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Albayati SH, Nezhad NG, Taki AG, Rahman RNZRA. Efficient and easible biocatalysts: Strategies for enzyme improvement. A review. Int J Biol Macromol 2024; 276:133978. [PMID: 39038570 DOI: 10.1016/j.ijbiomac.2024.133978] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2024] [Revised: 06/19/2024] [Accepted: 07/16/2024] [Indexed: 07/24/2024]
Abstract
Owing to the environmental friendliness and vast advantages that enzymes offer in the biotechnology and industry fields, biocatalysts are a prolific investigation field. However, the low catalytic activity, stability, and specific selectivity of the enzyme limit the range of the reaction enzymes involved in. A comprehensive understanding of the protein structure and dynamics in terms of molecular details enables us to tackle these limitations effectively and enhance the catalytic activity by enzyme engineering or modifying the supports and solvents. Along with different strategies including computational, enzyme engineering based on DNA recombination, enzyme immobilization, additives, chemical modification, and physicochemical modification approaches can be promising for the wide spread of industrial enzyme usage. This is attributed to the successful application of biocatalysts in industrial and synthetic processes requires a system that exhibits stability, activity, and reusability in a continuous flow process, thereby reducing the production cost. The main goal of this review is to display relevant approaches for improving enzyme characteristics to overcome their industrial application.
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Affiliation(s)
- Samah Hashim Albayati
- Enzyme and Microbial Technology Research Centre, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang 43400, Selangor, Malaysia; Department of Microbiology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang 43400, Selangor, Malaysia
| | - Nima Ghahremani Nezhad
- Enzyme and Microbial Technology Research Centre, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang 43400, Selangor, Malaysia; Department of Microbiology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang 43400, Selangor, Malaysia
| | - Anmar Ghanim Taki
- Department of Radiology Techniques, Health and Medical Techniques College, Alnoor University, Mosul, Iraq
| | - Raja Noor Zaliha Raja Abd Rahman
- Enzyme and Microbial Technology Research Centre, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang 43400, Selangor, Malaysia; Department of Microbiology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang 43400, Selangor, Malaysia; Institute Bioscience, Universiti Putra Malaysia, Serdang 43400, Selangor, Malaysia.
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2
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Zhu L, McNamara HM, Toettcher JE. Light-switchable transcription factors obtained by direct screening in mammalian cells. Nat Commun 2023; 14:3185. [PMID: 37268649 PMCID: PMC10238501 DOI: 10.1038/s41467-023-38993-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Accepted: 05/24/2023] [Indexed: 06/04/2023] Open
Abstract
Optogenetic tools can provide fine spatial and temporal control over many biological processes. Yet the development of new light-switchable protein variants remains challenging, and the field still lacks general approaches to engineering or discovering protein variants with light-switchable biological functions. Here, we adapt strategies for protein domain insertion and mammalian-cell expression to generate and screen a library of candidate optogenetic tools directly in mammalian cells. The approach is based on insertion of the AsLOV2 photoswitchable domain at all possible positions in a candidate protein of interest, introduction of the library into mammalian cells, and light/dark selection for variants with photoswitchable activity. We demonstrate the approach's utility using the Gal4-VP64 transcription factor as a model system. Our resulting LightsOut transcription factor exhibits a > 150-fold change in transcriptional activity between dark and blue light conditions. We show that light-switchable function generalizes to analogous insertion sites in two additional Cys6Zn2 and C2H2 zinc finger domains, providing a starting point for optogenetic regulation of a broad class of transcription factors. Our approach can streamline the identification of single-protein optogenetic switches, particularly in cases where structural or biochemical knowledge is limited.
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Affiliation(s)
- Liyuan Zhu
- Department of Chemistry, Princeton University, Princeton, NJ, 08544, USA
| | - Harold M McNamara
- Department of Molecular Biology, Princeton University, Princeton, NJ, 08544, USA
- Lewis Sigler Institute, Princeton University, Princeton, NJ, 08544, USA
| | - Jared E Toettcher
- Department of Molecular Biology, Princeton University, Princeton, NJ, 08544, USA.
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3
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Sellés Vidal L, Isalan M, Heap JT, Ledesma-Amaro R. A primer to directed evolution: current methodologies and future directions. RSC Chem Biol 2023; 4:271-291. [PMID: 37034405 PMCID: PMC10074555 DOI: 10.1039/d2cb00231k] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Accepted: 01/18/2023] [Indexed: 01/30/2023] Open
Abstract
Directed evolution is one of the most powerful tools for protein engineering and functions by harnessing natural evolution, but on a shorter timescale. It enables the rapid selection of variants of biomolecules with properties that make them more suitable for specific applications. Since the first in vitro evolution experiments performed by Sol Spiegelman in 1967, a wide range of techniques have been developed to tackle the main two steps of directed evolution: genetic diversification (library generation), and isolation of the variants of interest. This review covers the main modern methodologies, discussing the advantages and drawbacks of each, and hence the considerations for designing directed evolution experiments. Furthermore, the most recent developments are discussed, showing how advances in the handling of ever larger library sizes are enabling new research questions to be tackled.
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Affiliation(s)
- Lara Sellés Vidal
- Imperial College Centre for Synthetic Biology, Imperial College London London SW7 2AZ UK
- Department of Bioengineering, Imperial College London London SW7 2AZ UK
| | - Mark Isalan
- Imperial College Centre for Synthetic Biology, Imperial College London London SW7 2AZ UK
- Department of Life Sciences, Imperial College London London SW7 2AZ UK
| | - John T Heap
- Imperial College Centre for Synthetic Biology, Imperial College London London SW7 2AZ UK
- Department of Life Sciences, Imperial College London London SW7 2AZ UK
- School of Life Sciences, The University of Nottingham, University Park Nottingham NG7 2RD UK
| | - Rodrigo Ledesma-Amaro
- Imperial College Centre for Synthetic Biology, Imperial College London London SW7 2AZ UK
- Department of Bioengineering, Imperial College London London SW7 2AZ UK
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4
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Rasila TS, Pulkkinen E, Kiljunen S, Haapa-Paananen S, Pajunen MI, Salminen A, Paulin L, Vihinen M, Rice PA, Savilahti H. Mu transpososome activity-profiling yields hyperactive MuA variants for highly efficient genetic and genome engineering. Nucleic Acids Res 2019; 46:4649-4661. [PMID: 29294068 PMCID: PMC5961161 DOI: 10.1093/nar/gkx1281] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2017] [Accepted: 12/21/2017] [Indexed: 11/22/2022] Open
Abstract
The phage Mu DNA transposition system provides a versatile species non-specific tool for molecular biology, genetic engineering and genome modification applications. Mu transposition is catalyzed by MuA transposase, with DNA cleavage and integration reactions ultimately attaching the transposon DNA to target DNA. To improve the activity of the Mu DNA transposition machinery, we mutagenized MuA protein and screened for hyperactivity-causing substitutions using an in vivo assay. The individual activity-enhancing substitutions were mapped onto the MuA–DNA complex structure, containing a tetramer of MuA transposase, two Mu end segments and a target DNA. This analysis, combined with the varying effect of the mutations in different assays, implied that the mutations exert their effects in several ways, including optimizing protein–protein and protein–DNA contacts. Based on these insights, we engineered highly hyperactive versions of MuA, by combining several synergistically acting substitutions located in different subdomains of the protein. Purified hyperactive MuA variants are now ready for use as second-generation tools in a variety of Mu-based DNA transposition applications. These variants will also widen the scope of Mu-based gene transfer technologies toward medical applications such as human gene therapy. Moreover, the work provides a platform for further design of custom transposases.
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Affiliation(s)
- Tiina S Rasila
- Division of Genetics and Physiology, Department of Biology, FI-20014 University of Turku, Turku, Finland.,Institute of Biotechnology, Viikki Biocenter, P. O. Box 56, FI-00014 University of Helsinki, Helsinki, Finland
| | - Elsi Pulkkinen
- Division of Genetics and Physiology, Department of Biology, FI-20014 University of Turku, Turku, Finland
| | - Saija Kiljunen
- Division of Genetics and Physiology, Department of Biology, FI-20014 University of Turku, Turku, Finland
| | - Saija Haapa-Paananen
- Division of Genetics and Physiology, Department of Biology, FI-20014 University of Turku, Turku, Finland
| | - Maria I Pajunen
- Division of Biochemistry and Biotechnology, Department of Biosciences, FI-00014 University of Helsinki, Helsinki, Finland
| | - Anu Salminen
- Department of Biochemistry, FI-20014 University of Turku, Turku, Finland
| | - Lars Paulin
- Institute of Biotechnology, Viikki Biocenter, P. O. Box 56, FI-00014 University of Helsinki, Helsinki, Finland
| | - Mauno Vihinen
- Department of Experimental Medical Science, Lund University, SE-221 84, Lund, Sweden
| | - Phoebe A Rice
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL 60637, USA
| | - Harri Savilahti
- Division of Genetics and Physiology, Department of Biology, FI-20014 University of Turku, Turku, Finland.,Institute of Biotechnology, Viikki Biocenter, P. O. Box 56, FI-00014 University of Helsinki, Helsinki, Finland
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5
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Younger AKD, Su PY, Shepard AJ, Udani SV, Cybulski TR, Tyo KEJ, Leonard JN. Development of novel metabolite-responsive transcription factors via transposon-mediated protein fusion. Protein Eng Des Sel 2018; 31:55-63. [PMID: 29385546 DOI: 10.1093/protein/gzy001] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Accepted: 01/07/2018] [Indexed: 12/22/2022] Open
Abstract
Naturally evolved metabolite-responsive biosensors enable applications in metabolic engineering, ranging from screening large genetic libraries to dynamically regulating biosynthetic pathways. However, there are many metabolites for which a natural biosensor does not exist. To address this need, we developed a general method for converting metabolite-binding proteins into metabolite-responsive transcription factors-Biosensor Engineering by Random Domain Insertion (BERDI). This approach takes advantage of an in vitro transposon insertion reaction to generate all possible insertions of a DNA-binding domain into a metabolite-binding protein, followed by fluorescence activated cell sorting to isolate functional biosensors. To develop and evaluate the BERDI method, we generated a library of candidate biosensors in which a zinc finger DNA-binding domain was inserted into maltose binding protein, which served as a model well-studied metabolite-binding protein. Library diversity was characterized by several methods, a selection scheme was deployed, and ultimately several distinct and functional maltose-responsive transcriptional biosensors were identified. We hypothesize that the BERDI method comprises a generalizable strategy that may ultimately be applied to convert a wide range of metabolite-binding proteins into novel biosensors for applications in metabolic engineering and synthetic biology.
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Affiliation(s)
- Andrew K D Younger
- Interdisciplinary Biological Sciences (IBiS) Graduate Program, Northwestern University, 2-100 Hogan Hall, 2205 Tech Drive, Evanston, IL 60208, USA
| | - Peter Y Su
- Department of Chemical and Biological Engineering, McCormick School of Engineering and Applied Science, Northwestern University, 2145 Sheridan Road, Room E-136, Evanston, IL 60208, USA
| | - Andrea J Shepard
- Department of Chemical and Biological Engineering, McCormick School of Engineering and Applied Science, Northwestern University, 2145 Sheridan Road, Room E-136, Evanston, IL 60208, USA
| | - Shreya V Udani
- Department of Biomedical Engineering, McCormick School of Engineering and Applied Science, 2145 Sheridan Road, Evanston, IL 60208, USA
| | - Thaddeus R Cybulski
- Department of Physical Medicine and Rehabilitation, Northwestern University and Rehabilitation Institute of Chicago, 710 North Lake Shore Drive, #1022, Chicago, IL 60611, USA
| | - Keith E J Tyo
- Department of Chemical and Biological Engineering, McCormick School of Engineering and Applied Science, Northwestern University, 2145 Sheridan Road, Room E-136, Evanston, IL 60208, USA.,Chemistry of Life Processes Institute, 2170 Campus Dr, Evanston, IL 60208, USA.,Center for Synthetic Biology, Technological Institute, 2145 Sheridan Road, Evanston, IL 60208, USA
| | - Joshua N Leonard
- Department of Chemical and Biological Engineering, McCormick School of Engineering and Applied Science, Northwestern University, 2145 Sheridan Road, Room E-136, Evanston, IL 60208, USA.,Chemistry of Life Processes Institute, 2170 Campus Dr, Evanston, IL 60208, USA.,Center for Synthetic Biology, Technological Institute, 2145 Sheridan Road, Evanston, IL 60208, USA.,Robert H. Lurie Comprehensive Cancer Center, Northwestern University, 303 E. Superior L3-125, Chicago, IL 60611, USA
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6
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Applications of the Bacteriophage Mu In Vitro Transposition Reaction and Genome Manipulation via Electroporation of DNA Transposition Complexes. Methods Mol Biol 2018; 1681:279-286. [PMID: 29134602 DOI: 10.1007/978-1-4939-7343-9_20] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The capacity of transposable elements to insert into the genomes has been harnessed during the past decades to various in vitro and in vivo applications. This chapter describes in detail the general protocols and principles applicable for the Mu in vitro transposition reaction as well as the assembly of DNA transposition complexes that can be electroporated into bacterial cells to accomplish efficient gene delivery. These techniques with their modifications potentiate various gene and genome modification applications, which are discussed briefly here, and the reader is referred to the original publications for further details.
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7
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Rapid construction of metabolite biosensors using domain-insertion profiling. Nat Commun 2016; 7:12266. [PMID: 27470466 PMCID: PMC4974565 DOI: 10.1038/ncomms12266] [Citation(s) in RCA: 82] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2015] [Accepted: 06/15/2016] [Indexed: 12/15/2022] Open
Abstract
Single-fluorescent protein biosensors (SFPBs) are an important class of probes that enable the single-cell quantification of analytes in vivo. Despite advantages over other detection technologies, their use has been limited by the inherent challenges of their construction. Specifically, the rational design of green fluorescent protein (GFP) insertion into a ligand-binding domain, generating the requisite allosteric coupling, remains a rate-limiting step. Here, we describe an unbiased approach, termed domain-insertion profiling with DNA sequencing (DIP-seq), that combines the rapid creation of diverse libraries of potential SFPBs and high-throughput activity assays to identify functional biosensors. As a proof of concept, we construct an SFPB for the important regulatory sugar trehalose. DIP-seq analysis of a trehalose-binding-protein reveals allosteric hotspots for GFP insertion and results in high-dynamic range biosensors that function robustly in vivo. Taken together, DIP-seq simultaneously accelerates metabolite biosensor construction and provides a novel tool for interrogating protein allostery. In the construction of single fluorescent protein biosensors, selection of the insertion point of a fluorescent protein into a ligand-binding domain is a rate-limiting step. Here, the authors develop an unbiased, high-throughput approach, called domain insertion profiling with DNA sequencing (DIP-seq), to generate a novel trehalose biosensor.
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8
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Pulkkinen E, Haapa-Paananen S, Turakainen H, Savilahti H. A set of mini-Mu transposons for versatile cloning of circular DNA and novel dual-transposon strategy for increased efficiency. Plasmid 2016; 86:46-53. [PMID: 27387339 DOI: 10.1016/j.plasmid.2016.07.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2016] [Revised: 06/29/2016] [Accepted: 07/02/2016] [Indexed: 12/22/2022]
Abstract
Mu transposition-based cloning of DNA circles employs in vitro transposition reaction to deliver both the plasmid origin of replication and a selectable marker into the target DNA of interest. We report here the construction of a platform for the purpose that contains ten mini-Mu transposons with five different replication origins, enabling a variety of research approaches for the discovery and study of circular DNA. We also demonstrate that the simultaneous use of two transposons, one with the origin of replication and the other with selectable marker, is beneficial as it improves the cloning efficiency by reducing the fraction of autointegration-derived plasmid clones. The constructed transposons now provide a set of new tools for the studies on DNA circles and widen the applicability of Mu transposition based approaches to clone circular DNA from various sources.
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Affiliation(s)
- Elsi Pulkkinen
- Division of Genetics and Physiology, Department of Biology, University of Turku, Vesilinnantie 5, FI-20500 Turku, Finland
| | - Saija Haapa-Paananen
- Division of Genetics and Physiology, Department of Biology, University of Turku, Vesilinnantie 5, FI-20500 Turku, Finland
| | - Hilkka Turakainen
- Institute of Biotechnology, Viikki Biocenter, P.O. Box 56, Viikinkaari 9, FI-00014, University of Helsinki, Helsinki, Finland
| | - Harri Savilahti
- Division of Genetics and Physiology, Department of Biology, University of Turku, Vesilinnantie 5, FI-20500 Turku, Finland; Institute of Biotechnology, Viikki Biocenter, P.O. Box 56, Viikinkaari 9, FI-00014, University of Helsinki, Helsinki, Finland.
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9
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MuA-mediated in vitro cloning of circular DNA: transpositional autointegration and the effect of MuB. Mol Genet Genomics 2016; 291:1181-91. [DOI: 10.1007/s00438-016-1175-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2015] [Accepted: 01/21/2016] [Indexed: 11/26/2022]
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10
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Pulkkinen E, Haapa-Paananen S, Savilahti H. An assay to monitor the activity of DNA transposition complexes yields a general quality control measure for transpositional recombination reactions. Mob Genet Elements 2014; 4:1-8. [PMID: 26442171 PMCID: PMC4590003 DOI: 10.4161/21592543.2014.969576] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2014] [Revised: 08/22/2014] [Accepted: 09/01/2014] [Indexed: 12/20/2022] Open
Abstract
Transposon-based technologies have many applications in molecular biology and can be used for gene delivery into prokaryotic and eukaryotic cells. Common transpositional activity measurement assays suitable for many types of transposons would be beneficial, as diverse transposon systems could be compared for their performance attributes. Therefore, we developed a general-purpose assay to enable and standardize the activity measurement for DNA transposition complexes (transpososomes), using phage Mu transposition as a test platform. This assay quantifies transpositional recombination efficiency and is based on an in vitro transposition reaction with a target plasmid carrying a lethal ccdB gene. If transposition targets ccdB, this gene becomes inactivated, enabling plasmid-receiving Escherichia coli cells to survive and to be scored as colonies on selection plates. The assay was validated with 3 mini-Mu transposons varying in size and differing in their marker gene constitution. Tests with different amounts of transposon DNA provided a linear response and yielded a 10-fold operational range for the assay. The colony formation capacity was linearly correlated with the competence status of the E.coli cells, enabling normalization of experimental data obtained with different batches of recipient cells. The developed assay can now be used to directly compare transpososome activities with all types of mini-Mu transposons, regardless of their aimed use. Furthermore, the assay should be directly applicable to other transposition-based systems with a functional in vitro reaction, and it provides a dependable quality control measure that previously has been lacking but is highly important for the evaluation of current and emerging transposon-based applications.
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Affiliation(s)
- Elsi Pulkkinen
- Division of Genetics and Physiology; Department of Biology; University of Turku; Turku, Finland
| | - Saija Haapa-Paananen
- Division of Genetics and Physiology; Department of Biology; University of Turku; Turku, Finland
| | - Harri Savilahti
- Division of Genetics and Physiology; Department of Biology; University of Turku; Turku, Finland
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11
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Rasila TS, Vihinen M, Paulin L, Haapa-Paananen S, Savilahti H. Flexibility in MuA transposase family protein structures: functional mapping with scanning mutagenesis and sequence alignment of protein homologues. PLoS One 2012; 7:e37922. [PMID: 22666413 PMCID: PMC3362531 DOI: 10.1371/journal.pone.0037922] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2012] [Accepted: 04/26/2012] [Indexed: 12/13/2022] Open
Abstract
MuA transposase protein is a member of the retroviral integrase superfamily (RISF). It catalyzes DNA cleavage and joining reactions via an initial assembly and subsequent structural transitions of a protein-DNA complex, known as the Mu transpososome, ultimately attaching transposon DNA to non-specific target DNA. The transpososome functions as a molecular DNA-modifying machine and has been used in a wide variety of molecular biology and genetics/genomics applications. To analyze structure-function relationships in MuA action, a comprehensive pentapeptide insertion mutagenesis was carried out for the protein. A total of 233 unique insertion variants were generated, and their activity was analyzed using a quantitative in vivo DNA transposition assay. The results were then correlated with the known MuA structures, and the data were evaluated with regard to the protein domain function and transpososome development. To complement the analysis with an evolutionary component, a protein sequence alignment was produced for 44 members of MuA family transposases. Altogether, the results pinpointed those regions, in which insertions can be tolerated, and those where insertions are harmful. Most insertions within the subdomains Iγ, IIα, IIβ, and IIIα completely destroyed the transposase function, yet insertions into certain loop/linker regions of these subdomains increased the protein activity. Subdomains Iα and IIIβ were largely insertion-tolerant. The comprehensive structure-function data set will be useful for designing MuA transposase variants with improved properties for biotechnology/genomics applications, and is informative with regard to the function of RISF proteins in general.
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Affiliation(s)
- Tiina S. Rasila
- Institute of Biotechnology, Viikki Biocenter, University of Helsinki, Helsinki, Finland
| | - Mauno Vihinen
- Institute of Biomedical Technology, University of Tampere, Tampere, Finland
- BioMediTech, Tampere, Finland
- Department of Experimental Medical Science, Lund University, Lund, Sweden
| | - Lars Paulin
- Institute of Biotechnology, Viikki Biocenter, University of Helsinki, Helsinki, Finland
| | - Saija Haapa-Paananen
- Institute of Biotechnology, Viikki Biocenter, University of Helsinki, Helsinki, Finland
| | - Harri Savilahti
- Institute of Biotechnology, Viikki Biocenter, University of Helsinki, Helsinki, Finland
- Division of Genetics and Physiology, Department of Biology, University of Turku, Turku, Finland
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12
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Chen Y, Holtman CK, Taton A, Golden SS. Functional Analysis of the Synechococcus elongatus PCC 7942 Genome. FUNCTIONAL GENOMICS AND EVOLUTION OF PHOTOSYNTHETIC SYSTEMS 2012. [DOI: 10.1007/978-94-007-1533-2_5] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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13
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Kant R, Paulin L, Alatalo E, de Vos WM, Palva A. Genome sequence of Lactobacillus amylovorus GRL1118, isolated from pig ileum. J Bacteriol 2011; 193:3147-8. [PMID: 21478337 PMCID: PMC3133193 DOI: 10.1128/jb.00423-11] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2011] [Accepted: 04/04/2011] [Indexed: 11/20/2022] Open
Abstract
Lactobacillus amylovorus is a common member of the beneficial microbiota present in the pig gastrointestinal tract. Here, we report the genome sequence of the surface layer (S-layer) protein-carrying and potentially probiotic strain L. amylovorus GRL1118, which was isolated from porcine ileum and which shows strong adherence to pig intestinal epithelial cells.
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Affiliation(s)
- Ravi Kant
- Department of Veterinary Biosciences, Faculty of Veterinary Medicine, FIN-00014 University of Helsinki, Finland
| | - Lars Paulin
- Institute of Biotechnology, FIN-00014 University of Helsinki, Helsinki, Finland
| | - Edward Alatalo
- Institute of Biotechnology, FIN-00014 University of Helsinki, Helsinki, Finland
| | - Willem M. de Vos
- Department of Veterinary Biosciences, Faculty of Veterinary Medicine, FIN-00014 University of Helsinki, Finland
- Laboratory of Microbiology, Wageningen University, Wageningen, the Netherlands
| | - Airi Palva
- Department of Veterinary Biosciences, Faculty of Veterinary Medicine, FIN-00014 University of Helsinki, Finland
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14
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Krupovic M, Vilen H, Bamford JKH, Kivelä HM, Aalto JM, Savilahti H, Bamford DH. Genome characterization of lipid-containing marine bacteriophage PM2 by transposon insertion mutagenesis. J Virol 2006; 80:9270-8. [PMID: 16940538 PMCID: PMC1563929 DOI: 10.1128/jvi.00536-06] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2006] [Accepted: 06/27/2006] [Indexed: 11/20/2022] Open
Abstract
Bacteriophage PM2 presently is the only member of the Corticoviridae family. The virion consists of a protein-rich lipid vesicle, which is surrounded by an icosahedral protein capsid. The lipid vesicle encloses a supercoiled circular double-stranded DNA genome of 10,079 bp. PM2 belongs to the marine phage community and is known to infect two gram-negative Pseudoalteromonas species. In this study, we present a characterization of the PM2 genome made using the in vitro transposon insertion mutagenesis approach. Analysis of 101 insertion mutants yielded information on the essential and dispensable regions of the PM2 genome and led to the identification of several new genes. A number of lysis-deficient mutants as well as mutants displaying delayed- and/or incomplete-lysis phenotypes were identified. This enabled us to identify novel lysis-associated genes with no resemblance to those previously described from other bacteriophage systems. Nonessential genome regions are discussed in the context of PM2 genome evolution.
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Affiliation(s)
- Mart Krupovic
- Department of Biological and Environmental Sciences, Institute of Biotechnology, Viikki Biocenter 2, P.O. Box 56 (Viikinkaari 5), FIN-00014 University of Helsinki, Finland
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15
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Song MJ, Hwang S, Wong WH, Wu TT, Lee S, Liao HI, Sun R. Identification of viral genes essential for replication of murine gamma-herpesvirus 68 using signature-tagged mutagenesis. Proc Natl Acad Sci U S A 2005; 102:3805-10. [PMID: 15738413 PMCID: PMC553290 DOI: 10.1073/pnas.0404521102] [Citation(s) in RCA: 118] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Gamma-herpesviruses, Epstein-Barr virus, and Kaposi's sarcoma-associated herpesvirus are important human pathogens, because they are involved in tumor development. Murine gamma-herpesvirus-68 (MHV-68 or gammaHV-68) has emerged as a small animal model system for the study of gamma-herpesvirus pathogenesis and host-virus interactions. To identify the genes required for viral replication in vitro and in vivo, we generated 1,152 mutants using signature-tagged transposon mutagenesis on an infectious bacterial artificial chromosome of MHV-68. Almost every ORF was mutated by random insertion. For each ORF, a mutant with an insertion proximal to the N terminus of each ORF was examined for the ability to grow in fibroblasts. Our results indicate that 41 genes are essential for in vitro growth, whereas 26 are nonessential and 6 attenuated. Replication-competent mutants were pooled to infect mice, which led to the discovery of ORF 54 being important for MHV-68 to replicate in the lung. This genetic analysis of a tumor-associated herpesvirus at the whole genome level validates signature-tagged transposon mutagenesis screening as an effective genetic system to identify important virulent genes in vivo and define interactions with the host immune system.
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Affiliation(s)
- Moon Jung Song
- Department of Microbiology, College of Medicine, Hallym University, Chuncheon 200-702, Republic of Korea
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Vilen H, Aalto JM, Kassinen A, Paulin L, Savilahti H. A direct transposon insertion tool for modification and functional analysis of viral genomes. J Virol 2003; 77:123-34. [PMID: 12477817 PMCID: PMC140628 DOI: 10.1128/jvi.77.1.123-134.2003] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Advances in DNA transposition technology have recently generated efficient tools for various types of functional genetic analyses. We demonstrate here the power of the bacteriophage Mu-derived in vitro DNA transposition system for modification and functional characterization of a complete bacterial virus genome. The linear double-stranded DNA genome of Escherichia coli bacteriophage PRD1 was studied by insertion mutagenesis with reporter mini-Mu transposons that were integrated in vitro into isolated genomic DNA. After introduction into bacterial cells by electroporation, recombinant transposon-containing virus clones were identified by autoradiography or visual blue-white screening employing alpha-complementation of E. coli beta-galactosidase. Additionally, a modified transposon with engineered NotI sites at both ends was used to introduce novel restriction sites into the phage genome. Analysis of the transposon integration sites in the genomes of viable recombinant phage generated a functional map, collectively indicating genes and genomic regions essential and nonessential for virus propagation. Moreover, promoterless transposons defined the direction of transcription within several insert-tolerant genomic regions. These strategies for the analysis of viral genomes are of a general nature and therefore may be applied to functional genomics studies in all prokaryotic and eukaryotic cell viruses.
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Affiliation(s)
- Heikki Vilen
- Program in Cellular Biotechnology, Institute of Biotechnology, Viikki Biocenter, University of Helsinki, Finland
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Kekarainen T, Savilahti H, Valkonen JPT. Functional genomics on potato virus A: virus genome-wide map of sites essential for virus propagation. Genome Res 2002; 12:584-94. [PMID: 11932242 PMCID: PMC187510 DOI: 10.1101/gr.220702] [Citation(s) in RCA: 60] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Transposition-based in vitro insertional mutagenesis strategies provide promising new approaches for functional characterization of any cloned gene or genome region. We have extended the methodology and scope of such analysis to a complete viral genome. To map genome regions both essential and nonessential for Potato virus A propagation, we generated a genomic 15-bp insertion mutant library utilizing the efficient in vitro DNA transposition reaction of phage Mu. We then determined the proficiency of 1125 mutants to propagate in tobacco protoplasts by using a genetic footprinting strategy that simultaneously mapped the genomic insertion sites. Over 300 sites critical for virus propagation were identified, and many of them were located in positions previously not assigned to any viral functions. Many genome regions tolerated insertions indicating less important sites for virus propagation and thus pinpointed potential locations for further genome manipulation. The methodology described is applicable to a detailed functional analysis of any viral nucleic acid cloned as DNA and can be used to address many different processes during viral infection cycles.
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Affiliation(s)
- Tuija Kekarainen
- Department of Plant Biology, Swedish University of Agricultural Sciences (SLU), S-75007 Uppsala, Sweden
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Lamberg A, Nieminen S, Qiao M, Savilahti H. Efficient insertion mutagenesis strategy for bacterial genomes involving electroporation of in vitro-assembled DNA transposition complexes of bacteriophage mu. Appl Environ Microbiol 2002; 68:705-12. [PMID: 11823210 PMCID: PMC126711 DOI: 10.1128/aem.68.2.705-712.2002] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
An efficient insertion mutagenesis strategy for bacterial genomes based on the phage Mu DNA transposition reaction was developed. Incubation of MuA transposase protein with artificial mini-Mu transposon DNA in the absence of divalent cations in vitro resulted in stable but inactive Mu DNA transposition complexes, or transpososomes. Following delivery into bacterial cells by electroporation, the complexes were activated for DNA transposition chemistry after encountering divalent metal ions within the cells. Mini-Mu transposons were integrated into bacterial chromosomes with efficiencies ranging from 10(4) to 10(6) CFU/microg of input transposon DNA in the four species tested, i.e., Escherichia coli, Salmonella enterica serovar Typhimurium, Erwinia carotovora, and Yersinia enterocolitica. Efficiency of integration was influenced mostly by the competence status of a given strain or batch of bacteria. An accurate 5-bp target site duplication flanking the transposon, a hallmark of Mu transposition, was generated upon mini-Mu integration into the genome, indicating that a genuine DNA transposition reaction was reproduced within the cells of the bacteria studied. This insertion mutagenesis strategy for microbial genomes may be applicable to a variety of organisms provided that a means to introduce DNA into their cells is available.
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Affiliation(s)
- Arja Lamberg
- Program in Cellular Biotechnology, Institute of Biotechnology, Viikki Biocenter, University of Helsinki, Viikinkaari 9, 00014 Helsinki, Finland
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Haapa-Paananen S, Rita H, Savilahti H. DNA transposition of bacteriophage Mu. A quantitative analysis of target site selection in vitro. J Biol Chem 2002; 277:2843-51. [PMID: 11700310 DOI: 10.1074/jbc.m108044200] [Citation(s) in RCA: 72] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The Mu transpositional DNA recombination machinery selects target sites by assembling a protein-DNA complex that interacts with the target DNA and reacts whenever it locates a favorable sequence composition. Splicing of a transposon into the target generates a 5-bp duplication that reflects the original target site. Preferential usage of different target pentamers was examined with a minimal Mu in vitro system and quantitatively compiled consensus sequences for the most preferred and the least preferred sites were generated. When analyzed as base steps, preferences toward certain steps along the 5-bp target site were detected. We further show that insertion sites can be predicted on the basis of additively calculated base step values. Also surrounding sequences influence the preference of a given pentamer; a symmetrical structural component was revealed, suggesting potential hinges at and around the target site.
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Affiliation(s)
- Saija Haapa-Paananen
- Program in Cellular Biotechnology, Institute of Biotechnology, Viikki Biocenter, PO Box 56, Viikinkaari 9, 00014 University of Helsinki, Finland
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