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Ribeiro NS, da Rosa DF, Xavier MA, Dos Reis SV, Beys-da-Silva WO, Santi L, Bizarro CV, Dalberto PF, Basso LA, Macedo AJ. Unveiling antibiofilm potential: proteins from Priestia sp. targeting Staphylococcus aureus biofilm formation. Antonie Van Leeuwenhoek 2024; 117:78. [PMID: 38740670 DOI: 10.1007/s10482-024-01977-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Accepted: 05/06/2024] [Indexed: 05/16/2024]
Abstract
Staphylococcus aureus is the etiologic agent of many nosocomial infections, and its biofilm is frequently isolated from medical devices. Moreover, the dissemination of multidrug-resistant (MDR) strains from this pathogen, such as methicillin-resistant S. aureus (MRSA) strains, is a worldwide public health issue. The inhibition of biofilm formation can be used as a strategy to weaken bacterial resistance. Taking that into account, we analysed the ability of marine sponge-associated bacteria to produce antibiofilm molecules, and we found that marine Priestia sp., isolated from marine sponge Scopalina sp. collected on the Brazilian coast, secretes proteins that impair biofilm development from S. aureus. Partially purified proteins (PPP) secreted after 24 hours of bacterial growth promoted a 92% biofilm mass reduction and 4.0 µg/dL was the minimum concentration to significantly inhibit biofilm formation. This reduction was visually confirmed by light microscopy and Scanning Electron Microscopy (SEM). Furthermore, biochemical assays showed that the antibiofilm activity of PPP was reduced by ethylenediaminetetraacetic acid (EDTA) and 1,10 phenanthroline (PHEN), while it was stimulated by zinc ions, suggesting an active metallopeptidase in PPP. This result agrees with mass spectrometry (MS) identification, which indicated the presence of a metallopeptidase from the M28 family. Additionally, whole-genome sequencing analysis of Priestia sp. shows that gene ywad, a metallopeptidase-encoding gene, was present. Therefore, the results presented herein indicate that PPP secreted by the marine Priestia sp. can be explored as a potential antibiofilm agent and help to treat chronic infections.
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Affiliation(s)
- Nicole Sartori Ribeiro
- Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil
| | - Deisiane Fernanda da Rosa
- Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil
| | - Marina Amaral Xavier
- Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil
| | - Sharon Vieira Dos Reis
- Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil
| | - Walter O Beys-da-Silva
- Faculdade de Farmácia, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil
| | - Lucélia Santi
- Faculdade de Farmácia, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil
| | - Cristiano Valim Bizarro
- Instituto Nacional de Ciência e Tecnologia em Tuberculose (INCT-TB), Centro de Pesquisas em Biologia Molecular e Funcional (CPBMF), and Programa de Pós-Graduação em Biologia Celular e Molecular, Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), 92A TECNOPUC, Av. Ipiranga 6681, Partenon, Porto Alegre, 90616-900, Brazil
| | - Pedro Ferrari Dalberto
- Instituto Nacional de Ciência e Tecnologia em Tuberculose (INCT-TB), Centro de Pesquisas em Biologia Molecular e Funcional (CPBMF), and Programa de Pós-Graduação em Biologia Celular e Molecular, Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), 92A TECNOPUC, Av. Ipiranga 6681, Partenon, Porto Alegre, 90616-900, Brazil
| | - Luiz Augusto Basso
- Instituto Nacional de Ciência e Tecnologia em Tuberculose (INCT-TB), Centro de Pesquisas em Biologia Molecular e Funcional (CPBMF), and Programa de Pós-Graduação em Biologia Celular e Molecular, Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), 92A TECNOPUC, Av. Ipiranga 6681, Partenon, Porto Alegre, 90616-900, Brazil
| | - Alexandre José Macedo
- Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil.
- Faculdade de Farmácia, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil.
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Reis SVD, Ribeiro NS, Rocha DA, Fortes IS, Trentin DDS, Andrade SFD, Macedo AJ. N 4 -benzyl-N 2 -phenylquinazoline-2,4-diamine compound presents antibacterial and antibiofilm effect against Staphylococcus aureus and Staphylococcus epidermidis. Chem Biol Drug Des 2020; 96:1372-1379. [PMID: 32542979 DOI: 10.1111/cbdd.13745] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2019] [Revised: 05/16/2020] [Accepted: 05/31/2020] [Indexed: 01/09/2023]
Abstract
Staphylococcus aureus and Staphylococcus epidermidis are the main agents involved with implant-related infections. Their ability to adhere to medical devices with subsequent biofilm formation is crucial to the development of these infections. Herein, we described the antibacterial and antibiofilm activities of a quinazoline-based compound, N4 -benzyl-N2 -phenylquinazoline-2,4-diamine, against both biofilm-forming pathogens. The minimum inhibitory concentrations (MIC) were determined as 25 µM for S. aureus and 15 µM for S. epidermidis. At sub-MIC concentrations (20 µM for S. aureus and 10 µM for S. epidermidis), the compound was able to inhibit biofilm formation without interfere with bacterial growth, confirmed by scanning electron microscopy. Moreover, surfaces coated with the quinazoline-based compound were able to prevent bacterial adherence. In addition, this compound presented no toxicity to human red blood cells at highest MIC 25 µM and in vivo toxicity assay using Galleria mellonella larvae resulted in 82% survival with a high dose of 500 mg/kg body weight. These features evidence quinazoline-based compound as interesting entities to promising applications in biomedical fields, such as antimicrobial and in anti-infective approaches.
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Affiliation(s)
- Sharon Vieira Dos Reis
- Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Nicole Sartori Ribeiro
- Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | | | | | - Danielle da Silva Trentin
- Departamento de Ciências Básicas da Saúde, Programa de Pós-Graduação em Biociências, Universidade Federal de Ciências da Saúde de Porto Alegre (UFCSPA), Porto Alegre, Brazil
| | | | - Alexandre José Macedo
- Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil.,Faculdade de Farmácia, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
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Dos Santos FM, Piffer AC, Schneider RDO, Ribeiro NS, Garcia AWA, Schrank A, Kmetzsch L, Vainstein MH, Staats CC. Alterations of zinc homeostasis in response to Cryptococcus neoformans in a murine macrophage cell line. Future Microbiol 2017; 12:491-504. [DOI: 10.2217/fmb-2016-0160] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Aim: To evaluate alterations of zinc homeostasis in macrophages exposed to Cryptococcus neoformans. Materials & methods: Using a fluorescent zinc probe-based flow cytometry and atomic absorption spectrometry, zinc levels were evaluated in J774.A1 cell lines exposed to C. neoformans H99 cells. The transcription profile of macrophage zinc related homeostasis genes – metallothioneins and zinc transporters (ZnTs) of the SLC30 and SLC39 (Zrt-Irt-protein) families – was analyzed by quantitative PCR. Results: Macrophage intracellular labile zinc levels decreased following exposure to C. neoformans. A significant decrease in transcription levels was detected in specific ZnTs from both the Zrt-Irt-protein and ZnT families, especially 24 h after infection. Conclusion: These findings suggest that macrophages may exhibit zinc depletion in response to C. neoformans infection.
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Affiliation(s)
- Francine Melise Dos Santos
- Programa de Pós-Graduação em Biologia Celular e Molecular, Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Av. Bento Gonçalves 9500, 43421, Caixa Postal 15005, Porto Alegre, RS 91501-970, Brazil
| | - Alícia Corbellini Piffer
- Programa de Pós-Graduação em Biologia Celular e Molecular, Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Av. Bento Gonçalves 9500, 43421, Caixa Postal 15005, Porto Alegre, RS 91501-970, Brazil
| | - Rafael de Oliveira Schneider
- Programa de Pós-Graduação em Biologia Celular e Molecular, Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Av. Bento Gonçalves 9500, 43421, Caixa Postal 15005, Porto Alegre, RS 91501-970, Brazil
| | - Nicole Sartori Ribeiro
- Programa de Pós-Graduação em Biologia Celular e Molecular, Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Av. Bento Gonçalves 9500, 43421, Caixa Postal 15005, Porto Alegre, RS 91501-970, Brazil
| | - Ane Wichine Acosta Garcia
- Programa de Pós-Graduação em Biologia Celular e Molecular, Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Av. Bento Gonçalves 9500, 43421, Caixa Postal 15005, Porto Alegre, RS 91501-970, Brazil
| | - Augusto Schrank
- Programa de Pós-Graduação em Biologia Celular e Molecular, Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Av. Bento Gonçalves 9500, 43421, Caixa Postal 15005, Porto Alegre, RS 91501-970, Brazil
- Departamento de Biologia Molecular e Biotecnologia, Universidade Federal do Rio Grande do Sul, Av. Bento Gonçalves 9500, 43421, Caixa Postal 15005, Porto Alegre, RS 91501-970, Brazil
| | - Lívia Kmetzsch
- Programa de Pós-Graduação em Biologia Celular e Molecular, Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Av. Bento Gonçalves 9500, 43421, Caixa Postal 15005, Porto Alegre, RS 91501-970, Brazil
- Departamento de Biologia Molecular e Biotecnologia, Universidade Federal do Rio Grande do Sul, Av. Bento Gonçalves 9500, 43421, Caixa Postal 15005, Porto Alegre, RS 91501-970, Brazil
| | - Marilene Henning Vainstein
- Programa de Pós-Graduação em Biologia Celular e Molecular, Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Av. Bento Gonçalves 9500, 43421, Caixa Postal 15005, Porto Alegre, RS 91501-970, Brazil
- Departamento de Biologia Molecular e Biotecnologia, Universidade Federal do Rio Grande do Sul, Av. Bento Gonçalves 9500, 43421, Caixa Postal 15005, Porto Alegre, RS 91501-970, Brazil
| | - Charley Christian Staats
- Programa de Pós-Graduação em Biologia Celular e Molecular, Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Av. Bento Gonçalves 9500, 43421, Caixa Postal 15005, Porto Alegre, RS 91501-970, Brazil
- Departamento de Biologia Molecular e Biotecnologia, Universidade Federal do Rio Grande do Sul, Av. Bento Gonçalves 9500, 43421, Caixa Postal 15005, Porto Alegre, RS 91501-970, Brazil
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Tiago FCP, Porto BAA, Ribeiro NS, Moreira LMC, Arantes RME, Vieira AT, Teixeira MM, Generoso SV, Nascimento VN, Martins FS, Nicoli JR. Effect of Saccharomyces cerevisiae strain UFMG A-905 in experimental model of inflammatory bowel disease. Benef Microbes 2015; 6:807-15. [PMID: 26322540 DOI: 10.3920/bm2015.0018] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
In the present study, the protective potential of Saccharomyces cerevisiae strain UFMG A-905 was evaluated in a murine model of acute ulcerative colitis (UC). Six groups of Balb/c mice were used: not treated with yeast and not challenged with dextran sulphate sodium (DSS) (control); treated with S. cerevisiae UFMG A-905 (905); treated with the non-probiotic S. cerevisiae W303 (W303); challenged with DSS (DSS); treated with S. cerevisiae UFMG A-905 and challenged with DSS (905 + DSS); and treated with S. cerevisiae W303 and challenged with DSS (W303 + DSS). Seven days after induction of UC, mice were euthanised to remove colon for enzymatic, immunological, and histopathological analysis. In vivo intestinal permeability was also evaluated. An improvement of clinical manifestations of experimental UC was observed only in mice of the 905 + DSS group when compared to animals from DSS and W303 + DSS groups. This observation was confirmed by histological and morphometrical data and determination of myeloperoxidase and eosinophil peroxidase activities, intestinal permeability and some pro-inflammatory cytokines. S. cerevisiae UFMG A-905 showed to be a potential alternative treatment for UC when used in an experimental animal model of the disease.
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Affiliation(s)
- F C P Tiago
- 1 Department of Microbiology, Institute of Biological Sciences, Federal University of Minas Gerais, Avenida Presidente Antônio Carlos 6627, C.P. 486, Pampulha - Campus UFMG, 31270-901, Belo Horizonte, MG, Brazil
| | - B A A Porto
- 1 Department of Microbiology, Institute of Biological Sciences, Federal University of Minas Gerais, Avenida Presidente Antônio Carlos 6627, C.P. 486, Pampulha - Campus UFMG, 31270-901, Belo Horizonte, MG, Brazil
| | - N S Ribeiro
- 1 Department of Microbiology, Institute of Biological Sciences, Federal University of Minas Gerais, Avenida Presidente Antônio Carlos 6627, C.P. 486, Pampulha - Campus UFMG, 31270-901, Belo Horizonte, MG, Brazil
| | - L M C Moreira
- 1 Department of Microbiology, Institute of Biological Sciences, Federal University of Minas Gerais, Avenida Presidente Antônio Carlos 6627, C.P. 486, Pampulha - Campus UFMG, 31270-901, Belo Horizonte, MG, Brazil
| | - R M E Arantes
- 2 Department of General Pathology, Institute of Biological Sciences, Federal University of Minas Gerais, Avenida Presidente Antônio Carlos 6627, C.P. 486, Pampulha - Campus UFMG, 31270-901, Belo Horizonte, MG, Brazil
| | - A T Vieira
- 3 Department of Biochemistry and Immunology, Institute of Biological Sciences, Federal University of Minas Gerais, Avenida Presidente Antônio Carlos 6627, C.P. 486, Pampulha - Campus UFMG, 31270-901, Belo Horizonte, MG, Brazil
| | - M M Teixeira
- 3 Department of Biochemistry and Immunology, Institute of Biological Sciences, Federal University of Minas Gerais, Avenida Presidente Antônio Carlos 6627, C.P. 486, Pampulha - Campus UFMG, 31270-901, Belo Horizonte, MG, Brazil
| | - S V Generoso
- 4 School of Pharmacy, Federal University of Minas Gerais, Avenida Presidente Antônio Carlos 6627, C.P. 486, Pampulha - Campus UFMG, 31270-901, Belo Horizonte, MG, Brazil
| | - V N Nascimento
- 4 School of Pharmacy, Federal University of Minas Gerais, Avenida Presidente Antônio Carlos 6627, C.P. 486, Pampulha - Campus UFMG, 31270-901, Belo Horizonte, MG, Brazil
| | - F S Martins
- 1 Department of Microbiology, Institute of Biological Sciences, Federal University of Minas Gerais, Avenida Presidente Antônio Carlos 6627, C.P. 486, Pampulha - Campus UFMG, 31270-901, Belo Horizonte, MG, Brazil
| | - J R Nicoli
- 1 Department of Microbiology, Institute of Biological Sciences, Federal University of Minas Gerais, Avenida Presidente Antônio Carlos 6627, C.P. 486, Pampulha - Campus UFMG, 31270-901, Belo Horizonte, MG, Brazil
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5
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Abstract
The effects of different cations on the hydrodynamic radius (RH) of a 48-bp synthetic DNA are measured by time-resolved fluorescence polarization anisotropy of intercalated ethidium. Relative statistical errors in RH are only approximately 1%. With increasing cation concentration, Na+ causes a small decrease in RH, Cs+ causes a somewhat larger decrease by up to 0.5 A at 100 mM, and (CH3CH2)4N+ causes an increase in RH by approximately 0.5 A at 100 mM. The qualitatively different effects of these monovalent cations indicates that the changes in RH with cation concentration do not arise primarily from electrolyte friction. Divalent cations cause much larger increases in RH with increasing cation concentration. Mg2+ causes an increase in RH by up to 1.0 A at 24.4 mM, and Mn2+ causes an increase in RH by up to 1.6 A at 24.4 mM. These effects are independent of DNA concentration. There is some positive correlation between the order of effects of the different cations on RH and the order of their effects on interhelical hydration forces. It is suggested that these different ions affect RH either by altering the hydration layer or possibly by some effect on DNA structure, such as stabilizing bends.
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Affiliation(s)
- B S Fujimoto
- Department of Chemistry, University of Washington, Seattle 98195
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6
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Abstract
Nuclear magnetic resonance and optical experiments are combined to determine the rms amplitude of local angular motion of purines in DNA in solution. A 12 base-pair duplex DNA with the sequence d(CGCGAATTCGCG)2 is deuterated at the H8 positions of adenine and guanine by exchange with solvent at 55 degrees C. The deuterium nmr spectrum of this DNA is measured at 30 mg/mL at 30 degrees C in an 11.76 Tesla magnet (76.75 MHz). The time-resolved fluorescence polarization anisotropies (FPA) of this same sample and also a greatly diluted sample (0.215 mg/mL) were measured after addition of ethidium. FPA measurements of the dilute sample yield the hydrodynamic radius, RH = 9.94 +/- 0.2 A, while those at the nmr concentration are employed to characterize the collective motions in terms of either an enhanced viscosity or dimer formation. The rms amplitude of local angular motion was determined by analyzing the 2H-nmr spectrum, in particular the line width, using recently developed theory for the transverse relaxation rate (RQ2) together with essential information about the collective motions from these and other optical studies. When the principal-axis frame of the electric field gradient tensor is assumed to undergo overdamped libration around each of its three body-fixed axes in an isotropic deflection potential, then the rms amplitude of local angular motion around any single axis is found to lie in the range 10 degrees-11 degrees, provided the high DNA concentration acts to enhance the viscosity, and is about 9 degrees-11 degrees, if it acts to produce end-to-end dimers. The proton nmr relaxation data of Eimer et al. are reanalyzed and shown to yield an rms amplitude of angular motion of the cytosine H5-H6 internuclear vector of 9 degrees-10 degrees, depending upon its orientation with respect to the helix axis. In all of these analyses, full account is taken of the collective twisting and bending deformations, which have a small but significant effect on the results. It is shown that the rms amplitudes of local angular motion do not depend strongly on the model (potential), provided that isotropic rotation around the same number of axes is allowed and that one compares rms angles of the same dimensionality. The rms amplitudes of local angular motion in solution are comparable to those observed for the same sequence at low levels of hydration in the solid state.
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Affiliation(s)
- S Nuutero
- Department of Chemistry, University of Washington, Seattle 98195
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7
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Abstract
The structure of the DNA.RNA hybrid (GTCACATG).(caugugac), where lowercase letters designate RNA residues, has been determined on the basis of J-coupling analysis and 2D-NOE studies. The central hexamer in this sequence has been previously studied [Reid, D. G., Salisbury, S. A., Brown, T., Williams, D. H., Vasseur, J.-J., Rayner, B., & Imabach, J.-L. (1983) Eur. J. Biochem. 135, 307-314] via one-dimensional NOE methods and circular dichroism studies. Contrary to their results, we find that this duplex does not assume a B-form conformation in solution. Instead, the RNA residues retain their C3'-endo (A-form) conformation, as indicated by the absence of H1'-H2' couplings and by strong H6/H8 to (n-1) H2'NOEs. The sugars of the DNA residues, on the other hand, do not assume an A-form (or a B-form) conformation but an intermediate conformation in the O4'-endo range (P approximately 72-110 degrees), as indicated by the presence of strong H1'-H4' NOEs, medium-strength H2"-H3' COSY cross peaks, strong H3'-H4' DQF-COSY cross peaks, and H1'-H2' coupling constants that are of approximately the same magnitude as the H1'-H2" coupling constants. These results suggest that the RNA strand not only retains its N-type structure but also exerts an influence on the conformation of the DNA strand. Our results provide strong evidence that DNA.RNA hybrid duplexes do not assume an all-C2'-endo B-type conformation; neither do they assume an all-C3'-endo A-type conformation in solution. Furthermore, although not the main focus of this study, a comparison of the longitudinal relaxation times of the DNA and RNA residues indicates the need for extended relaxation delays in two-dimensional NMR spectra of hybrid duplexes, as has been previously observed for DNA.RNA chimeric duplexes (Wang, A. C., Kim, S.-G., Chou, S.-H., Orban, J., Flynn, P., & Reid, B. R. (1992) Biochemistry 31, 3940-3946).
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Affiliation(s)
- M Salazar
- Department of Chemistry, University of Washington, Seattle 98195
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8
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Hare DR, Ribeiro NS, Wemmer DE, Reid BR. Complete assignment of the imino protons of Escherichia coli valine transfer RNA: two-dimensional NMR studies in water. Biochemistry 1985; 24:4300-6. [PMID: 3902082 DOI: 10.1021/bi00337a008] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
The imino proton spectrum of Escherichia coli valine tRNA has been studied by two-dimensional nuclear Overhauser effect spectroscopy (NOESY) in H2O solution. The small nuclear Overhauser effects from the imino proton of an internal base pair to the imino protons of each nearest neighbor can be observed as off-diagonal cross-peaks. In this way most of the sequential NOE connectivity trains for all the helices in this molecule can be determined in a single experiment. AU resonances can be distinguished from GC resonances by the AU imino NOE to the aromatic adenine C2-H, thus leading to specific base-pair assignments. In general, the NOESY spectrum alone is not capable of assigning every imino proton resonance even in well-resolved tRNA spectra. Multiple proton peaks exhibit more than two cross-peaks, resulting in ambiguous connectivities, and coupling between protons with similar chemical shifts produces cross-peaks that are incompletely resolved from the diagonal. The sequence of the particular tRNA determines the occurrence of the latter problem, which can often be solved by careful one-dimensional experiments. The complete imino proton assignments of E. coli valine tRNA are presented.
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Thomas JC, Schurr JM, Reid BR, Ribeiro NS, Hare DR. Effect of Mg2+ on solution conformation of two different transfer ribonucleic acids. Biochemistry 1984; 23:5414-20. [PMID: 6210103 DOI: 10.1021/bi00318a006] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
We have investigated the effect of Mg2+ on the solution conformation of two different tRNAs by studying the decay of the fluorescence polarization anisotropy of intercalated ethidium on a nanosecond time scale. In the presence of endogenous Mg2+, yeast tRNAPhe and Escherichia coli tRNAVal1 exhibit similar behavior; i.e., the fluorescence from the intercalated ethidium decays biexponentially with lifetimes of approximately 25 and approximately 5 ns, and the fluorescence polarization anisotropy decays with a lifetime of approximately 25 ns. However, once Mg2+ is removed from the two tRNAs, their behavior is no longer similar. In the case of yeast tRNAPhe, it appears that titrating with Mg2+ restores the tRNA to the condition that it was in prior to the Mg2+ removal. This is not so for E. coli tRNAVal1, in which case titrating with Mg2+ results in a two-component anisotropy decay with lifetimes of approximately 25 and approximately 6 ns. Rudimentary calculations indicate that the 6-ns component does not result simply from a change in conformation of the tRNA. However, torsional motions in the tRNA facilitated by a torsion "joint" with a rigidity approximately 1/40 that of intact linear phi 29 DNA would yield a decay component on this time scale with about the right amplitude. We are thus left with the possibility that (after initially removing magnesium) titrating tRNAVal1 with Mg2+ leads to increased internal flexibility and a significant amplitude of a deformational relaxation mode. At any rate, there is no question that after removal of Mg2+ tRNAPhe and tRNAVal1 display quite different solution conformation behavior. These findings are in qualitative agreement with recent 500-MHz 1H NMR results from solutions of these two tRNAs.
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10
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Louie A, Ribeiro NS, Reid BR, Jurnak F. Relative affinities of all Escherichia coli aminoacyl-tRNAs for elongation factor Tu-GTP. J Biol Chem 1984; 259:5010-6. [PMID: 6370998] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
The relative affinities of all Escherichia coli amino-acyl-tRNAs for E. coli elongation factor (EF) Tu-GTP have been measured by two independent applications of the competition form of the ribonuclease resistance assay. The set of aminoacyl-tRNAs includes at least one tRNA for each of the 20 amino acids as well as purified isoacceptor tRNA species for arginine, glycine, leucine, lysine, and tyrosine. In the first competition study, [3H]Phe-tRNA was used as the competing aminoacyl-tRNA against [14C]aminoacyl-tRNA in the set of all tRNAs; in the second study, [3H]Leu-tRNALeu4 was used as the competing aminoacyl-tRNA. The relative order of aminoacyl-tRNA affinities for EF-Tu-GTP was the same in each study. The results indicate that the affinity of EF-Tu-GTP at 4 degrees C, pH 7.4, is strongest for Gln-tRNA and weakest for Val-tRNA. Both Gly-tRNA and Pro-tRNA bind very strongly to EF-Tu-GTP relative to other aminoacyl-tRNAs. Various models of ternary complex interactions are discussed in light of the new data. Although the properties of the amino acid substituent are primarily responsible for the differences in relative affinities among the noninitiator aminoacyl-tRNAs, the results for the four isoacceptor species of Leu-tRNALeu indicate that the secondary structural features of the tRNA are also influential.
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12
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Reid BR, McCollum L, Ribeiro NS, Abbate J, Hurd RE. Identification of tertiary base pair resonances in the nuclear magnetic resonance spectra of transfer ribonucleic acid. Biochemistry 1979; 18:3996-4005. [PMID: 385039 DOI: 10.1021/bi00585a024] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The low-field hydrogen-bond ring NH proton nuclear magnetic resonance (NMR) spectra of several transfer ribonucleic acids (tRNAs) related to yeast tRNAPhe have been examined in detail. Several resonances are sensitive to magnesium ion and temperature, suggesting that they are derived from tertiary base pairs. These same resonances cannot be attributed to cloverleaf base pairs as shown by experimental assignment and ring current shift calculation of the secondary base pair resonances. The crystal structure of yeast tRNAPhe reveals at least six tertiary base pairs involving ring NH hydrogen bonds, which we conclude are responsible for the extra resonances observed in the low-field NMR spectrum. In several tRNAs with the same tertiary folding potential and dihydrouridine helix sequence as yeast tRNAPhe, the extra resonances from tertiary base pairs are observed at the same position in the spectrum.
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Reid BR, Ribeiro NS, McCollum L, Abbate J, Hurd RE. High-resolution nuclear magnetic resonance determination of transfer RNA tertiary base pairs in solution. 1. Species containing a small variable loop. Biochemistry 1977; 16:2086-94. [PMID: 324514 DOI: 10.1021/bi00629a006] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Eight class I tRNA species have been purified to homogeneity and their proton nuclear magnetic resonance (NMR) spectra in the low-field region (-11 to -15 ppm) have been studied at 360 MHz. The low-field spectra contain only one low-field resonance from each base pair (the ring NH hydrogen bond) and hence directly monitor the number of long-lived secondary and tertiary base pairs in solution. The tRNA species were chosen on the basis of their sequence homology with yeast phenylalanine tRNA in the regions which form tertiary base pairs in the crystal structure of this tRNA. All of the spectra show 26 or 27 low-field resonances approximately 7 of which are derived from tertiary base pairs. These results are contrary to previous claims that the NMR spectra indicate the presence of resonances from secondary base pairs only, as well as more recent claims of only 1-3 tertiary resonances, but are in good agreement with the number of tertiary base pairs expected in solution based on the crystal structure. The tertiary base pair resonances are stable up to at least 46 degrees C. Removal of magnesium ions causes structural changes in the tRNA but does not result in the loss of any secondary or tertiary base pairs.
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Reid BR, Ribeiro NS, Gould G, Robillard G, Hilbers CW, Shulman RG. Tertiary hydrogen bonds in the solution structure of transfer RNA. Proc Natl Acad Sci U S A 1975; 72:2049-53. [PMID: 1094451 PMCID: PMC432690 DOI: 10.1073/pnas.72.6.2049] [Citation(s) in RCA: 43] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
The high resolution nuclear magnetic resonance (NMR) spectra of hydrogen-bonded protons in four tRNAs have been studied at 270 MHz. The relative intensity of the resonances between -11 ppm and -15 ppm of Escherichia coli tRNA1-Va1 indicate that there are 26 plus or minus 3 protons, while only 20 are expected from secondary structure Watson-Crick hydrogen bonds inthe cloverleaf structure. Several possible candidates for these extra resonances are suggested by tertiary interactions observed in recent crystallographic studies. Of the four tRNAs studied, three, e.g., E. coli tRNA1Va1, E. coli tRNA-Arg and E. coli tRNA-Phe have one "GU pair" in their cloverleaf structure, while the fourth, yeast tRNA-Asp,has three "GU pairs" and one "G pair". Correlating these with the NMR spectra in the -10 ppm to -11 ppm region allows us to conclude that the "GU pairs" are not hydrogen-bonded by tautomerization to the lactim form. At the very low field region, near -14.9 ppm, the three E. coli tRNAs show a single resonance which is attributed to the 4-thiouracil 8 to adenine 14 hydrogen bond of the tertiary structure, by analogy with the recent crystal structure of yeast tRNA-Phe. This assignment is confirmed by the disappearance of this resonance after treatment with cyanogen bromide.
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