1
|
Mielinis P, Sukackaitė R, Serapinaitė A, Samoilovas F, Alzbutas G, Matjošaitis K, Lubys A. MuA-based Molecular Indexing for Rare Mutation Detection by Next-Generation Sequencing. J Mol Biol 2021; 433:167209. [PMID: 34419430 DOI: 10.1016/j.jmb.2021.167209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Revised: 08/12/2021] [Accepted: 08/12/2021] [Indexed: 12/12/2022]
Abstract
Detection of low-frequency mutations in cancer genomes or other heterogeneous cell populations requires high-fidelity sequencing. Molecular barcoding is one of the key technologies that enables the differentiation of true mutations from errors, which can be caused by sequencing or library preparation processes. However, current approaches where barcodes are introduced via primer extension or adaptor ligation do not utilize the full power of barcoding, due to complicated library preparation workflows and biases. Here we demonstrate the remarkable tolerance of MuA transposase to the presence of multiple replacements in transposon sequence, and explore this unique feature to engineer the MuA transposome complex with randomised nucleotides in 12 transposon positions, which can be introduced as a barcode into the target molecule after transposition event. We applied the approach of Unique MuA-based Molecular Indexing (UMAMI) to assess the power of rare mutation detection by shortgun sequencing on the Illumina platform. Our results show that UMAMI allows detection of rare mutations readily and reliably, and in this paper we report error rate values for the number of thermophilic DNA polymerases measured by using UMAMI.
Collapse
Affiliation(s)
- Paulius Mielinis
- Thermo Fisher Scientific Baltics UAB, V. A. Graičiūno 8, Vilnius LT-02241, Lithuania
| | - Rasa Sukackaitė
- Thermo Fisher Scientific Baltics UAB, V. A. Graičiūno 8, Vilnius LT-02241, Lithuania.
| | - Aistė Serapinaitė
- Thermo Fisher Scientific Baltics UAB, V. A. Graičiūno 8, Vilnius LT-02241, Lithuania
| | - Faustas Samoilovas
- Thermo Fisher Scientific Baltics UAB, V. A. Graičiūno 8, Vilnius LT-02241, Lithuania
| | - Gediminas Alzbutas
- Thermo Fisher Scientific Baltics UAB, V. A. Graičiūno 8, Vilnius LT-02241, Lithuania
| | - Karolis Matjošaitis
- Thermo Fisher Scientific Baltics UAB, V. A. Graičiūno 8, Vilnius LT-02241, Lithuania
| | - Arvydas Lubys
- Thermo Fisher Scientific Baltics UAB, V. A. Graičiūno 8, Vilnius LT-02241, Lithuania
| |
Collapse
|
2
|
Adachi H, Contreras MP, Harant A, Wu CH, Derevnina L, Sakai T, Duggan C, Moratto E, Bozkurt TO, Maqbool A, Win J, Kamoun S. An N-terminal motif in NLR immune receptors is functionally conserved across distantly related plant species. eLife 2019; 8:e49956. [PMID: 31774397 PMCID: PMC6944444 DOI: 10.7554/elife.49956] [Citation(s) in RCA: 123] [Impact Index Per Article: 24.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Accepted: 11/23/2019] [Indexed: 12/19/2022] Open
Abstract
The molecular codes underpinning the functions of plant NLR immune receptors are poorly understood. We used in vitro Mu transposition to generate a random truncation library and identify the minimal functional region of NLRs. We applied this method to NRC4-a helper NLR that functions with multiple sensor NLRs within a Solanaceae receptor network. This revealed that the NRC4 N-terminal 29 amino acids are sufficient to induce hypersensitive cell death. This region is defined by the consensus MADAxVSFxVxKLxxLLxxEx (MADA motif) that is conserved at the N-termini of NRC family proteins and ~20% of coiled-coil (CC)-type plant NLRs. The MADA motif matches the N-terminal α1 helix of Arabidopsis NLR protein ZAR1, which undergoes a conformational switch during resistosome activation. Immunoassays revealed that the MADA motif is functionally conserved across NLRs from distantly related plant species. NRC-dependent sensor NLRs lack MADA sequences indicating that this motif has degenerated in sensor NLRs over evolutionary time.
Collapse
Affiliation(s)
- Hiroaki Adachi
- The Sainsbury LaboratoryUniversity of East Anglia, Norwich Research ParkNorwichUnited Kingdom
| | - Mauricio P Contreras
- The Sainsbury LaboratoryUniversity of East Anglia, Norwich Research ParkNorwichUnited Kingdom
| | - Adeline Harant
- The Sainsbury LaboratoryUniversity of East Anglia, Norwich Research ParkNorwichUnited Kingdom
| | - Chih-hang Wu
- The Sainsbury LaboratoryUniversity of East Anglia, Norwich Research ParkNorwichUnited Kingdom
| | - Lida Derevnina
- The Sainsbury LaboratoryUniversity of East Anglia, Norwich Research ParkNorwichUnited Kingdom
| | - Toshiyuki Sakai
- The Sainsbury LaboratoryUniversity of East Anglia, Norwich Research ParkNorwichUnited Kingdom
| | - Cian Duggan
- Department of Life SciencesImperial College LondonLondonUnited Kingdom
| | - Eleonora Moratto
- Department of Life SciencesImperial College LondonLondonUnited Kingdom
| | - Tolga O Bozkurt
- Department of Life SciencesImperial College LondonLondonUnited Kingdom
| | - Abbas Maqbool
- The Sainsbury LaboratoryUniversity of East Anglia, Norwich Research ParkNorwichUnited Kingdom
| | - Joe Win
- The Sainsbury LaboratoryUniversity of East Anglia, Norwich Research ParkNorwichUnited Kingdom
| | - Sophien Kamoun
- The Sainsbury LaboratoryUniversity of East Anglia, Norwich Research ParkNorwichUnited Kingdom
| |
Collapse
|
3
|
Savitskaya J, Protzko RJ, Li FZ, Arkin AP, Dueber JE. Iterative screening methodology enables isolation of strains with improved properties for a FACS-based screen and increased L-DOPA production. Sci Rep 2019; 9:5815. [PMID: 30967567 PMCID: PMC6456618 DOI: 10.1038/s41598-019-41759-0] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Accepted: 03/05/2019] [Indexed: 12/20/2022] Open
Abstract
Optimizing microbial hosts for the large-scale production of valuable metabolites often requires multiple mutations and modifications to the host's genome. We describe a three-round screen for increased L-DOPA production in S. cerevisiae using FACS enrichment of an enzyme-coupled biosensor for L-DOPA. Multiple rounds of screening were enabled by a single build of a barcoded in vitro transposon-mediated disruption library. New background strains for screening were built for each iteration using results from previous iterations. The same in vitro transposon-mediated disruption library was integrated by homologous recombination into new background strains in each round of screening. Compared with creating new transposon insertions in each round, this method takes less time and saves the cost of additional sequencing to characterize transposon insertion sites. In the first two rounds of screening, we identified deletions that improved biosensor compartmentalization and, consequently, improved our ability to screen for L-DOPA production. In a final round, we discovered that deletion of heme oxygenase (HMX1) increases total heme concentration and increases L-DOPA production, using dopamine measurement as a proxy. We further demonstrated that deleting HMX1 may represent a general strategy for P450 function improvement by improving activity of a second P450 enzyme, BM3, which performs a distinct reaction.
Collapse
Affiliation(s)
- Judy Savitskaya
- University of California, Berkeley - UCSF Graduate Program in Bioengineering, Berkeley, CA, 94720, USA.,Department of Bioengineering, University of California, Berkeley, Berkeley, CA, 94720, USA
| | - Ryan J Protzko
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, 94720, USA
| | - Francesca-Zhoufan Li
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, 94720, USA
| | - Adam P Arkin
- University of California, Berkeley - UCSF Graduate Program in Bioengineering, Berkeley, CA, 94720, USA. .,Department of Bioengineering, University of California, Berkeley, Berkeley, CA, 94720, USA. .,Environmental Genomics & System Biology, Lawrence Berkeley National Lab, Berkeley, California, USA.
| | - John E Dueber
- University of California, Berkeley - UCSF Graduate Program in Bioengineering, Berkeley, CA, 94720, USA. .,Department of Bioengineering, University of California, Berkeley, Berkeley, CA, 94720, USA. .,Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.
| |
Collapse
|
4
|
Atkinson JT, Wu B, Segatori L, Silberg JJ. Overcoming component limitations in synthetic biology through transposon-mediated protein engineering. Methods Enzymol 2019; 621:191-212. [DOI: 10.1016/bs.mie.2019.02.014] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
|
5
|
Horikawa T, Hung LW, Kim HB, Shaya D, Kim CY, Terwilliger TC, Yamashita E, Aoki M, Okada U, Murakami S. BpeB, a major resistance-nodulation-cell division transporter from Burkholderia cenocepacia: construct design, crystallization and preliminary structural analysis. Acta Crystallogr F Struct Biol Commun 2018; 74:710-716. [PMID: 30387776 PMCID: PMC6213979 DOI: 10.1107/s2053230x18013547] [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: 08/01/2018] [Accepted: 09/24/2018] [Indexed: 11/11/2022] Open
Abstract
Burkholderia cenocepacia is an opportunistic pathogen that infects cystic fibrosis patients, causing pneumonia and septicemia. B. cenocepacia has intrinsic antibiotic resistance against monobactams, aminoglycosides, chloramphenicol and fluoroquinolones that is contributed by a homologue of BpeB, which is a member of the resistance-nodulation-cell division (RND)-type multidrug-efflux transporters. Here, the cloning, overexpression, purification, construct design for crystallization and preliminary X-ray diffraction analysis of this BpeB homologue from B. cenocepacia are reported. Two truncation variants were designed to remove possible disordered regions based on comparative sequence and structural analysis to salvage the wild-type protein, which failed to crystallize. The 17-residue carboxyl-terminal truncation yielded crystals that diffracted to 3.6 Å resolution. The efflux function measured using minimal inhibitory concentration assays indicated that the truncation decreased, but did not eliminate, the efflux activity of the transporter.
Collapse
Affiliation(s)
- Tomonari Horikawa
- Department of Life Science and Technology, Tokyo Institute of Technology, Yokohama 226-8501, Japan
| | - Li-Wei Hung
- Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - Heung-Bok Kim
- Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - David Shaya
- Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - Chang-Yub Kim
- Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - Thomas C. Terwilliger
- Los Alamos National Laboratory, Los Alamos, NM 87545, USA
- New Mexico Consortium, Los Alamos, NM 87544, USA
| | - Eiki Yamashita
- Institute for Protein Research, Osaka University, Osaka 565-0871, Japan
| | - Maho Aoki
- Department of Life Science and Technology, Tokyo Institute of Technology, Yokohama 226-8501, Japan
| | - Ui Okada
- Department of Life Science and Technology, Tokyo Institute of Technology, Yokohama 226-8501, Japan
| | - Satoshi Murakami
- Department of Life Science and Technology, Tokyo Institute of Technology, Yokohama 226-8501, Japan
| |
Collapse
|
6
|
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.
Collapse
|
7
|
Morelli A, Cabezas Y, Mills LJ, Seelig B. Extensive libraries of gene truncation variants generated by in vitro transposition. Nucleic Acids Res 2017; 45:e78. [PMID: 28130425 PMCID: PMC5449547 DOI: 10.1093/nar/gkx030] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2016] [Accepted: 01/20/2017] [Indexed: 11/14/2022] Open
Abstract
The detailed analysis of the impact of deletions on proteins or nucleic acids can reveal important functional regions and lead to variants with improved macromolecular properties. We present a method to generate large libraries of mutants with deletions of varying length that are randomly distributed throughout a given gene. This technique facilitates the identification of crucial sequence regions in nucleic acids or proteins. The approach utilizes in vitro transposition to generate 5΄ and 3΄ fragment sub-libraries of a given gene, which are then randomly recombined to yield a final library comprising both terminal and internal deletions. The method is easy to implement and can generate libraries in three to four days. We used this approach to produce a library of >9000 random deletion mutants of an artificial RNA ligase enzyme representing 32% of all possible deletions. The quality of the library was assessed by next-generation sequencing and detailed bioinformatics analysis. Finally, we subjected this library to in vitro selection and obtained fully functional variants with deletions of up to 18 amino acids of the parental enzyme that had been 95 amino acids in length.
Collapse
Affiliation(s)
- Aleardo Morelli
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA.,BioTechnology Institute, University of Minnesota, St. Paul, MN 55108, USA
| | - Yari Cabezas
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA.,BioTechnology Institute, University of Minnesota, St. Paul, MN 55108, USA
| | - Lauren J Mills
- Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, MN 55455, USA
| | - Burckhard Seelig
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA.,BioTechnology Institute, University of Minnesota, St. Paul, MN 55108, USA
| |
Collapse
|
8
|
Jones AM, Atkinson JT, Silberg JJ. PERMutation Using Transposase Engineering (PERMUTE): A Simple Approach for Constructing Circularly Permuted Protein Libraries. Methods Mol Biol 2017; 1498:295-308. [PMID: 27709583 DOI: 10.1007/978-1-4939-6472-7_19] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Rearrangements that alter the order of a protein's sequence are used in the lab to study protein folding, improve activity, and build molecular switches. One of the simplest ways to rearrange a protein sequence is through random circular permutation, where native protein termini are linked together and new termini are created elsewhere through random backbone fission. Transposase mutagenesis has emerged as a simple way to generate libraries encoding different circularly permuted variants of proteins. With this approach, a synthetic transposon (called a permuteposon) is randomly inserted throughout a circularized gene to generate vectors that express different permuted variants of a protein. In this chapter, we outline the protocol for constructing combinatorial libraries of circularly permuted proteins using transposase mutagenesis, and we describe the different permuteposons that have been developed to facilitate library construction.
Collapse
Affiliation(s)
- Alicia M Jones
- Biosciences Department, Rice University, MS-140, 6100 Main Street, Houston, TX, 77005, USA
| | - Joshua T Atkinson
- Systems, Synthetic, and Physical Biology Graduate Program, Rice University, 6100 Main MS-180, Houston, TX, 77005, USA
| | - Jonathan J Silberg
- Biosciences Department, Rice University, MS-140, 6100 Main Street, Houston, TX, 77005, USA.
| |
Collapse
|
9
|
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.
Collapse
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.
| |
Collapse
|
10
|
Liu SS, Wei X, Ji Q, Xin X, Jiang B, Liu J. A facile and efficient transposon mutagenesis method for generation of multi-codon deletions in protein sequences. J Biotechnol 2016; 227:27-34. [DOI: 10.1016/j.jbiotec.2016.03.038] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Revised: 03/17/2016] [Accepted: 03/21/2016] [Indexed: 12/17/2022]
|
11
|
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]
|
12
|
Kiljunen S, Pajunen MI, Dilks K, Storf S, Pohlschroder M, Savilahti H. Generation of comprehensive transposon insertion mutant library for the model archaeon, Haloferax volcanii, and its use for gene discovery. BMC Biol 2014; 12:103. [PMID: 25488358 PMCID: PMC4300041 DOI: 10.1186/s12915-014-0103-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2014] [Accepted: 11/26/2014] [Indexed: 12/04/2022] Open
Abstract
Background Archaea share fundamental properties with bacteria and eukaryotes. Yet, they also possess unique attributes, which largely remain poorly characterized. Haloferax volcanii is an aerobic, moderately halophilic archaeon that can be grown in defined media. It serves as an excellent archaeal model organism to study the molecular mechanisms of biological processes and cellular responses to changes in the environment. Studies on haloarchaea have been impeded by the lack of efficient genetic screens that would facilitate the identification of protein functions and respective metabolic pathways. Results Here, we devised an insertion mutagenesis strategy that combined Mu in vitro DNA transposition and homologous-recombination-based gene targeting in H. volcanii. We generated an insertion mutant library, in which the clones contained a single genomic insertion. From the library, we isolated pigmentation-defective and auxotrophic mutants, and the respective insertions pinpointed a number of genes previously known to be involved in carotenoid and amino acid biosynthesis pathways, thus validating the performance of the methodologies used. We also identified mutants that had a transposon insertion in a gene encoding a protein of unknown or putative function, demonstrating that novel roles for non-annotated genes could be assigned. Conclusions We have generated, for the first time, a random genomic insertion mutant library for a halophilic archaeon and used it for efficient gene discovery. The library will facilitate the identification of non-essential genes behind any specific biochemical pathway. It represents a significant step towards achieving a more complete understanding of the unique characteristics of halophilic archaea. Electronic supplementary material The online version of this article (doi:10.1186/s12915-014-0103-3) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Saija Kiljunen
- Division of Genetics and Physiology, Department of Biology, University of Turku, Turku, Finland.
| | - Maria I Pajunen
- Division of Genetics and Physiology, Department of Biology, University of Turku, Turku, Finland. .,Current address: Department of Biosciences, Division of Biochemistry and Biotechnology, University of Helsinki, Helsinki, Finland.
| | - Kieran Dilks
- Department of Biology, University of Pennsylvania, Philadelphia, PA, USA.
| | - Stefanie Storf
- Department of Biology, University of Pennsylvania, Philadelphia, PA, USA.
| | | | - Harri Savilahti
- Division of Genetics and Physiology, Department of Biology, University of Turku, Turku, Finland.
| |
Collapse
|
13
|
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.
Collapse
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
| |
Collapse
|
14
|
Segall-Shapiro TH, Meyer AJ, Ellington AD, Sontag ED, Voigt CA. A 'resource allocator' for transcription based on a highly fragmented T7 RNA polymerase. Mol Syst Biol 2014; 10:742. [PMID: 25080493 PMCID: PMC4299498 DOI: 10.15252/msb.20145299] [Citation(s) in RCA: 127] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Synthetic genetic systems share resources with the host, including machinery for transcription
and translation. Phage RNA polymerases (RNAPs) decouple transcription from the host and generate
high expression. However, they can exhibit toxicity and lack accessory proteins (σ factors
and activators) that enable switching between different promoters and modulation of activity. Here,
we show that T7 RNAP (883 amino acids) can be divided into four fragments that have to be
co-expressed to function. The DNA-binding loop is encoded in a C-terminal 285-aa ‘σ
fragment’, and fragments with different specificity can direct the remaining 601-aa
‘core fragment’ to different promoters. Using these parts, we have built a resource
allocator that sets the core fragment concentration, which is then shared by multiple σ
fragments. Adjusting the concentration of the core fragment sets the maximum transcriptional
capacity available to a synthetic system. Further, positive and negative regulation is implemented
using a 67-aa N-terminal ‘α fragment’ and a null (inactivated) σ
fragment, respectively. The α fragment can be fused to recombinant proteins to make promoters
responsive to their levels. These parts provide a toolbox to allocate transcriptional resources via
different schemes, which we demonstrate by building a system which adjusts promoter activity to
compensate for the difference in copy number of two plasmids.
Collapse
Affiliation(s)
- Thomas H Segall-Shapiro
- Department of Biological Engineering, Synthetic Biology Center Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Adam J Meyer
- Institute for Cellular and Molecular Biology University of Texas at Austin, Austin, TX, USA
| | - Andrew D Ellington
- Institute for Cellular and Molecular Biology University of Texas at Austin, Austin, TX, USA
| | - Eduardo D Sontag
- Department of Mathematics, Rutgers University, Piscataway, NJ, USA
| | - Christopher A Voigt
- Department of Biological Engineering, Synthetic Biology Center Massachusetts Institute of Technology, Cambridge, MA, USA
| |
Collapse
|
15
|
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.
Collapse
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
| |
Collapse
|
16
|
Mehta MM, Liu S, Silberg JJ. A transposase strategy for creating libraries of circularly permuted proteins. Nucleic Acids Res 2012; 40:e71. [PMID: 22319214 PMCID: PMC3351165 DOI: 10.1093/nar/gks060] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
A simple approach for creating libraries of circularly permuted proteins is described that is called PERMutation Using Transposase Engineering (PERMUTE). In PERMUTE, the transposase MuA is used to randomly insert a minitransposon that can function as a protein expression vector into a plasmid that contains the open reading frame (ORF) being permuted. A library of vectors that express different permuted variants of the ORF-encoded protein is created by: (i) using bacteria to select for target vectors that acquire an integrated minitransposon; (ii) excising the ensemble of ORFs that contain an integrated minitransposon from the selected vectors; and (iii) circularizing the ensemble of ORFs containing integrated minitransposons using intramolecular ligation. Construction of a Thermotoga neapolitana adenylate kinase (AK) library using PERMUTE revealed that this approach produces vectors that express circularly permuted proteins with distinct sequence diversity from existing methods. In addition, selection of this library for variants that complement the growth of Escherichia coli with a temperature-sensitive AK identified functional proteins with novel architectures, suggesting that PERMUTE will be useful for the directed evolution of proteins with new functions.
Collapse
Affiliation(s)
- Manan M Mehta
- Department of Biochemistry and Cell Biology Rice University, Houston, TX 77251, USA
| | | | | |
Collapse
|
17
|
Pajunen MI, Rasila TS, Happonen LJ, Lamberg A, Haapa-Paananen S, Kiljunen S, Savilahti H. Universal platform for quantitative analysis of DNA transposition. Mob DNA 2010; 1:24. [PMID: 21110848 PMCID: PMC3003695 DOI: 10.1186/1759-8753-1-24] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2010] [Accepted: 11/26/2010] [Indexed: 01/16/2023] Open
Abstract
Background Completed genome projects have revealed an astonishing diversity of transposable genetic elements, implying the existence of novel element families yet to be discovered from diverse life forms. Concurrently, several better understood transposon systems have been exploited as efficient tools in molecular biology and genomics applications. Characterization of new mobile elements and improvement of the existing transposition technology platforms warrant easy-to-use assays for the quantitative analysis of DNA transposition. Results Here we developed a universal in vivo platform for the analysis of transposition frequency with class II mobile elements, i.e., DNA transposons. For each particular transposon system, cloning of the transposon ends and the cognate transposase gene, in three consecutive steps, generates a multifunctional plasmid, which drives inducible expression of the transposase gene and includes a mobilisable lacZ-containing reporter transposon. The assay scores transposition events as blue microcolonies, papillae, growing within otherwise whitish Escherichia coli colonies on indicator plates. We developed the assay using phage Mu transposition as a test model and validated the platform using various MuA transposase mutants. For further validation and to illustrate universality, we introduced IS903 transposition system components into the assay. The developed assay is adjustable to a desired level of initial transposition via the control of a plasmid-borne E. coli arabinose promoter. In practice, the transposition frequency is modulated by varying the concentration of arabinose or glucose in the growth medium. We show that variable levels of transpositional activity can be analysed, thus enabling straightforward screens for hyper- or hypoactive transposase mutants, regardless of the original wild-type activity level. Conclusions The established universal papillation assay platform should be widely applicable to a variety of mobile elements. It can be used for mechanistic studies to dissect transposition and provides a means to screen or scrutinise transposase mutants and genes encoding host factors. In succession, improved versions of transposition systems should yield better tools for molecular biology and offer versatile genome modification vehicles for many types of studies, including gene therapy and stem cell research.
Collapse
Affiliation(s)
- Maria I Pajunen
- Division of Genetics and Physiology, Department of Biology, Vesilinnantie 5, FIN-20014 University of Turku, Finland.
| | | | | | | | | | | | | |
Collapse
|
18
|
Weber M, Chernov K, Turakainen H, Wohlfahrt G, Pajunen M, Savilahti H, Jäntti J. Mso1p regulates membrane fusion through interactions with the putative N-peptide-binding area in Sec1p domain 1. Mol Biol Cell 2010; 21:1362-74. [PMID: 20181830 PMCID: PMC2854094 DOI: 10.1091/mbc.e09-07-0546] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
We show that the putative N-peptide binding area in Sec1p domain 1 is important for Mso1p binding and that Mso1p can interact with Sso1p and Sso2p. Our results suggest that Mso1p mimics N-peptide binding to facilitate membrane fusion. Sec1p/Munc18 (SM) family proteins regulate SNARE complex function in membrane fusion through their interactions with syntaxins. In addition to syntaxins, only a few SM protein interacting proteins are known and typically, their binding modes with SM proteins are poorly characterized. We previously identified Mso1p as a Sec1p-binding protein and showed that it is involved in membrane fusion regulation. Here we demonstrate that Mso1p and Sec1p interact at sites of exocytosis and that the Mso1p–Sec1p interaction site depends on a functional Rab GTPase Sec4p and its GEF Sec2p. Random and targeted mutagenesis of Sec1p, followed by analysis of protein interactions, indicates that Mso1p interacts with Sec1p domain 1 and that this interaction is important for membrane fusion. In many SM family proteins, domain 1 binds to a N-terminal peptide of a syntaxin family protein. The Sec1p-interacting syntaxins Sso1p and Sso2p lack the N-terminal peptide. We show that the putative N-peptide binding area in Sec1p domain 1 is important for Mso1p binding, and that Mso1p can interact with Sso1p and Sso2p. Our results suggest that Mso1p mimics N-peptide binding to facilitate membrane fusion.
Collapse
Affiliation(s)
- Marion Weber
- Research Program in Cell and Molecular Biology, Institute of Biotechnology, University of Helsinki, 00014 Helsinki, Finland
| | | | | | | | | | | | | |
Collapse
|
19
|
Turakainen H, Saarimäki-Vire J, Sinjushina N, Partanen J, Savilahti H. Transposition-based method for the rapid generation of gene-targeting vectors to produce Cre/Flp-modifiable conditional knock-out mice. PLoS One 2009; 4:e4341. [PMID: 19194496 PMCID: PMC2632748 DOI: 10.1371/journal.pone.0004341] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2008] [Accepted: 12/24/2008] [Indexed: 11/18/2022] Open
Abstract
Conditional gene targeting strategies are progressively used to study gene function tissue-specifically and/or at a defined time period. Instrumental to all of these strategies is the generation of targeting vectors, and any methodology that would streamline the procedure would be highly beneficial. We describe a comprehensive transposition-based strategy to produce gene-targeting vectors for the generation of mouse conditional alleles. The system employs a universal cloning vector and two custom-designed mini-Mu transposons. It produces targeting constructions directly from BAC clones, and the alleles generated are modifiable by Cre and Flp recombinases. We demonstrate the applicability of the methodology by modifying two mouse genes, Chd22 and Drapc1. This straightforward strategy should be readily suitable for high-throughput targeting vector production.
Collapse
Affiliation(s)
- Hilkka Turakainen
- Program in Cellular Biotechnology, Institute of Biotechnology, Viikki Biocenter, University of Helsinki, Helsinki, Finland
| | - Jonna Saarimäki-Vire
- Program in Developmental Biology, Institute of Biotechnology, Viikki Biocenter, University of Helsinki, Helsinki, Finland
| | - Natalia Sinjushina
- Program in Developmental Biology, Institute of Biotechnology, Viikki Biocenter, University of Helsinki, Helsinki, Finland
| | - Juha Partanen
- Program in Developmental Biology, Institute of Biotechnology, Viikki Biocenter, University of Helsinki, Helsinki, Finland
| | - Harri Savilahti
- Program in Cellular Biotechnology, Institute of Biotechnology, Viikki Biocenter, University of Helsinki, Helsinki, Finland
- Division of Genetics and Physiology, Department of Biology, University of Turku, Turku, Finland
- * E-mail:
| |
Collapse
|
20
|
Wu Z, Xuanyuan Z, Li R, Jiang D, Li C, Xu H, Bai Y, Zhang X, Turakainen H, Saris P, Savilahti H, Qiao M. Mu transposition complex mutagenesis inLactococcus lactis- identification of genes affecting nisin production. J Appl Microbiol 2009; 106:41-8. [DOI: 10.1111/j.1365-2672.2008.03962.x] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
|
21
|
Paatero AO, Turakainen H, Happonen LJ, Olsson C, Palomäki T, Pajunen MI, Meng X, Otonkoski T, Tuuri T, Berry C, Malani N, Frilander MJ, Bushman FD, Savilahti H. Bacteriophage Mu integration in yeast and mammalian genomes. Nucleic Acids Res 2008; 36:e148. [PMID: 18953026 PMCID: PMC2602771 DOI: 10.1093/nar/gkn801] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2008] [Revised: 10/09/2008] [Accepted: 10/10/2008] [Indexed: 11/14/2022] Open
Abstract
Genomic parasites have evolved distinctive lifestyles to optimize replication in the context of the genomes they inhabit. Here, we introduced new DNA into eukaryotic cells using bacteriophage Mu DNA transposition complexes, termed 'transpososomes'. Following electroporation of transpososomes and selection for marker gene expression, efficient integration was verified in yeast, mouse and human genomes. Although Mu has evolved in prokaryotes, strong biases were seen in the target site distributions in eukaryotic genomes, and these biases differed between yeast and mammals. In Saccharomyces cerevisiae transposons accumulated outside of genes, consistent with selection against gene disruption. In mouse and human cells, transposons accumulated within genes, which previous work suggests is a favorable location for efficient expression of selectable markers. Naturally occurring transposons and viruses in yeast and mammals show related, but more extreme, targeting biases, suggesting that they are responding to the same pressures. These data help clarify the constraints exerted by genome structure on genomic parasites, and illustrate the wide utility of the Mu transpososome technology for gene transfer in eukaryotic cells.
Collapse
Affiliation(s)
- Anja O. Paatero
- Program in Cellular Biotechnology, Institute of Biotechnology, Viikki Biocenter, Biomedicum Stem Cell Center, Biomedicum Helsinki, University of Helsinki, Helsinki, Division of Genetics and Physiology, Department of Biology, University of Turku, Turku, Program in Developmental Biology, Institute of Biotechnology, Viikki Biocenter, University of Helsinki, Hospital for Children and Adolescents, University of Helsinki, Family Federation of Finland, Helsinki, Finland and Department of Microbiology, University of Pennsylvania School of Medicine, Philadelphia, PA, USA
| | - Hilkka Turakainen
- Program in Cellular Biotechnology, Institute of Biotechnology, Viikki Biocenter, Biomedicum Stem Cell Center, Biomedicum Helsinki, University of Helsinki, Helsinki, Division of Genetics and Physiology, Department of Biology, University of Turku, Turku, Program in Developmental Biology, Institute of Biotechnology, Viikki Biocenter, University of Helsinki, Hospital for Children and Adolescents, University of Helsinki, Family Federation of Finland, Helsinki, Finland and Department of Microbiology, University of Pennsylvania School of Medicine, Philadelphia, PA, USA
| | - Lotta J. Happonen
- Program in Cellular Biotechnology, Institute of Biotechnology, Viikki Biocenter, Biomedicum Stem Cell Center, Biomedicum Helsinki, University of Helsinki, Helsinki, Division of Genetics and Physiology, Department of Biology, University of Turku, Turku, Program in Developmental Biology, Institute of Biotechnology, Viikki Biocenter, University of Helsinki, Hospital for Children and Adolescents, University of Helsinki, Family Federation of Finland, Helsinki, Finland and Department of Microbiology, University of Pennsylvania School of Medicine, Philadelphia, PA, USA
| | - Cia Olsson
- Program in Cellular Biotechnology, Institute of Biotechnology, Viikki Biocenter, Biomedicum Stem Cell Center, Biomedicum Helsinki, University of Helsinki, Helsinki, Division of Genetics and Physiology, Department of Biology, University of Turku, Turku, Program in Developmental Biology, Institute of Biotechnology, Viikki Biocenter, University of Helsinki, Hospital for Children and Adolescents, University of Helsinki, Family Federation of Finland, Helsinki, Finland and Department of Microbiology, University of Pennsylvania School of Medicine, Philadelphia, PA, USA
| | - Tiina Palomäki
- Program in Cellular Biotechnology, Institute of Biotechnology, Viikki Biocenter, Biomedicum Stem Cell Center, Biomedicum Helsinki, University of Helsinki, Helsinki, Division of Genetics and Physiology, Department of Biology, University of Turku, Turku, Program in Developmental Biology, Institute of Biotechnology, Viikki Biocenter, University of Helsinki, Hospital for Children and Adolescents, University of Helsinki, Family Federation of Finland, Helsinki, Finland and Department of Microbiology, University of Pennsylvania School of Medicine, Philadelphia, PA, USA
| | - Maria I. Pajunen
- Program in Cellular Biotechnology, Institute of Biotechnology, Viikki Biocenter, Biomedicum Stem Cell Center, Biomedicum Helsinki, University of Helsinki, Helsinki, Division of Genetics and Physiology, Department of Biology, University of Turku, Turku, Program in Developmental Biology, Institute of Biotechnology, Viikki Biocenter, University of Helsinki, Hospital for Children and Adolescents, University of Helsinki, Family Federation of Finland, Helsinki, Finland and Department of Microbiology, University of Pennsylvania School of Medicine, Philadelphia, PA, USA
| | - Xiaojuan Meng
- Program in Cellular Biotechnology, Institute of Biotechnology, Viikki Biocenter, Biomedicum Stem Cell Center, Biomedicum Helsinki, University of Helsinki, Helsinki, Division of Genetics and Physiology, Department of Biology, University of Turku, Turku, Program in Developmental Biology, Institute of Biotechnology, Viikki Biocenter, University of Helsinki, Hospital for Children and Adolescents, University of Helsinki, Family Federation of Finland, Helsinki, Finland and Department of Microbiology, University of Pennsylvania School of Medicine, Philadelphia, PA, USA
| | - Timo Otonkoski
- Program in Cellular Biotechnology, Institute of Biotechnology, Viikki Biocenter, Biomedicum Stem Cell Center, Biomedicum Helsinki, University of Helsinki, Helsinki, Division of Genetics and Physiology, Department of Biology, University of Turku, Turku, Program in Developmental Biology, Institute of Biotechnology, Viikki Biocenter, University of Helsinki, Hospital for Children and Adolescents, University of Helsinki, Family Federation of Finland, Helsinki, Finland and Department of Microbiology, University of Pennsylvania School of Medicine, Philadelphia, PA, USA
| | - Timo Tuuri
- Program in Cellular Biotechnology, Institute of Biotechnology, Viikki Biocenter, Biomedicum Stem Cell Center, Biomedicum Helsinki, University of Helsinki, Helsinki, Division of Genetics and Physiology, Department of Biology, University of Turku, Turku, Program in Developmental Biology, Institute of Biotechnology, Viikki Biocenter, University of Helsinki, Hospital for Children and Adolescents, University of Helsinki, Family Federation of Finland, Helsinki, Finland and Department of Microbiology, University of Pennsylvania School of Medicine, Philadelphia, PA, USA
| | - Charles Berry
- Program in Cellular Biotechnology, Institute of Biotechnology, Viikki Biocenter, Biomedicum Stem Cell Center, Biomedicum Helsinki, University of Helsinki, Helsinki, Division of Genetics and Physiology, Department of Biology, University of Turku, Turku, Program in Developmental Biology, Institute of Biotechnology, Viikki Biocenter, University of Helsinki, Hospital for Children and Adolescents, University of Helsinki, Family Federation of Finland, Helsinki, Finland and Department of Microbiology, University of Pennsylvania School of Medicine, Philadelphia, PA, USA
| | - Nirav Malani
- Program in Cellular Biotechnology, Institute of Biotechnology, Viikki Biocenter, Biomedicum Stem Cell Center, Biomedicum Helsinki, University of Helsinki, Helsinki, Division of Genetics and Physiology, Department of Biology, University of Turku, Turku, Program in Developmental Biology, Institute of Biotechnology, Viikki Biocenter, University of Helsinki, Hospital for Children and Adolescents, University of Helsinki, Family Federation of Finland, Helsinki, Finland and Department of Microbiology, University of Pennsylvania School of Medicine, Philadelphia, PA, USA
| | - Mikko J. Frilander
- Program in Cellular Biotechnology, Institute of Biotechnology, Viikki Biocenter, Biomedicum Stem Cell Center, Biomedicum Helsinki, University of Helsinki, Helsinki, Division of Genetics and Physiology, Department of Biology, University of Turku, Turku, Program in Developmental Biology, Institute of Biotechnology, Viikki Biocenter, University of Helsinki, Hospital for Children and Adolescents, University of Helsinki, Family Federation of Finland, Helsinki, Finland and Department of Microbiology, University of Pennsylvania School of Medicine, Philadelphia, PA, USA
| | - Frederic D. Bushman
- Program in Cellular Biotechnology, Institute of Biotechnology, Viikki Biocenter, Biomedicum Stem Cell Center, Biomedicum Helsinki, University of Helsinki, Helsinki, Division of Genetics and Physiology, Department of Biology, University of Turku, Turku, Program in Developmental Biology, Institute of Biotechnology, Viikki Biocenter, University of Helsinki, Hospital for Children and Adolescents, University of Helsinki, Family Federation of Finland, Helsinki, Finland and Department of Microbiology, University of Pennsylvania School of Medicine, Philadelphia, PA, USA
| | - Harri Savilahti
- Program in Cellular Biotechnology, Institute of Biotechnology, Viikki Biocenter, Biomedicum Stem Cell Center, Biomedicum Helsinki, University of Helsinki, Helsinki, Division of Genetics and Physiology, Department of Biology, University of Turku, Turku, Program in Developmental Biology, Institute of Biotechnology, Viikki Biocenter, University of Helsinki, Hospital for Children and Adolescents, University of Helsinki, Family Federation of Finland, Helsinki, Finland and Department of Microbiology, University of Pennsylvania School of Medicine, Philadelphia, PA, USA
| |
Collapse
|
22
|
Pajunen M, Turakainen H, Poussu E, Peränen J, Vihinen M, Savilahti H. High-precision mapping of protein protein interfaces: an integrated genetic strategy combining en masse mutagenesis and DNA-level parallel analysis on a yeast two-hybrid platform. Nucleic Acids Res 2007; 35:e103. [PMID: 17702760 PMCID: PMC2018616 DOI: 10.1093/nar/gkm563] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Understanding networks of protein–protein interactions constitutes an essential component on a path towards comprehensive description of cell function. Whereas efficient techniques are readily available for the initial identification of interacting protein partners, practical strategies are lacking for the subsequent high-resolution mapping of regions involved in protein–protein interfaces. We present here a genetic strategy to accurately map interacting protein regions at amino acid precision. The system is based on parallel construction, sampling and analysis of a comprehensive insertion mutant library. The methodology integrates Mu in vitro transposition-based random pentapeptide mutagenesis of proteins, yeast two-hybrid screening and high-resolution genetic footprinting. The strategy is general and applicable to any interacting protein pair. We demonstrate the feasibility of the methodology by mapping the region in human JFC1 that interacts with Rab8A, and we show that the association is mediated by the Slp homology domain 1.
Collapse
Affiliation(s)
- Maria Pajunen
- Program in Cellular Biotechnology, Institute of Biotechnology, Viikki Biocenter, University of Helsinki, Institute of Medical Technology, University of Tampere, Research Unit, Tampere University Hospital, Tampere and Division of Genetics and Physiology, Department of Biology, University of Turku, Finland
| | - Hilkka Turakainen
- Program in Cellular Biotechnology, Institute of Biotechnology, Viikki Biocenter, University of Helsinki, Institute of Medical Technology, University of Tampere, Research Unit, Tampere University Hospital, Tampere and Division of Genetics and Physiology, Department of Biology, University of Turku, Finland
| | - Eini Poussu
- Program in Cellular Biotechnology, Institute of Biotechnology, Viikki Biocenter, University of Helsinki, Institute of Medical Technology, University of Tampere, Research Unit, Tampere University Hospital, Tampere and Division of Genetics and Physiology, Department of Biology, University of Turku, Finland
| | - Johan Peränen
- Program in Cellular Biotechnology, Institute of Biotechnology, Viikki Biocenter, University of Helsinki, Institute of Medical Technology, University of Tampere, Research Unit, Tampere University Hospital, Tampere and Division of Genetics and Physiology, Department of Biology, University of Turku, Finland
| | - Mauno Vihinen
- Program in Cellular Biotechnology, Institute of Biotechnology, Viikki Biocenter, University of Helsinki, Institute of Medical Technology, University of Tampere, Research Unit, Tampere University Hospital, Tampere and Division of Genetics and Physiology, Department of Biology, University of Turku, Finland
| | - Harri Savilahti
- Program in Cellular Biotechnology, Institute of Biotechnology, Viikki Biocenter, University of Helsinki, Institute of Medical Technology, University of Tampere, Research Unit, Tampere University Hospital, Tampere and Division of Genetics and Physiology, Department of Biology, University of Turku, Finland
- *To whom correspondence should be addressed. +358 9 191 59516+358 9 191 59366
| |
Collapse
|
23
|
Orsini L, Pajunen M, Hanski I, Savilahti H. SNP discovery by mismatch-targeting of Mu transposition. Nucleic Acids Res 2007; 35:e44. [PMID: 17311815 PMCID: PMC1874615 DOI: 10.1093/nar/gkm070] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Single nucleotide polymorphisms (SNPs) represent a valuable resource for the mapping of human disease genes and induced mutations in model organisms. SNPs may become the markers of choice also for population ecology and evolutionary studies, but their isolation for non-model organisms with unsequenced genomes is often difficult. Here, we describe a rapid and cost-effective strategy to isolate SNPs that exploits the property of the bacteriophage Mu transposition machinery to target mismatched DNA sites and thereby to effectively detect polymorphic loci. To demonstrate the methodology, we isolated 164 SNPs from the unsequenced genome of the Glanville fritillary butterfly (Melitaea cinxia), a much-studied species in population biology, and we validated 24 of them. The strategy involves standard molecular biology techniques as well as undemanding MuA transposase-catalyzed in vitro transposition reactions, and it is applicable to any organism.
Collapse
Affiliation(s)
- Luisa Orsini
- Metapopulation Research Group, Department of Biological and Environmental Sciences, PO Box 65, and Research Program in Cellular Biotechnology, Institute of Biotechnology, PO Box 56, FIN-00014, University of Helsinki, Finland and Division of Genetics and Physiology, Department of Biology, FIN-20014, University of Turku, Finland
| | - Maria Pajunen
- Metapopulation Research Group, Department of Biological and Environmental Sciences, PO Box 65, and Research Program in Cellular Biotechnology, Institute of Biotechnology, PO Box 56, FIN-00014, University of Helsinki, Finland and Division of Genetics and Physiology, Department of Biology, FIN-20014, University of Turku, Finland
| | - Ilkka Hanski
- Metapopulation Research Group, Department of Biological and Environmental Sciences, PO Box 65, and Research Program in Cellular Biotechnology, Institute of Biotechnology, PO Box 56, FIN-00014, University of Helsinki, Finland and Division of Genetics and Physiology, Department of Biology, FIN-20014, University of Turku, Finland
| | - Harri Savilahti
- Metapopulation Research Group, Department of Biological and Environmental Sciences, PO Box 65, and Research Program in Cellular Biotechnology, Institute of Biotechnology, PO Box 56, FIN-00014, University of Helsinki, Finland and Division of Genetics and Physiology, Department of Biology, FIN-20014, University of Turku, Finland
- *To whom correspondence should be addressed. +358 9 191 59516+358 9 191 59366
| |
Collapse
|
24
|
Current awareness on yeast. Yeast 2006. [DOI: 10.1002/yea.1172] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
|