1
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Nutrient Sensing and Biofilm Modulation: The Example of L-arginine in Pseudomonas. Int J Mol Sci 2022; 23:ijms23084386. [PMID: 35457206 PMCID: PMC9028604 DOI: 10.3390/ijms23084386] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 04/12/2022] [Accepted: 04/13/2022] [Indexed: 12/01/2022] Open
Abstract
Bacterial biofilm represents a multicellular community embedded within an extracellular matrix attached to a surface. This lifestyle confers to bacterial cells protection against hostile environments, such as antibiotic treatment and host immune response in case of infections. The Pseudomonas genus is characterised by species producing strong biofilms difficult to be eradicated and by an extraordinary metabolic versatility which may support energy and carbon/nitrogen assimilation under multiple environmental conditions. Nutrient availability can be perceived by a Pseudomonas biofilm which, in turn, readapts its metabolism to finally tune its own formation and dispersion. A growing number of papers is now focusing on the mechanism of nutrient perception as a possible strategy to weaken the biofilm barrier by environmental cues. One of the most important nutrients is amino acid L-arginine, a crucial metabolite sustaining bacterial growth both as a carbon and a nitrogen source. Under low-oxygen conditions, L-arginine may also serve for ATP production, thus allowing bacteria to survive in anaerobic environments. L-arginine has been associated with biofilms, virulence, and antibiotic resistance. L-arginine is also a key precursor of regulatory molecules such as polyamines, whose involvement in biofilm homeostasis is reported. Given the biomedical and biotechnological relevance of biofilm control, the state of the art on the effects mediated by the L-arginine nutrient on biofilm modulation is presented, with a special focus on the Pseudomonas biofilm. Possible biotechnological and biomedical applications are also discussed.
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2
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Guanidinium binding to proteins: The intriguing effects on the D1 and D2 domains of Thermotoga maritima Arginine Binding Protein and a comprehensive analysis of the Protein Data Bank. Int J Biol Macromol 2020; 163:375-385. [PMID: 32629051 DOI: 10.1016/j.ijbiomac.2020.06.290] [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: 05/24/2020] [Accepted: 06/30/2020] [Indexed: 10/23/2022]
Abstract
Thermotoga maritima Arginine Binding Protein has been extensively characterized because of its peculiar features and its possible use as a biosensor. In this characterization, deletion of the C-terminal helix to obtain the monomeric protein TmArgBP20-233 and dissection of the monomer in its two domains, D1 and D2, have been performed. In the present study the stability of these three forms against guanidinium chloride is investigated by means of circular dichroism and differential scanning calorimetry measurements. All three proteins show a high conformational stability; moreover, D1 shows an unusual behavior in the presence of low concentrations of guanidinium chloride. This finding has led us to investigate a possible binding interaction by means of isothermal titration calorimetry and X-ray crystallography; the results indicate that D1 is able to bind the guanidinium ion (GuH+), due to its similarity with the arginine terminal moiety. The analysis of the structural and dynamic properties of the D1-GuH+ complex indicates that the protein binds the ligand through multiple and diversified interactions. An exhaustive survey of the binding modes of GuH+ to proteins indicates that this is a rather common feature. These observations provide interesting insights into the effects that GuH+ is able to induce in protein structures.
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3
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Capo A, Natalello A, Marienhagen J, Pennacchio A, Camarca A, Di Giovanni S, Staiano M, D'Auria S, Varriale A. Structural features of the glutamate-binding protein from Corynebacterium glutamicum. Int J Biol Macromol 2020; 162:903-912. [PMID: 32593757 DOI: 10.1016/j.ijbiomac.2020.06.197] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Revised: 06/05/2020] [Accepted: 06/21/2020] [Indexed: 10/24/2022]
Abstract
L-glutamate (Glu) is the major excitatory transmitter in mammalian brain. Inadequate concentration of Glu in the brain correlates to mood disorder. In industry, Glu is used as a flavour enhancer in food and in foodstuff processing. A high concentration of Glu has several effects on human health such as hypersensitive effects, headache and stomach pain. The presence of Glu in food can be detected by different analytical methods based on chromatography, or capillary electrophoresis or amperometric techniques. We have isolated and characterized a glutamate-binding protein (GluB) from the Gram-positive bacteria Corynebacterium glutamicum. Together with GluC protein, GluD protein and the cytoplasmic protein GluA, GluB permits the transport of Glu in/out of cell. In this study, we have investigated the binding features of GluB as well as the effect of temperature on its structure both in the absence and in the presence of Glu. The results have showed that GluB has a high affinity and selectivity versus Glu (nanomolar range) and the presence of the ligand induces a higher thermal stability of the protein structure.
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Affiliation(s)
- Alessandro Capo
- Institute of Food Science CNR, via Roma 64, 83100 Avellino, Italy
| | - Antonino Natalello
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, P.zza della Scienza 2, 20126 Milano, Italy
| | - Jan Marienhagen
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich, 52425 Jülich, Germany; Institute of Biotechnology, RWTH Aachen University, Worringer Weg 3, D-52074 Aachen, Germany
| | | | | | | | - Maria Staiano
- Institute of Food Science CNR, via Roma 64, 83100 Avellino, Italy
| | - Sabato D'Auria
- Institute of Food Science CNR, via Roma 64, 83100 Avellino, Italy.
| | - Antonio Varriale
- Institute of Food Science CNR, via Roma 64, 83100 Avellino, Italy
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4
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Smaldone G, Ruggiero A, Balasco N, Vitagliano L. Development of a Protein Scaffold for Arginine Sensing Generated through the Dissection of the Arginine-Binding Protein from Thermotoga maritima. Int J Mol Sci 2020; 21:ijms21207503. [PMID: 33053818 PMCID: PMC7589609 DOI: 10.3390/ijms21207503] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Revised: 10/05/2020] [Accepted: 10/08/2020] [Indexed: 12/21/2022] Open
Abstract
Arginine is one of the most important nutrients of living organisms as it plays a major role in important biological pathways. However, the accumulation of arginine as consequence of metabolic defects causes hyperargininemia, an autosomal recessive disorder. Therefore, the efficient detection of the arginine is a field of relevant biomedical/biotechnological interest. Here, we developed protein variants suitable for arginine sensing by mutating and dissecting the multimeric and multidomain structure of Thermotoga maritima arginine-binding protein (TmArgBP). Indeed, previous studies have shown that TmArgBP domain-swapped structure can be manipulated to generate simplified monomeric and single domain scaffolds. On both these stable scaffolds, to measure tryptophan fluorescence variations associated with the arginine binding, a Phe residue of the ligand binding pocket was mutated to Trp. Upon arginine binding, both mutants displayed a clear variation of the Trp fluorescence. Notably, the single domain scaffold variant exhibited a good affinity (~3 µM) for the ligand. Moreover, the arginine binding to this variant could be easily reverted under very mild conditions. Atomic-level data on the recognition process between the scaffold and the arginine were obtained through the determination of the crystal structure of the adduct. Collectively, present data indicate that TmArgBP scaffolds represent promising candidates for developing arginine biosensors.
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Affiliation(s)
- Giovanni Smaldone
- IRCCS SDN, Via Emanuele Gianturco, 113 80143 Naples, Italy
- Correspondence: (G.S.); (A.R.)
| | - Alessia Ruggiero
- Institute of Biostructures and Bioimaging, CNR, Via Mezzocannone 16. I-80134 Naples, Italy; (N.B.); (L.V.)
- Correspondence: (G.S.); (A.R.)
| | - Nicole Balasco
- Institute of Biostructures and Bioimaging, CNR, Via Mezzocannone 16. I-80134 Naples, Italy; (N.B.); (L.V.)
| | - Luigi Vitagliano
- Institute of Biostructures and Bioimaging, CNR, Via Mezzocannone 16. I-80134 Naples, Italy; (N.B.); (L.V.)
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5
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Mattossovich R, Merlo R, Miggiano R, Valenti A, Perugino G. O6-alkylguanine-DNA Alkyltransferases in Microbes Living on the Edge: From Stability to Applicability. Int J Mol Sci 2020; 21:E2878. [PMID: 32326075 PMCID: PMC7216122 DOI: 10.3390/ijms21082878] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Revised: 04/09/2020] [Accepted: 04/16/2020] [Indexed: 02/06/2023] Open
Abstract
The genome of living cells is continuously exposed to endogenous and exogenous attacks, and this is particularly amplified at high temperatures. Alkylating agents cause DNA damage, leading to mutations and cell death; for this reason, they also play a central role in chemotherapy treatments. A class of enzymes known as AGTs (alkylguanine-DNA-alkyltransferases) protects the DNA from mutations caused by alkylating agents, in particular in the recognition and repair of alkylated guanines in O6-position. The peculiar irreversible self-alkylation reaction of these enzymes triggered numerous studies, especially on the human homologue, in order to identify effective inhibitors in the fight against cancer. In modern biotechnology, engineered variants of AGTs are developed to be used as protein tags for the attachment of chemical ligands. In the last decade, research on AGTs from (hyper)thermophilic sources proved useful as a model system to clarify numerous phenomena, also common for mesophilic enzymes. This review traces recent progress in this class of thermozymes, emphasizing their usefulness in basic research and their consequent advantages for in vivo and in vitro biotechnological applications.
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Affiliation(s)
- Rosanna Mattossovich
- Institute of Bioscience and BioResources, National Research Council of Italy, Via Pietro Castellino 111, 80131 Naples, Italy; (R.M.); (R.M.)
| | - Rosa Merlo
- Institute of Bioscience and BioResources, National Research Council of Italy, Via Pietro Castellino 111, 80131 Naples, Italy; (R.M.); (R.M.)
| | - Riccardo Miggiano
- Department of Pharmaceutical Sciences, University of Piemonte Orientale, Via Bovio 6, 28100 Novara, Italy;
| | - Anna Valenti
- Institute of Bioscience and BioResources, National Research Council of Italy, Via Pietro Castellino 111, 80131 Naples, Italy; (R.M.); (R.M.)
| | - Giuseppe Perugino
- Institute of Bioscience and BioResources, National Research Council of Italy, Via Pietro Castellino 111, 80131 Naples, Italy; (R.M.); (R.M.)
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6
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Smaldone G, Ruggiero A, Balasco N, Abuhammad A, Autiero I, Caruso D, Esposito D, Ferraro G, Gelardi ELM, Moreira M, Quareshy M, Romano M, Saaret A, Selvam I, Squeglia F, Troisi R, Kroon-Batenburg LMJ, Esposito L, Berisio R, Vitagliano L. The non-swapped monomeric structure of the arginine-binding protein from Thermotoga maritima. Acta Crystallogr F Struct Biol Commun 2019; 75:707-713. [PMID: 31702584 PMCID: PMC6839819 DOI: 10.1107/s2053230x1901464x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Accepted: 10/29/2019] [Indexed: 01/07/2023] Open
Abstract
Domain swapping is a widespread oligomerization process that is observed in a large variety of protein families. In the large superfamily of substrate-binding proteins, non-monomeric members have rarely been reported. The arginine-binding protein from Thermotoga maritima (TmArgBP), a protein endowed with a number of unusual properties, presents a domain-swapped structure in its dimeric native state in which the two polypeptide chains mutually exchange their C-terminal helices. It has previously been shown that mutations in the region connecting the last two helices of the TmArgBP structure lead to the formation of a variety of oligomeric states (monomers, dimers, trimers and larger aggregates). With the aim of defining the structural determinants of domain swapping in TmArgBP, the monomeric form of the P235GK mutant has been structurally characterized. Analysis of this arginine-bound structure indicates that it consists of a closed monomer with its C-terminal helix folded against the rest of the protein, as typically observed for substrate-binding proteins. Notably, the two terminal helices are joined by a single nonhelical residue (Gly235). Collectively, the present findings indicate that extending the hinge region and conferring it with more conformational freedom makes the formation of a closed TmArgBP monomer possible. On the other hand, the short connection between the helices may explain the tendency of the protein to also adopt alternative oligomeric states (dimers, trimers and larger aggregates). The data reported here highlight the importance of evolutionary control to avoid the uncontrolled formation of heterogeneous and potentially harmful oligomeric species through domain swapping.
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Affiliation(s)
- Giovanni Smaldone
- AIC School Crystallographic Information Fiesta 2019, Naples, Italy
- IRCCS SDN, Via Gianturco 113, 80143 Naples, Italy
| | - Alessia Ruggiero
- AIC School Crystallographic Information Fiesta 2019, Naples, Italy
- Institute of Biostructures and Bioimaging (IBB), CNR, Naples, Italy
| | - Nicole Balasco
- AIC School Crystallographic Information Fiesta 2019, Naples, Italy
- Institute of Biostructures and Bioimaging (IBB), CNR, Naples, Italy
| | - Areej Abuhammad
- AIC School Crystallographic Information Fiesta 2019, Naples, Italy
- Department of Pharmaceutical Sciences, School of Pharmacy, The University of Jordan, Amman, Jordan
| | - Ida Autiero
- AIC School Crystallographic Information Fiesta 2019, Naples, Italy
- Institute of Biostructures and Bioimaging (IBB), CNR, Naples, Italy
| | - Daniela Caruso
- AIC School Crystallographic Information Fiesta 2019, Naples, Italy
- Università degli Studi della Campania ‘Luigi Vanvitelli’, Caserta, Italy
| | - Davide Esposito
- AIC School Crystallographic Information Fiesta 2019, Naples, Italy
- Institute of Biostructures and Bioimaging (IBB), CNR, Naples, Italy
| | - Giarita Ferraro
- AIC School Crystallographic Information Fiesta 2019, Naples, Italy
| | | | - Miguel Moreira
- AIC School Crystallographic Information Fiesta 2019, Naples, Italy
- Institute of Biostructures and Bioimaging (IBB), CNR, Naples, Italy
| | - Mussa Quareshy
- AIC School Crystallographic Information Fiesta 2019, Naples, Italy
| | - Maria Romano
- AIC School Crystallographic Information Fiesta 2019, Naples, Italy
| | - Annica Saaret
- AIC School Crystallographic Information Fiesta 2019, Naples, Italy
| | - Irwin Selvam
- AIC School Crystallographic Information Fiesta 2019, Naples, Italy
| | - Flavia Squeglia
- AIC School Crystallographic Information Fiesta 2019, Naples, Italy
- Institute of Biostructures and Bioimaging (IBB), CNR, Naples, Italy
| | - Romualdo Troisi
- AIC School Crystallographic Information Fiesta 2019, Naples, Italy
| | - Loes M. J. Kroon-Batenburg
- AIC School Crystallographic Information Fiesta 2019, Naples, Italy
- Crystal and Structural Chemistry, Utrecht University, Padualaan 8, Utrecht, The Netherlands
| | - Luciana Esposito
- AIC School Crystallographic Information Fiesta 2019, Naples, Italy
- Institute of Biostructures and Bioimaging (IBB), CNR, Naples, Italy
| | - Rita Berisio
- AIC School Crystallographic Information Fiesta 2019, Naples, Italy
- Institute of Biostructures and Bioimaging (IBB), CNR, Naples, Italy
| | - Luigi Vitagliano
- AIC School Crystallographic Information Fiesta 2019, Naples, Italy
- Institute of Biostructures and Bioimaging (IBB), CNR, Naples, Italy
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7
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Dennis ML, Esquirol L, Nebl T, Newman J, Scott C, Peat TS. The evolving story of AtzT, a periplasmic binding protein. Acta Crystallogr D Struct Biol 2019; 75:995-1002. [PMID: 31692473 PMCID: PMC6834077 DOI: 10.1107/s2059798319013883] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2019] [Accepted: 10/11/2019] [Indexed: 11/20/2022] Open
Abstract
Atrazine is an s-triazine-based herbicide that is used in many countries around the world in many millions of tons per year. A small number of organisms, such as Pseudomonas sp. strain ADP, have evolved to use this modified s-triazine as a food source, and the various genes required to metabolize atrazine can be found on a single plasmid. The atomic structures of seven of the eight proteins involved in the breakdown of atrazine by Pseudomonas sp. strain ADP have been determined by X-ray crystallography, but the structures of the proteins required by the cell to import atrazine for use as an energy source are still lacking. The structure of AtzT, a periplasmic binding protein that may be involved in the transport of a derivative of atrazine, 2-hydroxyatrazine, into the cell for mineralization, has now been determined. The structure was determined by SAD phasing using an ethylmercury phosphate derivative that diffracted X-rays to beyond 1.9 Å resolution. `Native' (guanine-bound) and 2-hydroxyatrazine-bound structures were also determined to high resolution (1.67 and 1.65 Å, respectively), showing that 2-hydroxyatrazine binds in a similar way to the purportedly native ligand. Structural similarities led to the belief that it may be possible to evolve AtzT from a purine-binding protein to a protein that can bind and detect atrazine in the environment.
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Affiliation(s)
- Matthew L. Dennis
- Biomedical Manufacturing Program, CSIRO, 343 Royal Parade, Parkville, VIC 3052, Australia
| | - Lygie Esquirol
- CSIRO Synthetic Biology Future Science Platform, GPO Box 1700, Acton, Canberra, ACT 2601, Australia
| | - Tom Nebl
- Biomedical Manufacturing Program, CSIRO, 343 Royal Parade, Parkville, VIC 3052, Australia
| | - Janet Newman
- Biomedical Manufacturing Program, CSIRO, 343 Royal Parade, Parkville, VIC 3052, Australia
| | - Colin Scott
- CSIRO Synthetic Biology Future Science Platform, GPO Box 1700, Acton, Canberra, ACT 2601, Australia
| | - Thomas S. Peat
- Biomedical Manufacturing Program, CSIRO, 343 Royal Parade, Parkville, VIC 3052, Australia
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8
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Mattossovich R, Merlo R, Fontana A, d'Ippolito G, Terns MP, Watts EA, Valenti A, Perugino G. A journey down to hell: new thermostable protein-tags for biotechnology at high temperatures. Extremophiles 2019; 24:81-91. [PMID: 31555904 DOI: 10.1007/s00792-019-01134-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Accepted: 09/13/2019] [Indexed: 12/14/2022]
Abstract
The specific labelling of proteins in recent years has made use of self-labelling proteins, such as the SNAP-tag® and the Halotag®. These enzymes, by their nature or suitably engineered, have the ability to specifically react with their respective substrates, but covalently retaining a part of them in the catalytic site upon reaction. This led to the synthesis of substrates conjugated with, e.g., fluorophores (proposing them as alternatives to fluorescent proteins), but also with others chemical groups, for numerous biotechnological applications. Recently, a mutant of the OGT from Saccharolobus solfataricus (H5) very stable to high temperatures and in the presence of physical and chemical denaturing agents has been proposed as a thermostable SNAP-tag® for in vivo and in vitro harsh reaction conditions. Here, we show two new thermostable OGTs from Thermotoga neapolitana and Pyrococcus furiosus, which, respectively, display a higher catalytic activity and thermostability respect to H5, proposing them as alternatives for in vivo studies in these extreme model organisms.
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Affiliation(s)
- Rosanna Mattossovich
- Institute of Biosciences and BioResources, National Council of Research of Italy, Via P. Castellino 111, 80131, Naples, Italy
| | - Rosa Merlo
- Institute of Biosciences and BioResources, National Council of Research of Italy, Via P. Castellino 111, 80131, Naples, Italy
| | - Angelo Fontana
- Institute of Biomolecular Chemistry, National Council of Research of Italy, Via Campi Flegrei, 34, 80078, Pozzuoli, NA, Italy
| | - Giuliana d'Ippolito
- Institute of Biomolecular Chemistry, National Council of Research of Italy, Via Campi Flegrei, 34, 80078, Pozzuoli, NA, Italy
| | - Michael P Terns
- Departments of Biochemistry and Molecular Biology, Genetics, and Microbiology, University of Georgia, Athens, GA, USA
| | - Elizabeth A Watts
- Departments of Biochemistry and Molecular Biology, Genetics, and Microbiology, University of Georgia, Athens, GA, USA
| | - Anna Valenti
- Institute of Biosciences and BioResources, National Council of Research of Italy, Via P. Castellino 111, 80131, Naples, Italy
| | - Giuseppe Perugino
- Institute of Biosciences and BioResources, National Council of Research of Italy, Via P. Castellino 111, 80131, Naples, Italy.
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9
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Cormann KU, Baumgart M, Bott M. Structure-Based Design of Versatile Biosensors for Small Molecules Based on the PAS Domain of a Thermophilic Histidine Kinase. ACS Synth Biol 2018; 7:2888-2897. [PMID: 30525476 DOI: 10.1021/acssynbio.8b00348] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The development of biosensors for in vitro quantification of small molecules such as metabolites or man-made chemicals is still a major challenge. Here we show that engineered variants of the sensory PAS domain of the histidine kinase CitA of the thermophilic bacterium Geobacillus thermoleovorans represent promising alternatives to established biorecognition elements. By combining binding site grafting and rational design we constructed protein variants binding l-malate, ethylmalonate, or the aromatic compound phthalate instead of the native ligand citrate. Due to more favorable entropy contributions, the wild-type protein and its engineered variants exhibited increased (nano- to micromolar) affinities and improved enantioselectivity compared to CitA homologues of mesophilic organisms. Ligand binding was directly converted into an optical signal that was preserved after immobilization of the protein. A fluorescently labeled variant was used to quantify ethylmalonate, an urinary biomarker for ethylmalonic encephalopathy, in synthetic urine, thereby demonstrating the applicability of the sensor in complex samples.
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Affiliation(s)
- Kai U. Cormann
- IBG-1: Biotechnology, Institute of Bio- and Geosciences, Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Meike Baumgart
- IBG-1: Biotechnology, Institute of Bio- and Geosciences, Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Michael Bott
- IBG-1: Biotechnology, Institute of Bio- and Geosciences, Forschungszentrum Jülich, 52425 Jülich, Germany
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10
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Smaldone G, Balasco N, Vigorita M, Ruggiero A, Cozzolino S, Berisio R, Del Vecchio P, Graziano G, Vitagliano L. Domain communication in Thermotoga maritima Arginine Binding Protein unraveled through protein dissection. Int J Biol Macromol 2018; 119:758-769. [PMID: 30059738 DOI: 10.1016/j.ijbiomac.2018.07.172] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Revised: 07/24/2018] [Accepted: 07/26/2018] [Indexed: 10/28/2022]
Abstract
Substrate binding proteins represent a large protein family that plays fundamental roles in selective transportation of metabolites across membrane. The function of these proteins relies on the relative motions of their two domains. Insights into domain communication in this class of proteins have been here collected using Thermotoga maritima Arginine Binding Protein (TmArgBP) as model system. TmArgBP was dissected into two domains (D1 and D2) that were exhaustively characterized using a repertoire of different experimental and computational techniques. Indeed, stability, crystalline structure, ability to recognize the arginine substrate, and dynamics of the two individual domains have been here studied. Present data demonstrate that, although in the parent protein both D1 and D2 cooperate for the arginine anchoring; only D1 is intrinsically able to bind the substrate. The implications of this finding on the mechanism of arginine binding and release by TmArgBP have been discussed. Interestingly, both D1 and D2 retain the remarkable thermal/chemical stability of the parent protein. The analysis of the structural and dynamic properties of TmArgBP and of the individual domains highlights possible routes of domain communication. Finally, this study generated two interesting molecular tools, the two stable isolated domains that could be used in future investigations.
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Affiliation(s)
| | - Nicole Balasco
- Institute of Biostructures and Bioimaging, CNR, Via Mezzocannone 16, 80134 Napoli, Italy
| | - Marilisa Vigorita
- Department of Sciences and Technologies, Università del Sannio, via Port'arsa 11, 82100 Benevento, Italy
| | - Alessia Ruggiero
- Institute of Biostructures and Bioimaging, CNR, Via Mezzocannone 16, 80134 Napoli, Italy
| | - Serena Cozzolino
- Department of Chemical Sciences, University of Naples Federico II, via Cintia, 80126 Napoli, Italy
| | - Rita Berisio
- Institute of Biostructures and Bioimaging, CNR, Via Mezzocannone 16, 80134 Napoli, Italy
| | - Pompea Del Vecchio
- Department of Chemical Sciences, University of Naples Federico II, via Cintia, 80126 Napoli, Italy
| | - Giuseppe Graziano
- Department of Sciences and Technologies, Università del Sannio, via Port'arsa 11, 82100 Benevento, Italy
| | - Luigi Vitagliano
- Institute of Biostructures and Bioimaging, CNR, Via Mezzocannone 16, 80134 Napoli, Italy.
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11
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Domain swapping dissection in Thermotoga maritima arginine binding protein: How structural flexibility may compensate destabilization. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2018; 1866:952-962. [PMID: 29860047 DOI: 10.1016/j.bbapap.2018.05.016] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Revised: 05/11/2018] [Accepted: 05/28/2018] [Indexed: 11/21/2022]
Abstract
Thermotoga maritima Arginine Binding Protein (TmArgBP) is a valuable candidate for arginine biosensing in diagnostics. This protein is endowed with unusual structural properties that include an extraordinary thermal/chemical stability, a domain swapped structure that undergoes large tertiary and quaternary structural transition, and the ability to form non-canonical oligomeric species. As the intrinsic stability of TmArgBP allows for extensive protein manipulations, we here dissected its structure in two parts: its main body deprived of the swapping fragment (TmArgBP20-233) and the C-terminal peptide corresponding to the helical swapping element. Both elements have been characterized independently or in combination using a repertoire of biophysical/structural techniques. Present investigations clearly indicate that TmArgBP20-233 represents a better scaffold for arginine sensing compared to the wild-type protein. Moreover, our data demonstrate that the ligand-free and the ligand-bound forms respond very differently to this helix deletion. This drastic perturbation has an important impact on the ligand-bound form of TmArgBP20-233 stability whereas it barely affects its ligand-free state. The crystallographic structures of these forms provide a rationale to this puzzling observation. Indeed, the arginine-bound state is very rigid and virtually unchanged upon protein truncation. On the other hand, the flexible ligand-free TmArgBP20-233 is able to adopt a novel state as a consequence of the helix deletion. Therefore, the flexibility of the ligand-free form endows this state with a remarkable robustness upon severe perturbations. In this scenario, TmArgBP dissection highlights an intriguing connection between destabilizing/stabilizing effects and the overall flexibility that could operate also in other proteins.
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