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Chkaiban L, Tosi L, Parekkadan B. Assembly of Long-Adapter Single-Strand Oligonucleotide (LASSO) Probes for Massively Parallel Capture of Kilobase Size DNA Targets. Curr Protoc 2021; 1:e278. [PMID: 34807521 PMCID: PMC8669654 DOI: 10.1002/cpz1.278] [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] [Indexed: 11/06/2022]
Abstract
Genome DNA sequencing has become an affordable means to resolve questions about the genetic background of life. However, the biological functions of many DNA-encoded sequences are still relatively unknown. A highly scalable and cost-effective cloning method to select natural DNA targets from genomic templates is therefore urgently needed to enable rapid understanding of the biological products of genomes. One such method involves LASSO probes, which are long single-stranded DNA oligonucleotides designed with a universal adapter that is used to link two sequences that are complementary to a genomic target of interest. Through a pooled assembly method, LASSOs can be made for multiplex DNA capture. Herein, we describe a robust, efficient method to assemble LASSO probe libraries using a Cre-recombinase-mediated reaction and a protocol for multiplex genome target capture. The starting components are a pre-LASSO probe library comprising short DNA oligo pools designed in silico and an Escherichia coli plasmid (pLASSO) that incorporates the pre-LASSO library. Through internal recombination of pLASSO with its inserts, a mature LASSO library in final configuration can be made with high purity. Assembly of a LASSO probe library takes 4 days, and target capture can be performed in a single day. With an exponentially growing list of new genomes available for investigation, this method can enable the rapid production of ORFeome libraries for high-throughput screening to identify biological functions as a complementary approach to understand genome functional biology. © 2021 Wiley Periodicals LLC. Basic Protocol 1: Assembly of LASSO probes Support Protocol 1: Generation of pLASSO vectors Support Protocol 2: Preparation of pre-LASSOs Basic Protocol 2: Massively parallel capture of large DNAs using LASSO probes.
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Affiliation(s)
- Lamia Chkaiban
- Department of Biomedical Engineering, Rutgers, The State University of New Jersey, Piscataway, NJ
| | - Lorenzo Tosi
- Department of Biomedical Engineering, Rutgers, The State University of New Jersey, Piscataway, NJ
| | - Biju Parekkadan
- Department of Biomedical Engineering, Rutgers, The State University of New Jersey, Piscataway, NJ
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2
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Abstract
The Mos1-mediated Single-Copy Insertion (MosSCI) method is widely used to establish stable Caenorhabditis elegans transgenic strains. Cloning MosSCI targeting plasmids can be cumbersome because it requires assembling multiple genetic elements including a promoter, a 3'UTR and gene fragments. Recently, Schwartz and Jorgensen developed the SapTrap method for the one-step assembly of plasmids containing components of the CRISPR/Cas9 system for C. elegans Here, we report on the adaptation of the SapTrap method for the efficient and modular assembly of a promoter, 3'UTR and either 2 or 3 gene fragments in a MosSCI targeting vector in a single reaction. We generated a toolkit that includes several fluorescent tags, components of the ePDZ/LOV optogenetic system and regulatory elements that control gene expression in the C. elegans germline. As a proof of principle, we generated a collection of strains that fluorescently label the endoplasmic reticulum and mitochondria in the hermaphrodite germline and that enable the light-stimulated recruitment of mitochondria to centrosomes in the one-cell worm embryo. The method described here offers a flexible and efficient method for assembly of custom MosSCI targeting vectors.
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Bradley M, Ramirez I, Cheung K, Gholkar AA, Torres JZ. Inducible LAP-tagged Stable Cell Lines for Investigating Protein Function, Spatiotemporal Localization and Protein Interaction Networks. J Vis Exp 2016. [PMID: 28060263 PMCID: PMC5226453 DOI: 10.3791/54870] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Multi-protein complexes, rather than single proteins acting in isolation, often govern molecular pathways regulating cellular homeostasis. Based on this principle, the purification of critical proteins required for the functioning of these pathways along with their native interacting partners has not only allowed the mapping of the protein constituents of these pathways, but has also provided a deeper understanding of how these proteins coordinate to regulate these pathways. Within this context, understanding a protein's spatiotemporal localization and its protein-protein interaction network can aid in defining its role within a pathway, as well as how its misregulation may lead to disease pathogenesis. To address this need, several approaches for protein purification such as tandem affinity purification (TAP) and localization and affinity purification (LAP) have been designed and used successfully. Nevertheless, in order to apply these approaches to pathway-scale proteomic analyses, these strategies must be supplemented with modern technological developments in cloning and mammalian stable cell line generation. Here, we describe a method for generating LAP-tagged human inducible stable cell lines for investigating protein subcellular localization and protein-protein interaction networks. This approach has been successfully applied to the dissection of multiple cellular pathways including cell division and is compatible with high-throughput proteomic analyses.
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Affiliation(s)
- Michelle Bradley
- Department of Chemistry and Biochemistry, University of California, Los Angeles
| | - Ivan Ramirez
- Department of Chemistry and Biochemistry, University of California, Los Angeles
| | - Keith Cheung
- Department of Chemistry and Biochemistry, University of California, Los Angeles
| | - Ankur A Gholkar
- Department of Chemistry and Biochemistry, University of California, Los Angeles
| | - Jorge Z Torres
- Department of Chemistry and Biochemistry, University of California, Los Angeles; Molecular Biology Institute, University of California, Los Angeles; Jonsson Comprehensive Cancer Center, University of California, Los Angeles;
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4
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Grant IM, Balcha D, Hao T, Shen Y, Trivedi P, Patrushev I, Fortriede JD, Karpinka JB, Liu L, Zorn AM, Stukenberg PT, Hill DE, Gilchrist MJ. The Xenopus ORFeome: A resource that enables functional genomics. Dev Biol 2015; 408:345-57. [PMID: 26391338 PMCID: PMC4684507 DOI: 10.1016/j.ydbio.2015.09.004] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2014] [Revised: 08/18/2015] [Accepted: 09/09/2015] [Indexed: 12/18/2022]
Abstract
Functional characterisation of proteins and large-scale, systems-level studies are enabled by extensive sets of cloned open reading frames (ORFs) in an easily-accessible format that enables many different applications. Here we report the release of the first stage of the Xenopus ORFeome, which contains 8673 ORFs from the Xenopus Gene Collection (XGC) for Xenopus laevis, cloned into a Gateway® donor vector enabling rapid in-frame transfer of the ORFs to expression vectors. This resource represents an estimated 7871 unique genes, approximately 40% of the non-redundant X. laevis gene complement, and includes 2724 genes where the human ortholog has an association with disease. Transfer into the Gateway system was validated by 5' and 3' end sequencing of the entire collection and protein expression of a set of test clones. In a parallel process, the underlying ORF predictions from the original XGC collection were re-analysed to verify quality and full-length status, identifying those proteins likely to exhibit truncations when translated. These data are integrated into Xenbase, the Xenopus community database, which associates genomic, expression, function and human disease model metadata to each ORF, enabling end-users to search for ORFeome clones with links to commercial distributors of the collection. When coupled with the experimental advantages of Xenopus eggs and embryos, the ORFeome collection represents a valuable resource for functional genomics and disease modelling.
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Affiliation(s)
- Ian M Grant
- The Francis Crick Institute, Mill Hill Laboratory, The Ridgeway, Mill Hill, London NW7 1AA, UK
| | - Dawit Balcha
- Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Tong Hao
- Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Yun Shen
- Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Prasad Trivedi
- University of Virginia, School of Medicine, Charlottesville, VA 22908, USA
| | - Ilya Patrushev
- The Francis Crick Institute, Mill Hill Laboratory, The Ridgeway, Mill Hill, London NW7 1AA, UK
| | - Joshua D Fortriede
- Xenbase, Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - John B Karpinka
- Xenbase, Department of Biological Science, University of Calgary, Calgary, AB, Canada
| | - Limin Liu
- University of Virginia, School of Medicine, Charlottesville, VA 22908, USA
| | - Aaron M Zorn
- Xenbase, Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - P Todd Stukenberg
- University of Virginia, School of Medicine, Charlottesville, VA 22908, USA
| | - David E Hill
- Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA.
| | - Michael J Gilchrist
- The Francis Crick Institute, Mill Hill Laboratory, The Ridgeway, Mill Hill, London NW7 1AA, UK.
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5
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Kogame T. 4-Fragment Gateway cloning format for MosSCI-compatible vectors integrating Promoterome and 3'UTRome libraries of Caenorhabditis elegans. THE JOURNAL OF MEDICAL INVESTIGATION 2015; 62:161-6. [PMID: 26399341 DOI: 10.2152/jmi.62.161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
The technique of Mos1-mediated Single Copy Insertion (MosSCI) now has become the essential technique which facilitates transgenic experiments for Caenohabditis elegans (C. elegans). Gateway system which is adopted to MosSCI-compatible vectors offers an advantage of simultaneous cloning with entry vectors cloned in the Gateway system format. On the other hand, the format for MosSCI-compatible vectors restricts flexibility in designing the vectors to only 3-fragment integration. Thus, construct of complex transgene such as the expression vector for translational gene fusion is tedious work even with Gateway system. We have developed the new recombination format called LeGaSCI (Library-enhanced Gateway for MosSCI) to expand the conventional 3-fragment to 4-fragment format which still retains the capacity to accept Promoterome and 3'UTRome libraries of C. elegans. In the new recombination format, 2 different Gateway format were combined. Cloning reaction for the tissue-specific expression vector of GFP-tagged protein with 3'UTR successfully occurred without any expected insertion, deletion or frame-shift mutation. Moreover, The MosSCI transgenic line was successfully generated with the construct. Collectively, we established the new Gateway system format which allows us to assemble 4-fragment insertion with the widest variety of entry clone vectors from C. elegans libraries.
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Affiliation(s)
- Toshiaki Kogame
- Systems Biology of Gene Regulatory Elements, Max-Delbruck-Center for Molecular Medicine
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Fuxman Bass JI, Sahni N, Shrestha S, Garcia-Gonzalez A, Mori A, Bhat N, Yi S, Hill DE, Vidal M, Walhout AJM. Human gene-centered transcription factor networks for enhancers and disease variants. Cell 2015; 161:661-673. [PMID: 25910213 PMCID: PMC4409666 DOI: 10.1016/j.cell.2015.03.003] [Citation(s) in RCA: 65] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2014] [Revised: 11/26/2014] [Accepted: 01/30/2015] [Indexed: 01/16/2023]
Abstract
Gene regulatory networks (GRNs) comprising interactions between transcription factors (TFs) and regulatory loci control development and physiology. Numerous disease-associated mutations have been identified, the vast majority residing in non-coding regions of the genome. As current GRN mapping methods test one TF at a time and require the use of cells harboring the mutation(s) of interest, they are not suitable to identify TFs that bind to wild-type and mutant loci. Here, we use gene-centered yeast one-hybrid (eY1H) assays to interrogate binding of 1,086 human TFs to 246 enhancers, as well as to 109 non-coding disease mutations. We detect both loss and gain of TF interactions with mutant loci that are concordant with target gene expression changes. This work establishes eY1H assays as a powerful addition to the toolkit of mapping human GRNs and for the high-throughput characterization of genomic variants that are rapidly being identified by genome-wide association studies.
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Affiliation(s)
- Juan I Fuxman Bass
- Program in Systems Biology and Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Nidhi Sahni
- Department of Cancer Biology, Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Shaleen Shrestha
- Program in Systems Biology and Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Aurian Garcia-Gonzalez
- Program in Systems Biology and Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Akihiro Mori
- Program in Systems Biology and Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Numana Bhat
- Program in Systems Biology and Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Song Yi
- Department of Cancer Biology, Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - David E Hill
- Department of Cancer Biology, Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Marc Vidal
- Department of Cancer Biology, Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Albertha J M Walhout
- Program in Systems Biology and Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA; Department of Cancer Biology, Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA 02215, USA.
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7
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Blasche S, Arens S, Ceol A, Siszler G, Schmidt MA, Häuser R, Schwarz F, Wuchty S, Aloy P, Uetz P, Stradal T, Koegl M. The EHEC-host interactome reveals novel targets for the translocated intimin receptor. Sci Rep 2014; 4:7531. [PMID: 25519916 PMCID: PMC4269881 DOI: 10.1038/srep07531] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2014] [Accepted: 11/21/2014] [Indexed: 12/20/2022] Open
Abstract
Enterohemorrhagic E. coli (EHEC) manipulate their human host through at least 39 effector proteins which hijack host processes through direct protein-protein interactions (PPIs). To identify their protein targets in the host cells, we performed yeast two-hybrid screens, allowing us to find 48 high-confidence protein-protein interactions between 15 EHEC effectors and 47 human host proteins. In comparison to other bacteria and viruses we found that EHEC effectors bind more frequently to hub proteins as well as to proteins that participate in a higher number of protein complexes. The data set includes six new interactions that involve the translocated intimin receptor (TIR), namely HPCAL1, HPCAL4, NCALD, ARRB1, PDE6D, and STK16. We compared these TIR interactions in EHEC and enteropathogenic E. coli (EPEC) and found that five interactions were conserved. Notably, the conserved interactions included those of serine/threonine kinase 16 (STK16), hippocalcin-like 1 (HPCAL1) as well as neurocalcin-delta (NCALD). These proteins co-localize with the infection sites of EPEC. Furthermore, our results suggest putative functions of poorly characterized effectors (EspJ, EspY1). In particular, we observed that EspJ is connected to the microtubule system while EspY1 appears to be involved in apoptosis/cell cycle regulation.
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Affiliation(s)
- Sonja Blasche
- Genomics and Proteomics Core Facilities, German Cancer Research Center, Im Neuenheimer Feld 580, 69120 Heidelberg, Germany
| | - Stefan Arens
- Institute of Molecular Cell Biology, University of Münster, Schlossplatz 5, D-48149 Münster
| | - Arnaud Ceol
- 1] Joint IRB-BSC Program in Computational Biology, Institute for Research in Biomedicine (IRB Barcelona), Barcelona, Spain [2] Center for Genomic Science of IIT@SEMM, Fondazione Istituto Italiano di Tecnologia (IIT), Via Adamello 16, 20139 Milan - Italy
| | - Gabriella Siszler
- Genomics and Proteomics Core Facilities, German Cancer Research Center, Im Neuenheimer Feld 580, 69120 Heidelberg, Germany
| | - M Alexander Schmidt
- Institute of Infectiology, ZMBE, University of Münster, Von-Esmarch-Str. 56, D-48149 Münster
| | - Roman Häuser
- Genomics and Proteomics Core Facilities, German Cancer Research Center, Im Neuenheimer Feld 580, 69120 Heidelberg, Germany
| | - Frank Schwarz
- Genomics and Proteomics Core Facilities, German Cancer Research Center, Im Neuenheimer Feld 580, 69120 Heidelberg, Germany
| | - Stefan Wuchty
- 1] Dept. of Computer Science, Univ. of Miami, 1365 Memorial Drive, Coral Gables, FL 33146, USA [2] Center for Computational Science, Univ. of Miami, 1365 Memorial Drive, Coral Gables, FL 33146, USA
| | - Patrick Aloy
- 1] Joint IRB-BSC Program in Computational Biology, Institute for Research in Biomedicine (IRB Barcelona), Barcelona, Spain [2] Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - Peter Uetz
- Center for the Study of Biological Complexity, Virginia Commonwealth University, Richmond, VA 23284, USA
| | - Theresia Stradal
- 1] Institute of Molecular Cell Biology, University of Münster, Schlossplatz 5, D-48149 Münster [2] Helmholtz Centre for Infection Research, Inhoffenstrasse 7, D-38124 Braunschweig
| | - Manfred Koegl
- Genomics and Proteomics Core Facilities, German Cancer Research Center, Im Neuenheimer Feld 580, 69120 Heidelberg, Germany
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Lehtonen SI, Taskinen B, Ojala E, Kukkurainen S, Rahikainen R, Riihimaki TA, Laitinen OH, Kulomaa MS, Hytonen VP. Efficient preparation of shuffled DNA libraries through recombination (Gateway) cloning. Protein Eng Des Sel 2014; 28:23-8. [DOI: 10.1093/protein/gzu050] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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9
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Abstract
Hedgehog (Hh) pathway activation and Gli-dependent transcription play critical roles in embryonic patterning, tissue homeostasis, and tumorigenesis. By conducting a genome-scale cDNA overexpression screen, we have identified the Rho GAP family member Arhgap36 as a positive regulator of the Hh pathway in vitro and in vivo. Arhgap36 acts in a Smoothened (Smo)-independent manner to inhibit Gli repressor formation and to promote the activation of full-length Gli proteins. Arhgap36 concurrently induces the accumulation of Gli proteins in the primary cilium, and its ability to induce Gli-dependent transcription requires kinesin family member 3a and intraflagellar transport protein 88, proteins that are essential for ciliogenesis. Arhgap36 also functionally and biochemically interacts with Suppressor of Fused. Transcriptional profiling further reveals that Arhgap36 is overexpressed in murine medulloblastomas that acquire resistance to chemical Smo inhibitors and that ARHGAP36 isoforms capable of Gli activation are up-regulated in a subset of human medulloblastomas. Our findings reveal a new mechanism of Gli transcription factor activation and implicate ARHGAP36 dysregulation in the onset and/or progression of GLI-dependent cancers.
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Zhu J, Larman HB, Gao G, Somwar R, Zhang Z, Laserson U, Ciccia A, Pavlova N, Church G, Zhang W, Kesari S, Elledge SJ. Discovery of protein interactions using parallel analysis of translated ORFs (PLATO). Nat Protoc 2014; 9:90-103. [PMID: 24336473 PMCID: PMC4129458 DOI: 10.1038/nprot.2013.167] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Parallel analysis of translated open reading frames (ORFs) (PLATO) can be used for the unbiased discovery of interactions between full-length proteins encoded by a library of 'prey' ORFs and surface-immobilized 'bait' antibodies, polypeptides or small-molecular-weight compounds. PLATO uses ribosome display (RD) to link ORF-derived mRNA molecules to the proteins they encode, and recovered mRNA from affinity enrichment is subjected to analysis using massively parallel DNA sequencing. Compared with alternative in vitro methods, PLATO provides several advantages including library size and cost. A unique advantage of PLATO is that an alternative reverse transcription-quantitative PCR (RT-qPCR) protocol can be used to test binding of specific, individual proteins. To illustrate a typical experimental workflow, we demonstrate PLATO for the identification of the immune target of serum antibodies from patients with inclusion body myositis (IBM). Beginning with an ORFeome library in an RD vector, the protocol can produce samples for deep sequencing or RT-qPCR within 4 d.
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Affiliation(s)
- Jian Zhu
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital, Boston, MA
- Department of Genetics, Harvard University Medical School, Boston, MA
- Howard Hughes Medical Institute
| | - H. Benjamin Larman
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital, Boston, MA
- Harvard-MIT Division of Health Sciences and Technology, Cambridge, MA
- Department of Materials Science and Engineering, Massachusetts Institute of Technology, Cambridge, MA
- Department of Genetics, Harvard University Medical School, Boston, MA
- Howard Hughes Medical Institute
| | - Geng Gao
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital, Boston, MA
- Department of Genetics, Harvard University Medical School, Boston, MA
- Howard Hughes Medical Institute
| | - Romel Somwar
- Human Oncology and Pathogenesis Program, Memorial Sloan-Kettering Cancer Center, New York, NY
| | - Zijuan Zhang
- Department of Chemistry, University of Massachusetts Boston, Boston, MA
| | - Uri Laserson
- Harvard-MIT Division of Health Sciences and Technology, Cambridge, MA
- Department of Genetics, Harvard University Medical School, Boston, MA
- Department of Mathematics, Massachusetts Institute of Technology, Cambridge, MA
| | - Alberto Ciccia
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital, Boston, MA
- Department of Genetics, Harvard University Medical School, Boston, MA
- Howard Hughes Medical Institute
| | - Natalya Pavlova
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital, Boston, MA
- Department of Genetics, Harvard University Medical School, Boston, MA
- Howard Hughes Medical Institute
| | - George Church
- Harvard-MIT Division of Health Sciences and Technology, Cambridge, MA
- Department of Genetics, Harvard University Medical School, Boston, MA
| | - Wei Zhang
- Department of Chemistry, University of Massachusetts Boston, Boston, MA
| | - Santosh Kesari
- Division of Neuro-Oncology, Translational Neuro-Oncology Laboratories, Department of Neurosciences, U.C. San Diego, Moores Cancer Center, La Jolla, CA
| | - Stephen J. Elledge
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital, Boston, MA
- Department of Genetics, Harvard University Medical School, Boston, MA
- Howard Hughes Medical Institute
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Buj R, Iglesias N, Planas AM, Santalucía T. A plasmid toolkit for cloning chimeric cDNAs encoding customized fusion proteins into any Gateway destination expression vector. BMC Mol Biol 2013; 14:18. [PMID: 23957834 PMCID: PMC3765358 DOI: 10.1186/1471-2199-14-18] [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: 04/08/2013] [Accepted: 08/12/2013] [Indexed: 12/31/2022] Open
Abstract
Background Valuable clone collections encoding the complete ORFeomes for some model organisms have been constructed following the completion of their genome sequencing projects. These libraries are based on Gateway cloning technology, which facilitates the study of protein function by simplifying the subcloning of open reading frames (ORF) into any suitable destination vector. The expression of proteins of interest as fusions with functional modules is a frequent approach in their initial functional characterization. A limited number of Gateway destination expression vectors allow the construction of fusion proteins from ORFeome-derived sequences, but they are restricted to the possibilities offered by their inbuilt functional modules and their pre-defined model organism-specificity. Thus, the availability of cloning systems that overcome these limitations would be highly advantageous. Results We present a versatile cloning toolkit for constructing fully-customizable three-part fusion proteins based on the MultiSite Gateway cloning system. The fusion protein components are encoded in the three plasmids integral to the kit. These can recombine with any purposely-engineered destination vector that uses a heterologous promoter external to the Gateway cassette, leading to the in-frame cloning of an ORF of interest flanked by two functional modules. In contrast to previous systems, a third part becomes available for peptide-encoding as it no longer needs to contain a promoter, resulting in an increased number of possible fusion combinations. We have constructed the kit’s component plasmids and demonstrate its functionality by providing proof-of-principle data on the expression of prototype fluorescent fusions in transiently-transfected cells. Conclusions We have developed a toolkit for creating fusion proteins with customized N- and C-term modules from Gateway entry clones encoding ORFs of interest. Importantly, our method allows entry clones obtained from ORFeome collections to be used without prior modifications. Using this technology, any existing Gateway destination expression vector with its model-specific properties could be easily adapted for expressing fusion proteins.
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Affiliation(s)
- Raquel Buj
- Department of Brain Ischemia and Neurodegeneration, Institut d'Investigacions Biomèdiques de Barcelona (IIBB)-Consejo Superior de Investigaciones Científicas (CSIC), Barcelona, Spain
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12
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Rid R, Abdel-Hadi O, Maier R, Wagner M, Hundsberger H, Hintner H, Bauer J, Onder K. From the ORFeome concept to highly comprehensive, full-genome screening libraries. Assay Drug Dev Technol 2012; 11:52-7. [PMID: 22621725 DOI: 10.1089/adt.2012.450] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Recombination-based cloning techniques have in recent times facilitated the establishment of genome-scale single-gene ORFeome repositories. Their further handling and downstream application in systematic fashion is, however, practically impeded because of logistical plus economic challenges. At this juncture, simultaneously transferring entire gene collections in compiled pool format could represent an advanced compromise between systematic ORFeome (an organism's entire set of protein-encoding open reading frames) projects and traditional random library approaches, but has not yet been considered in great detail. In our endeavor to merge the comprehensiveness of ORFeomes with a basically simple, streamlined, and easily executable single-tube design, we have here produced five different pooled screening-ready libraries for both Staphylococcus aureus and Homo sapiens. By evaluating the parallel transfer efficiencies of differentially sized genes from initial polymerase chain reaction (PCR) product amplification to entry and final destination library construction via quantitative real-time PCR, we found that the complexity of the gene population is fairly stably maintained once an entry resource has been successfully established, and that no apparent size-selection bias loss of large inserts takes place. Recombinational transfer processes are hence robust enough for straightforwardly achieving such pooled screening libraries.
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Affiliation(s)
- Raphaela Rid
- Division of Molecular Dermatology, Department of Dermatology, Paracelsus Private Medical University Salzburg, Austria
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13
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D'Angelo S, Velappan N, Mignone F, Santoro C, Sblattero D, Kiss C, Bradbury ARM. Filtering "genic" open reading frames from genomic DNA samples for advanced annotation. BMC Genomics 2011; 12 Suppl 1:S5. [PMID: 21810207 PMCID: PMC3223728 DOI: 10.1186/1471-2164-12-s1-s5] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Background In order to carry out experimental gene annotation, DNA encoding open reading frames (ORFs) derived from real genes (termed "genic") in the correct frame is required. When genes are correctly assigned, isolation of genic DNA for functional annotation can be carried out by PCR. However, not all genes are correctly assigned, and even when correctly assigned, gene products are often incorrectly folded when expressed in heterologous hosts. This is a problem that can sometimes be overcome by the expression of protein fragments encoding domains, rather than full-length proteins. One possible method to isolate DNA encoding such domains would to "filter" complex DNA (cDNA libraries, genomic and metagenomic DNA) for gene fragments that confer a selectable phenotype relying on correct folding, with all such domains present in a complex DNA sample, termed the “domainome”. Results In this paper we discuss the preparation of diverse genic ORF libraries from randomly fragmented genomic DNA using ß-lactamase to filter out the open reading frames. By cloning DNA fragments between leader sequences and the mature ß-lactamase gene, colonies can be selected for resistance to ampicillin, conferred by correct folding of the lactamase gene. Our experiments demonstrate that the majority of surviving colonies contain genic open reading frames, suggesting that ß-lactamase is acting as a selectable folding reporter. Furthermore, different leaders (Sec, TAT and SRP), normally translocating different protein classes, filter different genic fragment subsets, indicating that their use increases the fraction of the “domainone” that is accessible. Conclusions The availability of ORF libraries, obtained with the filtering method described here, combined with screening methods such as phage display and protein-protein interaction studies, or with protein structure determination projects, can lead to the identification and structural determination of functional genic ORFs. ORF libraries represent, moreover, a useful tool to proceed towards high-throughput functional annotation of newly sequenced genomes.
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Affiliation(s)
- Sara D'Angelo
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM, USA
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14
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Abstract
Phage display has been extensively used to study protein-protein interactions, receptor- and antibody-binding sites, and immune responses, to modify protein properties, and to select antibodies against a wide range of different antigens. In the format most often used, a polypeptide is displayed on the surface of a filamentous phage by genetic fusion to one of the coat proteins, creating a chimeric coat protein, and coupling phenotype (the protein) to genotype (the gene within). As the gene encoding the chimeric coat protein is packaged within the phage, selection of the phage on the basis of the binding properties of the polypeptide displayed on the surface simultaneously results in the isolation of the gene encoding the polypeptide. This unit describes the background to the technique, and illustrates how it has been applied to a number of different problems, each of which has its neurobiological counterparts. Although this overview concentrates on the use of filamentous phage, which is the most popular platform, other systems are also described.
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Abstract
The ever-increasing number of sequenced genomes and subsequent sequence-based analysis has provided tremendous insight into cellular processes; however, the ability to experimentally manipulate this genomic information in the laboratory requires the development of new high-throughput methods. To translate this genomic information into information on protein function, molecular and cell biological techniques are required. One strategy to gain insight into protein function is to observe where each specific protein is subcellularly localized. We have developed a pipeline of methods that allows rapid, efficient, and scalable gene cloning, imaging, and image analysis. This work focuses on a high-throughput screen of the Caulobacter crescentus proteome to identify proteins with unique subcellular localization patterns. The cloning, imaging, and image analysis techniques described here are applicable to any organism of interest.
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Affiliation(s)
- John N Werner
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, USA
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De Backer P, De Waele D, Van Speybroeck L. Ins and outs of systems biology vis-à-vis molecular biology: continuation or clear cut? Acta Biotheor 2010; 58:15-49. [PMID: 19855930 DOI: 10.1007/s10441-009-9089-6] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2008] [Accepted: 09/17/2009] [Indexed: 01/24/2023]
Abstract
The comprehension of living organisms in all their complexity poses a major challenge to the biological sciences. Recently, systems biology has been proposed as a new candidate in the development of such a comprehension. The main objective of this paper is to address what systems biology is and how it is practised. To this end, the basic tools of a systems biological approach are explored and illustrated. In addition, it is questioned whether systems biology 'revolutionizes' molecular biology and 'transcends' its assumed reductionism. The strength of this claim appears to depend on how molecular and systems biology are characterised and on how reductionism is interpreted. Doing credit to molecular biology and to methodological reductionism, it is argued that the distinction between molecular and systems biology is gradual rather than sharp. As such, the classical challenge in biology to manage, interpret and integrate biological data into functional wholes is further intensified by systems biology's use of modelling and bioinformatics, and by its scale enlargement.
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Affiliation(s)
- Philippe De Backer
- VIB, Department of Molecular Genetics/Department of Plant Systems Biology, Ghent University, Technologiepark 927, 9052 Ghent, Belgium
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17
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Pellet J, Tafforeau L, Lucas-Hourani M, Navratil V, Meyniel L, Achaz G, Guironnet-Paquet A, Aublin-Gex A, Caignard G, Cassonnet P, Chaboud A, Chantier T, Deloire A, Demeret C, Le Breton M, Neveu G, Jacotot L, Vaglio P, Delmotte S, Gautier C, Combet C, Deleage G, Favre M, Tangy F, Jacob Y, Andre P, Lotteau V, Rabourdin-Combe C, Vidalain PO. ViralORFeome: an integrated database to generate a versatile collection of viral ORFs. Nucleic Acids Res 2009; 38:D371-8. [PMID: 20007148 PMCID: PMC2808970 DOI: 10.1093/nar/gkp1000] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Large collections of protein-encoding open reading frames (ORFs) established in a versatile recombination-based cloning system have been instrumental to study protein functions in high-throughput assays. Such ‘ORFeome’ resources have been developed for several organisms but in virology, plasmid collections covering a significant fraction of the virosphere are still needed. In this perspective, we present ViralORFeome 1.0 (http://www.viralorfeome.com), an open-access database and management system that provides an integrated set of bioinformatic tools to clone viral ORFs in the Gateway® system. ViralORFeome provides a convenient interface to navigate through virus genome sequences, to design ORF-specific cloning primers, to validate the sequence of generated constructs and to browse established collections of virus ORFs. Most importantly, ViralORFeome has been designed to manage all possible variants or mutants of a given ORF so that the cloning procedure can be applied to any emerging virus strain. A subset of plasmid constructs generated with ViralORFeome platform has been tested with success for heterologous protein expression in different expression systems at proteome scale. ViralORFeome should provide our community with a framework to establish a large collection of virus ORF clones, an instrumental resource to determine functions, activities and binding partners of viral proteins.
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Affiliation(s)
- J Pellet
- INSERM U851, Lyon, IFR128-BioSciences, Université Lyon 1, Université de Lyon, Lyon, France
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Cai Y, Lux MW, Adam L, Peccoud J. Modeling structure-function relationships in synthetic DNA sequences using attribute grammars. PLoS Comput Biol 2009; 5:e1000529. [PMID: 19816554 PMCID: PMC2748682 DOI: 10.1371/journal.pcbi.1000529] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2009] [Accepted: 09/03/2009] [Indexed: 11/18/2022] Open
Abstract
Recognizing that certain biological functions can be associated with specific DNA sequences has led various fields of biology to adopt the notion of the genetic part. This concept provides a finer level of granularity than the traditional notion of the gene. However, a method of formally relating how a set of parts relates to a function has not yet emerged. Synthetic biology both demands such a formalism and provides an ideal setting for testing hypotheses about relationships between DNA sequences and phenotypes beyond the gene-centric methods used in genetics. Attribute grammars are used in computer science to translate the text of a program source code into the computational operations it represents. By associating attributes with parts, modifying the value of these attributes using rules that describe the structure of DNA sequences, and using a multi-pass compilation process, it is possible to translate DNA sequences into molecular interaction network models. These capabilities are illustrated by simple example grammars expressing how gene expression rates are dependent upon single or multiple parts. The translation process is validated by systematically generating, translating, and simulating the phenotype of all the sequences in the design space generated by a small library of genetic parts. Attribute grammars represent a flexible framework connecting parts with models of biological function. They will be instrumental for building mathematical models of libraries of genetic constructs synthesized to characterize the function of genetic parts. This formalism is also expected to provide a solid foundation for the development of computer assisted design applications for synthetic biology.
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Affiliation(s)
- Yizhi Cai
- Virginia Bioinformatics Institute, Virginia Polytechnic Institute and State University, Blacksburg, Virginia, United States of America
| | - Matthew W. Lux
- Virginia Bioinformatics Institute, Virginia Polytechnic Institute and State University, Blacksburg, Virginia, United States of America
| | - Laura Adam
- Virginia Bioinformatics Institute, Virginia Polytechnic Institute and State University, Blacksburg, Virginia, United States of America
| | - Jean Peccoud
- Virginia Bioinformatics Institute, Virginia Polytechnic Institute and State University, Blacksburg, Virginia, United States of America
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19
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Torres JZ, Miller JJ, Jackson PK. High-throughput generation of tagged stable cell lines for proteomic analysis. Proteomics 2009; 9:2888-91. [PMID: 19405035 DOI: 10.1002/pmic.200800873] [Citation(s) in RCA: 89] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
We present an optimized system for rapid generation of localization and affinity purification-tagged mammalian stable cell lines that facilitates complex purification and interacting protein identification. The improved components of this method, including the flexibility of inducible expression, circumvent issues associated with toxicity, clonal selection, sample yields and time to data acquisition. We have applied this method to the study of cell-cycle regulators and novel microtubule-associated proteins.
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Affiliation(s)
- Jorge Z Torres
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA.
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20
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Autiero I, Costantini S, Colonna G. Modeling of the bacterial mechanism of methicillin-resistance by a systems biology approach. PLoS One 2009; 4:e6226. [PMID: 19593454 PMCID: PMC2707609 DOI: 10.1371/journal.pone.0006226] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2009] [Accepted: 06/15/2009] [Indexed: 02/06/2023] Open
Abstract
Background A microorganism is a complex biological system able to preserve its functional features against external perturbations and the ability of the living systems to oppose to these external perturbations is defined “robustness”. The antibiotic resistance, developed by different bacteria strains, is a clear example of robustness and of ability of the bacterial system to acquire a particular functional behaviour in response to environmental changes. In this work we have modeled the whole mechanism essential to the methicillin-resistance through a systems biology approach. The methicillin is a β-lactamic antibiotic that act by inhibiting the penicillin-binding proteins (PBPs). These PBPs are involved in the synthesis of peptidoglycans, essential mesh-like polymers that surround cellular enzymes and are crucial for the bacterium survival. Methodology The network of genes, mRNA, proteins and metabolites was created using CellDesigner program and the data of molecular interactions are stored in Systems Biology Markup Language (SBML). To simulate the dynamic behaviour of this biochemical network, the kinetic equations were associated with each reaction. Conclusions Our model simulates the mechanism of the inactivation of the PBP by methicillin, as well as the expression of PBP2a isoform, the regulation of the SCCmec elements (SCC: staphylococcal cassette chromosome) and the synthesis of peptidoglycan by PBP2a. The obtained results by our integrated approach show that the model describes correctly the whole phenomenon of the methicillin resistance and is able to respond to the external perturbations in the same way of the real cell. Therefore, this model can be useful to develop new therapeutic approaches for the methicillin control and to understand the general mechanism regarding the cellular resistance to some antibiotics.
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Affiliation(s)
- Ida Autiero
- CRISCEB (Interdepartmental Research Center for Computational and Biotechnological Sciences), Second University of Naples, Naples, Italy
| | - Susan Costantini
- CRISCEB (Interdepartmental Research Center for Computational and Biotechnological Sciences), Second University of Naples, Naples, Italy
- CROM (Oncology Research Centre of Mercogliano) “Fiorentino Lo Vuolo”, Mercogliano, Italy
- Department of Biochemistry and Biophysics, Second University of Naples, Naples, Italy
- * E-mail:
| | - Giovanni Colonna
- CRISCEB (Interdepartmental Research Center for Computational and Biotechnological Sciences), Second University of Naples, Naples, Italy
- Department of Biochemistry and Biophysics, Second University of Naples, Naples, Italy
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Quantitative genome-scale analysis of protein localization in an asymmetric bacterium. Proc Natl Acad Sci U S A 2009; 106:7858-63. [PMID: 19416866 DOI: 10.1073/pnas.0901781106] [Citation(s) in RCA: 138] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Despite the importance of subcellular localization for cellular activities, the lack of high-throughput, high-resolution imaging and quantitation methodologies has limited genomic localization analysis to a small number of archival studies focused on C-terminal fluorescent protein fusions. Here, we develop a high-throughput pipeline for generating, imaging, and quantitating fluorescent protein fusions that we use for the quantitative genomic assessment of the distributions of both N- and C-terminal fluorescent protein fusions. We identify nearly 300 localized Caulobacter crescentus proteins, up to 10-fold more than were previously characterized. The localized proteins tend to be involved in spatially or temporally dynamic processes and proteins that function together and often localize together as well. The distributions of the localized proteins were quantitated by using our recently described projected system of internal coordinates from interpolated contours (PSICIC) image analysis toolkit, leading to the identification of cellular regions that are over- or under-enriched in localized proteins and of potential differences in the mechanisms that target proteins to different subcellular destinations. The Caulobacter localizome data thus represent a resource for studying both global properties of protein localization and specific protein functions, whereas the localization analysis pipeline is a methodological resource that can be readily applied to other systems.
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22
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Abstract
Current classification of medical diagnosis derives from observational correlation between clinical syndromes and pathologic analysis. Limited understanding of the molecular determinants of diseases encountered in the critically ill remains a major obstacle to the rationale selection of therapeutic targets. Indeed, many human diseases reflect a disorder in physiologic processes that are known to involve the interaction of many complex control loops and to respond to a variety of pharmacologic agents and environmental factors. The advent of whole-genome sequencing and other high-throughput technologies have changed biomedical research into a data-rich discipline. "Omics" data sets that describe virtually all biomolecules in the cell are now publicly available. One of the challenges faced by investigators now lies in the interpretation of vast amounts of biological data sets to derive fundamental and applied biological information about whole systems. As mechanistic understanding of disease requires more than an agglomeration of information on the expression and activities of disease-associated molecules, network analysis has been applied to biological problems. Network analysis of the biological integratome promises to identify factors that influence disease phenotype, providing unique insight into disease mechanism. Network analysis also provides a mechanistic basis for defining phenotypic differences through consideration of unique genetic and environmental factors that govern intermediate phenotypes contributing to disease expression. Lastly, network analysis offers a unique method for identifying therapeutic targets that can alter disease expression.
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Abstract
We describe a plate-based cloning and expression strategy for efficient high-throughput generation of validated expression clones in Escherichia coli. The process incorporates 48- or 96-well plates at all stages including the cloning and colony selection phases which are often performed manually. A 48-grid agar growth plate has been integrated into the colony selection component to improve throughput at the cloning stage. The combinations of 48- and 96-well plate formats are compatible with automated liquid handlers and multichannel pipettes. This revised cloning and expression pipeline increases throughput significantly, and also results in a reduction in both time and material requirements. The system has been validated by the production and screening of several thousand clones at the Midwest Center for Structural Genomics.
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Abstract
Reverse chemical genomic approach is expected to greatly expedite the discovery of new compounds, which modulate biological phenotypes in various ways. However, toward this end, various contents and platforms must be well prepared in the research community. In this regard, genome-wide preparation of clones for production of proteins in either a native or a fusion form, which are conventionally called ORFeome clones, would play a crucial role in realizing reverse chemical genomics as an approach of choice. In this chapter, currently available ORFeome cloning technologies are overviewed and a selection guideline for them is provided.
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Affiliation(s)
- Osamu Ohara
- Department of Human Genome Research, Kazusa DNA Research Institute, Chiba, Japan
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25
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Abstract
Predicting the behavior of living organisms is an enormous challenge given their vast complexity. Efforts to model biological systems require large datasets generated by physical binding experiments and perturbation studies. Genetic perturbations have proven important and are greatly facilitated by the advent of comprehensive mutant libraries in model organisms. Small-molecule chemical perturbagens provide a complementary approach, especially for systems that lack mutant libraries, and can easily probe the function of essential genes. Though single chemical or genetic perturbations provide crucial information associating individual components (for example, genes, proteins or small molecules) with pathways or phenotypes, functional relationships between pathways and modules of components are most effectively obtained from combined perturbation experiments. Here we review the current state of and discuss some future directions for 'combination chemical genetics', the systematic application of multiple chemical or mixed chemical and genetic perturbations, both to gain insight into biological systems and to facilitate medical discoveries.
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Affiliation(s)
- Joseph Lehár
- CombinatoRx Incorporated, 245 First Street, Cambridge, Massachusetts 02142, USA.
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26
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Maier R, Brandner C, Hintner H, Bauer J, Onder K. Construction of a reading frame-independent yeast two-hybrid vector system for site-specific recombinational cloning and protein interaction screening. Biotechniques 2008; 45:235-44. [PMID: 18778248 DOI: 10.2144/000112897] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
The yeast two-hybrid (Y2H) system is a powerful method to identify protein-protein inter-actions (PPI) in vivo, requiring minimal prior information of the putative interactors. The time and effort required for each experiment can be significantly reduced if the "bait" and the "prey" proteins are cloned into specific recombination-amenable two-hybrid vectors. We describe the construction of a reading frame-independent vector system for Y2H PPI studies. The described vector system knits together the advantages of site-specific recombination cloning with the Y2H system. The produced plasmids enable recombination-based cloning of genes or gene fragments in all possible reading frames into Y2H library vectors. Thus, Y2H screening libraries can be rapidly constructed and will present more amino termini in the correct reading frame. Additionally, advantageous for small-scale Y2H studies, there is no need to know the natural reading frame of the genes of interest, because the bait and prey genes can be transferred into the vectors by a single reaction and are present in all possible reading frames. Since the Y2H system per se is a positive selection system, only pairs of bait and prey genes harboring the correct reading frames will emerge. We tested the new vectors within the Y2H system and demonstrated full functionality without any undesired effects on the Y2H system itself. Besides the vector construction, we investigated the utility of the system for Y2H analysis and demonstrated clearly its practicability in genome-wide Y2H screenings and the advantage of using additional reading-frame Y2H cDNA libraries. We performed a series of genome-wide Y2H library screenings with the human vitamin D receptor protein (VDR) as bait. We investigated: (i) whether more protein interactors are found by using three instead of one reading-frame destination vectors; (ii) how much overlap between the different reading-frame libraries exists; and (iii) the rate of possible additional autoactivators. We conclude that our vectors deliver significantly more interactors and outperform a single reading-frame library. This new system could enable simple and fast large-scale PPI studies and the construction of high-quality screening libraries.
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Affiliation(s)
- Richard Maier
- Department of Cell Biology, University of Salzburg, Hellbrunnerstrasse 34, Salzburg, Vienna.
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27
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Kudva IT, Calderwood SB, John M. Proteomics-based expression library screening - a platform technology for rapid discovery of pathogen-specific markers of infection. ACTA ACUST UNITED AC 2008; 2:979-89. [PMID: 23495870 DOI: 10.1517/17530059.2.8.979] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
BACKGROUND The development of new management modalities is imperative for reducing the global burden of infectious diseases. OBJECTIVE To develop a platform technology for rapid definition of comprehensive pathogen immunoproteomes (the repertoire of microbial proteins that elicit and interact with host immune responses). METHODS Standard molecular biology techniques were coupled with cutting-edge proteomics to develop proteomics-based expression library screening (PELS). RESULTS Proof of principle of PELS was demonstrated by defining a comprehensive immunoproteome of the human gastrointestinal pathogen, Escherichia coli O157:H7, in bovine reservoirs in just 3 weeks. CONCLUSIONS PELS, an immunoproteomics-based platform technology, is a rapid and inexpensive alternative to protein/antigen arrays/chips. It is applicable to any parasitic, fungal, viral or bacterial pathogen (or commensal) that: has a sequenced genome; can be cultured in the laboratory; and elicits host humoral immune responses during the process of infection/disease.
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Affiliation(s)
- Indira T Kudva
- Massachusetts General Hospital, Division of Infectious Diseases, Boston, MA 02114, USA +1 781 244 4505 ;
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28
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Shetty RP, Endy D, Knight TF. Engineering BioBrick vectors from BioBrick parts. J Biol Eng 2008; 2:5. [PMID: 18410688 PMCID: PMC2373286 DOI: 10.1186/1754-1611-2-5] [Citation(s) in RCA: 490] [Impact Index Per Article: 30.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2008] [Accepted: 04/14/2008] [Indexed: 11/13/2022] Open
Abstract
Background The underlying goal of synthetic biology is to make the process of engineering biological systems easier. Recent work has focused on defining and developing standard biological parts. The technical standard that has gained the most traction in the synthetic biology community is the BioBrick standard for physical composition of genetic parts. Parts that conform to the BioBrick assembly standard are BioBrick standard biological parts. To date, over 2,000 BioBrick parts have been contributed to, and are available from, the Registry of Standard Biological Parts. Results Here we extended the same advantages of BioBrick standard biological parts to the plasmid-based vectors that are used to provide and propagate BioBrick parts. We developed a process for engineering BioBrick vectors from BioBrick parts. We designed a new set of BioBrick parts that encode many useful vector functions. We combined the new parts to make a BioBrick base vector that facilitates BioBrick vector construction. We demonstrated the utility of the process by constructing seven new BioBrick vectors. We also successfully used the resulting vectors to assemble and propagate other BioBrick standard biological parts. Conclusion We extended the principles of part reuse and standardization to BioBrick vectors. As a result, myriad new BioBrick vectors can be readily produced from all existing and newly designed BioBrick parts. We invite the synthetic biology community to (1) use the process to make and share new BioBrick vectors; (2) expand the current collection of BioBrick vector parts; and (3) characterize and improve the available collection of BioBrick vector parts.
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Affiliation(s)
- Reshma P Shetty
- Department of Biological Engineering, MIT, 32 Vassar Street Rm 32-311, Cambridge, MA 02139, USA.
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Karimi M, Bleys A, Vanderhaeghen R, Hilson P. Building blocks for plant gene assembly. PLANT PHYSIOLOGY 2007; 145:1183-91. [PMID: 17965171 PMCID: PMC2151724 DOI: 10.1104/pp.107.110411] [Citation(s) in RCA: 186] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/14/2023]
Abstract
The MultiSite Gateway cloning system, based on site-specific recombination, enables the assembly of multiple DNA fragments in predefined order, orientation, and frame register. To streamline the construction of recombinant genes for functional analysis in plants, we have built a collection of 36 reference Gateway entry clones carrying promoters, terminators, and reporter genes, as well as elements of the LhG4/LhGR two-component system. This collection obeys simple engineering rules. The genetic elements (parts) are designed in a standard format. They are interchangeable, fully documented, and can be combined at will according to the desired output. We also took advantage of the MultiSite Gateway recombination sites to create vectors in which two or three genes can be cloned simultaneously in separate expression cassettes. To illustrate the flexibility of these core resources for the construction of a wide variety of plant transformation vectors, we generated various transgenes encoding fluorescent proteins and tested their activity in plant cells. The structure and sequence of all described plasmids are accessible online at http://www.psb.ugent.be/gateway/. All accessions can be requested via the same Web site.
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Affiliation(s)
- Mansour Karimi
- Department of Plant Systems Biology, Flanders Institute for Biotechnology, Ghent University, 9052 Gent, Belgium
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30
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Goodin MM, Chakrabarty R, Banerjee R, Yelton S, Debolt S. New gateways to discovery. PLANT PHYSIOLOGY 2007; 145:1100-9. [PMID: 18056860 PMCID: PMC2151732 DOI: 10.1104/pp.107.106641] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2007] [Accepted: 08/28/2007] [Indexed: 05/19/2023]
Affiliation(s)
- Michael M Goodin
- Department of Plant Pathology , University of Kentucky, Lexington, Kentucky 40546, USA.
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Roure A, Rothbächer U, Robin F, Kalmar E, Ferone G, Lamy C, Missero C, Mueller F, Lemaire P. A multicassette Gateway vector set for high throughput and comparative analyses in ciona and vertebrate embryos. PLoS One 2007; 2:e916. [PMID: 17878951 PMCID: PMC1976267 DOI: 10.1371/journal.pone.0000916] [Citation(s) in RCA: 105] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2007] [Accepted: 08/01/2007] [Indexed: 01/26/2023] Open
Abstract
Background The past few years have seen a vast increase in the amount of genomic data available for a growing number of taxa, including sets of full length cDNA clones and cis-regulatory sequences. Large scale cross-species comparisons of protein function and cis-regulatory sequences may help to understand the emergence of specific traits during evolution. Principal Findings To facilitate such comparisons, we developed a Gateway compatible vector set, which can be used to systematically dissect cis-regulatory sequences, and overexpress wild type or tagged proteins in a variety of chordate systems. It was developed and first characterised in the embryos of the ascidian Ciona intestinalis, in which large scale analyses are easier to perform than in vertebrates, owing to the very efficient embryo electroporation protocol available in this organism. Its use was then extended to fish embryos and cultured mammalian cells. Conclusion This versatile vector set opens the way to the mid- to large-scale comparative analyses of protein function and cis-regulatory sequences across chordate evolution. A complete user manual is provided as supplemental material.
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Affiliation(s)
- Agnès Roure
- Institut de Biologie du Développement de Marseille Luminy, UMR 6216 CNRS/Université de la Méditerranée, Marseille, France
- * To whom correspondence should be addressed. E-mail: (AR); (PL)
| | - Ute Rothbächer
- Institut de Biologie du Développement de Marseille Luminy, UMR 6216 CNRS/Université de la Méditerranée, Marseille, France
| | - François Robin
- Institut de Biologie du Développement de Marseille Luminy, UMR 6216 CNRS/Université de la Méditerranée, Marseille, France
| | - Eva Kalmar
- Institute of Toxicology and Genetics, Forschungszentrum Karlsruhe, Karlsruhe, Germany
| | - Giustina Ferone
- CEINGE Biotecnologie Avanzate SCarl (Center for Genetic Engineering), Napoli, Italy
| | - Clément Lamy
- Institut de Biologie du Développement de Marseille Luminy, UMR 6216 CNRS/Université de la Méditerranée, Marseille, France
| | - Caterina Missero
- CEINGE Biotecnologie Avanzate SCarl (Center for Genetic Engineering), Napoli, Italy
| | - Ferenc Mueller
- Institute of Toxicology and Genetics, Forschungszentrum Karlsruhe, Karlsruhe, Germany
| | - Patrick Lemaire
- Institut de Biologie du Développement de Marseille Luminy, UMR 6216 CNRS/Université de la Méditerranée, Marseille, France
- * To whom correspondence should be addressed. E-mail: (AR); (PL)
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Katzen F. Gateway®recombinational cloning: a biological operating system. Expert Opin Drug Discov 2007; 2:571-89. [DOI: 10.1517/17460441.2.4.571] [Citation(s) in RCA: 162] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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Zavzavadjian JR, Couture S, Park WS, Whalen J, Lyon S, Lee G, Fung E, Mi Q, Liu J, Wall E, Santat L, Dhandapani K, Kivork C, Driver A, Zhu X, Chang MS, Randhawa B, Gehrig E, Bryan H, Verghese M, Maer A, Saunders B, Ning Y, Subramaniam S, Meyer T, Simon MI, O’Rourke N, Chandy G, Fraser IDC. The alliance for cellular signaling plasmid collection: a flexible resource for protein localization studies and signaling pathway analysis. Mol Cell Proteomics 2007; 6:413-24. [PMID: 17192258 PMCID: PMC3579516 DOI: 10.1074/mcp.m600437-mcp200] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Cellular responses to inputs that vary both temporally and spatially are determined by complex relationships between the components of cell signaling networks. Analysis of these relationships requires access to a wide range of experimental reagents and techniques, including the ability to express the protein components of the model cells in a variety of contexts. As part of the Alliance for Cellular Signaling, we developed a robust method for cloning large numbers of signaling ORFs into Gateway entry vectors, and we created a wide range of compatible expression platforms for proteomics applications. To date, we have generated over 3000 plasmids that are available to the scientific community via the American Type Culture Collection. We have established a website at www.signaling-gateway.org/data/plasmid/ that allows users to browse, search, and blast Alliance for Cellular Signaling plasmids. The collection primarily contains murine signaling ORFs with an emphasis on kinases and G protein signaling genes. Here we describe the cloning, databasing, and application of this proteomics resource for large scale subcellular localization screens in mammalian cell lines.
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Affiliation(s)
- Joelle R. Zavzavadjian
- Alliance for Cellular Signaling, California Institute of Technology, Pasadena, California, 91125
- Molecular Biology Laboratory, California Institute of Technology, Pasadena, California, 91125
| | - Sam Couture
- Alliance for Cellular Signaling, California Institute of Technology, Pasadena, California, 91125
- Molecular Biology Laboratory, California Institute of Technology, Pasadena, California, 91125
| | - Wei Sun Park
- Alliance for Cellular Signaling, California Institute of Technology, Pasadena, California, 91125
- Microscopy Laboratory, Stanford University, Palo Alto, California, 94305
| | - James Whalen
- Alliance for Cellular Signaling, California Institute of Technology, Pasadena, California, 91125
- Microscopy Laboratory, Stanford University, Palo Alto, California, 94305
| | - Stephen Lyon
- Alliance for Cellular Signaling, California Institute of Technology, Pasadena, California, 91125
- Bioinformatics and Data Coordination Laboratory, University of California San Diego, La Jolla, California 92093
| | - Genie Lee
- Alliance for Cellular Signaling, California Institute of Technology, Pasadena, California, 91125
- Molecular Biology Laboratory, California Institute of Technology, Pasadena, California, 91125
| | - Eileen Fung
- Alliance for Cellular Signaling, California Institute of Technology, Pasadena, California, 91125
- Molecular Biology Laboratory, California Institute of Technology, Pasadena, California, 91125
| | - Qingli Mi
- Alliance for Cellular Signaling, California Institute of Technology, Pasadena, California, 91125
- Molecular Biology Laboratory, California Institute of Technology, Pasadena, California, 91125
| | - Jamie Liu
- Alliance for Cellular Signaling, California Institute of Technology, Pasadena, California, 91125
- Molecular Biology Laboratory, California Institute of Technology, Pasadena, California, 91125
| | - Estelle Wall
- Alliance for Cellular Signaling, California Institute of Technology, Pasadena, California, 91125
- Molecular Biology Laboratory, California Institute of Technology, Pasadena, California, 91125
| | - Leah Santat
- Alliance for Cellular Signaling, California Institute of Technology, Pasadena, California, 91125
- Molecular Biology Laboratory, California Institute of Technology, Pasadena, California, 91125
| | - Kavitha Dhandapani
- Alliance for Cellular Signaling, California Institute of Technology, Pasadena, California, 91125
- Molecular Biology Laboratory, California Institute of Technology, Pasadena, California, 91125
| | - Christine Kivork
- Alliance for Cellular Signaling, California Institute of Technology, Pasadena, California, 91125
- Molecular Biology Laboratory, California Institute of Technology, Pasadena, California, 91125
| | - Adrienne Driver
- Alliance for Cellular Signaling, California Institute of Technology, Pasadena, California, 91125
- Molecular Biology Laboratory, California Institute of Technology, Pasadena, California, 91125
| | - Xiaocui Zhu
- Alliance for Cellular Signaling, California Institute of Technology, Pasadena, California, 91125
- Molecular Biology Laboratory, California Institute of Technology, Pasadena, California, 91125
| | - Mi Sook Chang
- Alliance for Cellular Signaling, California Institute of Technology, Pasadena, California, 91125
- Molecular Biology Laboratory, California Institute of Technology, Pasadena, California, 91125
| | - Baljinder Randhawa
- Alliance for Cellular Signaling, California Institute of Technology, Pasadena, California, 91125
- Molecular Biology Laboratory, California Institute of Technology, Pasadena, California, 91125
| | - Elizabeth Gehrig
- Alliance for Cellular Signaling, California Institute of Technology, Pasadena, California, 91125
- Microscopy Laboratory, Stanford University, Palo Alto, California, 94305
| | - Heather Bryan
- Alliance for Cellular Signaling, California Institute of Technology, Pasadena, California, 91125
- Microscopy Laboratory, Stanford University, Palo Alto, California, 94305
| | - Mary Verghese
- Alliance for Cellular Signaling, California Institute of Technology, Pasadena, California, 91125
- Microscopy Laboratory, Stanford University, Palo Alto, California, 94305
| | - Andreia Maer
- Alliance for Cellular Signaling, California Institute of Technology, Pasadena, California, 91125
- Bioinformatics and Data Coordination Laboratory, University of California San Diego, La Jolla, California 92093
| | - Brian Saunders
- Alliance for Cellular Signaling, California Institute of Technology, Pasadena, California, 91125
- Bioinformatics and Data Coordination Laboratory, University of California San Diego, La Jolla, California 92093
| | - Yuhong Ning
- Alliance for Cellular Signaling, California Institute of Technology, Pasadena, California, 91125
- Bioinformatics and Data Coordination Laboratory, University of California San Diego, La Jolla, California 92093
| | - Shankar Subramaniam
- Alliance for Cellular Signaling, California Institute of Technology, Pasadena, California, 91125
- Bioinformatics and Data Coordination Laboratory, University of California San Diego, La Jolla, California 92093
| | - Tobias Meyer
- Alliance for Cellular Signaling, California Institute of Technology, Pasadena, California, 91125
- Microscopy Laboratory, Stanford University, Palo Alto, California, 94305
| | - Melvin I. Simon
- Alliance for Cellular Signaling, California Institute of Technology, Pasadena, California, 91125
- Molecular Biology Laboratory, California Institute of Technology, Pasadena, California, 91125
| | - Nancy O’Rourke
- Alliance for Cellular Signaling, California Institute of Technology, Pasadena, California, 91125
- Microscopy Laboratory, Stanford University, Palo Alto, California, 94305
| | - Grischa Chandy
- Alliance for Cellular Signaling, California Institute of Technology, Pasadena, California, 91125
- Microscopy Laboratory, Stanford University, Palo Alto, California, 94305
| | - Iain D. C. Fraser
- Alliance for Cellular Signaling, California Institute of Technology, Pasadena, California, 91125
- Molecular Biology Laboratory, California Institute of Technology, Pasadena, California, 91125
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Lamesch P, Li N, Milstein S, Fan C, Hao T, Szabo G, Hu Z, Venkatesan K, Bethel G, Martin P, Rogers J, Lawlor S, McLaren S, Dricot A, Borick H, Cusick ME, Vandenhaute J, Dunham I, Hill DE, Vidal M. hORFeome v3.1: a resource of human open reading frames representing over 10,000 human genes. Genomics 2007; 89:307-15. [PMID: 17207965 PMCID: PMC4647941 DOI: 10.1016/j.ygeno.2006.11.012] [Citation(s) in RCA: 188] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2006] [Revised: 10/29/2006] [Accepted: 11/21/2006] [Indexed: 11/24/2022]
Abstract
Complete sets of cloned protein-encoding open reading frames (ORFs), or ORFeomes, are essential tools for large-scale proteomics and systems biology studies. Here we describe human ORFeome version 3.1 (hORFeome v3.1), currently the largest publicly available resource of full-length human ORFs (available at www.openbiosystems.com). Generated by Gateway recombinational cloning, this collection contains 12,212 ORFs, representing 10,214 human genes, and corresponds to a 51% expansion of the original hORFeome v1.1. An online human ORFeome database, hORFDB, was built and serves as the central repository for all cloned human ORFs (http://horfdb.dfci.harvard.edu). This expansion of the original ORFeome resource greatly increases the potential experimental search space for large-scale proteomics studies, which will lead to the generation of more comprehensive datasets.
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Affiliation(s)
- Philippe Lamesch
- Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana-Farber Cancer Institute, and Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
- Unité de Recherche en Biologie Moléculaire, Facultés Universitaires Notre-Dame de la Paix, 5000 Namur, Belgium
| | - Ning Li
- Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana-Farber Cancer Institute, and Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Stuart Milstein
- Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana-Farber Cancer Institute, and Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Changyu Fan
- Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana-Farber Cancer Institute, and Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Tong Hao
- Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana-Farber Cancer Institute, and Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Gabor Szabo
- Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana-Farber Cancer Institute, and Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
- Department of Physics and Center for Complex Network Research, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Zhenjun Hu
- Department of Biomedical Engineering, Boston University, Boston, MA 02115, USA
| | - Kavitha Venkatesan
- Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana-Farber Cancer Institute, and Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Graeme Bethel
- The Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK
| | - Paul Martin
- The Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK
| | - Jane Rogers
- The Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK
| | - Stephanie Lawlor
- The Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK
| | - Stuart McLaren
- The Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK
| | - Amélie Dricot
- Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana-Farber Cancer Institute, and Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
- Unité de Recherche en Biologie Moléculaire, Facultés Universitaires Notre-Dame de la Paix, 5000 Namur, Belgium
| | - Heather Borick
- Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana-Farber Cancer Institute, and Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Michael E. Cusick
- Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana-Farber Cancer Institute, and Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Jean Vandenhaute
- Unité de Recherche en Biologie Moléculaire, Facultés Universitaires Notre-Dame de la Paix, 5000 Namur, Belgium
| | - Ian Dunham
- The Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK
| | - David E. Hill
- Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana-Farber Cancer Institute, and Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
- Corresponding authors. Fax: +1 617 632 5739.
| | - Marc Vidal
- Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana-Farber Cancer Institute, and Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
- Corresponding authors. Fax: +1 617 632 5739.
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Kornienko M, Montalvo A, Carpenter BE, Lenard M, Abeywickrema P, Hall DL, Darke PL, Kuo LC. Protein expression plasmids produced rapidly: streamlining cloning protocols and robotic handling. Assay Drug Dev Technol 2006; 3:661-74. [PMID: 16438661 DOI: 10.1089/adt.2005.3.661] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
As many processes in the preclinical drug discovery process become highly parallel, the need to also produce a large number of different proteins in parallel has become acute, such as for protein crystallization and activity screening. In turn, the requisite DNA constructions to produce these proteins must now be done at a rate that requires automated cloning procedures, each with an intrinsic low failure probability per sample. The high-throughput cloning solutions presented here achieve production of 192 different expression plasmids at a success rate of greater than 95% of the targeted open reading frames. Time for completion of the set by one person is reduced to approximately 11 working days, starting with polymerase chain reactions for a number of source clones and ending with purified expression plasmids. Achievement of this throughput utilizes the following: (1) the Beckman Coulter (Fullerton, CA) Biomek FX liquid handler for most manipulations, (2) Gateway cloning technology (Invitrogen Corp., Carlsbad, CA), and (3) computer programs designed for parallel processing of all sample information, including primer design and the resulting DNA and protein sequence assembly. Exemplary data are presented for discovery of a form of the Rho-kinase that crystallizes (ROCK2).
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Affiliation(s)
- Maria Kornienko
- Department of Structural Biology, Merck Research Laboratories, West Point, PA 19486, USA.
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36
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Hallez R, Letesson JJ, Vandenhaute J, De Bolle X. Gateway-based destination vectors for functional analyses of bacterial ORFeomes: application to the Min system in Brucella abortus. Appl Environ Microbiol 2006; 73:1375-9. [PMID: 17172460 PMCID: PMC1828643 DOI: 10.1128/aem.01873-06] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Twenty Gateway-compatible destination vectors were constructed. The vectors comprise fluorescent and epitope fusion tags, various drug markers, and replication origins that should make them useful for exploring existing microbial ORFeomes. In an attempt to validate several of these vectors, we observed polar and oscillating localization of MinD in Brucella abortus.
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Affiliation(s)
- Régis Hallez
- Unité de Recherche en Biologie Moléculaire, University of Namur, 61 rue de Bruxelles, B-5000 Namur, Belgium
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37
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Weeks SD, Drinker M, Loll PJ. Ligation independent cloning vectors for expression of SUMO fusions. Protein Expr Purif 2006; 53:40-50. [PMID: 17251035 PMCID: PMC1892228 DOI: 10.1016/j.pep.2006.12.006] [Citation(s) in RCA: 113] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2006] [Revised: 12/04/2006] [Accepted: 12/07/2006] [Indexed: 11/19/2022]
Abstract
With demand increasing for the production of many different proteins for biophysical or biochemical analyses, rapid methods are needed for the cloning, expression and purification of native recombinant proteins. In particular, generic methods are required that are independent of the target gene sequence. To address this challenge we have constructed four Escherichia coli expression vectors that can be used for ligation independent cloning (LIC) of an amplified target gene sequence. These vectors represent the combinatorial pairing of two different parent vector backbones with two different affinity tags. The target gene is cloned downstream of the sequence coding for an affinity-tagged small ubiquitin related modifier (SUMO). Using enhanced green fluorescent protein (eGFP) as an example we demonstrate that the LIC procedure works with high efficiency for all four of the vectors. We also show that the resultant recombinant SUMO fusion proteins can be overexpressed in E. coli and readily isolated by standard affinity purification techniques. Importantly, the purified fusion product can be treated with recombinant SUMO hydrolase to yield a mature target protein with any residue except proline at the amino terminus. We demonstrate an application of this by generating recombinant eGFP containing a non-native amino terminal cysteine residue and using it as a substrate for expressed protein ligation (EPL). The reagents and techniques described here represent a generic method for the rapid cloning and production of a target protein, and would be appropriate for a high throughput genomic scale expression project.
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Affiliation(s)
- Stephen D. Weeks
- Department of Biochemistry & Molecular Biology, Drexel University College of Medicine, 245 N 15th Street, Mailstop 497, Philadelphia, PA 19102-1192, USA
| | - Mark Drinker
- Division of Infectious Diseases, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Patrick J. Loll
- Department of Biochemistry & Molecular Biology, Drexel University College of Medicine, 245 N 15th Street, Mailstop 497, Philadelphia, PA 19102-1192, USA
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38
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Abstract
Protein chips have emerged as a promising approach for a wide variety of applications including the identification of protein-protein interactions, protein-phospholipid interactions, small molecule targets, and substrates of proteins kinases. They can also be used for clinical diagnostics and monitoring disease states. This article reviews current methods in the generation and applications of protein microarrays.
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Affiliation(s)
| | | | - Michael Snyder
- Corresponding author. Tel.: +1 203 432 6139; fax: +1 203 432 3597.
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Jalanko A, Tyynelä J, Peltonen L. From genes to systems: new global strategies for the characterization of NCL biology. Biochim Biophys Acta Mol Basis Dis 2006; 1762:934-44. [PMID: 17045465 DOI: 10.1016/j.bbadis.2006.09.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2006] [Revised: 09/01/2006] [Accepted: 09/05/2006] [Indexed: 11/20/2022]
Abstract
Neuronal ceroid lipofuscinoses (NCL) are rare neurological disorders with a uniform phenotype, caused by mutations in seven known genes. NCL provide a unique model to characterize molecular pathways critical for normal neuronal development and pathological neuronal degeneration. Systems biology based approach utilizes the rapidly developing tools of genomics, proteomics, lipidomics and metabolomics and aims at thorough understanding of the functions of cells, tissues and whole organisms by molecular analysis and biocomputing-assisted modeling. The systems level understanding of NCL is now possible by utilizing different model organisms. Initial work has revealed disturbed metabolic pathways in several NCL disorders and most analyses have utilized the infantile (INCL/CLN1) and juvenile (JNCL/CLN3) disease modeling and utilized mainly human and mouse samples. To date, the data obtained from transcript and lipidomic profiling has pinpointed the role of lipid metabolism and synaptic function in the infantile NCL. Changes in glutamate utilization and amino acid metabolism have been a common theme emerging from the transcript and metabolite profiling of the juvenile NCL. Further experimental models are being developed and systematic sample collection as well as data integration projects are needed. The combined analyses of the global information should provide means to expose all the NCL-associated molecular pathways.
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Affiliation(s)
- Anu Jalanko
- National Public Health Institute, Department of Molecular Medicine, Biomedicum Helsinki, Helsinki, Finland.
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40
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Itoh M, Yasunishi A, Imamura K, Kanamori-Katayama M, Suzuki H, Suzuki M, Carninci P, Kawai J, Hayashizaki Y. Constructing ORFeome resources with removable termination codons. Biotechniques 2006; 41:44, 46, 48 passim. [PMID: 16869512 DOI: 10.2144/000112209] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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41
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Kudva IT, Krastins B, Sheng H, Griffin RW, Sarracino DA, Tarr PI, Hovde CJ, Calderwood SB, John M. Proteomics-based expression library screening (PELS): a novel method for rapidly defining microbial immunoproteomes. Mol Cell Proteomics 2006; 5:1514-9. [PMID: 16737953 PMCID: PMC2754196 DOI: 10.1074/mcp.t600013-mcp200] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Current methodologies for global identification of microbial proteins that elicit host humoral immune responses have several limitations and are not ideally suited for use in the postgenomic era. Here we describe a novel application of proteomics, proteomics-based expression library screening, to rapidly define microbial immunoproteomes. Proteomics-based expression library screening is broadly applicable to any cultivable, sequenced pathogen eliciting host antibody responses and hence is ideal for rapidly mining microbial proteomes for targets with diagnostic, prophylactic, and therapeutic potential. In this report, we demonstrate "proof-of-principle" by identifying 207 proteins of the Escherichia coli O157:H7 immunome in bovine reservoirs in only 3 weeks.
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Affiliation(s)
- Indira T. Kudva
- Division of Infectious Diseases, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts 02114
- Department of Medicine, Harvard Medical School, Boston, Massachusetts 02114
| | - Bryan Krastins
- Harvard Partners Center For Genetics and Genomics, Cambridge, Massachusetts 02139
| | - Haiqing Sheng
- Department of Microbiology, Molecular Biology, and Biochemistry, University of Idaho, Moscow, Idaho 83844
| | - Robert W. Griffin
- Division of Infectious Diseases, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts 02114
| | - David A. Sarracino
- Harvard Partners Center For Genetics and Genomics, Cambridge, Massachusetts 02139
| | - Phillip I. Tarr
- Departments of Pediatrics and Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri 63110
| | - Carolyn J. Hovde
- Department of Microbiology, Molecular Biology, and Biochemistry, University of Idaho, Moscow, Idaho 83844
| | - Stephen B. Calderwood
- Division of Infectious Diseases, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts 02114
- Department of Medicine, Harvard Medical School, Boston, Massachusetts 02114
- Department of Microbiology and Molecular Genetics, Harvard Medical School, Boston, Massachusetts 02114
| | - Manohar John
- Division of Infectious Diseases, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts 02114
- Department of Medicine, Harvard Medical School, Boston, Massachusetts 02114
- To whom correspondence should be addressed. Tel.: 617−724−7528; Fax: 617−726−7416; E-mail:
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42
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Joyce AR, Palsson BØ. The model organism as a system: integrating 'omics' data sets. Nat Rev Mol Cell Biol 2006; 7:198-210. [PMID: 16496022 DOI: 10.1038/nrm1857] [Citation(s) in RCA: 445] [Impact Index Per Article: 24.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Various technologies can be used to produce genome-scale, or 'omics', data sets that provide systems-level measurements for virtually all types of cellular components in a model organism. These data yield unprecedented views of the cellular inner workings. However, this abundance of information also presents many hurdles, the main one being the extraction of discernable biological meaning from multiple omics data sets. Nevertheless, researchers are rising to the challenge by using omics data integration to address fundamental biological questions that would increase our understanding of systems as a whole.
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Affiliation(s)
- Andrew R Joyce
- Bioinformatics Program, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0412, USA.
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43
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Underwood BA, Vanderhaeghen R, Whitford R, Town CD, Hilson P. Simultaneous high-throughput recombinational cloning of open reading frames in closed and open configurations. PLANT BIOTECHNOLOGY JOURNAL 2006; 4:317-24. [PMID: 17147637 DOI: 10.1111/j.1467-7652.2006.00183.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Comprehensive open reading frame (ORF) clone collections, ORFeomes, are key components of functional genomics projects. When recombinational cloning systems are used to capture ORFs in master clones, these DNA sequences can be easily transferred into a variety of expression plasmids, each designed for a specific assay. Depending on downstream applications, an ORF is cloned either with or without a stop codon at its original position, referred to as closed or open configuration, respectively. The former is preferred when the encoded protein is produced in its native form or with an amino-terminal tag; the latter is obligatory when the protein is produced as a fusion with a carboxyl-terminal tag. We developed a streamlined protocol for high-throughput, simultaneous cloning of both open and closed ORF entry clones with the Gateway recombinational cloning system. The protocol is straightforward to set up in large-scale ORF cloning projects, and is cost-effective, because the initial ORF amplification and the cloning in a pDONR vector are performed only once to obtain the two ORF configurations. We illustrated its implementation for the isolation and validation of 346 Arabidopsis ORF entry clones.
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Affiliation(s)
- Beverly A Underwood
- The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA
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44
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Hilson P. Cloned sequence repertoires for small- and large-scale biology. TRENDS IN PLANT SCIENCE 2006; 11:133-41. [PMID: 16481211 DOI: 10.1016/j.tplants.2006.01.006] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2005] [Revised: 12/14/2005] [Accepted: 01/30/2006] [Indexed: 05/06/2023]
Abstract
How to assign function to the tens of thousands of genes discovered in the chromosomes of a few model species? How to complement the classical genetic approaches that are not always ideally suited to decode complex mechanisms? The solutions to these pressing questions are not simple and rely on the development of novel resources and technologies. Here I critically review what clone collections are available and how they can be exploited for the systematic analysis of gene functions in plants.
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Affiliation(s)
- Pierre Hilson
- Department of Plant Systems Biology, Flanders Interuniversity Institute for Biotechnology (VIB), Ghent University, B-9052 Gent, Belgium.
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45
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Lievens S, Lemmens I, Montoye T, Eyckerman S, Tavernier J. Two-hybrid and its recent adaptations. DRUG DISCOVERY TODAY. TECHNOLOGIES 2006; 3:317-324. [PMID: 24980535 DOI: 10.1016/j.ddtec.2006.09.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Interactions between proteins play a pivotal role in virtually all cellular processes, and many of these interactions represent interesting targets for drug development. Among the wide array of interactor-hunting technologies that has emerged, genetic two-hybrid methods account for a large amount of the currently available interaction data and is being successfully applied in interactome-scale mapping projects. Reverse two-hybrid approaches have been developed that allow selected interactions to be assayed for disrupting compounds.:
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Affiliation(s)
- Sam Lievens
- Flanders Interuniversity Institute for Biotechnology (VIB), Department of Medical Protein Research, Ghent University, Faculty of Medicine and Health Sciences, A. Baertsoenkaai 3, 9000 Ghent, Belgium
| | - Irma Lemmens
- Flanders Interuniversity Institute for Biotechnology (VIB), Department of Medical Protein Research, Ghent University, Faculty of Medicine and Health Sciences, A. Baertsoenkaai 3, 9000 Ghent, Belgium
| | - Tony Montoye
- Flanders Interuniversity Institute for Biotechnology (VIB), Department of Medical Protein Research, Ghent University, Faculty of Medicine and Health Sciences, A. Baertsoenkaai 3, 9000 Ghent, Belgium
| | - Sven Eyckerman
- Flanders Interuniversity Institute for Biotechnology (VIB), Department of Medical Protein Research, Ghent University, Faculty of Medicine and Health Sciences, A. Baertsoenkaai 3, 9000 Ghent, Belgium
| | - Jan Tavernier
- Flanders Interuniversity Institute for Biotechnology (VIB), Department of Medical Protein Research, Ghent University, Faculty of Medicine and Health Sciences, A. Baertsoenkaai 3, 9000 Ghent, Belgium.
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46
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Sasuga Y, Tani T, Hayashi M, Yamakawa H, Ohara O, Harada Y. Development of a microscopic platform for real-time monitoring of biomolecular interactions. Genome Res 2005; 16:132-9. [PMID: 16344567 PMCID: PMC1356137 DOI: 10.1101/gr.4235806] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
We developed a new microscopic platform for the real-time analysis of molecular interactions by combining microbead-tagging techniques with total internal reflection fluorescent microscopy (TIRFM). The optical manipulation of probe microbeads, followed by photo immobilization on a solid surface, enabled us to generate arrays with extremely high density (>100 microbeads in a 25 microm x 25 microm area), and TIRFM made it possible to monitor the binding reactions of fluorescently labeled targets onto probe microbeads without removal of free targets. We demonstrated the high performance of this platform through analyses of interactions between antigen and antibody and between small compounds and proteins. Then, recombinant protein levels in total cellular lysates of Escherichia coli were quantified from the association kinetics using antibody-immobilized microbead arrays, which served as a model for a protein-profiling array. Furthermore, in combination with in vitro synthesis-coupled protein labeling, we could kinematically analyze the interaction of nuclear factor kappaB (p50) with DNA. These results demonstrated that this platform enabled us to: (1) monitor binding processes of fluorescently labeled targets to multiple probes in real-time without removal of free targets, (2) determine concentrations of free targets only from the association kinetics at an early phase, and (3) greatly reduce the required volume of the target solution, in principle to subnanoliter, for molecular interaction analysis. The unique features of this microbead-based microarray system open the way to explore molecular interactions with a wide range of affinities in extremely small volumes of target solutions, such as extracts from single cells.
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Affiliation(s)
- Yasuhiro Sasuga
- The Tokyo Metropolitan Institute of Medical Science, Bunkyo-ku, Tokyo 113-8613, Japan
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47
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Blommel PG, Martin PA, Wrobel RL, Steffen E, Fox BG. High efficiency single step production of expression plasmids from cDNA clones using the Flexi Vector cloning system. Protein Expr Purif 2005; 47:562-70. [PMID: 16377204 DOI: 10.1016/j.pep.2005.11.007] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2005] [Revised: 11/10/2005] [Accepted: 11/11/2005] [Indexed: 10/25/2022]
Abstract
The success of structural genomics and proteomics initiatives is dependent on the availability of target genes in vectors suitable for protein production. Here, we compare two high-throughput methods for producing expression vectors from plasmid-derived cDNA fragments. Expression vectors were constructed for compatibility with the Gateway recombination cloning system and the Flexi Vector restriction-based cloning system. Cloning protocols for each system were conducted in parallel for 96 different target genes from PCR through the production of sequence-verified expression clones. The short nucleotide sequences required to prepare the target open reading frames for Flexi Vector cloning allowed a single-step PCR protocol, resulting in fewer mutations relative to the Gateway protocol. Furthermore, through initial cloning of the target open reading frames directly into an expression vector, the Flexi Vector system gave time and cost savings compared to the protocol required for the Gateway system. Within the Flexi Vector system, genes were transferred between four different expression vectors. The efficiency of gene transfer between Flexi Vectors depended on including a region of sequence identity adjacent to one of the restriction sites. With the proper construction in the flanking sequence of the vector, gene transfer efficiencies of 95-98% were demonstrated.
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Affiliation(s)
- Paul G Blommel
- Department of Biochemistry, Center for Eukaryotic Structural Genomics, University of Wisconsin, Madison, 53706-1549, USA
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48
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Schroeder BK, House BL, Mortimer MW, Yurgel SN, Maloney SC, Ward KL, Kahn ML. Development of a functional genomics platform for Sinorhizobium meliloti: construction of an ORFeome. Appl Environ Microbiol 2005; 71:5858-64. [PMID: 16204497 PMCID: PMC1265944 DOI: 10.1128/aem.71.10.5858-5864.2005] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The nitrogen-fixing, symbiotic bacterium Sinorhizobium meliloti reduces molecular dinitrogen to ammonia in a specific symbiotic context, supporting the nitrogen requirements of various forage legumes, including alfalfa. Determining the DNA sequence of the S. meliloti genome was an important step in plant-microbe interaction research, adding to the considerable information already available about this bacterium by suggesting possible functions for many of the >6,200 annotated open reading frames (ORFs). However, the predictive power of bioinformatic analysis is limited, and putting the role of these genes into a biological context will require more definitive functional approaches. We present here a strategy for genetic analysis of S. meliloti on a genomic scale and report the successful implementation of the first step of this strategy by constructing a set of plasmids representing 100% of the 6,317 annotated ORFs cloned into a mobilizable plasmid by using efficient PCR and recombination protocols. By using integrase recombination to insert these ORFs into other plasmids in vitro or in vivo (B. L. House et al., Appl. Environ. Microbiol. 70:2806-2815, 2004), this ORFeome can be used to generate various specialized genetic materials for functional analysis of S. meliloti, such as operon fusions, mutants, and protein expression plasmids. The strategy can be generalized to many other genome projects, and the S. meliloti clones should be useful for investigators wanting an accessible source of cloned genes encoding specific enzymes.
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Affiliation(s)
- Brenda K Schroeder
- Institute of Biological Chemistry, Washington State University, Pullman, WA 99164-6340, USA
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49
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De Sutter V, Vanderhaeghen R, Tilleman S, Lammertyn F, Vanhoutte I, Karimi M, Inzé D, Goossens A, Hilson P. Exploration of jasmonate signalling via automated and standardized transient expression assays in tobacco cells. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2005; 44:1065-76. [PMID: 16359398 DOI: 10.1111/j.1365-313x.2005.02586.x] [Citation(s) in RCA: 95] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Although sequence information and genome annotation are improving at an impressive pace, functional ontology is still non-existent or rudimentary for most genes. In this regard, transient expression assays are very valuable for identification of short functional segments in particular pathways, because they can be performed rapidly and at a scale unattainable in stably transformed tissues. Vectors were constructed and protocols developed for systematic transient assays in plant protoplasts. To enhance throughput and reproducibility, protoplast treatments were performed entirely by a liquid-handling robot in multiwell plates, including polyethylene glycol/Ca2+ cell transfection with plasmid mixtures, washes and lysis. All transcriptional readouts were measured using a dual firefly/Renilla luciferase assay, in which the former was controlled by a reporter promoter and the latter by the 35S CaMV promoter, which served as internal normalization standard. The automated protocols were suitable for transient assays in protoplasts prepared from cell cultures of Nicotiana tabacum Bright Yellow-2 and Arabidopsis thaliana. They were implemented in a screen to discover potential regulators of genes coding for key enzymes in nicotine biosynthesis. Two novel tobacco transcription factors were found, NtORC1 and NtJAP1, that positively regulate the putrescine N-methyltransferase (PMT) promoter. In addition, combinatorial tests showed that these two factors act synergistically to induce PMT transcriptional activity. The development and use of high-throughput plant transient expression assays are discussed.
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Affiliation(s)
- Valerie De Sutter
- Department of Plant Systems Biology, Flanders Interuniversity Institute for Biotechnology, Ghent University, Technologiepark 927, B-9052 Gent, Belgium
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50
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Cusick ME, Klitgord N, Vidal M, Hill DE. Interactome: gateway into systems biology. Hum Mol Genet 2005; 14 Spec No. 2:R171-81. [PMID: 16162640 DOI: 10.1093/hmg/ddi335] [Citation(s) in RCA: 263] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Protein-protein interactions are fundamental to all biological processes, and a comprehensive determination of all protein-protein interactions that can take place in an organism provides a framework for understanding biology as an integrated system. The availability of genome-scale sets of cloned open reading frames has facilitated systematic efforts at creating proteome-scale data sets of protein-protein interactions, which are represented as complex networks or 'interactome' maps. Protein-protein interaction mapping projects that follow stringent criteria, coupled with experimental validation in orthogonal systems, provide high-confidence data sets immanently useful for interrogating developmental and disease mechanisms at a system level as well as elucidating individual protein function and interactome network topology. Although far from complete, currently available maps provide insight into how biochemical properties of proteins and protein complexes are integrated into biological systems. Such maps are also a useful resource to predict the function(s) of thousands of genes.
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Affiliation(s)
- Michael E Cusick
- Center for Cancer Systems Biology and Department of Cancer Biology, Dana-Farber Cancer Institute, 44 Binney Street, Boston, MA 02115, USA.
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