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Schlüter L, Busche T, Bondzio L, Hütten A, Niehaus K, Schneiker-Bekel S, Pühler A, Kalinowski J. Sigma Factor Engineering in Actinoplanes sp. SE50/110: Expression of the Alternative Sigma Factor Gene ACSP50_0507 (σH As) Enhances Acarbose Yield and Alters Cell Morphology. Microorganisms 2024; 12:1241. [PMID: 38930623 PMCID: PMC11205660 DOI: 10.3390/microorganisms12061241] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2024] [Revised: 06/11/2024] [Accepted: 06/17/2024] [Indexed: 06/28/2024] Open
Abstract
Sigma factors are transcriptional regulators that are part of complex regulatory networks for major cellular processes, as well as for growth phase-dependent regulation and stress response. Actinoplanes sp. SE50/110 is the natural producer of acarbose, an α-glucosidase inhibitor that is used in diabetes type 2 treatment. Acarbose biosynthesis is dependent on growth, making sigma factor engineering a promising tool for metabolic engineering. ACSP50_0507 is a homolog of the developmental and osmotic-stress-regulating Streptomyces coelicolor σHSc. Therefore, the protein encoded by ACSP50_0507 was named σHAs. Here, an Actinoplanes sp. SE50/110 expression strain for the alternative sigma factor gene ACSP50_0507 (sigHAs) achieved a two-fold increased acarbose yield with acarbose production extending into the stationary growth phase. Transcriptome sequencing revealed upregulation of acarbose biosynthesis genes during growth and at the late stationary growth phase. Genes that are transcriptionally activated by σHAs frequently code for secreted or membrane-associated proteins. This is also mirrored by the severely affected cell morphology, with hyperbranching, deformed and compartmentalized hyphae. The dehydrated cell morphology and upregulation of further genes point to a putative involvement in osmotic stress response, similar to its S. coelicolor homolog. The DNA-binding motif of σHAs was determined based on transcriptome sequencing data and shows high motif similarity to that of its homolog. The motif was confirmed by in vitro binding of recombinantly expressed σHAs to the upstream sequence of a strongly upregulated gene. Autoregulation of σHAs was observed, and binding to its own gene promoter region was also confirmed.
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Affiliation(s)
- Laura Schlüter
- Microbial Genomics and Biotechnology, Center for Biotechnology, Bielefeld University, 33594 Bielefeld, Germany; (L.S.); (S.S.-B.)
| | - Tobias Busche
- Technology Platform Genomics, Center for Biotechnology, Bielefeld University, 33594 Bielefeld, Germany;
- Medical School East Westphalia-Lippe, Bielefeld University, 33594 Bielefeld, Germany
| | - Laila Bondzio
- Faculty of Physics, Bielefeld University, 33594 Bielefeld, Germany; (L.B.); (A.H.)
| | - Andreas Hütten
- Faculty of Physics, Bielefeld University, 33594 Bielefeld, Germany; (L.B.); (A.H.)
| | - Karsten Niehaus
- Proteome and Metabolome Research, Faculty of Biology, Bielefeld University, 33594 Bielefeld, Germany;
| | - Susanne Schneiker-Bekel
- Microbial Genomics and Biotechnology, Center for Biotechnology, Bielefeld University, 33594 Bielefeld, Germany; (L.S.); (S.S.-B.)
- Genome Research of Industrial Microorganisms, Center for Biotechnology (CeBiTec), Bielefeld University, 33594 Bielefeld, Germany;
| | - Alfred Pühler
- Genome Research of Industrial Microorganisms, Center for Biotechnology (CeBiTec), Bielefeld University, 33594 Bielefeld, Germany;
| | - Jörn Kalinowski
- Microbial Genomics and Biotechnology, Center for Biotechnology, Bielefeld University, 33594 Bielefeld, Germany; (L.S.); (S.S.-B.)
- Technology Platform Genomics, Center for Biotechnology, Bielefeld University, 33594 Bielefeld, Germany;
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Allaert Y, Leyder A, Franceus J, Desmet T. Strategies for the synthesis of the osmolyte glucosylglycerate and its precursor glycerate. Appl Microbiol Biotechnol 2024; 108:297. [PMID: 38607564 PMCID: PMC11009771 DOI: 10.1007/s00253-024-13139-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2024] [Revised: 03/25/2024] [Accepted: 04/04/2024] [Indexed: 04/13/2024]
Abstract
Glycosidic osmolytes are widespread natural compounds that protect microorganisms and their macromolecules from the deleterious effects of various environmental stresses. Their protective properties have attracted considerable interest for industrial applications, especially as active ingredients in cosmetics and healthcare products. In that regard, the osmolyte glucosylglycerate is somewhat overlooked. Glucosylglycerate is typically accumulated by certain organisms when they are exposed to high salinity and nitrogen starvation, and its potent stabilizing effects have been demonstrated in vitro. However, the applications of this osmolyte have not been thoroughly explored due to the lack of a cost-efficient production process. Here, we present an overview of the progress that has been made in developing promising strategies for the synthesis of glucosylglycerate and its precursor glycerate, and discuss the remaining challenges. KEY POINTS: • Bacterial milking could be explored for fermentative production of glucosylglycerate • Glycoside phosphorylases of GH13_18 represent attractive alternatives for biocatalytic production • Conversion of glycerol with alditol oxidase is a promising strategy for generating the precursor glycerate.
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Affiliation(s)
- Yentl Allaert
- Centre for Synthetic Biology (CSB), Department of Biotechnology, Ghent University, Coupure Links 653, B-9000, Ghent, Belgium
| | - Arthur Leyder
- Centre for Synthetic Biology (CSB), Department of Biotechnology, Ghent University, Coupure Links 653, B-9000, Ghent, Belgium
| | - Jorick Franceus
- Centre for Synthetic Biology (CSB), Department of Biotechnology, Ghent University, Coupure Links 653, B-9000, Ghent, Belgium
| | - Tom Desmet
- Centre for Synthetic Biology (CSB), Department of Biotechnology, Ghent University, Coupure Links 653, B-9000, Ghent, Belgium.
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Mukherjee K, Narindoshvili T, Raushel FM. Discovery of a Kojibiose Phosphorylase in Escherichia coli K-12. Biochemistry 2018; 57:2857-2867. [PMID: 29684280 DOI: 10.1021/acs.biochem.8b00392] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The substrate profiles for three uncharacterized enzymes (YcjM, YcjT, and YcjU) that are expressed from a cluster of 12 genes ( ycjM-W and ompG) of unknown function in Escherichia coli K-12 were determined. Through a comprehensive bioinformatic and steady-state kinetic analysis, the catalytic function of YcjT was determined to be kojibiose phosphorylase. In the presence of saturating phosphate and kojibiose (α-(1,2)-d-glucose-d-glucose), this enzyme catalyzes the formation of d-glucose and β-d-glucose-1-phosphate ( kcat = 1.1 s-1, Km = 1.05 mM, and kcat/ Km = 1.12 × 103 M-1 s-1). Additionally, it was also shown that in the presence of β-d-glucose-1-phosphate, YcjT can catalyze the formation of other disaccharides using 1,5-anhydro-d-glucitol, l-sorbose, d-sorbitol, or l-iditol as a substitute for d-glucose. Kojibiose is a component of cell wall lipoteichoic acids in Gram-positive bacteria and is of interest as a potential low-calorie sweetener and prebiotic. YcjU was determined to be a β-phosphoglucomutase that catalyzes the isomerization of β-d-glucose-1-phosphate ( kcat = 21 s-1, Km = 18 μM, and kcat/ Km = 1.1 × 106 M-1 s-1) to d-glucose-6-phosphate. YcjU was also shown to exhibit catalytic activity with β-d-allose-1-phosphate, β-d-mannose-1-phosphate, and β-d-galactose-1-phosphate. YcjM catalyzes the phosphorolysis of α-(1,2)-d-glucose-d-glycerate with a kcat = 2.1 s-1, Km = 69 μM, and kcat/ Km = 3.1 × 104 M-1 s-1.
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Affiliation(s)
- Keya Mukherjee
- Department of Biochemistry & Biophysics , Texas A&M University , College Station , Texas 77844 , United States
| | - Tamari Narindoshvili
- Department of Chemistry , Texas A&M University , College Station , Texas 77843 , United States
| | - Frank M Raushel
- Department of Biochemistry & Biophysics , Texas A&M University , College Station , Texas 77844 , United States.,Department of Chemistry , Texas A&M University , College Station , Texas 77843 , United States
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Nunes-Costa D, Maranha A, Costa M, Alarico S, Empadinhas N. Glucosylglycerate metabolism, bioversatility and mycobacterial survival. Glycobiology 2016; 27:213-227. [DOI: 10.1093/glycob/cww132] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2016] [Accepted: 12/14/2016] [Indexed: 12/17/2022] Open
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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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Alarico S, Costa M, Sousa MS, Maranha A, Lourenço EC, Faria TQ, Ventura MR, Empadinhas N. Mycobacterium hassiacum recovers from nitrogen starvation with up-regulation of a novel glucosylglycerate hydrolase and depletion of the accumulated glucosylglycerate. Sci Rep 2014; 4:6766. [PMID: 25341489 PMCID: PMC5381378 DOI: 10.1038/srep06766] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2014] [Accepted: 09/17/2014] [Indexed: 01/24/2023] Open
Abstract
Some microorganisms accumulate glucosylglycerate (GG) during growth under nitrogen deprivation. However, the molecular mechanisms underlying the role of GG and the regulation of its levels in the nitrogen stress response are elusive. Since GG is required for biosynthesis of mycobacterial methylglucose lipopolysaccharides (MGLP) we examined the molecular mechanisms linking replenishment of assimilable nitrogen to nitrogen-starved M. hassiacum with depletion of GG accumulated during nitrogen deficiency. To probe the involvement of a newly identified glycoside hydrolase in GG depletion, we produced the mycobacterial enzyme recombinantly and confirmed the specific hydrolysis of GG (GG hydrolase, GgH) in vitro. We have also observed a pronounced up-regulation of GgH mRNA in response to the nitrogen shock, which positively correlates with GG depletion in vivo and growth stimulation, implicating GgH in the recovery process. Since GgH orthologs seem to be absent from most slowly-growing mycobacteria including M. tuberculosis, the disclosure of the GgH function allows reconfiguration of the MGLP pathway in rapidly-growing species and accommodation of this possible regulatory step. This new link between GG metabolism, MGLP biosynthesis and recovery from nitrogen stress furthers our knowledge on the mycobacterial strategies to endure a frequent stress faced in some environments and during long-term infection.
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Affiliation(s)
- Susana Alarico
- CNC - Center for Neuroscience and Cell Biology, University of Coimbra, Portugal
| | - Mafalda Costa
- CNC - Center for Neuroscience and Cell Biology, University of Coimbra, Portugal
| | - Marta S Sousa
- CNC - Center for Neuroscience and Cell Biology, University of Coimbra, Portugal
| | - Ana Maranha
- CNC - Center for Neuroscience and Cell Biology, University of Coimbra, Portugal
| | - Eva C Lourenço
- ITQB - Instituto de Tecnologia Química e Biológica, Oeiras, Portugal
| | - Tiago Q Faria
- CNC - Center for Neuroscience and Cell Biology, University of Coimbra, Portugal
| | - M Rita Ventura
- ITQB - Instituto de Tecnologia Química e Biológica, Oeiras, Portugal
| | - Nuno Empadinhas
- 1] CNC - Center for Neuroscience and Cell Biology, University of Coimbra, Portugal [2] III/UC - Institute for Interdisciplinary Research, University of Coimbra, Portugal
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Organic solutes in the deepest phylogenetic branches of the Bacteria: identification of α(1–6)glucosyl-α(1–2)glucosylglycerate in Persephonella marina. Extremophiles 2012. [DOI: 10.1007/s00792-012-0500-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Luley-Goedl C, Nidetzky B. Glycosides as compatible solutes: biosynthesis and applications. Nat Prod Rep 2011; 28:875-96. [DOI: 10.1039/c0np00067a] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Empadinhas N, da Costa MS. Diversity, biological roles and biosynthetic pathways for sugar-glycerate containing compatible solutes in bacteria and archaea. Environ Microbiol 2010; 13:2056-77. [PMID: 21176052 DOI: 10.1111/j.1462-2920.2010.02390.x] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
A decade ago the compatible solutes mannosylglycerate (MG) and glucosylglycerate (GG) were considered to be rare in nature. Apart from two species of thermophilic bacteria, Thermus thermophilus and Rhodothermus marinus, and a restricted group of hyperthermophilic archaea, the Thermococcales, MG had only been identified in a few red algae. Glucosylglycerate was considered to be even rarer and had only been detected as an insignificant solute in two halophilic microorganisms, a cyanobacterium, as a component of a polysaccharide and of a glycolipid in two actinobacteria. Unlike the hyper/thermophilic MG-accumulating microorganisms, branching close to the root of the Tree of Life, those harbouring GG shared a mesophilic lifestyle. Exceptionally, the thermophilic bacterium Persephonella marina was reported to accumulate GG. However, and especially owing to the identification of the key-genes for MG and GG synthesis and to the escalating numbers of genomes available, a plethora of new organisms with the resources to synthesize these solutes has been recognized. The accumulation of GG as an 'emergency' compatible solute under combined salt stress and nitrogen-deficient conditions now seems to be a disseminated survival strategy from enterobacteria to marine cyanobacteria. In contrast, the thermophilic and extremely radiation-resistant bacterium Rubrobacter xylanophilus is the only actinobacterium known to accumulate MG, and under all growth conditions tested. This review addresses the environmental factors underlying the accumulation of MG, GG and derivatives in bacteria and archaea and their roles during stress adaptation or as precursors for more elaborated macromolecules. The diversity of pathways for MG and GG synthesis as well as those for some of their derivatives is also discussed. The importance of glycerate-derived organic solutes in the microbial world is only now being recognized. Their stress-dependent accumulation and the molecular aspects of their interactions with biomolecules have already fuelled several emerging applications in biotechnology and biomedicine.
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Affiliation(s)
- Nuno Empadinhas
- Center for Neuroscience and Cell Biology, University of Coimbra, 3004-517 Coimbra, Portugal.
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Empadinhas N, Pereira PJB, Albuquerque L, Costa J, Sá-Moura B, Marques AT, Macedo-Ribeiro S, da Costa MS. Functional and structural characterization of a novel mannosyl-3-phosphoglycerate synthase from Rubrobacter xylanophilus reveals its dual substrate specificity. Mol Microbiol 2010; 79:76-93. [PMID: 21166895 DOI: 10.1111/j.1365-2958.2010.07432.x] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Rubrobacter xylanophilus is the only actinobacterium known to accumulate the organic solute mannosylglycerate (MG); moreover, the accumulation of MG is constitutive. The key enzyme for MG synthesis, catalysing the conversion of GDP-mannose (GDP-Man) and D-3-phosphoglycerate (3-PGA) into the phosphorylated intermediate mannosyl-3-phosphoglycerate and GDP, was purified from R. xylanophilus cell extracts and the corresponding gene was expressed in E. coli. Despite the related solute glucosylglycerate (GG) having never been detected in R. xylanophilus, the cell extracts and the pure recombinant mannosyl-3-phosphoglycerate synthase (MpgS) could also synthesize glucosyl-3-phosphoglycerate (GPG), the precursor of GG, in agreement with the higher homology of the novel MpgS towards GPG-synthesizing mycobacterial glucosyl-3-phosphoglycerate synthases (GpgS) than towards MpgSs from hyper/thermophiles, known to accumulate MG under salt or thermal stress. To understand the specificity and substrate ambiguity of this novel enzyme, we determined the crystal structure of the unliganded MpgS and of its complexes with the nucleotide and sugar donors, at 2.2, 2.8 and 2.5 Å resolution respectively. The first three-dimensional structures of a protein from this extremely gamma-radiation-resistant thermophile here reported show that MpgS (GT81 family) contains a GT-A like fold and clearly explain its nucleotide and sugar-donor specificity. In the GDP-Man complex, a flexible loop ((254) RQNRHQ(259) ), located close to the active site moves towards the incoming sugar moiety, providing the ligands for both magnesium ion co-ordination and sugar binding. A triple mutant of R. xylanophilus MpgS, mimicking the (206) PLAGE(210) loop stabilizing hydrogen bond network observed for mycobacterial GpgSs, reduces significantly the affinity to GDP-Man, implicating this loop in the sugar-donor discrimination.
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Affiliation(s)
- Nuno Empadinhas
- Center for Neuroscience and Cell Biology, University of Coimbra, 3004-517 Coimbra, Portugal
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Sawangwan T, Goedl C, Nidetzky B. Single-step enzymatic synthesis of (R)-2-O-alpha-D-glucopyranosyl glycerate, a compatible solute from micro-organisms that functions as a protein stabiliser. Org Biomol Chem 2009; 7:4267-70. [PMID: 19795066 DOI: 10.1039/b912621j] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Regioselective glucosylation of R-glycerate catalysed by sucrose phosphorylase in the presence of sucrose as the donor substrate provided the natural compatible solute (R)-2-O-alpha-D-glucopyranosyl glycerate with complete regioselectivity in an optimised synthetic yield of 90% R-glycerate converted and a concentration of about 270 mM.
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Affiliation(s)
- Thornthan Sawangwan
- Institute of Biotechnology and Biochemical Engineering, Graz University of Technology, Petersgasse 12/1, Graz, Austria
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Sedmera P, Halada P, Pospísil S. New carbasugars from Streptomyces lincolnensis. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2009; 47:519-522. [PMID: 19224545 DOI: 10.1002/mrc.2408] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Two new carbasugars (9 and 10) were isolated from Streptomyces lincolnensis DSM 40355 along with streptol (valienol, 8), gabosine I (valienone, 14), and glucosylglycerate. The reported (1)H and (13)C assignments are based on 1D ((1)H, (13)C, 1D-TOCSY, homodecoupling) and 2D (gCOSY, J-resolved, TOCSY, ROESY, gHSQC, gHMBC) NMR techniques and electrospray ionization FT mass spectrometry (ESI FTMS).
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Affiliation(s)
- Petr Sedmera
- Institute of Microbiology, Academy of Sciences of the Czech Republic, Vídenská 1083, 142 20 Prague, Czech Republic.
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