Mohd Faheem Khan
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, 781039, Assam, India
| | - Sanjukta Patra
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, 781039, Assam, India.
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Salar-García MJ, Bernal V, Pastor JM, Salvador M, Argandoña M, Nieto JJ, Vargas C, Cánovas M. Understanding the interplay of carbon and nitrogen supply for ectoines production and metabolic overflow in high density cultures of Chromohalobacter salexigens. Microb Cell Fact 2017; 16:23. [PMID: 28179004 PMCID: PMC5299690 DOI: 10.1186/s12934-017-0643-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2016] [Accepted: 02/01/2017] [Indexed: 01/27/2023] Open
Abstract
Background The halophilic bacterium Chromohalobacter salexigens has been proposed as promising cell factory for the production of the compatible solutes ectoine and hydroxyectoine. This bacterium has evolved metabolic adaptations to efficiently grow under high salt concentrations by accumulating ectoines as compatible solutes. However, metabolic overflow, which is a major drawback for the efficient conversion of biological feedstocks, occurs as a result of metabolic unbalances during growth and ectoines production. Optimal production of ectoines is conditioned by the interplay of carbon and nitrogen metabolisms. In this work, we set out to determine how nitrogen supply affects the production of ectoines. Results Chromohalobacter salexigens was challenged to grow in media with unbalanced carbon/nitrogen ratio. In C. salexigens, overflow metabolism and ectoines production are a function of medium composition. At low ammonium conditions, the growth rate decreased importantly, up to 80%. Shifts in overflow metabolism were observed when changing the C/N ratio in the culture medium. 13C-NMR analysis of ectoines labelling revealed a high metabolic rigidity, with almost constant flux ratios in all conditions assayed. Unbalanced C/N ratio led to pyruvate accumulation, especially upon N-limitation. Analysis of an ect− mutant demonstrated the link between metabolic overflow and ectoine biosynthesis. Under non ectoine synthesizing conditions, glucose uptake and metabolic overflow decreased importantly. Finally, in fed-batch cultures, biomass yield was affected by the feeding scheme chosen. High growth (up to 42.4 g L−1) and volumetric ectoine yields (up to 4.21 g L−1) were obtained by minimizing metabolite overflow and nutrient accumulation in high density cultures in a low nitrogen fed-batch culture. Moreover, the yield coefficient calculated for the transformation of glucose into biomass was 30% higher in fed-batch than in the batch culture, demonstrating that the metabolic efficiency of C. salexigens can be improved by careful design of culture feeding schemes. Conclusions Metabolic shifts observed at low ammonium concentrations were explained by a shift in the energy required for nitrogen assimilation. Carbon-limited fed-batch cultures with reduced ammonium supply were the best conditions for cultivation of C. salexigens, supporting high density growth and maintaining high ectoines production. Electronic supplementary material The online version of this article (doi:10.1186/s12934-017-0643-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- María J Salar-García
- Departamento de Bioquímica y Biología Molecular B e Inmunología, Facultad de Química, Universidad de Murcia, Campus Regional de Excelencia Internacional "Campus Mare Nostrum", 30100, Murcia, Spain.,Departamento de Ingeniería Química y Ambiental, Universidad Politécnica de Cartagena, Campus Regional de Excelencia Internacional "Campus Mare Nostrum", Campus Muralla del MarCalle Doctor Fleming S/N, 30202, Cartagena, Spain
| | - Vicente Bernal
- Departamento de Bioquímica y Biología Molecular B e Inmunología, Facultad de Química, Universidad de Murcia, Campus Regional de Excelencia Internacional "Campus Mare Nostrum", 30100, Murcia, Spain. .,Área de Biología, Dirección de Tecnología Química y Nuevas Energías, Centro de Tecnología de Repsol S.A., Ctra. de Extremadura A-5, Km. 18, 28375, Móstoles, Spain.
| | - José M Pastor
- Departamento de Bioquímica y Biología Molecular B e Inmunología, Facultad de Química, Universidad de Murcia, Campus Regional de Excelencia Internacional "Campus Mare Nostrum", 30100, Murcia, Spain
| | - Manuel Salvador
- Departamento de Microbiología y Parasitología, Facultad de Farmacia, Universidad de Sevilla, 41012, Seville, Spain
| | - Montserrat Argandoña
- Departamento de Microbiología y Parasitología, Facultad de Farmacia, Universidad de Sevilla, 41012, Seville, Spain
| | - Joaquín J Nieto
- Departamento de Microbiología y Parasitología, Facultad de Farmacia, Universidad de Sevilla, 41012, Seville, Spain
| | - Carmen Vargas
- Departamento de Microbiología y Parasitología, Facultad de Farmacia, Universidad de Sevilla, 41012, Seville, Spain
| | - Manuel Cánovas
- Departamento de Bioquímica y Biología Molecular B e Inmunología, Facultad de Química, Universidad de Murcia, Campus Regional de Excelencia Internacional "Campus Mare Nostrum", 30100, Murcia, Spain.
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169
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Kohn T, Heuer A, Jogler M, Vollmers J, Boedeker C, Bunk B, Rast P, Borchert D, Glöckner I, Freese HM, Klenk HP, Overmann J, Kaster AK, Rohde M, Wiegand S, Jogler C. Fuerstia marisgermanicae gen. nov., sp. nov., an Unusual Member of the Phylum Planctomycetes from the German Wadden Sea. Front Microbiol 2016; 7:2079. [PMID: 28066393 PMCID: PMC5177795 DOI: 10.3389/fmicb.2016.02079] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Accepted: 12/08/2016] [Indexed: 11/23/2022] Open
Abstract
Members of the phylum Planctomycetes are ubiquitous bacteria that dwell in aquatic and terrestrial habitats. While planctomycetal species are important players in the global carbon and nitrogen cycle, this phylum is still undersampled and only few genome sequences are available. Here we describe strain NH11T, a novel planctomycete obtained from a crustacean shell (Wadden Sea, Germany). The phylogenetically closest related cultivated species is Gimesia maris, sharing only 87% 16S rRNA sequence identity. Previous isolation attempts have mostly yielded members of the genus Rhodopirellula from water of the German North Sea. On the other hand, only one axenic culture of the genus Pirellula was obtained from a crustacean thus far. However, the 16S rRNA gene sequence of strain NH11T shares only 80% sequence identity with the closest relative of both genera, Rhodopirellula and Pirellula. Thus, strain NH11T is unique in terms of origin and phylogeny. While the pear to ovoid shaped cells of strain NH11T are typical planctomycetal, light-, and electron microscopic observations point toward an unusual variation of cell division through budding: during the division process daughter- and mother cells are connected by an unseen thin tubular-like structure. Furthermore, the periplasmic space of strain NH11T was unusually enlarged and differed from previously known planctomycetes. The complete genome of strain NH11T, with almost 9 Mb in size, is among the largest planctomycetal genomes sequenced thus far, but harbors only 6645 protein-coding genes. The acquisition of genomic components by horizontal gene transfer is indicated by the presence of numerous putative genomic islands. Strikingly, 45 “giant genes” were found within the genome of NH11T. Subsequent analysis of all available planctomycetal genomes revealed that Planctomycetes as such are especially rich in “giant genes”. Furthermore, Multilocus Sequence Analysis (MLSA) tree reconstruction support the phylogenetic distance of strain NH11T from other cultivated Planctomycetes of the same phylogenetic cluster. Thus, based on our findings, we propose to classify strain NH11T as Fuerstia marisgermanicae gen. nov., sp. nov., with the type strain NH11T, within the phylum Planctomycetes.
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Affiliation(s)
- Timo Kohn
- Leibniz Institut Deutsche Sammlung Von Mikroorganismen und Zellkulturen Braunschweig, Germany
| | - Anja Heuer
- Leibniz Institut Deutsche Sammlung Von Mikroorganismen und Zellkulturen Braunschweig, Germany
| | - Mareike Jogler
- Leibniz Institut Deutsche Sammlung Von Mikroorganismen und Zellkulturen Braunschweig, Germany
| | - John Vollmers
- Leibniz Institut Deutsche Sammlung Von Mikroorganismen und Zellkulturen Braunschweig, Germany
| | - Christian Boedeker
- Leibniz Institut Deutsche Sammlung Von Mikroorganismen und Zellkulturen Braunschweig, Germany
| | - Boyke Bunk
- Leibniz Institut Deutsche Sammlung Von Mikroorganismen und Zellkulturen Braunschweig, Germany
| | - Patrick Rast
- Leibniz Institut Deutsche Sammlung Von Mikroorganismen und Zellkulturen Braunschweig, Germany
| | - Daniela Borchert
- Leibniz Institut Deutsche Sammlung Von Mikroorganismen und Zellkulturen Braunschweig, Germany
| | - Ines Glöckner
- Leibniz Institut Deutsche Sammlung Von Mikroorganismen und Zellkulturen Braunschweig, Germany
| | - Heike M Freese
- Leibniz Institut Deutsche Sammlung Von Mikroorganismen und Zellkulturen Braunschweig, Germany
| | | | - Jörg Overmann
- Leibniz Institut Deutsche Sammlung Von Mikroorganismen und Zellkulturen Braunschweig, Germany
| | - Anne-Kristin Kaster
- Leibniz Institut Deutsche Sammlung Von Mikroorganismen und Zellkulturen Braunschweig, Germany
| | - Manfred Rohde
- Helmholtz Centre for Infectious Disease Braunschweig, Germany
| | - Sandra Wiegand
- Leibniz Institut Deutsche Sammlung Von Mikroorganismen und Zellkulturen Braunschweig, Germany
| | - Christian Jogler
- Leibniz Institut Deutsche Sammlung Von Mikroorganismen und Zellkulturen Braunschweig, Germany
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170
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Cantera S, Lebrero R, Sadornil L, García-Encina PA, Muñoz R. Valorization of CH4 emissions into high-added-value products: Assessing the production of ectoine coupled with CH4 abatement. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2016; 182:160-165. [PMID: 27472052 DOI: 10.1016/j.jenvman.2016.07.064] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2016] [Revised: 07/17/2016] [Accepted: 07/18/2016] [Indexed: 06/06/2023]
Abstract
This study assessed an innovative strategy for the valorization of dilute methane emissions based on the bio-conversion of CH4 (the second most important greenhouse gas (GHG)) into ectoine by the methanotrophic ectoine-producing strain Methylomicrobium alcaliphilum 20 Z. The influence of CH4 (2-20%), Cu(2+) (0.05-50 μM) and NaCl (0-9%) concentration as well as temperature (25-35 °C) on ectoine synthesis and specific CH4 biodegradation rate was evaluated for the first time. Concentrations of 20% CH4 (at 3% NaCl, 0.05 μM Cu(2+), 25 °C) and 6% NaCl (at 4% CH4, 0.05 μM Cu(2+), 25 °C) supported the maximum intra-cellular ectoine production yield (31.0 ±1.7 and 66.9 ±4.2 mg g biomass(-1), respectively). On the other hand, extra-cellular ectoine concentrations of up to 4.7 ± 0.1 mg L(-1) were detected at high Cu(2+)concentrations (50 μM), despite this methanotroph has not been previously classified as an ectoine-excreting strain. This research demonstrated the feasibility of the bio-conversion of dilute emissions of methane into high-added value products in an attempt to develop a sustainable GHG bioeconomy.
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Affiliation(s)
- Sara Cantera
- Department of Chemical Engineering and Environmental Technology, Valladolid University, Dr. Mergelina, s/n, Valladolid, Spain
| | - Raquel Lebrero
- Department of Chemical Engineering and Environmental Technology, Valladolid University, Dr. Mergelina, s/n, Valladolid, Spain
| | - Lidia Sadornil
- Department of Chemical Engineering and Environmental Technology, Valladolid University, Dr. Mergelina, s/n, Valladolid, Spain
| | - Pedro A García-Encina
- Department of Chemical Engineering and Environmental Technology, Valladolid University, Dr. Mergelina, s/n, Valladolid, Spain
| | - Raúl Muñoz
- Department of Chemical Engineering and Environmental Technology, Valladolid University, Dr. Mergelina, s/n, Valladolid, Spain.
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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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172
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Beblo-Vranesevic K, Galinski EA, Rachel R, Huber H, Rettberg P. Influence of osmotic stress on desiccation and irradiation tolerance of (hyper)-thermophilic microorganisms. Arch Microbiol 2016; 199:17-28. [PMID: 27443666 DOI: 10.1007/s00203-016-1269-6] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2016] [Revised: 06/27/2016] [Accepted: 07/13/2016] [Indexed: 11/25/2022]
Abstract
This study examined the influence of prior salt adaptation on the survival rate of (hyper)-thermophilic bacteria and archaea after desiccation and UV or ionizing irradiation treatment. Survival rates after desiccation of Hydrogenothermus marinus and Archaeoglobus fulgidus increased considerably when the cells were cultivated at higher salt concentrations before drying. By doubling the concentration of NaCl, a 30 times higher survival rate of H. marinus after desiccation was observed. Under salt stress, the compatible solute diglycerol phosphate in A. fulgidus and glucosylglycerate in H. marinus accumulated in the cytoplasm. Several different compatible solutes were added as protectants to A. fulgidus and H. marinus before desiccation treatment. Some of these had similar effects as intracellularly produced compatible solutes. The survival rates of H. marinus and A. fulgidus after exposure to UV-C (254 nm) or ionizing X-ray/gamma radiation were irrespective of the salt-induced synthesis or the addition of compatible solutes.
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Affiliation(s)
- Kristina Beblo-Vranesevic
- Institute of Aerospace Medicine, Radiation Biology Division, German Aerospace Center (DLR e.V.), Linder Höhe, 51147, Cologne, Germany.
| | - Erwin A Galinski
- Institute of Microbiology and Biotechnology, Rheinische Friedrich-Wilhelms University, Bonn, Germany
| | - Reinhard Rachel
- Faculty of Biology and Preclinical Medicine, Center for Electron Microscopy, University Regensburg, Regensburg, Germany
| | - Harald Huber
- Faculty of Biology and Preclinical Medicine, Institute for Microbiology and Archaea Center, University of Regensburg, Regensburg, Germany
| | - Petra Rettberg
- Institute of Aerospace Medicine, Radiation Biology Division, German Aerospace Center (DLR e.V.), Linder Höhe, 51147, Cologne, Germany
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173
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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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174
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Pathway construction and metabolic engineering for fermentative production of ectoine in Escherichia coli. Metab Eng 2016; 36:10-18. [DOI: 10.1016/j.ymben.2016.02.013] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2015] [Revised: 02/09/2016] [Accepted: 02/23/2016] [Indexed: 11/19/2022]
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175
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Tanimura K, Matsumoto T, Nakayama H, Tanaka T, Kondo A. Improvement of ectoine productivity by using sugar transporter-overexpressing Halomonas elongata. Enzyme Microb Technol 2016; 89:63-8. [DOI: 10.1016/j.enzmictec.2016.03.006] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2015] [Revised: 02/12/2016] [Accepted: 03/16/2016] [Indexed: 10/22/2022]
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176
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Obruca S, Sedlacek P, Krzyzanek V, Mravec F, Hrubanova K, Samek O, Kucera D, Benesova P, Marova I. Accumulation of Poly(3-hydroxybutyrate) Helps Bacterial Cells to Survive Freezing. PLoS One 2016; 11:e0157778. [PMID: 27315285 PMCID: PMC4912086 DOI: 10.1371/journal.pone.0157778] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2016] [Accepted: 06/03/2016] [Indexed: 11/19/2022] Open
Abstract
Accumulation of polyhydroxybutyrate (PHB) seems to be a common metabolic strategy adopted by many bacteria to cope with cold environments. This work aimed at evaluating and understanding the cryoprotective effect of PHB. At first a monomer of PHB, 3-hydroxybutyrate, was identified as a potent cryoprotectant capable of protecting model enzyme (lipase), yeast (Saccharomyces cerevisiae) and bacterial cells (Cupriavidus necator) against the adverse effects of freezing-thawing cycles. Further, the viability of the frozen-thawed PHB accumulating strain of C. necator was compared to that of the PHB non-accumulating mutant. The presence of PHB granules in cells was revealed to be a significant advantage during freezing. This might be attributed to the higher intracellular level of 3-hydroxybutyrate in PHB accumulating cells (due to the action of parallel PHB synthesis and degradation, the so-called PHB cycle), but the cryoprotective effect of PHB granules seems to be more complex. Since intracellular PHB granules retain highly flexible properties even at extremely low temperatures (observed by cryo-SEM), it can be expected that PHB granules protect cells against injury from extracellular ice. Finally, thermal analysis indicates that PHB-containing cells exhibit a higher rate of transmembrane water transport, which protects cells against the formation of intracellular ice which usually has fatal consequences.
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Affiliation(s)
- Stanislav Obruca
- Materials Research Centre, Faculty of Chemistry, Brno University of Technology, Purkynova 118, 612 00, Brno, Czech Republic
| | - Petr Sedlacek
- Materials Research Centre, Faculty of Chemistry, Brno University of Technology, Purkynova 118, 612 00, Brno, Czech Republic
| | - Vladislav Krzyzanek
- Institute of Scientific Instruments, Academy of Sciences of The Czech Republic, Vvi, Kralovopolska 147, 612 64, Brno, Czech Republic
| | - Filip Mravec
- Materials Research Centre, Faculty of Chemistry, Brno University of Technology, Purkynova 118, 612 00, Brno, Czech Republic
| | - Kamila Hrubanova
- Institute of Scientific Instruments, Academy of Sciences of The Czech Republic, Vvi, Kralovopolska 147, 612 64, Brno, Czech Republic
| | - Ota Samek
- Institute of Scientific Instruments, Academy of Sciences of The Czech Republic, Vvi, Kralovopolska 147, 612 64, Brno, Czech Republic
| | - Dan Kucera
- Materials Research Centre, Faculty of Chemistry, Brno University of Technology, Purkynova 118, 612 00, Brno, Czech Republic
| | - Pavla Benesova
- Materials Research Centre, Faculty of Chemistry, Brno University of Technology, Purkynova 118, 612 00, Brno, Czech Republic
| | - Ivana Marova
- Materials Research Centre, Faculty of Chemistry, Brno University of Technology, Purkynova 118, 612 00, Brno, Czech Republic
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177
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Tao P, Li H, Yu Y, Gu J, Liu Y. Ectoine and 5-hydroxyectoine accumulation in the halophile Virgibacillus halodenitrificans PDB-F2 in response to salt stress. Appl Microbiol Biotechnol 2016; 100:6779-6789. [PMID: 27106915 DOI: 10.1007/s00253-016-7549-x] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2016] [Revised: 03/20/2016] [Accepted: 04/12/2016] [Indexed: 11/28/2022]
Abstract
The moderately halophilic bacterium Virgibacillus halodenitrificans PDB-F2 copes with salinity by synthesizing or taking up compatible solutes. The main compatible solutes in this strain were ectoine and hydroxyectoine, as determined by (1)H nuclear magnetic resonance spectroscopy ((1)H-NMR). A high-performance liquid chromatography (HPLC) analysis showed that ectoine was the major solute that was synthesized in response to elevated salinity, while hydroxyectoine was a minor solute. However, the hydroxyectoine/ectoine ratio increased from 0.04 at 3 % NaCl to 0.45 at 15 % NaCl in the late exponential growth phase. A cluster of ectoine biosynthesis genes was identified, including three genes in the order of ectA, ectB, and ectC. The hydroxyectoine biosynthesis gene ectD was not part of the ectABC gene cluster. Reverse transcription-quantitative polymerase chain reactions (RT-qPCR) showed that the expression of the ect genes was salinity dependent. The expression of ectABC reached a maximum at 12 % NaCl, while ectD expression increased up to 15 % NaCl. Ectoine and hydroxyectoine production was growth phase dependent. The hydroxyectoine/ectoine ratio increased from 0.018 in the early exponential phase to 0.11 in the stationary phase at 5 % NaCl. Hydroxyectoine biosynthesis started much later than ectoine biosynthesis after osmotic shock, and the temporal expression of the ect genes differed under these conditions, with the ectABC genes being expressed first, followed by ectD gene. Increased culture salinity triggered ectoine or hydroxyectoine uptake when they were added to the medium. Hydroxyectoine was accumulated preferentially when both ectoine and hydroxyectoine were provided exogenously.
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Affiliation(s)
- Ping Tao
- State Environmental Protection Key Laboratory of Environmental Risk Assessment and Control on Chemical Process, State Key Laboratory of Biological Reactor Engineering, School of Resource and Environmental Engineering, East China University of Science and Technology, Shanghai, 200237, People's Republic of China
| | - Hui Li
- State Environmental Protection Key Laboratory of Environmental Risk Assessment and Control on Chemical Process, State Key Laboratory of Biological Reactor Engineering, School of Resource and Environmental Engineering, East China University of Science and Technology, Shanghai, 200237, People's Republic of China.
| | - Yunjiang Yu
- Center for Environmental Health Research, South China Institute of Environmental Sciences, Guangzhou, 510535, People's Republic of China
| | - Jidong Gu
- School of Biological Sciences, Swire Institute of Marine Science, The University of Hong Kong, Pokfulam Road, Hong Kong, SAR, People's Republic of China
| | - Yongdi Liu
- State Environmental Protection Key Laboratory of Environmental Risk Assessment and Control on Chemical Process, State Key Laboratory of Biological Reactor Engineering, School of Resource and Environmental Engineering, East China University of Science and Technology, Shanghai, 200237, People's Republic of China.
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178
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Jorge CD, Borges N, Bagyan I, Bilstein A, Santos H. Potential applications of stress solutes from extremophiles in protein folding diseases and healthcare. Extremophiles 2016; 20:251-9. [PMID: 27071404 DOI: 10.1007/s00792-016-0828-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2015] [Accepted: 03/24/2016] [Indexed: 11/26/2022]
Abstract
Protein misfolding, aggregation and deposition in the brain, in the form of amyloid, are implicated in the etiology of several neurodegenerative disorders, such as Alzheimer's, Parkinson's and prion diseases. Drugs available on the market reduce the symptoms, but they are not a cure. Therefore, it is urgent to identify promising targets and develop effective drugs. Preservation of protein native conformation and/or inhibition of protein aggregation seem pertinent targets for drug development. Several studies have shown that organic solutes, produced by extremophilic microorganisms in response to osmotic and/or heat stress, prevent denaturation and aggregation of model proteins. Among these stress solutes, mannosylglycerate, mannosylglyceramide, di-myo-inositol phosphate, diglycerol phosphate and ectoine are effective in preventing amyloid formation by Alzheimer's Aβ peptide and/or α-synuclein in vitro. Moreover, mannosylglycerate is a potent inhibitor of Aβ and α-synuclein aggregation in living cells, and mannosylglyceramide and ectoine inhibit aggregation and reduce prion peptide-induced toxicity in human cells. This review focuses on the efficacy of stress solutes from hyper/thermophiles and ectoines to prevent amyloid formation in vitro and in vivo and their potential application in drug development against protein misfolding diseases. Current and envisaged applications of these extremolytes in neurodegenerative diseases and healthcare will also be addressed.
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Affiliation(s)
- Carla D Jorge
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República-EAN, 2780-157, Oeiras, Portugal.
| | - Nuno Borges
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República-EAN, 2780-157, Oeiras, Portugal
| | - Irina Bagyan
- Bitop AG, Stockumer Straße 28, 58453, Witten, Germany
| | | | - Helena Santos
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República-EAN, 2780-157, Oeiras, Portugal
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179
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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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180
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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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181
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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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182
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Cha JY, Han S, Hong HJ, Cho H, Kim D, Kwon Y, Kwon SK, Crüsemann M, Bok Lee Y, Kim JF, Giaever G, Nislow C, Moore BS, Thomashow LS, Weller DM, Kwak YS. Microbial and biochemical basis of a Fusarium wilt-suppressive soil. THE ISME JOURNAL 2016; 10:119-29. [PMID: 26057845 PMCID: PMC4681868 DOI: 10.1038/ismej.2015.95] [Citation(s) in RCA: 208] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2014] [Revised: 04/26/2015] [Accepted: 05/03/2015] [Indexed: 01/21/2023]
Abstract
Crops lack genetic resistance to most necrotrophic pathogens. To compensate for this disadvantage, plants recruit antagonistic members of the soil microbiome to defend their roots against pathogens and other pests. The best examples of this microbially based defense of roots are observed in disease-suppressive soils in which suppressiveness is induced by continuously growing crops that are susceptible to a pathogen, but the molecular basis of most is poorly understood. Here we report the microbial characterization of a Korean soil with specific suppressiveness to Fusarium wilt of strawberry. In this soil, an attack on strawberry roots by Fusarium oxysporum results in a response by microbial defenders, of which members of the Actinobacteria appear to have a key role. We also identify Streptomyces genes responsible for the ribosomal synthesis of a novel heat-stable antifungal thiopeptide antibiotic inhibitory to F. oxysporum and the antibiotic's mode of action against fungal cell wall biosynthesis. Both classical- and community-oriented approaches were required to dissect this suppressive soil from the field to the molecular level, and the results highlight the role of natural antibiotics as weapons in the microbial warfare in the rhizosphere that is integral to plant health, vigor and development.
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Affiliation(s)
- Jae-Yul Cha
- IALS and Department of Plant Medicine, Gyeongsang National University, Jinju, Republic of Korea
| | - Sangjo Han
- Bioinformatics Tech Lab, SK Telecom, Sungnam, Republic of Korea
| | - Hee-Jeon Hong
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Hyunji Cho
- RILS and Division of Applied Life Science, Gyeongsang National University, Jinju, Republic of Korea
| | - Daran Kim
- IALS and Department of Plant Medicine, Gyeongsang National University, Jinju, Republic of Korea
| | - Youngho Kwon
- IALS and Department of Plant Medicine, Gyeongsang National University, Jinju, Republic of Korea
| | - Soon-Kyeong Kwon
- Department of Systems Biology and Division of Life Sciences, Yonsei University, Seoul, Republic of Korea
| | - Max Crüsemann
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Yong Bok Lee
- RILS and Division of Applied Life Science, Gyeongsang National University, Jinju, Republic of Korea
| | - Jihyun F Kim
- Department of Systems Biology and Division of Life Sciences, Yonsei University, Seoul, Republic of Korea
| | - Guri Giaever
- Pharmaceutical Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - Corey Nislow
- Pharmaceutical Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - Bradley S Moore
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Linda S Thomashow
- US Department of Agriculture, Agricultural Research Service, Root Disease and Biological Control Research Unit, Pullman, WA, USA
| | - David M Weller
- US Department of Agriculture, Agricultural Research Service, Root Disease and Biological Control Research Unit, Pullman, WA, USA
| | - Youn-Sig Kwak
- IALS and Department of Plant Medicine, Gyeongsang National University, Jinju, Republic of Korea
- RILS and Division of Applied Life Science, Gyeongsang National University, Jinju, Republic of Korea
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183
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Comprehensive Genomic Analyses of the OM43 Clade, Including a Novel Species from the Red Sea, Indicate Ecotype Differentiation among Marine Methylotrophs. Appl Environ Microbiol 2015; 82:1215-1226. [PMID: 26655752 DOI: 10.1128/aem.02852-15] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2015] [Accepted: 12/03/2015] [Indexed: 12/16/2022] Open
Abstract
The OM43 clade within the family Methylophilaceae of Betaproteobacteria represents a group of methylotrophs that play important roles in the metabolism of C1 compounds in marine environments and other aquatic environments around the globe. Using dilution-to-extinction cultivation techniques, we successfully isolated a novel species of this clade (here designated MBRS-H7) from the ultraoligotrophic open ocean waters of the central Red Sea. Phylogenomic analyses indicate that MBRS-H7 is a novel species that forms a distinct cluster together with isolate KB13 from Hawaii (Hawaii-Red Sea [H-RS] cluster) that is separate from the cluster represented by strain HTCC2181 (from the Oregon coast). Phylogenetic analyses using the robust 16S-23S internal transcribed spacer revealed a potential ecotype separation of the marine OM43 clade members, which was further confirmed by metagenomic fragment recruitment analyses that showed trends of higher abundance in low-chlorophyll and/or high-temperature provinces for the H-RS cluster but a preference for colder, highly productive waters for the HTCC2181 cluster. This potential environmentally driven niche differentiation is also reflected in the metabolic gene inventories, which in the case of the H-RS cluster include those conferring resistance to high levels of UV irradiation, temperature, and salinity. Interestingly, we also found different energy conservation modules between these OM43 subclades, namely, the existence of the NADH:quinone oxidoreductase complex I (NUO) system in the H-RS cluster and the nonhomologous NADH:quinone oxidoreductase (NQR) system in the HTCC2181 cluster, which might have implications for their overall energetic yields.
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184
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Eiberweiser A, Nazet A, Kruchinin SE, Fedotova MV, Buchner R. Hydration and Ion Binding of the Osmolyte Ectoine. J Phys Chem B 2015; 119:15203-11. [PMID: 26565946 DOI: 10.1021/acs.jpcb.5b09276] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Ectoine is a widespread osmolyte enabling halophilic bacteria to withstand high osmotic stress that has many potential applications ranging from cosmetics to its use as a therapeutic agent. In this contribution, combining experiment and theory, the hydration and ion-binding of this zwitterionic compound was studied to gain information on the functioning of ectoine in particular and of osmolytes in general. Dielectric relaxation spectroscopy was used to determine the effective hydration number of ectoine and its effective dipole moment in aqueous solutions with and without added NaCl. The obtained experimental data were compared with structural results from 1D-RISM and 3D-RISM calculations. It was found that ectoine is strongly hydrated, even in the presence of high salt concentrations. Upon addition of NaCl, ions are bound to ectoine but the formed complexes are not very stable. Interestingly, this osmolyte strongly rises the static relative permittivity of its solutions, shielding thus effectively long-range Coulomb interactions among ions in ectoine-containing solutions. We believe that via this effect, which should be common to all zwitterionic osmolytes, ectoine protects against excessive ions within the cell in addition to its strong osmotic activity protecting against ions outside.
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Affiliation(s)
- Andreas Eiberweiser
- Institut für Physikalische und Theoretische Chemie, Universität Regensburg , D-93040 Regensburg, Germany
| | - Andreas Nazet
- Institut für Physikalische und Theoretische Chemie, Universität Regensburg , D-93040 Regensburg, Germany
| | - Sergey E Kruchinin
- G. A. Krestov Institute of Solution Chemistry, Russian Academy of Sciences , Akademicheskaya st. 1, Ivanovo, Russia
| | - Marina V Fedotova
- G. A. Krestov Institute of Solution Chemistry, Russian Academy of Sciences , Akademicheskaya st. 1, Ivanovo, Russia
| | - Richard Buchner
- Institut für Physikalische und Theoretische Chemie, Universität Regensburg , D-93040 Regensburg, Germany
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185
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Evaluation of 3-hydroxybutyrate as an enzyme-protective agent against heating and oxidative damage and its potential role in stress response of poly(3-hydroxybutyrate) accumulating cells. Appl Microbiol Biotechnol 2015; 100:1365-1376. [DOI: 10.1007/s00253-015-7162-4] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2015] [Revised: 11/02/2015] [Accepted: 11/07/2015] [Indexed: 10/22/2022]
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186
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Yoruk HM, Sayar NA. Topological analysis of carbon flux during multi-stress adaptation in Halomonas sp. AAD12. ELECTRON J BIOTECHN 2015. [DOI: 10.1016/j.ejbt.2015.09.010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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187
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Raddadi N, Cherif A, Daffonchio D, Neifar M, Fava F. Biotechnological applications of extremophiles, extremozymes and extremolytes. Appl Microbiol Biotechnol 2015; 99:7907-13. [PMID: 26272092 DOI: 10.1007/s00253-015-6874-9] [Citation(s) in RCA: 122] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2015] [Revised: 07/20/2015] [Accepted: 07/22/2015] [Indexed: 11/24/2022]
Abstract
In the last decade, attention to extreme environments has increased because of interests to isolate previously unknown extremophilic microorganisms in pure culture and to profile their metabolites. Microorganisms that live in extreme environments produce extremozymes and extremolytes that have the potential to be valuable resources for the development of a bio-based economy through their application to white, red, and grey biotechnologies. Here, we provide an overview of extremophile ecology, and we review the most recent applications of microbial extremophiles and the extremozymes and extremolytes they produce to biotechnology.
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Affiliation(s)
- Noura Raddadi
- Department of Civil, Chemical, Environmental and Materials Engineering (DICAM), University of Bologna, via Terracini 28, 40131, Bologna, Italy,
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188
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Osaki T, Kurozumi S, Sato K, Terashi T, Azuma K, Murahata Y, Tsuka T, Ito N, Imagawa T, Minami S, Okamoto Y. Metabolomic Analysis of Blood Plasma after Oral Administration of N-acetyl-d-Glucosamine in Dogs. Mar Drugs 2015; 13:5007-15. [PMID: 26262626 PMCID: PMC4557012 DOI: 10.3390/md13085007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2015] [Accepted: 07/24/2015] [Indexed: 01/25/2023] Open
Abstract
N-acetyl-d-glucosamine (GlcNAc) is a monosaccharide that polymerizes linearly through (1,4)-β-linkages. GlcNAc is the monomeric unit of the polymer chitin. GlcNAc is a basic component of hyaluronic acid and keratin sulfate found on the cell surface. The aim of this study was to examine amino acid metabolism after oral GlcNAc administration in dogs. Results showed that plasma levels of ectoine were significantly higher after oral administration of GlcNAc than prior to administration (p < 0.001). To our knowledge, there have been no reports of increased ectoine concentrations in the plasma. The mechanism by which GlcNAc administration leads to increased ectoine plasma concentration remains unclear; future studies are required to clarify this mechanism.
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Affiliation(s)
- Tomohiro Osaki
- Department of Veterinary Clinical Medicine, School of Veterinary Medicine, Tottori University, 4-101 Koyama-cho Minami, Tottori 680-8553, Japan.
| | - Seiji Kurozumi
- Koyo Chemical Co. Ltd., 1-17 Taiyuji-cho, Kita-ku, Osaka 530-0051, Japan.
| | - Kimihiko Sato
- Koyo Chemical Co. Ltd., 1-17 Taiyuji-cho, Kita-ku, Osaka 530-0051, Japan.
| | - Taro Terashi
- Koyo Chemical Co. Ltd., 1-17 Taiyuji-cho, Kita-ku, Osaka 530-0051, Japan.
| | - Kazuo Azuma
- Department of Veterinary Clinical Medicine, School of Veterinary Medicine, Tottori University, 4-101 Koyama-cho Minami, Tottori 680-8553, Japan.
| | - Yusuke Murahata
- Department of Veterinary Clinical Medicine, School of Veterinary Medicine, Tottori University, 4-101 Koyama-cho Minami, Tottori 680-8553, Japan.
| | - Takeshi Tsuka
- Department of Veterinary Clinical Medicine, School of Veterinary Medicine, Tottori University, 4-101 Koyama-cho Minami, Tottori 680-8553, Japan.
| | - Norihiko Ito
- Department of Veterinary Clinical Medicine, School of Veterinary Medicine, Tottori University, 4-101 Koyama-cho Minami, Tottori 680-8553, Japan.
| | - Tomohiro Imagawa
- Department of Veterinary Clinical Medicine, School of Veterinary Medicine, Tottori University, 4-101 Koyama-cho Minami, Tottori 680-8553, Japan.
| | - Saburo Minami
- Department of Veterinary Clinical Medicine, School of Veterinary Medicine, Tottori University, 4-101 Koyama-cho Minami, Tottori 680-8553, Japan.
| | - Yoshiharu Okamoto
- Department of Veterinary Clinical Medicine, School of Veterinary Medicine, Tottori University, 4-101 Koyama-cho Minami, Tottori 680-8553, Japan.
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Diken E, Ozer T, Arikan M, Emrence Z, Oner ET, Ustek D, Arga KY. Genomic analysis reveals the biotechnological and industrial potential of levan producing halophilic extremophile, Halomonas smyrnensis AAD6T. SPRINGERPLUS 2015; 4:393. [PMID: 26251777 PMCID: PMC4523562 DOI: 10.1186/s40064-015-1184-3] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/09/2015] [Accepted: 07/27/2015] [Indexed: 01/21/2023]
Abstract
Halomonas smyrnensis AAD6T is a gram negative, aerobic, and moderately halophilic bacterium, and is known to produce high levels of levan with many potential uses in foods, feeds, cosmetics, pharmaceutical and chemical industries due to its outstanding properties. Here, the whole-genome analysis was performed to gain more insight about the biological mechanisms, and the whole-genome organization of the bacterium. Industrially crucial genes, including the levansucrase, were detected and the genome-scale metabolic model of H. smyrnensis AAD6T was reconstructed. The bacterium was found to have many potential applications in biotechnology not only being a levan producer, but also because of its capacity to produce Pel exopolysaccharide, polyhydroxyalkanoates, and osmoprotectants. The genomic information presented here will not only provide additional information to enhance our understanding of the genetic and metabolic network of halophilic bacteria, but also accelerate the research on systematical design of engineering strategies for biotechnology applications.
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Affiliation(s)
- Elif Diken
- />Department of Bioengineering, Marmara University, Goztepe, 34722 Istanbul, Turkey
| | - Tugba Ozer
- />Department of Bioengineering, Marmara University, Goztepe, 34722 Istanbul, Turkey
| | - Muzaffer Arikan
- />Department of Genetics, Institute for Experimental Medicine, Istanbul University, Capa, 34093 Istanbul, Turkey
| | - Zeliha Emrence
- />Department of Genetics, Institute for Experimental Medicine, Istanbul University, Capa, 34093 Istanbul, Turkey
| | - Ebru Toksoy Oner
- />Department of Bioengineering, Marmara University, Goztepe, 34722 Istanbul, Turkey
| | - Duran Ustek
- />Department of Medical Genetics, School of Medicine, REMER, Medipol University, 34810 Istanbul, Turkey
| | - Kazim Yalcin Arga
- />Department of Bioengineering, Marmara University, Goztepe, 34722 Istanbul, Turkey
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190
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Kobus S, Widderich N, Hoeppner A, Bremer E, Smits SHJ. Overproduction, crystallization and X-ray diffraction data analysis of ectoine synthase from the cold-adapted marine bacterium Sphingopyxis alaskensis. ACTA CRYSTALLOGRAPHICA SECTION F-STRUCTURAL BIOLOGY COMMUNICATIONS 2015; 71:1027-32. [PMID: 26249694 DOI: 10.1107/s2053230x15011115] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2015] [Accepted: 06/08/2015] [Indexed: 11/10/2022]
Abstract
Ectoine biosynthetic genes (ectABC) are widely distributed in bacteria. Microorganisms that carry them make copious amounts of ectoine as a cell protectant in response to high-osmolarity challenges. Ectoine synthase (EctC; EC 4.2.1.108) is the key enzyme for the production of this compatible solute and mediates the last step of ectoine biosynthesis. It catalyzes the ring closure of the cyclic ectoine molecule. A codon-optimized version of ectC from Sphingopyxis alaskensis (Sa) was used for overproduction of SaEctC protein carrying a Strep-tag II peptide at its carboxy-terminus. The recombinant SaEctC-Strep-tag II protein was purified to near-homogeneity from Escherichia coli cell extracts by affinity chromatography. Size-exclusion chromatography revealed that it is a dimer in solution. The SaEctC-Strep-tag II protein was crystallized using the sitting-drop vapour-diffusion method and crystals that diffracted to 1.0 Å resolution were obtained.
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Affiliation(s)
- Stefanie Kobus
- Crystal Farm and X-ray Facility, Heinrich-Heine-University, Universitaetsstrasse 1, 40225 Düsseldorf, Germany
| | - Nils Widderich
- Department of Biology, Laboratory for Microbiology, Philipps-University Marburg, Karl-von-Frisch Strasse 8, 35043 Marburg, Germany
| | - Astrid Hoeppner
- Crystal Farm and X-ray Facility, Heinrich-Heine-University, Universitaetsstrasse 1, 40225 Düsseldorf, Germany
| | - Erhard Bremer
- Department of Biology, Laboratory for Microbiology, Philipps-University Marburg, Karl-von-Frisch Strasse 8, 35043 Marburg, Germany
| | - Sander H J Smits
- Institute of Biochemistry, Heinrich-Heine-University, Universitaetsstrasse 1, 40225 Düsseldorf, Germany
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191
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GlnR-Mediated Regulation of ectABCD Transcription Expands the Role of the GlnR Regulon to Osmotic Stress Management. J Bacteriol 2015; 197:3041-7. [PMID: 26170409 DOI: 10.1128/jb.00185-15] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2015] [Accepted: 07/03/2015] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED Ectoine and hydroxyectoine are excellent compatible solutes for bacteria to deal with environmental osmotic stress and temperature damages. The biosynthesis cluster of ectoine and hydroxyectoine is widespread among microorganisms, and its expression is activated by high salinity and temperature changes. So far, little is known about the mechanism of the regulation of the transcription of ect genes and only two MarR family regulators (EctR1 in methylobacteria and the EctR1-related regulator CosR in Vibrio cholerae) have been found to negatively regulate the expression of ect genes. Here, we characterize GlnR, the global regulator for nitrogen metabolism in actinomycetes, as a negative regulator for the transcription of ectoine/hydroxyectoine biosynthetic genes (ect operon) in Streptomyces coelicolor. The physiological role of this transcriptional repression by GlnR is proposed to protect the intracellular glutamate pool, which acts as a key nitrogen donor for both the nitrogen metabolism and the ectoine/hydroxyectoine biosynthesis. IMPORTANCE High salinity is deleterious, and cells must evolve sophisticated mechanisms to cope with this osmotic stress. Although production of ectoine and hydroxyectoine is one of the most frequently adopted strategies, the in-depth mechanism of regulation of their biosynthesis is less understood. So far, only two MarR family negative regulators, EctR1 and CosR, have been identified in methylobacteria and Vibrio, respectively. Here, our work demonstrates that GlnR, the global regulator for nitrogen metabolism, is a negative transcriptional regulator for ect genes in Streptomyces coelicolor. Moreover, a close relationship is found between nitrogen metabolism and osmotic resistance, and GlnR-mediated regulation of ect transcription is proposed to protect the intracellular glutamate pool. Meanwhile, the work reveals the multiple roles of GlnR in bacterial physiology.
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192
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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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193
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Bownik A, Stępniewska Z. Protective effects of bacterial osmoprotectant ectoine on bovine erythrocytes subjected to staphylococcal alpha-haemolysin. Toxicon 2015; 99:130-5. [PMID: 25841345 DOI: 10.1016/j.toxicon.2015.03.022] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2015] [Revised: 03/27/2015] [Accepted: 03/31/2015] [Indexed: 10/23/2022]
Abstract
Ectoine (ECT) is a bacterial compatible solute with documented protective action however no data are available on its effects on various cells against bacterial toxins. Therefore, we determined the in vitro influence of ECT on bovine erythrocytes subjected to staphylococcal α-haemolysin (HlyA). The cells exposed to HlyA alone showed a distinct haemolysis and reduced glutathione (GSH)/oxidised glutathione (GSSG) level, however the toxic effects were attenuated in the combinations of HlyA + ECT suggesting ECT-induced protection of erythrocytes from HlyA.
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Affiliation(s)
- Adam Bownik
- Department of Animal Physiology and Toxicology, Faculty of Biotechnology and Environmental Sciences, The John Paul II Catholic University of Lublin, Kontstantynów 1 "I", 20-708 Lublin, Poland.
| | - Zofia Stępniewska
- Department of Biochemistry and Environmental Chemistry, Faculty of Biotechnology and Environmental Sciences, The John Paul II Catholic University of Lublin, Kontstantynów 1 "I", 20-708 Lublin, Poland
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194
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Lu ZY, Guo XJ, Li H, Huang ZZ, Lin KF, Liu YD. High-throughput screening for a moderately halophilic phenol-degrading strain and its salt tolerance response. Int J Mol Sci 2015; 16:11834-48. [PMID: 26020478 PMCID: PMC4490417 DOI: 10.3390/ijms160611834] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2015] [Accepted: 05/06/2015] [Indexed: 11/24/2022] Open
Abstract
A high-throughput screening system for moderately halophilic phenol-degrading bacteria from various habitats was developed to replace the conventional strain screening owing to its high efficiency. Bacterial enrichments were cultivated in 48 deep well microplates instead of shake flasks or tubes. Measurement of phenol concentrations was performed in 96-well microplates instead of using the conventional spectrophotometric method or high-performance liquid chromatography (HPLC). The high-throughput screening system was used to cultivate forty-three bacterial enrichments and gained a halophilic bacterial community E3 with the best phenol-degrading capability. Halomonas sp. strain 4-5 was isolated from the E3 community. Strain 4-5 was able to degrade more than 94% of the phenol (500 mg·L−1 starting concentration) over a range of 3%–10% NaCl. Additionally, the strain accumulated the compatible solute, ectoine, with increasing salt concentrations. PCR detection of the functional genes suggested that the largest subunit of multicomponent phenol hydroxylase (LmPH) and catechol 1,2-dioxygenase (C12O) were active in the phenol degradation process.
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Affiliation(s)
- Zhi-Yan Lu
- State Environmental Protection Key Laboratory of Environmental Risk Assessment and Control on Chemical Process, School of Resources and Environmental Engineering, East China University of Science and Technology, Shanghai 200237, China.
| | - Xiao-Jue Guo
- State Environmental Protection Key Laboratory of Environmental Risk Assessment and Control on Chemical Process, School of Resources and Environmental Engineering, East China University of Science and Technology, Shanghai 200237, China.
| | - Hui Li
- State Environmental Protection Key Laboratory of Environmental Risk Assessment and Control on Chemical Process, School of Resources and Environmental Engineering, East China University of Science and Technology, Shanghai 200237, China.
| | - Zhong-Zi Huang
- State Environmental Protection Key Laboratory of Environmental Risk Assessment and Control on Chemical Process, School of Resources and Environmental Engineering, East China University of Science and Technology, Shanghai 200237, China.
- School of Chemical Engineering, Shanghai University of Engineering Science, Shanghai 201620, China.
| | - Kuang-Fei Lin
- State Environmental Protection Key Laboratory of Environmental Risk Assessment and Control on Chemical Process, School of Resources and Environmental Engineering, East China University of Science and Technology, Shanghai 200237, China.
| | - Yong-Di Liu
- State Environmental Protection Key Laboratory of Environmental Risk Assessment and Control on Chemical Process, School of Resources and Environmental Engineering, East China University of Science and Technology, Shanghai 200237, China.
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195
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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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196
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Salvador M, Argandoña M, Pastor JM, Bernal V, Cánovas M, Csonka LN, Nieto JJ, Vargas C. Contribution of RpoS to metabolic efficiency and ectoines synthesis during the osmo- and heat-stress response in the halophilic bacterium Chromohalobacter salexigens. ENVIRONMENTAL MICROBIOLOGY REPORTS 2015; 7:301-311. [PMID: 25417903 DOI: 10.1111/1758-2229.12249] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2014] [Accepted: 10/16/2014] [Indexed: 06/04/2023]
Abstract
Chromohalobacter salexigens is a halophilic γ-proteobacterium that responds to osmotic and heat stresses by accumulating ectoine and hydroxyectoine respectively. Evolution has optimized its metabolism to support high production of ectoines. We analysed the effect of an rpoS mutation in C. salexigens metabolism and ectoines synthesis. In long-term adapted cells, the rpoS strain was osmosensitive but not thermosensitive and showed unaltered ectoines content, suggesting that RpoS regulates ectoine(s)-independent osmoadaptive mechanisms. RpoS is involved in the regulation of C. salexigens metabolic adaptation to stress, as early steps of glucose oxidation through the Entner-Doudoroff pathway were deregulated in the rpoS mutant, leading to improved metabolic efficiency at low salinity. Moreover, a reduced pyruvate (but not acetate) overflow was displayed by the rpoS strain at low salt, probably linked to a slowdown in gluconate production and/or subsequent metabolism. Interestingly, RpoS does not seem to be the main regulator triggering the immediate transcriptional response of ectoine synthesis to osmotic or thermal upshifts. However, it contributed to the expression of the ect genes in cells previously adapted to low or high salinity.
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Affiliation(s)
- Manuel Salvador
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Seville, Seville, 41012, Spain
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197
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Bennur T, Kumar AR, Zinjarde S, Javdekar V. Nocardiopsis species: Incidence, ecological roles and adaptations. Microbiol Res 2015; 174:33-47. [PMID: 25946327 DOI: 10.1016/j.micres.2015.03.010] [Citation(s) in RCA: 69] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2014] [Revised: 03/13/2015] [Accepted: 03/16/2015] [Indexed: 12/23/2022]
Abstract
Members of the genus Nocardiopsis are ecologically versatile and biotechnologically important. They produce a variety of bioactive compounds such as antimicrobial agents, anticancer substances, tumor inducers, toxins and immunomodulators. They also secrete novel extracellular enzymes such as amylases, chitinases, cellulases, β-glucanases, inulinases, xylanases and proteases. Nocardiopsis species are aerobic, Gram-positive, non-acid-fast, catalase-positive actinomycetes with nocardioform substrate mycelia and their aerial mycelia bear long chains of spores. Their DNA possesses high contents of guanine and cytosine. There is a marked variation in properties of the isolates obtained from different ecological niches and their products. An important feature of several species is their halophilic or halotolerant nature. They are associated with a variety of marine and terrestrial biological forms wherein they produce antibiotics and toxins that help their hosts in evading pathogens and predators. Two Nocardiopsis species, namely, N. dassonvillei and N. synnemataformans (among the thirty nine reported ones) are opportunistic human pathogens and cause mycetoma, suppurative infections and abscesses. Nocardiopsis species are present in some plants (as endophytes or surface microflora) and their rhizospheres. Here, they are reported to produce enzymes such as α-amylases and antifungal agents that are effective in warding-off plant pathogens. They are prevalent as free-living entities in terrestrial locales, indoor locations, marine ecosystems and hypersaline habitats on account of their salt-, alkali- and desiccation-resistant behavior. In such natural locations, Nocardiopsis species mainly help in recycling organic compounds. Survival under these diverse conditions is mediated by the production of extracellular enzymes, antibiotics, surfactants, and the accumulation of compatible solutes. The accommodative genomic features of Nocardiopsis species support their existence under the diverse conditions where they prevail.
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Affiliation(s)
- Tahsin Bennur
- Institute of Bioinformatics and Biotechnology, Savitribai Phule Pune University, Pune 411007, India
| | - Ameeta Ravi Kumar
- Institute of Bioinformatics and Biotechnology, Savitribai Phule Pune University, Pune 411007, India
| | - Smita Zinjarde
- Institute of Bioinformatics and Biotechnology, Savitribai Phule Pune University, Pune 411007, India.
| | - Vaishali Javdekar
- Department of Biotechnology, Abasaheb Garware College, Pune 411004, India.
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198
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Asghar W, El Assal R, Shafiee H, Anchan RM, Demirci U. Preserving human cells for regenerative, reproductive, and transfusion medicine. Biotechnol J 2015; 9:895-903. [PMID: 24995723 DOI: 10.1002/biot.201300074] [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: 07/09/2013] [Revised: 05/21/2014] [Accepted: 05/30/2014] [Indexed: 12/15/2022]
Abstract
Cell cryopreservation maintains cellular life at sub-zero temperatures by slowing down biochemical processes. Various cell types are routinely cryopreserved in modern reproductive, regenerative, and transfusion medicine. Current cell cryopreservation methods involve freezing (slow/rapid) or vitrifying cells in the presence of a cryoprotective agent (CPA). Although these methods are clinically utilized, cryo-injury due to ice crystals, osmotic shock, and CPA toxicity cause loss of cell viability and function. Recent approaches using minimum volume vitrification provide alternatives to the conventional cryopreservation methods. Minimum volume vitrification provides ultra-high cooling and rewarming rates that enable preserving cells without ice crystal formation. Herein, we review recent advances in cell cryopreservation technology and provide examples of techniques that are utilized in oocyte, stem cell, and red blood cell cryopreservation.
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Affiliation(s)
- Waseem Asghar
- Bio-Acoustic-MEMS in Medicine (BAMM) Laboratories, Department of Radiology, Canary Center at Stanford for Cancer Early Detection, Stanford School of Medicine, Stanford University, Palo Alto, CA, USA
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199
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Kamanda Ngugi D, Blom J, Alam I, Rashid M, Ba-Alawi W, Zhang G, Hikmawan T, Guan Y, Antunes A, Siam R, El Dorry H, Bajic V, Stingl U. Comparative genomics reveals adaptations of a halotolerant thaumarchaeon in the interfaces of brine pools in the Red Sea. THE ISME JOURNAL 2015; 9:396-411. [PMID: 25105904 PMCID: PMC4303633 DOI: 10.1038/ismej.2014.137] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2014] [Revised: 05/29/2014] [Accepted: 06/21/2014] [Indexed: 02/05/2023]
Abstract
The bottom of the Red Sea harbors over 25 deep hypersaline anoxic basins that are geochemically distinct and characterized by vertical gradients of extreme physicochemical conditions. Because of strong changes in density, particulate and microbial debris get entrapped in the brine-seawater interface (BSI), resulting in increased dissolved organic carbon, reduced dissolved oxygen toward the brines and enhanced microbial activities in the BSI. These features coupled with the deep-sea prevalence of ammonia-oxidizing archaea (AOA) in the global ocean make the BSI a suitable environment for studying the osmotic adaptations and ecology of these important players in the marine nitrogen cycle. Using phylogenomic-based approaches, we show that the local archaeal community of five different BSI habitats (with up to 18.2% salinity) is composed mostly of a single, highly abundant Nitrosopumilus-like phylotype that is phylogenetically distinct from the bathypelagic thaumarchaea; ammonia-oxidizing bacteria were absent. The composite genome of this novel Nitrosopumilus-like subpopulation (RSA3) co-assembled from multiple single-cell amplified genomes (SAGs) from one such BSI habitat further revealed that it shares ∼54% of its predicted genomic inventory with sequenced Nitrosopumilus species. RSA3 also carries several, albeit variable gene sets that further illuminate the phylogenetic diversity and metabolic plasticity of this genus. Specifically, it encodes for a putative proline-glutamate 'switch' with a potential role in osmotolerance and indirect impact on carbon and energy flows. Metagenomic fragment recruitment analyses against the composite RSA3 genome, Nitrosopumilus maritimus, and SAGs of mesopelagic thaumarchaea also reiterate the divergence of the BSI genotypes from other AOA.
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Affiliation(s)
- David Kamanda Ngugi
- Red Sea Research Centre, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Jochen Blom
- Bioinformatics and Systems Biology, Justus Liebig University, Giessen, Germany
| | - Intikhab Alam
- Computational Bioscience Research Centre, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Mamoon Rashid
- Red Sea Research Centre, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Wail Ba-Alawi
- Computational Bioscience Research Centre, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Guishan Zhang
- Red Sea Research Centre, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Tyas Hikmawan
- Red Sea Research Centre, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Yue Guan
- Red Sea Research Centre, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Andre Antunes
- Red Sea Research Centre, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Rania Siam
- Department of Biology, American University in Cairo, Cairo, Egypt
| | - Hamza El Dorry
- Department of Biology, American University in Cairo, Cairo, Egypt
| | - Vladimir Bajic
- Computational Bioscience Research Centre, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Ulrich Stingl
- Red Sea Research Centre, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
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200
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Kuwano R, Hashiguchi Y, Ikeda R, Ishizuka K. Catalytic Asymmetric Hydrogenation of Pyrimidines. Angew Chem Int Ed Engl 2015; 54:2393-6. [DOI: 10.1002/anie.201410607] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2014] [Revised: 12/06/2014] [Indexed: 11/06/2022]
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