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Caetano DG, Napoleão-Pêgo P, Villela LM, Côrtes FH, Cardoso SW, Hoagland B, Grinsztejn B, Veloso VG, De-Simone SG, Guimarães ML. Patterns of Diversity and Humoral Immunogenicity for HIV-1 Antisense Protein (ASP). Vaccines (Basel) 2024; 12:771. [PMID: 39066409 PMCID: PMC11281420 DOI: 10.3390/vaccines12070771] [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: 05/28/2024] [Revised: 07/01/2024] [Accepted: 07/06/2024] [Indexed: 07/28/2024] Open
Abstract
HIV-1 has an antisense gene overlapping env that encodes the ASP protein. ASP functions are still unknown, but it has been associated with gp120 in the viral envelope and membrane of infected cells, making it a potential target for immune response. Despite this, immune response patterns against ASP are poorly described and can be influenced by the high genetic variability of the env gene. To explore this, we analyzed 100k HIV-1 ASP sequences from the Los Alamos HIV sequence database using phylogenetic, Shannon entropy (Hs), and logo tools to study ASP variability in worldwide and Brazilian sequences from the most prevalent HIV-1 subtypes in Brazil (B, C, and F1). Data obtained in silico guided the design and synthesis of 15-mer overlapping peptides through spot synthesis on cellulose membranes. Peptide arrays were screened to assess IgG and IgM responses in pooled plasma samples from HIV controllers and individuals with acute or recent HIV infection. Excluding regions with low alignment accuracy, several sites with higher variability (Hs > 1.5) were identified among the datasets (25 for worldwide sequences, 20 for Brazilian sequences). Among sites with Hs < 1.5, sequence logos allowed the identification of 23 other sites with subtype-specific signatures. Altogether, amino acid variations with frequencies > 20% in the 48 variable sites identified were included in 92 peptides, divided into 15 sets, representing near full-length ASP. During the immune screening, the strongest responses were observed in three sets, one in the middle and one at the C-terminus of the protein. While some sets presented variations potentially associated with epitope displacement between IgG and IgM targets and subtype-specific signatures appeared to impact the level of response for some peptides, signals of cross-reactivity were observed for some sets despite the presence of B/C/F1 signatures. Our data provides a map of ASP regions preferentially targeted by IgG and IgM responses. Despite B/C/F1 subtype signatures in ASP, the amino acid variation in some areas preferentially targeted by IgM and IgG did not negatively impact the response against regions with higher immunogenicity.
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Affiliation(s)
- Diogo Gama Caetano
- AIDS and Molecular Immunology Laboratory, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro 21040-360, Brazil (M.L.G.)
| | - Paloma Napoleão-Pêgo
- Epidemiology and Molecular Systematics Laboratory (LEMS), Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro 21040-360, Brazil
| | - Larissa Melo Villela
- Epidemiology and Molecular Systematics Laboratory (LEMS), Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro 21040-360, Brazil
| | - Fernanda Heloise Côrtes
- AIDS and Molecular Immunology Laboratory, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro 21040-360, Brazil (M.L.G.)
| | - Sandra Wagner Cardoso
- Instituto Nacional de Infectologia Evandro Chagas, Oswaldo Cruz Foundation, Rio de Janeiro 21040-360, Brazil
| | - Brenda Hoagland
- Instituto Nacional de Infectologia Evandro Chagas, Oswaldo Cruz Foundation, Rio de Janeiro 21040-360, Brazil
| | - Beatriz Grinsztejn
- Instituto Nacional de Infectologia Evandro Chagas, Oswaldo Cruz Foundation, Rio de Janeiro 21040-360, Brazil
| | - Valdilea Gonçalves Veloso
- Instituto Nacional de Infectologia Evandro Chagas, Oswaldo Cruz Foundation, Rio de Janeiro 21040-360, Brazil
| | - Salvatore Giovanni De-Simone
- Epidemiology and Molecular Systematics Laboratory (LEMS), Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro 21040-360, Brazil
- Center for Technological Development in Health (CDTS), National Institute of Science and Technology for Innovation in Neglected Population Diseases (INCT-IDPN), Oswaldo Cruz Foundation, Rio de Janeiro 21040-900, Brazil
- Program of Post-Graduation on Science and Biotechnology, Department of Molecular and Cellular Biology, Biology Institute, Federal Fluminense University, Niterói 22040-036, Brazil
| | - Monick Lindenmeyer Guimarães
- AIDS and Molecular Immunology Laboratory, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro 21040-360, Brazil (M.L.G.)
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Meloni M, Rossi J, Fanti S, Carloni G, Tedesco D, Treffon P, Piccinini L, Falini G, Trost P, Vierling E, Licausi F, Giuntoli B, Musiani F, Fermani S, Zaffagnini M. Structural and biochemical characterization of Arabidopsis alcohol dehydrogenases reveals distinct functional properties but similar redox sensitivity. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 118:1054-1070. [PMID: 38308388 DOI: 10.1111/tpj.16651] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Revised: 01/07/2024] [Accepted: 01/18/2024] [Indexed: 02/04/2024]
Abstract
Alcohol dehydrogenases (ADHs) are a group of zinc-binding enzymes belonging to the medium-length dehydrogenase/reductase (MDR) protein superfamily. In plants, these enzymes fulfill important functions involving the reduction of toxic aldehydes to the corresponding alcohols (as well as catalyzing the reverse reaction, i.e., alcohol oxidation; ADH1) and the reduction of nitrosoglutathione (GSNO; ADH2/GSNOR). We investigated and compared the structural and biochemical properties of ADH1 and GSNOR from Arabidopsis thaliana. We expressed and purified ADH1 and GSNOR and determined two new structures, NADH-ADH1 and apo-GSNOR, thus completing the structural landscape of Arabidopsis ADHs in both apo- and holo-forms. A structural comparison of these Arabidopsis ADHs revealed a high sequence conservation (59% identity) and a similar fold. In contrast, a striking dissimilarity was observed in the catalytic cavity supporting substrate specificity and accommodation. Consistently, ADH1 and GSNOR showed strict specificity for their substrates (ethanol and GSNO, respectively), although both enzymes had the ability to oxidize long-chain alcohols, with ADH1 performing better than GSNOR. Both enzymes contain a high number of cysteines (12 and 15 out of 379 residues for ADH1 and GSNOR, respectively) and showed a significant and similar responsivity to thiol-oxidizing agents, indicating that redox modifications may constitute a mechanism for controlling enzyme activity under both optimal growth and stress conditions.
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Affiliation(s)
- Maria Meloni
- Department of Pharmacy and Biotechnology, University of Bologna, 40126, Bologna, Italy
| | - Jacopo Rossi
- Department of Pharmacy and Biotechnology, University of Bologna, 40126, Bologna, Italy
| | - Silvia Fanti
- Department of Chemistry "G. Ciamician", University of Bologna, 40126, Bologna, Italy
| | - Giacomo Carloni
- Department of Chemistry "G. Ciamician", University of Bologna, 40126, Bologna, Italy
| | - Daniele Tedesco
- Institute for Organic Synthesis and Photoreactivity (ISOF), National Research Council of Italy (CNR), 40129, Bologna, Italy
| | - Patrick Treffon
- Department of Biochemistry and Molecular Biology, University of Massachusetts Amherst, Amherst, Massachusetts, USA
| | - Luca Piccinini
- Department of Biology, University of Pisa, Pisa, 56127, Italy
- Center for Plant Sciences, Scuola Superiore Sant'Anna, Pisa, 56124, Italy
| | - Giuseppe Falini
- Department of Chemistry "G. Ciamician", University of Bologna, 40126, Bologna, Italy
| | - Paolo Trost
- Department of Pharmacy and Biotechnology, University of Bologna, 40126, Bologna, Italy
| | - Elizabeth Vierling
- Department of Biochemistry and Molecular Biology, University of Massachusetts Amherst, Amherst, Massachusetts, USA
| | | | - Beatrice Giuntoli
- Department of Biology, University of Pisa, Pisa, 56127, Italy
- Center for Plant Sciences, Scuola Superiore Sant'Anna, Pisa, 56124, Italy
| | - Francesco Musiani
- Department of Pharmacy and Biotechnology, University of Bologna, 40126, Bologna, Italy
| | - Simona Fermani
- Department of Chemistry "G. Ciamician", University of Bologna, 40126, Bologna, Italy
- Interdepartmental Centre for Industrial Research Health Sciences & Technologies, University of Bologna, 40064, Bologna, Italy
| | - Mirko Zaffagnini
- Department of Pharmacy and Biotechnology, University of Bologna, 40126, Bologna, Italy
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3
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Orzel B, Pelucelli A, Ostrowska M, Potocki S, Kozlowski H, Peana M, Gumienna-Kontecka E. Fe(II), Mn(II), and Zn(II) Binding to the C-Terminal Region of FeoB Protein: An Insight into the Coordination Chemistry and Specificity of the Escherichia coli Fe(II) Transporter. Inorg Chem 2023; 62:18607-18624. [PMID: 37910812 PMCID: PMC10647171 DOI: 10.1021/acs.inorgchem.3c02910] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Revised: 10/03/2023] [Accepted: 10/03/2023] [Indexed: 11/03/2023]
Abstract
The interactions between two peptide ligands [Ac763CCAASTTGDCH773 (P1) and Ac743RRARSRVDIELLATRKSVSSCCAASTTGDCH773 (P2)] derived from the cytoplasmic C-terminal region of Eschericha coli FeoB protein and Fe(II), Mn(II), and Zn(II) ions were investigated. The Feo system is regarded as the most important bacterial Fe(II) acquisition system, being one of the key virulence factors, especially in anaerobic conditions. Located in the inner membrane of Gram-negative bacteria, FeoB protein transports Fe(II) from the periplasm to the cytoplasm. Despite its crucial role in bacterial pathogenicity, the mechanism in which the metal ion is trafficked through the membrane is not yet elucidated. In the gammaproteobacteria class, the cytoplasmic C-terminal part of FeoB contains conserved cysteine, histidine, and glutamic and aspartic acid residues, which could play a vital role in Fe(II) binding in the cytoplasm, receiving the metal ion from the transmembrane helices. In this work, we characterized the complexes formed between the whole cytosolic C-terminal sequence of E. coli FeoB (P2) and its key polycysteine region (P1) with Fe(II), Mn(II), and Zn(II) ions, exploring the specificity of the C-terminal region of FeoB. With the help of a variety of potentiometric, spectroscopic (electron paramagnetic resonance and NMR), and spectrometric (electrospray ionization mass spectrometry) techniques and molecular dynamics, we propose the metal-binding modes of the ligands, compare their affinities toward the metal ions, and discuss the possible physiological role of the C-terminal region of E. coli FeoB.
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Affiliation(s)
- Bartosz Orzel
- Faculty
of Chemistry, University of Wrocław, 50-383 Wrocław, Poland
| | - Alessio Pelucelli
- Department
of Chemical, Physical, Mathematical and Natural Sciences, University of Sassari, 07100 Sassari, Italy
| | | | - Slawomir Potocki
- Faculty
of Chemistry, University of Wrocław, 50-383 Wrocław, Poland
| | - Henryk Kozlowski
- Faculty
of Chemistry, University of Wrocław, 50-383 Wrocław, Poland
- Department
of Health Sciences, University of Opole, Katowicka 68, 45-060 Opole, Poland
| | - Massimiliano Peana
- Department
of Chemical, Physical, Mathematical and Natural Sciences, University of Sassari, 07100 Sassari, Italy
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Timm J, Pike DH, Mancini JA, Tyryshkin AM, Poudel S, Siess JA, Molinaro PM, McCann JJ, Waldie KM, Koder RL, Falkowski PG, Nanda V. Design of a minimal di-nickel hydrogenase peptide. SCIENCE ADVANCES 2023; 9:eabq1990. [PMID: 36897954 PMCID: PMC10005181 DOI: 10.1126/sciadv.abq1990] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Accepted: 02/07/2023] [Indexed: 06/07/2023]
Abstract
Ancestral metabolic processes involve the reversible oxidation of molecular hydrogen by hydrogenase. Extant hydrogenase enzymes are complex, comprising hundreds of amino acids and multiple cofactors. We designed a 13-amino acid nickel-binding peptide capable of robustly producing molecular hydrogen from protons under a wide variety of conditions. The peptide forms a di-nickel cluster structurally analogous to a Ni-Fe cluster in [NiFe] hydrogenase and the Ni-Ni cluster in acetyl-CoA synthase, two ancient, extant proteins central to metabolism. These experimental results demonstrate that modern enzymes, despite their enormous complexity, likely evolved from simple peptide precursors on early Earth.
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Affiliation(s)
- Jennifer Timm
- Environmental Biophysics and Molecular Ecology Program, Department of Marine and Coastal Sciences and Department of Earth and Planetary Sciences, Rutgers University, New Brunswick, NJ 08901, USA
- Center for Advanced Biotechnology and Medicine and the Department of Biochemistry and Molecular Biology, Robert Wood Johnson Medical School, Rutgers University, Piscataway, NJ 08854, USA
| | - Douglas H. Pike
- Center for Advanced Biotechnology and Medicine and the Department of Biochemistry and Molecular Biology, Robert Wood Johnson Medical School, Rutgers University, Piscataway, NJ 08854, USA
| | - Joshua A. Mancini
- Environmental Biophysics and Molecular Ecology Program, Department of Marine and Coastal Sciences and Department of Earth and Planetary Sciences, Rutgers University, New Brunswick, NJ 08901, USA
- Center for Advanced Biotechnology and Medicine and the Department of Biochemistry and Molecular Biology, Robert Wood Johnson Medical School, Rutgers University, Piscataway, NJ 08854, USA
| | - Alexei M. Tyryshkin
- Environmental Biophysics and Molecular Ecology Program, Department of Marine and Coastal Sciences and Department of Earth and Planetary Sciences, Rutgers University, New Brunswick, NJ 08901, USA
- Center for Advanced Biotechnology and Medicine and the Department of Biochemistry and Molecular Biology, Robert Wood Johnson Medical School, Rutgers University, Piscataway, NJ 08854, USA
| | - Saroj Poudel
- Environmental Biophysics and Molecular Ecology Program, Department of Marine and Coastal Sciences and Department of Earth and Planetary Sciences, Rutgers University, New Brunswick, NJ 08901, USA
- Center for Advanced Biotechnology and Medicine and the Department of Biochemistry and Molecular Biology, Robert Wood Johnson Medical School, Rutgers University, Piscataway, NJ 08854, USA
| | - Jan A. Siess
- Center for Advanced Biotechnology and Medicine and the Department of Biochemistry and Molecular Biology, Robert Wood Johnson Medical School, Rutgers University, Piscataway, NJ 08854, USA
| | - Paul M. Molinaro
- Department of Physics, The City College of New York, New York, NY 10016, USA
| | - James J. McCann
- Department of Physics, The City College of New York, New York, NY 10016, USA
| | - Kate M. Waldie
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA
| | - Ronald L. Koder
- Department of Physics, The City College of New York, New York, NY 10016, USA
| | - Paul G. Falkowski
- Environmental Biophysics and Molecular Ecology Program, Department of Marine and Coastal Sciences and Department of Earth and Planetary Sciences, Rutgers University, New Brunswick, NJ 08901, USA
| | - Vikas Nanda
- Center for Advanced Biotechnology and Medicine and the Department of Biochemistry and Molecular Biology, Robert Wood Johnson Medical School, Rutgers University, Piscataway, NJ 08854, USA
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