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Gupta K, Tölzer C, Sari-Ak D, Fitzgerald DJ, Schaffitzel C, Berger I. MultiBac: Baculovirus-Mediated Multigene DNA Cargo Delivery in Insect and Mammalian Cells. Viruses 2019; 11:E198. [PMID: 30813511 PMCID: PMC6466381 DOI: 10.3390/v11030198] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Revised: 02/14/2019] [Accepted: 02/21/2019] [Indexed: 12/22/2022] Open
Abstract
The baculovirus/insect cell system (BICS) is widely used in academia and industry to produce eukaryotic proteins for many applications, ranging from structure analysis to drug screening and the provision of protein biologics and therapeutics. Multi-protein complexes have emerged as vital catalysts of cellular function. In order to unlock the structure and mechanism of these essential molecular machines and decipher their function, we developed MultiBac, a BICS particularly tailored for heterologous multigene transfer and multi-protein complex production. Baculovirus is unique among common viral vectors in its capacity to accommodate very large quantities of heterologous DNA and to faithfully deliver this cargo to a host cell of choice. We exploited this beneficial feature to outfit insect cells with synthetic DNA circuitry conferring new functionality during heterologous protein expression, and developing customized MultiBac baculovirus variants in the process. By altering its tropism, recombinant baculovirions can be used for the highly efficient delivery of a customized DNA cargo in mammalian cells and tissues. Current advances in synthetic biology greatly facilitate the construction or recombinant baculoviral genomes for gene editing and genome engineering, mediated by a MultiBac baculovirus tailored to this purpose. Here, recent developments and exploits of the MultiBac system are presented and discussed.
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Berger I, van der Hout M, Hoogenboom AMCH, Berger E, Mulder CL. [Modifications in therapy for patients with severe mental illness and intellectual disability: a qualitative study]. TIJDSCHRIFT VOOR PSYCHIATRIE 2019; 61:375-383. [PMID: 31243747] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
In ambulant psychiatric care, intellectual disability (id) is often not recognised. Therefore, a Screener for Intelligence and Learning disabilities (scil) was recently introduced to assist recognition. However, because, current therapy is not adjusted for id-related problems, its effectiveness remains unknown.<br/> AIM: To gain insight into adequate adaptation of interventions by professionals for patients with severe mental illness (smi) and id, to improve the quality of care without the need to develop a completely new program of therapy.<br/> METHOD: A qualitative design (n=15) including 8 interviews and one focus group, among psychiatric practitioners and id experts.<br/> RESULTS: Five main themes were identified to adjust therapy: treatment, communication, inclusion of the network, estimation of support needs and self-management. CONCLUSIONS To align therapy with the requirements of patients with smi and id, a patient-oriented approach to care is necessary. Simple but effective modifications, summarised in a toolkit, appear to contribute to this. To offer appropriate care to patients with smi and id, attention is needed for both a support-oriented and a recovery-oriented approach.
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Sari-Ak D, Bahrami S, Laska MJ, Drncova P, Fitzgerald DJ, Schaffitzel C, Garzoni F, Berger I. High-Throughput Production of Influenza Virus-Like Particle (VLP) Array by Using VLP-factory ™, a MultiBac Baculoviral Genome Customized for Enveloped VLP Expression. Methods Mol Biol 2019; 2025:213-226. [PMID: 31267455 DOI: 10.1007/978-1-4939-9624-7_10] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Baculovirus-based expression of proteins in insect cell cultures has emerged as a powerful technology to produce complex protein biologics for many applications ranging from multiprotein complex structural biology to manufacturing of therapeutic proteins including virus-like particles (VLPs). VLPs are protein assemblies that mimic live viruses but typically do not contain any genetic material, and therefore are safe and attractive alternatives to life attenuated or inactivated viruses for vaccination purposes. MultiBac is an advanced baculovirus expression vector system (BEVS) which consists of an engineered viral genome that can be customized for tailored applications. Here we describe the creation of a MultiBac-based VLP-factory™, based on the M1 capsid protein from influenza, and its application to produce in a parallelized fashion an array of influenza-derived VLPs containing functional mutations in influenza hemagglutinin (HA) thought to modulate the immune response elicited by the VLP.
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Nemoz C, Ropars V, Frit P, Gontier A, Drevet P, Yu J, Guerois R, Pitois A, Comte A, Delteil C, Barboule N, Legrand P, Baconnais S, Yin Y, Tadi S, Barbet-Massin E, Berger I, Le Cam E, Modesti M, Rothenberg E, Calsou P, Charbonnier JB. XLF and APLF bind Ku80 at two remote sites to ensure DNA repair by non-homologous end joining. Nat Struct Mol Biol 2018; 25:971-980. [PMID: 30291363 PMCID: PMC6234012 DOI: 10.1038/s41594-018-0133-6] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2017] [Accepted: 08/21/2018] [Indexed: 12/20/2022]
Abstract
The Ku70-Ku80 (Ku) heterodimer binds rapidly and tightly to the ends of DNA double-strand breaks and recruits factors of the non-homologous end-joining (NHEJ) repair pathway through molecular interactions that remain unclear. We have determined crystal structures of the Ku-binding motifs (KBM) of the NHEJ proteins APLF (A-KBM) and XLF (X-KBM) bound to a Ku-DNA complex. The two KBM motifs bind remote sites of the Ku80 α/β domain. The X-KBM occupies an internal pocket formed by an unprecedented large outward rotation of the Ku80 α/β domain. We observe independent recruitment of the APLF-interacting protein XRCC4 and of XLF to laser-irradiated sites via binding of A- and X-KBMs, respectively, to Ku80. Finally, we show that mutation of the X-KBM and A-KBM binding sites in Ku80 compromises both the efficiency and accuracy of end joining and cellular radiosensitivity. A- and X-KBMs may represent two initial anchor points to build the intricate interaction network required for NHEJ.
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Khan I, Krishnaswamy S, Sabale M, Groth D, Wijaya L, Morici M, Berger I, Schaffitzel C, Fraser PE, Martins RN, Verdile G. Efficient production of a mature and functional gamma secretase protease. Sci Rep 2018; 8:12834. [PMID: 30150752 PMCID: PMC6110731 DOI: 10.1038/s41598-018-30788-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Accepted: 08/06/2018] [Indexed: 12/27/2022] Open
Abstract
Baculoviral protein expression in insect cells has been previously used to generate large quantities of a protein of interest for subsequent use in biochemical and structural analyses. The MultiBac baculovirus protein expression system has enabled, the use of a single baculovirus to reconstitute a protein complex of interest, resulting in a larger protein yield. Using this system, we aimed to reconstruct the gamma (γ)-secretase complex, a multiprotein enzyme complex essential for the production of amyloid-β (Aβ) protein. A MultiBac vector containing all components of the γ-secretase complex was generated and expression was observed for all components. The complex was active in processing APP and Notch derived γ-secretase substrates and proteolysis could be inhibited with γ-secretase inhibitors, confirming specificity of the recombinant γ-secretase enzyme. Finally, affinity purification was used to purify an active recombinant γ-secretase complex. In this study we demonstrated that the MultiBac protein expression system can be used to generate an active γ-secretase complex and provides a new tool to study γ-secretase enzyme and its variants.
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El-Saafin F, Curry C, Ye T, Garnier JM, Kolb-Cheynel I, Stierle M, Downer NL, Dixon MP, Negroni L, Berger I, Thomas T, Voss AK, Dobyns W, Devys D, Tora L. Homozygous TAF8 mutation in a patient with intellectual disability results in undetectable TAF8 protein, but preserved RNA polymerase II transcription. Hum Mol Genet 2018; 27:2171-2186. [PMID: 29648665 PMCID: PMC5985725 DOI: 10.1093/hmg/ddy126] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Revised: 04/04/2018] [Accepted: 04/06/2018] [Indexed: 01/21/2023] Open
Abstract
The human general transcription factor TFIID is composed of the TATA-binding protein (TBP) and 13 TBP-associated factors (TAFs). In eukaryotic cells, TFIID is thought to nucleate RNA polymerase II (Pol II) preinitiation complex formation on all protein coding gene promoters and thus, be crucial for Pol II transcription. In a child with intellectual disability, mild microcephaly, corpus callosum agenesis and poor growth, we identified a homozygous splice-site mutation in TAF8 (NM_138572.2: c.781-1G > A). Our data indicate that the patient's mutation generates a frame shift and an unstable TAF8 mutant protein with an unrelated C-terminus. The mutant TAF8 protein could not be detected in extracts from the patient's fibroblasts, indicating a loss of TAF8 function and that the mutation is most likely causative. Moreover, our immunoprecipitation and proteomic analyses show that in patient cells only partial TAF complexes exist and that the formation of the canonical TFIID is impaired. In contrast, loss of TAF8 in mouse embryonic stem cells and blastocysts leads to cell death and to a global decrease in Pol II transcription. Astonishingly however, in human TAF8 patient cells, we could not detect any cellular phenotype, significant changes in genome-wide Pol II occupancy and pre-mRNA transcription. Thus, the disorganization of the essential holo-TFIID complex did not affect global Pol II transcription in the patient's fibroblasts. Our observations further suggest that partial TAF complexes, and/or an altered TFIID containing a mutated TAF8, could support human development and thus, the absence of holo-TFIID is less deleterious for transcription than originally predicted.
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Bing F, Berger I, Rodier G, Casile C, Morel N, M’Biene S, Vadot W, Moroni AL, Guellerin J, Pignal-Jacquard C. Étude par binômes radiologue/neurologue des corrélations inter- et intra-observateurs du DWI-ASPECTS en phase aiguë de l’infarctus cérébral. J Neuroradiol 2018. [DOI: 10.1016/j.neurad.2018.01.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Nie Y, Zhang F, Yuan C, Li L, Sun Y, Wang Y, Zhao L, Robinson PJ, Berger I, Kornberg RD. Streamlining protein complex production using multiprotein expression technologies. Acta Crystallogr A Found Adv 2017. [DOI: 10.1107/s2053273317082997] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
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Gupta K, Watson AA, Baptista T, Scheer E, Chambers AL, Koehler C, Zou J, Obong-Ebong I, Kandiah E, Temblador A, Round A, Forest E, Man P, Bieniossek C, Laue ED, Lemke EA, Rappsilber J, Robinson CV, Devys D, Tora L, Berger I. Architecture of TAF11/TAF13/TBP complex suggests novel regulation properties of general transcription factor TFIID. eLife 2017; 6:e30395. [PMID: 29111974 PMCID: PMC5690282 DOI: 10.7554/elife.30395] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2017] [Accepted: 11/03/2017] [Indexed: 11/13/2022] Open
Abstract
General transcription factor TFIID is a key component of RNA polymerase II transcription initiation. Human TFIID is a megadalton-sized complex comprising TATA-binding protein (TBP) and 13 TBP-associated factors (TAFs). TBP binds to core promoter DNA, recognizing the TATA-box. We identified a ternary complex formed by TBP and the histone fold (HF) domain-containing TFIID subunits TAF11 and TAF13. We demonstrate that TAF11/TAF13 competes for TBP binding with TATA-box DNA, and also with the N-terminal domain of TAF1 previously implicated in TATA-box mimicry. In an integrative approach combining crystal coordinates, biochemical analyses and data from cross-linking mass-spectrometry (CLMS), we determine the architecture of the TAF11/TAF13/TBP complex, revealing TAF11/TAF13 interaction with the DNA binding surface of TBP. We identify a highly conserved C-terminal TBP-interaction domain (CTID) in TAF13, which is essential for supporting cell growth. Our results thus have implications for cellular TFIID assembly and suggest a novel regulatory state for TFIID function.
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Pelosse M, Crocker H, Gorda B, Lemaire P, Rauch J, Berger I. MultiBac: from protein complex structures to synthetic viral nanosystems. BMC Biol 2017; 15:99. [PMID: 29084535 PMCID: PMC5661938 DOI: 10.1186/s12915-017-0447-6] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
The MultiBac baculovirus/insect cell expression vector system was conceived as a user-friendly, modular tool-kit for producing multiprotein complexes for structural biology applications. MultiBac has allowed the structure and function of many molecular machines to be elucidated, including previously inaccessible high-value drug targets. More recently, MultiBac developments have shifted to customized baculoviral genomes that are tailored for a range of applications, including synthesizing artificial proteins by genetic code expansion. We review some of these developments, including the ongoing rewiring of the MultiBac system for mammalian applications, notably CRISPR/Cas9-mediated gene editing.
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McNally KE, Faulkner R, Steinberg F, Gallon M, Ghai R, Pim D, Langton P, Pearson N, Danson CM, Nägele H, Morris LL, Singla A, Overlee BL, Heesom KJ, Sessions R, Banks L, Collins BM, Berger I, Billadeau DD, Burstein E, Cullen PJ. Retriever is a multiprotein complex for retromer-independent endosomal cargo recycling. Nat Cell Biol 2017; 19:1214-1225. [PMID: 28892079 PMCID: PMC5790113 DOI: 10.1038/ncb3610] [Citation(s) in RCA: 201] [Impact Index Per Article: 28.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2017] [Accepted: 08/10/2017] [Indexed: 02/08/2023]
Abstract
Following endocytosis into the endosomal network, integral membrane proteins undergo sorting for lysosomal degradation or are retrieved and recycled back to the cell surface. Here we describe the discovery of an ancient and conserved multiprotein complex that orchestrates cargo retrieval and recycling and, importantly, is biochemically and functionally distinct from the established retromer pathway. We have called this complex 'retriever'; it is a heterotrimer composed of DSCR3, C16orf62 and VPS29, and bears striking similarity to retromer. We establish that retriever associates with the cargo adaptor sorting nexin 17 (SNX17) and couples to CCC (CCDC93, CCDC22, COMMD) and WASH complexes to prevent lysosomal degradation and promote cell surface recycling of α5β1 integrin. Through quantitative proteomic analysis, we identify over 120 cell surface proteins, including numerous integrins, signalling receptors and solute transporters, that require SNX17-retriever to maintain their surface levels. Our identification of retriever establishes a major endosomal retrieval and recycling pathway.
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Pelosse M, Cottet-Rousselle C, Grichine A, Berger I, Schlattner U. Genetically Encoded Fluorescent Biosensors to Explore AMPK Signaling and Energy Metabolism. ACTA ACUST UNITED AC 2017; 107:491-523. [PMID: 27812993 DOI: 10.1007/978-3-319-43589-3_20] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Maintenance of energy homeostasis is a basic requirement for cell survival. Different mechanisms have evolved to cope with spatial and temporal mismatch between energy-providing and -consuming processes. Among these, signaling by AMP-activated protein kinase (AMPK) is one of the key players, regulated by and itself regulating cellular adenylate levels. Further understanding its complex cellular function requires deeper insight into its activation patterns in space and time at a single cell level. This may become possible with an increasing number of genetically encoded fluorescent biosensors, mostly based on fluorescence resonance energy transfer, which have been engineered to monitor metabolic parameters and kinase activities. Here, we review basic principles of biosensor design and function and the advantages and limitations of their use and provide an overview on existing FRET biosensors to monitor AMPK activation, ATP concentration, and ATP/ADP ratios, together with other key metabolites and parameters of energy metabolism.
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Berger MR, Zepp M, Westphal G, Berger I, Armbruster FP. Abstract P2-04-23: A monoclonal antibody against hypo-glycosylated bone sialoprotein II has application for diagnostic purposes in samples of breast cancer patients and for treatment of skeletal metastasis caused by MDA-MB-231 breast cancer cells in rats. Cancer Res 2017. [DOI: 10.1158/1538-7445.sabcs16-p2-04-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
The SIBLING protein bone sialoprotein II (BSP) has been implicated in lytic skeletal metastasis as it is expressed in a subset of primary breast cancers and can be detected at elevated levels in the serum of patients with increased risk to develop skeletal metastasis. The aim of this study was to investigate the potential application of a rat monoclonal antibody against hypo-glycosylated BSP (IDK1) for diagnostic and therapeutic purposes.
The diagnostic part of this study was based on breast cancer specimens from the biobank / repository of the Institute of Pathology of the Municipal Hospital Kassel, Germany. Immune-histochemical analyses were performed with IDK1 for comparing BSP expression between ten human primary breast tumor sections and their corresponding bone metastatic tissue samples. The therapeutic part of this study was based on a model in nude rats, in which the rats were implanted with human MDA-MB-231 breast cancer cells for selective and orthotopic appearance of osteolytic skeletal lesions. Tumor bearing rats were treated with IDK1 starting at two or four weeks after tumor cell inoculation into the femoral artery of one hind leg. Tumor growth was monitored by light emission, caused by luciferase mediated metabolism of luciferin. Photon emission was recorded at regular intervals by a Xenogen IVIS 100 imaging system. After sacrifice, samples of lesions and apparently healthy tissues were investigated by H&E staining as well as by immune-histological staining for BSP.
BSP staining was found within the cytoplasm of tumor cells. Increased expression of BSP was also detected in healthy bone cells, e.g. osteoblasts, as soon as breast tumor cells invaded bone tissue. An elevation of BSP expression near necrotic centers was also found. Expression of BSP in primary breast tumors was positively correlated with BSP expression in bone metastases. Furthermore, bone metastases showed higher and more intensive expression of BSP than their respective primary breast tumors (p<0.0039).
In the experimental treatment part, all but one untreated tumor bearing rats showed rapid tumor growth accompanied with lytic destruction of femur and tibia of the respective hind leg (18/19; tumor take rate 95%). In contrast, rats treated with the anti-BSP antibody did not show a significant increase in light emission nor a clinical deterioration. In fact, 8 of 10 rats receiving the antibody at a dose of 10 mg/kg/week starting at two weeks after tumor implantation did not show any light emission after 4 to 6 weeks (p = 0.01 versus control) as well as 6 of 10 rats receiving the antibody at the same dose starting at four weeks after tumor implantation (p < 0.05). Radiological and histological examination confirmed that animals without light emission were free of tumor growth, corresponding to a complete remission.
In conclusion, the rat monoclonal antibody directed against BSP is a powerful tool with potential for diagnostic and therapeutic applications in breast cancer skeletal metastasis and warrants further development.
Citation Format: Berger MR, Zepp M, Westphal G, Berger I, Armbruster FP. A monoclonal antibody against hypo-glycosylated bone sialoprotein II has application for diagnostic purposes in samples of breast cancer patients and for treatment of skeletal metastasis caused by MDA-MB-231 breast cancer cells in rats [abstract]. In: Proceedings of the 2016 San Antonio Breast Cancer Symposium; 2016 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2017;77(4 Suppl):Abstract nr P2-04-23.
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Berger I, Jiang Q, Schulze RJ, Collinson I, Schaffitzel C. Multiprotein Complex Production in E. coli: The SecYEG-SecDFYajC-YidC Holotranslocon. Methods Mol Biol 2017; 1586:279-290. [PMID: 28470612 DOI: 10.1007/978-1-4939-6887-9_18] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
A modular approach for balanced overexpression of recombinant multiprotein complexes in E. coli is described, with the prokaryotic protein secretase/insertase complex, the SecYEG-SecDFYajC-YidC holotranslocon (HTL), used as an example. This procedure has been implemented here in the ACEMBL system. The protocol details the design principles of the monocistronic or polycistronic DNA constructs, the expression and purification of functional HTL and its association with translating ribosome nascent chain (RNC) complexes into a RNC-HTL supercomplex.
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Huber N, Bieniossek C, Wagner KM, Elsässer HP, Suter U, Berger I, Niemann A. Glutathione-conjugating and membrane-remodeling activity of GDAP1 relies on amphipathic C-terminal domain. Sci Rep 2016; 6:36930. [PMID: 27841286 PMCID: PMC5107993 DOI: 10.1038/srep36930] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2016] [Accepted: 10/21/2016] [Indexed: 11/09/2022] Open
Abstract
Mutations in the ganglioside-induced differentiation associated protein 1 (GDAP1) cause severe peripheral motor and sensory neuropathies called Charcot-Marie-Tooth disease. GDAP1 expression induces fission of mitochondria and peroxisomes by a currently elusive mechanism, while disease causing mutations in GDAP1 impede the protein's role in mitochondrial dynamics. In silico analysis reveals sequence similarities of GDAP1 to glutathione S-transferases (GSTs). However, a proof of GST activity and its possible impact on membrane dynamics are lacking to date. Using recombinant protein, we demonstrate for the first time theta-class-like GST activity for GDAP1, and it's activity being regulated by the C-terminal hydrophobic domain 1 (HD1) of GDAP1 in an autoinhibitory manner. Moreover, we show that the HD1 amphipathic pattern is required to induce membrane dynamics by GDAP1. As both, fission and GST activities of GDAP1, are critically dependent on HD1, we propose that GDAP1 undergoes a molecular switch, turning from a pro-fission active to an auto-inhibited inactive conformation.
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Abstract
Since its inception more than 30 years ago, the baculovirus expression vector system (BEVS) has been used prolifically to produce heterologous proteins for research and development. In the cell, a cornerstone of biological activity are multiprotein complexes, catalyzing essential functions. BEVS has been uniquely successful to unlock such complex assemblies for high-resolution structural and functional analysis. Synthetic biology approaches have been implemented to optimize multigene assembly methods, accelerating upstream processes. Specialized baculoviral genomes are being created with functions tailored to enhance production of particular target protein classes. Here we comment on current and emerging developments in the field and their potential to accelerate protein complex research.
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Monteiro F, Bernal V, Chaillet M, Berger I, Alves PM. Targeted supplementation design for improved production and quality of enveloped viral particles in insect cell-baculovirus expression system. J Biotechnol 2016; 233:34-41. [DOI: 10.1016/j.jbiotec.2016.06.029] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2016] [Revised: 06/20/2016] [Accepted: 06/30/2016] [Indexed: 12/18/2022]
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Mansouri M, Bellon-Echeverria I, Rizk A, Ehsaei Z, Cianciolo Cosentino C, Silva CS, Xie Y, Boyce FM, Davis MW, Neuhauss SCF, Taylor V, Ballmer-Hofer K, Berger I, Berger P. Highly efficient baculovirus-mediated multigene delivery in primary cells. Nat Commun 2016; 7:11529. [PMID: 27143231 PMCID: PMC4857464 DOI: 10.1038/ncomms11529] [Citation(s) in RCA: 74] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2016] [Accepted: 04/04/2016] [Indexed: 12/11/2022] Open
Abstract
Multigene delivery and subsequent cellular expression is emerging as a key technology required in diverse research fields including, synthetic and structural biology, cellular reprogramming and functional pharmaceutical screening. Current viral delivery systems such as retro- and adenoviruses suffer from limited DNA cargo capacity, thus impeding unrestricted multigene expression. We developed MultiPrime, a modular, non-cytotoxic, non-integrating, baculovirus-based vector system expediting highly efficient transient multigene expression from a variety of promoters. MultiPrime viruses efficiently transduce a wide range of cell types, including non-dividing primary neurons and induced-pluripotent stem cells (iPS). We show that MultiPrime can be used for reprogramming, and for genome editing and engineering by CRISPR/Cas9. Moreover, we implemented dual-host-specific cassettes enabling multiprotein expression in insect and mammalian cells using a single reagent. Our experiments establish MultiPrime as a powerful and highly efficient tool, to deliver multiple genes for a wide range of applications in primary and established mammalian cells. Current viral gene delivery systems are limited in the amount of foreign DNA they can deliver to cells. Here the authors develop MultiPrime, a baculovirus-based vector system capable of multigene delivery into a wide variety of cells, and use Multiprime for genome engineering by CRISPR/Cas9.
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Zhang W, Aubert A, Gomez de Segura JM, Karuppasamy M, Basu S, Murthy AS, Diamante A, Drury TA, Balmer J, Cramard J, Watson AA, Lando D, Lee SF, Palayret M, Kloet SL, Smits AH, Deery MJ, Vermeulen M, Hendrich B, Klenerman D, Schaffitzel C, Berger I, Laue ED. The Nucleosome Remodeling and Deacetylase Complex NuRD Is Built from Preformed Catalytically Active Sub-modules. J Mol Biol 2016; 428:2931-42. [PMID: 27117189 PMCID: PMC4942838 DOI: 10.1016/j.jmb.2016.04.025] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2016] [Accepted: 04/18/2016] [Indexed: 11/26/2022]
Abstract
The nucleosome remodeling deacetylase (NuRD) complex is a highly conserved regulator of chromatin structure and transcription. Structural studies have shed light on this and other chromatin modifying machines, but much less is known about how they assemble and whether stable and functional sub-modules exist that retain enzymatic activity. Purification of the endogenous Drosophila NuRD complex shows that it consists of a stable core of subunits, while others, in particular the chromatin remodeler CHD4, associate transiently. To dissect the assembly and activity of NuRD, we systematically produced all possible combinations of different components using the MultiBac system, and determined their activity and biophysical properties. We carried out single-molecule imaging of CHD4 in live mouse embryonic stem cells, in the presence and absence of one of core components (MBD3), to show how the core deacetylase and chromatin-remodeling sub-modules associate in vivo. Our experiments suggest a pathway for the assembly of NuRD via preformed and active sub-modules. These retain enzymatic activity and are present in both the nucleus and the cytosol, an outcome with important implications for understanding NuRD function. We have studied Drosophila nucleosome remodeling deacetylase (NuRD) assembly. NuRD consists of a core deacetylase complex, where MTA-like acts as the scaffold. This transiently associates with a chromatin remodeling sub-module including CHD4. Single-molecule imaging shows that the two sub-modules associate through MBD-like. NuRD comprises catalytically active sub-modules in both the cytosol and the nucleus.
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Sponer J, Berger I, Spačková N, Leszczynski J, Hobza P. Aromatic Base Stacking in DNA: From ab initio Calculations to Molecular Dynamics Simulations. J Biomol Struct Dyn 2016; 17 Suppl 1:1-24. [PMID: 22607400 DOI: 10.1080/07391102.2000.10506597] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
Abstract Aromatic stacking of nucleic acid bases is one of the key players in determining the structure and dynamics of nucleic acids. The arrangement of nucleic acid bases with extensive overlap of their aromatic rings gave rise to numerous often contradictory suggestions about the physical origins of stacking and the possible role of delocalized electrons in stacked aromatic π systems, leading to some confusion about the issue. The recent advance of computer hardware and software finally allowed the application of state of the art quantum-mechanical approaches with inclusion of electron correlation effects to study aromatic base stacking, now providing an ultimitate qualitative description of the phenomenon. Base stacking is determined by an interplay of the three most commonly encountered molecular interactions: dispersion attraction, electrostatic interaction, and short-range repulsion. Unusual (aromatic- stacking specific) energy contributions were in fact not evidenced and are not necessary to describe stacking. The currently used simple empirical potential form, relying on atom-centered constant point charges and Lennard-Jones van der Waals terms, is entirely able to reproduce the essential features of base stacking. Thus, we can conclude that base stacking is in principle one of the best described interactions in current molecular modeling and it allows to study base stacking in DNA using large-scale classical molecular dynamics simulations. Neglect of cooperativity of stacking appears to be the most serious approximation of the currently used force field form. This review summarizes recent developments in the field. It is written for an audience that is not necessarily expert in computational quantum chemistry and follows up on our previous contribution (Sponer et. al., J. Biomol. Struct. Dyn. 14, 117, (1997)). First, the applied methodology, its accuracy, and the physical nature of base stacking is briefly overviewed, including a comment on the accuracy of other molecular orbital methods and force fields. Then, base stacking is contrasted with hydrogen bonding, the other dominant force in nucleic acid structure. The sequence dependence and cooperativity of base stacking is commented on, and finally a brief introduction into recent progress in large-scale molecular dynamics simulations of nucleic acids is provided. Using four stranded DNA assemblies as an example, we demonstrate the efficacy of current molecular dynamics techniques that utilize refined and verified force fields in the study of stacking in nucleic acid molecules.
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Swale C, Monod A, Tengo L, Labaronne A, Garzoni F, Bourhis JM, Cusack S, Schoehn G, Berger I, Ruigrok RWH, Crépin T. Structural characterization of recombinant IAV polymerase reveals a stable complex between viral PA-PB1 heterodimer and host RanBP5. Sci Rep 2016; 6:24727. [PMID: 27095520 PMCID: PMC4837377 DOI: 10.1038/srep24727] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2015] [Accepted: 04/04/2016] [Indexed: 01/19/2023] Open
Abstract
The genome of influenza A virus (IAV) comprises eight RNA segments (vRNA) which are transcribed and replicated by the heterotrimeric IAV RNA-dependent RNA-polymerase (RdRp). RdRp consists of three subunits (PA, PB1 and PB2) and binds both the highly conserved 3′- and 5′-ends of the vRNA segment. The IAV RdRp is an important antiviral target, but its structural mechanism has remained largely elusive to date. By applying a polyprotein strategy, we produced RdRp complexes and define a minimal human IAV RdRp core complex. We show that PA-PB1 forms a stable heterodimeric submodule that can strongly interact with 5′-vRNA. In contrast, 3′-vRNA recognition critically depends on the PB2 N-terminal domain. Moreover, we demonstrate that PA-PB1 forms a stable and stoichiometric complex with host nuclear import factor RanBP5 that can be modelled using SAXS and we show that the PA-PB1-RanPB5 complex is no longer capable of 5′-vRNA binding. Our results provide further evidence for a step-wise assembly of IAV structural components, regulated by nuclear transport mechanisms and host factor binding.
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Gupta K, Sari-Ak D, Haffke M, Trowitzsch S, Berger I. Zooming in on Transcription Preinitiation. J Mol Biol 2016; 428:2581-2591. [PMID: 27067110 PMCID: PMC4906157 DOI: 10.1016/j.jmb.2016.04.003] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2016] [Revised: 04/01/2016] [Accepted: 04/01/2016] [Indexed: 02/08/2023]
Abstract
Class II gene transcription commences with the assembly of the Preinitiation Complex (PIC) from a plethora of proteins and protein assemblies in the nucleus, including the General Transcription Factors (GTFs), RNA polymerase II (RNA pol II), co-activators, co-repressors, and more. TFIID, a megadalton-sized multiprotein complex comprising 20 subunits, is among the first GTFs to bind the core promoter. TFIID assists in nucleating PIC formation, completed by binding of further factors in a highly regulated stepwise fashion. Recent results indicate that TFIID itself is built from distinct preformed submodules, which reside in the nucleus but also in the cytosol of cells. Here, we highlight recent insights in transcription factor assembly and the regulation of transcription preinitiation. Architectural models of human and yeast PIC were proposed. Mediator core–ITC complex structure reveals novel interactions. TFIID submodule residing in the cytoplasm has been discovered. Complex assembly emerges as key concept in transcription regulation.
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Koehler C, Sauter P, Wawryszyn M, Estrada Girona G, Fritz MH, Biskup M, Besir H, Berger I, Benes V, Korbel J, Braese S, Lemke EA. A New Tool for Custom Protein Design and Engineering - DH10 Bac-TAG. Biophys J 2016. [DOI: 10.1016/j.bpj.2015.11.1856] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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Sari D, Gupta K, Thimiri Govinda Raj DB, Aubert A, Drncová P, Garzoni F, Fitzgerald D, Berger I. The MultiBac Baculovirus/Insect Cell Expression Vector System for Producing Complex Protein Biologics. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2015; 896:199-215. [PMID: 27165327 PMCID: PMC7122245 DOI: 10.1007/978-3-319-27216-0_13] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Multiprotein complexes regulate most if not all cellular functions. Elucidating the structure and function of these complex cellular machines is essential for understanding biology. Moreover, multiprotein complexes by themselves constitute powerful reagents as biologics for the prevention and treatment of human diseases. Recombinant production by the baculovirus/insect cell expression system is particularly useful for expressing proteins of eukaryotic origin and their complexes. MultiBac, an advanced baculovirus/insect cell system, has been widely adopted in the last decade to produce multiprotein complexes with many subunits that were hitherto inaccessible, for academic and industrial research and development. The MultiBac system, its development and numerous applications are presented. Future opportunities for utilizing MultiBac to catalyze discovery are outlined.
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