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Davenport BI, Tica J, Isalan M. Reducing metabolic burden in the PACEmid evolver system by remastering high-copy phagemid vectors. ENGINEERING BIOLOGY 2022; 6:50-61. [PMID: 36969104 PMCID: PMC9996709 DOI: 10.1049/enb2.12021] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Revised: 04/07/2022] [Accepted: 04/20/2022] [Indexed: 01/12/2023] Open
Abstract
Orthogonal or non-cross-reacting transcription factors are used in synthetic biology as components of genetic circuits. Brödel et al. (2016) engineered 12 such cIλ transcription factor variants using a directed evolution 'PACEmid' system. The variants operate as dual activator/repressors and expand gene circuit construction possibilities. However, the high-copy phagemid vectors carrying the cIλ variants imposed high metabolic burden upon cells. Here, the authors 'remaster' the phagemid backbones to relieve their burden substantially, exhibited by a recovery in Escherichia coli growth. The remastered phagemids' ability to function within the PACEmid evolver system is maintained, as is the cIλ transcription factors' activity within these vectors. The low-burden phagemid versions are more suitable for use in PACEmid experiments and synthetic gene circuits; the authors have, therefore, replaced the original high-burden phagemids on the Addgene repository. The authors' work emphasises the importance of understanding metabolic burden and incorporating it into design steps in future synthetic biology ventures.
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Affiliation(s)
- Beth India Davenport
- Department of Life SciencesImperial College LondonSouth Kensington CampusLondonUK
| | - Jure Tica
- Department of Life SciencesImperial College LondonSouth Kensington CampusLondonUK
| | - Mark Isalan
- Department of Life SciencesImperial College LondonSouth Kensington CampusLondonUK
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Arpino JAJ, Hancock EJ, Anderson J, Barahona M, Stan GBV, Papachristodoulou A, Polizzi K. Tuning the dials of Synthetic Biology. MICROBIOLOGY-SGM 2013; 159:1236-1253. [PMID: 23704788 PMCID: PMC3749727 DOI: 10.1099/mic.0.067975-0] [Citation(s) in RCA: 76] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Abstract
Synthetic Biology is the ‘Engineering of Biology’ – it aims to use a forward-engineering design cycle based on specifications, modelling, analysis, experimental implementation, testing and validation to modify natural or design new, synthetic biology systems so that they behave in a predictable fashion. Motivated by the need for truly plug-and-play synthetic biological components, we present a comprehensive review of ways in which the various parts of a biological system can be modified systematically. In particular, we review the list of ‘dials’ that are available to the designer and discuss how they can be modelled, tuned and implemented. The dials are categorized according to whether they operate at the global, transcriptional, translational or post-translational level and the resolution that they operate at. We end this review with a discussion on the relative advantages and disadvantages of some dials over others.
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Affiliation(s)
- James A J Arpino
- Centre for Synthetic Biology and Innovation, Imperial College London, South Kensington Campus, London SW7 2AZ, UK.,Department of Mathematics, Imperial College London, South Kensington Campus, London SW7 2AZ, UK.,Department of Life Sciences, Imperial College London, South Kensington Campus, London SW7 2AZ, UK
| | - Edward J Hancock
- Department of Engineering Science, University of Oxford, Parks Road, Oxford OX1 3PJ, UK
| | - James Anderson
- St John's College, St Giles, Oxford OX1 3JP, UK.,Department of Engineering Science, University of Oxford, Parks Road, Oxford OX1 3PJ, UK
| | - Mauricio Barahona
- Department of Mathematics, Imperial College London, South Kensington Campus, London SW7 2AZ, UK
| | - Guy-Bart V Stan
- Department of Bioengineering, Imperial College London, South Kensington Campus, London SW7 2AZ, UK.,Centre for Synthetic Biology and Innovation, Imperial College London, South Kensington Campus, London SW7 2AZ, UK
| | | | - Karen Polizzi
- Department of Life Sciences, Imperial College London, South Kensington Campus, London SW7 2AZ, UK.,Centre for Synthetic Biology and Innovation, Imperial College London, South Kensington Campus, London SW7 2AZ, UK
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Stotzky G, Devanas MA, Zeph LR. Methods for studying bacterial gene transfer in soil by conjugation and transduction. ADVANCES IN APPLIED MICROBIOLOGY 1990; 35:57-169. [PMID: 2205084 DOI: 10.1016/s0065-2164(08)70243-0] [Citation(s) in RCA: 29] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- G Stotzky
- Department of Biology, New York University, New York 10003
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Nijkamp HJ, de Lang R, Stuitje AR, van den Elzen PJ, Veltkamp E, van Putten AJ. The complete nucleotide sequence of the bacteriocinogenic plasmid CloDF13. Plasmid 1986; 16:135-60. [PMID: 3749334 DOI: 10.1016/0147-619x(86)90072-7] [Citation(s) in RCA: 33] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
The complete nucleotide sequence of the bacteriocinogenic plasmid CloDF13 has been determined. The plasmid consists of 9957 base pairs (molecular weight 6.64 X 10(6] with a GC content of 54.4%. At this moment 16 identified biological functions can be assigned to the primary structure of the CloDF13 DNA. The functions include those of eight protein encoding genes, two untranslated RNA species, and six DNA sites. We discuss these functions in relation to the structure of CloDF13 DNA. For convenience we have divided the CloDF13 genome into five defined regions: region I (origin of vegetative replication, priming and control of replication, type I incompatibility), region II (cloacin DF13, cloacin immunity, cloacin release, cloacin operon control), region III (double-stranded DNA-phage interaction, type II incompatibility, multimer resolution), region IV (inhibition of male specific RNA phages and transfer of Flac), and region V (mobility proteins, basis of mobility).
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Warnes A, Stephenson JR. The insertion of large pieces of foreign genetic material reduces the stability of bacterial plasmids. Plasmid 1986; 16:116-23. [PMID: 3529147 DOI: 10.1016/0147-619x(86)90070-3] [Citation(s) in RCA: 31] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
The stability of genetically engineered bacterial plasmids under continuous culture fermentation is of crucial importance in the application of microbiology to many processes of potential industrial importance. In order to determine the effect of inserting large pieces of foreign DNA on the stability of bacterial plasmids we have studied the behavior of pAT153 with DNA inserts of various sizes derived from cytomegalovirus. Foreign DNA up to 2 kb in length had no effect on stability, whereas the insertion of an 8-kb fragment resulted in a transient instability. This instability was overcome by the spontaneous appearance of leu+ cells in the culture. Insertion of a 21-kb DNA fragment resulted in a rapid loss of plasmid, which was not prevented by the appearance of leu+ cells. In all cases copy number analyses indicated that plasmid loss was due to segregational instability, probably because the plasmid placed an unacceptable metabolic load on the cell.
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