1
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Greenwich JL, Eagan JL, Feirer N, Boswinkle K, Minasov G, Shuvalova L, Inniss NL, Raghavaiah J, Ghosh AK, Satchell KJF, Allen KD, Fuqua C. Control of biofilm formation by an Agrobacterium tumefaciens pterin-binding periplasmic protein conserved among diverse Proteobacteria. Proc Natl Acad Sci U S A 2024; 121:e2319903121. [PMID: 38870058 PMCID: PMC11194511 DOI: 10.1073/pnas.2319903121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2023] [Accepted: 05/13/2024] [Indexed: 06/15/2024] Open
Abstract
Biofilm formation and surface attachment in multiple Alphaproteobacteria is driven by unipolar polysaccharide (UPP) adhesins. The pathogen Agrobacterium tumefaciens produces a UPP adhesin, which is regulated by the intracellular second messenger cyclic diguanylate monophosphate (c-di-GMP). Prior studies revealed that DcpA, a diguanylate cyclase-phosphodiesterase, is crucial in control of UPP production and surface attachment. DcpA is regulated by PruR, a protein with distant similarity to enzymatic domains known to coordinate the molybdopterin cofactor (MoCo). Pterins are bicyclic nitrogen-rich compounds, several of which are produced via a nonessential branch of the folate biosynthesis pathway, distinct from MoCo. The pterin-binding protein PruR controls DcpA activity, fostering c-di-GMP breakdown and dampening its synthesis. Pterins are excreted, and we report here that PruR associates with these metabolites in the periplasm, promoting interaction with the DcpA periplasmic domain. The pteridine reductase PruA, which reduces specific dihydro-pterin molecules to their tetrahydro forms, imparts control over DcpA activity through PruR. Tetrahydromonapterin preferentially associates with PruR relative to other related pterins, and the PruR-DcpA interaction is decreased in a pruA mutant. PruR and DcpA are encoded in an operon with wide conservation among diverse Proteobacteria including mammalian pathogens. Crystal structures reveal that PruR and several orthologs adopt a conserved fold, with a pterin-specific binding cleft that coordinates the bicyclic pterin ring. These findings define a pterin-responsive regulatory mechanism that controls biofilm formation and related c-di-GMP-dependent phenotypes in A. tumefaciens and potentially acts more widely in multiple proteobacterial lineages.
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Affiliation(s)
| | - Justin L. Eagan
- Department of Biology, Indiana University, Bloomington, IN47405
| | - Nathan Feirer
- Department of Biology, Indiana University, Bloomington, IN47405
| | - Kaleb Boswinkle
- Department of Biochemistry, Virginia Polytechnic Institute and State University, Blacksburg, VA24061
| | - George Minasov
- Department of Microbiology-Immunology, Feinberg School of Medicine, Northwestern University, Chicago, IL60611
- Center for Structural Biology of Infectious Diseases, Feinberg School of Medicine, Northwestern University, Chicago, IL60611
| | - Ludmilla Shuvalova
- Department of Pharmacology, Feinberg School of Medicine, Northwestern University, Chicago, IL60611
| | - Nicole L. Inniss
- Department of Microbiology-Immunology, Feinberg School of Medicine, Northwestern University, Chicago, IL60611
- Center for Structural Biology of Infectious Diseases, Feinberg School of Medicine, Northwestern University, Chicago, IL60611
| | - Jakka Raghavaiah
- Department of Chemistry, Purdue University, West Lafayette, IN47907
- Department of Medicinal Chemistry, Purdue University, West Lafayette, IN47907
| | - Arun K. Ghosh
- Department of Chemistry, Purdue University, West Lafayette, IN47907
- Department of Medicinal Chemistry, Purdue University, West Lafayette, IN47907
| | - Karla J. F. Satchell
- Department of Microbiology-Immunology, Feinberg School of Medicine, Northwestern University, Chicago, IL60611
- Center for Structural Biology of Infectious Diseases, Feinberg School of Medicine, Northwestern University, Chicago, IL60611
| | - Kylie D. Allen
- Department of Biochemistry, Virginia Polytechnic Institute and State University, Blacksburg, VA24061
| | - Clay Fuqua
- Department of Biology, Indiana University, Bloomington, IN47405
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2
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Kratzl F, Urban M, Pandhal J, Shi M, Meng C, Kleigrewe K, Kremling A, Pflüger-Grau K. Pseudomonas putida as saviour for troubled Synechococcus elongatus in a synthetic co-culture - interaction studies based on a multi-OMICs approach. Commun Biol 2024; 7:452. [PMID: 38609451 PMCID: PMC11014904 DOI: 10.1038/s42003-024-06098-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2023] [Accepted: 03/22/2024] [Indexed: 04/14/2024] Open
Abstract
In their natural habitats, microbes rarely exist in isolation; instead, they thrive in consortia, where various interactions occur. In this study, a defined synthetic co-culture of the cyanobacterium S. elongatus cscB, which supplies sucrose to the heterotrophic P. putida cscRABY, is investigated to identify potential interactions. Initial experiments reveal a remarkable growth-promoting effect of the heterotrophic partner on the cyanobacterium, resulting in an up to 80% increase in the growth rate and enhanced photosynthetic capacity. Vice versa, the presence of the cyanobacterium has a neutral effect on P. putida cscRABY, highlighting the resilience of pseudomonads against stress and their potential as co-culture partners. Next, a suitable reference process reinforcing the growth-promoting effect is established in a parallel photobioreactor system, which sets the basis for the analysis of the co-culture at the transcriptome, proteome, and metabolome levels. In addition to several moderate changes, including alterations in the metabolism and stress response in both microbes, this comprehensive multi-OMICs approach strongly hints towards the exchange of further molecules beyond the unidirectional feeding with sucrose. Taken together, these findings provide valuable insights into the complex dynamics between both co-culture partners, indicating multi-level interactions, which can be employed for further streamlining of the co-cultivation system.
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Affiliation(s)
- Franziska Kratzl
- Professorship for Systems Biotechnology, TUM School of Engineering and Design, Technical University of Munich, Garching, Germany
| | - Marlene Urban
- Professorship for Systems Biotechnology, TUM School of Engineering and Design, Technical University of Munich, Garching, Germany
| | - Jagroop Pandhal
- Department of Chemical and Biological Engineering, University of Sheffield, Sheffield, United Kingdom
| | - Mengxun Shi
- Department of Chemical and Biological Engineering, University of Sheffield, Sheffield, United Kingdom
| | - Chen Meng
- Bavarian Center for Biomolecular Mass Spectrometry (BayBioMS), TUM School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Karin Kleigrewe
- Bavarian Center for Biomolecular Mass Spectrometry (BayBioMS), TUM School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Andreas Kremling
- Professorship for Systems Biotechnology, TUM School of Engineering and Design, Technical University of Munich, Garching, Germany
| | - Katharina Pflüger-Grau
- Professorship for Systems Biotechnology, TUM School of Engineering and Design, Technical University of Munich, Garching, Germany.
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3
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Ochoa-Sánchez LE, Martínez JL, Gil-Gil T. Evolution of Resistance against Ciprofloxacin, Tobramycin, and Trimethoprim/Sulfamethoxazole in the Environmental Opportunistic Pathogen Stenotrophomonas maltophilia. Antibiotics (Basel) 2024; 13:330. [PMID: 38667006 PMCID: PMC11047544 DOI: 10.3390/antibiotics13040330] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Revised: 03/27/2024] [Accepted: 04/02/2024] [Indexed: 04/29/2024] Open
Abstract
Stenotrophomonas maltophilia is an opportunistic pathogen that produces respiratory infections in immunosuppressed and cystic fibrosis patients. The therapeutic options to treat S. maltophilia infections are limited since it exhibits resistance to a wide variety of antibiotics such as β-lactams, aminoglycosides, tetracyclines, cephalosporins, macrolides, fluoroquinolones, or carbapenems. The antibiotic combination trimethoprim/sulfamethoxazole (SXT) is the treatment of choice to combat infections caused by S. maltophilia, while ceftazidime, ciprofloxacin, or tobramycin are used in most SXT-resistant infections. In the current study, experimental evolution and whole-genome sequencing (WGS) were used to examine the evolutionary trajectories of S. maltophilia towards resistance against tobramycin, ciprofloxacin, and SXT. The genetic changes underlying antibiotic resistance, as well as the evolutionary trajectories toward that resistance, were determined. Our results determine that genomic changes in the efflux pump regulatory genes smeT and soxR are essential to confer resistance to ciprofloxacin, and the mutation in the rplA gene is significant in the resistance to tobramycin. We identified mutations in folP and the efflux pump regulator smeRV as the basis of SXT resistance. Detailed and reliable knowledge of ciprofloxacin, tobramycin, and SXT resistance is essential for safe and effective use in clinical settings. Herein, we were able to prove once again the extraordinary ability that S. maltophilia has to acquire resistance and the importance of looking for alternatives to combat this resistance.
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Affiliation(s)
- Luz Edith Ochoa-Sánchez
- Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas (CSIC), Darwin 3, 28049 Madrid, Spain;
| | - José Luis Martínez
- Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas (CSIC), Darwin 3, 28049 Madrid, Spain;
| | - Teresa Gil-Gil
- Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas (CSIC), Darwin 3, 28049 Madrid, Spain;
- Department of Biology, Emory University, Atlanta, GA 30322, USA
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4
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Shi T, Sun X, Yuan Q, Wang J, Shen X. Exploring the role of flavin-dependent monooxygenases in the biosynthesis of aromatic compounds. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2024; 17:46. [PMID: 38520003 PMCID: PMC10958861 DOI: 10.1186/s13068-024-02490-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2023] [Accepted: 03/13/2024] [Indexed: 03/25/2024]
Abstract
Hydroxylated aromatic compounds exhibit exceptional biological activities. In the biosynthesis of these compounds, three types of hydroxylases are commonly employed: cytochrome P450 (CYP450), pterin-dependent monooxygenase (PDM), and flavin-dependent monooxygenase (FDM). Among these, FDM is a preferred choice due to its small molecular weight, stable expression in both prokaryotic and eukaryotic fermentation systems, and a relatively high concentration of necessary cofactors. However, the catalytic efficiency of many FDMs falls short of meeting the demands of large-scale production. Additionally, challenges arise from the limited availability of cofactors and compatibility issues among enzyme components. Recently, significant progress has been achieved in improving its catalytic efficiency, but have not yet detailed and informative viewed so far. Therefore, this review emphasizes the advancements in FDMs for the biosynthesis of hydroxylated aromatic compounds and presents a summary of three strategies aimed at enhancing their catalytic efficiency: (a) Developing efficient enzyme mutants through protein engineering; (b) enhancing the supply and rapid circulation of critical cofactors; (c) facilitating cofactors delivery for enhancing FDMs catalytic efficiency. Furthermore, the current challenges and further perspectives on improving catalytic efficiency of FDMs are also discussed.
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Affiliation(s)
- Tong Shi
- State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, 15 Beisanhuan East Road, Chaoyang District, Beijing, 100029, China
| | - Xinxiao Sun
- State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, 15 Beisanhuan East Road, Chaoyang District, Beijing, 100029, China
| | - Qipeng Yuan
- State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, 15 Beisanhuan East Road, Chaoyang District, Beijing, 100029, China
| | - Jia Wang
- State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, 15 Beisanhuan East Road, Chaoyang District, Beijing, 100029, China.
| | - Xiaolin Shen
- State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, 15 Beisanhuan East Road, Chaoyang District, Beijing, 100029, China.
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5
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Greenwich JL, Eagan JL, Feirer N, Boswinkle K, Minasov G, Shuvalova L, Inniss NL, Raghavaiah J, Ghosh AK, Satchell KJ, Allen KD, Fuqua C. Control of Biofilm Formation by an Agrobacterium tumefaciens Pterin-Binding Periplasmic Protein Conserved Among Pathogenic Bacteria. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.18.567607. [PMID: 38014264 PMCID: PMC10680838 DOI: 10.1101/2023.11.18.567607] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
Biofilm formation and surface attachment in multiple Alphaproteobacteria is driven by unipolar polysaccharide (UPP) adhesins. The pathogen Agrobacterium tumefaciens produces a UPP adhesin, which is regulated by the intracellular second messenger cyclic diguanylate monophosphate (cdGMP). Prior studies revealed that DcpA, a diguanylate cyclase-phosphodiesterase (DGC-PDE), is crucial in control of UPP production and surface attachment. DcpA is regulated by PruR, a protein with distant similarity to enzymatic domains known to coordinate the molybdopterin cofactor (MoCo). Pterins are bicyclic nitrogen-rich compounds, several of which are formed via a non-essential branch of the folate biosynthesis pathway, distinct from MoCo. The pterin-binding protein PruR controls DcpA activity, fostering cdGMP breakdown and dampening its synthesis. Pterins are excreted and we report here that PruR associates with these metabolites in the periplasm, promoting interaction with the DcpA periplasmic domain. The pteridine reductase PruA, which reduces specific dihydro-pterin molecules to their tetrahydro forms, imparts control over DcpA activity through PruR. Tetrahydromonapterin preferentially associates with PruR relative to other related pterins, and the PruR-DcpA interaction is decreased in a pruA mutant. PruR and DcpA are encoded in an operon that is conserved amongst multiple Proteobacteria including mammalian pathogens. Crystal structures reveal that PruR and several orthologs adopt a conserved fold, with a pterin-specific binding cleft that coordinates the bicyclic pterin ring. These findings define a new pterin-responsive regulatory mechanism that controls biofilm formation and related cdGMP-dependent phenotypes in A. tumefaciens and is found in multiple additional bacterial pathogens.
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Affiliation(s)
| | - Justin L. Eagan
- Department of Biology, Indiana University, Bloomington, IN 47405 USA
| | - Nathan Feirer
- Department of Biology, Indiana University, Bloomington, IN 47405 USA
| | - Kaleb Boswinkle
- Department of Biochemistry, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061 USA
| | - George Minasov
- Department of Microbiology-Immunology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611 USA
- Center for Structural Biology of Infectious Diseases, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611 USA
| | - Ludmilla Shuvalova
- Department of Pharmacology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611 USA
| | - Nicole L. Inniss
- Department of Microbiology-Immunology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611 USA
- Center for Structural Biology of Infectious Diseases, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611 USA
| | - Jakka Raghavaiah
- Departments of Chemistry and Medicinal Chemistry, Purdue University, West Lafayette, IN 47907 USA
| | - Arun K. Ghosh
- Departments of Chemistry and Medicinal Chemistry, Purdue University, West Lafayette, IN 47907 USA
| | - Karla J.F. Satchell
- Department of Microbiology-Immunology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611 USA
- Center for Structural Biology of Infectious Diseases, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611 USA
| | - Kylie D. Allen
- Department of Biochemistry, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061 USA
| | - Clay Fuqua
- Department of Biology, Indiana University, Bloomington, IN 47405 USA
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6
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Abstract
The metabolism of a bacterial cell stretches beyond its boundaries, often connecting with the metabolism of other cells to form extended metabolic networks that stretch across communities, and even the globe. Among the least intuitive metabolic connections are those involving cross-feeding of canonically intracellular metabolites. How and why are these intracellular metabolites externalized? Are bacteria simply leaky? Here I consider what it means for a bacterium to be leaky, and I review mechanisms of metabolite externalization from the context of cross-feeding. Despite common claims, diffusion of most intracellular metabolites across a membrane is unlikely. Instead, passive and active transporters are likely involved, possibly purging excess metabolites as part of homeostasis. Re-acquisition of metabolites by a producer limits the opportunities for cross-feeding. However, a competitive recipient can stimulate metabolite externalization and initiate a positive-feedback loop of reciprocal cross-feeding.
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Affiliation(s)
- James B McKinlay
- Department of Biology, Indiana University, Bloomington, Indiana, USA;
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7
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Shaw M, Petzer A, Petzer JP, Cloete TT. The pterin binding site of dihydropteroate synthase (DHPS): in silico screening and in vitro antibacterial activity of existing drugs. RESULTS IN CHEMISTRY 2023. [DOI: 10.1016/j.rechem.2023.100863] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/27/2023] Open
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8
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Insights into Molecular Structure of Pterins Suitable for Biomedical Applications. Int J Mol Sci 2022; 23:ijms232315222. [PMID: 36499560 PMCID: PMC9737128 DOI: 10.3390/ijms232315222] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 11/22/2022] [Accepted: 11/30/2022] [Indexed: 12/07/2022] Open
Abstract
Pterins are an inseparable part of living organisms. Pterins participate in metabolic reactions mostly as tetrahydropterins. Dihydropterins are usually intermediates of these reactions, whereas oxidized pterins can be biomarkers of diseases. In this review, we analyze the available data on the quantum chemistry of unconjugated pterins as well as their photonics. This gives a comprehensive overview about the electronic structure of pterins and offers some benefits for biomedicine applications: (1) one can affect the enzymatic reactions of aromatic amino acid hydroxylases, NO synthases, and alkylglycerol monooxygenase through UV irradiation of H4pterins since UV provokes electron donor reactions of H4pterins; (2) the emission properties of H2pterins and oxidized pterins can be used in fluorescence diagnostics; (3) two-photon absorption (TPA) should be used in such pterin-related infrared therapy because single-photon absorption in the UV range is inefficient and scatters in vivo; (4) one can affect pathogen organisms through TPA excitation of H4pterin cofactors, such as the molybdenum cofactor, leading to its detachment from proteins and subsequent oxidation; (5) metal nanostructures can be used for the UV-vis, fluorescence, and Raman spectroscopy detection of pterin biomarkers. Therefore, we investigated both the biochemistry and physical chemistry of pterins and suggested some potential prospects for pterin-related biomedicine.
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9
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Tilocca B, Soggiu A, Iavarone F, Greco V, Putignani L, Ristori MV, Macari G, Spina AA, Morittu VM, Ceniti C, Piras C, Bonizzi L, Britti D, Urbani A, Figeys D, Roncada P. The Functional Characteristics of Goat Cheese Microbiota from a One-Health Perspective. Int J Mol Sci 2022; 23:ijms232214131. [PMID: 36430609 PMCID: PMC9698706 DOI: 10.3390/ijms232214131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 11/10/2022] [Accepted: 11/11/2022] [Indexed: 11/18/2022] Open
Abstract
Goat cheese is an important element of the Mediterranean diet, appreciated for its health-promoting features and unique taste. A pivotal role in the development of these characteristics is attributed to the microbiota and its continuous remodeling over space and time. Nevertheless, no thorough study of the cheese-associated microbiota using two metaomics approaches has previously been conducted. Here, we employed 16S rRNA gene sequencing and metaproteomics to explore the microbiota of a typical raw goat milk cheese at various ripening timepoints and depths of the cheese wheel. The 16S rRNA gene-sequencing and metaproteomics results described a stable microbiota ecology across the selected ripening timepoints, providing evidence for the microbiologically driven fermentation of goat milk products. The important features of the microbiota harbored on the surface and in the core of the cheese mass were highlighted in both compositional and functional terms. We observed the rind microbiota struggling to maintain the biosafety of the cheese through competition mechanisms and/or by preventing the colonization of the cheese by pathobionts of animal or environmental origin. The core microbiota was focused on other biochemical processes, supporting its role in the development of both the health benefits and the pleasant gustatory nuances of goat cheese.
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Affiliation(s)
- Bruno Tilocca
- Department of Health Sciences, University ‘Magna Græcia’ of Catanzaro, Viale Europa, 88100 Catanzaro, Italy
| | - Alessio Soggiu
- One Health Unit, Department of Biomedical, Surgical and Dental Sciences, University of Milano, Via della Commenda 10, 20133 Milano, Italy
| | - Federica Iavarone
- Department of Basic Biotechnological Sciences, Intensivological and Perioperative Clinics, Catholic University of Sacred Heart, Largo Vito, 00168 Rome, Italy
- Clinical Chemistry, Biochemistry and Molecular Biology Operations (UOC), Agostino Gemelli Foundation University Hospital IRCCS, Largo Agostino Gemelli 8, 00168 Rome, Italy
| | - Viviana Greco
- Department of Basic Biotechnological Sciences, Intensivological and Perioperative Clinics, Catholic University of Sacred Heart, Largo Vito, 00168 Rome, Italy
- Clinical Chemistry, Biochemistry and Molecular Biology Operations (UOC), Agostino Gemelli Foundation University Hospital IRCCS, Largo Agostino Gemelli 8, 00168 Rome, Italy
| | - Lorenza Putignani
- Unit of Parasitology, Unit of Human Microbiome, Bambino Gesù Children’s Hospital IRCCS, Piazza Sant’Onofrio, 4, 00165 Rome, Italy
| | - Maria Vittoria Ristori
- Unit of Parasitology, Unit of Human Microbiome, Bambino Gesù Children’s Hospital IRCCS, Piazza Sant’Onofrio, 4, 00165 Rome, Italy
| | | | - Anna Antonella Spina
- Department of Health Sciences, University ‘Magna Græcia’ of Catanzaro, Viale Europa, 88100 Catanzaro, Italy
| | - Valeria Maria Morittu
- Department of Health Sciences, University ‘Magna Græcia’ of Catanzaro, Viale Europa, 88100 Catanzaro, Italy
| | - Carlotta Ceniti
- Department of Health Sciences, University ‘Magna Græcia’ of Catanzaro, Viale Europa, 88100 Catanzaro, Italy
| | - Cristian Piras
- Department of Health Sciences, University ‘Magna Græcia’ of Catanzaro, Viale Europa, 88100 Catanzaro, Italy
| | - Luigi Bonizzi
- One Health Unit, Department of Biomedical, Surgical and Dental Sciences, University of Milano, Via della Commenda 10, 20133 Milano, Italy
| | - Domenico Britti
- Department of Health Sciences, University ‘Magna Græcia’ of Catanzaro, Viale Europa, 88100 Catanzaro, Italy
| | - Andrea Urbani
- Department of Basic Biotechnological Sciences, Intensivological and Perioperative Clinics, Catholic University of Sacred Heart, Largo Vito, 00168 Rome, Italy
- Clinical Chemistry, Biochemistry and Molecular Biology Operations (UOC), Agostino Gemelli Foundation University Hospital IRCCS, Largo Agostino Gemelli 8, 00168 Rome, Italy
| | - Daniel Figeys
- Ottawa Institute of Systems Biology, University of Ottawa, 451 Smyth Road, Ottawa, ON K1H 8M5, Canada
| | - Paola Roncada
- Department of Health Sciences, University ‘Magna Græcia’ of Catanzaro, Viale Europa, 88100 Catanzaro, Italy
- Correspondence: ; Tel.: +39-096-1369-4284
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10
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Ciavardini A, Galdenzi F, Coreno M, Ninno GD, Grazioli C, de Simone M, Totani R, Piccirillo S, Plekan O, Ponzi A. Valence and core-level X-ray photoemission spectroscopy of light-sensitive molecules: Lumazine and alloxazine. Chem Phys 2022. [DOI: 10.1016/j.chemphys.2022.111757] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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11
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Francescutti CM, Martin A, Hanly JJ. Knockdowns of red Malphigian tubules reveal pigmentation roles in the milkweed bug. JOURNAL OF EXPERIMENTAL ZOOLOGY. PART B, MOLECULAR AND DEVELOPMENTAL EVOLUTION 2022; 338:382-387. [PMID: 35189035 DOI: 10.1002/jez.b.23123] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Revised: 01/25/2022] [Accepted: 02/03/2022] [Indexed: 06/14/2023]
Abstract
Classical Drosophila eye color mutations have unearthed a toolkit of genes that have permitted candidate gene studies of the outstanding diversity of coloration patterns in other insects. The gene underlying the eye color phenotypes of the red Malphigian tubules (red) fly mutant was mapped to a LysM domain gene of unknown molecular function. Here, we used RNAi to test the role of a red ortholog in the pigmentation of the milkweed bug Oncopeltus fasciatus, and contrast its effect with the ommochrome biosynthetic pathway gene vermilion (ver). Pigmentation was reduced in the cuticle of embryonic legs and first instar abdomens following parental RNAi against red, but not against ver, likely reflecting an effect on pterin biogenesis. Nymphal RNAi of red and ver both resulted in adult eye depigmentation, consistent with an effect on ommochrome content. These results suggest red loss-of-function impacts biochemically distinct types of pigments, and we discuss its putative role in the biogenesis of lysosome-related organelles such as ommochromasomes and pterinosomes.
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Affiliation(s)
- Caroline M Francescutti
- Department of Biological Sciences, The George Washington University, Washington, District of Columbia, USA
| | - Arnaud Martin
- Department of Biological Sciences, The George Washington University, Washington, District of Columbia, USA
| | - Joseph J Hanly
- Department of Biological Sciences, The George Washington University, Washington, District of Columbia, USA
- Smithsonian Tropical Research Institute, Gamboa, Panama
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12
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An Overview of Emerging Cyanide Bioremediation Methods. Processes (Basel) 2022. [DOI: 10.3390/pr10091724] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/07/2022] Open
Abstract
Cyanide compounds are hazardous compounds which are extremely toxic to living organisms, especially free cyanide in the form of hydrogen cyanide gas (HCN) and cyanide ion (CN−). These cyanide compounds are metabolic inhibitors since they can tightly bind to the metals of metalloenzymes. Anthropogenic sources contribute significantly to CN− contamination in the environment, more specifically to surface and underground waters. The treatment processes, such as chemical and physical treatment processes, have been implemented. However, these processes have drawbacks since they generate additional contaminants which further exacerbates the environmental pollution. The biological treatment techniques are mostly overlooked as an alternative to the conventional physical and chemical methods. However, the recent research has focused substantially on this method, with different reactor configurations that were proposed. However, minimal attention was given to the emerging technologies that sought to accelerate the treatment with a subsequent resource recovery from the process. Hence, this review focuses on the recent emerging tools that can be used to accelerate cyanide biodegradation. These tools include, amongst others, electro-bioremediation, anaerobic biodegradation and the use of microbial fuel cell technology. These processes were demonstrated to have the possibility of producing value-added products, such as biogas, co-factors of neurotransmitters and electricity from the treatment process.
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13
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Koch M, Noonan AJC, Qiu Y, Dofher K, Kieft B, Mottahedeh S, Shastri M, Hallam SJ. The survivor strain: isolation and characterization of Phormidium yuhuli AB48, a filamentous phototactic cyanobacterium with biotechnological potential. Front Bioeng Biotechnol 2022; 10:932695. [PMID: 36046667 PMCID: PMC9420970 DOI: 10.3389/fbioe.2022.932695] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Accepted: 06/27/2022] [Indexed: 11/13/2022] Open
Abstract
Despite their recognized potential, current applications of cyanobacteria as microbial cell factories remain in early stages of development. This is partly due to the fact that engineered strains are often difficult to grow at scale. This technical challenge contrasts with the dense and highly productive cyanobacteria populations thriving in many natural environments. It has been proposed that the selection of strains pre-adapted for growth in industrial photobioreactors could enable more productive cultivation outcomes. Here, we described the initial morphological, physiological, and genomic characterization of Phormidium yuhuli AB48 isolated from an industrial photobioreactor environment. P. yuhuli AB48 is a filamentous phototactic cyanobacterium with a growth rate comparable to Synechocystis sp. PCC 6803. The isolate forms dense biofilms under high salinity and alkaline conditions and manifests a similar nutrient profile to Arthrospira platensis (Spirulina). We sequenced, assembled, and analyzed the P. yuhuli AB48 genome, the first closed circular isolate reference genome for a member of the Phormidium genus. We then used cultivation experiments in combination with proteomics and metabolomics to investigate growth characteristics and phenotypes related to industrial scale cultivation, including nitrogen and carbon utilization, salinity, and pH acclimation, as well as antibiotic resistance. These analyses provide insight into the biological mechanisms behind the desirable growth properties manifested by P. yuhuli AB48 and position it as a promising microbial cell factory for industrial-scale bioproduction[221, 1631].
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Affiliation(s)
- Moritz Koch
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada
| | - Avery J. C. Noonan
- Genome Science and Technology Program, University of British Columbia, Vancouver, BC, Canada
- ECOSCOPE Training Program, University of British Columbia, Vancouver, BC, Canada
| | - Yilin Qiu
- Genome Science and Technology Program, University of British Columbia, Vancouver, BC, Canada
| | - Kalen Dofher
- Genome Science and Technology Program, University of British Columbia, Vancouver, BC, Canada
| | - Brandon Kieft
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada
| | | | | | - Steven J. Hallam
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada
- Genome Science and Technology Program, University of British Columbia, Vancouver, BC, Canada
- ECOSCOPE Training Program, University of British Columbia, Vancouver, BC, Canada
- Graduate Program in Bioinformatics, University of British Columbia, Vancouver, BC, Canada
- Life Sciences Institute, University of British Columbia, Vancouver, BC, Canada
- *Correspondence: Steven J. Hallam,
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14
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Colston KJ, Basu P. Synthesis, Redox and Spectroscopic Properties of Pterin of Molybdenum Cofactors. Molecules 2022; 27:3324. [PMID: 35630801 PMCID: PMC9146068 DOI: 10.3390/molecules27103324] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Revised: 05/18/2022] [Accepted: 05/19/2022] [Indexed: 12/10/2022] Open
Abstract
Pterins are bicyclic heterocycles that are found widely across Nature and are involved in a variety of biological functions. Notably, pterins are found at the core of molybdenum cofactor (Moco) containing enzymes in the molybdopterin (MPT) ligand that coordinates molybdenum and facilitates cofactor activity. Pterins are diverse and can be widely functionalized to tune their properties. Herein, the general methods of synthesis, redox and spectroscopic properties of pterin are discussed to provide more insight into pterin chemistry and their importance to biological systems.
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Affiliation(s)
| | - Partha Basu
- Department of Chemistry and Chemical Biology, Indiana University-Purdue University Indianapolis, Indianapolis, IN 46202, USA;
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15
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Desruelle AV, de Maistre S, Gaillard S, Richard S, Tardivel C, Martin JC, Blatteau JE, Boussuges A, Rives S, Risso JJ, Vallee N. Cecal Metabolomic Fingerprint of Unscathed Rats: Does It Reflect the Good Response to a Provocative Decompression? Front Physiol 2022; 13:882944. [PMID: 35655958 PMCID: PMC9152359 DOI: 10.3389/fphys.2022.882944] [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: 02/24/2022] [Accepted: 04/27/2022] [Indexed: 11/23/2022] Open
Abstract
On one side, decompression sickness (DCS) with neurological disorders lead to a reshuffle of the cecal metabolome of rats. On the other side, there is also a specific and different metabolomic signature in the cecum of a strain of DCS-resistant rats, that are not exposed to hyperbaric protocol. We decide to study a conventional strain of rats that resist to an accident-provoking hyperbaric exposure, and we hypothesize that the metabolomic signature put forward may correspond to a physiological response adapted to the stress induced by diving. The aim is to verify and characterize whether the cecal compounds of rats resistant to the provocative dive have a cecal metabolomic signature different from those who do not dive. 35 asymptomatic diver rats are selected to be compared to 21 rats non-exposed to the hyperbaric protocol. Because our aim is essentially to study the differences in the cecal metabolome associated with the hyperbaric exposure, about half of the rats are fed soy and the other half of maize in order to better rule out the effect of the diet itself. Lower levels of IL-1β and glutathione peroxidase (GPX) activity are registered in blood of diving rats. No blood cell mobilization is noted. Conventional and ChemRICH approaches help the metabolomic interpretation of the 185 chemical compounds analyzed in the cecal content. Statistical analysis show a panel of 102 compounds diet related. 19 are in common with the hyperbaric protocol effect. Expression of 25 compounds has changed in the cecal metabolome of rats resistant to the provocative dive suggesting an alteration of biliary acids metabolism, most likely through actions on gut microbiota. There seem to be also weak changes in allocations dedicated to various energy pathways, including hormonal reshuffle. Some of the metabolites may also have a role in regulating inflammation, while some may be consumed for the benefit of oxidative stress management.
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Affiliation(s)
- Anne-Virginie Desruelle
- Institut de Recherche Biomédicale des Armées, Equipe de Recherche Subaquatique Opérationnelle, Toulon Cedex, France
| | - Sébastien de Maistre
- Service de Médecine Hyperbare Expertise Plongée, Hôpital d'Instruction des Armées Sainte-Anne, Toulon Cedex, France
| | | | | | - Catherine Tardivel
- C2VN, INRAE, INSERM, BIOMET, Aix Marseille University, Faculté de Médecine La Timone, Marseille, France
| | - Jean-Charles Martin
- C2VN, INRAE, INSERM, BIOMET, Aix Marseille University, Faculté de Médecine La Timone, Marseille, France
| | - Jean-Eric Blatteau
- Service de Médecine Hyperbare Expertise Plongée, Hôpital d'Instruction des Armées Sainte-Anne, Toulon Cedex, France
| | - Alain Boussuges
- Institut de Recherche Biomédicale des Armées, Equipe de Recherche Subaquatique Opérationnelle, Toulon Cedex, France
| | - Sarah Rives
- Institut de Recherche Biomédicale des Armées, Equipe de Recherche Subaquatique Opérationnelle, Toulon Cedex, France
| | - Jean-Jacques Risso
- Institut de Recherche Biomédicale des Armées, Equipe de Recherche Subaquatique Opérationnelle, Toulon Cedex, France
| | - Nicolas Vallee
- Institut de Recherche Biomédicale des Armées, Equipe de Recherche Subaquatique Opérationnelle, Toulon Cedex, France
- *Correspondence: Nicolas Vallee,
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16
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Bommasamudram J, Kumar P, Kapur S, Sharma D, Devappa S. Development of Thermotolerant Lactobacilli Cultures with Improved Probiotic Properties Using Adaptive Laboratory Evolution Method. Probiotics Antimicrob Proteins 2022:10.1007/s12602-021-09892-3. [PMID: 35060080 DOI: 10.1007/s12602-021-09892-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/14/2021] [Indexed: 12/20/2022]
Abstract
Probiotics play a significant role in functional foods. Heat stress and dehydration are the two principal mechanisms leading to inactivation and loss of probiotics viability in its production. There is a need to develop an industrial organism to withstand higher temperatures during its processing and storage. This current study aims to develop thermotolerant strains of Lacticaseibacillus casei N (N) and Lactobacillus helveticus NRRL B-4526 (H) by acclimatizing the wild-type strains to the higher temperature of 45 °C by adaptive laboratory evolution. A two-fold increase in biomass was observed in both acclimatized strains up to the 200th generation, which subsequently remained stable after 500 generations. The morphological change of these acclimatized strains was observed under scanning electron microscopy. Also, there was an increase in probiotic attributes of these acclimatized strains compared to their wild-types. Among two acclimatized strains, L. casei N-45 had shown higher tolerance in the acidic pH 3.0 (89.31%), the bile of 0.3% (84.45%), simulated gastric juice (79.12%), and simulated intestinal juice (73.86%). There was also an increase in salt tolerance (NaCl), radical scavenging activity, autoaggregation, coaggregation, and hydrophobicity of these adapted strains. The total protein profiling using 2D gel electrophoresis reveals the differences in protein expressions between wild-type and acclimatized strains. Specific protein spots from acclimatized strains of H-45 and N-45 were further subjected to MALDI-TOF MS/MS. Some of the identified proteins were recognized to play a role in RNA chaperones and protein synthesis during stress conditions.
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17
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Andrade P, Carneiro M. Pterin-based pigmentation in animals. Biol Lett 2021; 17:20210221. [PMID: 34403644 PMCID: PMC8370806 DOI: 10.1098/rsbl.2021.0221] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Accepted: 07/26/2021] [Indexed: 12/19/2022] Open
Abstract
Pterins are one of the major sources of bright coloration in animals. They are produced endogenously, participate in vital physiological processes and serve a variety of signalling functions. Despite their ubiquity in nature, pterin-based pigmentation has received little attention when compared to other major pigment classes. Here, we summarize major aspects relating to pterin pigmentation in animals, from its long history of research to recent genomic studies on the molecular mechanisms underlying its evolution. We argue that pterins have intermediate characteristics (endogenously produced, typically bright) between two well-studied pigment types, melanins (endogenously produced, typically cryptic) and carotenoids (dietary uptake, typically bright), providing unique opportunities to address general questions about the biology of coloration, from the mechanisms that determine how different types of pigmentation evolve to discussions on honest signalling hypotheses. Crucial gaps persist in our knowledge on the molecular basis underlying the production and deposition of pterins. We thus highlight the need for functional studies on systems amenable for laboratory manipulation, but also on systems that exhibit natural variation in pterin pigmentation. The wealth of potential model species, coupled with recent technological and analytical advances, make this a promising time to advance research on pterin-based pigmentation in animals.
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Affiliation(s)
- Pedro Andrade
- CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Vairão, Portugal
| | - Miguel Carneiro
- CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Vairão, Portugal
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18
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Shulpekova Y, Nechaev V, Kardasheva S, Sedova A, Kurbatova A, Bueverova E, Kopylov A, Malsagova K, Dlamini JC, Ivashkin V. The Concept of Folic Acid in Health and Disease. Molecules 2021; 26:molecules26123731. [PMID: 34207319 PMCID: PMC8235569 DOI: 10.3390/molecules26123731] [Citation(s) in RCA: 60] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Revised: 06/12/2021] [Accepted: 06/17/2021] [Indexed: 12/18/2022] Open
Abstract
Folates have a pterine core structure and high metabolic activity due to their ability to accept electrons and react with O-, S-, N-, C-bounds. Folates play a role as cofactors in essential one-carbon pathways donating methyl-groups to choline phospholipids, creatine, epinephrine, DNA. Compounds similar to folates are ubiquitous and have been found in different animals, plants, and microorganisms. Folates enter the body from the diet and are also synthesized by intestinal bacteria with consequent adsorption from the colon. Three types of folate and antifolate cellular transporters have been found, differing in tissue localization, substrate affinity, type of transferring, and optimal pH for function. Laboratory criteria of folate deficiency are accepted by WHO. Severe folate deficiencies, manifesting in early life, are seen in hereditary folate malabsorption and cerebral folate deficiency. Acquired folate deficiency is quite common and is associated with poor diet and malabsorption, alcohol consumption, obesity, and kidney failure. Given the observational data that folates have a protective effect against neural tube defects, ischemic events, and cancer, food folic acid fortification was introduced in many countries. However, high physiological folate concentrations and folate overload may increase the risk of impaired brain development in embryogenesis and possess a growth advantage for precancerous altered cells.
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Affiliation(s)
- Yulia Shulpekova
- Department of Internal Diseases Propedeutics, Sechenov University, 119121 Moscow, Russia; (Y.S.); (V.N.); (S.K.); (A.S.); (A.K.); (E.B.); (V.I.)
| | - Vladimir Nechaev
- Department of Internal Diseases Propedeutics, Sechenov University, 119121 Moscow, Russia; (Y.S.); (V.N.); (S.K.); (A.S.); (A.K.); (E.B.); (V.I.)
| | - Svetlana Kardasheva
- Department of Internal Diseases Propedeutics, Sechenov University, 119121 Moscow, Russia; (Y.S.); (V.N.); (S.K.); (A.S.); (A.K.); (E.B.); (V.I.)
| | - Alla Sedova
- Department of Internal Diseases Propedeutics, Sechenov University, 119121 Moscow, Russia; (Y.S.); (V.N.); (S.K.); (A.S.); (A.K.); (E.B.); (V.I.)
| | - Anastasia Kurbatova
- Department of Internal Diseases Propedeutics, Sechenov University, 119121 Moscow, Russia; (Y.S.); (V.N.); (S.K.); (A.S.); (A.K.); (E.B.); (V.I.)
| | - Elena Bueverova
- Department of Internal Diseases Propedeutics, Sechenov University, 119121 Moscow, Russia; (Y.S.); (V.N.); (S.K.); (A.S.); (A.K.); (E.B.); (V.I.)
| | - Arthur Kopylov
- Biobanking Group, Branch of Institute of Biomedical Chemistry “Scientific and Education Center”, 119121 Moscow, Russia;
| | - Kristina Malsagova
- Biobanking Group, Branch of Institute of Biomedical Chemistry “Scientific and Education Center”, 119121 Moscow, Russia;
- Correspondence: ; Tel.: +7-499-764-9878
| | | | - Vladimir Ivashkin
- Department of Internal Diseases Propedeutics, Sechenov University, 119121 Moscow, Russia; (Y.S.); (V.N.); (S.K.); (A.S.); (A.K.); (E.B.); (V.I.)
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19
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Bernardes JS, Eberle RJ, Vieira FRJ, Coronado MA. A comparative pan-genomic analysis of 53 C. pseudotuberculosis strains based on functional domains. J Biomol Struct Dyn 2020; 39:6974-6986. [PMID: 32779519 DOI: 10.1080/07391102.2020.1805017] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Corynebacterium pseudotuberculosis is a pathogenic bacterium with great veterinary and economic importance. It is classified into two biovars: ovis, nitrate-negative, that causes lymphadenitis in small ruminants and equi, nitrate-positive, causing ulcerative lymphangitis in equines. With the explosive growth of available genomes of several strains, pan-genome analysis has opened new opportunities for understanding the dynamics and evolution of C. pseudotuberculosis. However, few pan-genomic studies have compared biovars equi and ovis. Such studies have considered a reduced number of strains and compared entire genomes. Here we conducted an original pan-genome analysis based on protein sequences and their functional domains. We considered 53 C. pseudotuberculosis strains from both biovars isolated from different hosts and countries. We have analysed conserved domains, common domains more frequently found in each biovar and biovar-specific (unique) domains. Our results demonstrated that biovar equi is more variable; there is a significant difference in the number of proteins per strains, probably indicating the occurrence of more gene loss/gain events. Moreover, strains of biovar equi presented a higher number of biovar-specific domains, 77 against only eight in biovar ovis, most of them are associated with virulence mechanisms. With this domain analysis, we have identified functional differences among strains of biovars ovis and equi that could be related to niche-adaptation and probably help to better understanding mechanisms of virulence and pathogenesis. The distribution patterns of functional domains identified in this work might have impacts on bacterial physiology and lifestyle, encouraging the development of new diagnoses, vaccines, and treatments for C. pseudotuberculosis diseases.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Juliana S Bernardes
- Laboratoire de Biologie Computationelle et Quantitative, UMR 7238, CNRS, Sorbonne Université, Paris, France
| | - Raphael J Eberle
- Multiuser Center for Biomolecular Innovation, Department of Physics, Instituto de Biociências, Letras e Ciências Exatas (Ibilce), Universidade Estadual Paulista (UNESP), São Jose do Rio Preto, Brazil
| | - Fabio R J Vieira
- Institut de Biologie de l'École Normale Supérieure (IBENS), Paris, France
| | - Mônika A Coronado
- Multiuser Center for Biomolecular Innovation, Department of Physics, Instituto de Biociências, Letras e Ciências Exatas (Ibilce), Universidade Estadual Paulista (UNESP), São Jose do Rio Preto, Brazil.,Institute of Biological Information Processing (IBI-7: Strucutral Biochemistry), Forschungszentrum Juelich, Juelich, Germany
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20
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Labine M, DePledge L, Feirer N, Greenwich J, Fuqua C, Allen KD. Enzymatic and Mutational Analysis of the PruA Pteridine Reductase Required for Pterin-Dependent Control of Biofilm Formation in Agrobacterium tumefaciens. J Bacteriol 2020; 202:JB.00098-20. [PMID: 32482721 PMCID: PMC8404713 DOI: 10.1128/jb.00098-20] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Accepted: 05/22/2020] [Indexed: 11/20/2022] Open
Abstract
Pterins are ubiquitous biomolecules with diverse functions including roles as cofactors, pigments, and redox mediators. Recently, a novel pterin-dependent signaling pathway that controls biofilm formation was identified in the plant pathogen, Agrobacterium tumefaciens A key player in this pathway is a pteridine reductase termed PruA, where its enzymatic activity has been shown to control surface attachment and limit biofilm formation. Here, we biochemically characterize PruA to investigate the catalytic properties and substrate specificity of this pteridine reductase. PruA demonstrates maximal catalytic efficiency with dihydrobiopterin and comparable activities with the stereoisomers dihydromonapterin and dihydroneopterin. Since A. tumefaciens does not synthesize or utilize biopterins, the likely physiological substrate is dihydromonapterin or dihydroneopterin, or both. Notably, PruA does not exhibit pteridine reductase activity with dihydrofolate or fully oxidized pterins. Site-directed mutagenesis studies of a conserved tyrosine residue, the key component of a putative catalytic triad, indicate that this tyrosine is not directly involved in PruA catalysis but may be important for substrate or cofactor binding. Additionally, mutagenesis of the arginine residue in the N-terminal TGX3RXG motif significantly reduces the catalytic efficiency of PruA, supporting its proposed role in pterin binding and catalysis. Finally, we report the enzymatic characterization of PruA homologs from Pseudomonas aeruginosa and Brucella abortus, thus expanding the roles and potential significance of pteridine reductases in diverse bacteria.Importance Biofilms are complex multicellular communities that are formed by diverse bacteria. In the plant pathogen, Agrobacterium tumefaciens, the transition from a free-living motile state to a non-motile biofilm state is governed by a novel signaling pathway involving small molecules called pterins. The involvement of pterins in biofilm formation is unexpected and prompts many questions about the molecular details of this pathway. This work biochemically characterizes the PruA pteridine reductase involved in the signaling pathway to reveal its enzymatic properties and substrate preference, thus providing important insight into pterin biosynthesis and its role in A. tumefaciens biofilm control. Additionally, the enzymatic characteristics of related pteridine reductases from mammalian pathogens are examined to uncover potential roles of these enzymes in other bacteria.
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Affiliation(s)
- Monica Labine
- Department of Biochemistry, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA
| | - Lisa DePledge
- Department of Chemistry and Biochemistry, Gonzaga University, Spokane, WA, USA
| | - Nathan Feirer
- Department of Biology, Indiana University, Bloomington, Indiana, USA
| | | | - Clay Fuqua
- Department of Biology, Indiana University, Bloomington, Indiana, USA
| | - Kylie D Allen
- Department of Biochemistry, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA
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21
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Teimouri MB, Meydani A, Panji Z. A One-Pot Synthesis of 5-(1,3-Dimethyl-2,6-Dioxo-5-{[(1E)-Arylmethylene]Amino}-1,2,3,6-Tetrahydropyrimidin-4-yl)-1,3,7,9-Tetramethyl-5,10-Dihydropyrimido[5,4-g]Pteridine-2,4,6,8(1H,3H,7H,9H)-Tetrone via a Pseudo Four-Component Domino Reaction. Polycycl Aromat Compd 2019. [DOI: 10.1080/10406638.2019.1678182] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Affiliation(s)
| | - Ali Meydani
- Faculty of Chemistry, Kharazmi University, Tehran, Iran
| | - Zahra Panji
- Faculty of Chemistry, Kharazmi University, Tehran, Iran
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22
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Daniels BJ, Li FF, Furkert DP, Brimble MA. Naturally Occurring Lumazines. JOURNAL OF NATURAL PRODUCTS 2019; 82:2054-2065. [PMID: 31317731 DOI: 10.1021/acs.jnatprod.9b00351] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Natural products containing a lumazine motif were first isolated from natural sources in 1940. These natural products are relatively rare, with fewer than 100 lumazines known to occur in Nature. This review discusses the isolation of lumazines, their biological activity, and their biosynthesis, where known.
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Affiliation(s)
- Benjamin J Daniels
- School of Chemical Sciences , The University of Auckland , 23 Symonds Street , Auckland 1010 , New Zealand
| | - Freda F Li
- School of Chemical Sciences , The University of Auckland , 23 Symonds Street , Auckland 1010 , New Zealand
| | - Daniel P Furkert
- School of Chemical Sciences , The University of Auckland , 23 Symonds Street , Auckland 1010 , New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery , The University of Auckland , 3 Symonds Street , Auckland 1010 , New Zealand
| | - Margaret A Brimble
- School of Chemical Sciences , The University of Auckland , 23 Symonds Street , Auckland 1010 , New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery , The University of Auckland , 3 Symonds Street , Auckland 1010 , New Zealand
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23
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Floyd MAM, Williams AJ, Grubisic A, Emerson D. Metabolic Processes Preserved as Biosignatures in Iron-Oxidizing Microorganisms: Implications for Biosignature Detection on Mars. ASTROBIOLOGY 2019; 19:40-52. [PMID: 30044121 PMCID: PMC6338579 DOI: 10.1089/ast.2017.1745] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Iron-oxidizing bacteria occupy a distinct environmental niche. These chemolithoautotrophic organisms require very little oxygen (when neutrophilic) or outcompete oxygen for access to Fe(II) (when acidophilic). The utilization of Fe(II) as an electron donor makes them strong analog organisms for any potential life that could be found on Mars. Despite their importance to the elucidation of early life on, and potentially beyond, Earth, many details of their metabolism remain unknown. By using on-line thermochemolysis and gas chromatography-mass spectrometry (GC-MS), a distinct signal for a low-molecular-weight molecule was discovered in multiple iron-oxidizing isolates as well as several iron-dominated environmental samples, from freshwater and marine environments and in both modern and older iron rock samples. This GC-MS signal was neither detected in organisms that did not use Fe(II) as an electron donor nor present in iron mats in which organic carbon was destroyed by heating. Mass spectral analysis indicates that the molecule bears the hallmarks of a pterin-bearing molecule. Genomic analysis has previously identified a molybdopterin that could be part of the electron transport chain in a number of lithotrophic iron-oxidizing bacteria, suggesting one possible source for this signal is the pterin component of this protein. The rock samples indicate the possibility that the molecule can be preserved within lithified sedimentary rocks. The specificity of the signal to organisms requiring iron in their metabolism makes this a novel biosignature with which to investigate both the evolution of life on ancient Earth and potential life on Mars.
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Affiliation(s)
| | - Amy J Williams
- 1 NASA Goddard Space Flight Center , Greenbelt, Maryland
- 2 Department of Physics, Astronomy, and Geosciences, Towson University , Towson, Maryland
| | | | - David Emerson
- 3 Bigelow Laboratory for Ocean Sciences , East Boothbay, Maine
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24
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Function and Regulation of Agrobacterium tumefaciens Cell Surface Structures that Promote Attachment. Curr Top Microbiol Immunol 2018; 418:143-184. [PMID: 29998422 DOI: 10.1007/82_2018_96] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Agrobacterium tumefaciens attaches stably to plant host tissues and abiotic surfaces. During pathogenesis, physical attachment to the site of infection is a prerequisite to infection and horizontal gene transfer to the plant. Virulent and avirulent strains may also attach to plant tissue in more benign plant associations, and as with other soil microbes, to soil surfaces in the terrestrial environment. Although most A. tumefaciens virulence functions are encoded on the tumor-inducing plasmid, genes that direct general surface attachment are chromosomally encoded, and thus this process is not obligatorily tied to virulence, but is a more fundamental capacity. Several different cellular structures are known or suspected to contribute to the attachment process. The flagella influence surface attachment primarily via their propulsive activity, but control of their rotation during the transition to the attached state may be quite complex. A. tumefaciens produces several pili, including the Tad-type Ctp pili, and several plasmid-borne conjugal pili encoded by the Ti and At plasmids, as well as the so-called T-pilus, involved in interkingdom horizontal gene transfer. The Ctp pili promote reversible interactions with surfaces, whereas the conjugal and T-pili drive horizontal gene transfer (HGT) interactions with other cells and tissues. The T-pilus is likely to contribute to physical association with plant tissues during DNA transfer to plants. A. tumefaciens can synthesize a variety of polysaccharides including cellulose, curdlan (β-1,3 glucan), β-1,2 glucan (cyclic and linear), succinoglycan, and a localized polysaccharide(s) that is confined to a single cellular pole and is called the unipolar polysaccharide (UPP). Lipopolysaccharides are also in the outer leaflet of the outer membrane. Cellulose and curdlan production can influence attachment under certain conditions. The UPP is required for stable attachment under a range of conditions and on abiotic and biotic surfaces. Other factors that have been reported to play a role in attachment include the elusive protein called rhicadhesin. The process of surface attachment is under extensive regulatory control and can be modulated by environmental conditions, as well as by direct responses to surface contact. Complex transcriptional and post-transcriptional control circuitry underlies much of the production and deployment of these attachment functions.
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