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Bruckmann C, Tamburri S, De Lorenzi V, Doti N, Monti A, Mathiasen L, Cattaneo A, Ruvo M, Bachi A, Blasi F. Mapping the native interaction surfaces of PREP1 with PBX1 by cross-linking mass-spectrometry and mutagenesis. Sci Rep 2020; 10:16809. [PMID: 33033354 PMCID: PMC7545097 DOI: 10.1038/s41598-020-74032-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Accepted: 09/25/2020] [Indexed: 02/08/2023] Open
Abstract
Both onco-suppressor PREP1 and the oncogene MEIS1 bind to PBX1. This interaction stabilizes the two proteins and allows their translocation into the nucleus and thus their transcriptional activity. Here, we have combined cross-linking mass-spectrometry and systematic mutagenesis to detail the binding geometry of the PBX1-PREP1 (and PBX1-MEIS1) complexes, under native in vivo conditions. The data confirm the existence of two distinct interaction sites within the PBC domain of PBX1 and unravel differences among the highly similar binding sites of MEIS1 and PREP1. The HR2 domain has a fundamental role in binding the PBC-B domain of PBX1 in both PREP1 and MEIS1. The HR1 domain of MEIS1, however, seem to play a less stringent role in PBX1 interaction with respect to that of PREP1. This difference is also reflected by the different binding affinity of the two proteins to PBX1. Although partial, this analysis provides for the first time some ideas on the tertiary structure of the complexes not available before. Moreover, the extensive mutagenic analysis of PREP1 identifies the role of individual hydrophobic HR1 and HR2 residues, both in vitro and in vivo.
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Affiliation(s)
- Chiara Bruckmann
- IFOM (Foundation FIRC Institute of Molecular Oncology), Via Adamello 16, 20139, Milan, Italy.
| | - Simone Tamburri
- IFOM (Foundation FIRC Institute of Molecular Oncology), Via Adamello 16, 20139, Milan, Italy
- Department of Experimental Oncology, European Institute of Oncology, Via Adamello 16, 20139, Milan, Italy
| | - Valentina De Lorenzi
- IFOM (Foundation FIRC Institute of Molecular Oncology), Via Adamello 16, 20139, Milan, Italy
- Center for Nanotechnology Innovation@NEST, Istituto Italiano di Tecnologia, Piazza San Silvestro 12, 56124, Pisa, Italy
| | - Nunzianna Doti
- Institute of Biostructures and Bioimaging (IBB)-CNR, Via Mezzocannone 16, 80134, Naples, Italy
| | - Alessandra Monti
- Institute of Biostructures and Bioimaging (IBB)-CNR, Via Mezzocannone 16, 80134, Naples, Italy
| | - Lisa Mathiasen
- IFOM (Foundation FIRC Institute of Molecular Oncology), Via Adamello 16, 20139, Milan, Italy
| | - Angela Cattaneo
- IFOM (Foundation FIRC Institute of Molecular Oncology), Via Adamello 16, 20139, Milan, Italy
- Cogentech S.R.L. Benefit Corporation IT, Via Adamello 16, 20139, Milan, Italy
| | - Menotti Ruvo
- Institute of Biostructures and Bioimaging (IBB)-CNR, Via Mezzocannone 16, 80134, Naples, Italy
| | - Angela Bachi
- IFOM (Foundation FIRC Institute of Molecular Oncology), Via Adamello 16, 20139, Milan, Italy
| | - Francesco Blasi
- IFOM (Foundation FIRC Institute of Molecular Oncology), Via Adamello 16, 20139, Milan, Italy.
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2
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Doti N, Monti A, Bruckmann C, Calvanese L, Smaldone G, Caporale A, Falcigno L, D'Auria G, Blasi F, Ruvo M, Vitagliano L. Identification and characterization of cytotoxic amyloid-like regions in human Pbx-regulating protein-1. Int J Biol Macromol 2020; 163:618-629. [PMID: 32634512 DOI: 10.1016/j.ijbiomac.2020.06.271] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Revised: 03/19/2020] [Accepted: 06/30/2020] [Indexed: 01/05/2023]
Abstract
The ability of many proteins to fold into well-defined structures has been traditionally considered a prerequisite for fulfilling their functions. Protein folding is also regarded as a valuable loophole to escape uncontrolled and harmful aggregations. Here we show that the PBX-regulating protein-1 (PREP1), an important homeodomain transcription factor involved in cell growth and differentiation during embryogenesis, is endowed with an uncommon thermostability. Indeed, circular dichroism analyses indicate that it retains most of its secondary structure at very high temperatures. These findings have important implications for PREP1 functions since it is a stabilizing factor of its partner PBX1. Predictive analyses suggest that the observed PREP1 thermostability could be related to the presence of aggregation-prone regions. Interestingly, synthetic peptides corresponding to these regions exhibit a remarkable propensity to form toxic β-rich amyloid-like aggregates in physiological conditions. On this basis, we suggest that PREP1 stability is an effective way to prevent or limit the formation of harmful aggregates. Notably, one of these PREP1 fragments (residues 117-132) is able to reversibly switch from α-helical to β-rich states depending on the environmental conditions. The chameleon conformational behavior of this peptide makes it an ideal system to study this intriguing and widespread structural transition.
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Affiliation(s)
- Nunzianna Doti
- Institute of Biostructures and Bioimaging (IBB)-CNR, Via Mezzocannone 16, 80134 Naples, Italy
| | - Alessandra Monti
- Institute of Biostructures and Bioimaging (IBB)-CNR, Via Mezzocannone 16, 80134 Naples, Italy; Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, University of Campania "Luigi Vanvitelli", Via Vivaldi 43, 81100 Caserta, Italy
| | - Chiara Bruckmann
- IFOM, Foundation FIRC (Italian Foundation for Cancer Research), Institute of Molecular Oncology, Milan, Italy
| | - Luisa Calvanese
- Institute of Biostructures and Bioimaging (IBB)-CNR, Via Mezzocannone 16, 80134 Naples, Italy
| | | | - Andrea Caporale
- Institute of Biostructures and Bioimaging (IBB)-CNR, Via Mezzocannone 16, 80134 Naples, Italy
| | - Lucia Falcigno
- Institute of Biostructures and Bioimaging (IBB)-CNR, Via Mezzocannone 16, 80134 Naples, Italy; Department of Pharmacy, University of Naples "Federico II", via Mezzocannone 16, 80134 Naples, Italy
| | - Gabriella D'Auria
- Institute of Biostructures and Bioimaging (IBB)-CNR, Via Mezzocannone 16, 80134 Naples, Italy; Department of Pharmacy, University of Naples "Federico II", via Mezzocannone 16, 80134 Naples, Italy
| | - Francesco Blasi
- IFOM, Foundation FIRC (Italian Foundation for Cancer Research), Institute of Molecular Oncology, Milan, Italy
| | - Menotti Ruvo
- Institute of Biostructures and Bioimaging (IBB)-CNR, Via Mezzocannone 16, 80134 Naples, Italy.
| | - Luigi Vitagliano
- Institute of Biostructures and Bioimaging (IBB)-CNR, Via Mezzocannone 16, 80134 Naples, Italy.
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Kumar A, Kumar V, Kumar A. Functional characterization of host toxic EcdB transcription factor protein of echinocandin B biosynthetic gene cluster. Biotechnol Appl Biochem 2019; 66:626-633. [PMID: 31069846 DOI: 10.1002/bab.1763] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Accepted: 05/07/2019] [Indexed: 11/09/2022]
Abstract
The ecdB is a transcription factor, located in the echinocandin B biosynthetic gene cluster of Emericella rugulosa NRRL11440. Here, we validated the ecdB mRNA sequence for functional expression and to explore the role of EcdB protein in the echinocandin B regulation. The sequence alignment study revealed that the ecdB coding sequence was found 75 bp shorter than the reference mRNA sequence. This coding sequence encodes for EcdB protein and comprises three conserved domains; DNA binding domain (DBD), coiled-coil domain, and signature middle homology region. The full-length and DBD (truncated) DNA sequences were expressed in Escherichia coli BL21(DE3) under different tested conditions. The expression of EcdB protein was found to be toxic, which curbs the cell growth. In contrast to truncated protein (GST:EcdB1-54), the full-length (GST:EcdB) protein was expressed at very low titer and not detectable in SDS-PAGE under the varying isopropyl β-d-1-thiogalactopyranoside (IPTG), temperature, and media conditions. However, GST:EcdB1-54 was successfully purified under standard conditions (0.5 mM IPTG at 0.5OD) with 33 kDa expected size. The functionality of GST:EcdB1-54 was attained by electrophoretic mobility shift assay study as a clear band shifting showed with ecdA promoter. Taken together, we conclude that EcdB interacts with the ecdA promoter that reflected to require for echinocandin B regulation.
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Affiliation(s)
- Arvind Kumar
- Department of Biotechnology, Central University of South Bihar, Panchanpur, Gaya, India
| | - Vinay Kumar
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, India
| | - Antresh Kumar
- Department of Biotechnology, Central University of South Bihar, Panchanpur, Gaya, India
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Völkel S, Stielow B, Finkernagel F, Berger D, Stiewe T, Nist A, Suske G. Transcription factor Sp2 potentiates binding of the TALE homeoproteins Pbx1:Prep1 and the histone-fold domain protein Nf-y to composite genomic sites. J Biol Chem 2018; 293:19250-19262. [PMID: 30337366 DOI: 10.1074/jbc.ra118.005341] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Revised: 10/17/2018] [Indexed: 11/06/2022] Open
Abstract
Different transcription factors operate together at promoters and enhancers to regulate gene expression. Transcription factors either bind directly to their target DNA or are tethered to it by other proteins. The transcription factor Sp2 serves as a paradigm for indirect genomic binding. It does not require its DNA-binding domain for genomic DNA binding and occupies target promoters independently of whether they contain a cognate DNA-binding motif. Hence, Sp2 is strikingly different from its closely related paralogs Sp1 and Sp3, but how Sp2 recognizes its targets is unknown. Here, we sought to gain more detailed insights into the genomic targeting mechanism of Sp2. ChIP-exo sequencing in mouse embryonic fibroblasts revealed genomic binding of Sp2 to a composite motif where a recognition sequence for TALE homeoproteins and a recognition sequence for the trimeric histone-fold domain protein nuclear transcription factor Y (Nf-y) are separated by 11 bp. We identified a complex consisting of the TALE homeobox protein Prep1, its partner PBX homeobox 1 (Pbx1), and Nf-y as the major partners in Sp2-promoter interactions. We found that the Pbx1:Prep1 complex together with Nf-y recruits Sp2 to co-occupied regulatory elements. In turn, Sp2 potentiates binding of Pbx1:Prep1 and Nf-y. We also found that the Sp-box, a short sequence motif close to the Sp2 N terminus, is crucial for Sp2's cofactor function. Our findings reveal a mechanism by which the DNA binding-independent activity of Sp2 potentiates genomic loading of Pbx1:Prep1 and Nf-y to composite motifs present in many promoters of highly expressed genes.
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Affiliation(s)
- Sara Völkel
- From the Institute of Molecular Biology and Tumor Research (IMT) and
| | - Bastian Stielow
- From the Institute of Molecular Biology and Tumor Research (IMT) and
| | | | - Dana Berger
- From the Institute of Molecular Biology and Tumor Research (IMT) and
| | - Thorsten Stiewe
- the Genomics Core Facility, Center for Tumor Biology and Immunology (ZTI), Philipps-University of Marburg, 35043 Marburg, Germany
| | - Andrea Nist
- the Genomics Core Facility, Center for Tumor Biology and Immunology (ZTI), Philipps-University of Marburg, 35043 Marburg, Germany
| | - Guntram Suske
- From the Institute of Molecular Biology and Tumor Research (IMT) and
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5
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New Insights into Cooperative Binding of Homeodomain Transcription Factors PREP1 and PBX1 to DNA. Sci Rep 2017; 7:40665. [PMID: 28094776 PMCID: PMC5240567 DOI: 10.1038/srep40665] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2016] [Accepted: 12/09/2016] [Indexed: 01/13/2023] Open
Abstract
PREP1 and PBX1 are homeodomain (HD) transcription factors that play crucial roles in embryonic development. Here, we present the first biophysical characterization of a PREP1 HD, and the NMR spectroscopic study of its DNA binding pocket. The data show that residues flanking the HD participate in DNA binding. The kinetic parameters for DNA binding of individual PREP1 and PBX1 HDs, and of their combination, show that isolated PREP1 and PBX1 HDs bind to DNA in a cooperative manner. A novel PREP1 motif, flanking the HD at the C-terminus, is required for cooperativity.
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6
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Dardaei L, Penkov D, Mathiasen L, Bora P, Morelli MJ, Blasi F. Tumorigenesis by Meis1 overexpression is accompanied by a change of DNA target-sequence specificity which allows binding to the AP-1 element. Oncotarget 2016; 6:25175-87. [PMID: 26259236 PMCID: PMC4694823 DOI: 10.18632/oncotarget.4488] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2015] [Accepted: 07/23/2015] [Indexed: 11/25/2022] Open
Abstract
Meis1 overexpression induces tumorigenicity but its activity is inhibited by Prep1 tumor suppressor. Why does overexpression of Meis1 cause cancer and how does Prep1 inhibit? Tumor profiling and ChIP-sequencing data in a genetically-defined set of cell lines show that: 1) The number of Meis1 and Prep1 DNA binding sites increases linearly with their concentration resulting in a strong increase of “extra” target genes. 2) At high concentration, Meis1 DNA target specificity changes such that the most enriched consensus becomes that of the AP-1 regulatory element, whereas the specific OCTA consensus is not enriched because diluted within the many extra binding sites. 3) Prep1 inhibits Meis1 tumorigenesis preventing the binding to many of the “extra” genes containing AP-1 sites. 4) The overexpression of Prep1, but not of Meis1, changes the functional genomic distribution of the binding sites, increasing seven fold the number of its “enhancer” and decreasing its “promoter” targets. 5) A specific Meis1 “oncogenic” and Prep1 “tumor suppressing” signature has been identified selecting from the pool of genes bound by each protein those whose expression was modified uniquely by the “tumor-inducing” Meis1 or tumor-inhibiting Prep1 overexpression. In both signatures, the enriched gene categories are the same and are involved in signal transduction. However, Meis1 targets stimulatory genes while Prep1 targets genes that inhibit the tumorigenic signaling pathways.
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Affiliation(s)
- Leila Dardaei
- IFOM, FIRC Institute of Molecular Oncology, IFOM-IEO Campus, Milano, Italy.,Present Address: Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA, USA
| | - Dmitry Penkov
- IFOM, FIRC Institute of Molecular Oncology, IFOM-IEO Campus, Milano, Italy.,Department of Experimental Cardiology, Russian Cardiology Research and Production Complex, Moscow, Russia
| | - Lisa Mathiasen
- IFOM, FIRC Institute of Molecular Oncology, IFOM-IEO Campus, Milano, Italy
| | - Pranami Bora
- Center for Genomic Science of IIT@SEMM, Fondazione Istituto Italiano di Tecnologia (IIT), Milan, Italy
| | - Marco J Morelli
- Center for Genomic Science of IIT@SEMM, Fondazione Istituto Italiano di Tecnologia (IIT), Milan, Italy
| | - Francesco Blasi
- IFOM, FIRC Institute of Molecular Oncology, IFOM-IEO Campus, Milano, Italy
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7
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Mathiasen L, Valentini E, Boivin S, Cattaneo A, Blasi F, Svergun DI, Bruckmann C. The flexibility of a homeodomain transcription factor heterodimer and its allosteric regulation by DNA binding. FEBS J 2016; 283:3134-54. [PMID: 27390177 DOI: 10.1111/febs.13801] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2016] [Revised: 05/20/2016] [Accepted: 07/06/2016] [Indexed: 12/27/2022]
Abstract
UNLABELLED Transcription factors are known to modify the DNA that they bind. However, DNA can also serve as an allosteric ligand whose binding modifies the conformation of transcriptional regulators. Here, we describe how heterodimer PBX1:PREP1, formed by proteins playing major roles in embryonic development and tumorigenesis, undergoes an allosteric transition upon DNA binding. We demonstrate through a number of biochemical and biophysical methods that PBX1:PREP1 exhibits a structural change upon DNA binding. Small-angle X-ray scattering (SAXS), circular dichroism (CD), isothermal titration calorimetry (ITC), and limited proteolysis demonstrate a different shape, α-helical content, thermodynamic behavior, and solution environment of the holo-complex (with DNA) compared to the apo-complex (without DNA). Given that PBX1 as such does not have a defined DNA selectivity, structural changes upon DNA binding become major factors in the function of the PBX1:PREP1 complex. The observed changes are mapped at both the amino- and carboxy-terminal regions of the two proteins thereby providing important insights to determine how PBX1:PREP1 dimer functions. DATABASE Small-angle scattering data are available in SASBDB under accession numbers SASDAP7, SASDAQ7, and SASDAR7.
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Affiliation(s)
- Lisa Mathiasen
- FIRC (Foundation for Italian Cancer Research) Institute of Molecular Oncology (IFOM), Milan, Italy
| | | | | | - Angela Cattaneo
- FIRC (Foundation for Italian Cancer Research) Institute of Molecular Oncology (IFOM), Milan, Italy
| | - Francesco Blasi
- FIRC (Foundation for Italian Cancer Research) Institute of Molecular Oncology (IFOM), Milan, Italy
| | | | - Chiara Bruckmann
- FIRC (Foundation for Italian Cancer Research) Institute of Molecular Oncology (IFOM), Milan, Italy
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8
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Lorenzo V, Mascanzoni F, Vitagliano L, Ruvo M, Doti N. The Interacting Domains of PREP1 and p160 are Endowed with a Remarkable Structural Stability. Mol Biotechnol 2016; 58:328-39. [DOI: 10.1007/s12033-016-9932-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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