1
|
Baglivo I, Malgieri G, Roop RM, Barton IS, Wang X, Russo V, Pirone L, Pedone EM, Pedone PV. MucR protein: Three decades of studies have led to the identification of a new H-NS-like protein. Mol Microbiol 2024. [PMID: 38619026 DOI: 10.1111/mmi.15261] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Revised: 03/22/2024] [Accepted: 03/25/2024] [Indexed: 04/16/2024]
Abstract
MucR belongs to a large protein family whose members regulate the expression of virulence and symbiosis genes in α-proteobacteria species. This protein and its homologs were initially studied as classical transcriptional regulators mostly involved in repression of target genes by binding their promoters. Very recent studies have led to the classification of MucR as a new type of Histone-like Nucleoid Structuring (H-NS) protein. Thus this review is an effort to put together a complete and unifying story demonstrating how genetic and biochemical findings on MucR suggested that this protein is not a classical transcriptional regulator, but functions as a novel type of H-NS-like protein, which binds AT-rich regions of genomic DNA and regulates gene expression.
Collapse
Affiliation(s)
- Ilaria Baglivo
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, University of Campania "Luigi Vanvitelli", Caserta, Italy
| | - Gaetano Malgieri
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, University of Campania "Luigi Vanvitelli", Caserta, Italy
| | - Roy Martin Roop
- Department of Microbiology and Immunology, Brody School of Medicine, East Carolina University, Greenville, North Carolina, USA
| | - Ian S Barton
- Department of Microbiology and Immunology, Brody School of Medicine, East Carolina University, Greenville, North Carolina, USA
| | - Xindan Wang
- Department of Biology, Indiana University, Bloomington, Indiana, USA
| | | | - Luciano Pirone
- Institute of Biostructures and Bioimaging, CNR, Naples, Italy
| | - Emilia M Pedone
- Institute of Biostructures and Bioimaging, CNR, Naples, Italy
| | - Paolo V Pedone
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, University of Campania "Luigi Vanvitelli", Caserta, Italy
| |
Collapse
|
2
|
Slapakova M, Sgambati D, Pirone L, Russo V, D’Abrosca G, Valletta M, Russo R, Chambery A, Malgieri G, Pedone EM, Dame RT, Pedone PV, Baglivo I. MucR from Sinorhizobium meliloti: New Insights into Its DNA Targets and Its Ability to Oligomerize. Int J Mol Sci 2023; 24:14702. [PMID: 37834166 PMCID: PMC10572780 DOI: 10.3390/ijms241914702] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Revised: 09/21/2023] [Accepted: 09/25/2023] [Indexed: 10/15/2023] Open
Abstract
Proteins of the MucR/Ros family play a crucial role in bacterial infection or symbiosis with eukaryotic hosts. MucR from Sinorhizobium meliloti plays a regulatory role in establishing symbiosis with the host plant, both dependent and independent of Quorum Sensing. Here, we report the first characterization of MucR isolated from Sinorhizobium meliloti by mass spectrometry and demonstrate that this protein forms higher-order oligomers in its native condition of expression by SEC-MALS. We show that MucR purified from Sinorhizobium meliloti can bind DNA and recognize the region upstream of the ndvA gene in EMSA, revealing that this gene is a direct target of MucR. Although MucR DNA binding activity was already described, a detailed characterization of Sinorhizobium meliloti DNA targets has never been reported. We, thus, analyze sequences recognized by MucR in the rem gene promoter, showing that this protein recognizes AT-rich sequences and does not require a consensus sequence to bind DNA. Furthermore, we investigate the dependence of MucR DNA binding on the length of DNA targets. Taken together, our studies establish MucR from Sinorhizobium meliloti as a member of a new family of Histone-like Nucleoid Structuring (H-NS) proteins, thus explaining the multifaceted role of this protein in many species of alpha-proteobacteria.
Collapse
Affiliation(s)
- Martina Slapakova
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, University of Campania “Luigi Vanvitelli”, Via Vivaldi, 43, 81100 Caserta, Italy; (M.S.); (D.S.); (V.R.); (M.V.); (R.R.); (A.C.); (G.M.); (P.V.P.)
| | - Domenico Sgambati
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, University of Campania “Luigi Vanvitelli”, Via Vivaldi, 43, 81100 Caserta, Italy; (M.S.); (D.S.); (V.R.); (M.V.); (R.R.); (A.C.); (G.M.); (P.V.P.)
| | - Luciano Pirone
- Institute of Biostructures and Bioimaging, CNR, Via Pietro Castellino, 80134 Naples, Italy; (L.P.); (E.M.P.)
| | - Veronica Russo
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, University of Campania “Luigi Vanvitelli”, Via Vivaldi, 43, 81100 Caserta, Italy; (M.S.); (D.S.); (V.R.); (M.V.); (R.R.); (A.C.); (G.M.); (P.V.P.)
| | - Gianluca D’Abrosca
- Department of Clinical and Experimental Medicine, University of Foggia, Viale Pinto, 1, 71122 Foggia, Italy;
| | - Mariangela Valletta
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, University of Campania “Luigi Vanvitelli”, Via Vivaldi, 43, 81100 Caserta, Italy; (M.S.); (D.S.); (V.R.); (M.V.); (R.R.); (A.C.); (G.M.); (P.V.P.)
| | - Rosita Russo
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, University of Campania “Luigi Vanvitelli”, Via Vivaldi, 43, 81100 Caserta, Italy; (M.S.); (D.S.); (V.R.); (M.V.); (R.R.); (A.C.); (G.M.); (P.V.P.)
| | - Angela Chambery
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, University of Campania “Luigi Vanvitelli”, Via Vivaldi, 43, 81100 Caserta, Italy; (M.S.); (D.S.); (V.R.); (M.V.); (R.R.); (A.C.); (G.M.); (P.V.P.)
| | - Gaetano Malgieri
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, University of Campania “Luigi Vanvitelli”, Via Vivaldi, 43, 81100 Caserta, Italy; (M.S.); (D.S.); (V.R.); (M.V.); (R.R.); (A.C.); (G.M.); (P.V.P.)
| | - Emilia Maria Pedone
- Institute of Biostructures and Bioimaging, CNR, Via Pietro Castellino, 80134 Naples, Italy; (L.P.); (E.M.P.)
| | - Remus Thei Dame
- Leiden Institute of Chemistry, Leiden University, 2333 CC Leiden, The Netherlands;
- Centre for Microbial Cell Biology, Leiden University, 2333 CC Leiden, The Netherlands
| | - Paolo Vincenzo Pedone
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, University of Campania “Luigi Vanvitelli”, Via Vivaldi, 43, 81100 Caserta, Italy; (M.S.); (D.S.); (V.R.); (M.V.); (R.R.); (A.C.); (G.M.); (P.V.P.)
| | - Ilaria Baglivo
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, University of Campania “Luigi Vanvitelli”, Via Vivaldi, 43, 81100 Caserta, Italy; (M.S.); (D.S.); (V.R.); (M.V.); (R.R.); (A.C.); (G.M.); (P.V.P.)
| |
Collapse
|
3
|
Grazioso R, García-Viñuales S, D'Abrosca G, Baglivo I, Pedone PV, Milardi D, Fattorusso R, Isernia C, Russo L, Malgieri G. The change of conditions does not affect Ros87 downhill folding mechanism. Sci Rep 2020; 10:21067. [PMID: 33273582 PMCID: PMC7713307 DOI: 10.1038/s41598-020-78008-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Accepted: 11/19/2020] [Indexed: 11/20/2022] Open
Abstract
Downhill folding has been defined as a unique thermodynamic process involving a conformations ensemble that progressively loses structure with the decrease of protein stability. Downhill folders are estimated to be rather rare in nature as they miss an energetically substantial folding barrier that can protect against aggregation and proteolysis. We have previously demonstrated that the prokaryotic zinc finger protein Ros87 shows a bipartite folding/unfolding process in which a metal binding intermediate converts to the native structure through a delicate barrier-less downhill transition. Significant variation in folding scenarios can be detected within protein families with high sequence identity and very similar folds and for the same sequence by varying conditions. For this reason, we here show, by means of DSC, CD and NMR, that also in different pH and ionic strength conditions Ros87 retains its partly downhill folding scenario demonstrating that, at least in metallo-proteins, the downhill mechanism can be found under a much wider range of conditions and coupled to other different transitions. We also show that mutations of Ros87 zinc coordination sphere produces a different folding scenario demonstrating that the organization of the metal ion core is determinant in the folding process of this family of proteins.
Collapse
Affiliation(s)
- Rinaldo Grazioso
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, Via Vivaldi 43, 81100, Caserta, Italy
| | | | - Gianluca D'Abrosca
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, Via Vivaldi 43, 81100, Caserta, Italy
| | - Ilaria Baglivo
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, Via Vivaldi 43, 81100, Caserta, Italy
| | - Paolo Vincenzo Pedone
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, Via Vivaldi 43, 81100, Caserta, Italy
| | - Danilo Milardi
- Institute of Crystallography-CNR, Via Paolo Gaifami 18, 95126, Catania, Italy
| | - Roberto Fattorusso
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, Via Vivaldi 43, 81100, Caserta, Italy
| | - Carla Isernia
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, Via Vivaldi 43, 81100, Caserta, Italy
| | - Luigi Russo
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, Via Vivaldi 43, 81100, Caserta, Italy.
| | - Gaetano Malgieri
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, Via Vivaldi 43, 81100, Caserta, Italy.
| |
Collapse
|
4
|
Substitution of the Native Zn(II) with Cd(II), Co(II) and Ni(II) Changes the Downhill Unfolding Mechanism of Ros87 to a Completely Different Scenario. Int J Mol Sci 2020; 21:ijms21218285. [PMID: 33167398 PMCID: PMC7663847 DOI: 10.3390/ijms21218285] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Revised: 10/30/2020] [Accepted: 11/03/2020] [Indexed: 12/15/2022] Open
Abstract
The structural effects of zinc replacement by xenobiotic metal ions have been widely studied in several eukaryotic and prokaryotic zinc-finger-containing proteins. The prokaryotic zinc finger, that presents a bigger βββαα domain with a larger hydrophobic core with respect to its eukaryotic counterpart, represents a valuable model protein to study metal ion interaction with metallo-proteins. Several studies have been conducted on Ros87, the DNA binding domain of the prokaryotic zinc finger Ros, and have demonstrated that the domain appears to structurally tolerate Ni(II), albeit with important structural perturbations, but not Pb(II) and Hg(II), and it is in vitro functional when the zinc ion is replaced by Cd(II). We have previously shown that Ros87 unfolding is a two-step process in which a zinc binding intermediate converts to the native structure thorough a delicate downhill folding transition. Here, we explore the folding/unfolding behaviour of Ros87 coordinated to Co(II), Ni(II) or Cd(II), by UV-Vis, CD, DSC and NMR techniques. Interestingly, we show how the substitution of the native metal ion results in complete different folding scenarios. We found a two-state unfolding mechanism for Cd-Ros87 whose metal affinity Kd is comparable to the one obtained for the native Zn-Ros87, and a more complex mechanism for Co-Ros87 and Ni-Ros87, that show higher Kd values. Our data outline the complex cross-correlation between the protein-metal ion equilibrium and the folding mechanism proposing such an interplay as a key factor in the proper metal ion selection by a specific metallo-protein.
Collapse
|
5
|
Structural Insight of the Full-Length Ros Protein: A Prototype of the Prokaryotic Zinc-Finger Family. Sci Rep 2020; 10:9283. [PMID: 32518326 PMCID: PMC7283297 DOI: 10.1038/s41598-020-66204-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Accepted: 05/15/2020] [Indexed: 11/30/2022] Open
Abstract
Ros/MucR is a widespread family of bacterial zinc-finger (ZF) containing proteins that integrate multiple functions such as virulence, symbiosis and/or cell cycle transcription. NMR solution structure of Ros DNA-binding domain (region 56–142, i.e. Ros87) has been solved by our group and shows that the prokaryotic ZF domain shows interesting structural and functional features that differentiate it from its eukaryotic counterpart as it folds in a significantly larger zinc-binding globular domain. We have recently proposed a novel functional model for this family of proteins suggesting that they may act as H-NS-‘like’ gene silencers. Indeed, the N-terminal region of this family of proteins appears to be responsible for the formation of functional oligomers. No structural characterization of the Ros N-terminal domain (region 1–55) is available to date, mainly because of serious solubility problems of the full-length protein. Here we report the first structural characterization of the N-terminal domain of the prokaryotic ZF family examining by means of MD and NMR the structural preferences of the full-length Ros protein from Agrobacterium tumefaciens.
Collapse
|
6
|
Borriello G, Russo V, Paradiso R, Riccardi MG, Criscuolo D, Verde G, Marasco R, Pedone PV, Galiero G, Baglivo I. Different Impacts of MucR Binding to the babR and virB Promoters on Gene Expression in Brucella abortus 2308. Biomolecules 2020; 10:biom10050788. [PMID: 32438765 PMCID: PMC7277663 DOI: 10.3390/biom10050788] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Revised: 05/12/2020] [Accepted: 05/12/2020] [Indexed: 12/27/2022] Open
Abstract
The protein MucR from Brucella abortus has been described as a transcriptional regulator of many virulence genes. It is a member of the Ros/MucR family comprising proteins that control the expression of genes important for the successful interaction of α-proteobacteria with their eukaryotic hosts. Despite clear evidence of the role of MucR in repressing virulence genes, no study has been carried out so far demonstrating the direct interaction of this protein with the promoter of its target gene babR encoding a LuxR-like regulator repressing virB genes. In this study, we show for the first time the ability of MucR to bind the promoter of babR in electrophoretic mobility shift assays demonstrating a direct role of MucR in repressing this gene. Furthermore, we demonstrate that MucR can bind the virB gene promoter. Analyses by RT-qPCR showed no significant differences in the expression level of virB genes in Brucella abortus CC092 lacking MucR compared to the wild-type Brucella abortus strain, indicating that MucR binding to the virB promoter has little impact on virB gene expression in B. abortus 2308. The MucR modality to bind the two promoters analyzed supports our previous hypothesis that this is a histone-like protein never found before in Brucella.
Collapse
Affiliation(s)
- Giorgia Borriello
- Experimental Zooprophylactic Institute of Southern Italy, via Salute, 2, 80055 Portici, Italy; (G.B.); (R.P.); (M.G.R.); (D.C.)
| | - Veronica Russo
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, University of Campania “Luigi Vanvitelli”, via Vivaldi—43, 81100 Caserta, Italy; (V.R.); (R.M.); (P.V.P.)
| | - Rubina Paradiso
- Experimental Zooprophylactic Institute of Southern Italy, via Salute, 2, 80055 Portici, Italy; (G.B.); (R.P.); (M.G.R.); (D.C.)
| | - Marita Georgia Riccardi
- Experimental Zooprophylactic Institute of Southern Italy, via Salute, 2, 80055 Portici, Italy; (G.B.); (R.P.); (M.G.R.); (D.C.)
| | - Daniela Criscuolo
- Experimental Zooprophylactic Institute of Southern Italy, via Salute, 2, 80055 Portici, Italy; (G.B.); (R.P.); (M.G.R.); (D.C.)
| | - Gaetano Verde
- Institute of Genetics and Biophysics (IGB) “Adriano Buzzati-Traverso”, Consiglio Nazionale delle Ricerche (CNR), 80134 Naples, Italy;
- Flomics Biotech, Carrer Dr. Aiguader 88, 08003 Barcelona, Spain
| | - Rosangela Marasco
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, University of Campania “Luigi Vanvitelli”, via Vivaldi—43, 81100 Caserta, Italy; (V.R.); (R.M.); (P.V.P.)
| | - Paolo Vincenzo Pedone
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, University of Campania “Luigi Vanvitelli”, via Vivaldi—43, 81100 Caserta, Italy; (V.R.); (R.M.); (P.V.P.)
| | - Giorgio Galiero
- Experimental Zooprophylactic Institute of Southern Italy, via Salute, 2, 80055 Portici, Italy; (G.B.); (R.P.); (M.G.R.); (D.C.)
- Correspondence: (G.G.); (I.B.); Tel.: +39-081-7865201 (G.G.); +39-0823-274598 (I.B.)
| | - Ilaria Baglivo
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, University of Campania “Luigi Vanvitelli”, via Vivaldi—43, 81100 Caserta, Italy; (V.R.); (R.M.); (P.V.P.)
- Correspondence: (G.G.); (I.B.); Tel.: +39-081-7865201 (G.G.); +39-0823-274598 (I.B.)
| |
Collapse
|
7
|
Abstract
Zinc ion binding is a principal event in the achievement of the correct fold in classical zinc finger domains since the motif is largely unfolded in the absence of metal. In the case of a prokaryotic zinc finger, the larger βββαα domain contributes to the folding mechanism with a larger hydrophobic core. For these reasons, following the great amount of attention devoted to unveiling the effect of xenobiotic metal ion replacement in zinc fingers and in zinc-containing proteins in general, the prokaryotic zinc finger domain appears to be an interesting model for studying metal ion interaction with metalloproteins. Here, we explore the binding of Ni(II), Hg(II), and Pb(II) to Ros87, the DNA binding domain of the prokaryotic zinc finger protein Ros. We measured Ros87-metal ion dissociation constants and monitored the effects on the structure and function of the domain. Interestingly, we found that the protein folds in the presence of Ni(II) with important structural perturbations, while in the presence of Pb(II) and Hg(II) it does not appear to be significantly folded. Accordingly, an overall strong reduction in the DNA binding capability is observed for all of the examined proteins. Our data integrate and complement the information collected in the past few years concerning the functional and structural effects of metal ion substitution in classical zinc fingers in order to contribute to a better comprehension of the toxicity of these metals in biological systems.
Collapse
|
8
|
Identifying the region responsible for Brucella abortus MucR higher-order oligomer formation and examining its role in gene regulation. Sci Rep 2018; 8:17238. [PMID: 30467359 PMCID: PMC6250670 DOI: 10.1038/s41598-018-35432-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Accepted: 11/05/2018] [Indexed: 11/09/2022] Open
Abstract
MucR is a member of the Ros/MucR family of prokaryotic zinc-finger proteins found in the α-proteobacteria which regulate the expression of genes required for the successful pathogenic and symbiotic interactions of these bacteria with the eukaryotic hosts. The structure and function of their distinctive zinc-finger domain has been well-studied, but only recently the quaternary structure of the full length proteins was investigated demonstrating their ability to form higher-order oligomers. The aim of this study was to identify the region of MucR involved in higher-order oligomer formation by analysing deletion and point mutants of this protein by Light Scattering, and to determine the role that MucR oligomerization plays in the regulatory function of this protein. Here we demonstrate that a conserved hydrophobic region at the N-terminus of MucR is responsible for higher-order oligomer formation and that MucR oligomerization is essential for its regulatory function in Brucella. All these features of MucR are shared by the histone-like nucleoid structuring protein, (H-NS), leading us to propose that the prokaryotic zinc-finger proteins in the MucR/Ros family control gene expression employing a mechanism similar to that used by the H-NS proteins, rather than working as classical transcriptional regulators.
Collapse
|
9
|
Structural Characterization of the Lactobacillus Plantarum FlmC Protein Involved in Biofilm Formation. Molecules 2018; 23:molecules23092252. [PMID: 30181476 PMCID: PMC6225345 DOI: 10.3390/molecules23092252] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Revised: 08/27/2018] [Accepted: 08/31/2018] [Indexed: 12/25/2022] Open
Abstract
Lactobacillus plantarum is one of the most predominant species in the human gut microbiota of healthy individuals. We have previously characterized some probiotic features of L. plantarum LM3, as the high resistance to different stress, the binding ability toward some extracellular matrix proteins and plasminogen and the immunomodulatory role of the surface expressed adhesin EnoA1. We have also identified the flmA, flmB and flmC genes, coding for putative proteins named FlmA, FlmB and FlmC, whose null mutations partially impaired biofilm development; the L. plantarum LM3–6 strain, carrying a deletion in flmC, showed a high rate of autolysis, supporting the hypothesis that FlmC might be involved in cell wall integrity. Here, we report the in-silico characterization of ΔTM-FlmC, a portion of the FlmC protein. The protein has been also expressed, purified and characterized by means of CD spectroscopy, ICP-mass and UHPLC-HRMS. The obtained experimental data validated the predicted model unveiling also the presence of a bound lipid molecule and of a Mg(II) ion. Overall, we provide strong evidences that ΔTM-FlmC belongs to the LytR-CpsA-Psr (LCP) family of domains and is involved in cell envelope biogenesis.
Collapse
|
10
|
Baglivo I, Pirone L, Malgieri G, Fattorusso R, Roop II RM, Pedone EM, Pedone PV. MucR binds multiple target sites in the promoter of its own gene and is a heat-stable protein: Is MucR a H-NS-like protein? FEBS Open Bio 2018; 8:711-718. [PMID: 29632823 PMCID: PMC5881533 DOI: 10.1002/2211-5463.12411] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2018] [Revised: 02/17/2018] [Accepted: 02/21/2018] [Indexed: 01/08/2023] Open
Abstract
The protein MucR from Brucella spp. is involved in the expression regulation of genes necessary for host interaction and infection. MucR is a member of the Ros/MucR family, which comprises prokaryotic zinc-finger proteins and includes Ros from Agrobacterium tumefaciens and the Ml proteins from Mesorhizobium loti. MucR from Brucella spp. can regulate the expression of virulence genes and repress its own gene expression. Despite the well-known role played by MucR in the repression of its own gene, no target sequence has yet been identified in the mucR promoter gene. In this study, we provide the first evidence that MucR from Brucella abortus binds more than one target site in the promoter region of its own gene, suggesting a molecular mechanism by which this protein represses its own expression. Furthermore, a circular dichroism analysis reveals that MucR is a heat-stable protein. Overall, the results of this study suggest that MucR might resemble a H-NS protein.
Collapse
Affiliation(s)
- Ilaria Baglivo
- Department of Environmental, Biological and Pharmaceutical Sciences and TechnologiesUniversity of Campania ‘Luigi Vanvitelli’CasertaItaly
| | - Luciano Pirone
- Institute of Biostructures and BioimagingC.N.R.NaplesItaly
| | - Gaetano Malgieri
- Department of Environmental, Biological and Pharmaceutical Sciences and TechnologiesUniversity of Campania ‘Luigi Vanvitelli’CasertaItaly
| | - Roberto Fattorusso
- Department of Environmental, Biological and Pharmaceutical Sciences and TechnologiesUniversity of Campania ‘Luigi Vanvitelli’CasertaItaly
| | - Roy Martin Roop II
- Department of Microbiology and ImmunologyBrody School of MedicineEast Carolina UniversityGreenvilleNCUSA
| | | | - Paolo Vincenzo Pedone
- Department of Environmental, Biological and Pharmaceutical Sciences and TechnologiesUniversity of Campania ‘Luigi Vanvitelli’CasertaItaly
| |
Collapse
|
11
|
Malgieri G, D'Abrosca G, Pirone L, Toto A, Palmieri M, Russo L, Sciacca MFM, Tatè R, Sivo V, Baglivo I, Majewska R, Coletta M, Pedone PV, Isernia C, De Stefano M, Gianni S, Pedone EM, Milardi D, Fattorusso R. Folding mechanisms steer the amyloid fibril formation propensity of highly homologous proteins. Chem Sci 2018; 9:3290-3298. [PMID: 29780459 PMCID: PMC5933289 DOI: 10.1039/c8sc00166a] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2018] [Accepted: 02/28/2018] [Indexed: 12/16/2022] Open
Abstract
Understanding the molecular determinants of fibrillogenesis by studying the aggregation propensities of high homologous proteins with different folding pathways.
Significant advances in the understanding of the molecular determinants of fibrillogenesis can be expected from comparative studies of the aggregation propensities of proteins with highly homologous structures but different folding pathways. Here, we fully characterize, by means of stopped-flow, T-jump, CD and DSC experiments, the unfolding mechanisms of three highly homologous proteins, zinc binding Ros87 and Ml153–149 and zinc-lacking Ml452–151. The results indicate that the three proteins significantly differ in terms of stability and (un)folding mechanisms. Particularly, Ros87 and Ml153–149 appear to be much more stable to guanidine denaturation and are characterized by folding mechanisms including the presence of an intermediate. On the other hand, metal lacking Ml452–151 folds according to a classic two-state model. Successively, we have monitored the capabilities of Ros87, Ml452–151 and Ml153–149 to form amyloid fibrils under native conditions. Particularly, we show, by CD, fluorescence, DLS, TEM and SEM experiments, that after 168 hours, amyloid formation of Ros87 has started, while Ml153–149 has formed only amorphous aggregates and Ml452–151 is still monomeric in solution. This study shows how metal binding can influence protein folding pathways and thereby control conformational accessibility to aggregation-prone states, which in turn changes aggregation kinetics, shedding light on the role of metal ions in the development of protein deposition diseases.
Collapse
Affiliation(s)
- Gaetano Malgieri
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies , University of Campania "Luigi Vanvitelli" , Via Vivaldi 43 , 81100 Caserta , Italy .
| | - Gianluca D'Abrosca
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies , University of Campania "Luigi Vanvitelli" , Via Vivaldi 43 , 81100 Caserta , Italy .
| | - Luciano Pirone
- Institute of Biostructures and Bioimaging , CNR , Via Mezzocannone 16 , 80134 Naples , Italy
| | - Angelo Toto
- Department of Biochemical Sciences "Alessandro Rossi Fanelli" , University of Rome "La Sapienza" , Piazzale Aldo Moro 5 , 00185 , Roma , Italy
| | - Maddalena Palmieri
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies , University of Campania "Luigi Vanvitelli" , Via Vivaldi 43 , 81100 Caserta , Italy .
| | - Luigi Russo
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies , University of Campania "Luigi Vanvitelli" , Via Vivaldi 43 , 81100 Caserta , Italy .
| | | | - Rosarita Tatè
- Institute of Genetics and Biophysics "Adriano Buzzati-Traverso" , CNR , Via P. Castellino 111 , 80131 Napoli , Italy
| | - Valeria Sivo
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies , University of Campania "Luigi Vanvitelli" , Via Vivaldi 43 , 81100 Caserta , Italy .
| | - Ilaria Baglivo
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies , University of Campania "Luigi Vanvitelli" , Via Vivaldi 43 , 81100 Caserta , Italy .
| | - Roksana Majewska
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies , University of Campania "Luigi Vanvitelli" , Via Vivaldi 43 , 81100 Caserta , Italy .
| | - Massimo Coletta
- Department of Clinical Sciences and Translational Medicine , University of Rome "Tor Vergata" , Via Montpellier 1 , 00133 , Roma , Italy
| | - Paolo Vincenzo Pedone
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies , University of Campania "Luigi Vanvitelli" , Via Vivaldi 43 , 81100 Caserta , Italy .
| | - Carla Isernia
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies , University of Campania "Luigi Vanvitelli" , Via Vivaldi 43 , 81100 Caserta , Italy .
| | - Mario De Stefano
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies , University of Campania "Luigi Vanvitelli" , Via Vivaldi 43 , 81100 Caserta , Italy .
| | - Stefano Gianni
- Department of Biochemical Sciences "Alessandro Rossi Fanelli" , University of Rome "La Sapienza" , Piazzale Aldo Moro 5 , 00185 , Roma , Italy
| | - Emilia Maria Pedone
- Institute of Biostructures and Bioimaging , CNR , Via Mezzocannone 16 , 80134 Naples , Italy
| | - Danilo Milardi
- Institute of Biostructures and Bioimaging , CNR , Viale A. Doria 6 , 95125 Catania , Italy .
| | - Roberto Fattorusso
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies , University of Campania "Luigi Vanvitelli" , Via Vivaldi 43 , 81100 Caserta , Italy .
| |
Collapse
|
12
|
Co(II) Coordination in Prokaryotic Zinc Finger Domains as Revealed by UV-Vis Spectroscopy. Bioinorg Chem Appl 2017; 2017:1527247. [PMID: 29386985 PMCID: PMC5745721 DOI: 10.1155/2017/1527247] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Revised: 10/03/2017] [Accepted: 10/16/2017] [Indexed: 11/23/2022] Open
Abstract
Co(II) electronic configuration allows its use as a spectroscopic probe in UV-Vis experiments to characterize the metal coordination sphere that is an essential component of the functional structure of zinc-binding proteins and to evaluate the metal ion affinities of these proteins. Here, exploiting the capability of the prokaryotic zinc finger to use different combinations of residues to properly coordinate the structural metal ion, we provide the UV-Vis characterization of Co(II) addition to Ros87 and its mutant Ros87_C27D which bears an unusual CysAspHis2 coordination sphere. Zinc finger sites containing only one cysteine have been infrequently characterized. We show for the CysAspHis2 coordination an intense d-d transition band, blue-shifted with respect to the Cys2His2 sphere. These data complemented by NMR and CD data demonstrate that the tetrahedral geometry of the metal site is retained also in the case of a single-cysteine coordination sphere.
Collapse
|
13
|
Baglivo I, Pirone L, Pedone EM, Pitzer JE, Muscariello L, Marino MM, Malgieri G, Freschi A, Chambery A, Roop Ii RM, Pedone PV. Ml proteins from Mesorhizobium loti and MucR from Brucella abortus: an AT-rich core DNA-target site and oligomerization ability. Sci Rep 2017; 7:15805. [PMID: 29150637 PMCID: PMC5693944 DOI: 10.1038/s41598-017-16127-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Accepted: 11/07/2017] [Indexed: 11/09/2022] Open
Abstract
Mesorhizobium loti contains ten genes coding for proteins sharing high amino acid sequence identity with members of the Ros/MucR transcription factor family. Five of these Ros/MucR family members from Mesorhizobium loti (Ml proteins) have been recently structurally and functionally characterized demonstrating that Ml proteins are DNA-binding proteins. However, the DNA-binding studies were performed using the Ros DNA-binding site with the Ml proteins. Currently, there is no evidence as to when the Ml proteins are expressed during the Mesorhizobium lo ti life cycle as well as no information concerning their natural DNA-binding site. In this study, we examine the ml genes expression profile in Mesorhizobium loti and show that ml1, ml2, ml3 and ml5 are expressed during planktonic growth and in biofilms. DNA-binding experiments show that the Ml proteins studied bind a conserved AT-rich site in the promoter region of the exoY gene from Mesorhizobium loti and that the proteins make important contacts with the minor groove of DNA. Moreover, we demonstrate that the Ml proteins studied form higher-order oligomers through their N-terminal region and that the same AT-rich site is recognized by MucR from Brucella abortus using a similar mechanism involving contacts with the minor groove of DNA and oligomerization.
Collapse
Affiliation(s)
- Ilaria Baglivo
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, University of Campania "Luigi Vanvitelli", Caserta, 81100, Italy.
| | - Luciano Pirone
- Institute of Biostructures and Bioimaging, C.N.R., Naples, 80134, Italy
| | | | - Joshua Edison Pitzer
- Department of Microbiology and Immunology, Brody School of Medicine, East Carolina University, Greenville, NC, USA
| | - Lidia Muscariello
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, University of Campania "Luigi Vanvitelli", Caserta, 81100, Italy
| | - Maria Michela Marino
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, University of Campania "Luigi Vanvitelli", Caserta, 81100, Italy
| | - Gaetano Malgieri
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, University of Campania "Luigi Vanvitelli", Caserta, 81100, Italy
| | - Andrea Freschi
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, University of Campania "Luigi Vanvitelli", Caserta, 81100, Italy
| | - Angela Chambery
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, University of Campania "Luigi Vanvitelli", Caserta, 81100, Italy
| | - Roy-Martin Roop Ii
- Department of Microbiology and Immunology, Brody School of Medicine, East Carolina University, Greenville, NC, USA
| | - Paolo Vincenzo Pedone
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, University of Campania "Luigi Vanvitelli", Caserta, 81100, Italy.
| |
Collapse
|
14
|
D'Abrosca G, Russo L, Palmieri M, Baglivo I, Netti F, de Paola I, Zaccaro L, Farina B, Iacovino R, Pedone PV, Isernia C, Fattorusso R, Malgieri G. The (unusual) aspartic acid in the metal coordination sphere of the prokaryotic zinc finger domain. J Inorg Biochem 2016; 161:91-8. [PMID: 27238756 DOI: 10.1016/j.jinorgbio.2016.05.006] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2015] [Revised: 03/30/2016] [Accepted: 05/10/2016] [Indexed: 11/29/2022]
Abstract
The possibility of choices of protein ligands and coordination geometries leads to diverse Zn(II) binding sites in zinc-proteins, allowing a range of important biological roles. The prokaryotic Cys2His2 zinc finger domain (originally found in the Ros protein from Agrobacterium tumefaciens) tetrahedrally coordinates zinc through two cysteine and two histidine residues and it does not adopt a correct fold in the absence of the metal ion. Ros is the first structurally characterized member of a family of bacterial proteins that presents several amino acid changes in the positions occupied in Ros by the zinc coordinating residues. In particular, the second position is very often occupied by an aspartic acid although the coordination of structural zinc by an aspartate in eukaryotic zinc fingers is very unusual. Here, by appropriately mutating the protein Ros, we characterize the aspartate role within the coordination sphere of this family of proteins demonstrating how the presence of this residue only slightly perturbs the functional structure of the prokaryotic zinc finger domain while it greatly influences its thermodynamic properties.
Collapse
Affiliation(s)
- Gianluca D'Abrosca
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, Second University of Naples, Via Vivaldi 43, 81100 Caserta, Italy
| | - Luigi Russo
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, Second University of Naples, Via Vivaldi 43, 81100 Caserta, Italy
| | - Maddalena Palmieri
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, Second University of Naples, Via Vivaldi 43, 81100 Caserta, Italy
| | - Ilaria Baglivo
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, Second University of Naples, Via Vivaldi 43, 81100 Caserta, Italy
| | - Fortuna Netti
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, Second University of Naples, Via Vivaldi 43, 81100 Caserta, Italy
| | - Ivan de Paola
- Interuniversity Centre for Research on Bioactive Peptides (CIRPEB), University of Naples Federico II, Via Mezzocannone 16, 80134 Naples, Italy; Institute of Biostructures and Bioimaging - CNR, Via Mezzocannone 16, 80134 Naples, Italy
| | - Laura Zaccaro
- Interuniversity Centre for Research on Bioactive Peptides (CIRPEB), University of Naples Federico II, Via Mezzocannone 16, 80134 Naples, Italy; Institute of Biostructures and Bioimaging - CNR, Via Mezzocannone 16, 80134 Naples, Italy
| | - Biancamaria Farina
- Interuniversity Centre for Research on Bioactive Peptides (CIRPEB), University of Naples Federico II, Via Mezzocannone 16, 80134 Naples, Italy; Institute of Biostructures and Bioimaging - CNR, Via Mezzocannone 16, 80134 Naples, Italy
| | - Rosa Iacovino
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, Second University of Naples, Via Vivaldi 43, 81100 Caserta, Italy
| | - Paolo Vincenzo Pedone
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, Second University of Naples, Via Vivaldi 43, 81100 Caserta, Italy; Interuniversity Centre for Research on Bioactive Peptides (CIRPEB), University of Naples Federico II, Via Mezzocannone 16, 80134 Naples, Italy
| | - Carla Isernia
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, Second University of Naples, Via Vivaldi 43, 81100 Caserta, Italy; Interuniversity Centre for Research on Bioactive Peptides (CIRPEB), University of Naples Federico II, Via Mezzocannone 16, 80134 Naples, Italy
| | - Roberto Fattorusso
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, Second University of Naples, Via Vivaldi 43, 81100 Caserta, Italy; Interuniversity Centre for Research on Bioactive Peptides (CIRPEB), University of Naples Federico II, Via Mezzocannone 16, 80134 Naples, Italy
| | - Gaetano Malgieri
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, Second University of Naples, Via Vivaldi 43, 81100 Caserta, Italy.
| |
Collapse
|
15
|
Malgieri G, Palmieri M, Russo L, Fattorusso R, Pedone PV, Isernia C. The prokaryotic zinc-finger: structure, function and comparison with the eukaryotic counterpart. FEBS J 2015; 282:4480-96. [PMID: 26365095 DOI: 10.1111/febs.13503] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2015] [Revised: 07/23/2015] [Accepted: 08/24/2015] [Indexed: 01/18/2023]
Abstract
Classical zinc finger (ZF) domains were thought to be confined to the eukaryotic kingdom until the transcriptional regulator Ros protein was identified in Agrobacterium tumefaciens. The Ros Cys2 His2 ZF binds DNA in a peculiar mode and folds in a domain significantly larger than its eukaryotic counterpart consisting of 58 amino acids (the 9-66 region) arranged in a βββαα topology, and stabilized by a conserved, extensive, 15-residue hydrophobic core. The prokaryotic ZF domain, then, shows some intriguing new features that make it interestingly different from its eukaryotic counterpart. This review will focus on the prokaryotic ZFs, summarizing and discussing differences and analogies with the eukaryotic domains and providing important insights into their structure/function relationships.
Collapse
Affiliation(s)
- Gaetano Malgieri
- Department of Environmental, Biological and Pharmaceutical Science and Technology, II University of Naples, Caserta, Italy
| | - Maddalena Palmieri
- Department of Environmental, Biological and Pharmaceutical Science and Technology, II University of Naples, Caserta, Italy
| | - Luigi Russo
- Department of Environmental, Biological and Pharmaceutical Science and Technology, II University of Naples, Caserta, Italy
| | - Roberto Fattorusso
- Department of Environmental, Biological and Pharmaceutical Science and Technology, II University of Naples, Caserta, Italy.,Interuniversity Research Centre on Bioactive Peptides, University of Naples 'Federico II', Naples, Italy
| | - Paolo V Pedone
- Department of Environmental, Biological and Pharmaceutical Science and Technology, II University of Naples, Caserta, Italy.,Interuniversity Research Centre on Bioactive Peptides, University of Naples 'Federico II', Naples, Italy
| | - Carla Isernia
- Department of Environmental, Biological and Pharmaceutical Science and Technology, II University of Naples, Caserta, Italy.,Interuniversity Research Centre on Bioactive Peptides, University of Naples 'Federico II', Naples, Italy
| |
Collapse
|
16
|
Reddi AR, Pawlowska M, Gibney BR. Evaluation of the Intrinsic Zn(II) Affinity of a Cys3His1 Site in the Absence of Protein Folding Effects. Inorg Chem 2015; 54:5942-8. [DOI: 10.1021/acs.inorgchem.5b00718] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Amit R. Reddi
- Department of Chemistry & Biochemistry, Georgia Institute of Technology, 901 Atlantic Drive, Atlanta, Georgia 30332, United States
| | - Malgorzata Pawlowska
- Department of Chemistry, Brooklyn College, 2900 Bedford Avenue, Brooklyn, New York 11210, United States
| | - Brian R. Gibney
- Department of Chemistry, Brooklyn College, 2900 Bedford Avenue, Brooklyn, New York 11210, United States
- Ph.D. Program
in Chemistry, The Graduate Center of the City University of New York, 365 Fifth Avenue, New York, New York 10016, United States
| |
Collapse
|
17
|
Russo L, Palmieri M, Caso JV, D'Abrosca G, Diana D, Malgieri G, Baglivo I, Isernia C, Pedone PV, Fattorusso R. Towards understanding the molecular recognition process in prokaryotic zinc-finger domain. Eur J Med Chem 2014; 91:100-8. [PMID: 25240418 DOI: 10.1016/j.ejmech.2014.09.040] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2014] [Revised: 09/05/2014] [Accepted: 09/11/2014] [Indexed: 10/24/2022]
Abstract
Eukaryotic Cys2His2 zinc finger domain is one of the most common and important structural motifs involved in protein-DNA interaction. The recognition motif is characterized by the tetrahedral coordination of a zinc ion by conserved cysteine and histidine residues. We have characterized the prokaryotic Cys2His2 zinc finger motif, included in the DNA binding region (Ros87) of Ros protein from Agrobacterium tumefaciens, demonstrating that, although possessing a similar zinc coordination sphere, this domain presents significant differences from its eukaryotic counterpart. Furthermore, basic residues flanking the zinc binding region on either side have been demonstrated, by Electrophoretic Mobility Shift Assay (EMSA) experiments, to be essential for Ros DNA binding. In spite of this wealth of knowledge, the structural details of the mechanism through which the prokaryotic zinc fingers recognize their target genes are still unclear. Here, to gain insights into the molecular DNA recognition process of prokaryotic zinc finger domains we applied a strategy in which we performed molecular docking studies using a combination of Nuclear Magnetic Resonance (NMR) and Molecular Dynamics (MD) simulations data. The results demonstrate that the MD ensemble provides a reasonable picture of Ros87 backbone dynamics in solution. The Ros87-DNA model indicates that the interaction involves the first two residue of the first α-helix, and several residues located in the basic regions flanking the zinc finger domain. Interestingly, the prokaryotic zinc finger domain, mainly with the C-terminal tail that is wrapped around the DNA, binds a more extended recognition site than the eukaryotic counterpart. Our analysis demonstrates that the introduction of the protein flexibility in docking studies can improve, in terms of accuracy, the quality of the obtained models and could be particularly useful for protein showing high conformational heterogeneity as well as for computational drug design applications.
Collapse
Affiliation(s)
- Luigi Russo
- Department of Environmental, Biological and Pharmaceutical Sciences and Technology, Via Vivaldi 43, 81100 Caserta, Italy
| | - Maddalena Palmieri
- Department of Environmental, Biological and Pharmaceutical Sciences and Technology, Via Vivaldi 43, 81100 Caserta, Italy
| | - Jolanda Valentina Caso
- Department of Environmental, Biological and Pharmaceutical Sciences and Technology, Via Vivaldi 43, 81100 Caserta, Italy
| | - Gianluca D'Abrosca
- Department of Environmental, Biological and Pharmaceutical Sciences and Technology, Via Vivaldi 43, 81100 Caserta, Italy
| | - Donatella Diana
- Institute of Biostructures and Bioimaging -CNR, Via Mezzocannone 16, 80134 Naples, Italy
| | - Gaetano Malgieri
- Department of Environmental, Biological and Pharmaceutical Sciences and Technology, Via Vivaldi 43, 81100 Caserta, Italy
| | - Ilaria Baglivo
- Department of Environmental, Biological and Pharmaceutical Sciences and Technology, Via Vivaldi 43, 81100 Caserta, Italy
| | - Carla Isernia
- Department of Environmental, Biological and Pharmaceutical Sciences and Technology, Via Vivaldi 43, 81100 Caserta, Italy; Interuniversity Centre for Research on Bioactive Peptides (CIRPEB), University of Naples Federico II, Via Mezzocannone 16, 80134 Naples, Italy
| | - Paolo V Pedone
- Department of Environmental, Biological and Pharmaceutical Sciences and Technology, Via Vivaldi 43, 81100 Caserta, Italy
| | - Roberto Fattorusso
- Department of Environmental, Biological and Pharmaceutical Sciences and Technology, Via Vivaldi 43, 81100 Caserta, Italy; Interuniversity Centre for Research on Bioactive Peptides (CIRPEB), University of Naples Federico II, Via Mezzocannone 16, 80134 Naples, Italy.
| |
Collapse
|
18
|
Chan KL, Bakman I, Marts AR, Batir Y, Dowd TL, Tierney D, Gibney BR. Characterization of the Zn(II) binding properties of the human Wilms' tumor suppressor protein C-terminal zinc finger peptide. Inorg Chem 2014; 53:6309-20. [PMID: 24893204 PMCID: PMC4066921 DOI: 10.1021/ic500862b] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2014] [Indexed: 12/19/2022]
Abstract
Zinc finger proteins that bind Zn(II) using a Cys2His2 coordination motif within a ββα protein fold are the most abundant DNA binding transcription factor domains in eukaryotic systems. These classic zinc fingers are typically unfolded in the apo state and spontaneously fold into their functional ββα folds upon incorporation of Zn(II). These metal-induced protein folding events obscure the free energy cost of protein folding by coupling the protein folding and metal-ion binding thermodynamics. Herein, we determine the formation constant of a Cys2His2/ββα zinc finger domain, the C-terminal finger of the Wilms' tumor suppressor protein (WT1-4), for the purposes of determining its free energy cost of protein folding. Measurements of individual conditional dissociation constants, Kd values, at pH values from 5 to 9 were determined using fluorescence spectroscopy by direct or competition titration. Potentiometric titrations of apo-WT1-4 followed by NMR spectroscopy provided the intrinsic pKa values of the Cys2His2 residues, and corresponding potentiometric titrations of Zn(II)-WT1-4 followed by fluorescence spectroscopy yielded the effective pKa(eff) values of the Cys2His2 ligands bound to Zn(II). The Kd, pKa, and pKa(eff) values were combined in a minimal, complete equilibrium model to yield the pH-independent formation constant value for Zn(II)-WT1-4, Kf(ML) value of 7.5 × 10(12) M(-1), with a limiting Kd value of 133 fM. This shows that Zn(II) binding to the Cys2His2 site in WT1-4 provides at least -17.6 kcal/mol in driving force to fold the protein scaffold. A comparison of the conditional dissociation constants of Zn(II)-WT1-4 to those from the model peptide Zn(II)-GGG-Cys2His2 over the pH range 5.0 to 9.0 and a comparison of their pH-independent Kf(ML) values demonstrates that the free energy cost of protein folding in WT1-4 is less than +2.1 kcal/mol. These results validate our GGG model system for determining the cost of protein folding in natural zinc finger proteins and support the conclusion that the cost of protein folding in most zinc finger proteins is ≤+4.2 kcal/mol, a value that pales in comparison to the free energy contribution of Zn(II) binding, -17.6 kcal/mol.
Collapse
Affiliation(s)
- Ka Lam Chan
- Department of Chemistry, Brooklyn
College, 2900 Bedford
Avenue, Brooklyn, New York 11210, United States
| | - Inna Bakman
- Department of Chemistry, Brooklyn
College, 2900 Bedford
Avenue, Brooklyn, New York 11210, United States
- Ph.D. Program in Biochemistry, The City
University of New York, New York, New York 10016, United States
| | - Amy R. Marts
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio 45056, United States
| | - Yuksel Batir
- Department of Chemistry, Brooklyn
College, 2900 Bedford
Avenue, Brooklyn, New York 11210, United States
| | - Terry L. Dowd
- Department of Chemistry, Brooklyn
College, 2900 Bedford
Avenue, Brooklyn, New York 11210, United States
- Ph.D. Program in Biochemistry, The City
University of New York, New York, New York 10016, United States
| | - David
L. Tierney
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio 45056, United States
| | - Brian R. Gibney
- Department of Chemistry, Brooklyn
College, 2900 Bedford
Avenue, Brooklyn, New York 11210, United States
- Ph.D. Program in Biochemistry, The City
University of New York, New York, New York 10016, United States
| |
Collapse
|