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Moore V, Vermaas W. Functional consequences of modification of the photosystem I/photosystem II ratio in the cyanobacterium Synechocystis sp. PCC 6803. J Bacteriol 2024; 206:e0045423. [PMID: 38695523 PMCID: PMC11112997 DOI: 10.1128/jb.00454-23] [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: 12/27/2023] [Accepted: 03/16/2024] [Indexed: 05/24/2024] Open
Abstract
The stoichiometry of photosystem II (PSII) and photosystem I (PSI) varies between photoautotrophic organisms. The cyanobacterium Synechocystis sp. PCC 6803 maintains two- to fivefold more PSI than PSII reaction center complexes, and we sought to modify this stoichiometry by changing the promoter region of the psaAB operon. We thus generated mutants with varied psaAB expression, ranging from ~3% to almost 200% of the wild-type transcript level, but all showing a reduction in PSI levels, relative to wild type, suggesting a role of the psaAB promoter region in translational regulation. Mutants with 25%-70% of wild-type PSI levels were photoautotrophic, with whole-chain oxygen evolution rates on a per-cell basis comparable to that of wild type. In contrast, mutant strains with <10% of the wild-type level of PSI were obligate photoheterotrophs. Variable fluorescence yields of all mutants were much higher than those of wild type, indicating that the PSI content is localized differently than in wild type, with less transfer of PSII-absorbed energy to PSI. Strains with less PSI saturate at a higher light intensity, enhancing productivity at higher light intensities. This is similar to what is found in mutants with reduced antennae. With 3-(3,4-dichlorophenyl)-1,1-dimethylurea present, P700+ re-reduction kinetics in the mutants were slower than in wild type, consistent with the notion that there is less cyclic electron transport if less PSI is present. Overall, strains with a reduction in PSI content displayed surprisingly vigorous growth and linear electron transport. IMPORTANCE Consequences of reduction in photosystem I content were investigated in the cyanobacterium Synechocystis sp. PCC 6803 where photosystem I far exceeds the number of photosystem II complexes. Strains with less photosystem I displayed less cyclic electron transport, grew more slowly at lower light intensity and needed more light for saturation but were surprisingly normal in their whole-chain electron transport rates, implying that a significant fraction of photosystem I is dispensable for linear electron transport in cyanobacteria. These strains with reduced photosystem I levels may have biotechnological relevance as they grow well at higher light intensities.
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Affiliation(s)
- Vicki Moore
- School of Life Sciences and Center for Bioenergy and Photosynthesis, Arizona State University, Tempe, Arizona, USA
| | - Wim Vermaas
- School of Life Sciences and Center for Bioenergy and Photosynthesis, Arizona State University, Tempe, Arizona, USA
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2
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Santos SP, Garcés LFS, Silva FS, Santiago LF, Pinheiro CS, Alcantara-Neves NM, Pacheco LG. Engineering an optimized expression operating unit for improved recombinant protein production in Escherichia coli. Protein Expr Purif 2022; 199:106150. [DOI: 10.1016/j.pep.2022.106150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 07/26/2022] [Accepted: 07/27/2022] [Indexed: 10/31/2022]
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3
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Yu SJ, Cong L, Pan Q, Ding LL, Lei S, Cheng LY, Fang YH, Wei ZT, Liu HQ, Ran C. Whole genome sequencing and bulked segregant analysis suggest a new mechanism of amitraz resistance in the citrus red mite, Panonychus citri (Acari: Tetranychidae). PEST MANAGEMENT SCIENCE 2021; 77:5032-5048. [PMID: 34223705 DOI: 10.1002/ps.6544] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Revised: 06/17/2021] [Accepted: 07/05/2021] [Indexed: 06/13/2023]
Abstract
BACKGROUND Amitraz is a broad-spectrum insecticide/acaricide for the control of aphids, psyllids, ticks and mites. Current evidence suggests that ticks and phytophagous mites have developed strong resistance to amitraz. Previous studies have shown that multiple mechanisms are associated with amitraz resistance in ticks, but very few reports have involved Panonychus citri. We therefore used whole genome sequencing and bulked segregant analysis (BSA) to identify the mechanism underlying P. citri's resistance to amitraz. RESULTS High-quality assembly of the whole P. citri genome was completed, resulting in a genome of approximately 83.97 Mb and a contig N50 of approximately 1.81 Mb. Gene structure predictions revealed 11 577 genes, of which 10 940 genes were annotated. Trait-associated regions in the genome were mapped with bulked segregant analysis and 38 candidate SNPs were obtained, of which T752C had the strongest correlation with the resistant trait, located at the 5' untranslated region (UTR) of the β-2R adrenergic-like octopamine receptor gene. The mutation resulted in the formation of a short hairpin loop structure in mRNA and gene expression was down-regulated by more than 50% in the amitraz-resistant strain. Validation of the T752C mutation in field populations of P. citri found that the correlation between the resistance ratio and the base mutation was 94.40%. CONCLUSION Our results suggest that this 5' UTR mutation of the β-2R octopamine receptor gene, confers amitraz resistance in P. citri. This discovery provides a new explanation for the mechanism of pest resistance: base mutations in the 5' untranslated region of target gene may regulate the susceptibility of pests to pesticides.
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Affiliation(s)
- Shi-Jiang Yu
- Citrus Research Institute, Southwest University/Chinese Academy of Agricultural Sciences, National Engineering Research Center for Citrus, Chongqing, China
| | - Lin Cong
- Citrus Research Institute, Southwest University/Chinese Academy of Agricultural Sciences, National Engineering Research Center for Citrus, Chongqing, China
| | - Qi Pan
- Citrus Research Institute, Southwest University/Chinese Academy of Agricultural Sciences, National Engineering Research Center for Citrus, Chongqing, China
| | - Li-Li Ding
- Citrus Research Institute, Southwest University/Chinese Academy of Agricultural Sciences, National Engineering Research Center for Citrus, Chongqing, China
| | - Shuang Lei
- Citrus Research Institute, Southwest University/Chinese Academy of Agricultural Sciences, National Engineering Research Center for Citrus, Chongqing, China
| | - Lu-Yan Cheng
- Citrus Research Institute, Southwest University/Chinese Academy of Agricultural Sciences, National Engineering Research Center for Citrus, Chongqing, China
| | - Yun-Hong Fang
- Citrus Research Institute, Southwest University/Chinese Academy of Agricultural Sciences, National Engineering Research Center for Citrus, Chongqing, China
| | - Zhi-Tang Wei
- Citrus Research Institute, Southwest University/Chinese Academy of Agricultural Sciences, National Engineering Research Center for Citrus, Chongqing, China
| | - Hao-Qiang Liu
- Citrus Research Institute, Southwest University/Chinese Academy of Agricultural Sciences, National Engineering Research Center for Citrus, Chongqing, China
| | - Chun Ran
- Citrus Research Institute, Southwest University/Chinese Academy of Agricultural Sciences, National Engineering Research Center for Citrus, Chongqing, China
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Tietze L, Lale R. Importance of the 5' regulatory region to bacterial synthetic biology applications. Microb Biotechnol 2021; 14:2291-2315. [PMID: 34171170 PMCID: PMC8601185 DOI: 10.1111/1751-7915.13868] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 06/03/2021] [Accepted: 06/04/2021] [Indexed: 01/02/2023] Open
Abstract
The field of synthetic biology is evolving at a fast pace. It is advancing beyond single-gene alterations in single hosts to the logical design of complex circuits and the development of integrated synthetic genomes. Recent breakthroughs in deep learning, which is increasingly used in de novo assembly of DNA components with predictable effects, are also aiding the discipline. Despite advances in computing, the field is still reliant on the availability of pre-characterized DNA parts, whether natural or synthetic, to regulate gene expression in bacteria and make valuable compounds. In this review, we discuss the different bacterial synthetic biology methodologies employed in the creation of 5' regulatory regions - promoters, untranslated regions and 5'-end of coding sequences. We summarize methodologies and discuss their significance for each of the functional DNA components, and highlight the key advances made in bacterial engineering by concentrating on their flaws and strengths. We end the review by outlining the issues that the discipline may face in the near future.
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Affiliation(s)
- Lisa Tietze
- PhotoSynLabDepartment of BiotechnologyFaculty of Natural SciencesNorwegian University of Science and TechnologyTrondheimN‐7491Norway
| | - Rahmi Lale
- PhotoSynLabDepartment of BiotechnologyFaculty of Natural SciencesNorwegian University of Science and TechnologyTrondheimN‐7491Norway
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5
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Construction of an Efficient Nicotinate Dehydrogenase Expression System in Comamonas testosteroni CNB-2 with Multi-level N-Terminal Engineering. Appl Biochem Biotechnol 2020; 192:923-934. [DOI: 10.1007/s12010-020-03354-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Accepted: 05/22/2020] [Indexed: 10/23/2022]
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6
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Balzer Le S, Onsager I, Lorentzen JA, Lale R. Dual UTR-A novel 5' untranslated region design for synthetic biology applications. Synth Biol (Oxf) 2020; 5:ysaa006. [PMID: 32995550 PMCID: PMC7476403 DOI: 10.1093/synbio/ysaa006] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Revised: 04/29/2020] [Accepted: 05/29/2020] [Indexed: 01/07/2023] Open
Abstract
Bacterial 5' untranslated regions of mRNA (UTR) involve in a complex regulation of gene expression; however, the exact sequence features contributing to gene regulation are not yet fully understood. In this study, we report the design of a novel 5' UTR, dual UTR, utilizing the transcriptional and translational characteristics of 5' UTRs in a single expression cassette. The dual UTR consists of two 5' UTRs, each separately leading to either increase in transcription or translation of the reporter, that are separated by a spacer region, enabling de novo translation initiation. We rationally create dual UTRs with a wide range of expression profiles and demonstrate the functionality of the novel design concept in Escherichia coli and Pseudomonas putida using different promoter systems and coding sequences. Overall, we demonstrate the application potential of dual UTR design concept in various synthetic biology applications ranging from fine-tuning of gene expression to maximization of protein production.
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Affiliation(s)
- Simone Balzer Le
- PhotoSynLab, Department of Biotechnology, Faculty of Natural Sciences, Norwegian University of Science and Technology, N-7491, Trondheim, Norway
| | - Ingerid Onsager
- PhotoSynLab, Department of Biotechnology, Faculty of Natural Sciences, Norwegian University of Science and Technology, N-7491, Trondheim, Norway
| | - Jon Andreas Lorentzen
- PhotoSynLab, Department of Biotechnology, Faculty of Natural Sciences, Norwegian University of Science and Technology, N-7491, Trondheim, Norway
| | - Rahmi Lale
- PhotoSynLab, Department of Biotechnology, Faculty of Natural Sciences, Norwegian University of Science and Technology, N-7491, Trondheim, Norway
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The Impact of Leadered and Leaderless Gene Structures on Translation Efficiency, Transcript Stability, and Predicted Transcription Rates in Mycobacterium smegmatis. J Bacteriol 2020; 202:JB.00746-19. [PMID: 32094162 PMCID: PMC7148126 DOI: 10.1128/jb.00746-19] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Accepted: 02/19/2020] [Indexed: 12/31/2022] Open
Abstract
Regulation of gene expression is critical for Mycobacterium tuberculosis to tolerate stressors encountered during infection and for nonpathogenic mycobacteria such as Mycobacterium smegmatis to survive environmental stressors. Unlike better-studied models, mycobacteria express ∼14% of their genes as leaderless transcripts. However, the impacts of leaderless transcript structures on mRNA half-life and translation efficiency in mycobacteria have not been directly tested. For leadered transcripts, the contributions of 5' untranslated regions (UTRs) to mRNA half-life and translation efficiency are similarly unknown. In M. tuberculosis and M. smegmatis, the essential sigma factor, SigA, is encoded by a transcript with a relatively short half-life. We hypothesized that the long 5' UTR of sigA causes this instability. To test this, we constructed fluorescence reporters and measured protein abundance, mRNA abundance, and mRNA half-life and calculated relative transcript production rates. The sigA 5' UTR conferred an increased transcript production rate, shorter mRNA half-life, and decreased apparent translation rate compared to a synthetic 5' UTR commonly used in mycobacterial expression plasmids. Leaderless transcripts appeared to be translated with similar efficiency as those with the sigA 5' UTR but had lower predicted transcript production rates. A global comparison of M. tuberculosis mRNA and protein abundances failed to reveal systematic differences in protein/mRNA ratios for leadered and leaderless transcripts, suggesting that variability in translation efficiency is largely driven by factors other than leader status. Our data are also discussed in light of an alternative model that leads to different conclusions and suggests leaderless transcripts may indeed be translated less efficiently.IMPORTANCE Tuberculosis, caused by Mycobacterium tuberculosis, is a major public health problem killing 1.5 million people globally each year. During infection, M. tuberculosis must alter its gene expression patterns to adapt to the stress conditions it encounters. Understanding how M. tuberculosis regulates gene expression may provide clues for ways to interfere with the bacterium's survival. Gene expression encompasses transcription, mRNA degradation, and translation. Here, we used Mycobacterium smegmatis as a model organism to study how 5' untranslated regions affect these three facets of gene expression in multiple ways. We furthermore provide insight into the expression of leaderless mRNAs, which lack 5' untranslated regions and are unusually prevalent in mycobacteria.
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Rennig M, Mundhada H, Wordofa GG, Gerngross D, Wulff T, Worberg A, Nielsen AT, Nørholm MHH. Industrializing a Bacterial Strain for l-Serine Production through Translation Initiation Optimization. ACS Synth Biol 2019; 8:2347-2358. [PMID: 31550142 DOI: 10.1021/acssynbio.9b00169] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Turning a proof-of-concept synthetic biology design into a robust, high performing cell factory is a major time and money consuming task, which severely limits the growth of the white biotechnology sector. Here, we extend the use of tunable antibiotic resistance markers for synthetic evolution (TARSyn), a workflow for screening translation initiation region (TIR) libraries with antibiotic selection, to generic pathway engineering, and transform a proof-of-concept synbio design into a process that performs at industrially relevant levels. Using a combination of rational design and adaptive evolution, we recently engineered a high-performing bacterial strain for production of the important building block biochemical l-serine, based on two high-copy pET vectors facilitating expression of the serine biosynthetic genes serA, serC, and serB from three independent transcriptional units. Here, we prepare the bacterial strain for industrial scale up by transferring and reconfiguring the three genes into an operon encoded on a single low-copy plasmid. Not surprisingly, this initially reduces production titers considerably. We use TARSyn to screen both experimental and computational optimization designs resulting in high-performing synthetic serine operons and reach industrially relevant production levels of 50 g/L in fed-batch fermentations, the highest reported so far for serine production.
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Affiliation(s)
- Maja Rennig
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Building 220, Kemitorvet, 2800 Kgs. Lyngby, Denmark
- Mycropt IVS, 2800 Kgs. Lyngby, Denmark
| | - Hemanshu Mundhada
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Building 220, Kemitorvet, 2800 Kgs. Lyngby, Denmark
| | - Gossa G. Wordofa
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Building 220, Kemitorvet, 2800 Kgs. Lyngby, Denmark
| | - Daniel Gerngross
- Department of Biosystems Science and Engineering, ETH Zurich, 4058 Basel, Switzerland
| | - Tune Wulff
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Building 220, Kemitorvet, 2800 Kgs. Lyngby, Denmark
| | - Andreas Worberg
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Building 220, Kemitorvet, 2800 Kgs. Lyngby, Denmark
| | - Alex T. Nielsen
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Building 220, Kemitorvet, 2800 Kgs. Lyngby, Denmark
- Mycropt IVS, 2800 Kgs. Lyngby, Denmark
| | - Morten H. H. Nørholm
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Building 220, Kemitorvet, 2800 Kgs. Lyngby, Denmark
- Mycropt IVS, 2800 Kgs. Lyngby, Denmark
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9
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Nouaille S, Mondeil S, Finoux AL, Moulis C, Girbal L, Cocaign-Bousquet M. The stability of an mRNA is influenced by its concentration: a potential physical mechanism to regulate gene expression. Nucleic Acids Res 2017; 45:11711-11724. [PMID: 28977619 PMCID: PMC5714132 DOI: 10.1093/nar/gkx781] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2017] [Accepted: 08/28/2017] [Indexed: 01/19/2023] Open
Abstract
Changing mRNA stability is a major post-transcriptional way of controlling gene expression, particularly in newly encountered conditions. As the concentration of mRNA is the result of an equilibrium between transcription and degradation, it is generally assumed that at constant transcription, any change in mRNA concentration is the consequence of mRNA stabilization or destabilization. However, the literature reports many cases of opposite variations in mRNA concentration and stability in bacteria. Here, we analyzed the causal link between the concentration and stability of mRNA in two phylogenetically distant bacteria Escherichia coli and Lactococcus lactis. Using reporter mRNAs, we showed that modifying the stability of an mRNA had unpredictable effects, either higher or lower, on its concentration, whereas increasing its concentration systematically reduced stability. This inverse relationship between the concentration and stability of mRNA was generalized to native genes at the genome scale in both bacteria. Higher mRNA turnover in the case of higher concentrations appears to be a simple physical mechanism to regulate gene expression in the bacterial kingdom. The consequences for bacterial adaptation of this control of the stability of an mRNA by its concentration are discussed.
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Affiliation(s)
- Sébastien Nouaille
- LISBP, Université de Toulouse, CNRS, INRA, INSA, Toulouse, France. 135 av de Rangueil. 31077 Toulouse Cedex 4, France
| | - Sophie Mondeil
- LISBP, Université de Toulouse, CNRS, INRA, INSA, Toulouse, France. 135 av de Rangueil. 31077 Toulouse Cedex 4, France
| | - Anne-Laure Finoux
- LISBP, Université de Toulouse, CNRS, INRA, INSA, Toulouse, France. 135 av de Rangueil. 31077 Toulouse Cedex 4, France
| | - Claire Moulis
- LISBP, Université de Toulouse, CNRS, INRA, INSA, Toulouse, France. 135 av de Rangueil. 31077 Toulouse Cedex 4, France
| | - Laurence Girbal
- LISBP, Université de Toulouse, CNRS, INRA, INSA, Toulouse, France. 135 av de Rangueil. 31077 Toulouse Cedex 4, France
| | - Muriel Cocaign-Bousquet
- LISBP, Université de Toulouse, CNRS, INRA, INSA, Toulouse, France. 135 av de Rangueil. 31077 Toulouse Cedex 4, France
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10
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Gemperlein K, Hoffmann M, Huo L, Pilak P, Petzke L, Müller R, Wenzel SC. Synthetic biology approaches to establish a heterologous production system for coronatines. Metab Eng 2017; 44:213-222. [DOI: 10.1016/j.ymben.2017.09.009] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Revised: 08/19/2017] [Accepted: 09/18/2017] [Indexed: 11/28/2022]
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11
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Ojima-Kato T, Nagai S, Nakano H. N-terminal SKIK peptide tag markedly improves expression of difficult-to-express proteins in Escherichia coli and Saccharomyces cerevisiae. J Biosci Bioeng 2017; 123:540-546. [DOI: 10.1016/j.jbiosc.2016.12.004] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2016] [Revised: 11/23/2016] [Accepted: 12/06/2016] [Indexed: 11/27/2022]
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12
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Gawin A, Valla S, Brautaset T. The XylS/Pm regulator/promoter system and its use in fundamental studies of bacterial gene expression, recombinant protein production and metabolic engineering. Microb Biotechnol 2017; 10:702-718. [PMID: 28276630 PMCID: PMC5481539 DOI: 10.1111/1751-7915.12701] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2016] [Revised: 02/04/2017] [Accepted: 02/07/2017] [Indexed: 12/21/2022] Open
Abstract
The XylS/Pm regulator/promoter system originating from the Pseudomonas putida TOL plasmid pWW0 is widely used for regulated low‐ and high‐level recombinant expression of genes and gene clusters in Escherichia coli and other bacteria. Induction of this system can be graded by using different cheap benzoic acid derivatives, which enter cells by passive diffusion, operate in a dose‐dependent manner and are typically not metabolized by the host cells. Combinatorial mutagenesis and selection using the bla gene encoding β‐lactamase as a reporter have demonstrated that the Pm promoter, the DNA sequence corresponding to the 5′ untranslated end of its cognate mRNA and the xylS coding region can be modified and improved relative to various types of applications. By combining such mutant genetic elements, altered and extended expression profiles were achieved. Due to their unique properties, obtained systems serve as a genetic toolbox valuable for heterologous protein production and metabolic engineering, as well as for basic studies aiming at understanding fundamental parameters affecting bacterial gene expression. The approaches used to modify XylS/Pm should be adaptable for similar improvements also of other microbial expression systems. In this review, we summarize constructions, characteristics, refinements and applications of expression tools using the XylS/Pm system.
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Affiliation(s)
- Agnieszka Gawin
- Department of Biotechnology, Norwegian University of Science and Technology, Trondheim, Norway
| | - Svein Valla
- Department of Biotechnology, Norwegian University of Science and Technology, Trondheim, Norway
| | - Trygve Brautaset
- Department of Biotechnology, Norwegian University of Science and Technology, Trondheim, Norway
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13
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Šimčíková M, Alves CPA, Brito L, Prather KLJ, Prazeres DMF, Monteiro GA. Improvement of DNA minicircle production by optimization of the secondary structure of the 5′-UTR of ParA resolvase. Appl Microbiol Biotechnol 2016; 100:6725-6737. [DOI: 10.1007/s00253-016-7565-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2016] [Revised: 04/08/2016] [Accepted: 04/16/2016] [Indexed: 01/10/2023]
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Wörmann ME, Horien CL, Johnson E, Liu G, Aho E, Tang CM, Exley RM. Neisseria cinerea isolates can adhere to human epithelial cells by type IV pilus-independent mechanisms. MICROBIOLOGY-SGM 2016; 162:487-502. [PMID: 26813911 DOI: 10.1099/mic.0.000248] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
In pathogenic Neisseria species the type IV pili (Tfp) are of primary importance in host-pathogen interactions. Tfp mediate initial bacterial attachment to cell surfaces and formation of microcolonies via pilus-pilus interactions. Based on genome analysis, many non-pathogenic Neisseria species are predicted to express Tfp, but aside from studies on Neisseria elongata, relatively little is known about the formation and function of pili in these organisms. Here, we have analysed pilin expression and the role of Tfp in Neisseria cinerea. This non-pathogenic species shares a close taxonomic relationship to the pathogen Neisseria meningitidis and also colonizes the human oropharyngeal cavity. Through analysis of non-pathogenic Neisseria genomes we identified two genes with homology to pilE, which encodes the major pilin of N. meningitidis. We show which of the two genes is required for Tfp expression in N. cinerea and that Tfp in this species are required for DNA competence, similar to other Neisseria. However, in contrast to the meningococcus, deletion of the pilin gene did not impact the association of N. cinerea to human epithelial cells, demonstrating that N. cinerea isolates can adhere to human epithelial cells by Tfp-independent mechanisms.
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Affiliation(s)
- Mirka E Wörmann
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
| | - Corey L Horien
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
| | - Errin Johnson
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
| | - Guangyu Liu
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
| | - Ellen Aho
- Department of Biology, Concordia College, Moorhead, MN, USA
| | - Christoph M Tang
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
| | - Rachel M Exley
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
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15
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Gemperlein K, Zipf G, Bernauer HS, Müller R, Wenzel SC. Metabolic engineering of Pseudomonas putida for production of docosahexaenoic acid based on a myxobacterial PUFA synthase. Metab Eng 2016; 33:98-108. [DOI: 10.1016/j.ymben.2015.11.001] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2015] [Revised: 09/22/2015] [Accepted: 11/17/2015] [Indexed: 10/22/2022]
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16
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Bayer T, Milker S, Wiesinger T, Rudroff F, Mihovilovic MD. Designer Microorganisms for Optimized Redox Cascade Reactions - Challenges and Future Perspectives. Adv Synth Catal 2015. [DOI: 10.1002/adsc.201500202] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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17
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Courtade G, Balzer S, Forsberg Z, Vaaje-Kolstad G, Eijsink VGH, Aachmann FL. (1)H, (13)C, (15)N resonance assignment of the chitin-active lytic polysaccharide monooxygenase BlLPMO10A from Bacillus licheniformis. BIOMOLECULAR NMR ASSIGNMENTS 2015; 9:207-10. [PMID: 25204609 DOI: 10.1007/s12104-014-9575-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2014] [Accepted: 09/02/2014] [Indexed: 05/02/2023]
Abstract
The chitin-active 19.2 kDa lytic polysaccharide monooxygenase BlLPMO10A from Bacillus licheniformis has been isotopically labeled and recombinantly expressed. In this paper, we report the (1)H, (13)C, (15)N resonance assignment of BlLPMO10A.
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Affiliation(s)
- Gaston Courtade
- Department of Biotechnology, Norwegian University of Science and Technology, Sem Sælands vei 6/8, 7491, Trondheim, Norway
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Mahalik S, Sharma AK, Mukherjee KJ. Genome engineering for improved recombinant protein expression in Escherichia coli. Microb Cell Fact 2014; 13:177. [PMID: 25523647 PMCID: PMC4300154 DOI: 10.1186/s12934-014-0177-1] [Citation(s) in RCA: 72] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2014] [Accepted: 12/05/2014] [Indexed: 01/09/2023] Open
Abstract
A metabolic engineering perspective which views recombinant protein
expression as a multistep pathway allows us to move beyond vector design and
identify the downstream rate limiting steps in expression. In E.coli these are typically at the translational level
and the supply of precursors in the form of energy, amino acids and nucleotides.
Further recombinant protein production triggers a global cellular stress response
which feedback inhibits both growth and product formation. Countering this requires
a system level analysis followed by a rational host cell engineering to sustain
expression for longer time periods. Another strategy to increase protein yields
could be to divert the metabolic flux away from biomass formation and towards
recombinant protein production. This would require a growth stoppage mechanism which
does not affect the metabolic activity of the cell or the transcriptional or
translational efficiencies. Finally cells have to be designed for efficient export
to prevent buildup of proteins inside the cytoplasm and also simplify downstream
processing. The rational and the high throughput strategies that can be used for the
construction of such improved host cell platforms for recombinant protein expression
is the focus of this review.
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Affiliation(s)
- Shubhashree Mahalik
- School of Biotechnology, Jawaharlal Nehru University, New Delhi, 110067, India.
| | - Ashish K Sharma
- School of Biotechnology, Jawaharlal Nehru University, New Delhi, 110067, India.
| | - Krishna J Mukherjee
- School of Biotechnology, Jawaharlal Nehru University, New Delhi, 110067, India.
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Zwick F, Lale R, Valla S. Regulation of the expression level of transcription factor XylS reveals new functional insight into its induction mechanism at the Pm promoter. BMC Microbiol 2013; 13:262. [PMID: 24252441 PMCID: PMC4225500 DOI: 10.1186/1471-2180-13-262] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2013] [Accepted: 11/18/2013] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND XylS is the positive regulator of the inducible Pm promoter, originating from Pseudomonas putida, where the system controls a biochemical pathway involved in degradation of aromatic hydrocarbons, which also act as inducers. The XylS/Pm positive regulator/promoter system is used for recombinant gene expression and the output from Pm is known to be sensitive to the intracellular XylS concentration. RESULTS By constructing a synthetic operon consisting of xylS and luc, the gene encoding luciferase, relative XylS expression levels could be monitored indirectly at physiological concentrations. Expression of XylS from inducible promoters allowed control over a more than 800-fold range, however, the corresponding output from Pm covered only an about five-fold range. The maximum output from Pm could not be increased by introducing more copies of the promoter in the cells. Interestingly, a previously reported XylS variant (StEP-13), known to strongly stimulate expression from Pm, caused the same maximum activity from Pm as wild-type XylS at high XylS expression levels. Under uninduced conditions expression from Pm also increased as a function of XylS expression levels, and at very high concentrations the maximum activity from Pm was the same as in the presence of inducer. CONCLUSION According to our proposed model, which is in agreement with current knowledge, the regulator, XylS, can exist in three states: monomers, dimers, and aggregates. Only the dimers are active and able to induce expression from Pm. Their maximum intracellular concentration and the corresponding output from Pm are limited by the concentration-dependent conversion into inactive aggregates. Maximization of the induction ratio at Pm can be obtained by expression of XylS at the level where aggregation occurs, which might be exploited for recombinant gene expression. The results described here also indicate that there might exist variants of XylS which can exist at higher active dimer concentrations and thus lead to increased expression levels from Pm.
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Affiliation(s)
- Friederike Zwick
- Department of Biotechnology, Norwegian University of Science and Technology, Sem Sælands Vei 6/8, Trondheim N-7491, Norway.
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20
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Design and optimization of short DNA sequences that can be used as 5' fusion partners for high-level expression of heterologous genes in Escherichia coli. Appl Environ Microbiol 2013; 79:6655-64. [PMID: 23974137 DOI: 10.1128/aem.01676-13] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
The 5' terminal nucleotide sequence of a gene is often a bottleneck in recombinant protein production. The ifn-α2bS gene is poorly expressed in Escherichia coli unless a translocation signal sequence (pelB) is fused to the 5' end of the gene. A combined in silico and in vivo analysis reported here further indicates that the ifn-α2bS 5' coding sequence is suboptimal for efficient gene expression. ifn-α2bS therefore presents a suitable model gene for describing properties of 5' fusions promoting expression. We show that short DNA sequences corresponding to the 5' end of the highly expressed celB gene, whose protein product is cytosolic, can functionally replace pelB as a 5' fusion partner for efficient ifn-α2bS expression. celB fusions of various lengths (corresponding to a minimum of 8 codons) led to more than 7- and 60-fold stimulation of expression at the transcript and protein levels, respectively. Moreover, the presence of a celB-based fusion partner was found to moderately reduce the decay rate of the corresponding transcript. The 5' fusions thus appear to act by enhancing translation, and bound ribosomes may accordingly contribute to increased mRNA stability and reduced mRNA decay. However, other effects, such as altered protein stability, cannot be excluded. We also developed an experimental protocol that enabled us to identify improved variants of the celB fusion, and one of these (celBD11) could be used to additionally increase ifn-α2bS expression more than 4-fold at the protein level. Interestingly, celBD11 also stimulated greater protein production of three other medically important human genes than the wild-type celB fragment.
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High production of recombinant Norwegian salmonid alphavirus E1 and E2 proteins in Escherichia coli by fusion to secretion signal sequences and removal of hydrophobic domains. BIOTECHNOL BIOPROC E 2013. [DOI: 10.1007/s12257-013-0085-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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22
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Non-Invasive Analysis of Recombinant mRNA Stability in Escherichia coli by a Combination of Transcriptional Inducer Wash-Out and qRT-PCR. PLoS One 2013; 8:e66429. [PMID: 23840466 PMCID: PMC3686738 DOI: 10.1371/journal.pone.0066429] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2013] [Accepted: 05/04/2013] [Indexed: 01/27/2023] Open
Abstract
mRNA stability is one among many parameters that can potentially affect the level of recombinant gene expression in bacteria. Blocking of the entire prokaryotic transcription machinery by addition of rifampicin is commonly used in protocols for analysis of mRNA stability. Here we show that such treatment can be effectively replaced by a simple, non-invasive method based on removal of the relevant transcriptional inducers and that the mRNA decay can then be followed by qRT-PCR. To establish the methodology we first used the m-toluate-inducible XylS/Pm expression cassette as a model system and analyzed several examples of DNA modifications causing gene expression stimulation in Escherichia coli. The new method allowed us to clearly discriminate whether an improvement in mRNA stability contributes to observed increases in transcript amounts for each individual case. To support the experimental data a simple mathematical fitting model was developed to calculate relative decay rates. We extended the relevance of the method by demonstrating its application also for an IPTG-inducible expression cassette (LacI/Ptac) and by analyzing features of the bacteriophage T7-based expression system. The results suggest that the methodology is useful in elucidating factors controlling mRNA stability as well as other specific features of inducible expression systems. Moreover, as expression systems based on diffusible inducers are almost universally available, the concept can be most likely used to measure mRNA decay for any gene in any cell type that is heavily used in molecular biology research.
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Combinatorial mutagenesis and selection to understand and improve yeast promoters. BIOMED RESEARCH INTERNATIONAL 2013; 2013:926985. [PMID: 23841098 PMCID: PMC3690208 DOI: 10.1155/2013/926985] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/14/2013] [Revised: 05/03/2013] [Accepted: 05/08/2013] [Indexed: 11/22/2022]
Abstract
Microbial promoters are important targets both for understanding the global gene expression and developing genetic tools for heterologous expression of proteins and complex biosynthetic pathways. Previously, we have developed and used combinatorial mutagenesis methods to analyse and improve bacterial expression systems. Here, we present for the first time an analogous strategy for yeast. Our model promoter is the strong and inducible PAOX1 promoter in methylotrophic Pichia pastoris. The Zeocin resistance gene was applied as a valuable reporter for mutant PAOX1 promoter activity, and we used an episomal plasmid vector to ensure a constant reporter gene dosage in the yeast host cells. This novel design enabled direct selection for colonies of recombinant cells with altered Zeocin tolerance levels originating solely from randomly introduced point mutations in the PAOX1 promoter DNA sequence. We demonstrate that this approach can be used to select for PAOX1 promoter variants with abolished glucose repression in large mutant libraries. We also selected PAOX1 promoter variants with elevated expression level under induced conditions. The properties of the selected PAOX1 promoter variants were confirmed by expressing luciferase as an alternative reporter gene. The tools developed here should be useful for effective screening, characterization, and improvement of any yeast promoters.
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Zwick F, Lale R, Valla S. Combinatorial engineering for heterologous gene expression. Bioengineered 2013; 4:431-4. [PMID: 23644416 DOI: 10.4161/bioe.24703] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Tools for strain engineering with predictable outcome are of crucial importance for the nascent field of synthetic biology. The success of combining different DNA biological parts is often restricted by poorly understood factors deriving from the complexity of the systems. We have previously identified variants for different regulatory elements of the expression cassette XylS/Pm. When such elements are combined they act in a manner consistent with their individual behavior, as long as they affect different functions, such as transcription and translation. Interestingly, sequence context does not seem to influence the final outcome significantly. Expression of reporter gene bla could be increased up to 75 times at the protein level by combining three variants in one cassette. For other tested reporter genes similar results were obtained, except that the stimulatory effect was quantitatively less. Combination of individually characterized DNA parts thus stands as suitable method to achieve a desired phenotype.
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Affiliation(s)
- Friederike Zwick
- Department of Biotechnology; Norwegian University of Science and Technology; Trondheim, Norway
| | - Rahmi Lale
- Department of Biotechnology; Norwegian University of Science and Technology; Trondheim, Norway
| | - Svein Valla
- Department of Biotechnology; Norwegian University of Science and Technology; Trondheim, Norway
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25
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Overview of regulatory strategies and molecular elements in metabolic engineering of bacteria. Mol Biotechnol 2013; 52:300-8. [PMID: 22359157 DOI: 10.1007/s12033-012-9514-y] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
From a viewpoint of biotechnology, metabolic engineering mainly aims to change the natural status of a pathway in a microorganism towards the overproduction of certain bioproducts. The biochemical nature of a pathway implies us that changed pathway is often the collective results of altered behavior of the metabolic enzymes encoded by corresponding genes. By finely modulating the expression of these genes or the properties of the enzyme, we can gain efficient control on the pathway. In this article, we reviewed the typical methods that have been applied to regulate the expression of genes in metabolic engineering. These methods are grouped according to the operation targets in a typical gene. The transcription of a gene is controlled by an indispensable promoter. By utilizing promoters with different strengths, expected levels of expression can be easily achieved, and screening a promoter library may find suitable mutant promoters that can provide tunable expression of a gene. Auto-responsive promoter (quorum sensing (QS)-based or oxygen-inducible) simplifies the induction process by driving the expression of a gene in an automated manner. Light responsive promoter enables reversible and noninvasive control on gene activity, providing a promising method in controlling gene expression with time and space resolution in metabolic engineering involving complicated genetic circuits. Through directed evolution and/or rational design, the encoding sequences of a gene can be altered, leading to the possibly most profound changes in properties of a metabolic enzyme. Introducing an engineered riboswitch in mRNA can make it a regulatory molecule at the same time; ribosomal binding site is commonly engineered to be more attractive for a ribosome through design. Terminator of a gene will affect the stability of an mRNA, and intergenic region will influence the expression of many related genes. Improving the performance of these elements are generally the main activities in metabolic engineering.
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Balzer S, Kucharova V, Megerle J, Lale R, Brautaset T, Valla S. A comparative analysis of the properties of regulated promoter systems commonly used for recombinant gene expression in Escherichia coli. Microb Cell Fact 2013; 12:26. [PMID: 23506076 PMCID: PMC3621392 DOI: 10.1186/1475-2859-12-26] [Citation(s) in RCA: 93] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2012] [Accepted: 03/01/2013] [Indexed: 11/20/2022] Open
Abstract
Background Production of recombinant proteins in bacteria for academic and commercial purposes is a well established field; however the outcomes of process developments for specific proteins are still often unpredictable. One reason is the limited understanding of the performance of expression cassettes relative to each other due to different genetic contexts. Here we report the results of a systematic study aiming at exclusively comparing commonly used regulator/promoter systems by standardizing the designs of the replicon backbones. Results The vectors used in this study are based on either the RK2- or the pMB1- origin of replication and contain the regulator/promoter regions of XylS/Pm (wild-type), XylS/Pm ML1-17 (a Pm variant), LacI/PT7lac, LacI/Ptrc and AraC/PBAD to control expression of different proteins with various origins. Generally and not unexpected high expression levels correlate with high replicon copy number and the LacI/PT7lac system generates more transcript than all the four other cassettes. However, this transcriptional feature does not always lead to a correspondingly more efficient protein production, particularly if protein functionality is considered. In most cases the XylS/Pm ML1-17 and LacI/PT7lac systems gave rise to the highest amounts of functional protein production, and the XylS/Pm ML1-17 is the most flexible in the sense that it does not require any specific features of the host. The AraC/PBAD system is very good with respect to tightness, and a commonly used bioinformatics prediction tool (RBS calculator) suggested that it has the most translation-efficient UTR. Expression was also studied by flow cytometry in individual cells, and the results indicate that cell to cell heterogeneity is very relevant for understanding protein production at the population level. Conclusions The choice of expression system needs to be evaluated for each specific case, but we believe that the standardized vectors developed for this study can be used to more easily identify the nature of case-specific bottlenecks. By then taking into account the relevant characteristics of each expression cassette it will be easier to make the best choice with respect to the goal of achieving high levels of protein expression in functional or non-functional form.
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Affiliation(s)
- Simone Balzer
- Department of Biotechnology, NTNU, Sem Sælands vei 6, Trondheim 7491, Norway
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Combinatorial mutagenesis and selection of improved signal sequences and their application for high-level production of translocated heterologous proteins in Escherichia coli. Appl Environ Microbiol 2012; 79:559-68. [PMID: 23144128 DOI: 10.1128/aem.02407-12] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We previously designed the consensus signal peptide (CSP) and demonstrated that it can be used to strongly stimulate heterologous protein production in Escherichia coli. A comparative study using CSP and two bacterial signal sequences, pelB and ompA, showed that the effect of signal sequences on both expression level and translocation efficiency can be highly protein specific. We report here the generation of CSP mutant libraries by a combinatorial mutagenesis approach. Degenerated CSP oligonucleotides were cloned in frame with the 5' end of the bla gene, encoding the mature periplasmic β-lactamase released from its native signal sequence. This novel design allows for a direct selection of improved signal sequences that positively affect the expression level and/or translocation efficiency of β-lactamase, based on the ampicillin tolerance level of the E. coli host cells. By using this strategy, 61 different CSP mutants with up to 8-fold-increased ampicillin tolerance level and up to 5.5-fold-increased β-lactamase expression level were isolated and characterized genetically. A subset of the CSP mutants was then tested with the alternative reporter gene phoA, encoding periplasmic alkaline phosphatase (AP), resulting in an up to 8-fold-increased production level of active AP protein in E. coli. Moreover, it was demonstrated that the CSP mutants can improve the production of the medically important human interferon α2b under high-cell-density cultivations. Our results show that there is a clear potential for improving bacterial signal sequences by using combinatorial mutagenesis, and bioinformatics analyses indicated that the beneficial mutations could not be rationally predicted.
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28
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Zwick F, Lale R, Valla S. Strong stimulation of recombinant protein production in Escherichia coli by combining stimulatory control elements in an expression cassette. Microb Cell Fact 2012; 11:133. [PMID: 23031552 PMCID: PMC3526546 DOI: 10.1186/1475-2859-11-133] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2012] [Accepted: 09/22/2012] [Indexed: 11/22/2022] Open
Abstract
Background The XylS/Pm expression system has been used to produce recombinant proteins at industrial levels in Escherichia coli. Activation of transcription from the Pm promoter takes place in the presence of benzoic acid or derivatives of it. Previous mutagenesis studies resulted in identification of several variants of the expression control elements xylS (X), Pm (P) and the 5'-untranslated region (U) that individually gave rise to strongly stimulated expression. The goal of this study was to test if combination of such stimulatory mutations in the same expression vectors would lead to further increase of expression levels. Results We combined X, P and U variants that were originally identified due to their ability to strongly stimulate expression of the reporter gene bla (resistance to penicillin). Combination of optimized elements stimulated bla expression up to 75-fold (X, P and U combined) relative to the wild-type system, while accumulated transcript levels increased about 50-fold. This is much more than for the elements individually. We also tested combination of the variant elements on two other and unrelated genes, celB (encoding phosphoglucomutase) and the human growth factor gene gm-csf. Protein production from these genes is much more efficient than from bla in the wild-type system, but expression was still significantly stimulated by the combination of X, P and U variants, although not to the same extent as for bla. We also integrated a single copy of the expression cassette with each gene into the E. coli chromosome and found that the expression level from this single copy was higher for bla than for the wild-type plasmid system, while it was lower for celB and gm-csf. Conclusion Our results show that combination of stimulatory expression control elements can be used to further increase production of different proteins in E. coli. For one reporter gene (bla) this allowed for more protein production from a single gene copy integrated on the chromosome, compared to the wild-type plasmid system. The approach described here should in principle be applicable for improvement of any expression cassette.
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Affiliation(s)
- Friederike Zwick
- Department of Biotechnology, Norwegian University of Science and Technology, Sem Sælands Vei 6/8, N-7491, Trondheim, Norway
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Ceroni F, Furini S, Stefan A, Hochkoeppler A, Giordano E. A synthetic post-transcriptional controller to explore the modular design of gene circuits. ACS Synth Biol 2012; 1:163-71. [PMID: 23651154 DOI: 10.1021/sb200021s] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The assembly from modular parts is an efficient approach for creating new devices in Synthetic Biology. In the "bottom-up" designing strategy, modular parts are characterized in advance, and then mathematical modeling is used to predict the outcome of the final device. A prerequisite for bottom-up design is that the biological parts behave in a modular way when assembled together. We designed a new synthetic device for post-transcriptional regulation of gene expression and tested if the outcome of the device could be described from the features of its components. Modular parts showed unpredictable behavior when assembled in different complex circuits. This prevented a modular description of the device that was possible only under specific conditions. Our findings shed doubts into the feasibility of a pure bottom-up approach in synthetic biology, highlighting the urgency for new strategies for the rational design of synthetic devices.
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Affiliation(s)
- Francesca Ceroni
- Laboratory of Cellular and Molecular Engineering, University of Bologna, I-47521 Cesena, Italy
| | - Simone Furini
- Department of Medical Surgery and Bioengineering, University of Siena, I-53100 Siena, Italy
| | - Alessandra Stefan
- Department of Industrial Chemistry, University of Bologna, Viale Risorgimento 4, I-40136
Bologna, Italy
- CSGI, University of Firenze, Via della Lastruccia 3, I-50019
Sesto Fiorentino, Italy
| | - Alejandro Hochkoeppler
- Department of Industrial Chemistry, University of Bologna, Viale Risorgimento 4, I-40136
Bologna, Italy
- CSGI, University of Firenze, Via della Lastruccia 3, I-50019
Sesto Fiorentino, Italy
| | - Emanuele Giordano
- Laboratory of Cellular and Molecular Engineering, University of Bologna, I-47521 Cesena, Italy
- Department of Biochemistry “G. Moruzzi”, University of Bologna, I-40126 Bologna, Italy
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Exploring the 5'-UTR DNA region as a target for optimizing recombinant gene expression from the strong and inducible Pm promoter in Escherichia coli. J Biotechnol 2011; 158:224-30. [PMID: 21801767 DOI: 10.1016/j.jbiotec.2011.07.012] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2011] [Revised: 06/27/2011] [Accepted: 07/04/2011] [Indexed: 11/24/2022]
Abstract
By using the strong and inducible Pm promoter as a model, we recently reported that the β-lactamase production (encoded by bla) can be stimulated up to 20-fold in Escherichia coli by mutating the DNA region corresponding to the 5'-untranslated region of mRNA (UTR). One striking observation was the unexpected large stimulatory effect some of these UTR variants had on the bla transcript production level. We here demonstrate that such UTR variants can also be used to improve the expression level of the alternative genes celB (encoding phosphoglucomutase) and inf-α2b (encoding human cytokine interferon α2b), which both can be expressed to high levels even with the wild-type Pm UTR DNA sequence. Our data indicated some degree of context dependency between the UTR DNA and concomitant recombinant gene sequences. By constructing and using a synthetic operon, we demonstrated that UTR variants optimized for high-level expression of probably any recombinant gene can be efficiently selected from large UTR mutant libraries. The stimulation affected both the transcript production and translational level, and such modified UTR sequences therefore clearly have a significant applied potential for improvement of recombinant gene expression processes.
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Continuous control of the flow in biochemical pathways through 5' untranslated region sequence modifications in mRNA expressed from the broad-host-range promoter Pm. Appl Environ Microbiol 2011; 77:2648-55. [PMID: 21335387 DOI: 10.1128/aem.02091-10] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The inducible Pm promoter integrated into broad-host-range plasmid RK2 replicons can be fine-tuned continuously between the uninduced and maximally induced levels by varying the inducer concentrations. To lower the uninduced background level while still maintaining the inducibility for applications in, for example, metabolic engineering and synthetic (systems) biology, we report here the use of mutations in the Pm DNA region corresponding to the 5' untranslated region of mRNA (UTR). Five UTR variants obtained by doped oligonucleotide mutagenesis and selection, apparently reducing the efficiency of translation, were all found to display strongly reduced uninduced expression of three different reporter genes (encoding β-lactamase, luciferase, and phosphoglucomutase) in Escherichia coli. The ratio between induced and uninduced expression remained the same or higher compared to cells containing a corresponding plasmid with the wild-type UTR. Interestingly, the UTR variants also displayed similar effects on expression when substituted for the native UTR in another and constitutive promoter, P1 (P(antitet)), indicating a broad application potential of these UTR variants. Two of the selected variants were used to control the production of the C(50) carotenoid sarcinaxanthin in an engineered strain of E. coli that produces the precursor lycopene. Sarcinaxanthin is produced in this particular strain by expressing three Micrococcus luteus derived genes from the promoter Pm. The results indicated that UTR variants can be used to eliminate sarcinaxanthin production under uninduced conditions, whereas cells containing the corresponding plasmid with a wild-type UTR produced ca. 25% of the level observed under induced conditions.
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Vee Aune TE, Bakke I, Drabløs F, Lale R, Brautaset T, Valla S. Directed evolution of the transcription factor XylS for development of improved expression systems. Microb Biotechnol 2010; 3:38-47. [PMID: 21255304 PMCID: PMC3815945 DOI: 10.1111/j.1751-7915.2009.00126.x] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2009] [Revised: 04/29/2009] [Accepted: 05/03/2009] [Indexed: 11/28/2022] Open
Abstract
The inducible Pm promoter together with its cognate positive transcription regulator XylS has been shown to be useful for recombinant protein production under high cell density conditions. Here we report directed evolution of XylS resulting in mutant proteins with increased ability to stimulate transcription in Escherichia coli from Pm. A first round of mutagenesis using error-prone PCR on xylS was used to construct a library consisting of about 430,000 clones, and this library could be efficiently screened with respect to stimulation of expression from Pm due to a positive correlation between the level of expression of the reporter gene, bla (encoding β-lactamase), and the ampicillin tolerance of the corresponding host cells. Fourteen different amino acid substitutions in XylS were found to separately lead to up to nearly a threefold stimulation of expression under induced conditions, relative to wild type. These mutations were all located in the part corresponding to the N-terminal half of the protein. Varying combinations of the mutations resulted in further stimulation, and the best results (about 10-fold stimulation under induced conditions) were obtained by using a random shuffling procedure followed by a new round of screening. The uninduced levels of expression for the same mutants also increased, but only about four times. Through in silico 3D modelling of the N-terminal domain of XylS, it was observed that the evolved mutant proteins contained substitutions that were positioned in different parts of the predicted structure, including a β-barrel putatively responsible for effector binding and a coiled coil probably important for dimerization. The total production of the host-toxic antibody fragment scFv-phOx expressed from Pm with the evolved XylS mutant protein StEP-13 was about ninefold higher than with wild-type XylS, demonstrating that directed evolution of transcription factors can be an important new tool to achieve high-level recombinant protein production.
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Affiliation(s)
- Trond Erik Vee Aune
- Department of Biotechnology, Norwegian University of Science and Technology, 7491 Trondheim, Norway
| | - Ingrid Bakke
- Department of Biotechnology, Norwegian University of Science and Technology, 7491 Trondheim, Norway
| | - Finn Drabløs
- Department of Cancer Research and Molecular Medicine, Norwegian University of Science and Technology, 7006 Trondheim, Norway
| | - Rahmi Lale
- Department of Biotechnology, Norwegian University of Science and Technology, 7491 Trondheim, Norway
| | - Trygve Brautaset
- SINTEF Materials and Chemistry, Department of Biotechnology, SINTEF, 7465 Trondheim, Norway
| | - Svein Valla
- Department of Biotechnology, Norwegian University of Science and Technology, 7491 Trondheim, Norway
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Random mutagenesis of the PM promoter as a powerful strategy for improvement of recombinant-gene expression. Appl Environ Microbiol 2009; 75:2002-11. [PMID: 19201973 DOI: 10.1128/aem.02315-08] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The inducible Pm-xylS promoter system has proven useful for production of recombinant proteins in several gram-negative species and in high-cell-density cultivations of Escherichia coli. In this study we subjected a 24-bp region of Pm (including the -10 element) to random mutagenesis, leading to large mutant libraries in E. coli. Low-frequency-occurring Pm mutants displaying strongly increased promoter activity (up-mutants) could be efficiently identified by using beta-lactamase as a reporter. The up-mutants typically carried multiple point mutations positioned throughout the mutagenized region, combined with deletions around the transcription start site. Mutants displaying up to about a 14-fold increase in beta-lactamase expression (relative to wild-type Pm) were identified without loss of the inducible phenotype. The mutants also strongly stimulated the expression of two other reporter genes, luc (encoding firefly luciferase) and celB (encoding phosphoglucomutase), and were found to significantly improve (twofold) a previously optimized process for high-level recombinant production of the medically important granulocyte-macrophage colony-stimulating factor in E. coli under high-cell-density conditions. These results demonstrate the potential of using random mutagenesis of promoters to improve protein expression at industrial levels and indicate that targeted modifications of individual functional elements are not sufficient to obtain optimized promoter sequences.
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