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Adjeroud M, Kecha M, Escuder-Rodríguez JJ, Becerra M, González-Siso MI. AMWEst, a new thermostable and detergent-tolerant esterase retrieved from the Albian aquifer. Appl Microbiol Biotechnol 2024; 108:114. [PMID: 38204131 PMCID: PMC10781878 DOI: 10.1007/s00253-023-12844-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Revised: 09/22/2023] [Accepted: 10/02/2023] [Indexed: 01/12/2024]
Abstract
A fosmid library was constructed with the metagenomic DNA from the high-temperature sediment-rich water of the Albian aquifer (Algeria). Functional screening of this library was subsequently done looking for genes encoding lipolytic enzymes. We identified a novel gene named AMWEst (1209 base pairs) encoding a protein of 402 amino acids with a predicted molecular weight of 43.44 kDa and conferring esterase activity. AMWEst was successfully overexpressed in the yeast mesophilic host Saccharomyces cerevisiae, and the expression system used proved to be efficient and produced sufficient activity for its biochemical characterization. Multiple sequence alignment indicated that AMWEst contained a conserved pentapeptide motif (Gly120-His121-Ser122-Gln123-Gly124). The optimum pH and temperature of the recombinant esterase AMWEst were 8 and 80 °C, respectively. Additionally, AMWEst showed higher activity towards short carbon substrates and showed maximum activity for p-nitrophenyl hexanoate (C6). Notably, AMWEst has a remarkable thermostability, and the enzyme retains almost maximum activity at 70 °C after incubation for 1 h. Moreover, enzyme activity was enhanced by high concentrations of SDS and Triton X-100 detergents. KEY POINTS: • A novel thermostable esterase has been retrieved through functional metagenomics • The esterase is detergent-tolerant, which is attractive for some applications • The esterase can be expressed in a yeast mesophilic host to enhance its yield.
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Affiliation(s)
- Moussa Adjeroud
- Laboratoire de Mycologie, Département de Biologie Appliquée, de Biotechnologie Et de L'Activité Microbienne (LaMyBAM), Faculté Des Sciences de La Nature Et de La Vie, Université Des Frères Mentouri Constantine 1, 25000, Constantine, Algeria
- University of A Coruña, Grupo EXPRELA, Facultade de Ciencias, Centro Interdisciplinar de Química e Bioloxía (CICA), A Coruña, Spain
| | - Mouloud Kecha
- Laboratoire de Microbiologie Appliquée, Faculté Des Sciences de La Nature Et de La Vie, Département de Microbiologie, Université de Bejaia, Campus Targa Ouzemmour, 6000, Bejaia, Algeria
| | - Juan-José Escuder-Rodríguez
- University of A Coruña, Grupo EXPRELA, Facultade de Ciencias, Centro Interdisciplinar de Química e Bioloxía (CICA), A Coruña, Spain
| | - Manuel Becerra
- University of A Coruña, Grupo EXPRELA, Facultade de Ciencias, Centro Interdisciplinar de Química e Bioloxía (CICA), A Coruña, Spain.
| | - María-Isabel González-Siso
- University of A Coruña, Grupo EXPRELA, Facultade de Ciencias, Centro Interdisciplinar de Química e Bioloxía (CICA), A Coruña, Spain.
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Sword TT, Dinglasan JLN, Abbas GS, William Barker J, Spradley ME, Greene ER, Gooden DS, Emrich SJ, Gilchrist MA, Doktycz MJ, Bailey CB. Profiling Expression Strategies for a Type III Polyketide Synthase in a Lysate-Based, Cell-free System. bioRxiv 2023:2023.11.30.569483. [PMID: 38077034 PMCID: PMC10705458 DOI: 10.1101/2023.11.30.569483] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/17/2023]
Abstract
Some of the most metabolically diverse species of bacteria (e.g., Actinobacteria) have higher GC content in their DNA, differ substantially in codon usage, and have distinct protein folding environments compared to tractable expression hosts like Escherichia coli. Consequentially, expressing biosynthetic gene clusters (BGCs) from these bacteria in E. coli frequently results in a myriad of unpredictable issues with protein expression and folding, delaying the biochemical characterization of new natural products. Current strategies to achieve soluble, active expression of these enzymes in tractable hosts, such as BGC refactoring, can be a lengthy trial-and-error process. Cell-free expression (CFE) has emerged as 1) a valuable expression platform for enzymes that are challenging to synthesize in vivo, and as 2) a testbed for rapid prototyping that can improve cellular expression. Here, we use a type III polyketide synthase from Streptomyces griseus, RppA, which catalyzes the formation of the red pigment flaviolin, as a reporter to investigate BGC refactoring techniques. We synergistically tune promoter and codon usage to improve flaviolin production from cell-free expressed RppA. We then assess the utility of cell-free systems for prototyping these refactoring tactics prior to their implementation in cells. Overall, codon harmonization improves natural product synthesis more than traditional codon optimization across cell-free and cellular environments. Refactoring promoters and/or coding sequences via CFE can be a valuable strategy to rapidly screen for catalytically functional production of enzymes from BCGs. By showing the coordinators between CFE versus in vivo expression, this work advances CFE as a tool for natural product research.
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Affiliation(s)
- Tien T. Sword
- Department of Chemistry, University of Tennessee-Knoxville (Knoxville, TN USA)
| | - Jaime Lorenzo N. Dinglasan
- Biosciences Division, Oak Ridge National Laboratory (Oak Ridge, TN USA)
- Graduate School of Genome Science & Technology, University of Tennessee-Knoxville Knoxville (Knoxville, TN USA)
| | - Ghaeath S.K. Abbas
- Department of Chemistry, University of Tennessee-Knoxville (Knoxville, TN USA)
- University of Sydney, School of Chemistry (Sydney, NSW, Australia)
| | - J. William Barker
- Department of Chemistry, University of Tennessee-Knoxville (Knoxville, TN USA)
| | - Madeline E. Spradley
- Department of Biochemistry, Cellular, and Molecular Biology, University of Tennessee-Knoxville (Knoxville, TN USA)
| | - Elijah R. Greene
- Department of Chemistry, University of Tennessee-Knoxville (Knoxville, TN USA)
| | - Damian S. Gooden
- Department of Chemistry, University of Tennessee-Knoxville (Knoxville, TN USA)
| | - Scott J. Emrich
- Graduate School of Genome Science & Technology, University of Tennessee-Knoxville Knoxville (Knoxville, TN USA)
- Department of Electrical Engineering and Computer Science, University of Tennessee-Knoxville (Knoxville, TN USA)
- Department of Ecology & Evolutionary Biology, University of Tennessee-Knoxville (Knoxville, TN USA)
| | - Michael A. Gilchrist
- Graduate School of Genome Science & Technology, University of Tennessee-Knoxville Knoxville (Knoxville, TN USA)
- Department of Ecology & Evolutionary Biology, University of Tennessee-Knoxville (Knoxville, TN USA)
| | - Mitchel J. Doktycz
- Biosciences Division, Oak Ridge National Laboratory (Oak Ridge, TN USA)
- Graduate School of Genome Science & Technology, University of Tennessee-Knoxville Knoxville (Knoxville, TN USA)
| | - Constance B. Bailey
- Department of Chemistry, University of Tennessee-Knoxville (Knoxville, TN USA)
- Graduate School of Genome Science & Technology, University of Tennessee-Knoxville Knoxville (Knoxville, TN USA)
- University of Sydney, School of Chemistry (Sydney, NSW, Australia)
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Łubkowska B, Czajkowska E, Stodolna A, Sroczyński M, Zylicz-Stachula A, Sobolewski I, Skowron PM. A novel thermostable TP-84 capsule depolymerase: a method for rapid polyethyleneimine processing of a bacteriophage-expressed proteins. Microb Cell Fact 2023; 22:80. [PMID: 37098567 PMCID: PMC10131341 DOI: 10.1186/s12934-023-02086-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Accepted: 04/09/2023] [Indexed: 04/27/2023] Open
Abstract
BACKGROUND In spite of the fact that recombinant enzymes are preferably biotechnologically obtained using recombinant clones, the purification of proteins from native microorganisms, including those encoded by bacteriophages, continues. The native bacteriophage protein isolation is often troubled by large volumes of the infected bacterial cell lysates needed to be processed, which is highly undesired in scaled-up industrial processing. A well-known ammonium sulphate fractionation is often a method of choice during purification of the native bacteriophage protein. However, this method is time-consuming and cumbersome, and requires large amounts of the relatively expensive reagent. Thus, other effective and inexpensive methods of reversible protein precipitation are highly desirable. We have previously characterized thermophilic TP-84 bacteriophage, defined a new genus TP84virus within Siphoviridae family, conducted the TP-84 genome annotation and proteomic analysis. The longest Open Reading Frame (ORF) identified in the genome is TP84_26. We have previously annotated this ORF as a hydrolytic enzyme depolymerizing the thick polysaccharides host's capsule. RESULTS The TP84_26 'capsule depolymerase' (depolymerase) is a large, 112 kDa protein, biosynthesized by the infected Geobacillus stearothermophilus 10 (G. stearothermophilus 10) cells. The TP84_26 protein biosynthesis was confirmed by three approaches: (i) purification of the protein of the expected size; (ii) mass spectrometry (LC-MS) analysis and (iii) detection of the enzymatic activity toward G. stearothermophilus polysaccharide capsules. Streptomycin-resistant mutant of the host was generated and microbiological aspects of both the TP-84 and G. stearothermophilus 10 were determined. A new variant of polyethyleneimine (PEI)-mediated purification method was developed, using the novel TP-84 depolymerase as a model. The enzyme was characterized. Three depolymerase forms were detected: soluble, unbound proteins in the bacteriophage/cells lysate and another integrated into the TP-84 virion. CONCLUSIONS The novel TP-84 depolymerase was purified and characterized. The enzyme exists in three forms. The soluble, unbound forms are probably responsible for the weakening of the capsules of the uninfected bacterial cells. The form integrated into virion particles may generate a local passage for the invading TP-84. The developed PEI purification method appears well suited for the scaled-up or industrial production of bacteriophage proteins.
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Affiliation(s)
- Beata Łubkowska
- Faculty of Health and Life Sciences, Division of Biochemistry, Gdansk University of Physical Education and Sport, Gorskiego 1, 80-336, Gdansk, Poland.
- Faculty of Chemistry, Department of Molecular Biotechnology, University of Gdansk, Wita Stwosza 63, 80-308, Gdansk, Poland.
| | - Edyta Czajkowska
- Faculty of Chemistry, Department of Molecular Biotechnology, University of Gdansk, Wita Stwosza 63, 80-308, Gdansk, Poland
| | - Aleksandra Stodolna
- Faculty of Chemistry, Department of Molecular Biotechnology, University of Gdansk, Wita Stwosza 63, 80-308, Gdansk, Poland
| | - Michał Sroczyński
- Faculty of Chemistry, Department of Molecular Biotechnology, University of Gdansk, Wita Stwosza 63, 80-308, Gdansk, Poland
| | - Agnieszka Zylicz-Stachula
- Faculty of Chemistry, Department of Molecular Biotechnology, University of Gdansk, Wita Stwosza 63, 80-308, Gdansk, Poland
| | - Ireneusz Sobolewski
- Faculty of Chemistry, Department of Molecular Biotechnology, University of Gdansk, Wita Stwosza 63, 80-308, Gdansk, Poland
- BioGel Sp. z o.o. (Ltd.), ul. Promienista 83, 60-141, Poznań, Poland
| | - Piotr M Skowron
- Faculty of Chemistry, Department of Molecular Biotechnology, University of Gdansk, Wita Stwosza 63, 80-308, Gdansk, Poland
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Kruglikov A, Wei Y, Xia X. Proteins from Thermophilic Thermus thermophilus Often Do Not Fold Correctly in a Mesophilic Expression System Such as Escherichia coli. ACS Omega 2022; 7:37797-37806. [PMID: 36312379 PMCID: PMC9608423 DOI: 10.1021/acsomega.2c04786] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Accepted: 10/07/2022] [Indexed: 06/16/2023]
Abstract
Majority of protein structure studies use Escherichia coli (E. coli) and other model organisms as expression systems for other species' genes. However, protein folding depends on cellular environment factors, such as chaperone proteins, cytoplasmic pH, temperature, and ionic concentrations. Because of differences in these factors, especially temperature and chaperones, native proteins in organisms such as extremophiles may fold improperly when they are expressed in mesophilic model organisms. Here we present a methodology of assessing the effects of using E. coli as the expression system on protein structures. We compare these effects between eight mesophilic bacteria and Thermus thermophilus (T. thermophilus), a thermophile, and found that differences are significantly larger for T. thermophilus. More specifically, helical secondary structures in T. thermophilus proteins are often replaced by coil structures in E. coli. Our results show unique directionality in misfolding when proteins in thermophiles are expressed in mesophiles. This indicates that extremophiles, such as thermophiles, require unique protein expression systems in protein folding studies.
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Affiliation(s)
- Alibek Kruglikov
- Department
of Biology, University of Ottawa, Ottawa, Canada K1N 6N5
| | - Yulong Wei
- Department
of Biology, University of Ottawa, Ottawa, Canada K1N 6N5
| | - Xuhua Xia
- Department
of Biology, University of Ottawa, Ottawa, Canada K1N 6N5
- Ottawa
Institute of Systems Biology, University
of Ottawa, Ottawa, Canada K1N 6N5
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5
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Krefft D, Prusinowski M, Maciszka P, Skokowska A, Zebrowska J, Skowron PM. T7-lac promoter vectors spontaneous derepression caused by plant-derived growth media may lead to serious expression problems: a systematic evaluation. Microb Cell Fact 2022; 21:13. [PMID: 35090462 PMCID: PMC8796431 DOI: 10.1186/s12934-022-01740-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Accepted: 01/06/2022] [Indexed: 02/06/2023] Open
Abstract
Background The widespread usage of protein expression systems in Escherichia coli (E. coli) is a workhorse of molecular biology research that has practical applications in biotechnology industry, including the production of pharmaceutical drugs. Various factors can strongly affect the successful construction and stable maintenance of clones and the resulting biosynthesis levels. These include an appropriate selection of recombinant hosts, expression systems, regulation of promoters, the repression level at an uninduced state, growth temperature, codon usage, codon context, mRNA secondary structure, translation kinetics, the presence/absence of chaperons and others. However, optimization of the growth medium’s composition is often overlooked. We systematically evaluate this factor, which can have a dramatic effect on the expression of recombinant proteins, especially those which are toxic to a recombinant host. Results Commonly used animal tissue- and plant-based media were evaluated using a series of clones in pET vector, containing expressed Open Reading Frames (ORFs) with a wide spectrum of toxicity to the recombinant E. coli: (i) gfpuv (nontoxic); (ii) tp84_28—which codes for thermophilic endolysin (moderately toxic); and (iii) tthHB27IRM—which codes for thermophilic restriction endonuclease-methyltransferase (REase-MTase)—RM.TthHB27I (very toxic). The use of plant-derived peptones (soy peptone and malt extract) in a culture medium causes the T7-lac expression system to leak. We show that the presence of raffinose and stachyose (galactoside derivatives) in those peptones causes premature and uncontrolled induction of gene expression, which affects the course of the culture, the stability of clones and biosynthesis levels. Conclusions The use of plant-derived peptones in a culture medium when using T7-lac hybrid promoter expression systems, such as Tabor-Studier, can lead to uncontrolled production of a recombinant protein. These conclusions also extend to other, lac operator-controlled promoters. In the case of proteins which are toxic to a recombinant host, this can result in mutations or deletions in the expression vector and/or cloned gene, the death of the host or highly decreased expression levels. This phenomenon is caused by the content of certain saccharides in plant peptones, some of which (galactosides) may act as T7-lac promoter inducer by interacting with a Lac repressor. Thus, when attempting to overexpress toxic proteins, it is recommended to either not use plant-derived media or to use them with caution and perform a pilot-scale evaluation of the derepression effect on a case-by-case basis. Supplementary Information The online version contains supplementary material available at 10.1186/s12934-022-01740-5.
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Affiliation(s)
- Daria Krefft
- Department of Molecular Biotechnology, Faculty of Chemistry, University of Gdansk, Wita Stwosza 63 street, 80-308, Gdansk, Poland.
| | - Maciej Prusinowski
- Department of Molecular Biotechnology, Faculty of Chemistry, University of Gdansk, Wita Stwosza 63 street, 80-308, Gdansk, Poland
| | - Paulina Maciszka
- Department of Molecular Biotechnology, Faculty of Chemistry, University of Gdansk, Wita Stwosza 63 street, 80-308, Gdansk, Poland
| | - Aleksandra Skokowska
- Department of Molecular Biotechnology, Faculty of Chemistry, University of Gdansk, Wita Stwosza 63 street, 80-308, Gdansk, Poland
| | - Joanna Zebrowska
- Department of Molecular Biotechnology, Faculty of Chemistry, University of Gdansk, Wita Stwosza 63 street, 80-308, Gdansk, Poland
| | - Piotr M Skowron
- Department of Molecular Biotechnology, Faculty of Chemistry, University of Gdansk, Wita Stwosza 63 street, 80-308, Gdansk, Poland.,Department of Physical Education, University of Physical Education and Sport, Gdańsk, Poland
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Krawczun N, Bielawa M, Szemiako K, Łubkowska B, Sobolewski I, Zylicz-Stachula A, Skowron PM. Boosting toxic protein biosynthesis: transient in vivo inactivation of engineered bacterial alkaline phosphatase. Microb Cell Fact 2020; 19:166. [PMID: 32811518 PMCID: PMC7437050 DOI: 10.1186/s12934-020-01424-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Accepted: 08/11/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The biotechnology production of enzymes is often troubled by the toxicity of the recombinant products of cloned and expressed genes, which interferes with the recombinant hosts' metabolism. Various approaches have been taken to overcome these limitations, exemplified by tight control of recombinant genes or secretion of recombinant proteins. An industrial approach to protein production demands maximum possible yields of biosynthesized proteins, balanced with the recombinant host's viability. Bacterial alkaline phosphatase (BAP) from Escherichia coli (E. coli) is a key enzyme used in protein/antibody detection and molecular cloning. As it removes terminal phosphate from DNA, RNA and deoxyribonucleoside triphosphates, it is used to lower self-ligated vectors' background. The precursor enzyme contains a signal peptide at the N-terminus and is secreted to the E. coli periplasm. Then, the leader is clipped off and dimers are formed upon oxidation. RESULTS We present a novel approach to phoA gene cloning, engineering, expression, purification and reactivation of the transiently inactivated enzyme. The recombinant bap gene was modified by replacing a secretion leader coding section with a N-terminal His6-tag, cloned and expressed in E. coli in a PBAD promoter expression vector. The gene expression was robust, resulting in accumulation of His6-BAP in the cytoplasm, exceeding 50% of total cellular proteins. The His6-BAP protein was harmless to the cells, as its natural toxicity was inhibited by the reducing environment within the E. coli cytoplasm, preventing formation of the active enzyme. A simple protocol based on precipitation and immobilized metal affinity chromatography (IMAC) purification yielded homogeneous protein, which was reactivated by dialysis into a redox buffer containing reduced and oxidized sulfhydryl group compounds, as well as the protein structure stabilizing cofactors Zn2+, Mg2+ and phosphate. The reconstituted His6-BAP exhibited high activity and was used to develop an efficient protocol for all types of DNA termini, including problematic ones (blunt, 3'-protruding). CONCLUSIONS The developed method appears well suited for the industrial production of ultrapure BAP. Further, the method of transient inactivation of secreted toxic enzymes by conducting their biosynthesis in an inactive state in the cytoplasm, followed by in vitro reactivation, can be generally applied to other problematic proteins.
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Affiliation(s)
- Natalia Krawczun
- Department of Molecular Biotechnology, Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, 80-308, Gdansk, Poland
| | - Marta Bielawa
- Department of Molecular Biotechnology, Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, 80-308, Gdansk, Poland
| | - Kasjan Szemiako
- Department of Molecular Biotechnology, Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, 80-308, Gdansk, Poland
| | - Beata Łubkowska
- Department of Molecular Biotechnology, Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, 80-308, Gdansk, Poland
| | - Ireneusz Sobolewski
- Department of Molecular Biotechnology, Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, 80-308, Gdansk, Poland
| | - Agnieszka Zylicz-Stachula
- Department of Molecular Biotechnology, Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, 80-308, Gdansk, Poland
| | - Piotr M Skowron
- Department of Molecular Biotechnology, Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, 80-308, Gdansk, Poland.
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Jensen TØ, Tellgren-Roth C, Redl S, Maury J, Jacobsen SAB, Pedersen LE, Nielsen AT. Genome-wide systematic identification of methyltransferase recognition and modification patterns. Nat Commun 2019; 10:3311. [PMID: 31427571 PMCID: PMC6700114 DOI: 10.1038/s41467-019-11179-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Accepted: 06/27/2019] [Indexed: 01/25/2023] Open
Abstract
Genome-wide analysis of DNA methylation patterns using single molecule real-time DNA sequencing has boosted the number of publicly available methylomes. However, there is a lack of tools coupling methylation patterns and the corresponding methyltransferase genes. Here we demonstrate a high-throughput method for coupling methyltransferases with their respective motifs, using automated cloning and analysing the methyltransferases in vectors carrying a strain-specific cassette containing all potential target sites. To validate the method, we analyse the genomes of the thermophile Moorella thermoacetica and the mesophile Acetobacterium woodii, two acetogenic bacteria having substantially modified genomes with 12 methylation motifs and a total of 23 methyltransferase genes. Using our method, we characterize the 23 methyltransferases, assign motifs to the respective enzymes and verify activity for 11 of the 12 motifs. Single molecule real-time DNA sequencing allows genome-wide identification of DNA methylation patterns. Here, Jensen et al. present a high-throughput method that allows rapid coupling of DNA methylation patterns with their corresponding methyltransferase genes in bacteria.
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Affiliation(s)
- Torbjørn Ølshøj Jensen
- The Novo Nordisk Foundation Center for Biosustainability (CfB), Technical University of Denmark (DTU), DK-2800, Lyngby, Denmark
| | - Christian Tellgren-Roth
- Uppsala Genome Center, National Genomics Infrastructure, SciLifeLab, SE-751 08, Uppsala, Sweden
| | - Stephanie Redl
- The Novo Nordisk Foundation Center for Biosustainability (CfB), Technical University of Denmark (DTU), DK-2800, Lyngby, Denmark.,Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Jérôme Maury
- The Novo Nordisk Foundation Center for Biosustainability (CfB), Technical University of Denmark (DTU), DK-2800, Lyngby, Denmark
| | | | - Lasse Ebdrup Pedersen
- The Novo Nordisk Foundation Center for Biosustainability (CfB), Technical University of Denmark (DTU), DK-2800, Lyngby, Denmark
| | - Alex Toftgaard Nielsen
- The Novo Nordisk Foundation Center for Biosustainability (CfB), Technical University of Denmark (DTU), DK-2800, Lyngby, Denmark.
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8
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Meng DH, Du RR, Chen LZ, Li MT, Liu F, Hou J, Shi YK, Wang FS, Sheng JZ. Cascade synthesis of uridine-5'-diphosphate glucuronic acid by coupling multiple whole cells expressing hyperthermophilic enzymes. Microb Cell Fact 2019; 18:118. [PMID: 31262296 PMCID: PMC6604206 DOI: 10.1186/s12934-019-1168-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Accepted: 06/26/2019] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND Enzymatic glycan synthesis has leapt forward in recent years and a number of glucuronosyltransferase (EC 2.4.1.17) have been identified and prepared, which provides a guide to an efficient approach to prepare glycans containing glucuronic acid (GlcA) residues. The uridine 5'-diphosphate (UDP) activated form, UDP-GlcA, is the monosaccharide donor for these glucuronidation reactions. RESULTS To produce UDP-GlcA in a cost-effective way, an efficient three-step cascade route was developed using whole cells expressing hyperthermophilic enzymes to afford UDP-GlcA from starch. By coupling a coenzyme regeneration system with an appropriate expression level with UDP-glucose 6-dehydrogenase in a single strain, the cells were able to meet NAD+ requirements. Without addition of exogenous NAD+, the reaction produced 1.3 g L-1 UDP-GlcA, representing 100% and 46% conversion of UDP-Glc and UTP respectively. Finally, an anion exchange chromatography purification method was developed. UDP-GlcA was successfully obtained from the cascade system. The yield of UDP-GlcA during purification was about 92.0%. CONCLUSIONS This work built a de novo hyperthermophilic biosynthetic cascade into E. coli host cells, with the cells able to meet NAD+ cofactor requirements and act as microbial factories for UDP-GlcA synthesis, which opens a door to large-scale production of cheaper UDP-GlcA.
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Affiliation(s)
- Dan-Hua Meng
- Key Laboratory of Chemical Biology of Natural Products (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, Jinan, 250012, China
| | - Ran-Ran Du
- Key Laboratory of Chemical Biology of Natural Products (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, Jinan, 250012, China
| | - Lu-Zhou Chen
- Key Laboratory of Chemical Biology of Natural Products (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, Jinan, 250012, China
| | - Meng-Ting Li
- Key Laboratory of Chemical Biology of Natural Products (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, Jinan, 250012, China
| | - Fei Liu
- Key Laboratory of Biopharmaceuticals, Shandong Academy of Pharmaceutical Sciences, Jinan, 250101, China
| | - Jin Hou
- State Key Laboratory of Microbiology, Shandong University, Jinan, 250100, China
| | - Yi-Kang Shi
- National Glycoengineering Research Center, Shandong University, Jinan, 250012, China
| | - Feng-Shan Wang
- Key Laboratory of Chemical Biology of Natural Products (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, Jinan, 250012, China
- National Glycoengineering Research Center, Shandong University, Jinan, 250012, China
| | - Ju-Zheng Sheng
- Key Laboratory of Chemical Biology of Natural Products (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, Jinan, 250012, China.
- National Glycoengineering Research Center, Shandong University, Jinan, 250012, China.
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9
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Zebrowska J, Jezewska-Frackowiak J, Wieczerzak E, Kasprzykowski F, Zylicz-Stachula A, Skowron PM. Novel parameter describing restriction endonucleases: Secondary-Cognate-Specificity and chemical stimulation of TsoI leading to substrate specificity change. Appl Microbiol Biotechnol 2019; 103:3439-3451. [PMID: 30879089 PMCID: PMC6449304 DOI: 10.1007/s00253-019-09731-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2018] [Revised: 02/22/2019] [Accepted: 02/27/2019] [Indexed: 11/30/2022]
Abstract
Over 470 prototype Type II restriction endonucleases (REases) are currently known. Most recognise specific DNA sequences 4–8 bp long, with very few exceptions cleaving DNA more frequently. TsoI is a thermostable Type IIC enzyme that recognises the DNA sequence TARCCA (R = A or G) and cleaves downstream at N11/N9. The enzyme exhibits extensive top-strand nicking of the supercoiled single-site DNA substrate. The second DNA strand of such substrate is specifically cleaved only in the presence of duplex oligonucleotides containing a cognate site. We have previously shown that some Type IIC/IIG/IIS enzymes from the Thermus-family exhibit ‘affinity star’ activity, which can be induced by the S-adenosyl-L-methionine (SAM) cofactor analogue—sinefungin (SIN). Here, we define a novel type of inherently built-in ‘star’ activity, exemplified by TsoI. The TsoI ‘star’ activity cannot be described under the definition of the classic ‘star’ activity as it is independent of the reaction conditions used and cannot be separated from the cognate specificity. Therefore, we define this phenomenon as Secondary-Cognate-Specificity (SCS). The TsoI SCS comprises several degenerated variants of the cognate site. Although the efficiency of TsoI SCS cleavage is lower in comparison to the cognate TsoI recognition sequence, it can be stimulated by S-adenosyl-L-cysteine (SAC). We present a new route for the chemical synthesis of SAC. The TsoI/SAC REase may serve as a novel tool for DNA manipulation.
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Affiliation(s)
- Joanna Zebrowska
- Department of Molecular Biotechnology, Faculty of Chemistry, University of Gdansk, 63 Wita Stwosza Street, 80-308, Gdansk, Poland
| | - Joanna Jezewska-Frackowiak
- Department of Molecular Biotechnology, Faculty of Chemistry, University of Gdansk, 63 Wita Stwosza Street, 80-308, Gdansk, Poland
| | - Ewa Wieczerzak
- Department of Biomedical Chemistry, Faculty of Chemistry, University of Gdansk, 63 Wita Stwosza Street, 80-308, Gdansk, Poland
| | - Franciszek Kasprzykowski
- Department of Biomedical Chemistry, Faculty of Chemistry, University of Gdansk, 63 Wita Stwosza Street, 80-308, Gdansk, Poland
| | - Agnieszka Zylicz-Stachula
- Department of Molecular Biotechnology, Faculty of Chemistry, University of Gdansk, 63 Wita Stwosza Street, 80-308, Gdansk, Poland.
| | - Piotr M Skowron
- Department of Molecular Biotechnology, Faculty of Chemistry, University of Gdansk, 63 Wita Stwosza Street, 80-308, Gdansk, Poland.
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Rekadwad B, Gonzalez JM. Multidisciplinary involvement and potential of thermophiles. Folia Microbiol (Praha) 2019; 64:389-406. [PMID: 30386965 DOI: 10.1007/s12223-018-0662-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Accepted: 10/25/2018] [Indexed: 12/15/2022]
Abstract
The full biotechnological exploitation of thermostable enzymes in industrial processes is necessary for their commercial interest and industrious value. The heat-tolerant and heat-resistant enzymes are a key for efficient and cost-effective translation of substrates into useful products for commercial applications. The thermophilic, hyperthermophilic, and microorganisms adapted to extreme temperatures (i.e., low-temperature lovers or psychrophiles) are a rich source of thermostable enzymes with broad-ranging thermal properties, which have structural and functional stability to underpin a variety of technologies. These enzymes are under scrutiny for their great biotechnological potential. Temperature is one of the most critical parameters that shape microorganisms and their biomolecules for stability under harsh environmental conditions. This review describes in detail the sources of thermophiles and thermostable enzymes from prokaryotes and eukaryotes (microbial cell factories). Furthermore, the review critically examines perspectives to improve modern biocatalysts, its production and performance aiming to increase their value for biotechnology through higher standards, specificity, resistance, lowing costs, etc. These thermostable and thermally adapted extremophilic enzymes have been used in a wide range of industries that span all six enzyme classes. Thus, in particular, target of this review paper is to show the possibility of both high-value-low-volume (e.g., fine-chemical synthesis) and low-value-high-volume by-products (e.g., fuels) by minimizing changes to current industrial processes.
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Krefft D, Papkov A, Prusinowski M, Zylicz-Stachula A, Skowron PM. Randomized DNA libraries construction tool: a new 3-bp 'frequent cutter' TthHB27I/sinefungin endonuclease with chemically-induced specificity. BMC Genomics 2018; 19:361. [PMID: 29751745 PMCID: PMC5948728 DOI: 10.1186/s12864-018-4748-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Accepted: 04/30/2018] [Indexed: 12/14/2022] Open
Abstract
Background Acoustic or hydrodynamic shearing, sonication and enzymatic digestion are used to fragment DNA. However, these methods have several disadvantages, such as DNA damage, difficulties in fragmentation control, irreproducibility and under-representation of some DNA segments. The DNA fragmentation tool would be a gentle enzymatic method, offering cleavage frequency high enough to eliminate DNA fragments distribution bias and allow for easy control of partial digests. Only three such frequently cleaving natural restriction endonucleases (REases) were discovered: CviJI, SetI and FaiI. Therefore, we have previously developed two artificial enzymatic specificities, cleaving DNA approximately every ~ 3-bp: TspGWI/sinefungin (SIN) and TaqII/SIN. Results In this paper we present the third developed specificity: TthHB27I/SIN(SAM) - a new genomic tool, based on Type IIS/IIC/IIG Thermus-family REases-methyltransferases (MTases). In the presence of dimethyl sulfoxide (DMSO) and S-adenosyl-L-methionine (SAM) or its analogue SIN, the 6-bp cognate TthHB27I recognition sequence 5’-CAARCA-3′ is converted into a combined 3.2–3.0-bp ‘site’ or its statistical equivalent, while a cleavage distance of 11/9 nt is retained. Protocols for various modes of limited DNA digestions were developed. Conclusions In the presence of DMSO and SAM or SIN, TthHB27I is transformed from rare 6-bp cutter to a very frequent one, approximately 3-bp. Thus, TthHB27I/SIN(SAM) comprises a new tool in the very low-represented segment of such prototype REases specificities. Moreover, this modified TthHB27I enzyme is uniquely suited for controlled DNA fragmentation, due to partial DNA cleavage, which is an inherent feature of the Thermus-family enzymes. Such tool can be used for quasi-random libraries generation as well as for other DNA manipulations, requiring high frequency cleavage and uniform distribution of cuts along DNA. Electronic supplementary material The online version of this article (10.1186/s12864-018-4748-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Daria Krefft
- Department of Molecular Biotechnology, Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, 80-308, Gdansk, Poland
| | - Aliaksei Papkov
- Department of Molecular Biotechnology, Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, 80-308, Gdansk, Poland
| | - Maciej Prusinowski
- Department of Molecular Biotechnology, Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, 80-308, Gdansk, Poland
| | - Agnieszka Zylicz-Stachula
- Department of Molecular Biotechnology, Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, 80-308, Gdansk, Poland
| | - Piotr M Skowron
- Department of Molecular Biotechnology, Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, 80-308, Gdansk, Poland.
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