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Francis R, Kalyanaraman R, Boominathan V, Parthasarathy S, Chavaan A, Ansari IA, Ansari SA, Alkahtani HM, Chandran J, Tharumasivam SV. Piperine's potential in treating polycystic ovarian syndrome explored through in-silico docking. Sci Rep 2024; 14:21834. [PMID: 39294254 PMCID: PMC11411113 DOI: 10.1038/s41598-024-72800-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2024] [Accepted: 09/10/2024] [Indexed: 09/20/2024] Open
Abstract
Polycystic Ovarian Syndrome (PCOS) is a multifaceted metabolic and hormonal condition that impacts women in their procreative ages, identified by ovarian dysfunction, hyperandrogenaemia overweight and insulin insensitivity. The piperine, an important alkaloid compound of black pepper has shown promise in modulating various physiological processes. In this work, employed computational docking studies to explore the potential of piperine as a treatment for PCOS. Utilizing computational methods, we analyzed the binding interactions between piperine and key molecular targets implicated in PCOS pathogenesis, including hyperandrogenism, and "oligomenorrhea. The network pharmacology analysis report found 988 PCOS-related genes, 108 hyperandrogenism-related genes, and 377 oligomenorrhea-related genes, and we finally shortlisted 5 common genes in PCOS, hyperandrogenism, and "oligomenorrhea": NR3C1, PPARG, FOS, CYP17A1, and H6PD. Our results reveal favorable binding affinities with PPARG (-8.34 Kcal/mol) and H6PD (-8.70 Kcal/mol) and interaction patterns, suggesting the potential of piperine to modulate these targets. Moreover, the reliability of the piperine-target interactions was revealed by molecular simulations studies. These findings support further experimental investigations to validate the therapeutic efficacy of piperine in PCOS management. The integration of computational approaches with experimental studies has the potential to lay the groundwork for the creation of new therapies specifically targeting PCOS and related endocrine disorders.
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Affiliation(s)
- Rahul Francis
- Department of Biotechnology, Srimad Andavan Arts and Science College (Autonomous), Affiliated to Bharathidasan University, Tiruchirappalli, Tamil Nadu, India
| | - Ramanathan Kalyanaraman
- Department of Biotechnology, Srimad Andavan Arts and Science College (Autonomous), Affiliated to Bharathidasan University, Tiruchirappalli, Tamil Nadu, India
| | - Vasuki Boominathan
- Department of Biotechnology, Srimad Andavan Arts and Science College (Autonomous), Affiliated to Bharathidasan University, Tiruchirappalli, Tamil Nadu, India
| | | | - Ashajyothi Chavaan
- Department of Studies in Biotechnology, Vijayanagar Sri Krishnadevarya University, Ballari, Karnataka, 583-105, India
| | - Irfan Aamer Ansari
- Department of Drug Science and Technology, University of Turin, 10125, Turin, Italy
| | - Siddique Akber Ansari
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, P.O Box 2457, 11451, Riyadh, Saudi Arabia.
| | - Hamad M Alkahtani
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, P.O Box 2457, 11451, Riyadh, Saudi Arabia
| | - Janani Chandran
- Department of Biotechnology, Srimad Andavan Arts and Science College (Autonomous), Affiliated to Bharathidasan University, Tiruchirappalli, Tamil Nadu, India
| | - Siva Vijayakumar Tharumasivam
- Department of Biotechnology, Srimad Andavan Arts and Science College (Autonomous), Affiliated to Bharathidasan University, Tiruchirappalli, Tamil Nadu, India.
- Department of Biotechnology Engineering, School of Engineering and Technology, Dhanalakshmi Srinivasan University, Samayapuram, Trichy, Tamil Nadu, India.
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2
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Freda I, Exertier C, Barile A, Chaves-Sanjuan A, Vega M, Isupov M, Harmer N, Gugole E, Swuec P, Bolognesi M, Scipioni A, Savino C, Di Salvo M, Contestabile R, Vallone B, Tramonti A, Montemiglio L. Structural insights into the DNA recognition mechanism by the bacterial transcription factor PdxR. Nucleic Acids Res 2023; 51:8237-8254. [PMID: 37378428 PMCID: PMC10450172 DOI: 10.1093/nar/gkad552] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 06/08/2023] [Accepted: 06/22/2023] [Indexed: 06/29/2023] Open
Abstract
Specificity in protein-DNA recognition arises from the synergy of several factors that stem from the structural and chemical signatures encoded within the targeted DNA molecule. Here, we deciphered the nature of the interactions driving DNA recognition and binding by the bacterial transcription factor PdxR, a member of the MocR family responsible for the regulation of pyridoxal 5'-phosphate (PLP) biosynthesis. Single particle cryo-EM performed on the PLP-PdxR bound to its target DNA enabled the isolation of three conformers of the complex, which may be considered as snapshots of the binding process. Moreover, the resolution of an apo-PdxR crystallographic structure provided a detailed description of the transition of the effector domain to the holo-PdxR form triggered by the binding of the PLP effector molecule. Binding analyses of mutated DNA sequences using both wild type and PdxR variants revealed a central role of electrostatic interactions and of the intrinsic asymmetric bending of the DNA in allosterically guiding the holo-PdxR-DNA recognition process, from the first encounter through the fully bound state. Our results detail the structure and dynamics of the PdxR-DNA complex, clarifying the mechanism governing the DNA-binding mode of the holo-PdxR and the regulation features of the MocR family of transcription factors.
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Affiliation(s)
- Ida Freda
- Department of Biochemical Sciences “A. Rossi Fanelli”, Sapienza, University of Rome, Rome 00185, Italy
| | - Cécile Exertier
- Institute of Molecular Biology and Pathology, National Research Council, Rome 00185, Italy
| | - Anna Barile
- Institute of Molecular Biology and Pathology, National Research Council, Rome 00185, Italy
| | - Antonio Chaves-Sanjuan
- Department of Biosciences, Pediatric Clinical Research Center Romeo ed Enrica Invernizzi and NOLIMITS, University of Milano, Milano 20133, Italy
| | - Mirella Vivoli Vega
- School of Biochemistry, University of Bristol, University Walk, BS8 1TD Bristol, UK
| | - Michail N Isupov
- Geoffrey Pope Building, University of Exeter, Stocker Road, Exeter EX4 4QD, UK
| | - Nicholas J Harmer
- Living Systems Institute, University of Exeter, Stocker Road, Exeter EX4 4QD, UK
| | - Elena Gugole
- Institute of Molecular Biology and Pathology, National Research Council, Rome 00185, Italy
| | - Paolo Swuec
- Cryo-Electron Microscopy Core Facility, Human Technopole, Milano 20157, Italy
| | - Martino Bolognesi
- Department of Biosciences, Pediatric Clinical Research Center Romeo ed Enrica Invernizzi and NOLIMITS, University of Milano, Milano 20133, Italy
| | - Anita Scipioni
- Department of Chemistry, Sapienza, University of Rome, Rome 00185, Italy
| | - Carmelinda Savino
- Institute of Molecular Biology and Pathology, National Research Council, Rome 00185, Italy
| | - Martino Luigi Di Salvo
- Department of Biochemical Sciences “A. Rossi Fanelli”, Sapienza, University of Rome, Rome 00185, Italy
| | - Roberto Contestabile
- Department of Biochemical Sciences “A. Rossi Fanelli”, Sapienza, University of Rome, Rome 00185, Italy
- Istituto Pasteur-Fondazione Cenci Bolognetti, Sapienza, University of Rome, Rome 00185, Italy
| | - Beatrice Vallone
- Department of Biochemical Sciences “A. Rossi Fanelli”, Sapienza, University of Rome, Rome 00185, Italy
- Institute of Molecular Biology and Pathology, National Research Council, Rome 00185, Italy
| | - Angela Tramonti
- Institute of Molecular Biology and Pathology, National Research Council, Rome 00185, Italy
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3
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Roy S, Booth CE, Powell-Pierce AD, Schulz AM, Skare JT, Garcia BL. Conformational dynamics of complement protease C1r inhibitor proteins from Lyme disease- and relapsing fever-causing spirochetes. J Biol Chem 2023; 299:104972. [PMID: 37380082 PMCID: PMC10413161 DOI: 10.1016/j.jbc.2023.104972] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 06/16/2023] [Accepted: 06/19/2023] [Indexed: 06/30/2023] Open
Abstract
Borrelial pathogens are vector-borne etiological agents known to cause Lyme disease, relapsing fever, and Borrelia miyamotoi disease. These spirochetes each encode several surface-localized lipoproteins that bind components of the human complement system to evade host immunity. One borrelial lipoprotein, BBK32, protects the Lyme disease spirochete from complement-mediated attack via an alpha helical C-terminal domain that interacts directly with the initiating protease of the classical complement pathway, C1r. In addition, the B. miyamotoi BBK32 orthologs FbpA and FbpB also inhibit C1r, albeit via distinct recognition mechanisms. The C1r-inhibitory activities of a third ortholog termed FbpC, which is found exclusively in relapsing fever-causing spirochetes, remains unknown. Here, we report the crystal structure of the C-terminal domain of Borrelia hermsii FbpC to a limiting resolution of 1.5 Å. We used surface plasmon resonance and assays of complement function to demonstrate that FbpC retains potent BBK32-like anticomplement activities. Based on the structure of FbpC, we hypothesized that conformational dynamics of the complement inhibitory domains of borrelial C1r inhibitors may differ. To test this, we utilized the crystal structures of the C-terminal domains of BBK32, FbpA, FbpB, and FbpC to carry out molecular dynamics simulations, which revealed borrelial C1r inhibitors adopt energetically favored open and closed states defined by two functionally critical regions. Taken together, these results advance our understanding of how protein dynamics contribute to the function of bacterial immune evasion proteins and reveal a surprising plasticity in the structures of borrelial C1r inhibitors.
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Affiliation(s)
- Sourav Roy
- Department of Microbiology and Immunology, Brody School of Medicine, East Carolina University, Greenville, North Carolina, USA
| | - Charles E Booth
- Department of Microbiology and Immunology, Brody School of Medicine, East Carolina University, Greenville, North Carolina, USA
| | - Alexandra D Powell-Pierce
- Department of Microbial Pathogenesis and Immunology, School of Medicine, Texas A&M University, Bryan, Texas, USA
| | - Anna M Schulz
- Department of Microbiology and Immunology, Brody School of Medicine, East Carolina University, Greenville, North Carolina, USA
| | - Jon T Skare
- Department of Microbial Pathogenesis and Immunology, School of Medicine, Texas A&M University, Bryan, Texas, USA.
| | - Brandon L Garcia
- Department of Microbiology and Immunology, Brody School of Medicine, East Carolina University, Greenville, North Carolina, USA.
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4
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Roy S, Booth CE, Powell-Pierce AD, Schulz AM, Skare JT, Garcia BL. "Conformational dynamics of C1r inhibitor proteins from Lyme disease and relapsing fever spirochetes". BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.01.530473. [PMID: 36909632 PMCID: PMC10002728 DOI: 10.1101/2023.03.01.530473] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/06/2023]
Abstract
Borrelial pathogens are vector-borne etiological agents of Lyme disease, relapsing fever, and Borrelia miyamotoi disease. These spirochetes each encode several surface-localized lipoproteins that bind to components of the human complement system. BBK32 is an example of a borrelial lipoprotein that protects the Lyme disease spirochete from complement-mediated attack. The complement inhibitory activity of BBK32 arises from an alpha helical C-terminal domain that interacts directly with the initiating protease of the classical pathway, C1r. Borrelia miyamotoi spirochetes encode BBK32 orthologs termed FbpA and FbpB, and these proteins also inhibit C1r, albeit via distinct recognition mechanisms. The C1r-inhibitory activities of a third ortholog termed FbpC, which is found exclusively in relapsing fever spirochetes, remains unknown. Here we report the crystal structure of the C-terminal domain of B. hermsii FbpC to a limiting resolution of 1.5 Å. Surface plasmon resonance studies and assays of complement function demonstrate that FbpC retains potent BBK32-like anti-complement activities. Based on the structure of FbpC, we hypothesized that conformational dynamics of the complement inhibitory domains of borrelial C1r inhibitors may differ. To test this, we utilized the crystal structures of the C-terminal domains of BBK32, FbpA, FbpB, and FbpC to carry out 1 µs molecular dynamics simulations, which revealed borrelial C1r inhibitors adopt energetically favored open and closed states defined by two functionally critical regions. This study advances our understanding of how protein dynamics contribute to the function of bacterial immune evasion proteins and reveals a surprising plasticity in the structures of borrelial C1r inhibitors.
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Affiliation(s)
- Sourav Roy
- Department of Microbiology and Immunology, Brody School of Medicine, East Carolina University, Greenville, North Carolina, United States of America
| | - Charles E. Booth
- Department of Microbiology and Immunology, Brody School of Medicine, East Carolina University, Greenville, North Carolina, United States of America
| | - Alexandra D. Powell-Pierce
- Department of Microbial Pathogenesis and Immunology, College of Medicine, Texas A&M University, Bryan, TX, United States of America
| | - Anna M. Schulz
- Department of Microbiology and Immunology, Brody School of Medicine, East Carolina University, Greenville, North Carolina, United States of America
| | - Jon T. Skare
- Department of Microbial Pathogenesis and Immunology, College of Medicine, Texas A&M University, Bryan, TX, United States of America
| | - Brandon L. Garcia
- Department of Microbiology and Immunology, Brody School of Medicine, East Carolina University, Greenville, North Carolina, United States of America
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5
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Molecular Cloning, Purification and Characterization of Mce1R of Mycobacterium tuberculosis. Mol Biotechnol 2021; 63:200-220. [PMID: 33423211 DOI: 10.1007/s12033-020-00293-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/18/2020] [Indexed: 10/22/2022]
Abstract
The mce1 operon of Mycobacterium tuberculosis, important for lipid metabolism/transport, host cell invasion, modulation of host immune response and pathogenicity, is under the transcriptional control of Mce1R. Hence characterizing Mce1R is an important step for novel anti-tuberculosis drug discovery. The present study reports functional and in silico characterization of Mce1R. In this work, we have computationally modeled the structure of Mce1R and have validated the structure by computational and experimental methods. Mce1R has been shown to harbor the canonical VanR-like structure with a flexible N-terminal 'arm', carrying conserved positively charged residues, most likely involved in the operator DNA binding. The mce1R gene has been cloned, expressed, purified and its DNA-binding activity has been measured in vitro. The Kd value for Mce1R-operator DNA interaction has been determined to be 0.35 ± 0.02 µM which implies that Mce1R binds to DNA with moderate affinity compared to the other FCD family of regulators. So far, this is the first report for measuring the DNA-binding affinity of any VanR-type protein. Despite significant sequence similarity at the N-terminal domain, the wHTH motif of Mce1R exhibits poor conservancy of amino acid residues, critical for DNA-binding, thus results in moderate DNA-binding affinity. The N-terminal DNA-binding domain is structurally dynamic while the C-terminal domain showed significant stability and such profile of structural dynamics is most likely to be preserved in the structural orthologs of Mce1R. In addition to this, a cavity has been detected in the C-terminal domain of Mce1R which contains a few conserved residues. Comparison with other FCD family of regulators suggests that most of the conserved residues might be critical for binding to specific ligand. The max pKd value and drug score for the cavity are estimated to be 9.04 and 109 respectively suggesting that the cavity represents a suitable target site for novel anti-tuberculosis drug discovery approaches.
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6
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Frezzini M, Narzi D, Sciolari AM, Guidoni L, Pascarella S. Molecular dynamics of an asymmetric form of GabR, a bacterial transcriptional regulator. Biophys Chem 2020; 262:106380. [PMID: 32413777 DOI: 10.1016/j.bpc.2020.106380] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Revised: 04/14/2020] [Accepted: 04/15/2020] [Indexed: 01/20/2023]
Abstract
GabR is a bacterial transcription regulator with a dimeric structure in which each subunit includes a wHTH (winged Helix-Turn-Helix) domain connected through a peptide linker to a large C-terminal domain folded as the enzyme aspartate aminotransferase (AAT). In Bacillus subtilis, GabR activates the genes involved in the metabolism of γ-amino butyric acid (GABA) upon formation of a PLP-GABA adduct. Recently, the crystallographic structure of an asymmetric form of GabR has been solved. This form (semi-holo) has one active site binding PLP as internal aldimine and the other the PLP-GABA complex. This work reports a molecular dynamics (MD) study aimed at understanding the characteristics of the asymmetric GabR form and compare them to the dynamics properties of previously studied symmetric holo (internal PLP aldimine at both active sites) and holo-GABA (containing PLP-GABA adducts) GabRs. Standard molecular dynamics and data analysis techniques have been used. The results indicate a remarkable asymmetry in the mobility and interactions of the different structural portions of the semi-holo GabR and of a few residues at the active site. The pattern is different from that observed in the other symmetrical GabR forms. The asymmetric perturbation of the active site residues may suggest the existence of a form of allosteric interference between the two active sites.
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Affiliation(s)
- Mario Frezzini
- Department of Information Engineering, Computer Science and Mathematics, University of L'Aquila, 67100 L'Aquila, Italy.
| | - Daniele Narzi
- Department of Physics and Chemistry Sciences, University of L'Aquila, 67100 L'Aquila, Italy.
| | | | - Leonardo Guidoni
- Department of Physics and Chemistry Sciences, University of L'Aquila, 67100 L'Aquila, Italy.
| | - Stefano Pascarella
- Department of Biochemical Sciences "A. Rossi Fanelli", Sapienza University of Rome, 00185 Rome, Italy.
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7
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Nardella C, Barile A, di Salvo ML, Milano T, Pascarella S, Tramonti A, Contestabile R. Interaction of Bacillus subtilis GabR with the gabTD promoter: role of repeated sequences and effect of GABA in transcriptional activation. FEBS J 2020; 287:4952-4970. [PMID: 32147931 DOI: 10.1111/febs.15286] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Revised: 02/20/2020] [Accepted: 03/06/2020] [Indexed: 12/15/2022]
Abstract
Bacillus subtilis is able to use γ-aminobutyric acid (GABA) found in the soil as carbon and nitrogen source, through the action of GABA aminotransferase (GabT) and succinic semialdehyde dehydrogenase (GabD). GABA acts as molecular effector in the transcriptional activation of the gabTD operon by GabR. GabR is the most studied member of the MocR family of prokaryotic pyridoxal 5'-phosphate (PLP)-dependent transcriptional regulators, yet crucial aspects of its mechanism of action are unknown. GabR binds to the gabTD promoter, but transcription is activated only when GABA is present. Here, we demonstrated, in contrast with what had been previously proposed, that three repeated nucleotide sequences in the promoter region, two direct repeats and one inverted repeat, are specifically recognized by GabR. We carried out in vitro and in vivo experiments using mutant forms of the gabTD promoter. Our results showed that GABA activates transcription by changing the modality of interaction between GabR and the recognized sequence repeats. A hypothetical model is proposed in which GabR exists in two alternative conformations that, respectively, prevent or promote transcription. According to this model, in the absence of GABA, GabR binds to DNA interacting with all three sequence repeats, overlapping the RNA polymerase binding site and therefore preventing transcription activation. On the other hand, when GABA binds to GabR, a conformational change of the protein leads to the release of the interaction with the inverted repeat, allowing transcription initiation by RNA polymerase.
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Affiliation(s)
- Caterina Nardella
- Istituto Pasteur Italia-Fondazione Cenci Bolognetti, Dipartimento di Scienze Biochimiche 'A. Rossi Fanelli', Sapienza Università di Roma, Italy
| | - Anna Barile
- Istituto Pasteur Italia-Fondazione Cenci Bolognetti, Dipartimento di Scienze Biochimiche 'A. Rossi Fanelli', Sapienza Università di Roma, Italy.,Istituto di Biologia e Patologia Molecolari, Consiglio Nazionale delle Ricerche, Roma, Italy
| | - Martino L di Salvo
- Istituto Pasteur Italia-Fondazione Cenci Bolognetti, Dipartimento di Scienze Biochimiche 'A. Rossi Fanelli', Sapienza Università di Roma, Italy
| | - Teresa Milano
- Istituto Pasteur Italia-Fondazione Cenci Bolognetti, Dipartimento di Scienze Biochimiche 'A. Rossi Fanelli', Sapienza Università di Roma, Italy
| | - Stefano Pascarella
- Istituto Pasteur Italia-Fondazione Cenci Bolognetti, Dipartimento di Scienze Biochimiche 'A. Rossi Fanelli', Sapienza Università di Roma, Italy
| | - Angela Tramonti
- Istituto Pasteur Italia-Fondazione Cenci Bolognetti, Dipartimento di Scienze Biochimiche 'A. Rossi Fanelli', Sapienza Università di Roma, Italy.,Istituto di Biologia e Patologia Molecolari, Consiglio Nazionale delle Ricerche, Roma, Italy
| | - Roberto Contestabile
- Istituto Pasteur Italia-Fondazione Cenci Bolognetti, Dipartimento di Scienze Biochimiche 'A. Rossi Fanelli', Sapienza Università di Roma, Italy
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8
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Frezzini M, Guidoni L, Pascarella S. Conformational transitions induced by γ-amino butyrate binding in GabR, a bacterial transcriptional regulator. Sci Rep 2019; 9:19319. [PMID: 31848410 PMCID: PMC6917764 DOI: 10.1038/s41598-019-55581-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2019] [Accepted: 11/20/2019] [Indexed: 11/09/2022] Open
Abstract
GabR from Bacillus subtilis is a transcriptional regulator of the MocR subfamily of GntR regulators. The MocR architecture is characterized by the presence of an N-terminal winged-Helix-Turn-Helix domain and a C-terminal domain folded as the pyridoxal 5′-phosphate (PLP) dependent aspartate aminotransferase (AAT). The two domains are linked by a peptide bridge. GabR activates transcription of genes involved in γ-amino butyrate (GABA) degradation upon binding of PLP and GABA. This work is aimed at contributing to the understanding of the molecular mechanism underlying the GabR transcription activation upon GABA binding. To this purpose, the structure of the entire GabR dimer with GABA external aldimine (holo-GABA) has been reconstructed using available crystallographic data. The structure of the apo (without any ligand) and holo (with PLP) GabR forms have been derived from the holo-GABA. An extensive 1 μs comparative molecular dynamics (MD) has been applied to the three forms. Results showed that the presence of GABA external aldimine stiffens the GabR, stabilizes the AAT domain in the closed form and couples the AAT and HTH domains dynamics. Apo and holo GabR appear more flexible especially at the level of the HTH and linker portions and small AAT subdomain.
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Affiliation(s)
- Mario Frezzini
- Department of Information Engineering, Computer Science and Mathematics, University of L'Aquila, 67100, L'Aquila, Italy
| | - Leonardo Guidoni
- Department of Physics and Chemistry Sciences, University of L'Aquila, 67100, L'Aquila, Italy
| | - Stefano Pascarella
- Department of Biochemical Sciences "A Rossi Fanelli", Sapienza, University of Rome, 00185, Rome, Italy.
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9
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Richts B, Rosenberg J, Commichau FM. A Survey of Pyridoxal 5'-Phosphate-Dependent Proteins in the Gram-Positive Model Bacterium Bacillus subtilis. Front Mol Biosci 2019; 6:32. [PMID: 31134210 PMCID: PMC6522883 DOI: 10.3389/fmolb.2019.00032] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Accepted: 04/18/2019] [Indexed: 11/13/2022] Open
Abstract
The B6 vitamer pyridoxal 5′-phosphate (PLP) is a co-factor for proteins and enzymes that are involved in diverse cellular processes. Therefore, PLP is essential for organisms from all kingdoms of life. Here we provide an overview about the PLP-dependent proteins from the Gram-positive soil bacterium Bacillus subtilis. Since B. subtilis serves as a model system in basic research and as a production host in industry, knowledge about the PLP-dependent proteins could facilitate engineering the bacteria for biotechnological applications. The survey revealed that the majority of the PLP-dependent proteins are involved in metabolic pathways like amino acid biosynthesis and degradation, biosynthesis of antibacterial compounds, utilization of nucleotides as well as in iron and carbon metabolism. Many PLP-dependent proteins participate in de novo synthesis of the co-factors biotin, folate, heme, and NAD+ as well as in cell wall metabolism, tRNA modification, regulation of gene expression, sporulation, and biofilm formation. A surprisingly large group of PLP-dependent proteins (29%) belong to the group of poorly characterized proteins. This review underpins the need to characterize the PLP-dependent proteins of unknown function to fully understand the “PLP-ome” of B. subtilis.
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Affiliation(s)
- Björn Richts
- Department of General Microbiology, University of Goettingen, Göttingen, Germany
| | - Jonathan Rosenberg
- Department of General Microbiology, University of Goettingen, Göttingen, Germany
| | - Fabian M Commichau
- Department of General Microbiology, University of Goettingen, Göttingen, Germany
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10
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Pascarella S. Computational classification of MocR transcriptional regulators into subgroups as a support for experimental and functional characterization. Bioinformation 2019; 15:151-159. [PMID: 31435161 PMCID: PMC6677901 DOI: 10.6026/97320630015151] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Accepted: 02/03/2019] [Indexed: 11/23/2022] Open
Abstract
MocR bacterial transcriptional regulators are a subfamily within the GntR family. The MocR proteins possess an N-terminal domain containing the winged Helix-Turn-Helix (wHTH) motif and a C-terminal domain whose architecture is homologous to the fold type-I pyridoxal 5'-phosphate (PLP) dependent enzymes and whose archetypical protein is aspartate aminotransferase (AAT). The ancestor of the fold type-I PLP dependent super-family is considered one of the earliest enzymes. The members of this super-family are the product of evolution which resulted in a diversified protein population able to catalyze a set of reactions on substrates often containing amino groups. The MocR regulators are activators or repressors of gene control within many metabolic pathways often involving PLP enzymes. This diversity implies that MocR specifically responds to different classes of effector molecules. Therefore, it is of interest to compare the AAT domains of MocR from six bacteria phyla. Multi dimensional scaling and cluster analyses suggested that at least three subgroups exist within the population that reflects functional specialization rather than taxonomic origin. The AAT-domains of the three clusters display variable degree of similarity to different fold type-I PLP enzyme families. The results support the hypothesis that independent fusion events generated at least three different MocR subgroups.
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Affiliation(s)
- Stefano Pascarella
- Structural bioinformatics and Molecular modelling Lab;Dipartimento di Scienze biochimiche;Sapienza Universita di Roma;00185 Roma,Italy
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11
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Tramonti A, Nardella C, di Salvo ML, Pascarella S, Contestabile R. The MocR-like transcription factors: pyridoxal 5'-phosphate-dependent regulators of bacterial metabolism. FEBS J 2018; 285:3925-3944. [PMID: 29974999 DOI: 10.1111/febs.14599] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Revised: 06/14/2018] [Accepted: 06/25/2018] [Indexed: 12/22/2022]
Abstract
Many biological functions played by current proteins were not created by evolution from scratch, rather they were obtained combining already available protein scaffolds. This is the case of MocR-like bacterial transcription factors (MocR-TFs), a subclass of GntR transcription regulators, whose structure is the outcome of the fusion between DNA-binding proteins and pyridoxal 5'-phosphate (PLP)-dependent enzymes. The resultant chimeras can count on the properties of both protein classes, i.e. the capability to recognize specific DNA sequences and to bind PLP and amino-compounds; it is the modulation of such binding properties to confer to MocR-TFs chimeras the ability to interact with effector molecules and DNA so as to regulate transcription. MocR-TFs control different metabolic processes involving vitamin B6 and amino acids, which are canonical ligands of PLP-dependent enzymes. However, MocR-TFs are also implicated in the metabolism of compounds that are not substrates of PLP-dependent enzymes, such as rhizopine and ectoine. Genomic analyses show that MocR-TFs are widespread among eubacteria, implying an essential role in their metabolism and highlighting the scarcity of our knowledge on these important players in microbial metabolism. Although MocR-TFs have been discovered 15 years ago, the research activity on these transcriptional regulators has only recently intensified, producing a wealth of information that needs to be brought back to general principles. This is the main task of this review, which reports and analyses the available information concerning MocR-TFs functional role, structural features, interaction with effector molecules and the characteristics of DNA transcriptional factor-binding sites of MocR-based regulatory systems.
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Affiliation(s)
- Angela Tramonti
- Istituto di Biologia e Patologia Molecolari, Consiglio Nazionale delle Ricerche, Roma, Italy.,Dipartimento di Scienze Biochimiche "A. Rossi Fanelli", Istituto Pasteur Italia-Fondazione Cenci Bolognetti, Sapienza Università di Roma, Italy
| | - Caterina Nardella
- Dipartimento di Scienze Biochimiche "A. Rossi Fanelli", Istituto Pasteur Italia-Fondazione Cenci Bolognetti, Sapienza Università di Roma, Italy
| | - Martino L di Salvo
- Dipartimento di Scienze Biochimiche "A. Rossi Fanelli", Istituto Pasteur Italia-Fondazione Cenci Bolognetti, Sapienza Università di Roma, Italy
| | - Stefano Pascarella
- Dipartimento di Scienze Biochimiche "A. Rossi Fanelli", Istituto Pasteur Italia-Fondazione Cenci Bolognetti, Sapienza Università di Roma, Italy
| | - Roberto Contestabile
- Dipartimento di Scienze Biochimiche "A. Rossi Fanelli", Istituto Pasteur Italia-Fondazione Cenci Bolognetti, Sapienza Università di Roma, Italy
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