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The Facts and Family Secrets of Plasmids That Replicate via the Rolling-Circle Mechanism. Microbiol Mol Biol Rev 2021; 86:e0022220. [PMID: 34878299 DOI: 10.1128/mmbr.00222-20] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Plasmids are self-replicative DNA elements that are transferred between bacteria. Plasmids encode not only antibiotic resistance genes but also adaptive genes that allow their hosts to colonize new niches. Plasmid transfer is achieved by conjugation (or mobilization), phage-mediated transduction, and natural transformation. Thousands of plasmids use the rolling-circle mechanism for their propagation (RCR plasmids). They are ubiquitous, have a high copy number, exhibit a broad host range, and often can be mobilized among bacterial species. Based upon the replicon, RCR plasmids have been grouped into several families, the best known of them being pC194 and pUB110 (Rep_1 family), pMV158 and pE194 (Rep_2 family), and pT181 and pC221 (Rep_trans family). Genetic traits of RCR plasmids are analyzed concerning (i) replication mediated by a DNA-relaxing initiator protein and its interactions with the cognate DNA origin, (ii) lagging-strand origins of replication, (iii) antibiotic resistance genes, (iv) mobilization functions, (v) replication control, performed by proteins and/or antisense RNAs, and (vi) the participating host-encoded functions. The mobilization functions include a relaxase initiator of transfer (Mob), an origin of transfer, and one or two small auxiliary proteins. There is a family of relaxases, the MOBV family represented by plasmid pMV158, which has been revisited and updated. Family secrets, like a putative open reading frame of unknown function, are reported. We conclude that basic research on RCR plasmids is of importance, and our perspectives contemplate the concept of One Earth because we should incorporate bacteria into our daily life by diminishing their virulence and, at the same time, respecting their genetic diversity.
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Stefanucci A, Amato J, Brancaccio D, Pagano B, Randazzo A, Santoro F, Mayol L, Learte-Aymamí S, Rodriguez J, Mascareñas JL, Novellino E, Carotenuto A, Mollica A. A novel β-hairpin peptide derived from the ARC repressor selectively interacts with the major groove of B-DNA. Bioorg Chem 2021; 112:104836. [PMID: 33812270 DOI: 10.1016/j.bioorg.2021.104836] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Revised: 02/04/2021] [Accepted: 03/17/2021] [Indexed: 12/22/2022]
Abstract
Transcription factors (TFs) have a remarkable role in the homeostasis of the organisms and there is a growing interest in how they recognize and interact with specific DNA sequences. TFs recognize DNA using a variety of structural motifs. Among those, the ribbon-helix-helix (RHH) proteins, exemplified by the MetJ and ARC repressors, form dimers that insert antiparallel β-sheets into the major groove of DNA. A great chemical challenge consists of using the principles of DNA recognition by TFs to design minimized peptides that maintain the DNA affinity and specificity characteristics of the natural counterparts. In this context, a peptide mimic of an antiparallel β-sheet is very attractive since it can be obtained by a single peptide chain folding in a β-hairpin structure and can be as short as 14 amino acids or less. Herein, we designed eight linear and two cyclic dodeca-peptides endowed with β-hairpins. Their DNA binding properties have been investigated using fluorescence spectroscopy together with the conformational analysis through circular dichroism and solution NMR. We found that one of our peptides, peptide 6, is able to bind DNA, albeit without sequence selectivity. Notably, it shows a topological selectivity for the major groove of the DNA which is the interaction site of ARC and many other DNA-binding proteins. Moreover, we found that a type I' β-hairpin folding pattern is a favorite peptide structure for interaction with the B-DNA major groove. Peptide 6 is a valuable lead compound for the development of novel analogs with sequence selectivity.
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Affiliation(s)
- Azzurra Stefanucci
- Department of Pharmacy, University of Chieti-Pescara "G. d'Annunzio", Via dei Vestini 31, 66100 Chieti, Italy
| | - Jussara Amato
- Department of Pharmacy, University of Naples "Federico II", Via D. Montesano 49, 80131 Naples, Italy
| | - Diego Brancaccio
- Department of Pharmacy, University of Naples "Federico II", Via D. Montesano 49, 80131 Naples, Italy
| | - Bruno Pagano
- Department of Pharmacy, University of Naples "Federico II", Via D. Montesano 49, 80131 Naples, Italy
| | - Antonio Randazzo
- Department of Pharmacy, University of Naples "Federico II", Via D. Montesano 49, 80131 Naples, Italy
| | - Federica Santoro
- Department of Pharmacy, University of Naples "Federico II", Via D. Montesano 49, 80131 Naples, Italy
| | - Laura Mayol
- Department of Pharmacy, University of Naples "Federico II", Via D. Montesano 49, 80131 Naples, Italy
| | - Soraya Learte-Aymamí
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS), and Departamento de Química Orgánica. Universidade de Santiago de Compostela, 15782 Santiago de Compostela, Spain
| | - Jessica Rodriguez
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS), and Departamento de Química Orgánica. Universidade de Santiago de Compostela, 15782 Santiago de Compostela, Spain
| | - José Luis Mascareñas
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS), and Departamento de Química Orgánica. Universidade de Santiago de Compostela, 15782 Santiago de Compostela, Spain
| | - Ettore Novellino
- Department of Pharmacy, University of Naples "Federico II", Via D. Montesano 49, 80131 Naples, Italy
| | - Alfonso Carotenuto
- Department of Pharmacy, University of Naples "Federico II", Via D. Montesano 49, 80131 Naples, Italy.
| | - Adriano Mollica
- Department of Pharmacy, University of Chieti-Pescara "G. d'Annunzio", Via dei Vestini 31, 66100 Chieti, Italy.
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Dina NE, Muntean CM, Leopold N, Fălămaș A, Halmagyi A, Coste A. Structural Changes Induced in Grapevine (Vitis vinifera L.) DNA by Femtosecond IR Laser Pulses: A Surface-Enhanced Raman Spectroscopic Study. NANOMATERIALS 2016; 6:nano6060096. [PMID: 28335224 PMCID: PMC5302626 DOI: 10.3390/nano6060096] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/23/2016] [Revised: 04/25/2016] [Accepted: 05/17/2016] [Indexed: 11/25/2022]
Abstract
In this work, surface-enhanced Raman spectra of ten genomic DNAs extracted from leaf tissues of different grapevine (Vitis vinifera L.) varieties, respectively, are analyzed in the wavenumber range 300–1800 cm−1. Furthermore, structural changes induced in grapevine genomic nucleic acids upon femtosecond (170 fs) infrared (IR) laser pulse irradiation (λ = 1100 nm) are discussed in detail for seven genomic DNAs, respectively. Surface-enhanced Raman spectroscopy (SERS) signatures, vibrational band assignments and structural characterization of genomic DNAs are reported for each case. As a general observation, the wavenumber range between 1500 and 1660 cm−1 of the spectra seems to be modified upon laser treatment. This finding could reflect changes in the base-stacking interactions in DNA. Spectral shifts are mainly attributed to purines (dA, dG) and deoxyribose. Pyrimidine residues seem to be less affected by IR femtosecond laser pulse irradiation. Furthermore, changes in the conformational properties of nucleic acid segments are observed after laser treatment. We have found that DNA isolated from Feteasca Neagra grapevine leaf tissues is the most structurally-responsive system to the femtosecond IR laser irradiation process. In addition, using unbiased computational resources by means of principal component analysis (PCA), eight different grapevine varieties were discriminated.
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Affiliation(s)
- Nicoleta E Dina
- National Institute for Research & Development of Isotopic and Molecular Technologies, Donat 67-103, 400293 Cluj-Napoca, Romania.
| | - Cristina M Muntean
- National Institute for Research & Development of Isotopic and Molecular Technologies, Donat 67-103, 400293 Cluj-Napoca, Romania.
| | - Nicolae Leopold
- Babeş-Bolyai University, Faculty of Physics, Kogălniceanu 1, 400084 Cluj-Napoca, Romania.
| | - Alexandra Fălămaș
- National Institute for Research & Development of Isotopic and Molecular Technologies, Donat 67-103, 400293 Cluj-Napoca, Romania.
| | - Adela Halmagyi
- National Institute of Research and Development for Biological Sciences, branch Institute of Biological Research, Republicii Street 48, 400015 Cluj-Napoca, Romania.
| | - Ana Coste
- National Institute of Research and Development for Biological Sciences, branch Institute of Biological Research, Republicii Street 48, 400015 Cluj-Napoca, Romania.
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Stefanucci A, Mosquera J, Vázquez E, Mascareñas JL, Novellino E, Mollica A. Synthesis, Characterization, and DNA Binding Profile of a Macrocyclic β-Sheet Analogue of ARC Protein. ACS Med Chem Lett 2015; 6:1220-4. [PMID: 26713108 DOI: 10.1021/acsmedchemlett.5b00363] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2015] [Accepted: 10/29/2015] [Indexed: 12/29/2022] Open
Abstract
ARC repressor (apoptosis repressor with caspase recruitment domain) is a protein which binds selectively to a specific sequence of DNA. In humans, ARC is primarily expressed in striated muscle tissue, which normally does not undergo rapid cell turnover. This suggests that ARC may play a protective role in the prevention against Duchenne Muscular Dystrophy and several types of tumors. In this Letter we report the synthesis, characterization, and conformational analysis of a β-sheet ARC repressor mimetic, based on the amino acid sequence of the β-sheet domain in the ARC protein. The ability of this β-sheet macrocycle to bind to double-stranded DNA was also evaluated using spectroscopic methods. Our data show that the synthetic peptide has a defined conformation and is able to bind DNA with reasonable affinity. These initial results lay the groundwork for the design of novel β-sheets folded peptides as valuable substitutes of transcription factor proteins in drug therapy.
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Affiliation(s)
- Azzurra Stefanucci
- Dipartimento
di Chimica, Sapienza, Università di Roma, P.le A. Moro
5, 00187 Rome, Italy
| | - Jesús Mosquera
- Centro
Singular de Investigación en Química Biolóxica
e Materiais Moleculares (CIQUS), Departamento de Química Orgánica, Universidade de Santiago de Compostela, 15782 Santiago
de Compostela, Spain
| | - Eugènio Vázquez
- Centro
Singular de Investigación en Química Biolóxica
e Materiais Moleculares (CIQUS), Departamento de Química Orgánica, Universidade de Santiago de Compostela, 15782 Santiago
de Compostela, Spain
| | - José L. Mascareñas
- Centro
Singular de Investigación en Química Biolóxica
e Materiais Moleculares (CIQUS), Departamento de Química Orgánica, Universidade de Santiago de Compostela, 15782 Santiago
de Compostela, Spain
| | - Ettore Novellino
- Dipartimento
di Farmacia, Università di Napoli “Federico II”, Via D. Montesano, 49, 80131 Naples, Italy
| | - Adriano Mollica
- Dipartimento
di Farmacia, Università di Chieti-Pescara “G. d’Annunzio”, Via dei Vestini 31, 66100 Chieti, Italy
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Muntean CM, Leopold N, Tripon C, Coste A, Halmagyi A. Surface-enhanced Raman spectroscopy of genomic DNA from in vitro grown tomato (Lycopersicon esculentum Mill.) cultivars before and after plant cryopreservation. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2015; 144:107-114. [PMID: 25748988 DOI: 10.1016/j.saa.2015.02.085] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2014] [Revised: 12/18/2014] [Accepted: 02/19/2015] [Indexed: 06/04/2023]
Abstract
In this work the surface-enhanced Raman scattering (SERS) spectra of five genomic DNAs from non-cryopreserved control tomato plants (Lycopersicon esculentum Mill. cultivars Siriana, Darsirius, Kristin, Pontica and Capriciu) respectively, have been analyzed in the wavenumber range 400-1800 cm(-1). Structural changes induced in genomic DNAs upon cryopreservation were discussed in detail for four of the above mentioned tomato cultivars. The surface-enhanced Raman vibrational modes for each of these cases, spectroscopic band assignments and structural interpretations of genomic DNAs are reported. We have found, that DNA isolated from Siriana cultivar leaf tissues suffers the weakest structural changes upon cryogenic storage of tomato shoot apices. On the contrary, genomic DNA extracted from Pontica cultivar is the most responsive system to cryopreservation process. Particularly, both C2'-endo-anti and C3'-endo-anti conformations have been detected. As a general observation, the wavenumber range 1511-1652 cm(-1), being due to dA, dG and dT residues seems to be influenced by cryopreservation process. These changes could reflect unstacking of DNA bases. However, not significant structural changes of genomic DNAs from Siriana, Darsirius and Kristin have been found upon cryopreservation process of tomato cultivars. Based on this work, specific plant DNA-ligand interactions or accurate local structure of DNA in the proximity of a metallic surface, might be further investigated using surface-enhanced Raman spectroscopy.
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Affiliation(s)
- Cristina M Muntean
- National Institute for Research & Development of Isotopic and Molecular Technologies, Donat 67-103, 400293 Cluj-Napoca, Romania.
| | - Nicolae Leopold
- Babeş-Bolyai University, Faculty of Physics, Kogalniceanu 1, 400084 Cluj-Napoca, Romania
| | - Carmen Tripon
- National Institute for Research & Development of Isotopic and Molecular Technologies, Donat 67-103, 400293 Cluj-Napoca, Romania
| | - Ana Coste
- Institute of Biological Research, Branch of National Institute of Research and Development for Biological Sciences, Republicii 48, 400015 Cluj-Napoca, Romania
| | - Adela Halmagyi
- Institute of Biological Research, Branch of National Institute of Research and Development for Biological Sciences, Republicii 48, 400015 Cluj-Napoca, Romania
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Ivanova ME, Fletcher GC, O’Reilly N, Purkiss AG, Thompson BJ, McDonald NQ. Structures of the human Pals1 PDZ domain with and without ligand suggest gated access of Crb to the PDZ peptide-binding groove. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2015; 71:555-64. [PMID: 25760605 PMCID: PMC4356366 DOI: 10.1107/s139900471402776x] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/09/2014] [Accepted: 12/19/2014] [Indexed: 12/21/2022]
Abstract
Many components of epithelial polarity protein complexes possess PDZ domains that are required for protein interaction and recruitment to the apical plasma membrane. Apical localization of the Crumbs (Crb) transmembrane protein requires a PDZ-mediated interaction with Pals1 (protein-associated with Lin7, Stardust, MPP5), a member of the p55 family of membrane-associated guanylate kinases (MAGUKs). This study describes the molecular interaction between the Crb carboxy-terminal motif (ERLI), which is required for Drosophila cell polarity, and the Pals1 PDZ domain using crystallography and fluorescence polarization. Only the last four Crb residues contribute to Pals1 PDZ-domain binding affinity, with specificity contributed by conserved charged interactions. Comparison of the Crb-bound Pals1 PDZ structure with an apo Pals1 structure reveals a key Phe side chain that gates access to the PDZ peptide-binding groove. Removal of this side chain enhances the binding affinity by more than fivefold, suggesting that access of Crb to Pals1 may be regulated by intradomain contacts or by protein-protein interaction.
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Affiliation(s)
- Marina E. Ivanova
- Structural Biology Laboratories, Cancer Research UK, 44 Lincoln’s Inn Fields, London WC2A 3LY, England
| | - Georgina C. Fletcher
- Epithelial Biology Laboratories, Cancer Research UK, 44 Lincoln’s Inn Fields, London WC2A 3LY, England
| | - Nicola O’Reilly
- Peptide Chemistry Laboratories, Cancer Research UK, 44 Lincoln’s Inn Fields, London WC2A 3LY, England
| | - Andrew G. Purkiss
- Structural Biology Laboratories, Cancer Research UK, 44 Lincoln’s Inn Fields, London WC2A 3LY, England
| | - Barry J. Thompson
- Epithelial Biology Laboratories, Cancer Research UK, 44 Lincoln’s Inn Fields, London WC2A 3LY, England
| | - Neil Q. McDonald
- Structural Biology Laboratories, Cancer Research UK, 44 Lincoln’s Inn Fields, London WC2A 3LY, England
- Institute of Structural and Molecular Biology, Department of Biological Sciences, Birkbeck College, University of London, Malet Street, London WC1E 7HX, England
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