1
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He S, Abdallah II, van Merkerk R, Quax WJ. Insights into taxadiene synthase catalysis and promiscuity facilitated by mutability landscape and molecular dynamics. Planta 2024; 259:87. [PMID: 38460012 PMCID: PMC10924717 DOI: 10.1007/s00425-024-04363-9] [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] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Accepted: 02/07/2024] [Indexed: 03/11/2024]
Abstract
MAIN CONCLUSION Protein modeling, carbocation docking, and molecular dynamics along with structure-based mutability landscapes provided insight into taxadiene synthase catalysis (first step of the anticancer Taxol biosynthesis), protein structure-function correlations, and promiscuity. Plant terpenes belong to one of the largest and most diverse classes of natural products. This diversity is driven by the terpene synthase enzyme family which comprises numerous different synthases, several of which are promiscuous. Taxadiene synthase (TXS) is a class I diterpene synthase that catalyzes the first step in the biosynthesis pathway of the diterpene Taxol, an anticancer natural product produced by the Taxus plant. Exploring the molecular basis of TXS catalysis and its promiscuous potential garnered interest as a necessary means for understanding enzyme evolution and engineering possibilities to improve Taxol biosynthesis. A catalytically active closed conformation TXS model was designed using the artificial intelligence system, AlphaFold, accompanied by docking and molecular dynamics simulations. In addition, a mutability landscape of TXS including 14 residues was created to probe for structure-function relations. The mutability landscape revealed no mutants with improved catalytic activity compared to wild-type TXS. However, mutations of residues V584, Q609, V610, and Y688 showed high degree of promiscuity producing cembranoid-type and/or verticillene-type major products instead of taxanes. Mechanistic insights into V610F, V584M, Q609A, and Y688C mutants compared to the wild type revealed the trigger(s) for product profile change. Several mutants spanning residues V584, Q609, Y688, Y762, Q770, and F834 increased production of taxa-4(20),11(12)-diene which is a more favorable substrate for Taxol production compared to taxa-4(5),11(12)-diene. Finally, molecular dynamics simulations of the TXS reaction cascade revealed residues involved in ionization, carbocation stabilization, and cyclization ushering deeper understanding of the enzyme catalysis mechanism.
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Affiliation(s)
- Siqi He
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, Antonius Deusinglaan 1, 9713 AV, Groningen, The Netherlands
| | - Ingy I Abdallah
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, Antonius Deusinglaan 1, 9713 AV, Groningen, The Netherlands
- Department of Pharmacognosy, Faculty of Pharmacy, Alexandria University, Alexandria, Egypt
| | - Ronald van Merkerk
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, Antonius Deusinglaan 1, 9713 AV, Groningen, The Netherlands
| | - Wim J Quax
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, Antonius Deusinglaan 1, 9713 AV, Groningen, The Netherlands.
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2
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Guan Z, Song Y, de Vries M, Permentier H, Tepper P, van Merkerk R, Setroikromo R, Quax WJ. The Promiscuity of Squalene Synthase-Like Enzyme: Dehydrosqualene Synthase, a Natural Squalene Hyperproducer? J Agric Food Chem 2024; 72:3017-3024. [PMID: 38315649 PMCID: PMC10870770 DOI: 10.1021/acs.jafc.3c05770] [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] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Revised: 01/15/2024] [Accepted: 01/17/2024] [Indexed: 02/07/2024]
Abstract
Dehydrosqualene synthase (CrtM), as a squalene synthase-like enzyme from Staphylococcus aureus, can naturally utilize farnesyl diphosphate to produce dehydrosqualene (C30H48). However, no study has documented the natural production of squalene (C30H50) by CrtM. Here, based on an HPLC-Q-Orbitrap-MS/MS study, we report that the expression of crtM in vitro or in Bacillus subtilis 168 both results in the output of squalene, dehydrosqualene, and phytoene (C40H64). Notably, wild-type CrtM exhibits a significantly higher squalene yield compared to squalene synthase (SQS) from Bacillus megaterium with an approximately 2.4-fold increase. Moreover, the examination of presqualene diphosphate's stereostructures in both CrtM and SQS enzymes provides further understanding into the presence of multiple identified terpenoids. In summary, this study not only provides insights into the promiscuity demonstrated by squalene synthase-like enzymes but also highlights a new strategy of utilizing CrtM as a potential replacement for SQS in cell factories, thereby enhancing squalene production.
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Affiliation(s)
- Zheng Guan
- Department
of Chemical and Pharmaceutical Biology, Groningen Research Institute
of Pharmacy, University of Groningen, Groningen9713 AV, The Netherlands
| | - Yafeng Song
- Department
of Chemical and Pharmaceutical Biology, Groningen Research Institute
of Pharmacy, University of Groningen, Groningen9713 AV, The Netherlands
- Guangdong
Provincial Key Laboratory of Microbial Culture Collection and Application,
State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou510070, China
| | - Marcel de Vries
- Interfaculty
Mass Spectrometry Center, Groningen Research Institute of Pharmacy, University of Groningen, Groningen9713 AV, The Netherlands
| | - Hjalmar Permentier
- Interfaculty
Mass Spectrometry Center, Groningen Research Institute of Pharmacy, University of Groningen, Groningen9713 AV, The Netherlands
| | - Pieter Tepper
- Department
of Chemical and Pharmaceutical Biology, Groningen Research Institute
of Pharmacy, University of Groningen, Groningen9713 AV, The Netherlands
| | - Ronald van Merkerk
- Department
of Chemical and Pharmaceutical Biology, Groningen Research Institute
of Pharmacy, University of Groningen, Groningen9713 AV, The Netherlands
| | - Rita Setroikromo
- Department
of Chemical and Pharmaceutical Biology, Groningen Research Institute
of Pharmacy, University of Groningen, Groningen9713 AV, The Netherlands
| | - Wim J. Quax
- Department
of Chemical and Pharmaceutical Biology, Groningen Research Institute
of Pharmacy, University of Groningen, Groningen9713 AV, The Netherlands
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3
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Peng B, Zhang L, He S, Oerlemans R, Quax WJ, Groves MR, Haslinger K. Engineering a Plant Polyketide Synthase for the Biosynthesis of Methylated Flavonoids. J Agric Food Chem 2024; 72:529-539. [PMID: 38109879 PMCID: PMC10786038 DOI: 10.1021/acs.jafc.3c06785] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Revised: 11/30/2023] [Accepted: 12/06/2023] [Indexed: 12/20/2023]
Abstract
Homoeriodictyol and hesperetin are naturally occurring O-methylated flavonoids with many health-promoting properties. They are produced in plants in low abundance and as complex mixtures of similar compounds that are difficult to separate. Synthetic biology offers the opportunity to produce various flavonoids in a targeted, bottom-up approach in engineered microbes with high product titers. However, the production of O-methylated flavonoids is currently still highly inefficient. In this study, we investigated and engineered a combination of enzymes that had previously been shown to support homoeriodictyol and hesperetin production in Escherichia coli from fed O-methylated hydroxycinnamic acids. We determined the crystal structures of the enzyme catalyzing the first committed step of the pathway, chalcone synthase from Hordeum vulgare, in three ligand-bound states. Based on these structures and a multiple sequence alignment with other chalcone synthases, we constructed mutant variants and assessed their performance in E. coli toward producing methylated flavonoids. With our best mutant variant, HvCHS (Q232P, D234 V), we were able to produce homoeriodictyol and hesperetin at 2 times and 10 times higher titers than reported previously. Our findings will facilitate further engineering of this enzyme toward higher production of methylated flavonoids.
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Affiliation(s)
- Bo Peng
- Chemical
and Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, Antonius Deusinglaan 1, Groningen 9713AV, The Netherlands
| | - Lili Zhang
- XB20
Drug Design, Groningen Research Institute of Pharmacy, University of Groningen, Antonius Deusinglaan 1, Groningen 9713AV, The Netherlands
| | - Siqi He
- Chemical
and Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, Antonius Deusinglaan 1, Groningen 9713AV, The Netherlands
| | - Rick Oerlemans
- XB20
Drug Design, Groningen Research Institute of Pharmacy, University of Groningen, Antonius Deusinglaan 1, Groningen 9713AV, The Netherlands
| | - Wim J. Quax
- Chemical
and Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, Antonius Deusinglaan 1, Groningen 9713AV, The Netherlands
| | - Matthew R. Groves
- XB20
Drug Design, Groningen Research Institute of Pharmacy, University of Groningen, Antonius Deusinglaan 1, Groningen 9713AV, The Netherlands
| | - Kristina Haslinger
- Chemical
and Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, Antonius Deusinglaan 1, Groningen 9713AV, The Netherlands
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4
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Zhao C, Chen D, Suo F, Setroikromo R, Quax WJ, Dekker FJ. Discovery of highly potent HDAC8 PROTACs with anti-tumor activity. Bioorg Chem 2023; 136:106546. [PMID: 37098288 DOI: 10.1016/j.bioorg.2023.106546] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Revised: 04/11/2023] [Accepted: 04/12/2023] [Indexed: 04/27/2023]
Abstract
Various diseases are deeply associated with aberrations in HDAC8 functions. These aberrations can be assigned to either structural functions or catalytic functions of HDAC8. Therefore, development of HDAC8 degradation inducers might be more promising than HDAC8 inhibitors. We employed the proteolysis targeting chimera (PROTAC) strategy to develop a selective and potent HDAC8 degradation inducer CT-4 with single-digit nanomolar DC50 values and over 95% Dmax in both triple-negative breast cancer MDA-MB-231 cells and T-cell leukemia cells. Notably, CT-4 demonstrated potent anti-migration activity and limited anti-proliferative activity in MDA-MB-231 cells. In contrast, CT-4 effectively induced apototic cell death in Jurkat cells, as assessed by a caspase 3/7 activity assay and flow cytometry. Our findings suggest that the development of HDAC8 degradation inducers holds great potential for the treatment of HDAC8-related diseases.
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Affiliation(s)
- Chunlong Zhao
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy (GRIP), University of Groningen, Antonius Deusinglaan 1, 9713AV Groningen, The Netherlands
| | - Deng Chen
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy (GRIP), University of Groningen, Antonius Deusinglaan 1, 9713AV Groningen, The Netherlands
| | - Fengzhi Suo
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy (GRIP), University of Groningen, Antonius Deusinglaan 1, 9713AV Groningen, The Netherlands
| | - Rita Setroikromo
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy (GRIP), University of Groningen, Antonius Deusinglaan 1, 9713AV Groningen, The Netherlands
| | - Wim J Quax
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy (GRIP), University of Groningen, Antonius Deusinglaan 1, 9713AV Groningen, The Netherlands
| | - Frank J Dekker
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy (GRIP), University of Groningen, Antonius Deusinglaan 1, 9713AV Groningen, The Netherlands.
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5
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Song Y, He S, Jopkiewicz A, Setroikromo R, van Merkerk R, Quax WJ. Development and application of CRISPR-based genetic tools in Bacillus species and Bacillus phages. J Appl Microbiol 2022; 133:2280-2298. [PMID: 35797344 PMCID: PMC9796756 DOI: 10.1111/jam.15704] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 07/02/2022] [Accepted: 07/06/2022] [Indexed: 01/07/2023]
Abstract
Recently, the clustered regularly interspaced short palindromic repeats (CRISPR) system has been developed into a precise and efficient genome editing tool. Since its discovery as an adaptive immune system in prokaryotes, it has been applied in many different research fields including biotechnology and medical sciences. The high demand for rapid, highly efficient and versatile genetic tools to thrive in bacteria-based cell factories accelerates this process. This review mainly focuses on significant advancements of the CRISPR system in Bacillus subtilis, including the achievements in gene editing, and on problems still remaining. Next, we comprehensively summarize this genetic tool's up-to-date development and utilization in other Bacillus species, including B. licheniformis, B. methanolicus, B. anthracis, B. cereus, B. smithii and B. thuringiensis. Furthermore, we describe the current application of CRISPR tools in phages to increase Bacillus hosts' resistance to virulent phages and phage genetic modification. Finally, we suggest potential strategies to further improve this advanced technique and provide insights into future directions of CRISPR technologies for rendering Bacillus species cell factories more effective and more powerful.
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Affiliation(s)
- Yafeng Song
- Department of Chemical and Pharmaceutical BiologyGroningen Research Institute of Pharmacy, University of GroningenGroningenThe Netherlands,Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern ChinaInstitute of Microbiology, Guangdong Acadamy of SciencesGuangzhouChina
| | - Siqi He
- Department of Chemical and Pharmaceutical BiologyGroningen Research Institute of Pharmacy, University of GroningenGroningenThe Netherlands
| | - Anita Jopkiewicz
- Department of Chemical and Pharmaceutical BiologyGroningen Research Institute of Pharmacy, University of GroningenGroningenThe Netherlands
| | - Rita Setroikromo
- Department of Chemical and Pharmaceutical BiologyGroningen Research Institute of Pharmacy, University of GroningenGroningenThe Netherlands
| | - Ronald van Merkerk
- Department of Chemical and Pharmaceutical BiologyGroningen Research Institute of Pharmacy, University of GroningenGroningenThe Netherlands
| | - Wim J. Quax
- Department of Chemical and Pharmaceutical BiologyGroningen Research Institute of Pharmacy, University of GroningenGroningenThe Netherlands
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6
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Vogel JGT, Wibowo JP, Fan H, Setroikromo R, Wang K, Dömling A, Dekker FJ, Quax WJ. Discovery of chromene compounds as inhibitors of PvdQ acylase of Pseudomonas aeruginosa. Microbes Infect 2022; 24:105017. [PMID: 35709935 DOI: 10.1016/j.micinf.2022.105017] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Revised: 06/05/2022] [Accepted: 06/08/2022] [Indexed: 11/25/2022]
Abstract
The acquisition of iron is a crucial mechanism for the survival of pathogenic bacteria such as Pseudomonas aeruginosa in eukaryotic hosts. The key iron chelator in this organism is the siderophore pyoverdine, which was shown to be crucial for iron homeostasis. Pyoverdine is a non-ribosomal peptide with several maturation steps in the cytoplasm and others in the periplasmatic space. A key enzyme for its maturation is the acylase PvdQ. The inhibition of PvdQ stops the maturation of pyoverdine causing a significant imbalance in the iron homeostasis and hence can negatively influence the survival of P. aeruginosa. In this work, we successfully synthesized chromene-derived inhibitory molecules targeting PvdQ in a low micromolar range. In silico modeling as well as kinetic evaluations of the inhibitors suggest a competitive inhibition of the PvdQ function. Further, we evaluated the inhibitor in vivo on P. aeruginosa cells and report a dose-dependent reduction of pyoverdine formation. The compound also showed a protecting effect in a Galleria mellonella infection model.
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Affiliation(s)
- Jan G T Vogel
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, Antonius Deusinglaan 1, Groningen, 9713, AV, the Netherlands
| | - Joko P Wibowo
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, Antonius Deusinglaan 1, Groningen, 9713, AV, the Netherlands; Faculty of Pharmacy, University of Muhammadiyah Banjarmasin, Jl. Gubernur Syarkawi, Barito Kuala, 70582, Indonesia
| | - Hillina Fan
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, Antonius Deusinglaan 1, Groningen, 9713, AV, the Netherlands
| | - Rita Setroikromo
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, Antonius Deusinglaan 1, Groningen, 9713, AV, the Netherlands
| | - Kan Wang
- Department of Drug Design, Groningen Research Institute of Pharmacy, University of Groningen, Antonius Deusinglaan 1, Groningen, 9713, AV, the Netherlands
| | - Alexander Dömling
- Department of Drug Design, Groningen Research Institute of Pharmacy, University of Groningen, Antonius Deusinglaan 1, Groningen, 9713, AV, the Netherlands
| | - Frank J Dekker
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, Antonius Deusinglaan 1, Groningen, 9713, AV, the Netherlands
| | - Wim J Quax
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, Antonius Deusinglaan 1, Groningen, 9713, AV, the Netherlands.
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7
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Vogel J, Jansen L, Setroikromo R, Cavallo FM, van Dijl JM, Quax WJ. Fighting Acinetobacter baumannii infections with the acylase PvdQ. Microbes Infect 2022; 24:104951. [DOI: 10.1016/j.micinf.2022.104951] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 02/03/2022] [Accepted: 02/04/2022] [Indexed: 10/19/2022]
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8
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Arranz San Martín A, Vogel J, Wullich SC, Quax WJ, Fetzner S. Enzyme-Mediated Quenching of the Pseudomonas Quinolone Signal (PQS): A Comparison between Naturally Occurring and Engineered PQS-Cleaving Dioxygenases. Biomolecules 2022; 12:biom12020170. [PMID: 35204671 PMCID: PMC8961568 DOI: 10.3390/biom12020170] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 01/13/2022] [Accepted: 01/18/2022] [Indexed: 02/06/2023] Open
Abstract
The opportunistic pathogen Pseudomonas aeruginosa employs quorum sensing to govern the production of many virulence factors. Interference with quorum sensing signaling has therefore been put forward as an attractive approach to disarm this pathogen. Here, we analyzed the quorum quenching properties of natural and engineered (2-alkyl-)3-hydroxy-4(1H)-quinolone 2,4-dioxygenases (HQDs) that inactivate the P. aeruginosa signal molecule PQS (Pseudomonas quinolone signal; 2-heptyl-3-hydroxy-4(1H)-quinolone). When added exogenously to P. aeruginosa cultures, all HQDs tested significantly reduced the levels of PQS and other alkylquinolone-type secondary metabolites deriving from the biosynthetic pathway, such as the respiratory inhibitor 2-heptyl-4-hydroxyquinoline N-oxide. HQDs from Nocardia farcinica and Streptomyces bingchenggensis, which combine low KM values for PQS with thermal stability and resilience in the presence of P. aeruginosa exoproducts, respectively, attenuated production of the virulence factors pyocyanin and pyoverdine. A delay in mortality was observed when Galleria mellonella larvae were infected with P. aeruginosa suspensions treated with the S. bingchenggensis HQD or with inhibitors of alkylquinolone biosynthesis. Our data indicate that quenching of PQS signaling has potential as an anti-virulence strategy; however, an efficient anti-virulence therapy against P. aeruginosa likely requires a combination of agents addressing multiple targets.
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Affiliation(s)
- Alba Arranz San Martín
- Institute for Molecular Microbiology and Biotechnology, University of Münster, Corrensstraße 3, 48149 Münster, Germany; (A.A.S.M.); (S.C.W.)
| | - Jan Vogel
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, Antonius Deusinglaan 1, 9713 AV Groningen, The Netherlands; (J.V.); (W.J.Q.)
| | - Sandra C. Wullich
- Institute for Molecular Microbiology and Biotechnology, University of Münster, Corrensstraße 3, 48149 Münster, Germany; (A.A.S.M.); (S.C.W.)
| | - Wim J. Quax
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, Antonius Deusinglaan 1, 9713 AV Groningen, The Netherlands; (J.V.); (W.J.Q.)
| | - Susanne Fetzner
- Institute for Molecular Microbiology and Biotechnology, University of Münster, Corrensstraße 3, 48149 Münster, Germany; (A.A.S.M.); (S.C.W.)
- Correspondence: ; Tel.: +49-251-83-39824
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9
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Zhou X, Soto-Gamez A, Nijdam F, Setroikromo R, Quax WJ. Dihydroartemisinin-Transferrin Adducts Enhance TRAIL-Induced Apoptosis in Triple-Negative Breast Cancer in a P53-Independent and ROS-Dependent Manner. Front Oncol 2022; 11:789336. [PMID: 35047402 PMCID: PMC8762273 DOI: 10.3389/fonc.2021.789336] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [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: 10/04/2021] [Accepted: 12/03/2021] [Indexed: 01/25/2023] Open
Abstract
Triple-negative breast cancer (TNBC) is a highly aggressive breast cancer subtype independent of estrogen receptor, progesterone receptor, or human epidermal growth factor receptor 2. It has a poor prognosis and high recurrence. Due to its limited treatment options in the clinic, novel therapies are urgently needed. Single treatment with the death receptor ligand TRAIL was shown to be poorly effective. Recently, we have shown that artemisinin derivatives enhance TRAIL-induced apoptosis in colon cancer cells. Here, we utilized transferrin (TF) to enhance the effectiveness of dihydroartemisinin (DHA) in inducing cell death in TNBC cell lines (MDA-MB-231, MDA-MB-436, MDA-MB-468 and BT549). We found that the combination of DHA-TF and the death receptor 5-specific TRAIL variant DHER leads to an increase in DR5 expression in all four TNBC cell lines, while higher cytotoxicity was observed in MDA-MB-231, and MDA-MB-436. All the data point to the finding that DHA-TF stimulates cell death in TNBC cells, while the combination of DHA-TF with TRAIL variants will trigger more cell death in TRAIL-sensitive cells. Overall, DHA-TF in combination with TRAIL variants represents a potential novel combination therapy for triple-negative breast cancer.
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Affiliation(s)
- Xinyu Zhou
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, Groningen, Netherlands
| | - Abel Soto-Gamez
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, Groningen, Netherlands.,European Institute for the Biology of Aging (ERIBA), University Medical Center Groningen (UMCG), Groningen, Netherlands
| | - Fleur Nijdam
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, Groningen, Netherlands
| | - Rita Setroikromo
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, Groningen, Netherlands
| | - Wim J Quax
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, Groningen, Netherlands
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10
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Xiao Z, Osipyan A, Song S, Chen D, Schut RA, van Merkerk R, van der Wouden PE, Cool RH, Quax WJ, Melgert BN, Poelarends GJ, Dekker FJ. Thieno[2,3- d]pyrimidine-2,4(1 H,3 H)-dione Derivative Inhibits d-Dopachrome Tautomerase Activity and Suppresses the Proliferation of Non-Small Cell Lung Cancer Cells. J Med Chem 2022; 65:2059-2077. [PMID: 35041425 PMCID: PMC8842245 DOI: 10.1021/acs.jmedchem.1c01598] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [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] [Indexed: 02/07/2023]
Abstract
The homologous cytokines macrophage migration inhibitory factor (MIF) and d-dopachrome tautomerase (d-DT or MIF2) play key roles in cancers. Molecules binding to the MIF tautomerase active site interfere with its biological activity. In contrast, the lack of potent MIF2 inhibitors hinders the exploration of MIF2 as a drug target. In this work, screening of a focused compound collection enabled the identification of a MIF2 tautomerase inhibitor R110. Subsequent optimization provided inhibitor 5d with an IC50 of 1.0 μM for MIF2 tautomerase activity and a high selectivity over MIF. 5d suppressed the proliferation of non-small cell lung cancer cells in two-dimensional (2D) and three-dimensional (3D) cell cultures, which can be explained by the induction of cell cycle arrest via deactivation of the mitogen-activated protein kinase (MAPK) pathway. Thus, we discovered and characterized MIF2 inhibitors (5d) with improved antiproliferative activity in cellular models systems, which indicates the potential of targeting MIF2 in cancer treatment.
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Affiliation(s)
- Zhangping Xiao
- Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy (GRIP), University of Groningen, Antonius Deusinglaan 1, 9713 AV Groningen, The Netherlands
| | - Angelina Osipyan
- Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy (GRIP), University of Groningen, Antonius Deusinglaan 1, 9713 AV Groningen, The Netherlands
| | - Shanshan Song
- Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy (GRIP), University of Groningen, Antonius Deusinglaan 1, 9713 AV Groningen, The Netherlands.,Molecular Pharmacology, Groningen Research Institute of Pharmacy (GRIP), University of Groningen, Antonius Deusinglaan 1, 9713 AV Groningen, The Netherlands
| | - Deng Chen
- Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy (GRIP), University of Groningen, Antonius Deusinglaan 1, 9713 AV Groningen, The Netherlands
| | - Reinder A Schut
- Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy (GRIP), University of Groningen, Antonius Deusinglaan 1, 9713 AV Groningen, The Netherlands
| | - Ronald van Merkerk
- Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy (GRIP), University of Groningen, Antonius Deusinglaan 1, 9713 AV Groningen, The Netherlands
| | - Petra E van der Wouden
- Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy (GRIP), University of Groningen, Antonius Deusinglaan 1, 9713 AV Groningen, The Netherlands
| | - Robbert H Cool
- Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy (GRIP), University of Groningen, Antonius Deusinglaan 1, 9713 AV Groningen, The Netherlands
| | - Wim J Quax
- Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy (GRIP), University of Groningen, Antonius Deusinglaan 1, 9713 AV Groningen, The Netherlands
| | - Barbro N Melgert
- Molecular Pharmacology, Groningen Research Institute of Pharmacy (GRIP), University of Groningen, Antonius Deusinglaan 1, 9713 AV Groningen, The Netherlands.,University Medical Center Groningen, Groningen Research Institute of Asthma and COPD, University of Groningen, Hanzeplein 1, 9713 GZ Groningen, The Netherlands
| | - Gerrit J Poelarends
- Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy (GRIP), University of Groningen, Antonius Deusinglaan 1, 9713 AV Groningen, The Netherlands
| | - Frank J Dekker
- Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy (GRIP), University of Groningen, Antonius Deusinglaan 1, 9713 AV Groningen, The Netherlands
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11
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Suo F, Zhou X, Setroikromo R, Quax WJ. Receptor Specificity Engineering of TNF Superfamily Ligands. Pharmaceutics 2022; 14:181. [PMID: 35057080 PMCID: PMC8781899 DOI: 10.3390/pharmaceutics14010181] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 12/21/2021] [Accepted: 01/06/2022] [Indexed: 12/14/2022] Open
Abstract
The tumor necrosis factor (TNF) ligand family has nine ligands that show promiscuity in binding multiple receptors. As different receptors transduce into diverse pathways, the study on the functional role of natural ligands is very complex. In this review, we discuss the TNF ligands engineering for receptor specificity and summarize the performance of the ligand variants in vivo and in vitro. Those variants have an increased binding affinity to specific receptors to enhance the cell signal conduction and have reduced side effects due to a lowered binding to untargeted receptors. Refining receptor specificity is a promising research strategy for improving the application of multi-receptor ligands. Further, the settled variants also provide experimental guidance for engineering receptor specificity on other proteins with multiple receptors.
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Affiliation(s)
- Fengzhi Suo
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, Antonius Deusinglaan 1, 9713 AV Groningen, The Netherlands
| | - Xinyu Zhou
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, Antonius Deusinglaan 1, 9713 AV Groningen, The Netherlands
| | - Rita Setroikromo
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, Antonius Deusinglaan 1, 9713 AV Groningen, The Netherlands
| | - Wim J Quax
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, Antonius Deusinglaan 1, 9713 AV Groningen, The Netherlands
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12
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Xiao Z, Song S, Chen D, van Merkerk R, van der Wouden PE, Cool RH, Quax WJ, Poelarends GJ, Melgert BN, Dekker FJ. Proteolysis Targeting Chimera (PROTAC) for Macrophage Migration Inhibitory Factor (MIF) Has Anti-Proliferative Activity in Lung Cancer Cells. Angew Chem Int Ed Engl 2021; 60:17514-17521. [PMID: 34018657 PMCID: PMC8362126 DOI: 10.1002/anie.202101864] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [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: 02/05/2021] [Revised: 04/19/2021] [Indexed: 12/13/2022]
Abstract
Macrophage migration inhibitory factor (MIF) is involved in protein-protein interactions that play key roles in inflammation and cancer. Current strategies to develop small molecule modulators of MIF functions are mainly restricted to the MIF tautomerase active site. Here, we use this site to develop proteolysis targeting chimera (PROTAC) in order to eliminate MIF from its protein-protein interaction network. We report the first potent MIF-directed PROTAC, denoted MD13, which induced almost complete MIF degradation at low micromolar concentrations with a DC50 around 100 nM in A549 cells. MD13 suppresses the proliferation of A549 cells, which can be explained by deactivation of the MAPK pathway and subsequent induction of cell cycle arrest at the G2/M phase. MD13 also exhibits antiproliferative effect in a 3D tumor spheroid model. In conclusion, we describe the first MIF-directed PROTAC (MD13) as a research tool, which also demonstrates the potential of PROTACs in cancer therapy.
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Affiliation(s)
- Zhangping Xiao
- Department Chemical and Pharmaceutical BiologyGroningen Research Institute of Pharmacy (GRIP)University of GroningenAntonius Deusinglaan 19713AVGroningenThe Netherlands
| | - Shanshan Song
- Department Chemical and Pharmaceutical BiologyGroningen Research Institute of Pharmacy (GRIP)University of GroningenAntonius Deusinglaan 19713AVGroningenThe Netherlands
- Molecular PharmacologyGroningen Research Institute of Pharmacy (GRIP)University of GroningenAntonius Deusinglaan 19713AVGroningenThe Netherlands
| | - Deng Chen
- Department Chemical and Pharmaceutical BiologyGroningen Research Institute of Pharmacy (GRIP)University of GroningenAntonius Deusinglaan 19713AVGroningenThe Netherlands
| | | | - Petra E. van der Wouden
- Department Chemical and Pharmaceutical BiologyGroningen Research Institute of Pharmacy (GRIP)University of GroningenAntonius Deusinglaan 19713AVGroningenThe Netherlands
| | - Robbert H. Cool
- Department Chemical and Pharmaceutical BiologyGroningen Research Institute of Pharmacy (GRIP)University of GroningenAntonius Deusinglaan 19713AVGroningenThe Netherlands
| | - Wim J. Quax
- Department Chemical and Pharmaceutical BiologyGroningen Research Institute of Pharmacy (GRIP)University of GroningenAntonius Deusinglaan 19713AVGroningenThe Netherlands
| | - Gerrit J. Poelarends
- Department Chemical and Pharmaceutical BiologyGroningen Research Institute of Pharmacy (GRIP)University of GroningenAntonius Deusinglaan 19713AVGroningenThe Netherlands
| | - Barbro N. Melgert
- Molecular PharmacologyGroningen Research Institute of Pharmacy (GRIP)University of GroningenAntonius Deusinglaan 19713AVGroningenThe Netherlands
- University Medical Center GroningenGroningen Research Institute of Asthma and COPDUniversity of GroningenHanzeplein 19713 GZGroningenThe Netherlands
| | - Frank J. Dekker
- Department Chemical and Pharmaceutical BiologyGroningen Research Institute of Pharmacy (GRIP)University of GroningenAntonius Deusinglaan 19713AVGroningenThe Netherlands
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13
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Xiao Z, Song S, Chen D, Merkerk R, Wouden PE, Cool RH, Quax WJ, Poelarends GJ, Melgert BN, Dekker FJ. Proteolysis Targeting Chimera (PROTAC) for Macrophage Migration Inhibitory Factor (MIF) Has Anti‐Proliferative Activity in Lung Cancer Cells. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202101864] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Zhangping Xiao
- Department Chemical and Pharmaceutical Biology Groningen Research Institute of Pharmacy (GRIP) University of Groningen Antonius Deusinglaan 1 9713 AV Groningen The Netherlands
| | - Shanshan Song
- Department Chemical and Pharmaceutical Biology Groningen Research Institute of Pharmacy (GRIP) University of Groningen Antonius Deusinglaan 1 9713 AV Groningen The Netherlands
- Molecular Pharmacology Groningen Research Institute of Pharmacy (GRIP) University of Groningen Antonius Deusinglaan 1 9713 AV Groningen The Netherlands
| | - Deng Chen
- Department Chemical and Pharmaceutical Biology Groningen Research Institute of Pharmacy (GRIP) University of Groningen Antonius Deusinglaan 1 9713 AV Groningen The Netherlands
| | | | - Petra E. Wouden
- Department Chemical and Pharmaceutical Biology Groningen Research Institute of Pharmacy (GRIP) University of Groningen Antonius Deusinglaan 1 9713 AV Groningen The Netherlands
| | - Robbert H. Cool
- Department Chemical and Pharmaceutical Biology Groningen Research Institute of Pharmacy (GRIP) University of Groningen Antonius Deusinglaan 1 9713 AV Groningen The Netherlands
| | - Wim J. Quax
- Department Chemical and Pharmaceutical Biology Groningen Research Institute of Pharmacy (GRIP) University of Groningen Antonius Deusinglaan 1 9713 AV Groningen The Netherlands
| | - Gerrit J. Poelarends
- Department Chemical and Pharmaceutical Biology Groningen Research Institute of Pharmacy (GRIP) University of Groningen Antonius Deusinglaan 1 9713 AV Groningen The Netherlands
| | - Barbro N. Melgert
- Molecular Pharmacology Groningen Research Institute of Pharmacy (GRIP) University of Groningen Antonius Deusinglaan 1 9713 AV Groningen The Netherlands
- University Medical Center Groningen Groningen Research Institute of Asthma and COPD University of Groningen Hanzeplein 1 9713 GZ Groningen The Netherlands
| | - Frank J. Dekker
- Department Chemical and Pharmaceutical Biology Groningen Research Institute of Pharmacy (GRIP) University of Groningen Antonius Deusinglaan 1 9713 AV Groningen The Netherlands
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14
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Song Y, He S, Abdallah II, Jopkiewicz A, Setroikromo R, van Merkerk R, Tepper PG, Quax WJ. Engineering of Multiple Modules to Improve Amorphadiene Production in Bacillus subtilis Using CRISPR-Cas9. J Agric Food Chem 2021; 69:4785-4794. [PMID: 33877851 PMCID: PMC8154554 DOI: 10.1021/acs.jafc.1c00498] [Citation(s) in RCA: 15] [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] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Revised: 04/06/2021] [Accepted: 04/08/2021] [Indexed: 06/12/2023]
Abstract
Engineering strategies to improve terpenoids' production in Bacillus subtilis mainly focus on 2C-methyl-d-erythritol-4-phosphate (MEP) pathway overexpression. To systematically engineer the chassis strain for higher amorphadiene (precursor of artemisinin) production, a clustered regularly interspaced short palindromic repeat-Cas9 (CRISPR-Cas9) system was established in B. subtilis to facilitate precise and efficient genome editing. Then, this system was employed to engineer three more modules to improve amorphadiene production, including the terpene synthase module, the branch pathway module, and the central metabolic pathway module. Finally, our combination of all of the useful strategies within one strain significantly increased extracellular amorphadiene production from 81 to 116 mg/L after 48 h flask fermentation without medium optimization. For the first time, we attenuated the FPP-derived competing pathway to improve amorphadiene biosynthesis and investigated how the TCA cycle affects amorphadiene production in B. subtilis. Overall, this study provides a universal strategy for further increasing terpenoids' production in B. subtilis by comprehensive and systematic metabolic engineering.
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Affiliation(s)
- Yafeng Song
- Department
of Chemical and Pharmaceutical Biology, Groningen Research Institute
of Pharmacy, University of Groningen, Antonius Deusinglaan 1, 9713 AV Groningen, The Netherlands
| | - Siqi He
- Department
of Chemical and Pharmaceutical Biology, Groningen Research Institute
of Pharmacy, University of Groningen, Antonius Deusinglaan 1, 9713 AV Groningen, The Netherlands
| | - Ingy I. Abdallah
- Department
of Chemical and Pharmaceutical Biology, Groningen Research Institute
of Pharmacy, University of Groningen, Antonius Deusinglaan 1, 9713 AV Groningen, The Netherlands
- Department
of Pharmacognosy, Faculty of Pharmacy, Alexandria
University, 21521 Alexandria, Egypt
| | - Anita Jopkiewicz
- Department
of Chemical and Pharmaceutical Biology, Groningen Research Institute
of Pharmacy, University of Groningen, Antonius Deusinglaan 1, 9713 AV Groningen, The Netherlands
| | - Rita Setroikromo
- Department
of Chemical and Pharmaceutical Biology, Groningen Research Institute
of Pharmacy, University of Groningen, Antonius Deusinglaan 1, 9713 AV Groningen, The Netherlands
| | - Ronald van Merkerk
- Department
of Chemical and Pharmaceutical Biology, Groningen Research Institute
of Pharmacy, University of Groningen, Antonius Deusinglaan 1, 9713 AV Groningen, The Netherlands
| | - Pieter G. Tepper
- Department
of Chemical and Pharmaceutical Biology, Groningen Research Institute
of Pharmacy, University of Groningen, Antonius Deusinglaan 1, 9713 AV Groningen, The Netherlands
| | - Wim J. Quax
- Department
of Chemical and Pharmaceutical Biology, Groningen Research Institute
of Pharmacy, University of Groningen, Antonius Deusinglaan 1, 9713 AV Groningen, The Netherlands
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15
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Sagita R, Quax WJ, Haslinger K. Current State and Future Directions of Genetics and Genomics of Endophytic Fungi for Bioprospecting Efforts. Front Bioeng Biotechnol 2021; 9:649906. [PMID: 33791289 PMCID: PMC8005728 DOI: 10.3389/fbioe.2021.649906] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [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: 01/05/2021] [Accepted: 02/16/2021] [Indexed: 12/16/2022] Open
Abstract
The bioprospecting of secondary metabolites from endophytic fungi received great attention in the 1990s and 2000s, when the controversy around taxol production from Taxus spp. endophytes was at its height. Since then, hundreds of reports have described the isolation and characterization of putative secondary metabolites from endophytic fungi. However, only very few studies also report the genetic basis for these phenotypic observations. With low sequencing cost and fast sample turnaround, genetics- and genomics-based approaches have risen to become comprehensive approaches to study natural products from a wide-range of organisms, especially to elucidate underlying biosynthetic pathways. However, in the field of fungal endophyte biology, elucidation of biosynthetic pathways is still a major challenge. As a relatively poorly investigated group of microorganisms, even in the light of recent efforts to sequence more fungal genomes, such as the 1000 Fungal Genomes Project at the Joint Genome Institute (JGI), the basis for bioprospecting of enzymes and pathways from endophytic fungi is still rather slim. In this review we want to discuss the current approaches and tools used to associate phenotype and genotype to elucidate biosynthetic pathways of secondary metabolites in endophytic fungi through the lens of bioprospecting. This review will point out the reported successes and shortcomings, and discuss future directions in sampling, and genetics and genomics of endophytic fungi. Identifying responsible biosynthetic genes for the numerous secondary metabolites isolated from endophytic fungi opens the opportunity to explore the genetic potential of producer strains to discover novel secondary metabolites and enhance secondary metabolite production by metabolic engineering resulting in novel and more affordable medicines and food additives.
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Affiliation(s)
| | | | - Kristina Haslinger
- Groningen Institute of Pharmacy, Chemical and Pharmaceutical Biology, University of Groningen, Groningen, Netherlands
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16
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González-Ponce HA, Martínez-Saldaña MC, Tepper PG, Quax WJ, Buist-Homan M, Faber KN, Moshage H. Betacyanins, major components in Opuntia red-purple fruits, protect against acetaminophen-induced acute liver failure. Food Res Int 2020; 137:109461. [PMID: 33233135 DOI: 10.1016/j.foodres.2020.109461] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2019] [Revised: 04/05/2020] [Accepted: 06/16/2020] [Indexed: 01/06/2023]
Abstract
Acetaminophen (APAP) misuse or overdose is the most important cause of drug-induced acute liver failure. Overdoses of acetaminophen induce oxidative stress and liver injury by the electrophilic metabolite N-acetyl-p-benzoquinone imine (NAPQI). Plant-based medicine has been used for centuries against diseases or intoxications due to their biological activities. The aim of this study was to evaluate the therapeutic value of Opuntia robusta and Opuntia streptacantha fruit extracts against acetaminophen-induced liver damage and to identify the major biocomponents on them. Opuntia fruit extracts were obtained by peeling and squeezing each specie, followed by lyophilization. HPLC was used to characterize the extracts. The effect of the extracts against acetaminophen-induced acute liver injury was evaluated both in vivo and in vitro using biochemical, molecular and histological determinations. The results showed that betacyanins are the main components in the analyzed Opuntia fruit extracts, with betanin as the highest concentration. Therapeutic treatments with Opuntia extracts reduced biochemical, molecular and histological markers of liver (in vivo) and hepatocyte (in vitro) injury. Opuntia extracts reduced the APAP-increased expression of the stress-related gene Gadd45b. Furthermore, Opuntia extracts exerted diverse effects on the antioxidant related genes Sod2, Gclc and Hmox1, independent of their ROS-scavenging ability. Therefore, betacyanins as betanin from Opuntia robusta and Opuntia streptacantha fruits are promising nutraceutical compounds against oxidative liver damage.
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Affiliation(s)
- Herson Antonio González-Ponce
- Department of Gastroenterology and Hepatology, University Medical Center Groningen, University of Groningen, the Netherlands.
| | | | - Pieter G Tepper
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, the Netherlands
| | - Wim J Quax
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, the Netherlands
| | - Manon Buist-Homan
- Department of Gastroenterology and Hepatology, University Medical Center Groningen, University of Groningen, the Netherlands; Department of Laboratory Medicine, University Medical Center Groningen, University of Groningen, the Netherlands.
| | - Klaas Nico Faber
- Department of Gastroenterology and Hepatology, University Medical Center Groningen, University of Groningen, the Netherlands; Department of Laboratory Medicine, University Medical Center Groningen, University of Groningen, the Netherlands.
| | - Han Moshage
- Department of Gastroenterology and Hepatology, University Medical Center Groningen, University of Groningen, the Netherlands; Department of Laboratory Medicine, University Medical Center Groningen, University of Groningen, the Netherlands.
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17
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Pramastya H, Song Y, Elfahmi EY, Sukrasno S, Quax WJ. Positioning Bacillus subtilis as terpenoid cell factory. J Appl Microbiol 2020; 130:1839-1856. [PMID: 33098223 PMCID: PMC8247319 DOI: 10.1111/jam.14904] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [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: 06/11/2020] [Revised: 09/29/2020] [Accepted: 10/09/2020] [Indexed: 12/16/2022]
Abstract
Increasing demands for bioactive compounds have motivated researchers to employ micro‐organisms to produce complex natural products. Currently, Bacillus subtilis has been attracting lots of attention to be developed into terpenoids cell factories due to its generally recognized safe status and high isoprene precursor biosynthesis capacity by endogenous methylerythritol phosphate (MEP) pathway. In this review, we describe the up‐to‐date knowledge of each enzyme in MEP pathway and the subsequent steps of isomerization and condensation of C5 isoprene precursors. In addition, several representative terpene synthases expressed in B. subtilis and the engineering steps to improve corresponding terpenoids production are systematically discussed. Furthermore, the current available genetic tools are mentioned as along with promising strategies to improve terpenoids in B. subtilis, hoping to inspire future directions in metabolic engineering of B. subtilis for further terpenoid cell factory development.
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Affiliation(s)
- H Pramastya
- University of Groningen, Groningen, The Netherlands.,Pharmaceutical Biology Research Group, School of Pharmacy, Institut Teknologi Bandung, Bandung, Indonesia
| | - Y Song
- University of Groningen, Groningen, The Netherlands
| | - E Y Elfahmi
- Pharmaceutical Biology Research Group, School of Pharmacy, Institut Teknologi Bandung, Bandung, Indonesia
| | - S Sukrasno
- Pharmaceutical Biology Research Group, School of Pharmacy, Institut Teknologi Bandung, Bandung, Indonesia
| | - W J Quax
- University of Groningen, Groningen, The Netherlands
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18
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Pramastya H, Xue D, Abdallah II, Setroikromo R, Quax WJ. High level production of amorphadiene using Bacillus subtilis as an optimized terpenoid cell factory. N Biotechnol 2020; 60:159-167. [PMID: 33148534 DOI: 10.1016/j.nbt.2020.10.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Revised: 10/15/2020] [Accepted: 10/16/2020] [Indexed: 02/09/2023]
Abstract
The anti-malarial drug artemisinin, produced naturally in the plant Artemisia annua, experiences unstable and insufficient supply as its production relies heavily on the plant source. To meet the massive demand for this compound, metabolic engineering of microbes has been studied extensively. In this study, we focus on improving the production of amorphadiene, a crucial artemisinin precursor, in Bacillus subtilis. The expression level of the plant-derived amorphadiene synthase (ADS) was upregulated by fusion with green fluorescent protein (GFP). Furthermore, a co-expression system of ADS and a synthetic operon carrying the 2-C-methyl-D-erythritol-4-phosphate (MEP) pathway genes was established. Subsequently, farnesyl pyrophosphate synthase (FPPS), a key enzyme in formation of the sesquiterpene precursor farnesyl pyrophosphate (FPP), was expressed to supply sufficient substrate for ADS. The consecutive combination of these features yielded a B. subtilis strain expressing chromosomally integrated GFP-ADS followed by FPPS and a plasmid encoded synthetic operon showing a stepwise increased production of amorphadiene. An experimental design-aided systematic medium optimization was used to maximize the production level for the most promising engineered B. subtilis strain, resulting in an amorphadiene yield of 416 ± 15 mg/L, which is 20-fold higher than that previously reported in B. subtilis and more than double the production in Escherichia coli or Saccharomyces cerevisiae on a shake flask fermentation level.
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Affiliation(s)
- Hegar Pramastya
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, 9713 AV, Groningen, the Netherlands; Pharmaceutical Biology Research Group, School of Pharmacy, Institut Teknologi Bandung, 40132, Bandung, Indonesia
| | - Dan Xue
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, 9713 AV, Groningen, the Netherlands
| | - Ingy I Abdallah
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, 9713 AV, Groningen, the Netherlands; Department of Pharmacognosy, Faculty of Pharmacy, Alexandria University, Egypt
| | - Rita Setroikromo
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, 9713 AV, Groningen, the Netherlands
| | - Wim J Quax
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, 9713 AV, Groningen, the Netherlands.
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19
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Xiao Z, Chen D, Song S, van der Vlag R, van der Wouden PE, van Merkerk R, Cool RH, Hirsch AKH, Melgert BN, Quax WJ, Poelarends GJ, Dekker FJ. 7-Hydroxycoumarins Are Affinity-Based Fluorescent Probes for Competitive Binding Studies of Macrophage Migration Inhibitory Factor. J Med Chem 2020; 63:11920-11933. [PMID: 32940040 PMCID: PMC7586407 DOI: 10.1021/acs.jmedchem.0c01160] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
![]()
Macrophage
migration inhibitory factor (MIF) is a cytokine with
key roles in inflammation and cancer, which qualifies it as a potential
drug target. Apart from its cytokine activity, MIF also harbors enzyme
activity for keto–enol tautomerization. MIF enzymatic activity
has been used for identification of MIF binding molecules that also
interfere with its biological activity. However, MIF tautomerase activity
assays are troubled by irregularities, thus creating a need for alternative
methods. In this study, we identified a 7-hydroxycoumarin fluorophore
with high affinity for the MIF tautomerase active site (Ki = 18 ± 1 nM) that binds with concomitant quenching
of its fluorescence. This property enabled development of a novel
competition-based assay format to quantify MIF binding. We also demonstrated
that the 7-hydroxycoumarin fluorophore interfered with the MIF–CD74
interaction and inhibited proliferation of A549 cells. Thus, we provide
a high-affinity MIF binder as a novel tool to advance MIF-oriented
research.
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Affiliation(s)
- Zhangping Xiao
- Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy (GRIP), University of Groningen, Antonius Deusinglaan 1, 9713 AV Groningen, The Netherlands
| | - Deng Chen
- Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy (GRIP), University of Groningen, Antonius Deusinglaan 1, 9713 AV Groningen, The Netherlands
| | - Shanshan Song
- Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy (GRIP), University of Groningen, Antonius Deusinglaan 1, 9713 AV Groningen, The Netherlands.,Molecular Pharmacology, Groningen Research Institute of Pharmacy (GRIP), University of Groningen, Antonius Deusinglaan 1, 9713 AV Groningen, The Netherlands
| | - Ramon van der Vlag
- Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 7, 9747 AG Groningen, the Netherlands
| | - Petra E van der Wouden
- Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy (GRIP), University of Groningen, Antonius Deusinglaan 1, 9713 AV Groningen, The Netherlands
| | - Ronald van Merkerk
- Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy (GRIP), University of Groningen, Antonius Deusinglaan 1, 9713 AV Groningen, The Netherlands
| | - Robbert H Cool
- Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy (GRIP), University of Groningen, Antonius Deusinglaan 1, 9713 AV Groningen, The Netherlands
| | - Anna K H Hirsch
- Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 7, 9747 AG Groningen, the Netherlands.,Department of Drug Design and Optimization, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) - Helmholtz Centre for Infection Research (HZI) Campus Building E8.1, 66123 Saarbrücken, Germany.,Department of Pharmacy, Saarland University, Campus Building E8.1, 66123 Saarbrücken, Germany
| | - Barbro N Melgert
- Molecular Pharmacology, Groningen Research Institute of Pharmacy (GRIP), University of Groningen, Antonius Deusinglaan 1, 9713 AV Groningen, The Netherlands.,Groningen Research Institute of Asthma and COPD, University Medical Center Groningen, University of Groningen, Hanzeplein 1, 9713 GZ Groningen, The Netherlands
| | - Wim J Quax
- Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy (GRIP), University of Groningen, Antonius Deusinglaan 1, 9713 AV Groningen, The Netherlands
| | - Gerrit J Poelarends
- Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy (GRIP), University of Groningen, Antonius Deusinglaan 1, 9713 AV Groningen, The Netherlands
| | - Frank J Dekker
- Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy (GRIP), University of Groningen, Antonius Deusinglaan 1, 9713 AV Groningen, The Netherlands
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20
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Zhang BJ, Chen D, Dekker FJ, Quax WJ. Improving TRAIL-induced apoptosis in cancers by interfering with histone modifications. Cancer Drug Resist 2020; 3:791-803. [PMID: 35582230 PMCID: PMC8992553 DOI: 10.20517/cdr.2020.58] [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] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Revised: 08/17/2020] [Accepted: 08/19/2020] [Indexed: 11/12/2022]
Abstract
Epigenetic regulation refers to alterations to the chromatin template that collectively establish differential patterns of gene transcription. Post-translational modifications of the histones play a key role in epigenetic regulation of gene transcription. In this review, we provide an overview of recent studies on the role of histone modifications in carcinogenesis. Since tumour-selective ligands such as tumor necrosis factor-related apoptosis-inducing ligand (TRAIL) are well-considered as promising anti-tumour therapies, we summarise strategies for improving TRAIL sensitivity by inhibiting aberrant histone modifications in cancers. In this perspective we also discuss new epigenetic drug targets for enhancing TRAIL-mediated apoptosis.
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Affiliation(s)
- Bao-Jie Zhang
- University of Groningen, Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, Groningen 9713 AV, The Netherlands
| | - Deng Chen
- University of Groningen, Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, Groningen 9713 AV, The Netherlands
| | - Frank J. Dekker
- University of Groningen, Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, Groningen 9713 AV, The Netherlands
| | - Wim J. Quax
- University of Groningen, Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, Groningen 9713 AV, The Netherlands
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21
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Wójcik M, Vázquez Torres S, Quax WJ, Boersma YL. Sortase mutants with improved protein thermostability and enzymatic activity obtained by consensus design. Protein Eng Des Sel 2020; 32:555-564. [PMID: 32725168 DOI: 10.1093/protein/gzaa018] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2019] [Revised: 03/16/2020] [Accepted: 07/03/2020] [Indexed: 11/14/2022] Open
Abstract
Staphylococcus aureus sortase A (SaSrtA) is an enzyme that anchors proteins to the cell surface of Gram-positive bacteria. During the transpeptidation reaction performed by SaSrtA, proteins containing an N-terminal glycine can be covalently linked to another protein with a C-terminal LPXTG motif (X being any amino acid). Since the sortase reaction can be performed in vitro as well, it has found many applications in biotechnology. Although sortase-mediated ligation has many advantages, SaSrtA is limited by its low enzymatic activity and dependence on Ca2+. In our study, we evaluated the thermodynamic stability of the SaSrtA wild type and found the enzyme to be stable. We applied consensus analysis to further improve the enzyme's stability while at the same time enhancing the enzyme's activity. As a result, we found thermodynamically improved, more active and Ca2+-independent mutants. We envision that these new variants can be applied in conjugation reactions in low Ca2+ environments.
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Affiliation(s)
- Magdalena Wójcik
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, A. Deusinglaan 1, 9713 Groningen, The Netherlands
| | - Susana Vázquez Torres
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, A. Deusinglaan 1, 9713 Groningen, The Netherlands
| | - Wim J Quax
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, A. Deusinglaan 1, 9713 Groningen, The Netherlands
| | - Ykelien L Boersma
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, A. Deusinglaan 1, 9713 Groningen, The Netherlands
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22
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Wójcik M, Szala K, van Merkerk R, Quax WJ, Boersma YL. Engineering the specificity of Streptococcus pyogenes sortase A by loop grafting. Proteins 2020; 88:1394-1400. [PMID: 32501594 PMCID: PMC7586933 DOI: 10.1002/prot.25958] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [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: 02/04/2020] [Revised: 04/30/2020] [Accepted: 05/27/2020] [Indexed: 11/24/2022]
Abstract
Sortases are a group of enzymes displayed on the cell‐wall of Gram‐positive bacteria. They are responsible for the attachment of virulence factors onto the peptidoglycan in a transpeptidation reaction through recognition of a pentapeptide substrate. Most housekeeping sortases recognize one specific pentapeptide motif; however, Streptococcus pyogenes sortase A (SpSrtA WT) recognizes LPETG, LPETA and LPKLG motifs. Here, we examined SpSrtA's flexible substrate specificity by investigating the role of the β7/β8 loop in determining substrate specificity. We exchanged the β7/β8 loop in SpSrtA with corresponding β7/β8 loops from Staphylococcus aureus (SaSrtA WT) and Bacillus anthracis (BaSrtA WT). While the BaSrtA‐derived variant showed no enzymatic activity toward either LPETG or LPETA substrates, the activity of the SaSrtA‐derived mutant toward the LPETA substrate was completely abolished. Instead, the mutant had an improved activity toward LPETG, the preferred substrate of SaSrtA WT.
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Affiliation(s)
- Magdalena Wójcik
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, Groningen, The Netherlands
| | - Kamil Szala
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, Groningen, The Netherlands
| | - Ronald van Merkerk
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, Groningen, The Netherlands
| | - Wim J Quax
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, Groningen, The Netherlands
| | - Ykelien L Boersma
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, Groningen, The Netherlands
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23
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Setroikromo R, Zhang B, Reis CR, Mistry RH, Quax WJ. Death Receptor 5 Displayed on Extracellular Vesicles Decreases TRAIL Sensitivity of Colon Cancer Cells. Front Cell Dev Biol 2020; 8:318. [PMID: 32509779 PMCID: PMC7248226 DOI: 10.3389/fcell.2020.00318] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [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: 01/24/2020] [Accepted: 04/09/2020] [Indexed: 01/08/2023] Open
Abstract
Tumor necrosis factor–related apoptosis inducing ligand (TRAIL) is considered to be a promising antitumor drug because of its selective proapoptotic properties on tumor cells. However, the clinical application of TRAIL is until now limited because of the resistance of several cancer cells, which can occur at various levels in the TRAIL signaling pathway. The role of decoy receptors that can side-track TRAIL, thereby preventing the formation of an activated death receptor, has been extensively studied. In this study, we have focused on extracellular vesicles (EVs) that are known to play a role in cell-to-cell communication and that can be released by donor cells into the medium transferring their components to recipient cells. TRAIL-induced apoptotic signaling is triggered upon the binding of two death receptors, DR4 and DR5. Here, we found that DR5 but not DR4 is present in the conditioned medium (CM)–derived from various cancer cells. Moreover, we observed that DR5 was exposed on EVs and can act as “decoy receptor” for binding to TRAIL. This results in a strongly reduced number of apoptotic cells upon treatment with DR5-specific TRAIL variant DHER in CM. This reduction happened with EVs containing either the long or short isoform of DR5. Taken together, we demonstrated that colon rectal tumor cells can secrete DR5-coated EVs, and this can cause TRAIL resistance. This is to our knowledge a novel finding and provides new insights into understanding TRAIL sensitivity.
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Affiliation(s)
- Rita Setroikromo
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, Groningen, Netherlands
| | - Baojie Zhang
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, Groningen, Netherlands
| | - Carlos R Reis
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, Groningen, Netherlands
| | - Rima H Mistry
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, Groningen, Netherlands
| | - Wim J Quax
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, Groningen, Netherlands
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24
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Song Y, Guan Z, van Merkerk R, Pramastya H, Abdallah II, Setroikromo R, Quax WJ. Production of Squalene in Bacillus subtilis by Squalene Synthase Screening and Metabolic Engineering. J Agric Food Chem 2020; 68:4447-4455. [PMID: 32208656 PMCID: PMC7168599 DOI: 10.1021/acs.jafc.0c00375] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Squalene synthase (SQS) catalyzes the conversion of two farnesyl pyrophosphates to squalene, an important intermediate in between isoprene and valuable triterpenoids. In this study, we have constructed a novel biosynthesis pathway for squalene in Bacillus subtilis and performed metabolic engineering aiming at facilitating further exploitation and production of squalene-derived triterpenoids. Therefore, systematic studies and analysis were performed including selection of multiple SQS candidates from various organisms, comparison of expression vectors, optimization of cultivation temperatures, and examination of rate-limiting factors within the synthetic pathway. We were, for the first time, able to obtain squalene synthesis in B. subtilis. Furthermore, we achieved a 29-fold increase of squalene yield (0.26-7.5 mg/L) by expressing SQS from Bacillus megaterium and eliminating bottlenecks within the upstream methylerythritol-phosphate pathway. Moreover, our findings showed that also ispA could positively affect the production of squalene.
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Affiliation(s)
- Yafeng Song
- Department
of Chemical and Pharmaceutical Biology, Groningen Research Institute
of Pharmacy, University of Groningen, Antonius Deusinglaan 1, 9713 AV Groningen, The Netherlands
| | - Zheng Guan
- Department
of Chemical and Pharmaceutical Biology, Groningen Research Institute
of Pharmacy, University of Groningen, Antonius Deusinglaan 1, 9713 AV Groningen, The Netherlands
| | - Ronald van Merkerk
- Department
of Chemical and Pharmaceutical Biology, Groningen Research Institute
of Pharmacy, University of Groningen, Antonius Deusinglaan 1, 9713 AV Groningen, The Netherlands
| | - Hegar Pramastya
- Department
of Chemical and Pharmaceutical Biology, Groningen Research Institute
of Pharmacy, University of Groningen, Antonius Deusinglaan 1, 9713 AV Groningen, The Netherlands
- Pharmaceutical
Biology Research Group, School of Pharmacy, Institut Teknologi Bandung, 40132 Bandung, Indonesia
| | - Ingy I. Abdallah
- Department
of Chemical and Pharmaceutical Biology, Groningen Research Institute
of Pharmacy, University of Groningen, Antonius Deusinglaan 1, 9713 AV Groningen, The Netherlands
- Department
of Pharmacognosy, Faculty of Pharmacy, Alexandria
University, Alexandria 21521, Egypt
| | - Rita Setroikromo
- Department
of Chemical and Pharmaceutical Biology, Groningen Research Institute
of Pharmacy, University of Groningen, Antonius Deusinglaan 1, 9713 AV Groningen, The Netherlands
| | - Wim J. Quax
- Department
of Chemical and Pharmaceutical Biology, Groningen Research Institute
of Pharmacy, University of Groningen, Antonius Deusinglaan 1, 9713 AV Groningen, The Netherlands
- . Phone: +31 (0) 50 363 2558, (0) 50 363 8174. Fax: +31 (0) 50 363 3000
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25
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Zhang B, Chen D, Liu B, Dekker FJ, Quax WJ. A novel histone acetyltransferase inhibitor A485 improves sensitivity of non-small-cell lung carcinoma cells to TRAIL. Biochem Pharmacol 2020; 175:113914. [PMID: 32173363 DOI: 10.1016/j.bcp.2020.113914] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Accepted: 03/10/2020] [Indexed: 12/13/2022]
Abstract
Transcriptional coactivators p300 and CBP catalyze the acetylation of lysine residues in histone proteins. Upregulation of p300 and CBP has been associated with lung, colorectal and hepatocellular cancer, indicating an important role of p300 and CBP in tumorigenesis. Recently, the novel p300 and CBP-selective inhibitor A485 became available, which was shown to inhibit proliferation of 124 different cancer cell lines. Here, we found that downregulation of EP300 or CREBBP enhances apoptosis upon TRAIL stimulation in non-small-cell lung cancer (NSCLC) cells. A485 upregulates pro- and anti-apoptotic genes at the mRNA level, implying an apoptosis-modulating effect in NSCLC cells. However, A485 alone does not induce apoptosis. Interestingly, we observed that the number of apoptotic cells increases upon combined treatment with A485 and TRAIL. Therefore, A485, as a TRAIL-sensitizer, was used in combination with TRAIL in wild type of NSCLC cell lines (HCC827 and H1650) and cells with acquired erlotinib resistance (HCC827-ER and H1650-ER). Our results show that the combination of A485 and TRAIL synergistically increases cell death and inhibits long-term cell proliferation. Furthermore, this combination inhibits the growth of 3D spheroids of EGFR-TKI-resistant cells. Taken together, we demonstrate a successful combination of A485 and TRAIL in EGFR-TKI-sensitive and resistant NSCLC cells.
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Affiliation(s)
- Baojie Zhang
- University of Groningen, Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy, the Netherlands
| | - Deng Chen
- University of Groningen, Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy, the Netherlands
| | - Bin Liu
- University of Groningen, Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy, the Netherlands
| | - Frank J Dekker
- University of Groningen, Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy, the Netherlands
| | - Wim J Quax
- University of Groningen, Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy, the Netherlands.
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26
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Vogel J, Wakker-Havinga M, Setroikromo R, Quax WJ. Immobilized Acylase PvdQ Reduces Pseudomonas aeruginosa Biofilm Formation on PDMS Silicone. Front Chem 2020; 8:54. [PMID: 32117880 PMCID: PMC7012999 DOI: 10.3389/fchem.2020.00054] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [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: 08/21/2019] [Accepted: 01/17/2020] [Indexed: 11/13/2022] Open
Abstract
The bacterial biofilm plays a key role in nosocomial infections, especially those related to medical devices in sustained contact with patients. The active dispersion of bacterial cells out of biofilms acts as a reservoir for infectious diseases. The formation of such biofilms is a highly complex process, which is coordinated by many regulatory mechanisms of the pathogen including quorum sensing (QS). Many bacteria coordinate the expression of key virulence factors dependent on their population density through QS. The inhibition of this system is called quorum quenching (QQ). Thus, preventing the development of biofilms is considered a promising approach to prevent the development of hard to treat infections. Enzymatic QQ is the concept of interfering with the QS system of bacteria outside the cell. PvdQ is an acylase with an N-terminal nucleophile (Ntn-hydrolase) that is a part of the pyoverdine gene cluster (pvd). It is able to cleave irreversibly the amide bond of long chain N-acyl homoserine lactones (AHL) rendering them inactive. Long chain AHLs are the main signaling molecule in the QS system of the gram-negative pathogen Pseudomonas aeruginosa PA01, which is known for surface-associated biofilms on indwelling catheters and is also the cause of catheter-associated urinary tract infections. Furthermore, PA01 is a well characterized pathogen with respect to QS as well as QQ. In this study, we immobilized the acylase PvdQ on polydimethylsiloxane silicone (PDMS), creating a surface with quorum quenching properties. The goal is to control infections by minimizing the colonization of indwelling medical devices such as urinary catheters or intravascular catheters. The enzyme activity was confirmed by testing the degradation of the main auto-inducer that mediates QS in P. aeruginosa. In this article we report for the first time a successful immobilization of the quorum quenching acylase PvdQ on PDMS silicone. We could show that immobilized PvdQ retained its activity after the coating procedure and showed a 6-fold reduction of the auto-inducer 3-oxo-C12 in a biosensor setup. Further we report significant reduction of a P. aeruginosa PA01 biofilm on a coated PDMS surface compared to the same untreated material.
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Affiliation(s)
- Jan Vogel
- Chemical and Pharmaceutical Biology Department, University of Groningen, Groningen, Netherlands
| | - Marijke Wakker-Havinga
- Chemical and Pharmaceutical Biology Department, University of Groningen, Groningen, Netherlands
| | - Rita Setroikromo
- Chemical and Pharmaceutical Biology Department, University of Groningen, Groningen, Netherlands
| | - Wim J Quax
- Chemical and Pharmaceutical Biology Department, University of Groningen, Groningen, Netherlands
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27
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Abdallah II, Xue D, Pramastya H, van Merkerk R, Setroikromo R, Quax WJ. A regulated synthetic operon facilitates stable overexpression of multigene terpenoid pathway in Bacillus subtilis. ACTA ACUST UNITED AC 2020; 47:243-249. [DOI: 10.1007/s10295-019-02257-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Accepted: 12/14/2019] [Indexed: 01/17/2023]
Abstract
Abstract
The creation of microbial cell factories for sustainable production of natural products is important for medical and industrial applications. This requires stable expression of biosynthetic pathways in a host organism with favorable fermentation properties such as Bacillus subtilis. The aim of this study is to construct B. subtilis strains that produce valuable terpenoid compounds by overexpressing the innate methylerythritol phosphate (MEP) pathway. A synthetic operon allowing the concerted and regulated expression of multiple genes was developed. Up to 8 genes have been combined in this operon and a stably inherited plasmid-based vector was constructed resulting in a high production of C30 carotenoids. For this, two vectors were examined, one with rolling circle replication and another with theta replication. Theta-replication constructs were clearly superior in structural and segregational stability compared to rolling circle constructs. A strain overexpressing all eight genes of the MEP pathway on a theta-replicating plasmid clearly produced the highest level of carotenoids. The level of transcription for each gene in the operon was similar as RT-qPCR analysis indicated. Hence, that corresponding strain can be used as a stable cell factory for production of terpenoids. This is the first report of merging and stably expressing this large-size operon (eight genes) from a plasmid-based system in B. subtilis enabling high C30 carotenoid production.
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Affiliation(s)
- Ingy I Abdallah
- grid.4830.f 0000 0004 0407 1981 Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy University of Groningen Antonius Deusinglaan 1 9713 AV Groningen The Netherlands
| | - Dan Xue
- grid.4830.f 0000 0004 0407 1981 Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy University of Groningen Antonius Deusinglaan 1 9713 AV Groningen The Netherlands
| | - Hegar Pramastya
- grid.4830.f 0000 0004 0407 1981 Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy University of Groningen Antonius Deusinglaan 1 9713 AV Groningen The Netherlands
- grid.434933.a 0000 0004 1808 0563 Pharmaceutical Biology Research Group, School of Pharmacy Institut Teknologi Bandung 40132 Bandung Indonesia
| | - Ronald van Merkerk
- grid.4830.f 0000 0004 0407 1981 Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy University of Groningen Antonius Deusinglaan 1 9713 AV Groningen The Netherlands
| | - Rita Setroikromo
- grid.4830.f 0000 0004 0407 1981 Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy University of Groningen Antonius Deusinglaan 1 9713 AV Groningen The Netherlands
| | - Wim J Quax
- grid.4830.f 0000 0004 0407 1981 Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy University of Groningen Antonius Deusinglaan 1 9713 AV Groningen The Netherlands
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28
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Sahal G, Woerdenbag HJ, Hinrichs WLJ, Visser A, Tepper PG, Quax WJ, van der Mei HC, Bilkay IS. Antifungal and biofilm inhibitory effect of Cymbopogon citratus (lemongrass) essential oil on biofilm forming by Candida tropicalis isolates; an in vitro study. J Ethnopharmacol 2020; 246:112188. [PMID: 31470085 DOI: 10.1016/j.jep.2019.112188] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2019] [Revised: 08/08/2019] [Accepted: 08/26/2019] [Indexed: 06/10/2023]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE Cymbopogon citratus (lemongrass) essential oil has been widely used as a traditional medicine and is well known for antimicrobial properties. Therefore, it might be a potent anti-infective and biofilm inhibitive against Candida tropicalis infections. Until now, no ideal coating or cleaning method based on an essential oil has been described to prevent biofilm formation of Candida strains on silicone rubber maxillofacial prostheses, voice prostheses and medical devices susceptible to C. tropicalis infections. AIM OF THE STUDY To investigate the antifungal and biofilm inhibitory effects of Cymbopogon citratus oil. Clinical isolates of C. tropicalis biofilms on different biomaterials were used to study the inhibitory effect. MATERIALS AND METHODS The efficacy of Cymbopogon citratus, Cuminum cyminum, Citrus limon and Cinnamomum verum essential oils were compared on biofilm formation of three C. tropicalis isolates on 24 well polystyrene plates. C. citratus oil coated silicone rubber surfaces were prepared using hypromellose ointment as a vehicle. The antifungal tests to determine minimum inhibitory and minimum fungicidal concentrations were assessed by a microbroth dilution method and biofilm formation was determined by a crystal violet binding assay. RESULTS C. tropicalis strains formed more biofilm on hydrophobic materials than on hydrophilic glass. C. citratus oil showed a high antifungal effect against all C. tropicalis strains. For comparison, C. limon oil and C. cyminum oil showed minor to no killing effect against the C. tropicalis strains. C. citratus oil had the lowest minimal inhibitory concentration of all essential oils tested and inhibited biofilm formation of all C. tropicalis strains. C. citratus oil coating on silicone rubber resulted in a 45-76% reduction in biofilm formation of all C. tropicalis strains. CONCLUSION Cymbopogon citratus oil has good potential to be used as an antifungal and antibiofilm agent on silicone rubber prostheses and medical devices on which C. tropicalis biofilms pose a serious risk for skin infections and may cause a shorter lifespan of the prosthesis.
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Affiliation(s)
- Gulcan Sahal
- Hacettepe University, Faculty of Sciences, Department of Biology (Biotechnology Division) Beytepe, 06800, Ankara, Turkey.
| | - Herman J Woerdenbag
- University of Groningen, Department of Pharmaceutical Technology and Biopharmacy, Antonius Deusinglaan 1, 9713, AV, Groningen, the Netherlands.
| | - Wouter L J Hinrichs
- University of Groningen, Department of Pharmaceutical Technology and Biopharmacy, Antonius Deusinglaan 1, 9713, AV, Groningen, the Netherlands.
| | - Anita Visser
- University of Groningen, University Medical Center Groningen, Department of Oral and Maxillofacial Surgery and Maxillofacial Prosthodontics, PO Box 30.001, 9700, RB, Groningen, the Netherlands.
| | - Pieter G Tepper
- University of Groningen, Department of Chemical and Pharmaceutical Biology, Antonius Deusinglaan 1, 9713, AV, Groningen, the Netherlands.
| | - Wim J Quax
- University of Groningen, Department of Chemical and Pharmaceutical Biology, Antonius Deusinglaan 1, 9713, AV, Groningen, the Netherlands.
| | - Henny C van der Mei
- University of Groningen, University Medical Center Groningen, Department of Biomedical Engineering, Antonius Deusinglaan 1, 9713, AV, Groningen, the Netherlands.
| | - Isil Seyis Bilkay
- Hacettepe University, Faculty of Sciences, Department of Biology (Biotechnology Division) Beytepe, 06800, Ankara, Turkey.
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29
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Wibowo JP, Batista FA, van Oosterwijk N, Groves MR, Dekker FJ, Quax WJ. A novel mechanism of inhibition by phenylthiourea on PvdP, a tyrosinase synthesizing pyoverdine of Pseudomonas aeruginosa. Int J Biol Macromol 2019; 146:212-221. [PMID: 31899238 DOI: 10.1016/j.ijbiomac.2019.12.252] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Revised: 12/06/2019] [Accepted: 12/28/2019] [Indexed: 12/18/2022]
Abstract
The biosynthesis of pyoverdine, the major siderophore of Pseudomonas aeruginosa, is a well-organized process involving a discrete number of enzyme-catalyzed steps. The final step of this process involves the PvdP tyrosinase, which converts ferribactin into pyoverdine. Thus, inhibition of the PvdP tyrosinase activity provides an attractive strategy to interfere with siderophore synthesis to manage P. aeruginosa infections. Here, we report phenylthiourea as a non-competitive inhibitor of PvdP for which we solved a crystal structure in complex with PvdP. The crystal structure indicates that phenylthiourea binds to an allosteric binding site and thereby interferes with its tyrosinase activity. We further provide proofs that PvdP tyrosinase inhibition by phenylthiourea requires the C-terminal lid region. This provides opportunities to develop inhibitors that target the allosteric site, which seems to be confined to fluorescent pseudomonads, and not the tyrosinase active site. Furthermore, increases the chances to identify PvdP inhibitors that selectively interfere with siderophore synthesis.
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Affiliation(s)
- Joko P Wibowo
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, the Netherlands; Faculty of Pharmacy, University of Muhammadiyah Banjarmasin, Banjarmasin, Indonesia
| | - Fernando A Batista
- Department of Drug Design, Groningen Research Institute of Pharmacy, University of Groningen, the Netherlands
| | - Niels van Oosterwijk
- Department of Drug Design, Groningen Research Institute of Pharmacy, University of Groningen, the Netherlands
| | - Matthew R Groves
- Department of Drug Design, Groningen Research Institute of Pharmacy, University of Groningen, the Netherlands
| | - Frank J Dekker
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, the Netherlands
| | - Wim J Quax
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, the Netherlands.
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30
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Soto-Gamez A, Quax WJ, Demaria M. Regulation of Survival Networks in Senescent Cells: From Mechanisms to Interventions. J Mol Biol 2019; 431:2629-2643. [DOI: 10.1016/j.jmb.2019.05.036] [Citation(s) in RCA: 71] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Revised: 05/20/2019] [Accepted: 05/23/2019] [Indexed: 01/10/2023]
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31
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Zhao X, Palma Medina LM, Stobernack T, Glasner C, de Jong A, Utari P, Setroikromo R, Quax WJ, Otto A, Becher D, Buist G, van Dijl JM. Exoproteome Heterogeneity among Closely Related Staphylococcus aureus t437 Isolates and Possible Implications for Virulence. J Proteome Res 2019; 18:2859-2874. [PMID: 31119940 PMCID: PMC6617432 DOI: 10.1021/acs.jproteome.9b00179] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [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] [Indexed: 02/06/2023]
Abstract
Staphylococcus aureus with spa-type t437 has been identified as a predominant community-associated methicillin-resistant S. aureus clone from Asia, which is also encountered in Europe. Molecular typing has previously shown that t437 isolates are highly similar regardless of geographical regions or host environments. The present study was aimed at assessing to what extent this high similarity is actually reflected in the production of secreted virulence factors. We therefore profiled the extracellular proteome, representing the main reservoir of virulence factors, of 20 representative clinical isolates by mass spectrometry. The results show that these isolates can be divided into three groups and nine subgroups based on exoproteome abundance signatures. This implies that S. aureus t437 isolates show substantial exoproteome heterogeneity. Nonetheless, 30 highly conserved extracellular proteins, of which about 50% have a predicted role in pathogenesis, were dominantly identified. To approximate the virulence of the 20 investigated isolates, we employed infection models based on Galleria mellonella and HeLa cells. The results show that the grouping of clinical isolates based on their exoproteome profile can be related to virulence. We consider this outcome important as our approach provides a tool to pinpoint differences in virulence among seemingly highly similar clinical isolates of S. aureus.
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Affiliation(s)
- Xin Zhao
- University of Groningen , University Medical Center Groningen, Department of Medical Microbiology , Hanzeplein 1 , P.O. Box 30001, 9700 RB Groningen , The Netherlands
| | - Laura M Palma Medina
- University of Groningen , University Medical Center Groningen, Department of Medical Microbiology , Hanzeplein 1 , P.O. Box 30001, 9700 RB Groningen , The Netherlands
| | - Tim Stobernack
- University of Groningen , University Medical Center Groningen, Department of Medical Microbiology , Hanzeplein 1 , P.O. Box 30001, 9700 RB Groningen , The Netherlands
| | - Corinna Glasner
- University of Groningen , University Medical Center Groningen, Department of Medical Microbiology , Hanzeplein 1 , P.O. Box 30001, 9700 RB Groningen , The Netherlands
| | - Anne de Jong
- University of Groningen , Groningen Biomolecular Sciences and Biotechnology Institute, Department of Molecular Genetics , 9747 AG Groningen , The Netherlands
| | - Putri Utari
- University of Groningen , Groningen Research Institute of Pharmacy, Department of Chemical and Pharmaceutical Biology , A. Deusinglaan 1 , 9713 AV Groningen , The Netherlands
| | - Rita Setroikromo
- University of Groningen , Groningen Research Institute of Pharmacy, Department of Chemical and Pharmaceutical Biology , A. Deusinglaan 1 , 9713 AV Groningen , The Netherlands
| | - Wim J Quax
- University of Groningen , Groningen Research Institute of Pharmacy, Department of Chemical and Pharmaceutical Biology , A. Deusinglaan 1 , 9713 AV Groningen , The Netherlands
| | - Andreas Otto
- Institut für Mikrobiologie , University of Greifswald , Felix-Hausdorff-Str. 8 , 17475 Greifswald , Germany
| | - Dörte Becher
- Institut für Mikrobiologie , University of Greifswald , Felix-Hausdorff-Str. 8 , 17475 Greifswald , Germany
| | - Girbe Buist
- University of Groningen , University Medical Center Groningen, Department of Medical Microbiology , Hanzeplein 1 , P.O. Box 30001, 9700 RB Groningen , The Netherlands
| | - Jan Maarten van Dijl
- University of Groningen , University Medical Center Groningen, Department of Medical Microbiology , Hanzeplein 1 , P.O. Box 30001, 9700 RB Groningen , The Netherlands
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Wang Y, Michiels T, Setroikromo R, van Merkerk R, Cool RH, Quax WJ. Creation of RANKL mutants with low affinity for decoy receptor OPG and their potential anti-fibrosis activity. FEBS J 2019; 286:3582-3593. [PMID: 31081236 PMCID: PMC6852375 DOI: 10.1111/febs.14925] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Revised: 04/11/2019] [Accepted: 05/10/2019] [Indexed: 12/21/2022]
Abstract
Fibrosis is characterized by the progressive alteration of the tissue structure due to the excessive production of extracellular matrix (ECM). The signaling system encompassing Receptor Activator of Nuclear factor NF‐κB Ligand (RANKL)/RANK/Osteoprotegerin (OPG) was discovered to play an important role in the regulation of ECM formation and degradation in bone tissue. However, whether and how this signaling pathway plays a role in liver or pulmonary ECM degradation is unclear up to now. Interestingly, increased decoy receptor OPG levels are found in fibrotic tissues. We hypothesize that RANKL can stimulate RANK on macrophages and initiate the process of ECM degradation. This process may be inhibited by highly expressed OPG in fibrotic conditions. In this case, RANKL mutants that can bind to RANK without binding to OPG might become promising therapeutic candidates. In this study, we built a structure‐based library containing 44 RANKL mutants and found that the Q236 residue of RANKL is important for OPG binding. We show that RANKL_Q236D can activate RAW cells to initiate the process of ECM degradation and is able to escape from the obstruction by exogenous OPG. We propose that the generation of RANKL mutants with reduced affinity for OPG is a promising strategy for the exploration of new therapeutics against fibrosis.
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Affiliation(s)
- Yizhou Wang
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, The Netherlands
| | - Timo Michiels
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, The Netherlands
| | - Rita Setroikromo
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, The Netherlands
| | - Ronald van Merkerk
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, The Netherlands
| | - Robbert H Cool
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, The Netherlands
| | - Wim J Quax
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, The Netherlands
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Zhang B, Liu B, Chen D, Setroikromo R, Haisma HJ, Quax WJ. Histone Deacetylase Inhibitors Sensitize TRAIL-Induced Apoptosis in Colon Cancer Cells. Cancers (Basel) 2019; 11:cancers11050645. [PMID: 31083396 PMCID: PMC6562715 DOI: 10.3390/cancers11050645] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [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: 04/18/2019] [Revised: 05/03/2019] [Accepted: 05/08/2019] [Indexed: 01/04/2023] Open
Abstract
Tumor necrosis factor-related apoptosis-inducing ligand (TRAIL) is considered as a promising anti-cancer therapeutic. However, many cancers have been found to be or to become inherently resistant to TRAIL. A combination of epigenetic modifiers, such as histone deacetylase inhibitors (HDACi's), with TRAIL was effective to overcome TRAIL resistance in some cancers. Broad spectrum HDACi's, however, show considerable toxicity constraining clinical use. Since overexpression of class I histone deacetylase (HDAC) has been found in colon tumors relative to normal mucosa, we have focused on small spectrum HDACi's. We have now tested agonistic receptor-specific TRAIL variants rhTRAIL 4C7 and DHER in combination with several class I specific HDACi's on TRAIL-resistant colon cancer cells DLD-1 and WiDr. Our data show that TRAIL-mediated apoptosis is largely improved in WiDr cells by pre-incubation with Entinostat-a HDAC1, 2, and 3 inhibitor- and in DLD-1 cells by RGFP966-a HDAC3-specific inhibitor- or PCI34051-a HDAC8-specific inhibitor. We are the first to report that using RGFP966 or PCI34051 in combination with rhTRAIL 4C7 or DHER represents an effective cancer therapy. The intricate relation of HDACs and TRAIL-induced apoptosis was confirmed in cells by knockdown of HDAC1, 2, or 3 gene expression, which showed more early apoptotic cells upon adding rhTRAIL 4C7 or DHER. We observed that RGFP966 and PCI34051 increased DR4 expression after incubation on DLD-1 cells, while RGFP966 induced more DR5 expression on WiDr cells, indicating a different role for DR4 or DR5 in these combinations. At last, we show that combined treatment of RGFP966 with TRAIL variants (rhTRAIL 4C7/DHER) increases apoptosis on 3D tumor spheroid models.
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Affiliation(s)
- Baojie Zhang
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, Antonius Deusinglaan 1, 9713 AV Groningen, The Netherlands.
| | - Bin Liu
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, Antonius Deusinglaan 1, 9713 AV Groningen, The Netherlands.
| | - Deng Chen
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, Antonius Deusinglaan 1, 9713 AV Groningen, The Netherlands.
| | - Rita Setroikromo
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, Antonius Deusinglaan 1, 9713 AV Groningen, The Netherlands.
| | - Hidde J Haisma
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, Antonius Deusinglaan 1, 9713 AV Groningen, The Netherlands.
| | - Wim J Quax
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, Antonius Deusinglaan 1, 9713 AV Groningen, The Netherlands.
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Abdallah II, Pramastya H, van Merkerk R, Sukrasno, Quax WJ. Metabolic Engineering of Bacillus subtilis Toward Taxadiene Biosynthesis as the First Committed Step for Taxol Production. Front Microbiol 2019; 10:218. [PMID: 30842758 PMCID: PMC6391936 DOI: 10.3389/fmicb.2019.00218] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [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: 11/02/2018] [Accepted: 01/28/2019] [Indexed: 11/13/2022] Open
Abstract
Terpenoids are natural products known for their medicinal and commercial applications. Metabolic engineering of microbial hosts for the production of valuable compounds, such as artemisinin and Taxol, has gained vast interest in the last few decades. The Generally Regarded As Safe (GRAS) Bacillus subtilis 168 with its broad metabolic potential is considered one of these interesting microbial hosts. In the effort toward engineering B. subtilis as a cell factory for the production of the chemotherapeutic Taxol, we expressed the plant-derived taxadiene synthase (TXS) enzyme. TXS is responsible for the conversion of the precursor geranylgeranyl pyrophosphate (GGPP) to taxa-4,11-diene, which is the first committed intermediate in Taxol biosynthesis. Furthermore, overexpression of eight enzymes in the biosynthesis pathway was performed to increase the flux of the GGPP precursor. This was achieved by creating a synthetic operon harboring the B. subtilis genes encoding the 2-C-methyl-D-erythritol-4-phosphate (MEP) pathway (dxs, ispD, ispF, ispH, ispC, ispE, ispG) together with ispA (encoding geranyl and farnesyl pyrophosphate synthases) responsible for providing farnesyl pyrophosphate (FPP). In addition, a vector harboring the crtE gene (encoding geranylgeranyl pyrophosphate synthase, GGPPS, of Pantoea ananatis) to increase the supply of GGPP was introduced. The overexpression of the MEP pathway enzymes along with IspA and GGPPS caused an 83-fold increase in the amount of taxadiene produced compared to the strain only expressing TXS and relying on the innate pathway of B. subtilis. The total amount of taxadiene produced by that strain was 17.8 mg/l. This is the first account of the successful expression of taxadiene synthase in B. subtilis. We determined that the expression of GGPPS through the crtE gene is essential for the formation of sufficient precursor, GGPP, in B. subtilis as its innate metabolism is not efficient in producing it. Finally, the extracellular localization of taxadiene production by overexpressing the complete MEP pathway along with IspA and GGPPS presents the prospect for further engineering aiming for semisynthesis of Taxol.
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Affiliation(s)
- Ingy I Abdallah
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, Groningen, Netherlands
| | - Hegar Pramastya
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, Groningen, Netherlands.,Pharmaceutical Biology Research Group, School of Pharmacy, Institut Teknologi Bandung, Bandung, Indonesia
| | - Ronald van Merkerk
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, Groningen, Netherlands
| | - Sukrasno
- Pharmaceutical Biology Research Group, School of Pharmacy, Institut Teknologi Bandung, Bandung, Indonesia
| | - Wim J Quax
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, Groningen, Netherlands
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Zhang B, van Roosmalen IAM, Reis CR, Setroikromo R, Quax WJ. Death receptor 5 is activated by fucosylation in colon cancer cells. FEBS J 2019; 286:555-571. [PMID: 30589515 PMCID: PMC6849799 DOI: 10.1111/febs.14742] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [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: 03/15/2018] [Revised: 11/01/2018] [Accepted: 12/24/2018] [Indexed: 12/24/2022]
Abstract
The remarkable pro‐apoptotic properties of tumour necrosis factor (TNF)‐related apoptosis‐inducing ligand (TRAIL) have led to considerable interest in this protein as a potential anticancer therapeutic. However, TRAIL is largely ineffective in inducing apoptosis in certain cancer cells, and the mechanisms underlying this selectivity are unknown. In colon adenocarcinomas, posttranslational modifications including O‐ and N‐ glycosylation of death receptors were found to correlate with TRAIL‐induced apoptosis. Additionally, mRNA levels of fucosyltransferase 3 (FUT3) and 6 (FUT6) were found to be high in the TRAIL‐sensitive colon adenocarcinoma cell line COLO 205. In this study, we use agonistic receptor‐specific TRAIL variants to dissect the contribution of FUT3 and FUT6‐mediated fucosylation to TRAIL‐induced apoptosis via its two death receptors, DR4 and DR5. Triggering of apoptosis by TRAIL revealed that the low FUT3/6‐expressing cells DLD‐1 and HCT 116 are insensitive to DR5 but not to DR4‐mediated apoptosis. By contrast, efficient apoptosis is mediated via both receptors in high FUT3/6‐expressing COLO 205 cells. The reconstitution of FUT3/6 expression in DR5‐resistant cells completely restored TRAIL sensitivity via this receptor, while only marginally enhancing apoptosis via DR4 at lower TRAIL concentrations. Interestingly, we observed that induction of the salvage pathway by external administration of l‐fucose restores DR5‐mediated apoptosis in both DLD‐1 and HCT 116 cells. Finally, we show that fucosylation influences the ligand‐independent receptor association that leads to increased death inducing signalling complex (DISC) formation and caspase‐8 activation. Taken together, these results provide evidence for the differential impact of fucosylation on signalling via DR4 or DR5. These findings provide novel opportunities to enhance TRAIL sensitivity in colon adenocarcinoma cells that are highly resistant to DR5‐mediated apoptosis.
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Affiliation(s)
- Baojie Zhang
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, The Netherlands
| | - Ingrid A M van Roosmalen
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, The Netherlands
| | - Carlos R Reis
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, The Netherlands
| | - Rita Setroikromo
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, The Netherlands
| | - Wim J Quax
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, The Netherlands
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Abdallah II, van Merkerk R, Klumpenaar E, Quax WJ. Catalysis of amorpha-4,11-diene synthase unraveled and improved by mutability landscape guided engineering. Sci Rep 2018; 8:9961. [PMID: 29967474 PMCID: PMC6028579 DOI: 10.1038/s41598-018-28177-4] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [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: 03/22/2018] [Accepted: 06/13/2018] [Indexed: 01/02/2023] Open
Abstract
Amorpha-4,11-diene synthase (ADS) cyclizes the substrate farnesyl pyrophosphate to produce amorpha-4,11-diene as a major product. This is considered the first committed and rate-limiting step in the biosynthesis of the antimalarial artemisinin. Here, we utilize a reported 3D model of ADS to perform mutability landscape guided enzyme engineering. A mutant library of 258 variants along sixteen active site residues was created then screened for catalytic activity and product profile. This allowed for identification of the role of some of these residues in the mechanism. R262 constrains the released pyrophosphate group along with magnesium ions. The aromatic residues (W271, Y519 and F525) stabilize the intermediate carbocations while T296, G400, G439 and L515 help with the 1,6- and 1,10-ring closures. Finally, W271 is suggested to act as active site base along with T399, which ensures regioselective deprotonation. The mutability landscape also helped determine variants with improved catalytic activity. H448A showed ~4 fold increase in catalytic efficiency and the double mutation T399S/H448A improved kcat by 5 times. This variant can be used to enhance amorphadiene production and in turn artemisinin biosynthesis. Our findings provide the basis for the first step in improving industrial production of artemisinin and they open up possibilities for further engineering and understanding of ADS.
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Affiliation(s)
- Ingy I Abdallah
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, 9713 AV, Groningen, The Netherlands
| | - Ronald van Merkerk
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, 9713 AV, Groningen, The Netherlands
| | - Esmée Klumpenaar
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, 9713 AV, Groningen, The Netherlands
| | - Wim J Quax
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, 9713 AV, Groningen, The Netherlands.
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Seegers CLC, Tepper PG, Setroikromo R, Quax WJ. Cytotoxic Deoxypodophyllotoxin Can Be Extracted in High Purity from Anthriscus sylvestris Roots by Supercritical Carbon Dioxide. Planta Med 2018; 84:544-550. [PMID: 29253908 DOI: 10.1055/s-0043-123938] [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] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Deoxypodophyllotoxin is present in the roots of Anthriscus sylvestris. This compound is cytotoxic on its own, but it can also be converted into podophyllotoxin, which is in high demand as a precursor for the important anticancer drugs etoposide and teniposide. In this study, deoxypodophyllotoxin is extracted from A. sylvestris roots by supercritical carbon dioxide extraction. The process is simple and scalable. The supercritical carbon dioxide method extracts 75 - 80% of the total deoxypodophyllotoxin content, which is comparable to a single extraction by traditional Soxhlet. However, less polar components are extracted. The activity of the supercritical carbon dioxide extract containing deoxypodophyllotoxin was assessed by demonstrating that the extract arrests A549 and HeLa cells in the G2/M phase of the cell cycle. We conclude that biologically active deoxypodophyllotoxin can be extracted from A. sylvestris by supercritical carbon dioxide extraction. The method is solvent free and more sustainable compared to traditional methods.
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Affiliation(s)
- Christel L C Seegers
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, Groningen, Netherlands
| | - Pieter G Tepper
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, Groningen, Netherlands
| | - Rita Setroikromo
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, Groningen, Netherlands
| | - Wim J Quax
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, Groningen, Netherlands
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Utari PD, Setroikromo R, Melgert BN, Quax WJ. PvdQ Quorum Quenching Acylase Attenuates Pseudomonas aeruginosa Virulence in a Mouse Model of Pulmonary Infection. Front Cell Infect Microbiol 2018; 8:119. [PMID: 29755959 PMCID: PMC5932173 DOI: 10.3389/fcimb.2018.00119] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2018] [Accepted: 04/03/2018] [Indexed: 01/24/2023] Open
Abstract
Pseudomonas aeruginosa is the predominant pathogen in pulmonary infections associated with cystic fibrosis. Quorum sensing (QS) systems regulate the production of virulence factors and play an important role in the establishment of successful P. aeruginosa infections. Inhibition of the QS system (termed quorum quenching) renders the bacteria avirulent thus serving as an alternative approach in the development of novel antibiotics. Quorum quenching in Gram negative bacteria can be achieved by preventing the accumulation of N-acyl homoserine lactone (AHL) signaling molecule via enzymatic degradation. Previous work by us has shown that PvdQ acylase hydrolyzes AHL signaling molecules irreversibly, thereby inhibiting QS in P. aeruginosa in vitro and in a Caenorhabditis elegans model of P. aeruginosa infection. The aim of the present study is to assess the therapeutic efficacy of intranasally instilled PvdQ acylase in a mouse model of pulmonary P. aeruginosa infection. First, we evaluated the deposition pattern of intranasally administered fluorochrome-tagged PvdQ (PvdQ-VT) in mice at different stages of pulmonary infection by in vivo imaging studies. Following intranasal instillation, PvdQ-VT could be traced in all lung lobes with 42 ± 7.5% of the delivered dose being deposited at 0 h post-bacterial-infection, and 34 ± 5.2% at 72 h post bacterial-infection. We then treated mice with PvdQ during lethal P. aeruginosa pulmonary infection and that resulted in a 5-fold reduction of lung bacterial load and a prolonged survival of the infected animals with the median survival time of 57 hin comparison to 42 h for the PBS-treated group. In a sublethal P. aeruginosa pulmonary infection, PvdQ treatment resulted in less lung inflammation as well as decrease of CXCL2 and TNF-α levels at 24 h post-bacterial-infection by 15 and 20%, respectively. In conclusion, our study has shown therapeutic efficacy of PvdQ acylase as a quorum quenching agent during P. aeruginosa infection.
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Affiliation(s)
- Putri D. Utari
- Department of Chemical and Pharmaceutical Biology, University of Groningen, Groningen, Netherlands
| | - Rita Setroikromo
- Department of Chemical and Pharmaceutical Biology, University of Groningen, Groningen, Netherlands
| | - Barbro N. Melgert
- Department of Pharmacokinetics, Toxicology and Targeting, University of Groningen, Groningen, Netherlands
| | - Wim J. Quax
- Department of Chemical and Pharmaceutical Biology, University of Groningen, Groningen, Netherlands
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Li W, Guan Z, Brisset JC, Shi Q, Lou Q, Ma Y, Suriguga S, Ying H, Sa X, Chen Z, Quax WJ, Chu X. A nonalcoholic fatty liver disease cirrhosis model in gerbil: the dynamic relationship between hepatic lipid metabolism and cirrhosis. Int J Clin Exp Pathol 2018; 11:146-157. [PMID: 31938096 PMCID: PMC6957964] [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] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Accepted: 11/21/2017] [Indexed: 06/10/2023]
Abstract
Nonalcoholic fatty liver disease (NAFLD) usually takes decades to develop into cirrhosis, which limits the longitudinal study of NAFLD. This work aims at developing a NAFLD-caused cirrhosis model in gerbil and examining the dynamic relationship between hepatic lipid metabolism and cirrhosis. We fed gerbil a high-fat and high-cholesterol diet (HFHCD) for 24 weeks, and recorded the gerbil's phenotype at 3, 6, 9, 12, 15, 18, 21, 24 weeks. The model's pathological process, lipid metabolism, oxidative stress, liver collagen deposition and presence of relevant cytokines were tested and evaluated during the full-time frame of disease onset. The gerbil model can induce non-alcoholic steatohepatitis (NASH) within 9 weeks, and can develop cirrhosis after 21 weeks induction. The model's lipids metabolism disorder is accompanied with the liver damage development. During the NAFLD progression, triglycerides (TG) and free fatty acids (FFA) have presented distinct rise and fall tendency, and the turning points are at the fibrosis stage. Besides that, the ratios of total cholesterol (CHO) to high-density lipoprotein cholesterol (HDL-C) exhibited constant growth tendency, and have a good linear relationship with hepatic stellate cells (HSC) (R2 = 0.802, P < 0.001). The gerbil NAFLD cirrhosis model has been developed and possesses positive correlation between lipids metabolism and cirrhosis. The compelling rise and fall tendency of TG and FFA indicated that the fibrosis progression can lead to impairment in lipoprotein synthesis and engender decreased TG level. CHO/HDL-C ratios can imply the fibrosis progress and be used as a blood indicator for disease prediction and prevention.
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Affiliation(s)
- Wei Li
- Laboratory Animal Center, Zhejiang UniversityHangzhou, Zhejiang, China
- Laboratory Animal Center, Zhejiang Academy of Medical SciencesHangzhou, Zhejiang, China
| | - Zheng Guan
- Department of Chemical and Pharmaceutical Biology, GUIDE, University of GroningenGroningen, The Netherlands
| | - Jean C Brisset
- Department of Radiology, New York UniversityNew York, State of New York, The United States
| | - Qiaojuan Shi
- Laboratory Animal Center, Zhejiang Academy of Medical SciencesHangzhou, Zhejiang, China
| | - Qi Lou
- Laboratory Animal Center, Zhejiang Academy of Medical SciencesHangzhou, Zhejiang, China
| | - Yue Ma
- Laboratory Animal Center, Zhejiang Academy of Medical SciencesHangzhou, Zhejiang, China
| | - Su Suriguga
- Department of Pharmaceutical Technology and Biopharmacy, GUIDE, University of GroningenGroningen, The Netherlands
| | - Huazhong Ying
- Laboratory Animal Center, Zhejiang Academy of Medical SciencesHangzhou, Zhejiang, China
| | - Xiaoying Sa
- Laboratory Animal Center, Zhejiang Academy of Medical SciencesHangzhou, Zhejiang, China
| | - Zhenwen Chen
- Department of Laboratory Animal Science, School of Basic Medical Science, Capital Medical UniversityBeijing, China
| | - Wim J Quax
- Department of Chemical and Pharmaceutical Biology, GUIDE, University of GroningenGroningen, The Netherlands
| | - Xiaofeng Chu
- Laboratory Animal Center, Zhejiang Academy of Medical SciencesHangzhou, Zhejiang, China
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Abstract
<p>Terpenoids represent the largest class of natural products with a diverse array of structures and functions. Many terpenoids have reported therapeutic properties such as antimicrobial, anti-inflammatory, immunomodulatory and chemotherapeutic properties making them of great interest in the medical field. Also, they are widely used in the flavors and fragrances industries, in addition to being a source of biofuels. Terpenoids suffer from low natural yields and complicated chemical synthesis, hence the need for a more sustainable production method. Metabolic engineering provide an excellent opportunity to construct microbial cell factories producing the desired terpenoids. The biosynthetic mevalonate and non-mevalonate pathways involved in the production of terpenoid precursors are fully characterized so exploring methods to improve their flux would be the first step in creating a successful cell factory. The complexity and diversity of terpenoid structures depends mainly on the action of the terpene synthases responsible for their synthesis. These enzymes are classified into different classes and gaining insight into their catalytic mechanism will be useful in designing approaches to improve terpenoid production. This review focuses on the biosynthesis and biodiversity of terpenoids, understanding the terpene synthase enzyme family involved in their synthesis and the engineering efforts to create microbial cell factories for terpenoid production.</p>
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Wang Y, van Assen AH, Reis CR, Setroikromo R, van Merkerk R, Boersma YL, Cool RH, Quax WJ. Novel RANKL DE-loop mutants antagonize RANK-mediated osteoclastogenesis. FEBS J 2017. [PMID: 28627025 DOI: 10.1111/febs.14142] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Yizhou Wang
- Department of Chemical and Pharmaceutical Biology; Groningen Research Institute of Pharmacy; University of Groningen; The Netherlands
| | - Aart H.G. van Assen
- Department of Chemical and Pharmaceutical Biology; Groningen Research Institute of Pharmacy; University of Groningen; The Netherlands
| | - Carlos R. Reis
- Department of Chemical and Pharmaceutical Biology; Groningen Research Institute of Pharmacy; University of Groningen; The Netherlands
| | - Rita Setroikromo
- Department of Chemical and Pharmaceutical Biology; Groningen Research Institute of Pharmacy; University of Groningen; The Netherlands
| | - Ronald van Merkerk
- Department of Chemical and Pharmaceutical Biology; Groningen Research Institute of Pharmacy; University of Groningen; The Netherlands
| | - Ykelien L. Boersma
- Department of Chemical and Pharmaceutical Biology; Groningen Research Institute of Pharmacy; University of Groningen; The Netherlands
| | - Robbert H. Cool
- Department of Chemical and Pharmaceutical Biology; Groningen Research Institute of Pharmacy; University of Groningen; The Netherlands
| | - Wim J. Quax
- Department of Chemical and Pharmaceutical Biology; Groningen Research Institute of Pharmacy; University of Groningen; The Netherlands
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Abstract
N-Acylhomoserine lactone (AHL)-acylase (also known as amidase or amidohydrolase) is a class of enzyme that belongs to the Ntn-hydrolase superfamily. As the name implies, AHL-acylases are capable of hydrolysing AHLs, the most studied signaling molecules for quorum sensing in Gram-negative bacteria. Enzymatic degradation of AHLs can be beneficial in attenuating bacterial virulence, which can be exploited as a novel approach to fight infection of human pathogens, phytopathogens or aquaculture-related contaminations. Numerous acylases from both prokaryotic and eukaryotic sources have been characterized and tested for the interference of quorum sensing-regulated functions. The existence of AHL-acylases in a multitude of organisms from various ecological niches, raises the question of what the physiological roles of AHL-acylases actually are. In this review, we attempt to bring together recent studies to extend our understanding of the biological functions of these enzymes in nature.
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Affiliation(s)
- Putri D Utari
- Chemical and Pharmaceutical Biology Department, University of GroningenGroningen, Netherlands
| | - Jan Vogel
- Chemical and Pharmaceutical Biology Department, University of GroningenGroningen, Netherlands
| | - Wim J Quax
- Chemical and Pharmaceutical Biology Department, University of GroningenGroningen, Netherlands
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43
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Arabpour M, Cool RH, Faber KN, Quax WJ, Haisma HJ. Receptor-specific TRAIL as a means to achieve targeted elimination of activated hepatic stellate cells. J Drug Target 2016; 25:360-369. [PMID: 27885847 DOI: 10.1080/1061186x.2016.1262867] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Activated hepatic stellate cells (HSCs) are known to play a central role in liver fibrosis and their elimination is a crucial step toward the resolution and reversion of liver fibrosis. Tumor necrosis factor-related apoptosis-inducing ligand (TRAIL) is a molecule that may contribute to the apoptotic removal of activated HSC through binding to its dedicated receptors. In the present study, we investigated the potential application of recombinant receptor-specific TRAIL proteins in the efficient elimination of activated HSCs. Our finding revealed differential contribution of TRAIL receptors among HSCs populations with activated hepatic stellate cells expresses more TRAIL receptors DR5. In vitro treatment of activated HSCs with DR5-specific or wild-type TRAIL variants induced a significant reduction in viability and extracellular matrix production, whereas no significant decrease in viability was associated with the treatment of cells by DR4-specific TRAIL. Our analysis indicate the successful application of the DR5 receptor-specific TRAIL variant in the targeted elimination of activated HSCs via interference with collagen production and simultaneous induction of apoptosis via activation of the caspase pathway. DR5 receptor-specific TRAIL may thus represent a new therapeutic compound for the treatment of liver fibrosis.
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Affiliation(s)
- Mohammad Arabpour
- a Mivac Development , Arvid Wallgrens backe 20 , Gothenburg , Sweden.,b Department of Chemical and Pharmaceutical Biology , University of Groningen , Groningen , the Netherlands
| | - Robbert H Cool
- b Department of Chemical and Pharmaceutical Biology , University of Groningen , Groningen , the Netherlands
| | - Klaas Nico Faber
- c Department of Gastrointestinal and Liver Diseases , University Medical Center Groningen , Groningen , the Netherlands
| | - Wim J Quax
- b Department of Chemical and Pharmaceutical Biology , University of Groningen , Groningen , the Netherlands
| | - Hidde J Haisma
- b Department of Chemical and Pharmaceutical Biology , University of Groningen , Groningen , the Netherlands
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44
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Abdallah II, Czepnik M, van Merkerk R, Quax WJ. Insights into the Three-Dimensional Structure of Amorpha-4,11-diene Synthase and Probing of Plasticity Residues. J Nat Prod 2016; 79:2455-2463. [PMID: 27673334 DOI: 10.1021/acs.jnatprod.6b00236] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Amorphadiene synthase (ADS) is known for its vital role as a key enzyme in the biosynthesis of the antimalarial drug artemisinin. Despite the vast research targeting this enzyme, an X-ray crystal structure of the enzyme has not yet been reported. In spite of the remarkable difference in product profile among various sesquiterpene synthases, they all share a common α-helical fold with many highly conserved regions especially the bivalent metal ion binding motifs. Hence, to better understand the structural basis of the mechanism of ADS, a reliable 3D homology model representing the conformation of the ADS enzyme and the position of its substrate, farnesyl diphosphate, in the active site was constructed. The model was generated using the reported crystal structure of α-bisabolol synthase mutant, an enzyme with high sequence identity with ADS, as a template. Site-directed mutagenesis was used to probe the active site residues. Seven residues were probed showing their vital role in the ADS mechanism and/or their effect on product profile. The generated variants confirmed the validity of the ADS model. This model will serve as a basis for exploring structure-function relationships of all residues in the active site to obtain further insight into the ADS mechanism.
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Affiliation(s)
- Ingy I Abdallah
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen , 9713 AV, Groningen, The Netherlands
| | - Magdalena Czepnik
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen , 9713 AV, Groningen, The Netherlands
| | - Ronald van Merkerk
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen , 9713 AV, Groningen, The Netherlands
| | - Wim J Quax
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen , 9713 AV, Groningen, The Netherlands
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45
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Wilffert D, Donzelli R, Asselman A, Hermans J, Govorukhina N, Ten Hacken NH, Quax WJ, van de Merbel NC, Bischoff R. Quantitative antibody-free LC-MS/MS analysis of sTRAIL in sputum and saliva at the sub-ng/mL level. J Chromatogr B Analyt Technol Biomed Life Sci 2016; 1032:205-210. [PMID: 27250581 DOI: 10.1016/j.jchromb.2016.04.041] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Accepted: 04/22/2016] [Indexed: 11/28/2022]
Abstract
Soluble tumor necrosis factor-related apoptosis-inducing ligand (sTRAIL) induces apoptosis via the extrinsic death receptor pathway and may be a biomarker in the pathogenesis of a broad range of diseases. To investigate the role of sTRAIL in asthma, we developed a quantitative LC-MS/MS method with a lower limit of quantitation (LLOQ) of ≈3pM in induced sputum (174pg/mL) and saliva (198pg/mL) without the use of antibodies. sTRAIL was enriched by immobilized metal affinity chromatography (IMAC) solid-phase extraction (SPE) followed by tryptic digestion and subsequent enrichment of a signature peptide by strong cation exchange (SCX) SPE. The method was validated with respect to stability, accuracy and precision using the standard addition approach and fully metabolically (15)N-labelled hrTRAIL as internal standard. Our results indicate that it is possible to quantify cytokines like sTRAIL at the pM level by LC-MS/MS without the use of antibodies, which has, to our knowledge, never been shown before.
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Affiliation(s)
- Daniel Wilffert
- Analytical Biochemistry, Department of Pharmacy, University of Groningen, Antonius Deusinglaan 1, 9713 AV Groningen, The Netherlands
| | - Riccardo Donzelli
- Department of Pathology, University of Pisa, Via Roma 55, 56126 Pisa, Italy
| | - Angela Asselman
- Analytical Biochemistry, Department of Pharmacy, University of Groningen, Antonius Deusinglaan 1, 9713 AV Groningen, The Netherlands
| | - Jos Hermans
- Analytical Biochemistry, Department of Pharmacy, University of Groningen, Antonius Deusinglaan 1, 9713 AV Groningen, The Netherlands
| | - Natalia Govorukhina
- Analytical Biochemistry, Department of Pharmacy, University of Groningen, Antonius Deusinglaan 1, 9713 AV Groningen, The Netherlands
| | - Nick H Ten Hacken
- Department of Pulmonology, University Medical Center Groningen, University of Groningen, Hanzeplein 1, 9713 GZ Groningen, The Netherlands
| | - Wim J Quax
- Pharmaceutical Biology, Department of Pharmacy, University of Groningen, Antonius Deusinglaan 1, 9713 AV Groningen, The Netherlands
| | - Nico C van de Merbel
- Analytical Biochemistry, Department of Pharmacy, University of Groningen, Antonius Deusinglaan 1, 9713 AV Groningen, The Netherlands; PRA Health Sciences, Bioanalytical Laboratory, Amerikaweg 18, 9407 TK Assen, The Netherlands
| | - Rainer Bischoff
- Analytical Biochemistry, Department of Pharmacy, University of Groningen, Antonius Deusinglaan 1, 9713 AV Groningen, The Netherlands.
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46
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van der Meer JY, Poddar H, Baas BJ, Miao Y, Rahimi M, Kunzendorf A, van Merkerk R, Tepper PG, Geertsema EM, Thunnissen AMWH, Quax WJ, Poelarends GJ. Using mutability landscapes of a promiscuous tautomerase to guide the engineering of enantioselective Michaelases. Nat Commun 2016; 7:10911. [PMID: 26952338 PMCID: PMC4786785 DOI: 10.1038/ncomms10911] [Citation(s) in RCA: 67] [Impact Index Per Article: 8.4] [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: 07/24/2015] [Accepted: 02/02/2016] [Indexed: 01/24/2023] Open
Abstract
The Michael-type addition reaction is widely used in organic synthesis for carbon–carbon bond formation. However, biocatalytic methodologies for this type of reaction are scarce, which is related to the fact that enzymes naturally catalysing carbon–carbon bond-forming Michael-type additions are rare. A promising template to develop new biocatalysts for carbon–carbon bond formation is the enzyme 4-oxalocrotonate tautomerase, which exhibits promiscuous Michael-type addition activity. Here we present mutability landscapes for the expression, tautomerase and Michael-type addition activities, and enantioselectivity of 4-oxalocrotonate tautomerase. These maps of neutral, beneficial and detrimental amino acids for each residue position and enzyme property provide detailed insight into sequence–function relationships. This offers exciting opportunities for enzyme engineering, which is illustrated by the redesign of 4-oxalocrotonate tautomerase into two enantiocomplementary ‘Michaelases'. These ‘Michaelases' catalyse the asymmetric addition of acetaldehyde to various nitroolefins, providing access to both enantiomers of γ-nitroaldehydes, which are important precursors for pharmaceutically active γ-aminobutyric acid derivatives. The Michael-type addition reaction is used for carbon-carbon bond formation; however biocatalytic methods for this reaction are rare. Here, the authors generate and exploit mutability landscapes of 4-oxalocrotonate tautomerase to direct the redesign of this promiscuous enzyme into enantio-complementary Michaelases.
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Affiliation(s)
- Jan-Ytzen van der Meer
- Department of Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, Antonius Deusinglaan 1, Groningen 9713 AV, The Netherlands
| | - Harshwardhan Poddar
- Department of Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, Antonius Deusinglaan 1, Groningen 9713 AV, The Netherlands
| | - Bert-Jan Baas
- Department of Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, Antonius Deusinglaan 1, Groningen 9713 AV, The Netherlands
| | - Yufeng Miao
- Department of Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, Antonius Deusinglaan 1, Groningen 9713 AV, The Netherlands
| | - Mehran Rahimi
- Department of Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, Antonius Deusinglaan 1, Groningen 9713 AV, The Netherlands
| | - Andreas Kunzendorf
- Department of Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, Antonius Deusinglaan 1, Groningen 9713 AV, The Netherlands
| | - Ronald van Merkerk
- Department of Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, Antonius Deusinglaan 1, Groningen 9713 AV, The Netherlands
| | - Pieter G Tepper
- Department of Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, Antonius Deusinglaan 1, Groningen 9713 AV, The Netherlands
| | - Edzard M Geertsema
- Department of Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, Antonius Deusinglaan 1, Groningen 9713 AV, The Netherlands
| | - Andy-Mark W H Thunnissen
- Department of Biophysical Chemistry, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 7, Groningen 9747 AG, The Netherlands
| | - Wim J Quax
- Department of Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, Antonius Deusinglaan 1, Groningen 9713 AV, The Netherlands
| | - Gerrit J Poelarends
- Department of Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, Antonius Deusinglaan 1, Groningen 9713 AV, The Netherlands
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Yu R, Albarenque SM, Cool RH, Quax WJ, Mohr A, Zwacka RM. DR4 specific TRAIL variants are more efficacious than wild-type TRAIL in pancreatic cancer. Cancer Biol Ther 2015; 15:1658-66. [PMID: 25482930 DOI: 10.4161/15384047.2014.972183] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
Current treatment modalities for pancreatic carcinoma afford only modest survival benefits. TRAIL, as a potent and specific inducer of apoptosis in cancer cells, would be a promising new treatment option. However, since not all pancreatic cancer cells respond to TRAIL, further improvements and optimizations are still needed. One strategy to improve the effectiveness of TRAIL-based therapies is to specifically target one of the 2 cell death inducing TRAIL-receptors, TRAIL-R1 or TRAIL-R2 to overcome resistance. To this end, we designed constructs expressing soluble TRAIL (sTRAIL) variants that were rendered specific for either TRAIL-R1 or TRAIL-R2 by amino acid changes in the TRAIL ectodomain. When we expressed these constructs, including wild-type sTRAIL (sTRAIL(wt)), TRAIL-R1 (sTRAIL(DR4)) and TRAIL-R2 (sTRAIL(DR5)) specific variants, in 293 producer cells we found all to be readily expressed and secreted into the supernatant. These supernatants were subsequently transferred onto target cancer cells and apoptosis measured. We found that the TRAIL-R1 specific variant had higher apoptosis-inducing activity in human pancreatic carcinoma Colo357 cells as well as PancTu1 cells that were additionally sensitized by targeting of XIAP. Finally, we tested TRAIL-R1 specific recombinant TRAIL protein (rTRAIL(DR4)) on Colo357 xenografts in nude mice and found them to be more efficacious than rTRAIL(wt). Our results demonstrate the benefits of synthetic biological approaches and show that TRAIL-R1 specific variants can potentially enhance the therapeutic efficacy of TRAIL-based therapies in pancreatic cancer, suggesting that they can possibly become part of individualized and tumor specific combination treatments in the future.
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Key Words
- AML, Acute myeloid leukemia
- ANOVA, Analysis of variance between groups
- Apoptosis
- BSA, Bovine Serum Albumin
- Bcl-xL, B-cell lymphoma-extra large
- CMV, Cytomegalie virus
- CuZnSOD, Copper-Zinc Superoxide Dismutase
- DMEM, Dulbecco's modified Eagle's medium
- DNA, Deoxyribonucleic acid
- DR4 specific TRAIL variant
- EGFP, Enhanced green fluorescent protein
- ELISA, Enzyme-linked immunosorbent assay
- FACS, Fluorescence-activated cell sorting
- FADD, Fas-associated protein with death domain
- FBS, Fetal bovine serum
- FIB, Fibrillin
- FLIP, FLICE-like inhibitory protein
- Furin CS, Furin cleavage site
- IFN-g, Interferon-gamma
- ILZ, Isoleucine zipper
- MSC, Mesenchymal stem cell
- NF-κB, Nuclear factor kappa-light-chain-enhancer of activated B cells
- OPG, Osteoprogerin
- PBS, Phosphate buffered saline
- PCR, Polymerase chain reaction
- RANKL, Receptor activator of nuclear factor kappa-B ligand
- RNAi, RNA interference
- RPMI 1640 medium, Roswell Park Memorial Institute 1640 medium
- SDS, Sodium dodecyl sulphate
- SDS-PAGE, SDS-Polyacrylamide gel electrophoresis
- SEM, Standard error of the mean
- TNF, Tumor necrosis factor
- TRAIL
- TRAIL receptor
- TRAIL, TNF-related apoptosis-inducing ligand
- TRAIL-R1/DR4, TRAIL-receptor 1/Death – receptor 4
- TRAIL-R2/DR5, TRAIL-receptor 2/ Death – receptor 5
- TRAIL-R3/DcR1, TRAIL-receptor 3/Decoy-receptor 1
- TRAIL-R4/DcR2, TRAIL-receptor 4/Decoy-receptor 2
- XIAP
- XIAP, X-linked Inhibitor of apoptosis protein
- pancreatic cancer
- rTRAIL, recombinant TNF-related apoptosis-inducing ligand
- sTRAIL, soluble TNF-related apoptosis-inducing ligand
- sh-sequence, short-hairpin sequence
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Affiliation(s)
- Rui Yu
- a National University of Ireland; Galway; National Centre for Biomedical Engineering Science and Apoptosis Research Centre; Molecular Therapeutics Group ; Galway , Ireland
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O'Leary L, van der Sloot AM, Reis CR, Deegan S, Ryan AE, Dhami SPS, Murillo LS, Cool RH, Correa de Sampaio P, Thompson K, Murphy G, Quax WJ, Serrano L, Samali A, Szegezdi E. Decoy receptors block TRAIL sensitivity at a supracellular level: the role of stromal cells in controlling tumour TRAIL sensitivity. Oncogene 2015; 35:1261-70. [PMID: 26050621 DOI: 10.1038/onc.2015.180] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2014] [Revised: 03/02/2015] [Accepted: 03/27/2015] [Indexed: 12/22/2022]
Abstract
Tumour necrosis factor-related apoptosis-inducing ligand (TRAIL) is a death ligand cytokine known for its cytotoxic activity against malignantly transformed cells. TRAIL induces cell death through binding to death receptors DR4 and DR5. The inhibitory decoy receptors (DcR1 and DcR2) co-expressed with death receptor 4 (DR4)/DR5 on the same cell can block the transmission of the apoptotic signal. Here, we show that DcRs also regulate TRAIL sensitivity at a supracellular level and thus represent a mechanism by which the microenvironment can diminish tumour TRAIL sensitivity. Mathematical modelling and layered or spheroid stroma-extracellular matrix-tumour cultures were used to model the tumour microenvironment. By engineering TRAIL to escape binding by DcRs, we found that DcRs do not only act in a cell-autonomous or cis-regulatory manner, but also exert trans-cellular regulation originating from stromal cells and affect tumour cells, highlighting the potent inhibitory effect of DcRs in the tumour tissue and the necessity of selective targeting of the two death-inducing TRAIL receptors to maximise efficacy.
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Affiliation(s)
- L O'Leary
- Apoptosis Research Centre, National University of Ireland, Galway, Ireland
| | - A M van der Sloot
- EMBL/CRG Systems Biology Research Unit, Centre for Genomic Regulation (CRG), Barcelona, Spain.,Institute for Research in Immunology and Cancer, University of Montreal, 2950, Chemin de Polytechnique Pavillon Marcelle-Coutu, Dock 20, Montréal, Québec, Canada
| | - C R Reis
- Department of Pharmaceutical Biology, University of Groningen, Antonius Deusinglaan 1, 9713 AV, Groningen, The Netherlands
| | - S Deegan
- Apoptosis Research Centre, National University of Ireland, Galway, Ireland
| | - A E Ryan
- Discipline of Pharmacology and Therapeutics, School of Medicine, National University of Ireland, Galway, Ireland
| | - S P S Dhami
- Apoptosis Research Centre, National University of Ireland, Galway, Ireland
| | - L S Murillo
- National Centre for Biomedical Engineering Science, National University of Ireland, Galway, Ireland
| | - R H Cool
- Department of Pharmaceutical Biology, University of Groningen, Antonius Deusinglaan 1, 9713 AV, Groningen, The Netherlands
| | - P Correa de Sampaio
- Department of Oncology, University of Cambridge, Cancer Research UK Cambridge Research Institute, Li Ka Shing Centre, Cambridge, UK
| | - K Thompson
- Centre for Microscopy and Imaging, National University of Ireland, Galway, Ireland
| | - G Murphy
- Department of Oncology, University of Cambridge, Cancer Research UK Cambridge Research Institute, Li Ka Shing Centre, Cambridge, UK
| | - W J Quax
- Department of Pharmaceutical Biology, University of Groningen, Antonius Deusinglaan 1, 9713 AV, Groningen, The Netherlands
| | - L Serrano
- EMBL/CRG Systems Biology Research Unit, Centre for Genomic Regulation (CRG), Barcelona, Spain
| | - A Samali
- Apoptosis Research Centre, National University of Ireland, Galway, Ireland
| | - E Szegezdi
- Apoptosis Research Centre, National University of Ireland, Galway, Ireland
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49
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Xue D, Abdallah II, de Haan IEM, Sibbald MJJB, Quax WJ. Enhanced C30 carotenoid production in Bacillus subtilis by systematic overexpression of MEP pathway genes. Appl Microbiol Biotechnol 2015; 99:5907-15. [PMID: 25851715 PMCID: PMC4480331 DOI: 10.1007/s00253-015-6531-3] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2015] [Revised: 02/28/2015] [Accepted: 03/07/2015] [Indexed: 12/27/2022]
Abstract
Creating novel biosynthetic pathways and modulating the synthesis of important compounds are one of the hallmarks of synthetic biology. Understanding the key parameters controlling the flux of chemicals throughout a metabolic pathway is one of the challenges ahead. Isoprenoids are the most functionally and structurally diverse group of natural products from which numerous medicines and relevant fine chemicals are derived. The well-characterized and broadly used production organism Bacillus subtilis forms an ideal background for creating and studying novel synthetic routes. In comparison to other bacteria, B. subtilis emits the volatile compound isoprene, the smallest representative of isoprenoids, in high concentrations and thus represents an interesting starting point for an isoprenoid cell factory. In this study, the effect of systematic overexpression of the genes involved in the methylerythritol phosphate (MEP) pathway on isoprenoid production in B. subtilis was investigated. B. subtilis strains harboring a plasmid containing C30 carotenoid synthetic genes, crtM and crtN, were combined with pHCMC04G plasmids carrying various synthetic operons of the MEP pathway genes. The levels of produced carotenoids, diaponeurosporene and diapolycopene, were used as indication of the role of the various enzymes on the flux of the MEP pathway. It was shown that the production of carotenoids can be increased significantly by overexpressing the MEP pathway enzymes. More broadly, the strains developed in this study can be used as a starting point for various isoprenoid cell factories.
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Affiliation(s)
- Dan Xue
- Department of Pharmaceutical Biology, GRIP, University of Groningen, Antonius Deusinglaan 1, 9713 AV Groningen, The Netherlands
| | - Ingy I. Abdallah
- Department of Pharmaceutical Biology, GRIP, University of Groningen, Antonius Deusinglaan 1, 9713 AV Groningen, The Netherlands
| | - Ilse E. M. de Haan
- Department of Pharmaceutical Biology, GRIP, University of Groningen, Antonius Deusinglaan 1, 9713 AV Groningen, The Netherlands
| | - Mark J. J. B. Sibbald
- Department of Pharmaceutical Biology, GRIP, University of Groningen, Antonius Deusinglaan 1, 9713 AV Groningen, The Netherlands
| | - Wim J. Quax
- Department of Pharmaceutical Biology, GRIP, University of Groningen, Antonius Deusinglaan 1, 9713 AV Groningen, The Netherlands
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50
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Müller JEN, Meyer F, Litsanov B, Kiefer P, Potthoff E, Heux S, Quax WJ, Wendisch VF, Brautaset T, Portais JC, Vorholt JA. Engineering Escherichia coli for methanol conversion. Metab Eng 2015; 28:190-201. [PMID: 25596507 DOI: 10.1016/j.ymben.2014.12.008] [Citation(s) in RCA: 136] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2014] [Accepted: 12/31/2014] [Indexed: 11/24/2022]
Abstract
Methylotrophic bacteria utilize methanol and other reduced one-carbon compounds as their sole source of carbon and energy. For this purpose, these bacteria evolved a number of specialized enzymes and pathways. Here, we used a synthetic biology approach to select and introduce a set of "methylotrophy genes" into Escherichia coli based on in silico considerations and flux balance analysis to enable methanol dissimilation and assimilation. We determined that the most promising approach allowing the utilization of methanol was the implementation of NAD-dependent methanol dehydrogenase and the establishment of the ribulose monophosphate cycle by expressing the genes for hexulose-6-phosphate synthase (Hps) and 6-phospho-3-hexuloisomerase (Phi). To test for the best-performing enzymes in the heterologous host, a number of enzyme candidates from different donor organisms were selected and systematically analyzed for their in vitro and in vivo activities in E. coli. Among these, Mdh2, Hps and Phi originating from Bacillus methanolicus were found to be the most effective. Labeling experiments using (13)C methanol with E. coli producing these enzymes showed up to 40% incorporation of methanol into central metabolites. The presence of the endogenous glutathione-dependent formaldehyde oxidation pathway of E. coli did not adversely affect the methanol conversion rate. Taken together, the results of this study represent a major advancement towards establishing synthetic methylotrophs by gene transfer.
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Affiliation(s)
- Jonas E N Müller
- Institute of Microbiology, ETH Zurich, Vladimir-Prelog-Weg 4, 8093 Zurich, Switzerland
| | - Fabian Meyer
- Institute of Microbiology, ETH Zurich, Vladimir-Prelog-Weg 4, 8093 Zurich, Switzerland
| | - Boris Litsanov
- Institute of Microbiology, ETH Zurich, Vladimir-Prelog-Weg 4, 8093 Zurich, Switzerland
| | - Patrick Kiefer
- Institute of Microbiology, ETH Zurich, Vladimir-Prelog-Weg 4, 8093 Zurich, Switzerland
| | - Eva Potthoff
- Institute of Microbiology, ETH Zurich, Vladimir-Prelog-Weg 4, 8093 Zurich, Switzerland
| | - Stéphanie Heux
- Université de Toulouse; INSA, UPS, INP, LISBP, 135 Avenue de Rangueil, F-31077 Toulouse, France; INRA, UMR792, Ingénierie des Systèmes Biologiques et des Procédés, F-31400 Toulouse, France; CNRS, UMR5504, F-31400 Toulouse, France
| | - Wim J Quax
- Department of Pharmaceutical Biology, University of Groningen, Groningen, The Netherlands
| | - Volker F Wendisch
- Chair of Genetics of Prokaryotes, Faculty of Biology & CeBiTec, Bielefeld University, Universitätsstr. 25, D-33615 Bielefeld, Germany
| | - Trygve Brautaset
- Department of Molecular Biology, SINTEF Materials and Chemistry, Trondheim, Norway; Department of Biotechnology, Norwegian University of Science and Technology, Trondheim, Norway
| | - Jean-Charles Portais
- Université de Toulouse; INSA, UPS, INP, LISBP, 135 Avenue de Rangueil, F-31077 Toulouse, France; INRA, UMR792, Ingénierie des Systèmes Biologiques et des Procédés, F-31400 Toulouse, France; CNRS, UMR5504, F-31400 Toulouse, France
| | - Julia A Vorholt
- Institute of Microbiology, ETH Zurich, Vladimir-Prelog-Weg 4, 8093 Zurich, Switzerland.
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