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Pellizza L, Ramis L, Araoz IA, Aran M. 1H, 15N and 13C backbone and side chain solution NMR assignments of the TPM domain-containing protein of the thermophilic bacterium Rhodothermus marinus. BIOMOLECULAR NMR ASSIGNMENTS 2023; 17:229-233. [PMID: 37542635 DOI: 10.1007/s12104-023-10146-2] [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: 07/03/2023] [Accepted: 07/20/2023] [Indexed: 08/07/2023]
Abstract
The InterPro family IPR007621 TPM_phosphatase is a widely conserved family of protein domains found in prokaryotes, plants and invertebrates. Despite similar predicted protein folding, members of this family are involved in different cellular processes. In recent years, the structural and biochemical characterization of evolutionarily divergent TPM domains has shown their ability to hydrolyze phosphate groups of different substrates. However, there are still inaccurate functional annotations and uncertain relationships between the structure and function of this domain family. We here report the 1H, 13C, and 15N backbone and sidechain resonances of the TPM domain of a predicted TPM domain-containing protein of the thermophilic bacterium Rhodothermus marinus. These data will lay the groundwork for future NMR-based investigations, contributing to a thorough comprehension of the intricate aspects governing the interplay between structure and function of TPM domains. Additionally, they will unlock opportunities to explore dynamic structural changes, providing valuable insights into the molecular mechanisms underlying the evolutionary adaptations to extreme environmental conditions within this protein family.
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Affiliation(s)
- Leonardo Pellizza
- Fundación Instituto Leloir and Instituto de Investigaciones Bioquímicas de Buenos Aires (IIBBA)- CONICET, Patricias Argentinas 435 (C1405BWE), Buenos Aires, Argentina
| | - Lila Ramis
- Fundación Instituto Leloir and Instituto de Investigaciones Bioquímicas de Buenos Aires (IIBBA)- CONICET, Patricias Argentinas 435 (C1405BWE), Buenos Aires, Argentina
| | - Ignacio Argañaraz Araoz
- Fundación Instituto Leloir and Instituto de Investigaciones Bioquímicas de Buenos Aires (IIBBA)- CONICET, Patricias Argentinas 435 (C1405BWE), Buenos Aires, Argentina
| | - Martín Aran
- Fundación Instituto Leloir and Instituto de Investigaciones Bioquímicas de Buenos Aires (IIBBA)- CONICET, Patricias Argentinas 435 (C1405BWE), Buenos Aires, Argentina.
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Pellizza L, Bialer MG, Sieira R, Aran M. MliR, a novel MerR-like regulator of iron homeostasis, impacts metabolism, membrane remodeling, and cell adhesion in the marine Bacteroidetes Bizionia argentinensis. Front Microbiol 2022; 13:987756. [PMID: 36118216 PMCID: PMC9478572 DOI: 10.3389/fmicb.2022.987756] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Accepted: 08/08/2022] [Indexed: 11/13/2022] Open
Abstract
The MerR family is a group of transcriptional activators with conserved N-terminal helix-turn-helix DNA binding domains and variable C-terminal effector binding regions. In most MerR proteins the effector binding domain (EBD) contains a cysteine center suited for metal binding and mediates the response to environmental stimuli, such as oxidative stress, heavy metals or antibiotics. We here present a novel transcriptional regulator classified in the MerR superfamily that lacks an EBD domain and has neither conserved metal binding sites nor cysteine residues. This regulator from the psychrotolerant bacteria Bizionia argentinensis JUB59 is involved in iron homeostasis and was named MliR (MerR-like iron responsive Regulator). In silico analysis revealed that homologs of the MliR protein are widely distributed among different bacterial species. Deletion of the mliR gene led to decreased cell growth, increased cell adhesion and filamentation. Genome-wide transcriptomic analysis showed that genes associated with iron homeostasis were downregulated in mliR-deletion mutant. Through nuclear magnetic resonance-based metabolomics, ICP-MS, fluorescence microscopy and biochemical analysis we evaluated metabolic and phenotypic changes associated with mliR deletion. This work provides the first evidence of a MerR-family regulator involved in iron homeostasis and contributes to expanding our current knowledge on relevant metabolic pathways and cell remodeling mechanisms underlying in the adaptive response to iron availability in bacteria.
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Pellizza L, López JL, Vázquez S, Sycz G, Guimarães BG, Rinaldi J, Goldbaum FA, Aran M, Mac Cormack WP, Klinke S. Structure of the putative long tail fiber receptor-binding tip of a novel temperate bacteriophage from the Antarctic bacterium Bizionia argentinensis JUB59. J Struct Biol 2020; 212:107595. [PMID: 32736071 DOI: 10.1016/j.jsb.2020.107595] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2020] [Revised: 07/23/2020] [Accepted: 07/24/2020] [Indexed: 11/28/2022]
Abstract
Tailed bacteriophages are one of the most widespread biological entities on Earth. Their singular structures, such as spikes or fibers are of special interest given their potential use in a wide range of biotechnological applications. In particular, the long fibers present at the termini of the T4 phage tail have been studied in detail and are important for host recognition and adsorption. Although significant progress has been made in elucidating structural mechanisms of model phages, the high-resolution structural description of the vast population of marine phages is still unexplored. In this context, we present here the crystal structure of C24, a putative receptor-binding tip-like protein from Bizionia argentinensis JUB59, a psychrotolerant bacterium isolated from the marine surface waters of Potter Cove, Antarctica. The structure resembles the receptor-binding tip from the bacteriophage T4 long tail fiber yet showing marked differences in its domain organization, size, sequence identity and metal binding nature. We confirmed the viral origin of C24 by induction experiments using mitomycin C. Our results reveal the presence of a novel uncharacterized prophage in the genome of B. argentinensis JUB59, whose morphology is compatible with the order Caudovirales and that carries the nucleotide sequence of C24 in its genome. This work provides valuable information to expand our current knowledge on the viral machinery prevalent in the oceans.
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Affiliation(s)
- Leonardo Pellizza
- Fundación Instituto Leloir, IIBBA-CONICET, Patricias Argentinas 435 (C1405BWE), Buenos Aires, Argentina
| | - José L López
- Instituto de Bacteriología y Virología Molecular (IBAVIM), Cátedra de Virología, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Junín 956 (C1113AAZ), Buenos Aires, Argentina
| | - Susana Vázquez
- Instituto NANOBIOTEC - Cátedra de Biotecnología, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires - Consejo Nacional de Investigaciones Científicas y Técnicas, Junín 956 (C1113AAZ), Buenos Aires, Argentina
| | - Gabriela Sycz
- Fundación Instituto Leloir, IIBBA-CONICET, Patricias Argentinas 435 (C1405BWE), Buenos Aires, Argentina
| | - Beatriz G Guimarães
- Synchrotron SOLEIL, L'Orme des Merisiers, Saint-Aubin BP 48 (91192), Gif-sur-Yvette, France
| | - Jimena Rinaldi
- Fundación Instituto Leloir, IIBBA-CONICET, Patricias Argentinas 435 (C1405BWE), Buenos Aires, Argentina
| | - Fernando A Goldbaum
- Fundación Instituto Leloir, IIBBA-CONICET, Patricias Argentinas 435 (C1405BWE), Buenos Aires, Argentina; Plataforma Argentina de Biología Estructural y Metabolómica PLABEM, Patricias Argentinas 435 (C1405BWE), Buenos Aires, Argentina
| | - Martín Aran
- Fundación Instituto Leloir, IIBBA-CONICET, Patricias Argentinas 435 (C1405BWE), Buenos Aires, Argentina.
| | - Walter P Mac Cormack
- Instituto NANOBIOTEC - Cátedra de Biotecnología, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires - Consejo Nacional de Investigaciones Científicas y Técnicas, Junín 956 (C1113AAZ), Buenos Aires, Argentina; Instituto Antártico Argentino, 25 de Mayo 1143 (B1650HMK), San Martín, Provincia de Buenos Aires, Argentina.
| | - Sebastián Klinke
- Fundación Instituto Leloir, IIBBA-CONICET, Patricias Argentinas 435 (C1405BWE), Buenos Aires, Argentina; Plataforma Argentina de Biología Estructural y Metabolómica PLABEM, Patricias Argentinas 435 (C1405BWE), Buenos Aires, Argentina.
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Pellizza L, Smal C, Rodrigo G, Arán M. Codon usage clusters correlation: towards protein solubility prediction in heterologous expression systems in E. coli. Sci Rep 2018; 8:10618. [PMID: 30006617 PMCID: PMC6045634 DOI: 10.1038/s41598-018-29035-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Accepted: 06/21/2018] [Indexed: 12/15/2022] Open
Abstract
Production of soluble recombinant proteins is crucial to the development of industry and basic research. However, the aggregation due to the incorrect folding of the nascent polypeptides is still a mayor bottleneck. Understanding the factors governing protein solubility is important to grasp the underlying mechanisms and improve the design of recombinant proteins. Here we show a quantitative study of the expression and solubility of a set of proteins from Bizionia argentinensis. Through the analysis of different features known to modulate protein production, we defined two parameters based on the %MinMax algorithm to compare codon usage clusters between the host and the target genes. We demonstrate that the absolute difference between all %MinMax frequencies of the host and the target gene is significantly negatively correlated with protein expression levels. But most importantly, a strong positive correlation between solubility and the degree of conservation of codons usage clusters is observed for two independent datasets. Moreover, we evince that this correlation is higher in codon usage clusters involved in less compact protein secondary structure regions. Our results provide important tools for protein design and support the notion that codon usage may dictate translation rate and modulate co-translational folding.
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Affiliation(s)
- Leonardo Pellizza
- Laboratory of Nuclear Magnetic Resonance, Fundación Instituto Leloir, IIBBA-CONICET, Av. Patricias Argentinas 435, C1405BWE, CABA, Argentina
| | - Clara Smal
- Laboratory of Nuclear Magnetic Resonance, Fundación Instituto Leloir, IIBBA-CONICET, Av. Patricias Argentinas 435, C1405BWE, CABA, Argentina
| | - Guido Rodrigo
- Laboratory of Nuclear Magnetic Resonance, Fundación Instituto Leloir, IIBBA-CONICET, Av. Patricias Argentinas 435, C1405BWE, CABA, Argentina
| | - Martín Arán
- Laboratory of Nuclear Magnetic Resonance, Fundación Instituto Leloir, IIBBA-CONICET, Av. Patricias Argentinas 435, C1405BWE, CABA, Argentina.
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