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Wang R, Nji Wandi B, Schwartz N, Hecht J, Ponomareva L, Paige K, West A, Desanti K, Nguyen J, Niemi J, Thorson JS, Shaaban KA, Metsä-Ketelä M, Nybo SE. Diverse Combinatorial Biosynthesis Strategies for C-H Functionalization of Anthracyclinones. ACS Synth Biol 2024; 13:1523-1536. [PMID: 38662967 PMCID: PMC11101304 DOI: 10.1021/acssynbio.4c00043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Revised: 04/11/2024] [Accepted: 04/16/2024] [Indexed: 05/18/2024]
Abstract
Streptomyces spp. are "nature's antibiotic factories" that produce valuable bioactive metabolites, such as the cytotoxic anthracycline polyketides. While the anthracyclines have hundreds of natural and chemically synthesized analogues, much of the chemical diversity stems from enzymatic modifications to the saccharide chains and, to a lesser extent, from alterations to the core scaffold. Previous work has resulted in the generation of a BioBricks synthetic biology toolbox in Streptomyces coelicolor M1152ΔmatAB that could produce aklavinone, 9-epi-aklavinone, auramycinone, and nogalamycinone. In this work, we extended the platform to generate oxidatively modified analogues via two crucial strategies. (i) We swapped the ketoreductase and first-ring cyclase enzymes for the aromatase cyclase from the mithramycin biosynthetic pathway in our polyketide synthase (PKS) cassettes to generate 2-hydroxylated analogues. (ii) Next, we engineered several multioxygenase cassettes to catalyze 11-hydroxylation, 1-hydroxylation, 10-hydroxylation, 10-decarboxylation, and 4-hydroxyl regioisomerization. We also developed improved plasmid vectors and S. coelicolor M1152ΔmatAB expression hosts to produce anthracyclinones. This work sets the stage for the combinatorial biosynthesis of bespoke anthracyclines using recombinant Streptomyces spp. hosts.
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Affiliation(s)
- Rongbin Wang
- Department
of Life Technologies, University of Turku, FIN-20014 Turku, Finland
| | - Benjamin Nji Wandi
- Department
of Life Technologies, University of Turku, FIN-20014 Turku, Finland
| | - Nora Schwartz
- Department
of Pharmaceutical Sciences, College of Pharmacy, Ferris State University, Big Rapids, Michigan 49307, United States
| | - Jacob Hecht
- Department
of Pharmaceutical Sciences, College of Pharmacy, Ferris State University, Big Rapids, Michigan 49307, United States
| | - Larissa Ponomareva
- Center
for Pharmaceutical Research and Innovation, Department of Pharmaceutical Sciences,
College of Pharmacy, University of Kentucky, Lexington, Kentucky 40536, United States
| | - Kendall Paige
- Department
of Pharmaceutical Sciences, College of Pharmacy, Ferris State University, Big Rapids, Michigan 49307, United States
| | - Alexis West
- Department
of Pharmaceutical Sciences, College of Pharmacy, Ferris State University, Big Rapids, Michigan 49307, United States
| | - Kathryn Desanti
- Department
of Pharmaceutical Sciences, College of Pharmacy, Ferris State University, Big Rapids, Michigan 49307, United States
| | - Jennifer Nguyen
- Department
of Pharmaceutical Sciences, College of Pharmacy, Ferris State University, Big Rapids, Michigan 49307, United States
| | - Jarmo Niemi
- Department
of Life Technologies, University of Turku, FIN-20014 Turku, Finland
| | - Jon S. Thorson
- Center
for Pharmaceutical Research and Innovation, Department of Pharmaceutical Sciences,
College of Pharmacy, University of Kentucky, Lexington, Kentucky 40536, United States
| | - Khaled A. Shaaban
- Center
for Pharmaceutical Research and Innovation, Department of Pharmaceutical Sciences,
College of Pharmacy, University of Kentucky, Lexington, Kentucky 40536, United States
| | - Mikko Metsä-Ketelä
- Department
of Life Technologies, University of Turku, FIN-20014 Turku, Finland
| | - S. Eric Nybo
- Department
of Pharmaceutical Sciences, College of Pharmacy, Ferris State University, Big Rapids, Michigan 49307, United States
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2
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Gupta S, Pal D. Detection of intrinsic transcription termination sites in bacteria: consensus from hairpin detection approaches. J Biomol Struct Dyn 2024:1-11. [PMID: 38605579 DOI: 10.1080/07391102.2024.2325107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2023] [Accepted: 02/23/2024] [Indexed: 04/13/2024]
Abstract
We compare the WebGeSTer and INtrinsic transcription TERmination hairPIN (INTERPIN) databases used for intrinsic transcription termination (ITT) site prediction in bacteria. The former deploys inverted nucleotide repeat detection for identification of RNA hairpin, while the latter a pair-potential function - the hairpin energy score evaluation being identical for both. We find INTERPIN more sensitive than WebGeSTer with about 6% and 51% additional predictions for ITTs in chromosomal and plasmid operons, respectively. INTERPIN hairpins are relatively shorter in length with ungapped stem, and even located in AT-rich segments, compared to GC-rich longer hairpins with a gapped stem in WebGeSTer. The GC%, length, and energy score from INTERPIN transcription units (TUs) are best inter-correlated while the lowest energy single hairpins from WebGeSTer, considered suitable for ITT, being the worst. Around 72% TUs from the two databases overlap, and ∼60% of all alternate ITT sites downstream of TUs overlap, of which 65% are cluster hairpins. This helps highlight hairpin features that can be used to identify termination sites in bacteria across different prediction methods. Overall, the pair-potential-function-based hairpins screened appear to be more consistent with the kinetic and thermodynamics processes of ITT known to date.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Swati Gupta
- Department of Computational and Data Sciences, Indian Institute of Science, Bengaluru, India
| | - Debnath Pal
- Department of Computational and Data Sciences, Indian Institute of Science, Bengaluru, India
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Wang R, Nguyen J, Hecht J, Schwartz N, Brown KV, Ponomareva LV, Niemczura M, van Dissel D, van Wezel GP, Thorson JS, Metsä-Ketelä M, Shaaban KA, Nybo SE. A BioBricks Metabolic Engineering Platform for the Biosynthesis of Anthracyclinones in Streptomyces coelicolor. ACS Synth Biol 2022; 11:4193-4209. [PMID: 36378506 PMCID: PMC9764417 DOI: 10.1021/acssynbio.2c00498] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Actinomycetes produce a variety of clinically indispensable molecules, such as antineoplastic anthracyclines. However, the actinomycetes are hindered in their further development as genetically engineered hosts for the synthesis of new anthracycline analogues due to their slow growth kinetics associated with their mycelial life cycle and the lack of a comprehensive genetic toolbox for combinatorial biosynthesis. In this report, we tackled both issues via the development of the BIOPOLYMER (BIOBricks POLYketide Metabolic EngineeRing) toolbox: a comprehensive synthetic biology toolbox consisting of engineered strains, promoters, vectors, and biosynthetic genes for the synthesis of anthracyclinones. An improved derivative of the production host Streptomyces coelicolor M1152 was created by deleting the matAB gene cluster that specifies extracellular poly-β-1,6-N-acetylglucosamine (PNAG). This resulted in a loss of mycelial aggregation, with improved biomass accumulation and anthracyclinone production. We then leveraged BIOPOLYMER to engineer four distinct anthracyclinone pathways, identifying optimal combinations of promoters, genes, and vectors to produce aklavinone, 9-epi-aklavinone, auramycinone, and nogalamycinone at titers between 15-20 mg/L. Optimization of nogalamycinone production strains resulted in titers of 103 mg/L. We structurally characterized six anthracyclinone products from fermentations, including new compounds 9,10-seco-7-deoxy-nogalamycinone and 4-O-β-d-glucosyl-nogalamycinone. Lastly, we tested the antiproliferative activity of the anthracyclinones in a mammalian cancer cell viability assay, in which nogalamycinone, auramycinone, and aklavinone exhibited moderate cytotoxicity against several cancer cell lines. We envision that BIOPOLYMER will serve as a foundational platform technology for the synthesis of designer anthracycline analogues.
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Affiliation(s)
- Rongbin Wang
- Department
of Life Technologies, University of Turku, FIN-20014 Turku, Finland
| | - Jennifer Nguyen
- Department
of Pharmaceutical Sciences, College of Pharmacy, Ferris State University, Big Rapids, Michigan 49307, United States
| | - Jacob Hecht
- Department
of Pharmaceutical Sciences, College of Pharmacy, Ferris State University, Big Rapids, Michigan 49307, United States
| | - Nora Schwartz
- Department
of Pharmaceutical Sciences, College of Pharmacy, Ferris State University, Big Rapids, Michigan 49307, United States
| | - Katelyn V. Brown
- Department
of Pharmaceutical Sciences, College of Pharmacy, Ferris State University, Big Rapids, Michigan 49307, United States
| | - Larissa V. Ponomareva
- §Center for Pharmaceutical
Research and Innovation, ∥Department of Pharmaceutical Sciences,
College of Pharmacy, University of Kentucky, Lexington, Kentucky 40536, United States
| | - Magdalena Niemczura
- Department
of Life Technologies, University of Turku, FIN-20014 Turku, Finland
| | - Dino van Dissel
- Institute
of Biology, Leiden University, Sylviusweg 72, 2333
BE Leiden, The Netherlands,Department
of Biotechnology and Nanomedicine, SINTEF
AS, P.O. Box 4760 Torgarden, NO-7465 Trondheim, Norway
| | - Gilles P. van Wezel
- Institute
of Biology, Leiden University, Sylviusweg 72, 2333
BE Leiden, The Netherlands
| | - Jon S. Thorson
- §Center for Pharmaceutical
Research and Innovation, ∥Department of Pharmaceutical Sciences,
College of Pharmacy, University of Kentucky, Lexington, Kentucky 40536, United States
| | - Mikko Metsä-Ketelä
- Department
of Life Technologies, University of Turku, FIN-20014 Turku, Finland,
| | - Khaled A. Shaaban
- §Center for Pharmaceutical
Research and Innovation, ∥Department of Pharmaceutical Sciences,
College of Pharmacy, University of Kentucky, Lexington, Kentucky 40536, United States,
| | - S. Eric Nybo
- Department
of Pharmaceutical Sciences, College of Pharmacy, Ferris State University, Big Rapids, Michigan 49307, United States,
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A high-resolution map of bacteriophage ϕX174 transcription. Virology 2020; 547:47-56. [DOI: 10.1016/j.virol.2020.05.008] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Revised: 05/18/2020] [Accepted: 05/19/2020] [Indexed: 12/26/2022]
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Bilyk B, Horbal L, Luzhetskyy A. Chromosomal position effect influences the heterologous expression of genes and biosynthetic gene clusters in Streptomyces albus J1074. Microb Cell Fact 2017; 16:5. [PMID: 28052753 PMCID: PMC5209838 DOI: 10.1186/s12934-016-0619-z] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2016] [Accepted: 12/20/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Efforts to construct the Streptomyces host strain with enhanced yields of heterologous product have focussed mostly on engineering of primary metabolism and/or the deletion of endogenous biosynthetic gene clusters. However, other factors, such as chromosome compactization, have been shown to have a significant influence on gene expression levels in bacteria and fungi. The expression of genes and biosynthetic gene clusters may vary significantly depending on their location within the chromosome. Little is known about the position effect in actinomycetes, which are important producers of various industrially relevant bioactive molecules. RESULTS To demonstrate an impact of the chromosomal position effect on the heterologous expression of genes and gene clusters in Streptomyces albus J1074, a transposon mutant library with randomly distributed transposon that includes a β-glucuronidase reporter gene was generated. Reporter gene expression levels have been shown to depend on the position on the chromosome. Using a combination of the transposon system and a φC31-based vector, the aranciamycin biosynthetic cluster was introduced randomly into the S. albus genome. The production levels of aranciamycin varied up to eightfold depending on the location of the gene cluster within the chromosome of S. albus J1074. One of the isolated mutant strains with an artificially introduced attachment site produced approximately 50% more aranciamycin than strains with endogenous attBs. CONCLUSIONS In this study, we demonstrate that expression of the reporter gene and aranciamycin biosynthetic cluster in Streptomyces albus J1074 varies up to eightfold depending on its position on the chromosome. The integration of the heterologous cluster into different locations on the chromosome may significantly influence the titre of the produced substance. This knowledge can be used for the more efficient engineering of Actinobacteria via the relocation of the biosynthetic gene clusters and insertion of additional copies of heterologous constructs in a suitable chromosomal position.
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Affiliation(s)
- Bohdan Bilyk
- PharmBioTec GmbH, Science Park 1, 66123, Saarbrücken, Germany.,Helmholtz-Institute for Pharmaceutical Research Saarland, Campus, Building C2.3, 66123, Saarbrücken, Germany
| | - Liliya Horbal
- Department of Pharmaceutical Biotechnology, Saarland University, 66123, Saarbrücken, Germany
| | - Andriy Luzhetskyy
- PharmBioTec GmbH, Science Park 1, 66123, Saarbrücken, Germany. .,Helmholtz-Institute for Pharmaceutical Research Saarland, Campus, Building C2.3, 66123, Saarbrücken, Germany. .,Department of Pharmaceutical Biotechnology, Saarland University, 66123, Saarbrücken, Germany.
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Suzuki H, Kunisawa T, Otsuka J. Theoretical evaluation of transcriptional pausing effect on the attenuation in trp leader sequence. Biophys J 1986; 49:425-35. [PMID: 3513858 PMCID: PMC1329482 DOI: 10.1016/s0006-3495(86)83652-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
The effect of transcriptional pausing on attenuation is investigated theoretically on the basis of the attenuation control mechanism presented by Oxender et al. (Oxender, D. L., G. Zurawski, and C. Yanofsky, 1979, Proc. Natl. Acad. Sci. USA. 76:5524-5528). An extended stochastic model including the RNA polymerase pausing in the leader region is developed to calculate the probability of relative position between the RNA polymerase transcribing the trp leader sequence and the ribosome translating the transcript. The present study results in a new rationale that the transcriptional pausing site in the leader sequence makes the attenuation control both more sensitive as an on/off switch and less sensitive to variations in the concentration of cellular metabolites not connected with the need for expressing, or not expressing, the particular operon. It is also proposed that the transcriptional pausing diminishes the dependence of attenuation control characteristics on the number of nucleotides in the leader sequence. This result may be useful for understanding the attenuation control efficiencies of other amino acid leader sequences with different lengths of nucleotides.
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Wada A, Suyama A. Local stability of DNA and RNA secondary structure and its relation to biological functions. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 1986; 47:113-57. [PMID: 2424044 DOI: 10.1016/0079-6107(86)90012-x] [Citation(s) in RCA: 128] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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Tachibana H, Ishihama A. Correlation between the rate of productive transcription initiation and the strand-melting property of Escherichia coli promoters. Nucleic Acids Res 1985; 13:9031-42. [PMID: 2417199 PMCID: PMC318969 DOI: 10.1093/nar/13.24.9031] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
"Opening potential"s of DNA segments of about ten base pairs in length were calculated for eleven promoters of Escherichia coli using the thermodynamic parameter values [Gotoh and Tagashira (1981) Biopolymers 20, 1043-1058] for the stabilities of ten kinds of nearest neighbor base pair doublets in a melting reaction. They were compared with the strength of each promoter determined experimentally with a "mixed transcription" system [Kajitani and Ishihama (1983) Nucleic Acids Res. 11, 3873-3888]. A positive correlation was found between the calculated opening potential in the -9 to +3 region (+1 denotes the nucleotide position at which the transcription starts) and the rate of open complex formation.
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Brendel V. Mapping of transcription terminators of bacteriophages phi X174 and G4 by sequence analysis. J Virol 1985; 53:340-2. [PMID: 3155555 PMCID: PMC255051 DOI: 10.1128/jvi.53.1.340-342.1985] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
An algorithm to locate transcription terminators (V. Brendel and E. N. Trifonov, Nucleic Acids Res. 12:4411-4427, 1984) was applied to the genomes of bacteriophages phi x174 and G4. The proposed sites are similarly located in phiX and G4 and fit with transcript lengths previously observed in vivo and in vitro.
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Wada A, Suyama A. Stability distribution in the phage lambda-DNA double helix: a correlation between physical and genetic structure. J Biomol Struct Dyn 1984; 2:573-91. [PMID: 6242869 DOI: 10.1080/07391102.1984.10507592] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Statistical analyses on the positional correlation of physical-stability and base-sequence distribution maps with genetic map are made for the whole DNA (48502 bases) of lambda-phage. The susceptibility to a double-helix unfolding perturbation and the fraction of the transient opening of a particular region of the double helix are adopted to define this physical stability. The principal features obtained are: A) The DNA double strand of protein coding regions is found to have homostabilizing propensity around a defined stability which is characteristic to each individual gene. B) The stability of the double helix in non-protein coding region fluctuates, on average over the whole region, more than that in protein coding region. C) Boundary regions of protein coding and non-protein coding regions are regions of high stability-fluctuation. Stability especially fluctuates at the protein-coding-region side of the boundary. Contrary to the quiet feature of the interior part of protein coding region rather noisy part exists at its edge. D) One frequently opening region coincides with the attaching site for the site specific recombination between phage and bacterial DNA. There are two possible ways to explain the noisy feature in the stability distribution in non-protein coding regions: 1) The region has been used as the locus of recombination as evolution took place. Thus DNAs which were homostabilized around a different value characteristic to each individual DNA, have been joined there many times, so that the noise has accumulated as a remnant of evolutional history; and/or 2) the base-composition homogenizing or double-helix homostabilizing mechanism does not work in unneeded region such as non-protein coding region or introns. Since corresponding characteristics have been found in our previous analyses on other viral and globin-gene DNAs, the rules mentioned above may be comprehensively extended to other DNAs.
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Affiliation(s)
- A Wada
- Department of Physics, Faculty of Science, University of Tokyo, Japan
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