1
|
Chaillou S, Stamou PE, Torres LL, Riesco AB, Hazelton W, Pinheiro VB. Directed evolution of colE1 plasmid replication compatibility: a fast tractable tunable model for investigating biological orthogonality. Nucleic Acids Res 2022; 50:9568-9579. [PMID: 36018798 PMCID: PMC9458437 DOI: 10.1093/nar/gkac682] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Revised: 06/02/2022] [Accepted: 08/03/2022] [Indexed: 12/24/2022] Open
Abstract
Plasmids of the ColE1 family are among the most frequently used in molecular biology. They were adopted early for many biotechnology applications, and as models to study plasmid biology. Their mechanism of replication is well understood, involving specific interactions between a plasmid encoded sense-antisense gene pair (RNAI and RNAII). Due to such mechanism, two plasmids with the same origin cannot be stably maintained in cells-a process known as incompatibility. While mutations in RNAI and RNAII can make colE1 more compatible, there has been no systematic effort to engineer new compatible colE1 origins, which could bypass technical design constraints for multi-plasmid applications. Here, we show that by diversifying loop regions in RNAI (and RNAII), it is possible to select new viable colE1 origins compatible with the wild-type one. We demonstrate that sequence divergence is not sufficient to enable compatibility and pairwise interactions are not an accurate guide for higher order interactions. We identify potential principles to engineer plasmid copy number independently from other regulatory strategies and we propose plasmid compatibility as a tractable model to study biological orthogonality.
Collapse
Affiliation(s)
| | | | - Leticia L Torres
- University College London, Institute of Structural and Molecular Biology, University College London, Gower Street, London WC1E 6BT, UK
| | - Ana B Riesco
- University College London, Institute of Structural and Molecular Biology, University College London, Gower Street, London WC1E 6BT, UK
| | - Warren Hazelton
- University College London, Institute of Structural and Molecular Biology, University College London, Gower Street, London WC1E 6BT, UK
| | - Vitor B Pinheiro
- To whom correspondence should be addressed. Tel: +32 16 330 257;
| |
Collapse
|
2
|
Vincent AT, Emond-Rheault JG, Barbeau X, Attéré SA, Frenette M, Lagüe P, Charette SJ. Antibiotic resistance due to an unusual ColE1-type replicon plasmid in Aeromonas salmonicida. Microbiology (Reading) 2016; 162:942-953. [DOI: 10.1099/mic.0.000286] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Antony T. Vincent
- Centre de recherche de l’Institut universitaire de cardiologie et de pneumologie de Québec (Hôpital Laval), 2725 Chemin Sainte-Foy, Quebec City, QC, Canada, G1V 4G5
- Institut de biologie intégrative et des systèmes, Pavillon Charles-Eugène-Marchand, Université Laval, 1030 avenue de la Médecine, Quebec City, QC, Canada, G1V 0A6
- Département de biochimie, de microbiologie et de bio-informatique, Faculté des sciences et de génie, Université Laval, 1045 avenue de la Médecine, Quebec City, QC, Canada G1V 0A6
| | - Jean-Guillaume Emond-Rheault
- Institut de biologie intégrative et des systèmes, Pavillon Charles-Eugène-Marchand, Université Laval, 1030 avenue de la Médecine, Quebec City, QC, Canada, G1V 0A6
- Centre de recherche de l’Institut universitaire de cardiologie et de pneumologie de Québec (Hôpital Laval), 2725 Chemin Sainte-Foy, Quebec City, QC, Canada, G1V 4G5
- Département de biochimie, de microbiologie et de bio-informatique, Faculté des sciences et de génie, Université Laval, 1045 avenue de la Médecine, Quebec City, QC, Canada G1V 0A6
| | - Xavier Barbeau
- Institut de biologie intégrative et des systèmes, Pavillon Charles-Eugène-Marchand, Université Laval, 1030 avenue de la Médecine, Quebec City, QC, Canada, G1V 0A6
- Département de Chimie, Université Laval, Québec, Canada
| | - Sabrina A. Attéré
- Institut de biologie intégrative et des systèmes, Pavillon Charles-Eugène-Marchand, Université Laval, 1030 avenue de la Médecine, Quebec City, QC, Canada, G1V 0A6
- Centre de recherche de l’Institut universitaire de cardiologie et de pneumologie de Québec (Hôpital Laval), 2725 Chemin Sainte-Foy, Quebec City, QC, Canada, G1V 4G5
- Département de biochimie, de microbiologie et de bio-informatique, Faculté des sciences et de génie, Université Laval, 1045 avenue de la Médecine, Quebec City, QC, Canada G1V 0A6
| | - Michel Frenette
- Département de biochimie, de microbiologie et de bio-informatique, Faculté des sciences et de génie, Université Laval, 1045 avenue de la Médecine, Quebec City, QC, Canada G1V 0A6
- Groupe de Recherche en Écologie Buccale (GREB), Faculté de médecine dentaire, Université Laval, Quebec City, QC, Canada, G1V 0A6
| | - Patrick Lagüe
- Institut de biologie intégrative et des systèmes, Pavillon Charles-Eugène-Marchand, Université Laval, 1030 avenue de la Médecine, Quebec City, QC, Canada, G1V 0A6
- Département de biochimie, de microbiologie et de bio-informatique, Faculté des sciences et de génie, Université Laval, 1045 avenue de la Médecine, Quebec City, QC, Canada G1V 0A6
| | - Steve J. Charette
- Institut de biologie intégrative et des systèmes, Pavillon Charles-Eugène-Marchand, Université Laval, 1030 avenue de la Médecine, Quebec City, QC, Canada, G1V 0A6
- Centre de recherche de l’Institut universitaire de cardiologie et de pneumologie de Québec (Hôpital Laval), 2725 Chemin Sainte-Foy, Quebec City, QC, Canada, G1V 4G5
- Département de biochimie, de microbiologie et de bio-informatique, Faculté des sciences et de génie, Université Laval, 1045 avenue de la Médecine, Quebec City, QC, Canada G1V 0A6
| |
Collapse
|
3
|
Fujii R, Kitaoka M, Hayashi K. Random insertional-deletional strand exchange mutagenesis (RAISE): a simple method for generating random insertion and deletion mutations. Methods Mol Biol 2014; 1179:151-158. [PMID: 25055776 DOI: 10.1007/978-1-4939-1053-3_10] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Although proteins can be artificially improved by random insertion and deletion mutagenesis methods, these procedures are technically difficult. Here we describe a simple method called random insertional-deletional strand exchange mutagenesis (RAISE). This method is based on gene shuffling and can be used to introduce a wide variety of insertions, deletions, and substitutions. RAISE involves three steps: DNA fragmentation, attachment of a random short sequence, and reconstruction. This yields unique mutants and can be a powerful technique for protein engineering.
Collapse
Affiliation(s)
- Ryota Fujii
- Synthetic Chemicals Laboratory, Mitsui Chemicals, Inc., 580-32 Nagaura, Sodegaura, Chiba, 299-0265, Japan
| | | | | |
Collapse
|
4
|
Million-Weaver S, Alexander DL, Allen JM, Camps M. Quantifying plasmid copy number to investigate plasmid dosage effects associated with directed protein evolution. Methods Mol Biol 2012; 834:33-48. [PMID: 22144351 PMCID: PMC3804865 DOI: 10.1007/978-1-61779-483-4_3] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Our laboratory specializes in directed protein evolution, i.e., evolution of proteins under defined selective pressures in the laboratory. Our target genes are encoded in ColE1 plasmids to facilitate the generation of libraries in vivo. We have observed that when random mutations are not restricted to the coding sequence of the target genes, directed evolution results in a strong positive selection of plasmid origin of replication (ori) mutations. Surprisingly, this is true even during evolution of new biochemical activities, when the activity that is being selected was not originally present. The selected plasmid ori mutations are diverse and produce a range of plasmid copy numbers, suggesting a complex interplay between ori and coding mutations rather than a simple enhancement of level of expression of the target gene. Thus, plasmid dosage may contribute significantly to evolution by fine-tuning levels of activity. Here, we present examples illustrating these observations as well as our methods for efficient quantification of plasmid copy number.
Collapse
Affiliation(s)
- Samuel Million-Weaver
- Department of Microbiology and Environmental Toxicology, University of California Santa Cruz, Santa Cruz, CA, USA
| | | | | | | |
Collapse
|
5
|
Mao H, Graziano JJ, Chase TMA, Bentley CA, Bazirgan OA, Reddy NP, Song BD, Smider VV. Spatially addressed combinatorial protein libraries for recombinant antibody discovery and optimization. Nat Biotechnol 2010; 28:1195-202. [PMID: 20972421 DOI: 10.1038/nbt.1694] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2010] [Accepted: 09/27/2010] [Indexed: 12/21/2022]
Abstract
Antibody discovery typically uses hybridoma- or display-based selection approaches, which lack the advantages of directly screening spatially addressed compound libraries as in small-molecule discovery. Here we apply the latter strategy to antibody discovery, using a library of ∼10,000 human germline antibody Fabs created by de novo DNA synthesis and automated protein expression and purification. In multiplexed screening assays, we obtained specific hits against seven of nine antigens. Using sequence-activity relationships and iterative mutagenesis, we optimized the binding affinities of two hits to the low nanomolar range. The matured Fabs showed full and partial antagonism activities in cell-based assays. Thus, protein drug leads can be discovered using surprisingly small libraries of proteins with known sequences, questioning the requirement for billions of members in an antibody discovery library. This methodology also provides sequence, expression and specificity information at the first step of the discovery process, and could enable novel antibody discovery in functional screens.
Collapse
|
6
|
Evidence for the in vivo expression of a distant downstream gene under the control of ColE1 replication origin. Appl Microbiol Biotechnol 2010; 86:671-9. [DOI: 10.1007/s00253-009-2339-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2009] [Revised: 10/27/2009] [Accepted: 11/01/2009] [Indexed: 11/26/2022]
|
7
|
Wang Z, Yuan Z, Xiang L, Shao J, Węgrzyn G. tRNA-dependent cleavage of the ColE1 plasmid-encoded RNA I. MICROBIOLOGY-SGM 2007; 152:3467-3476. [PMID: 17159198 DOI: 10.1099/mic.0.29134-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Effects of tRNA(Ala)(UGC) and its derivative devoid of the 3'-ACCA motif [tRNA(Ala)(UGC)DeltaACCA] on the cleavage of the ColE1-like plasmid-derived RNA I were analysed in vivo and in vitro. In an amino-acid-starved relA mutant, in which uncharged tRNAs occur in large amounts, three products of specific cleavage of RNA I were observed, in contrast to an otherwise isogenic relA(+) host. Overexpression of tRNA(Ala)(UGC), which under such conditions occurs in Escherichia coli mostly in an uncharged form, induced RNA I cleavage and resulted in an increase in ColE1-like plasmid DNA copy number. Such effects were not observed during overexpression of the 3'-ACCA-truncated tRNA(Ala)(UGC). Moreover, tRNA(Ala)(UGC), but not tRNA(Ala)(UGC)DeltaACCA, caused RNA I cleavage in vitro in the presence of MgCl(2). These results strongly suggest that tRNA-dependent RNA I cleavage occurs in ColE1-like plasmid-bearing E. coli, and demonstrate that tRNA(Ala)(UGC) participates in specific degradation of RNA I in vivo and in vitro. This reaction is dependent on the presence of the 3'-ACCA motif of tRNA(Ala)(UGC).
Collapse
MESH Headings
- Bacteriocin Plasmids/genetics
- Base Sequence
- Blotting, Northern
- Coenzymes/pharmacology
- DNA, Bacterial/biosynthesis
- Escherichia coli/genetics
- Escherichia coli/metabolism
- Magnesium Chloride/pharmacology
- Models, Biological
- Molecular Sequence Data
- RNA Stability
- RNA, Antisense/genetics
- RNA, Antisense/metabolism
- RNA, Bacterial/genetics
- RNA, Bacterial/metabolism
- RNA, Catalytic/metabolism
- RNA, Transfer, Ala/metabolism
Collapse
Affiliation(s)
- Zhijun Wang
- Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University, Ithaca 14853, NY, USA
- Key Laboratory of Medical Molecular Virology, Shanghai Medical College, Fudan University, 200032, Shanghai, People's Republic of China
| | - Zhenghong Yuan
- Key Laboratory of Medical Molecular Virology, Shanghai Medical College, Fudan University, 200032, Shanghai, People's Republic of China
| | - Li Xiang
- Key Laboratory of Medical Molecular Virology, Shanghai Medical College, Fudan University, 200032, Shanghai, People's Republic of China
| | - Junjie Shao
- Key Laboratory of Medical Molecular Virology, Shanghai Medical College, Fudan University, 200032, Shanghai, People's Republic of China
| | - Grzegorz Węgrzyn
- Department of Genetics and Marine Biotechnology, Institute of Oceanology, Polish Academy of Sciences, Św. Wojciecha 5, 81-347 Gdynia, Poland
- Department of Molecular Biology, University of Gdańsk, 80-822, Gdańsk, Poland
| |
Collapse
|
8
|
Leonard B, Sharma V, Smider V. Co-expression of antibody fab heavy and light chain genes from separate evolved compatible replicons in E. coli. J Immunol Methods 2006; 317:56-63. [PMID: 17049550 DOI: 10.1016/j.jim.2006.09.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2006] [Revised: 08/17/2006] [Accepted: 09/07/2006] [Indexed: 11/23/2022]
Abstract
Antibody molecules bind to antigen with six complementary determining region (CDR) loops, three of which are located on each variable heavy (V(H)) and light (V(L)) chains. Discovery and optimization of antibodies that bind antigen using in vitro techniques require diversification of one or more of these CDRs. Since antibodies are dimeric, simultaneous diversification of heavy and light chains on separate genetic elements would allow "chain shuffling" to occur simply and efficiently. Efficient expression of antibody V(H) and V(L) requires that the two separate replicons be compatible with one another, but also have similar properties, such as copy number in E. coli. Standard plasmids that are compatible with one another in E. coli exist at widely variable copy numbers. Recently we described the isolation of ColE1 mutants that have similar copy numbers but different incompatibility characteristics. Thus, new compatibility groups in the ColE1 family were established. Herein we describe the E. coli expression of V(H) and V(L) genes to form a functional Fab. The ability to express antibody heavy and light chains from separate but compatible high copy plasmids should allow new opportunities in antibody engineering, such as rapid chain shuffling and generation of more complex antibody libraries.
Collapse
Affiliation(s)
- Brandon Leonard
- IntegriGen, Inc., 42 Digital Dr. Suite 6, Novato, CA 94949, USA
| | | | | |
Collapse
|
9
|
Walsh TR. Combinatorial genetic evolution of multiresistance. Curr Opin Microbiol 2006; 9:476-82. [PMID: 16942901 DOI: 10.1016/j.mib.2006.08.009] [Citation(s) in RCA: 55] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2006] [Accepted: 08/16/2006] [Indexed: 11/20/2022]
Abstract
The explosion in genetic information, whilst extending our knowledge, might not necessary increase our conceptual understanding on the complexities of bacterial genetics, or why some antibiotic resistant genotypes such as blaCTX-M-15 and blaVIM-2 appear to dominate. However, the information we have thus far suggests that clinical isolates have 'hijacked' plasmids, primarily built of backbone-DNA originating from environmental bacteria. Additionally, the combinatorial presence of other elements such as transposons, integrons, insertion sequence (IS) elements and the 'new' ISCR (IS common region) elements have also contributed to the increase in antibiotic resistance - an antibiotic resistant cluster composing four or five genes has become commonplace. In some instances, the presence of antibiotics themselves, such as fluoroquinolones, can mediate a bacterial SOS cell response, subsequently amplifying and/or augmenting the transfer of large genetic entities therefore, potentially promoting long-term detrimental effects.
Collapse
Affiliation(s)
- Timothy R Walsh
- Department of Molecular and Cellular Medicine, School of Medical Sciences, University of Bristol, Bristol BS8 1TD, UK.
| |
Collapse
|
10
|
Fujii R, Kitaoka M, Hayashi K. RAISE: a simple and novel method of generating random insertion and deletion mutations. Nucleic Acids Res 2006; 34:e30. [PMID: 16493137 PMCID: PMC1380258 DOI: 10.1093/nar/gnj032] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2005] [Revised: 01/24/2006] [Accepted: 02/04/2006] [Indexed: 11/12/2022] Open
Abstract
Although proteins may be artificially improved by random insertion and deletion mutagenesis methods, these procedures are technically difficult, and the mutations introduced are no more variable than those introduced by the introduction of random point mutations. We describe here a three-step method called RAISE, which is based on gene shuffling and can introduce a wide variety of insertions, deletions and substitutions. To test the efficacy of this method, we used it to mutate TEM beta-lactamase to generate improved antibiotic resistance. Some unique insertion or deletion mutations were observed in the improved mutants, some of which caused higher activities than point mutations. Our findings indicate that the RAISE method can yield unique mutants and may be a powerful technique of protein engineering.
Collapse
Affiliation(s)
- Ryota Fujii
- National Food Research Institute2-1-12 Kannondai, Tsukuba, Ibaraki, 305-8642, Japan
| | - Motomitsu Kitaoka
- National Food Research Institute2-1-12 Kannondai, Tsukuba, Ibaraki, 305-8642, Japan
| | - Kiyoshi Hayashi
- National Food Research Institute2-1-12 Kannondai, Tsukuba, Ibaraki, 305-8642, Japan
| |
Collapse
|