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de Raad M, Kooijmans SAA, Teunissen EA, Mastrobattista E. A solid-phase platform for combinatorial and scarless multipart gene assembly. ACS Synth Biol 2013; 2:316-26. [PMID: 23654269 DOI: 10.1021/sb300122q] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
With the emergence of standardized genetic modules as part of the synthetic biology toolbox, the need for universal and automatable assembly protocols increases. Although several methods and standards have been developed, these all suffer from drawbacks such as the introduction of scar sequences during ligation or the need for specific flanking sequences or a priori knowledge of the final sequence to be obtained. We have developed a method for scarless ligation of multipart gene segments in a truly sequence-independent fashion. The big advantage of this approach is that it is combinatorial, allowing the generation of all combinations of several variants of two or more modules to be ligated in less than a day. This method is based on the ligation of single-stranded or double-stranded oligodeoxynucleotides (ODN) and PCR products immobilized on a solid support. Different settings were tested to optimize the solid-support ligation. Finally, to show proof of concept for this novel multipart gene assembly platform a small library of all possible combinations of 4 BioBrick modules was generated and tested.
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Affiliation(s)
- Markus de Raad
- Department of Pharmaceutics, Utrecht Institute for Pharmaceutical
Sciences, Faculty of Science, University of Utrecht, Universiteitsweg 99, 3584 CG Utrecht, The Netherlands
| | - Sander A. A. Kooijmans
- Department of Clinical Chemistry
and Haematology, University Medical Center Utrecht, Heidelberglaan 100, 3584 CX Utrecht, The Netherlands
| | - Erik A. Teunissen
- Department of Pharmaceutics, Utrecht Institute for Pharmaceutical
Sciences, Faculty of Science, University of Utrecht, Universiteitsweg 99, 3584 CG Utrecht, The Netherlands
| | - Enrico Mastrobattista
- Department of Pharmaceutics, Utrecht Institute for Pharmaceutical
Sciences, Faculty of Science, University of Utrecht, Universiteitsweg 99, 3584 CG Utrecht, The Netherlands
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Abstract
A basic requirement for synthetic biology is the availability of efficient DNA assembly methods. We have previously reported the development of Golden Gate cloning, a method that allows parallel assembly of multiple DNA fragments in a one-tube reaction. Golden Gate cloning can be used for different levels of construct assembly: from gene fragments to complete gene coding sequences, from basic genetic elements to full transcription units, and finally from transcription units to multigene constructs. We provide here a protocol for DNA assembly using Golden Gate cloning, taking as an example the level of assembly of gene fragments to complete coding sequences, a level of cloning that can be used to perform DNA shuffling. Such protocol requires the following steps: (1) selecting fusion sites within parental sequences (sites at which parental sequences will be recombined), (2) amplifying all DNA fragments by PCR to add flanking restriction sites, (3) cloning the amplified fragments in intermediate constructs, and (4) assembling all or selected sets of intermediate constructs in a compatible recipient vector using a one-pot restriction-ligation.
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Affiliation(s)
- Carola Engler
- NOMAD BIOSCIENCE GMBH, Weinbergweg 22, Halle (Saale), Germany
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53
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Ulrich A, Andersen KR, Schwartz TU. Exponential megapriming PCR (EMP) cloning--seamless DNA insertion into any target plasmid without sequence constraints. PLoS One 2012; 7:e53360. [PMID: 23300917 PMCID: PMC3534072 DOI: 10.1371/journal.pone.0053360] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2012] [Accepted: 11/30/2012] [Indexed: 11/23/2022] Open
Abstract
We present a fast, reliable and inexpensive restriction-free cloning method for seamless DNA insertion into any plasmid without sequence limitation. Exponential megapriming PCR (EMP) cloning requires two consecutive PCR steps and can be carried out in one day. We show that EMP cloning has a higher efficiency than restriction-free (RF) cloning, especially for long inserts above 2.5 kb. EMP further enables simultaneous cloning of multiple inserts.
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Affiliation(s)
- Alexander Ulrich
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
- Institut für Chemie und Biochemie, Freie Universität Berlin, Berlin, Germany
| | - Kasper R. Andersen
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Thomas U. Schwartz
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
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Rizk M, Antranikian G, Elleuche S. End-to-end gene fusions and their impact on the production of multifunctional biomass degrading enzymes. Biochem Biophys Res Commun 2012; 428:1-5. [DOI: 10.1016/j.bbrc.2012.09.142] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2012] [Accepted: 09/30/2012] [Indexed: 11/29/2022]
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Tsai WL, Forbes JG, Wang K. Engineering of an elastic scaffolding polyprotein based on an SH3-binding intrinsically disordered titin PEVK module. Protein Expr Purif 2012; 85:187-99. [PMID: 22910563 PMCID: PMC3463739 DOI: 10.1016/j.pep.2012.08.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2012] [Revised: 07/24/2012] [Accepted: 08/03/2012] [Indexed: 01/21/2023]
Abstract
Titin is a large elastic protein found in muscle that maintains the elasticity and structural integrity of the sarcomere. The PEVK region of titin is intrinsically disordered, highly elastic and serves as a hub to bind signaling proteins. Systematic investigation of the structure and affinity profile of the PEVK region will provide important information about the functions of titin. Since PEVK is highly heterogeneous due to extensive differential splicing from more than one hundred exons, we engineered and expressed polyproteins that consist of a defined number of identical single exon modules. These customized polyproteins reduce heterogeneity, amplify interactions of less dominant modules, and most importantly, provide tags for atomic force microscopy and allow more readily interpretable data from single-molecule techniques. Expression and purification of recombinant polyprotein with repeat regions presented many technical challenges: recombination events in tandem repeats of identical DNA sequences exacerbated by high GC content, toxicity of polymer plasmid and expressed protein to the bacteria; early truncation of proteins expressed with different numbers of modules; and extreme sensitivity to proteolysis. We have investigated a number of in vitro and in vivo bacterial and yeast expression systems, as well as baculoviral systems as potential solutions to these problems. We successfully expressed and purified in gram quantities a polyprotein derived from human titin exon 172 using Pichia pastoris yeast. This study provides valuable insights into the technical challenges regarding the engineering and purification of a tandem repeat sequence of an intrinsically disordered biopolymer.
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Affiliation(s)
- Wanxia Li Tsai
- Muscle Proteomics and Nanotechnology Section, Laboratory of Muscle Biology, National Institute of Arthritis and Musculoskeletal and Skin Diseases, NIH/DHHS, Bethesda, MD 20892-8024, USA.
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Abstract
A number of molecular biology techniques are available to generate variants from a particular start gene for eventual protein expression. We discuss the basic principles of these methods in a repertoire that may be used to achieve the elemental steps in protein engineering. These include site-directed, deletion and insertion mutagenesis. We provide detailed case studies, drawn from our own experiences, packaged together with conceptual discussions and include an analysis of the techniques presented with regards to their uses in protein engineering.
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57
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Furtado GP, Ribeiro LF, Lourenzoni MR, Ward RJ. A designed bifunctional laccase/ -1,3-1,4-glucanase enzyme shows synergistic sugar release from milled sugarcane bagasse. Protein Eng Des Sel 2012; 26:15-23. [DOI: 10.1093/protein/gzs057] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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58
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Simplifying protein expression with ligation-free, traceless and tag-switching plasmids. Protein Expr Purif 2012; 85:9-17. [DOI: 10.1016/j.pep.2012.06.007] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2012] [Revised: 06/01/2012] [Accepted: 06/08/2012] [Indexed: 01/30/2023]
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Vaira AM, Lim HS, Bauchan GR, Owens RA, Natilla A, Dienelt MM, Reinsel MD, Hammond J. Lolium latent virus (Alphaflexiviridae) coat proteins: expression and functions in infected plant tissue. J Gen Virol 2012; 93:1814-1824. [PMID: 22573739 DOI: 10.1099/vir.0.042960-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2023] Open
Abstract
The genome of Lolium latent virus (LoLV; genus Lolavirus, family Alphaflexiviridae) is encapsidated by two carboxy-coterminal coat protein (CP) variants (about 28 and 33 kDa), in equimolar proportions. The CP ORF contains two 5'-proximal AUGs encoding Met 1 and Met 49, respectively promoting translation of the 33 and 28 kDa CP variants. The 33 kDa CP N-terminal domain includes a 42 aa sequence encoding a putative chloroplast transit peptide, leading to protein cleavage and alternative derivation of the approximately 28 kDa CP. Mutational analysis of the two in-frame start codons and of the putative proteolytic-cleavage site showed that the N-terminal sequence is crucial for efficient cell-to-cell movement, functional systemic movement, homologous CP interactions and particle formation, but is not required for virus replication. Blocking production of the 28 kDa CP by internal initiation shows no major outcome, whereas additional mutation to prevent proteolytic cleavage at the chloroplast membrane has a dramatic effect on virus infection.
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Affiliation(s)
- Anna Maria Vaira
- USDA-ARS, USNA, Floral and Nursery Plants Research Unit, 10300 Baltimore Avenue, Beltsville, MD, USA
- Istituto di Virologia Vegetale CNR, Strada delle Cacce 73, 10135, Torino, Italy
| | - Hyoun-Sub Lim
- Department of Applied Biology, Chungnam National University, Daejeon, 305-764, Republic of Korea
| | - Gary R Bauchan
- USDA-ARS, PSI, Electron and Confocal Microscopy Unit, 10300 Baltimore Avenue, Beltsville, MD, USA
| | - Robert A Owens
- USDA-ARS, PSI, Molecular Plant Pathology Laboratory, 10300 Baltimore Avenue, Beltsville, MD, USA
| | - Angela Natilla
- USDA-ARS, PSI, Molecular Plant Pathology Laboratory, 10300 Baltimore Avenue, Beltsville, MD, USA
| | - Margaret M Dienelt
- USDA-ARS, USNA, Floral and Nursery Plants Research Unit, 10300 Baltimore Avenue, Beltsville, MD, USA
| | - Michael D Reinsel
- USDA-ARS, USNA, Floral and Nursery Plants Research Unit, 10300 Baltimore Avenue, Beltsville, MD, USA
| | - John Hammond
- USDA-ARS, USNA, Floral and Nursery Plants Research Unit, 10300 Baltimore Avenue, Beltsville, MD, USA
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60
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Bi Y, Qiao X, Hua Z, Zhang L, Liu X, Li L, Hua W, Xiao H, Zhou J, Wei Q, Zheng X. An asymmetric PCR-based, reliable and rapid single-tube native DNA engineering strategy. BMC Biotechnol 2012; 12:39. [PMID: 22768962 PMCID: PMC3408372 DOI: 10.1186/1472-6750-12-39] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2012] [Accepted: 07/06/2012] [Indexed: 12/24/2022] Open
Abstract
Background Widely used restriction-dependent cloning methods are labour-intensive and time-consuming, while several types of ligase-independent cloning approaches have inherent limitations. A rapid and reliable method of cloning native DNA sequences into desired plasmids are highly desired. Results This paper introduces ABI-REC, a novel strategy combining asymmetric bridge PCR with intramolecular homologous recombination in bacteria for native DNA cloning. ABI-REC was developed to precisely clone inserts into defined location in a directional manner within recipient plasmids. It featured an asymmetric 3-primer PCR performed in a single tube that could robustly amplify a chimeric insert-plasmid DNA sequence with homologous arms at both ends. Intramolecular homologous recombination occurred to the chimera when it was transformed into E.coli and produced the desired recombinant plasmids with high efficiency and fidelity. It is rapid, and does not involve any operational nucleotides. We proved the reliability of ABI-REC using a double-resistance reporter assay, and investigated the effects of homology and insert length upon its efficiency. We found that 15 bp homology was sufficient to initiate recombination, while 25 bp homology had the highest cloning efficiency. Inserts up to 4 kb in size could be cloned by this method. The utility and advantages of ABI-REC were demonstrated through a series of pig myostatin (MSTN) promoter and terminator reporter plasmids, whose transcriptional activity was assessed in mammalian cells. We finally used ABI-REC to construct a pig MSTN promoter-terminator cassette reporter and showed that it could work coordinately to express EGFP. Conclusions ABI-REC has the following advantages: (i) rapid and highly efficient; (ii) native DNA cloning without introduction of extra bases; (iii) restriction-free; (iv) easy positioning of directional and site-specific recombination owing to formulated primer design. ABI-REC is a novel approach to DNA engineering and gene functional analysis.
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Affiliation(s)
- Yanzhen Bi
- Hubei Key Laboratory of Animal Embryo Engineering and Molecular Breeding, Institute of Animal Science and Veterinary Medicine, Hubei Academy of Agricultural Science, Wuhan 430064, China.
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Liang H, Wu Z, Jian J, Liu Z. Construction of a fusion flagellin complex and evaluation of the protective immunity of it in red snapper (Lutjanus sanguineus). Lett Appl Microbiol 2012; 55:115-21. [DOI: 10.1111/j.1472-765x.2012.03267.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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62
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Buey RM, Sen I, Kortt O, Mohan R, Gfeller D, Veprintsev D, Kretzschmar I, Scheuermann J, Neri D, Zoete V, Michielin O, de Pereda JM, Akhmanova A, Volkmer R, Steinmetz MO. Sequence determinants of a microtubule tip localization signal (MtLS). J Biol Chem 2012; 287:28227-42. [PMID: 22696216 DOI: 10.1074/jbc.m112.373928] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Microtubule plus-end-tracking proteins (+TIPs) specifically localize to the growing plus-ends of microtubules to regulate microtubule dynamics and functions. A large group of +TIPs contain a short linear motif, SXIP, which is essential for them to bind to end-binding proteins (EBs) and target microtubule ends. The SXIP sequence site thus acts as a widespread microtubule tip localization signal (MtLS). Here we have analyzed the sequence-function relationship of a canonical MtLS. Using synthetic peptide arrays on membrane supports, we identified the residue preferences at each amino acid position of the SXIP motif and its surrounding sequence with respect to EB binding. We further developed an assay based on fluorescence polarization to assess the mechanism of the EB-SXIP interaction and to correlate EB binding and microtubule tip tracking of MtLS sequences from different +TIPs. Finally, we investigated the role of phosphorylation in regulating the EB-SXIP interaction. Together, our results define the sequence determinants of a canonical MtLS and provide the experimental data for bioinformatics approaches to carry out genome-wide predictions of novel +TIPs in multiple organisms.
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Affiliation(s)
- Rubén M Buey
- Laboratory of Biomolecular Research, Paul Scherrer Institut, CH-5232 Villigen PSI, Switzerland
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Abstract
Inverse fusion PCR cloning (IFPC) is an easy, PCR based three-step cloning method that allows the seamless and directional insertion of PCR products into virtually all plasmids, this with a free choice of the insertion site. The PCR-derived inserts contain a vector-complementary 5′-end that allows a fusion with the vector by an overlap extension PCR, and the resulting amplified insert-vector fusions are then circularized by ligation prior transformation. A minimal amount of starting material is needed and experimental steps are reduced. Untreated circular plasmid, or alternatively bacteria containing the plasmid, can be used as templates for the insertion, and clean-up of the insert fragment is not urgently required. The whole cloning procedure can be performed within a minimal hands-on time and results in the generation of hundreds to ten-thousands of positive colonies, with a minimal background.
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Affiliation(s)
- Markus Spiliotis
- Institut für Parasitologie, Universität Bern, Bern, Switzerland.
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Structural characterization of CFA/III and Longus type IVb pili from enterotoxigenic Escherichia coli. J Bacteriol 2012; 194:2725-35. [PMID: 22447901 DOI: 10.1128/jb.00282-12] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The type IV pili are helical filaments found on many Gram-negative pathogenic bacteria, with multiple diverse roles in pathogenesis, including microcolony formation, adhesion, and twitching motility. Many pathogenic enterotoxigenic Escherichia coli (ETEC) isolates express one of two type IV pili belonging to the type IVb subclass: CFA/III or Longus. Here we show a direct correlation between CFA/III expression and ETEC aggregation, suggesting that these pili, like the Vibrio cholerae toxin-coregulated pili (TCP), mediate microcolony formation. We report a 1.26-Å resolution crystal structure of CofA, the major pilin subunit from CFA/III. CofA is very similar in structure to V. cholerae TcpA but possesses a 10-amino-acid insertion that replaces part of the α2-helix with an irregular loop containing a 3(10)-helix. Homology modeling suggests a very similar structure for the Longus LngA pilin. A model for the CFA/III pilus filament was generated using the TCP electron microscopy reconstruction as a template. The unique 3(10)-helix insert fits perfectly within the gap between CofA globular domains. This insert, together with differences in surface-exposed residues, produces a filament that is smoother and more negatively charged than TCP. To explore the specificity of the type IV pilus assembly apparatus, CofA was expressed heterologously in V. cholerae by replacing the tcpA gene with that of cofA within the tcp operon. Although CofA was synthesized and processed by V. cholerae, no CFA/III filaments were detected, suggesting that the components of the type IVb pilus assembly system are highly specific to their pilin substrates.
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Tsvetanova B, Peng L, Liang X, Li K, Hammond L, Peterson TC, Katzen F. Advanced DNA assembly technologies in drug discovery. Expert Opin Drug Discov 2012; 7:371-4. [PMID: 22468854 DOI: 10.1517/17460441.2012.672408] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Recombinant DNA technologies have had a fundamental impact on drug discovery. The continuous emergence of unique gene assembly techniques resulted in the generation of a variety of therapeutic reagents such as vaccines, cancer treatment molecules and regenerative medicine precursors. With the advent of synthetic biology there is a growing need for precise and concerted assembly of multiple DNA fragments of various sizes, including chromosomes. In this article, we summarize the highlights of the recombinant DNA technology since its inception in the early 1970s, emphasizing on the most recent advances, and underscoring their principles, advantages and shortcomings. Current and prior cloning trends are discussed in the context of sequence requirements and scars left behind. Our opinion is that despite the remarkable progress that has enabled the generation and manipulation of very large DNA sequences, a better understanding of the cell's natural circuits is needed in order to fully exploit the current state-of-the-art gene assembly technologies.
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66
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Abstract
Overlap extension or fusion PCR is thought to be a simple and easy method to produce fusion DNA fragments without the need for restriction enzyme digestion and DNA ligation. However, this method has not been used frequently, probably as it is not always reliable. When natural sequences are used for overlap sequences, sometimes either no fusion DNA is produced or only faint DNA bands are detected owing to low annealing between the overlap sequences selected. Here, we introduce several artificial overlap sequences, most of which are GC-rich, that can be used for reliable fusion PCR. We describe how these overlap sequences can be used for fusion DNA construction, in-frame gene fusion, and cloning in yeast.
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Affiliation(s)
- Kamonchai Cha-Aim
- Department of Applied Molecular Bioscience, Yamaguchi University Graduate School of Medicine, Ube, Japan
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67
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Kuzuya A, Tanaka K, Katada H, Komiyama M. Enzyme treatment-free and ligation-independent cloning using caged primers in polymerase chain reactions. Molecules 2011; 17:328-40. [PMID: 22210171 PMCID: PMC6290560 DOI: 10.3390/molecules17010328] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2011] [Revised: 12/26/2011] [Accepted: 12/27/2011] [Indexed: 11/29/2022] Open
Abstract
A new simple scheme for constructing recombinant vectors that does not require any restriction enzyme, ligase, or any other special enzyme treatment has been developed. By using caged primers in PCR, unnatural sticky-ends of any sequence, which are sufficiently long for ligation-independent cloning (LIC), are directly prepared on the product after a brief UVA irradiation. Target genes and vectors amplified by this light-assisted cohesive-ending (LACE) PCR join together in the desired arrangement in a simple mixture of them, tightly enough to be repaired and ligated in competent cells.
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Affiliation(s)
- Akinori Kuzuya
- Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro, Tokyo 153-8904, Japan; (K.T.); (H.K.)
- Department of Chemistry and Materials Engineering, Kansai University, 3-3-35 Yamate-cho, Suita, Osaka 564-8680, Japan
- Author to whom correspondence should be addressed; (A.K.); (M.K.); Tel.: +81-6-6368-0829 (A.K.); Fax: +81-6-6368-0829 (A.K.); Tel.: +81-3-5452-5200 (M.K.); Fax: +81-3-5452-5209 (M.K.)
| | - Keita Tanaka
- Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro, Tokyo 153-8904, Japan; (K.T.); (H.K.)
| | - Hitoshi Katada
- Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro, Tokyo 153-8904, Japan; (K.T.); (H.K.)
| | - Makoto Komiyama
- Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro, Tokyo 153-8904, Japan; (K.T.); (H.K.)
- Author to whom correspondence should be addressed; (A.K.); (M.K.); Tel.: +81-6-6368-0829 (A.K.); Fax: +81-6-6368-0829 (A.K.); Tel.: +81-3-5452-5200 (M.K.); Fax: +81-3-5452-5209 (M.K.)
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Nunez D, Antonescu C, Mettlen M, Liu A, Schmid SL, Loerke D, Danuser G. Hotspots organize clathrin-mediated endocytosis by efficient recruitment and retention of nucleating resources. Traffic 2011; 12:1868-78. [PMID: 21883765 DOI: 10.1111/j.1600-0854.2011.01273.x] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The formation of clathrin-coated pits (CCPs) at the plasma membrane has been reported to sometimes occur repeatedly at predefined sites. However, defining such CCP 'hotspots' structurally and mechanistically has been difficult due to the dynamic and heterogeneous nature of CCPs. Here, we explore the molecular requirements for hotspots using a global assay of CCP dynamics. Our data confirmed that a subset of CCPs is nucleated at spatially distinct sites. The degree of clustering of nucleation events at these sites is dependent on the integrity of cortical actin, and the availability of certain resources, including the adaptor protein AP-2 and the phospholipid PI(4,5)P(2) . We observe that modulation in the expression level of FCHo1 and 2, which have been reported to initiate CCPs, affects only the number of nucleations. Modulation in the expression levels of other accessory proteins, such as SNX9, affects the spatial clustering of CCPs but not the number of nucleations. On the basis of these findings, we distinguish two classes of accessory proteins in clathrin-mediated endocytosis (CME): nucleation factors and nucleation organizers. Finally, we observe that clustering of transferrin receptors spatially randomizes pit nucleation and thus reduces the role of hotspots. On the basis of these data, we propose that hotspots are specialized cortical actin patches that organize CCP nucleations from within the cell by more efficient recruitment and/or retention of the resources required for CCP nucleation partially due to the action of nucleation organizers.
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Affiliation(s)
- Daniel Nunez
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
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Scior A, Preissler S, Koch M, Deuerling E. Directed PCR-free engineering of highly repetitive DNA sequences. BMC Biotechnol 2011; 11:87. [PMID: 21943395 PMCID: PMC3187725 DOI: 10.1186/1472-6750-11-87] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2011] [Accepted: 09/23/2011] [Indexed: 01/24/2023] Open
Abstract
BACKGROUND Highly repetitive nucleotide sequences are commonly found in nature e.g. in telomeres, microsatellite DNA, polyadenine (poly(A)) tails of eukaryotic messenger RNA as well as in several inherited human disorders linked to trinucleotide repeat expansions in the genome. Therefore, studying repetitive sequences is of biological, biotechnological and medical relevance. However, cloning of such repetitive DNA sequences is challenging because specific PCR-based amplification is hampered by the lack of unique primer binding sites resulting in unspecific products. RESULTS For the PCR-free generation of repetitive DNA sequences we used antiparallel oligonucleotides flanked by restriction sites of Type IIS endonucleases. The arrangement of recognition sites allowed for stepwise and seamless elongation of repetitive sequences. This facilitated the assembly of repetitive DNA segments and open reading frames encoding polypeptides with periodic amino acid sequences of any desired length. By this strategy we cloned a series of polyglutamine encoding sequences as well as highly repetitive polyadenine tracts. Such repetitive sequences can be used for diverse biotechnological applications. As an example, the polyglutamine sequences were expressed as His6-SUMO fusion proteins in Escherichia coli cells to study their aggregation behavior in vitro. The His6-SUMO moiety enabled affinity purification of the polyglutamine proteins, increased their solubility, and allowed controlled induction of the aggregation process. We successfully purified the fusions proteins and provide an example for their applicability in filter retardation assays. CONCLUSION Our seamless cloning strategy is PCR-free and allows the directed and efficient generation of highly repetitive DNA sequences of defined lengths by simple standard cloning procedures.
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Affiliation(s)
- Annika Scior
- Molecular Microbiology, Department of Biology, University of Konstanz, 78457 Konstanz, Germany
- Konstanz Research School Chemical Biology, University of Konstanz, 78457 Konstanz, Germany
| | - Steffen Preissler
- Molecular Microbiology, Department of Biology, University of Konstanz, 78457 Konstanz, Germany
- Konstanz Research School Chemical Biology, University of Konstanz, 78457 Konstanz, Germany
| | - Miriam Koch
- Molecular Microbiology, Department of Biology, University of Konstanz, 78457 Konstanz, Germany
- Konstanz Research School Chemical Biology, University of Konstanz, 78457 Konstanz, Germany
| | - Elke Deuerling
- Molecular Microbiology, Department of Biology, University of Konstanz, 78457 Konstanz, Germany
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Encephalomyocarditis virus 2A protein is required for viral pathogenesis and inhibition of apoptosis. J Virol 2011; 85:10741-54. [PMID: 21849462 DOI: 10.1128/jvi.00394-11] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
The encephalomyocarditis virus (EMCV), a Picornaviridae virus, has a wide host spectrum and can cause various diseases. EMCV virulence factors, however, are as yet ill defined. Here, we demonstrate that the EMCV 2A protein is essential for the pathogenesis of EMCV. Infection of mice with the B279/95 strain of EMCV resulted in acute fatal disease, while the clone C9, derived by serial in vitro passage of the B279/95 strain, was avirulent. C9 harbored a large deletion in the gene encoding the 2A protein. This deletion was incorporated into the cDNA of a pathogenic EMCV1.26 strain. The new virus, EMCV1.26Δ2A, was capable of replicating in vitro, albeit more slowly than EMCV1.26. Only mice inoculated with EMCV1.26 triggered death within a few days. Mice infected with EMCV1.26Δ2A did not exhibit clinical signs, and histopathological analyses showed no damage in the central nervous system, unlike EMCV1.26-infected mice. In vitro, EMCV1.26Δ2A presented a defect in viral particle release correlating with prolonged cell viability. Unlike EMCV1.26, which induced cytopathic cell death, EMCV1.26Δ2A induced apoptosis via caspase 3 activation. This strongly suggests that the 2A protein is required for inhibition of apoptosis during EMCV infection. All together, our data indicate that the EMCV 2A protein is important for the virus in counteracting host defenses, since Δ2A viruses were no longer pathogenic and were unable to inhibit apoptosis in vitro.
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71
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Differential curvature sensing and generating activities of dynamin isoforms provide opportunities for tissue-specific regulation. Proc Natl Acad Sci U S A 2011; 108:E234-42. [PMID: 21670293 DOI: 10.1073/pnas.1102710108] [Citation(s) in RCA: 79] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Dynamin 1 (Dyn1) and Dyn2 are neuronal and ubiquitously expressed isoforms, respectively, of the multidomain GTPase required for clathrin-mediated endocytosis (CME). Although they are 79% identical, Dyn1 and Dyn2 are not fully functionally redundant. Through direct measurements of basal and assembly-stimulated GTPase activities, membrane binding, self-assembly, and membrane fission on planar and curved templates, we have shown that Dyn1 is an efficient curvature generator, whereas Dyn2 is primarily a curvature sensor. Using Dyn1/Dyn2 chimeras, we identified the lipid-binding pleckstrin homology domain as being responsible for the differential in vitro properties of these two isoforms. Remarkably, their in vitro activities were reversed by a single amino acid change in the membrane-binding variable loop 3. Reconstitution of KO mouse embryo fibroblasts showed that both the pleckstrin homology and the Pro/Arg-rich domains determine the differential abilities of these two isoforms to support CME. These domains are specific to classical dynamins and are involved in regulating their activity. Our findings reveal opportunities for fundamental differences in the regulation of Dyn1, which mediates rapid endocytosis at the synapse, vs. Dyn2, which regulates early and late events in CME in nonneuronal cells.
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72
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An efficient and rapid method for cDNA cloning from difficult templates using codon optimization and SOE-PCR: with human RANK and TIMP2 gene as examples. Biotechnol Lett 2011; 33:1939-47. [PMID: 21660576 DOI: 10.1007/s10529-011-0656-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2011] [Accepted: 05/26/2011] [Indexed: 10/18/2022]
Abstract
As gene cloning from difficult templates with regionalized high GC content is a long recognized problem, we have developed a novel and reliable method to clone such genes. Firstly, the high GC content region of the target cDNA was synthesized directly after codon optimization and the remaining cDNA fragment without high GC content was generated by routine RT-PCR. Then the entire redesigned coding sequence of the target gene was obtained by fusing the above available two cDNA fragments with SOE-PCR (splicing by overlapping extension-PCR). We have cloned the human RANK gene (ten exons; CDS 1851 bp) using this strategy. The redesigned cDNA was transfected into an eukaryotic expression system (A459 cells) to verify its expression. RT-PCR and western blotting confirmed this. To validate our method, we also successfully cloned human TIMP2 gene (five exons; CDS 660 bp) also having a regionalized high GC content. Our strategy for combining codon optimization and SOE-PCR to clone difficult genes is thus feasible and potentially universally applicable.
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73
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Wang X, Teng D, Yang Y, Tian F, Guan Q, Wang J. Construction of a reference plasmid molecule containing eight targets for the detection of genetically modified crops. Appl Microbiol Biotechnol 2011; 90:721-31. [PMID: 21336925 DOI: 10.1007/s00253-011-3159-9] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2010] [Revised: 01/18/2011] [Accepted: 01/23/2011] [Indexed: 12/17/2022]
Abstract
A standard plasmid containing eight targets was developed for quantitative detection of genetically modified (GM) soybeans and cotton. These eight targets were joined in tandem to form the pTLE8 plasmid with a length of 3,680 bp. This plasmid contains part of the endogenous soybean Lec1 gene, the Cauliflower mosaic virus (CaMV) 35S promoter, the Agrobacterium tumefaciens nopaline synthase (NOS) terminator, the PAT gene of the soybean line A2704-12, the event-specific 5'-junction region of Roundup-Ready Soya (RRS, 35SG), the Cry1A(c) gene from Bacillus thuringiensis (Bt), the endogenous cotton Sad1 gene, and a part of RRS EPSPS gene. The PCR efficiencies with pTLE8 as a calibrator ranged from 99.4% to 100.2% for the standard curves of the RRS EPSPS gene and the taxon-specific Lec1 gene (R(2)≥0.996). The limits of detection and quantification were nine and 15 copies, respectively. The standard deviation (SD) and relative standard deviation (RSD) values of repeatability were from 0.09 to 0.52 and from 0.28% to 2.11%, and those for reproducibility were from 0.12 to 1.15 and 0.42% to 3.85%, respectively. The average conversion factor (Cf) for the CRMs RRS quantification was 0.91. The RSD of the mean values for known samples ranged from 3.09% to 18.53%, and the biases were from 0.5% to 40%. These results show that our method using the pTLE8 plasmid as a reference material (RM) is reliable and feasible in the identification of GM soybeans, thus paving the way for the establishment of identification management systems for various products containing GMO components.
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Affiliation(s)
- Xiumin Wang
- Key Laboratory of Feed Biotechnology, Ministry of Agriculture, Beijing 100081, People's Republic of China
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74
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Engler C, Marillonnet S. Generation of families of construct variants using golden gate shuffling. Methods Mol Biol 2011; 729:167-81. [PMID: 21365490 DOI: 10.1007/978-1-61779-065-2_11] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/24/2023]
Abstract
Current standard cloning methods based on the use of restriction enzymes and ligase are very versatile, but are not well suited for high-throughput cloning projects or for assembly of many DNA fragments from several parental plasmids in a single step. We have previously reported the development of an efficient cloning method based on the use of type IIs restriction enzymes and restriction-ligation. Such method allows seamless assembly of multiple fragments from several parental plasmids with high efficiency, and also allows performing DNA shuffling if fragments prepared from several homologous genes are assembled together in a single restriction-ligation. Such protocol, called Golden Gate shuffling, requires performing the following steps: (1) sequences from several homologous genes are aligned, and recombination sites defined on conserved sequences; (2) modules defined by the position of these recombination sites are amplified by PCR with primers designed to equip them with flanking BsaI sites; (3) the amplified fragments are cloned as intermediate constructs and sequenced; and (4) finally, the intermediate modules are assembled together in a compatible recipient vector in a one-pot restriction-ligation. Depending on the needs of the user, and because of the high cloning efficiency, the resulting constructs can either be screened and analyzed individually, or, if required in larger numbers, directly used in functional screens to detect improved protein variants.
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Affiliation(s)
- Carola Engler
- Icon Genetics GmbH, Biozentrum Halle, Halle, Germany
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75
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Chen JH, Jung JW, Wang Y, Ha KS, Lu F, Lim CS, Takeo S, Tsuboi T, Han ET. Immunoproteomics Profiling of Blood Stage Plasmodium vivax Infection by High-Throughput Screening Assays. J Proteome Res 2010; 9:6479-89. [DOI: 10.1021/pr100705g] [Citation(s) in RCA: 91] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Jun-Hu Chen
- Department of Parasitology, School of Medicine, Kangwon National University, Chunchon, Gangwon-do, Republic of Korea, Institute of Parasitic Diseases, Zhejiang Academy of Medical Sciences, Hangzhou, Zhejiang, People’s Republic of China, Department of Molecular and Cellular Biochemistry, School of Medicine, Kangwon National University, Chunchon, Gangwon-do, Republic of Korea, Department of Laboratory Medicine, College of Medicine, Korea University, Seoul, Republic of Korea, Cell-free Science and
| | - Jae-Wan Jung
- Department of Parasitology, School of Medicine, Kangwon National University, Chunchon, Gangwon-do, Republic of Korea, Institute of Parasitic Diseases, Zhejiang Academy of Medical Sciences, Hangzhou, Zhejiang, People’s Republic of China, Department of Molecular and Cellular Biochemistry, School of Medicine, Kangwon National University, Chunchon, Gangwon-do, Republic of Korea, Department of Laboratory Medicine, College of Medicine, Korea University, Seoul, Republic of Korea, Cell-free Science and
| | - Yue Wang
- Department of Parasitology, School of Medicine, Kangwon National University, Chunchon, Gangwon-do, Republic of Korea, Institute of Parasitic Diseases, Zhejiang Academy of Medical Sciences, Hangzhou, Zhejiang, People’s Republic of China, Department of Molecular and Cellular Biochemistry, School of Medicine, Kangwon National University, Chunchon, Gangwon-do, Republic of Korea, Department of Laboratory Medicine, College of Medicine, Korea University, Seoul, Republic of Korea, Cell-free Science and
| | - Kwon-Soo Ha
- Department of Parasitology, School of Medicine, Kangwon National University, Chunchon, Gangwon-do, Republic of Korea, Institute of Parasitic Diseases, Zhejiang Academy of Medical Sciences, Hangzhou, Zhejiang, People’s Republic of China, Department of Molecular and Cellular Biochemistry, School of Medicine, Kangwon National University, Chunchon, Gangwon-do, Republic of Korea, Department of Laboratory Medicine, College of Medicine, Korea University, Seoul, Republic of Korea, Cell-free Science and
| | - Feng Lu
- Department of Parasitology, School of Medicine, Kangwon National University, Chunchon, Gangwon-do, Republic of Korea, Institute of Parasitic Diseases, Zhejiang Academy of Medical Sciences, Hangzhou, Zhejiang, People’s Republic of China, Department of Molecular and Cellular Biochemistry, School of Medicine, Kangwon National University, Chunchon, Gangwon-do, Republic of Korea, Department of Laboratory Medicine, College of Medicine, Korea University, Seoul, Republic of Korea, Cell-free Science and
| | - Chae Seung Lim
- Department of Parasitology, School of Medicine, Kangwon National University, Chunchon, Gangwon-do, Republic of Korea, Institute of Parasitic Diseases, Zhejiang Academy of Medical Sciences, Hangzhou, Zhejiang, People’s Republic of China, Department of Molecular and Cellular Biochemistry, School of Medicine, Kangwon National University, Chunchon, Gangwon-do, Republic of Korea, Department of Laboratory Medicine, College of Medicine, Korea University, Seoul, Republic of Korea, Cell-free Science and
| | - Satoru Takeo
- Department of Parasitology, School of Medicine, Kangwon National University, Chunchon, Gangwon-do, Republic of Korea, Institute of Parasitic Diseases, Zhejiang Academy of Medical Sciences, Hangzhou, Zhejiang, People’s Republic of China, Department of Molecular and Cellular Biochemistry, School of Medicine, Kangwon National University, Chunchon, Gangwon-do, Republic of Korea, Department of Laboratory Medicine, College of Medicine, Korea University, Seoul, Republic of Korea, Cell-free Science and
| | - Takafumi Tsuboi
- Department of Parasitology, School of Medicine, Kangwon National University, Chunchon, Gangwon-do, Republic of Korea, Institute of Parasitic Diseases, Zhejiang Academy of Medical Sciences, Hangzhou, Zhejiang, People’s Republic of China, Department of Molecular and Cellular Biochemistry, School of Medicine, Kangwon National University, Chunchon, Gangwon-do, Republic of Korea, Department of Laboratory Medicine, College of Medicine, Korea University, Seoul, Republic of Korea, Cell-free Science and
| | - Eun-Taek Han
- Department of Parasitology, School of Medicine, Kangwon National University, Chunchon, Gangwon-do, Republic of Korea, Institute of Parasitic Diseases, Zhejiang Academy of Medical Sciences, Hangzhou, Zhejiang, People’s Republic of China, Department of Molecular and Cellular Biochemistry, School of Medicine, Kangwon National University, Chunchon, Gangwon-do, Republic of Korea, Department of Laboratory Medicine, College of Medicine, Korea University, Seoul, Republic of Korea, Cell-free Science and
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76
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Leisner M, Bleris L, Lohmueller J, Xie Z, Benenson Y. Rationally designed logic integration of regulatory signals in mammalian cells. NATURE NANOTECHNOLOGY 2010; 5:666-670. [PMID: 20622866 PMCID: PMC2934882 DOI: 10.1038/nnano.2010.135] [Citation(s) in RCA: 81] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/25/2010] [Accepted: 06/08/2010] [Indexed: 05/29/2023]
Abstract
Molecular-level information processing is essential for 'smart' in vivo nanosystems. Natural molecular computing, such as the regulation of messenger RNA (mRNA) synthesis by special proteins called transcription factors, has inspired engineered systems that can control the levels of mRNA with certain combinations of transcription factors. Here, we show an alternative approach to achieving general-purpose control of mRNA and protein levels by logic integration of transcription factor input signals in mammalian cells. The transcription factors regulate synthetic genes coding for small regulatory RNAs (called microRNAs), which, in turn, control the mRNA of interest (the output) via an RNA interference pathway. The simplicity of these modular interactions makes it possible, in theory, to implement any arbitrary logic relation between the transcription factors and the output. We construct, test and optimize increasingly complex circuits with up to three transcription factor inputs, establishing a platform for in vivo molecular computing.
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Affiliation(s)
- Madeleine Leisner
- FAS Centre for Systems Biology, Harvard University, 52 Oxford Street, Cambridge Massachussetts 02138 USA
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77
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Olieric N, Kuchen M, Wagen S, Sauter M, Crone S, Edmondson S, Frey D, Ostermeier C, Steinmetz MO, Jaussi R. Automated seamless DNA co-transformation cloning with direct expression vectors applying positive or negative insert selection. BMC Biotechnol 2010; 10:56. [PMID: 20691119 PMCID: PMC2924254 DOI: 10.1186/1472-6750-10-56] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2010] [Accepted: 08/09/2010] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Molecular DNA cloning is crucial to many experiments and with the trend to higher throughput of modern approaches automated techniques are urgently required. We have established an automated, fast and flexible low-cost expression cloning approach requiring only vector and insert amplification by PCR and co-transformation of the products. RESULTS Our vectors apply positive selection for the insert or negative selection against empty vector molecules and drive strong expression of target proteins in E.coli cells. Variable tags are available both in N-terminal or C-terminal position. A newly developed beta-lactamase (DeltaW290) selection cassette contains a segment inside the beta-lactamase open reading frame encoding a stretch of hydrophilic amino acids that result in a T7 promoter when back-translated. This position of the promoter permits positive selection and attenuated expression of fusion proteins with C-terminal tags. We have tested eight vectors by inserting six target sequences of variable length, provenience and function. The target proteins were cloned, expressed and detected using an automated Tecan Freedom Evo II liquid handling work station. Only two colonies had to be picked to score with 85% correct inserts while 80% of those were positive in expression tests. CONCLUSIONS Our results establish co-transformation and positive/negative selection cloning in conjunction with the provided vectors and selection cassettes as an automatable alternative to commercialized high-throughput cloning systems like Gateway or ligase-independent cloning (LIC) .
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Affiliation(s)
- Natacha Olieric
- Paul Scherrer Institut, Biomolecular Research, Villigen PSI, Switzerland
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78
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Abstract
Proteins are the most versatile among the various biological building blocks and a mature field of protein engineering has lead to many industrial and biomedical applications. But the strength of proteins—their versatility, dynamics and interactions—also complicates and hinders systems engineering. Therefore, the design of more sophisticated, multi-component protein systems appears to lag behind, in particular, when compared to the engineering of gene regulatory networks. Yet, synthetic biologists have started to tinker with the information flow through natural signaling networks or integrated protein switches. A successful strategy common to most of these experiments is their focus on modular interactions between protein domains or domains and peptide motifs. Such modular interaction swapping has rewired signaling in yeast, put mammalian cell morphology under the control of light, or increased the flux through a synthetic metabolic pathway. Based on this experience, we outline an engineering framework for the connection of reusable protein interaction devices into self-sufficient circuits. Such a framework should help to ‘refacture’ protein complexity into well-defined exchangeable devices for predictive engineering. We review the foundations and initial success stories of protein synthetic biology and discuss the challenges and promises on the way from protein- to protein systems design.
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Affiliation(s)
- Raik Grünberg
- EMBL/CRG Systems Biology Research Unit, Centre for Genomic Regulation (CRG), UPF, 08003 Barcelona, Spain.
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79
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Atanassov II, Atanassov II, Etchells JP, Turner SR. A simple, flexible and efficient PCR-fusion/Gateway cloning procedure for gene fusion, site-directed mutagenesis, short sequence insertion and domain deletions and swaps. PLANT METHODS 2009; 5:14. [PMID: 19863796 PMCID: PMC2775020 DOI: 10.1186/1746-4811-5-14] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2009] [Accepted: 10/28/2009] [Indexed: 05/17/2023]
Abstract
BACKGROUND The progress and completion of various plant genome sequencing projects has paved the way for diverse functional genomic studies that involve cloning, modification and subsequent expression of target genes. This requires flexible and efficient procedures for generating binary vectors containing: gene fusions, variants from site-directed mutagenesis, addition of protein tags together with domain swaps and deletions. Furthermore, efficient cloning procedures, ideally high throughput, are essential for pyramiding of multiple gene constructs. RESULTS Here, we present a simple, flexible and efficient PCR-fusion/Gateway cloning procedure for construction of binary vectors for a range of gene fusions or variants with single or multiple nucleotide substitutions, short sequence insertions, domain deletions and swaps. Results from selected applications of the procedure which include ORF fusion, introduction of Cys>Ser mutations, insertion of StrepII tag sequence and domain swaps for Arabidopsis secondary cell wall AtCesA genes are demonstrated. CONCLUSION The PCR-fusion/Gateway cloning procedure described provides an elegant, simple and efficient solution for a wide range of diverse and complicated cloning tasks. Through streamlined cloning of sets of gene fusions and modification variants into binary vectors for systematic functional studies of gene families, our method allows for efficient utilization of the growing sequence and expression data.
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Affiliation(s)
- Ivan I Atanassov
- Faculty of Life Sciences, The University of Manchester, Oxford Road, Manchester, UK, M13 9PT
| | - Ilian I Atanassov
- Faculty of Life Sciences, The University of Manchester, Oxford Road, Manchester, UK, M13 9PT
| | - J Peter Etchells
- Faculty of Life Sciences, The University of Manchester, Oxford Road, Manchester, UK, M13 9PT
| | - Simon R Turner
- Faculty of Life Sciences, The University of Manchester, Oxford Road, Manchester, UK, M13 9PT
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80
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Xiao C, Chen F, Yu X, Lin C, Fu YF. Over-expression of an AT-hook gene, AHL22, delays flowering and inhibits the elongation of the hypocotyl in Arabidopsis thaliana. PLANT MOLECULAR BIOLOGY 2009; 71:39-50. [PMID: 19517252 DOI: 10.1007/s11103-009-9507-9] [Citation(s) in RCA: 88] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2009] [Accepted: 05/24/2009] [Indexed: 05/08/2023]
Abstract
The Arabidopsis genome encodes 29 AHL (AT-hook motif nuclear localized) proteins, but the function for most of them remains unknown. We report here a study of the AHL22 gene, which was originally identified as a gain-of-function allele that enhanced the phenotype of the cry1 cry2 mutant. AHL22 is a nuclear protein with the binding activity for an AT-rich DNA sequence. AHL22 overexpression delayed flowering and caused a constitutive photomorphogenic phenotype. The loss-of-function AHL22 mutant showed no clear phenotype on flowering, but slightly longer hypocotyls. However, silencing four AHL genes (AHL22, AHL18, AHL27, and AHL29) resulted in early flowering and enhanced ahl22-1 mutant phenotype on the growth of hypocotyls, suggesting genetic redundancy of AHL22 with other AHL genes on these plant developmental events. Further analysis showed that AHL22 controlled flowering and hypocotyl elongation might result from primarily the regulation of FT and PIF4 expression, respectively.
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Affiliation(s)
- Chaowen Xiao
- Institute of Crop Sciences, The National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Nandajie 12, Zhongguancun, Haidian District, Beijing, People's Republic of China
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81
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Lu Q, Burns MC, McDevitt PJ, Graham TL, Sukman AJ, Fornwald JA, Tang X, Gallagher KT, Hunsberger GE, Foley JJ, Schmidt DB, Kerrigan JJ, Lewis TS, Ames RS, Johanson KO. Optimized procedures for producing biologically active chemokines. Protein Expr Purif 2009; 65:251-60. [PMID: 19297698 DOI: 10.1016/j.pep.2009.01.017] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
We describe here two strategies to produce biologically active chemokines with authentic N-terminal amino acid residues. The first involves producing the target chemokine with an N-terminal 6xHis-SUMO tag in Escherichia coli as inclusion bodies. The fusion protein is solubilized and purified with Ni-NTA-agarose in denaturing reagents. This is further followed by tag removal and refolding in a redox refolding buffer. The second approach involves expressing the target chemokine with an N-terminal 6xHis-Trx-SUMO tag in an engineered E. coli strain that facilitates formation of disulfide bonds in the cytoplasm. Following purification of the fusion protein via Ni-NTA and tag removal, the target chemokine is refolded without redox buffer and purified by reverse phase chromatography. Using the procedures, we have produced more than 15 biologically active chemokines, with a yield of up to 15 mg/L.
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Affiliation(s)
- Quinn Lu
- GlaxoSmithKline, Biological Reagents & Assay Development, Mail Code: UE0548, 709 Swedeland Road, King of Prussia, PA 19406, USA.
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82
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A one pot, one step, precision cloning method with high throughput capability. PLoS One 2008; 3:e3647. [PMID: 18985154 PMCID: PMC2574415 DOI: 10.1371/journal.pone.0003647] [Citation(s) in RCA: 1483] [Impact Index Per Article: 92.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2008] [Accepted: 10/20/2008] [Indexed: 11/19/2022] Open
Abstract
Current cloning technologies based on site-specific recombination are efficient, simple to use, and flexible, but have the drawback of leaving recombination site sequences in the final construct, adding an extra 8 to 13 amino acids to the expressed protein. We have devised a simple and rapid subcloning strategy to transfer any DNA fragment of interest from an entry clone into an expression vector, without this shortcoming. The strategy is based on the use of type IIs restriction enzymes, which cut outside of their recognition sequence. With proper design of the cleavage sites, two fragments cut by type IIs restriction enzymes can be ligated into a product lacking the original restriction site. Based on this property, a cloning strategy called ‘Golden Gate’ cloning was devised that allows to obtain in one tube and one step close to one hundred percent correct recombinant plasmids after just a 5 minute restriction-ligation. This method is therefore as efficient as currently used recombination-based cloning technologies but yields recombinant plasmids that do not contain unwanted sequences in the final construct, thus providing precision for this fundamental process of genetic manipulation.
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83
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Structural studies of hen egg-white lysozyme dimer: Comparison with monomer. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2008; 1784:1043-9. [DOI: 10.1016/j.bbapap.2008.03.010] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2007] [Revised: 03/02/2008] [Accepted: 03/14/2008] [Indexed: 11/18/2022]
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84
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Tanaka K, Kuzuya A, Komiyama M. Site-selective Termination of DNA Replication by Using a Caged Template. CHEM LETT 2008. [DOI: 10.1246/cl.2008.584] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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85
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Yaghoubi H, Khajeh K, Hosseinkhani S, Ranjbar B, Naderi-Manesh H. Application of zero-length cross-linking to form lysozyme, horseradish peroxidase and lysozyme–peroxidase dimers: Activity and stability. Int J Biol Macromol 2007; 41:624-30. [PMID: 17915308 DOI: 10.1016/j.ijbiomac.2007.08.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2007] [Revised: 08/12/2007] [Accepted: 08/13/2007] [Indexed: 11/21/2022]
Abstract
A facile method for the formation of covalent bonds between protein molecules is zero-length cross-linking. This method enables the formation of cross-links without use of any chemical reagents. Here, the cross-linking is performed for lysozyme, peroxidase (a glycoprotein) and between lysozyme-peroxidase by the method of Simons et al. [B.L. Simons, M.C. King, T. Cyr, M.A. Hefford, H. Kaplan, Covalent cross-linking of protein without chemical reagents, Protein Sci. 2002, 11, 1558-1564]. Approximately one-third of the total lysozyme becomes cross-linked and the dimer form was the major product for both enzymes. This modification induced some changes in the kinetic properties of the dimer peroxidase, as evident by two-fold increasing of V(max) compared to the monomer but the enzymatic activity of cross-linked lysozyme dimer was the same as monomer. The activity of lysozyme dimer remained constant up to 10min at 80 degrees C, while peroxidase activity of both monomer and dimer began to decrease after heating. The structural changes of the enzymes were investigated by circular dichroism and intrinsic fluorescence techniques. Near UV result showed lysozyme possess a compact structure in the dimer form but disruption of tertiary structure of peroxidase dimer was observed. Also conformational changes were detected and discussed by intrinsic fluorescence experiments. Effect of several metals in the formation of lysozyme dimer showed that Co(2+) is the most effective one but its effect was marginal. At the end formation of heterogeneous dimer, peroxidase-lysozyme, was achieved using this method.
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Affiliation(s)
- Hashem Yaghoubi
- Department of Biochemistry and Biophysics, Faculty of Science, Tarbiat Modares University, P.O. Box 14115-175, Tehran, Iran
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86
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Geu-Flores F, Nour-Eldin HH, Nielsen MT, Halkier BA. USER fusion: a rapid and efficient method for simultaneous fusion and cloning of multiple PCR products. Nucleic Acids Res 2007; 35:e55. [PMID: 17389646 PMCID: PMC1874642 DOI: 10.1093/nar/gkm106] [Citation(s) in RCA: 223] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
We present a method that allows simultaneous fusion and cloning of multiple PCR products in a rapid and efficient manner. The procedure is based on the use of PCR primers that contain a single deoxyuridine residue near their 5′ end. Treatment of the PCR products with a commercial deoxyuridine-excision reagent generates long 3′ overhangs designed to specifically complement each other. The combination of this principle with the improved USER cloning technique provides a simple, fast and very efficient method to simultaneously fuse and clone multiple PCR fragments into a vector of interest. Around 90% positive clones were obtained when three different PCR products were fused and cloned into a USER-compatible vector in a simple procedure that, apart from the single PCR amplification step and the bacterial transformation, took approximately one hour. We expect this method to replace overlapping PCR and the use of type IIS restriction enzymes in many of their applications.
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Affiliation(s)
- Fernando Geu-Flores
- Plant Biochemistry Laboratory, Institute of Plant Biology, Faculty of Life Sciences, University of Copenhagen, Thorvaldsensvej 40, Frederiksberg C, Denmark
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87
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Hong SY, Lee JS, Cho KM, Math RK, Kim YH, Hong SJ, Cho YU, Cho SJ, Kim H, Yun HD. Construction of the bifunctional enzyme cellulase-beta-glucosidase from the hyperthermophilic bacterium Thermotoga maritima. Biotechnol Lett 2007; 29:931-6. [PMID: 17333463 DOI: 10.1007/s10529-007-9334-5] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2006] [Revised: 01/18/2007] [Accepted: 01/22/2007] [Indexed: 11/25/2022]
Abstract
An artificial bifunctional enzyme, cellulase-beta-glucosidase, was prepared by gene fusion from the hyperthermophilic bacterium Thermotoga maritima MSB8. The fusion protein exhibited both cellulase (Cel5C) and beta-glucosidase (BglB) activity when the bglB gene was fused to downstream of cel5C, but not when cel5C was fused to downstream of bglB. The specific activity of the bifunctional enzyme was 70% lower than that of cellulase or beta-glucosidase. The fusion enzyme was purified, and the MW was estimated as 114 kDa. The fusion enzyme displayed optimum cellulase activity at pH 8.0 and 70 degrees C over 30 min, and optimal beta-glucosidase activity at pH 7.0 and 80 degrees C over 30 min.
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Affiliation(s)
- Su-Young Hong
- Division of Applied Life Science, Gyeongsang National University, Chinju, Korea
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88
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Li W, Gao F. Creation of DNA overhangs by using modified DNA overhang cloning method. Appl Microbiol Biotechnol 2007; 75:703-9. [PMID: 17308905 DOI: 10.1007/s00253-007-0852-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2006] [Revised: 01/11/2007] [Accepted: 01/21/2007] [Indexed: 11/24/2022]
Abstract
DNA overhang cloning (DOC) method was invented by Kevin A. Jarrell and colleagues to create DNA overhangs at the ends of polymerase chain reaction (PCR) fragments. To increase the ligation products of DOC and make it possible to join the ligation products together to yield a larger DNA fragment without amplification by using the secondary PCR, we modified the original method by lengthening RNA-DNA hybrids to 8 bp, using RNase H to digest RNA chains, and so on. We found that the ligation of PCR fragments with DNA overhangs could be improved significantly by using the modified DOC. The ligation products of the modified DOC were rich enough to be separated by using agarose gel and joined together to yield a larger DNA fragment without amplification by using the secondary PCR. The modified DOC is simpler and much more effective than the original one. The creation of DNA overhangs by using complementary DNA oligonucleotides, T4 ligase, and RNase H is simpler and cheaper than that by using reverse transcriptase and RNase H.
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Affiliation(s)
- Wei Li
- Laboratory of Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, 530021, People's Republic of China.
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89
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Hong SY, Lee JS, Cho KM, Math RK, Kim YH, Hong SJ, Cho YU, Kim H, Yun HD. Assembling a novel bifunctional cellulase–xylanase from Thermotoga maritima by end-to-end fusion. Biotechnol Lett 2006; 28:1857-62. [PMID: 16988785 DOI: 10.1007/s10529-006-9166-8] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2006] [Accepted: 07/21/2006] [Indexed: 01/15/2023]
Abstract
An artificial, bifunctional, thermostable cellulase-xylanase enzyme from Thermotoga maritima by gene fusion. The fusion protein exhibited both cellulase and xylanase activity when xynA was fused downstream of cel5C but no activities were shown when xynA was fused upstream of cel5C. The enzyme was optimally active at pH 5.0 and 80 degrees C over 30 min. E. coli expressed the fusion enzyme, with an apparent molecular mass of approximately 152 kDa by carboxymethyl cellulose- and xylan-SDS-PAGE.
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Affiliation(s)
- Su Young Hong
- Division of Applied Life Science, Gyeongsang National University, Chinju, 660-701, Republic of Korea
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