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Ahmed S, Bhat AR, Rahiman AK, Dongre RS, Hasan AH, Niranjan V, C L, Sheikh SA, Jamalis J, Berredjem M, Kawsar SMA. Green synthesis, antibacterial and antifungal evaluation of new thiazolidine-2,4-dione derivatives: molecular dynamic simulation, POM study and identification of antitumor pharmacophore sites. J Biomol Struct Dyn 2023:1-17. [PMID: 37768136 DOI: 10.1080/07391102.2023.2258404] [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: 05/12/2023] [Accepted: 09/06/2023] [Indexed: 09/29/2023]
Abstract
In this study, a series of thiazolidine-2,4-dione derivatives 3a-i were synthesized and evaluated for antibacterial activity against Gram-positive and Gram-negative strains of Bacillus licheniformis, Escherichia coli, Pseudomonas aeruginosa and Staphylococcus aureus. Newly prepared thiazolidine (TZD) derivatives were further screened separately for in vitro antifungal activity against cultures of fungal species, namely, Aspergillus niger, Alternaria brassicicola, Chaetomium murorum, Fusarium oxysporum, Lycopodium sp. and Penicillium notatum. The electron-donating substituents (-OH and -OCH3) and electron-withdrawing substituents (-Cl and -NO2) on the attached arylidene moieties of five-membered heterocyclic ring enhanced the broad spectrum of antimicrobial and antifungal activities. The molecular docking study has revealed that compound 3h strongly interacts with the catalytic residues of the active site of the β-carbonic anhydrase (P. aeruginosa) and has the best docking score. In silico pharmacokinetics studies showed the drug-likeness and non-toxic nature of the synthesized compounds, which indicates the combined antibacterial, antiviral and antitumor pharmacophore sites of the targeted drug. This work demonstrates that potential TZD derivatives bind to different types of bacterial and fungal pathogens for circumventing their activities and opens avenues for the development of newer drug candidates that can target bacterial and fungal pathogens.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Sumeer Ahmed
- Post-Graduate and Research Department of Chemistry, The New College (Autonomous), University of Madras, Chennai, India
| | - Ajmal R Bhat
- Department of Chemistry, RTM Nagpur University, Nagpur, India
| | - Aziz Kalilur Rahiman
- Post-Graduate and Research Department of Chemistry, The New College (Autonomous), University of Madras, Chennai, India
| | | | - Aso Hameed Hasan
- Department of Chemistry, College of Science, University of Garmian, Kalar, Iraq
| | - Vidya Niranjan
- Department of Biotechnology, R V College of Engineering, Bengaluru, India
| | - Lavanya C
- Department of Biotechnology, R V College of Engineering, Bengaluru, India
| | - S A Sheikh
- Department of Physics, National Institute of Technology, Srinagar, Kashmir, India
| | - Joazaizulfazli Jamalis
- Faculty of Science, Department of Chemistry, Universiti Teknologi Malaysia, Johor, Malaysia
| | - Malika Berredjem
- Laboratory of Applied Organic Chemistry LCOA, Synthesis of Biomolecules and Molecular Modelling Group, Badji-Mokhtar - Annaba University, Annaba, Algeria
| | - Sarkar M A Kawsar
- Laboratory of Carbohydrate and Nucleoside Chemistry (LCNC), Department of Chemistry, Faculty of Science, University of Chittagong, Chittagong, Bangladesh
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Capasso C. Carbonic Anhydrases: A Superfamily of Ubiquitous Enzymes. Int J Mol Sci 2023; 24:ijms24087014. [PMID: 37108175 PMCID: PMC10138334 DOI: 10.3390/ijms24087014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Accepted: 03/24/2023] [Indexed: 04/29/2023] Open
Abstract
Numerous physiological and pathological cellular processes depend on the ability [...].
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Affiliation(s)
- Clemente Capasso
- Institute of Biosciences and Bioresources, National Research Council (CNR), via Pietro Castellino 111, 80131 Napoli, Italy
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3
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Nocentini A, Capasso C, Supuran CT. Carbonic Anhydrase Inhibitors as Novel Antibacterials in the Era of Antibiotic Resistance: Where Are We Now? Antibiotics (Basel) 2023; 12:antibiotics12010142. [PMID: 36671343 PMCID: PMC9854953 DOI: 10.3390/antibiotics12010142] [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: 12/21/2022] [Revised: 12/29/2022] [Accepted: 01/09/2023] [Indexed: 01/12/2023] Open
Abstract
Resistance to antibiotic treatment developed by bacteria in humans and animals occurs when the microorganisms resist treatment with clinically approved antibiotics. Actions must be implemented to stop the further development of antibiotic resistance and the subsequent emergence of superbugs. Medication repurposing/repositioning is one strategy that can help find new antibiotics, as it speeds up drug development phases. Among them, the Zn2+ ion binders, such as sulfonamides and their bioisosteres, are considered the most promising compounds to obtain novel antibacterials, thus avoiding antibiotic resistance. Sulfonamides and their bioisosteres have drug-like properties well-known for decades and are suitable lead compounds for developing new pharmacological agent families for inhibiting carbonic anhydrases (CAs). CAs are a superfamily of metalloenzymes catalyzing the reversible reaction of CO2 hydration to HCO3- and H+, being present in most bacteria in multiple genetic families (α-, β-, γ- and ι-classes). These enzymes, acting as CO2 transducers, are promising drug targets because their activity influences microbe proliferation, biosynthetic pathways, and pathogen persistence in the host. In their natural or slightly modified scaffolds, sulfonamides/sulfamates/sulamides inhibit CAs in vitro and in vivo, in mouse models infected with antibiotic-resistant strains, confirming thus their role in contrasting bacterial antibiotic resistance.
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Affiliation(s)
- Alessio Nocentini
- NEUROFARBA Department, Section of Pharmaceutical and Nutraceutical Sciences, University of Florence, 50019 Firenze, Italy
| | - Clemente Capasso
- Department of Biology, Agriculture and Food Sciences, Institute of Biosciences and Bioresources, CNR, 80131 Napoli, Italy
- Correspondence: (C.C.); (C.T.S.)
| | - Claudiu T. Supuran
- NEUROFARBA Department, Section of Pharmaceutical and Nutraceutical Sciences, University of Florence, 50019 Firenze, Italy
- Correspondence: (C.C.); (C.T.S.)
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Maheshwari N, Thakur IS, Srivastava S. Role of carbon-dioxide sequestering bacteria for clean air environment and prospective production of biomaterials: a sustainable approach. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:38950-38971. [PMID: 35304714 DOI: 10.1007/s11356-022-19393-7] [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: 10/20/2021] [Accepted: 02/20/2022] [Indexed: 06/14/2023]
Abstract
The increase in demand of fossil fuel uses for developmental activity and manufacturing of goods have resulted a huge emission of global warming gases (GWGs) in the atmosphere. Among all GWGs, CO2 is the major contributor that inevitably causes global warming and climate change. Mitigation strategies like biological CO2 capture through sequestration and their storage into biological organic form are used to minimize the concentration of atmospheric CO2 with the goal to control climate change. Since increasing atmospheric CO2 level supports microbial growth and productivity thus microbial-based CO2 sequestration has remarkable advantages as compared to plant-based sequestration. This review focuses on CO2 sequestration mechanism in bacteria through different carbon fixation pathways, involved enzymes, their role in calcite, and other environmentally friendly biomaterials such as biofuel, bioplastic, and biosurfactant.
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Affiliation(s)
- Neha Maheshwari
- Amity School of Earth and Environmental Science, Amity University, Gurugram, Haryana, India
| | - Indu Shekhar Thakur
- Amity School of Earth and Environmental Science, Amity University, Gurugram, Haryana, India
- School of Environmental Sciences, Jawaharlal Nehru University, New Delhi, 110067, India
| | - Shaili Srivastava
- Amity School of Earth and Environmental Science, Amity University, Gurugram, Haryana, India.
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Mares SE, King MM, Kubo A, Khanov AA, Lutter EI, Youssef N, Patrauchan MA. carP, encoding a Ca 2+-regulated putative phytase, is evolutionarily conserved in Pseudomonas aeruginosa and has potential as a biomarker. MICROBIOLOGY (READING, ENGLAND) 2021; 167:001004. [PMID: 33295862 PMCID: PMC8131022 DOI: 10.1099/mic.0.001004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2020] [Accepted: 11/24/2020] [Indexed: 01/16/2023]
Abstract
Pseudomonas aeruginosa infects patients with cystic fibrosis, burns, wounds and implants. Previously, our group showed that elevated Ca2+ positively regulates the production of several virulence factors in P. aeruginosa, such as biofilm formation, production of pyocyanin and secreted proteases. We have identified a Ca2+-regulated β-propeller putative phytase, CarP, which is required for Ca2+ tolerance, regulation of the intracellular Ca2+ levels, and plays a role in Ca2+ regulation of P. aeruginosa virulence. Here, we studied the conservation of carP sequence and its occurrence in diverse phylogenetic groups of bacteria. In silico analysis revealed that carP and its two paralogues PA2017 and PA0319 are primarily present in P. aeruginosa and belong to the core genome of the species. We identified 155 single nucleotide alterations within carP, 42 of which lead to missense mutations with only three that affected the predicted 3D structure of the protein. PCR analyses with carP-specific primers detected P. aeruginosa specifically in 70 clinical and environmental samples. Sequence comparison demonstrated that carP is overall highly conserved in P. aeruginosa isolated from diverse environments. Such evolutionary preservation of carP illustrates its importance for P. aeruginosa adaptations to diverse environments and demonstrates its potential as a biomarker.
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Affiliation(s)
- Sergio E. Mares
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK 74078, USA
| | - Michelle M. King
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK 74078, USA
| | - Aya Kubo
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK 74078, USA
| | - Anna A. Khanov
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK 74078, USA
| | - Erika I. Lutter
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK 74078, USA
| | - Noha Youssef
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK 74078, USA
| | - Marianna A. Patrauchan
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK 74078, USA
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Keren-Paz A, Kolodkin-Gal I. A brick in the wall: Discovering a novel mineral component of the biofilm extracellular matrix. N Biotechnol 2020; 56:9-15. [DOI: 10.1016/j.nbt.2019.11.002] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Revised: 11/01/2019] [Accepted: 11/02/2019] [Indexed: 01/09/2023]
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7
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Lotlikar SR, Kayastha BB, Vullo D, Khanam SS, Braga RE, Murray AB, McKenna R, Supuran CT, Patrauchan MA. Pseudomonas aeruginosa β-carbonic anhydrase, psCA1, is required for calcium deposition and contributes to virulence. Cell Calcium 2019; 84:102080. [PMID: 31589941 DOI: 10.1016/j.ceca.2019.102080] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Revised: 08/16/2019] [Accepted: 09/07/2019] [Indexed: 01/07/2023]
Abstract
Calcification of soft tissue leads to serious diseases and has been associated with bacterial chronic infections. However, the origin and the molecular mechanisms of calcification remain unclear. Here we hypothesized that a human pathogen Pseudomonas aeruginosa deposits extracellular calcium, a process requiring carbonic anhydrases (CAs). Transmission electron microscopy confirmed the formation of 0.1-0.2 μm deposits by P. aeruginosa PAO1 growing at 5 mM CaCl2, and X-ray elemental analysis confirmed they contain calcium. Quantitative analysis of deposited calcium showed that PAO1 deposits 0.35 and 0.75 mM calcium/mg protein when grown at 5 mM and 10 mM CaCl2, correspondingly. Fluorescent microscopy indicated that deposition initiates at the cell surface. We have previously characterized three PAO1 β-class CAs: psCA1, psCA2, and psCA3 that hydrate CO2 to HCO3-, among which psCA1 showed the highest catalytic activity (Lotlikar et. al. 2013). According to immunoblot and RT-qPCR, growth at elevated calcium levels increases the expression of psCA1. Analyses of the deletion mutants lacking one, two or all three psCA genes, determined that psCA1 plays a major role in calcium deposition and contributes to the pathogen's virulence. In-silico modeling of the PAO1 β-class CAs identified four amino acids that differ in psCA1 compared to psCA2, and psCA3 (T59, A61A, A101, and A108), and these differences may play a role in catalytic rate and thus calcium deposition. A series of inhibitors were tested against the recombinant psCA1, among which aminobenzene sulfonamide (ABS) and acetazolamide (AAZ), which inhibited psCA1 catalytic activity with KIs of 19 nM and 37 nM, correspondingly. The addition of ABS and AAZ to growing PAO1 reduced calcium deposition by 41 and 78, respectively. Hence, for the first time, we showed that the β-CA psCA1 in P. aeruginosa contributes to virulence likely by enabling calcium salt deposition, which can be partially controlled by inhibiting its catalytic activity.
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Affiliation(s)
- Shalaka R Lotlikar
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK 74078, USA
| | - Biraj B Kayastha
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK 74078, USA
| | - Daniela Vullo
- Università degli Studi di Firenze, Polo Scientifico, Laboratorio di Chimica Bioinorganica, Rm. 188, Via della Lastruccia 3, 50019 Sesto Fiorentino, Florence, Italy
| | - Sharmily S Khanam
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK 74078, USA
| | - Reygan E Braga
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK 74078, USA
| | - Akilah B Murray
- Department of Biochemistry and Molecular Biology, College of Medicine, University of Florida, Gainesville, FL 32610, USA
| | - Robert McKenna
- Department of Biochemistry and Molecular Biology, College of Medicine, University of Florida, Gainesville, FL 32610, USA
| | - Claudiu T Supuran
- Università degli Studi di Firenze, Polo Scientifico, Dipartimento Neurofarba, Sezione di Scienze Farmaceutiche, Via Ugo Schiff 6, 50019 Sesto Fiorentino, Florence, Italy
| | - Marianna A Patrauchan
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK 74078, USA.
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Jaya P, Nathan VK, Ammini P. Characterization of marine bacterial carbonic anhydrase and their CO 2 sequestration abilities based on a soil microcosm. Prep Biochem Biotechnol 2019; 49:891-899. [PMID: 31244362 DOI: 10.1080/10826068.2019.1633669] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The novel technology of biological carbon sequestration using microbial enzymes have numerous advantages over conventional sequestration strategies. In the present study, extracellular carbonic anhydrase (CA) producing bacteria were isolated from water samples in the Arabian Sea, India. A potential isolate, Bacillus safensis isolate AS-75 was identified based on 16S rDNA sequence analysis. The culture conditions suitable for CA production were 32 °C incubation temperature with 4% NaCl and 10 mM Zn supplementation. Experimental optimization of culture conditions enhanced enzyme activity to 265 U mL-1. CA specific gene was characterized and based on the analysis, the CA of B. safensis isolate AS-75 was a leucine (11.3%) with α-helices as the dominant component in its secondary structure. Based on soil microcosm studies, CA could sequester CO2 by 95.4% ± 0.11% in sterilized soil with enzyme microcosm. Hence, the application of enzyme was found to be more effective in removing CO2.
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Affiliation(s)
- Panchami Jaya
- Regional Centre, National Institute of Oceanography-CSIR , Cochin , India
| | - Vinod Kumar Nathan
- Regional Centre, National Institute of Oceanography-CSIR , Cochin , India.,School of Chemical and Biotechnology, SASTRA University , Thanjavur , India
| | - Parvathi Ammini
- Regional Centre, National Institute of Oceanography-CSIR , Cochin , India
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Maheshwari N, Kumar M, Thakur IS, Srivastava S. Cloning, expression and characterization of β- and γ‑carbonic anhydrase from Bacillus sp. SS105 for biomimetic sequestration of CO2. Int J Biol Macromol 2019; 131:445-452. [DOI: 10.1016/j.ijbiomac.2019.03.082] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2019] [Revised: 03/04/2019] [Accepted: 03/12/2019] [Indexed: 11/25/2022]
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10
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Esparza M, Jedlicki E, González C, Dopson M, Holmes DS. Effect of CO 2 Concentration on Uptake and Assimilation of Inorganic Carbon in the Extreme Acidophile Acidithiobacillus ferrooxidans. Front Microbiol 2019; 10:603. [PMID: 31019493 PMCID: PMC6458275 DOI: 10.3389/fmicb.2019.00603] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Accepted: 03/11/2019] [Indexed: 02/01/2023] Open
Abstract
This study was motivated by surprising gaps in the current knowledge of microbial inorganic carbon (Ci) uptake and assimilation at acidic pH values (pH < 3). Particularly striking is the limited understanding of the differences between Ci uptake mechanisms in acidic versus circumneutral environments where the Ci predominantly occurs either as a dissolved gas (CO2) or as bicarbonate (HCO3 -), respectively. In order to gain initial traction on the problem, the relative abundance of transcripts encoding proteins involved in Ci uptake and assimilation was studied in the autotrophic, polyextreme acidophile Acidithiobacillus ferrooxidans whose optimum pH for growth is 2.5 using ferrous iron as an energy source, although they are able to grow at pH 5 when using sulfur as an energy source. The relative abundance of transcripts of five operons (cbb1-5) and one gene cluster (can-sulP) was monitored by RT-qPCR and, in selected cases, at the protein level by Western blotting, when cells were grown under different regimens of CO2 concentration in elemental sulfur. Of particular note was the absence of a classical bicarbonate uptake system in A. ferrooxidans. However, bioinformatic approaches predict that sulP, previously annotated as a sulfate transporter, is a novel type of bicarbonate transporter. A conceptual model of CO2 fixation was constructed from combined bioinformatic and experimental approaches that suggests strategies for providing ecological flexibility under changing concentrations of CO2 and provides a portal to elucidating Ci uptake and regulation in acidic conditions. The results could advance the understanding of industrial bioleaching processes to recover metals such as copper at acidic pH. In addition, they may also shed light on how chemolithoautotrophic acidophiles influence the nutrient and energy balance in naturally occurring low pH environments.
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Affiliation(s)
- Mario Esparza
- Laboratorio de Biominería, Departamento de Biotecnología, Facultad de Ciencias del Mar y Recursos Biológicos, Universidad de Antofagasta, Antofagasta, Chile
| | - Eugenia Jedlicki
- Center for Bioinformatics and Genome Biology, Fundación Ciencia & Vida, Santiago, Chile
| | - Carolina González
- Center for Bioinformatics and Genome Biology, Fundación Ciencia & Vida, Santiago, Chile
| | - Mark Dopson
- Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Linnaeus University, Kalmar, Sweden
| | - David S. Holmes
- Center for Bioinformatics and Genome Biology, Fundación Ciencia & Vida, Santiago, Chile
- Centro de Genómica y Bioinformática, Facultad de Ciencias, Universidad Mayor, Santiago, Chile
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11
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Giri A, Banerjee UC, Kumar M, Pant D. Intracellular carbonic anhydrase from Citrobacter freundii and its role in bio-sequestration. BIORESOURCE TECHNOLOGY 2018; 267:789-792. [PMID: 30072238 DOI: 10.1016/j.biortech.2018.07.089] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Revised: 07/16/2018] [Accepted: 07/18/2018] [Indexed: 06/08/2023]
Abstract
The aim of this work was to study the CO2 bio-sequestration application of indigenous Citrobacter species and its carbonic anhydrase (CA). Intracellular CA was purified from Citrobacter freundii (CF; accession no: MH283871) isolated from limestone rock site in Kumaun region of Indian Himalaya studied for the sequestration of carbon dioxide and the formation of calcite. CF showed maximum CA enzyme activity at 11.3 EU/ml at pH 7.0 and 37 °C. Hydration of CO2 into carbonate was characterized by calcite phase of calcium carbonate using absorption spectroscopy and imaging technique. Purified CA showed a significantly high CO2 sequestration capacity of 230 mg CaCO3/mg of purified as compared to crude enzyme (50 mg CaCO3/ml of enzyme).
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Affiliation(s)
- Anand Giri
- School of Earth and Environmental Sciences, Central University of Himachal Pradesh, Dharamshala, Himachal Pradesh, India
| | - Uttam Chand Banerjee
- National Institute of Pharmaceutical Education and Research, Mohali, Punjab, India
| | - Manoj Kumar
- Indian Oil Corporation R&D Centre, Sector 13, Faridabad, India
| | - Deepak Pant
- School of Earth and Environmental Sciences, Central University of Himachal Pradesh, Dharamshala, Himachal Pradesh, India.
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Maheshwari N, Kumar M, Thakur IS, Srivastava S. Carbon dioxide biofixation by free air CO2 enriched (FACE) bacterium for biodiesel production. J CO2 UTIL 2018. [DOI: 10.1016/j.jcou.2018.08.010] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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13
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Murray AB, Aggarwal M, Pinard M, Vullo D, Patrauchan M, Supuran CT, McKenna R. Structural Mapping of Anion Inhibitors to β-Carbonic Anhydrase psCA3 from Pseudomonas aeruginosa. ChemMedChem 2018; 13:2024-2029. [PMID: 30088334 DOI: 10.1002/cmdc.201800375] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Indexed: 11/06/2022]
Abstract
Pseudomonas aeruginosa is a Gram-negative facultative anaerobe belonging to the Pseudomonadaceae family. It is a multidrug-resistant opportunistic human pathogen, a common cause of life-threatening nosocomial infections, and a key bacterial agent in cystic fibrosis and endocarditis. The bacterium exhibits intrinsic resistance to most antibacterial agents, including aminoglycosides and quinolones. Hence, the identification of new drug targets for P. aeruginosa is ongoing. PsCA3 is a β-class carbonic anhydrase (β-CA) that catalyzes the reversible hydration of carbon dioxide to bicarbonate and represents a new class of antimicrobial target. Previously, inhibitor screening studies of psCA3 have shown that a series of small anions including sulfamide (SFN), imidazole (IMD), and 4-methylimidazole (4MI), and thiocyanate (SCN) inhibit the enzyme with efficiencies in the micro- to millimolar range. Herein the X-ray crystal structures of these inhibitors in complex with psCA3 are presented and compared with human CA II. This structural survey into the binding modes of small anions forms the foundation for the development of inhibitors against β-CAs and more selective inhibitors against P. aeruginosa.
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Affiliation(s)
- Akilah B Murray
- Department of Biochemistry and Molecular Biology, College of Medicine, University of Florida, Gainesville, FL, 32610, USA
| | - Mayank Aggarwal
- Division of Biology and Soft Matter, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Melissa Pinard
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Daniela Vullo
- Università degli Studi di Firenze, Polo Scientifico, Dipartimento Neurofaba, Sezione di Scienze Farmaceutiche e Nutraceutiche, Via Ugo Schiff 6, 50019, Sesto Fiorentino, Firenze, Italy
| | - Marianna Patrauchan
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, 74078, USA
| | - Claudiu T Supuran
- Università degli Studi di Firenze, Polo Scientifico, Dipartimento Neurofaba, Sezione di Scienze Farmaceutiche e Nutraceutiche, Via Ugo Schiff 6, 50019, Sesto Fiorentino, Firenze, Italy
| | - Robert McKenna
- Department of Biochemistry and Molecular Biology, College of Medicine, University of Florida, Gainesville, FL, 32610, USA
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14
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Pérez-Etayo L, de Miguel MJ, Conde-Álvarez R, Muñoz PM, Khames M, Iriarte M, Moriyón I, Zúñiga-Ripa A. The CO 2-dependence of Brucella ovis and Brucella abortus biovars is caused by defective carbonic anhydrases. Vet Res 2018; 49:85. [PMID: 30185220 PMCID: PMC6126018 DOI: 10.1186/s13567-018-0583-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Accepted: 08/03/2018] [Indexed: 12/14/2022] Open
Abstract
Brucella bacteria cause brucellosis, a major zoonosis whose control requires efficient diagnosis and vaccines. Identification of classical Brucella spp. has traditionally relied on phenotypic characterization, including surface antigens and 5–10% CO2 necessity for growth (CO2-dependence), a trait of Brucella ovis and most Brucella abortus biovars 1–4 strains. Although molecular tests are replacing phenotypic methods, CO2-dependence remains of interest as it conditions isolation and propagation and reflects Brucella metabolism, an area of active research. Here, we investigated the connection of CO2-dependence and carbonic anhydrases (CA), the enzymes catalyzing the hydration of CO2 to the bicarbonate used by anaplerotic and biosynthetic carboxylases. Based on the previous demonstration that B. suis carries two functional CAs (CAI and CAII), we analyzed the CA sequences of CO2-dependent and -independent brucellae and spontaneous mutants. The comparisons strongly suggested that CAII is not functional in CO2-dependent B. abortus and B. ovis, and that a modified CAII sequence explains the CO2-independent phenotype of spontaneous mutants. Then, by mutagenesis and heterologous plasmid complementation and chromosomal insertion we proved that CAI alone is enough to support CO2-independent growth of B. suis in rich media but not of B. abortus in rich media or B. suis in minimal media. Finally, we also found that insertion of a heterologous active CAII into B. ovis reverted the CO2-dependence but did not alter its virulence in the mouse model. These results allow a better understanding of central aspects of Brucella metabolism and, in the case of B. ovis, provide tools for large-scale production of diagnostic antigens and vaccines.
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Affiliation(s)
- Lara Pérez-Etayo
- Instituto de Salud Tropical y Departamento de Microbiología y Parasitología-IDISNA, Universidad de Navarra, 31008, Pamplona, Spain
| | - María Jesús de Miguel
- Unidad de Producción y Sanidad Animal del Centro de Investigación y Tecnología Agroalimentaria de Aragón (CITA), Instituto Agroalimentario de Aragón (IA2), Zaragoza, Spain
| | - Raquel Conde-Álvarez
- Instituto de Salud Tropical y Departamento de Microbiología y Parasitología-IDISNA, Universidad de Navarra, 31008, Pamplona, Spain
| | - Pilar M Muñoz
- Unidad de Producción y Sanidad Animal del Centro de Investigación y Tecnología Agroalimentaria de Aragón (CITA), Instituto Agroalimentario de Aragón (IA2), Zaragoza, Spain
| | - Mammar Khames
- Department of Biology, University of Medea, 26000, Medea, Algeria.,National Veterinary High School, Algiers, Algeria
| | - Maite Iriarte
- Instituto de Salud Tropical y Departamento de Microbiología y Parasitología-IDISNA, Universidad de Navarra, 31008, Pamplona, Spain
| | - Ignacio Moriyón
- Instituto de Salud Tropical y Departamento de Microbiología y Parasitología-IDISNA, Universidad de Navarra, 31008, Pamplona, Spain
| | - Amaia Zúñiga-Ripa
- Instituto de Salud Tropical y Departamento de Microbiología y Parasitología-IDISNA, Universidad de Navarra, 31008, Pamplona, Spain.
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15
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Involvement of β-Carbonic Anhydrase Genes in Bacterial Genomic Islands and Their Horizontal Transfer to Protists. Appl Environ Microbiol 2018; 84:AEM.00771-18. [PMID: 29802189 DOI: 10.1128/aem.00771-18] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Accepted: 05/19/2018] [Indexed: 11/20/2022] Open
Abstract
Genomic islands (GIs) are a type of mobile genetic element (MGE) that are present in bacterial chromosomes. They consist of a cluster of genes that produce proteins that contribute to a variety of functions, including, but not limited to, the regulation of cell metabolism, antimicrobial resistance, pathogenicity, virulence, and resistance to heavy metals. The genes carried in MGEs can be used as a trait reservoir in times of adversity. Transfer of genes using MGEs, occurring outside reproduction, is called horizontal gene transfer (HGT). Previous data have shown that numerous HGT events have occurred through endosymbiosis between prokaryotes and eukaryotes. β-Carbonic anhydrase (β-CA) enzymes play a critical role in the biochemical pathways of many prokaryotes and eukaryotes. We previously suggested the horizontal transfer of β-CA genes from plasmids of some prokaryotic endosymbionts to their protozoan hosts. In this study, we set out to identify β-CA genes that might have been transferred between prokaryotic and protist species through HGT in GIs. Therefore, we investigated prokaryotic chromosomes containing β-CA-encoding GIs and utilized multiple bioinformatics tools to reveal the distinct movements of β-CA genes among a wide variety of organisms. Our results identify the presence of β-CA genes in GIs of several medically and industrially relevant bacterial species, and phylogenetic analyses reveal multiple cases of likely horizontal transfer of β-CA genes from GIs of ancestral prokaryotes to protists.IMPORTANCE The evolutionary process is mediated by mobile genetic elements (MGEs), such as genomic islands (GIs). A gene or set of genes in the GIs is exchanged between and within various species through horizontal gene transfer (HGT). Based on the crucial role that GIs can play in bacterial survival and proliferation, they were introduced as environment- and pathogen-associated factors. Carbonic anhydrases (CAs) are involved in many critical biochemical pathways, such as the regulation of pH homeostasis and electrolyte transfer. Among the six evolutionary families of CAs, β-CA gene sequences are present in many bacterial species, which can be horizontally transferred to protists during evolution. This study shows the involvement of bacterial β-CA gene sequences in the GIs and suggests their horizontal transfer to protists during evolution.
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16
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Dade-Robertson M, Keren-Paz A, Zhang M, Kolodkin-Gal I. Architects of nature: growing buildings with bacterial biofilms. Microb Biotechnol 2017; 10:1157-1163. [PMID: 28815998 PMCID: PMC5609236 DOI: 10.1111/1751-7915.12833] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Revised: 07/18/2017] [Accepted: 07/18/2017] [Indexed: 12/22/2022] Open
Abstract
In his text 'On Architecture', Vitruvius suggested that architecture is an imitation of nature. Here we discuss what happens when we begin using nature in architecture. We describe recent developments in the study of biofilm structure, and propose combining modern architecture and synthetic microbiology to develop sustainable construction approaches. Recently, Kolodkin-Gal laboratory and others revealed a role for precipitation of calcium carbonate in the maturation and assembly of bacterial communities with complex structures. Importantly, they demonstrated that different secreted organic materials shape the calcium carbonate crystals formed by the bacterial cells. This provides a proof-of-concept for a potential use of bacteria in designing rigid construction materials and altering crystal morphology and function. In this study, we discuss how these recent discoveries may change the current strategies of architecture and construction. We believe that biofilm communities enhanced by synthetic circuits may be used to construct buildings and to sequester carbon dioxide in the process.
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Affiliation(s)
- Martyn Dade-Robertson
- Faculty of Humanities and Social Sciences, School of Architecture, Planning and Landscape, Newcastle University, Newcastle upon Tyne, UK
| | - Alona Keren-Paz
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Meng Zhang
- Department of Applied Sciences, Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne, UK
| | - Ilana Kolodkin-Gal
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
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17
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Sahuquillo-Arce JM, Chouman-Arcas R, Molina-Moreno JM, Hernández-Cabezas A, Frasquet-Artés J, López-Hontangas JL. Capnophilic Enterobacteriaceae. Diagn Microbiol Infect Dis 2017; 87:318-319. [PMID: 28139278 DOI: 10.1016/j.diagmicrobio.2017.01.010] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2016] [Revised: 01/13/2017] [Accepted: 01/16/2017] [Indexed: 10/20/2022]
Abstract
Bacteria use bicarbonate as substrate for crucial metabolic reactions. We report the first case of bacteremia by capnophilic E. coli without the YadF gene (also known as CynT2 or Can2) that needs high concentrations of CO2 to non-enzymatically produce bicarbonate. This lack may also apply to previously reported capnophilic Enterobacteriaceae.
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Affiliation(s)
- J M Sahuquillo-Arce
- Microbiology Department, Hospital Universitari i Politècnic La Fe, Valencia, Spain.
| | - R Chouman-Arcas
- Microbiology Department, Hospital Universitari i Politècnic La Fe, Valencia, Spain
| | - J M Molina-Moreno
- Microbiology Department, Hospital Universitari i Politècnic La Fe, Valencia, Spain
| | - A Hernández-Cabezas
- Microbiology Department, Hospital Universitari i Politècnic La Fe, Valencia, Spain
| | - J Frasquet-Artés
- Microbiology Department, Hospital Universitari i Politècnic La Fe, Valencia, Spain
| | - J L López-Hontangas
- Microbiology Department, Hospital Universitari i Politècnic La Fe, Valencia, Spain
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18
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Pinard MA, Kurian JJ, Aggarwal M, Agbandje-McKenna M, McKenna R. Cryoannealing-induced space-group transition of crystals of the carbonic anhydrase psCA3. Acta Crystallogr F Struct Biol Commun 2016; 72:573-7. [PMID: 27380376 PMCID: PMC4933009 DOI: 10.1107/s2053230x16009286] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Accepted: 06/08/2016] [Indexed: 11/10/2022] Open
Abstract
Cryoannealing has been demonstrated to improve the diffraction quality and resolution of crystals of the β-carbonic anhydrase psCA3 concomitant with a change in space group. After initial flash-cooling in a liquid-nitrogen cryostream an X-ray diffraction data set from a psCA3 crystal was indexed in space group P21212 and was scaled to 2.6 Å resolution, but subsequent cryoannealing studies revealed induced protein rearrangements in the crystal contacts, which transformed the space group to I222, with a corresponding improvement of 0.7 Å in resolution. Although the change in diffraction resolution was significant, only minor changes in the psCA3 structure, which retained its catalytic `open' conformation, were observed. These findings demonstrate that cryoannealing can be successfully utilized to induce higher diffraction-quality crystals while maintaining enzymatically relevant conformations and may be useful as an experimental tool for structural studies of other enzymes where the initial diffraction quality is poor.
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Affiliation(s)
- Melissa A. Pinard
- Department of Biochemistry and Molecular Biology, University of Florida College of Medicine, 1200 Newell Drive, PO Box 100245, Gainesville, FL 32610, USA
| | - Justin J. Kurian
- Department of Biochemistry and Molecular Biology, University of Florida College of Medicine, 1200 Newell Drive, PO Box 100245, Gainesville, FL 32610, USA
| | - Mayank Aggarwal
- Division of Biology and Soft Matter, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Mavis Agbandje-McKenna
- Department of Biochemistry and Molecular Biology, University of Florida College of Medicine, 1200 Newell Drive, PO Box 100245, Gainesville, FL 32610, USA
| | - Robert McKenna
- Department of Biochemistry and Molecular Biology, University of Florida College of Medicine, 1200 Newell Drive, PO Box 100245, Gainesville, FL 32610, USA
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19
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Kentache T, Jouenne T, Dé E, Hardouin J. Proteomic characterization of Nα- and Nε-acetylation in Acinetobacter baumannii. J Proteomics 2016; 144:148-58. [PMID: 27222042 DOI: 10.1016/j.jprot.2016.05.021] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2016] [Revised: 05/12/2016] [Accepted: 05/18/2016] [Indexed: 12/25/2022]
Abstract
Nα- and Nε-acetylation represent a pivotal post-translational modification used by both eukaryotes and prokaryotes to modulate diverse biological processes. Acinetobacter baumannii has been described as an important nosocomial pathogen for the past 30 years, frequently involved in ventilator-associated pneumonia, bloodstream and urinary tract infections. Many aspects of the biology of A. baumannii remain elusive, in particular the extent and function of N-acetylation. We investigated here N-acetylation in A. baumannii strain ATCC 17978 by proteomic analysis, and we showed the usefulness of using different analytical approaches. Overall, we identified 525 N-acetylated proteins in which, 145 were Nα-acetylated and 411 were Nε-acetylated. Among them, 41 proteins carried both types of N-acetylation. We found that N-acetylation may play a role in biofilm formation, bacterial virulence (e.g. in several iron acquisition pathways), as well as a number of phenotypes, such as, stress adaptation and drug resistance. BIOLOGICAL SIGNIFICANCE This study is the first to perform the N-acetylome of A. baumannii using different analytical approaches. Each analytical tool permitted to characterize distinctive modified peptides. The combination of all these methods allowed us to identify 145 and 411 Nα- and Nε-acetylated proteins. Besides the fact that acetylation was involved in central metabolism as previously described in other bacteria, some N-acetylated proteins showed interesting role in bacterial virulence (iron acquisition), biofilm formation, stress adaptation and drug resistance of A. baumannii.
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Affiliation(s)
- Takfarinas Kentache
- CNRS, UMR 6270, Polymères, Biopolymères, Surfaces Laboratory, F-76821 Mont-Saint-Aignan, France; Normandie Univ, UR, France
| | - Thierry Jouenne
- CNRS, UMR 6270, Polymères, Biopolymères, Surfaces Laboratory, F-76821 Mont-Saint-Aignan, France; Normandie Univ, UR, France; PISSARO proteomic facility, IRIB, F-76821 Mont-Saint-Aignan, France
| | - Emmanuelle Dé
- CNRS, UMR 6270, Polymères, Biopolymères, Surfaces Laboratory, F-76821 Mont-Saint-Aignan, France; Normandie Univ, UR, France; PISSARO proteomic facility, IRIB, F-76821 Mont-Saint-Aignan, France
| | - Julie Hardouin
- CNRS, UMR 6270, Polymères, Biopolymères, Surfaces Laboratory, F-76821 Mont-Saint-Aignan, France; Normandie Univ, UR, France; PISSARO proteomic facility, IRIB, F-76821 Mont-Saint-Aignan, France.
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20
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Shah A, Eikmanns BJ. Transcriptional Regulation of the β-Type Carbonic Anhydrase Gene bca by RamA in Corynebacterium glutamicum. PLoS One 2016; 11:e0154382. [PMID: 27119954 PMCID: PMC4847777 DOI: 10.1371/journal.pone.0154382] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2016] [Accepted: 04/12/2016] [Indexed: 11/25/2022] Open
Abstract
Carbonic anhydrase catalyzes the reversible hydration of carbon dioxide to bicarbonate and maintains the balance of CO2/HCO3- in the intracellular environment, specifically for carboxylation/decarboxylation reactions. In Corynebacterium glutamicum, two putative genes, namely the bca (cg2954) and gca (cg0155) genes, coding for β-type and γ-type carbonic anhydrase, respectively, have been identified. We here analyze the transcriptional organization of these genes. The transcriptional start site (TSS) of the bca gene was shown to be the first nucleotide "A" of its putative translational start codon (ATG) and thus, bca codes for a leaderless transcript. The TSS of the gca gene was identified as an "A" residue located at position -20 relative to the first nucleotide of the annotated translational start codon of the cg0154 gene, which is located immediately upstream of gca. Comparative expression analysis revealed carbon source-dependent regulation of the bca gene, with 1.5- to 2-fold lower promoter activity in cells grown on acetate as compared to glucose as sole carbon source. Based on higher expression of bca in a mutant deficient of the regulator of acetate metabolism RamA as compared to the wild-type of C. glutamicum and based on the binding of His-tagged RamA protein to the bca promoter region, we here present evidence that RamA negatively regulates expression of bca in C. glutamicum. Functional characterization of a gca deletion mutant of C. glutamicum revealed the same growth characteristics of C. glutamicum ∆gca as that of wild-type C. glutamicum and no effect on expression of the bca gene.
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Affiliation(s)
- Adnan Shah
- Institute of Microbiology and Biotechnology, University of Ulm, D-89069 Ulm, Germany
| | - Bernhard J. Eikmanns
- Institute of Microbiology and Biotechnology, University of Ulm, D-89069 Ulm, Germany
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21
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Al-Haideri H, White MA, Kelly DJ. Major contribution of the type II beta carbonic anhydrase CanB (Cj0237) to the capnophilic growth phenotype ofCampylobacter jejuni. Environ Microbiol 2015; 18:721-35. [DOI: 10.1111/1462-2920.13092] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2015] [Revised: 10/11/2015] [Accepted: 10/12/2015] [Indexed: 11/28/2022]
Affiliation(s)
- Halah Al-Haideri
- Department of Molecular Biology and Biotechnology; The University of Sheffield; Firth Court, Western Bank Sheffield S10 2TN UK
| | - Michael A. White
- Department of Molecular Biology and Biotechnology; The University of Sheffield; Firth Court, Western Bank Sheffield S10 2TN UK
| | - David J. Kelly
- Department of Molecular Biology and Biotechnology; The University of Sheffield; Firth Court, Western Bank Sheffield S10 2TN UK
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22
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Aggarwal M, Chua TK, Pinard MA, Szebenyi DM, McKenna R. Carbon Dioxide "Trapped" in a β-Carbonic Anhydrase. Biochemistry 2015; 54:6631-8. [PMID: 26457866 DOI: 10.1021/acs.biochem.5b00987] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Carbonic anhydrases (CAs) are enzymes that catalyze the hydration/dehydration of CO2/HCO3(-) with rates approaching diffusion-controlled limits (kcat/KM ∼ 10(8) M(-1) s(-1)). This family of enzymes has evolved disparate protein folds that all perform the same reaction at near catalytic perfection. Presented here is a structural study of a β-CA (psCA3) expressed in Pseudomonas aeruginosa, in complex with CO2, using pressurized cryo-cooled crystallography. The structure has been refined to 1.6 Å resolution with R(cryst) and R(free) values of 17.3 and 19.9%, respectively, and is compared with the α-CA, human CA isoform II (hCA II), the only other CA to have CO2 captured in its active site. Despite the lack of structural similarity between psCA3 and hCA II, the CO2 binding orientation relative to the zinc-bound solvent is identical. In addition, a second CO2 binding site was located at the dimer interface of psCA3. Interestingly, all β-CAs function as dimers or higher-order oligomeric states, and the CO2 bound at the interface may contribute to the allosteric nature of this family of enzymes or may be a convenient alternative binding site as this pocket has been previously shown to be a promiscuous site for a variety of ligands, including bicarbonate, sulfate, and phosphate ions.
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Affiliation(s)
- Mayank Aggarwal
- Division of Biology and Soft Matter, Oak Ridge National Laboratory , Oak Ridge, Tennessee 37831, United States
| | - Teck Khiang Chua
- Cornell High Energy Synchrotron Source (CHESS), Cornell University , Ithaca, New York 14853, United States
| | - Melissa A Pinard
- Department of Biochemistry and Molecular Biology, College of Medicine, University of Florida , Gainesville, Florida 32610, United States
| | - Doletha M Szebenyi
- Cornell High Energy Synchrotron Source (CHESS), Cornell University , Ithaca, New York 14853, United States
| | - Robert McKenna
- Department of Biochemistry and Molecular Biology, College of Medicine, University of Florida , Gainesville, Florida 32610, United States
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23
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Zhou G, Shi QS, Huang XM, Xie XB, Chen YB. Insights intoPseudomonas aeruginosaATCC9027 Resistance to Isothiazolones Through Proteomics. Microb Drug Resist 2015; 21:140-8. [DOI: 10.1089/mdr.2014.0113] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Gang Zhou
- Guangdong Institute of Microbiology, State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangzhou, Guangdong, People's Republic of China
| | - Qing-Shan Shi
- Guangdong Institute of Microbiology, State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangzhou, Guangdong, People's Republic of China
| | - Xiao-Mo Huang
- Guangdong Institute of Microbiology, State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangzhou, Guangdong, People's Republic of China
| | - Xiao-Bao Xie
- Guangdong Institute of Microbiology, State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangzhou, Guangdong, People's Republic of China
| | - Yi-Ben Chen
- Guangdong Institute of Microbiology, State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangzhou, Guangdong, People's Republic of China
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24
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Abstract
Zampieri and colleagues used sophisticated statistical methods to create a picture of acid-base pattern and inflammation relationship in a clinical context. The observed independent relationship between acidosis and albumin concentration and inflammatory pattern opens up a new area for research. It has become clear that, in addition to the characterization of mediators, receptors, and cellular phenotypes, the inflammatory response has to be interpreted in light of acid-base status, albumin concentration, and probably also carbon dioxide level.
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25
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de Lorenzo V, Sekowska A, Danchin A. Chemical reactivity drives spatiotemporal organisation of bacterial metabolism. FEMS Microbiol Rev 2014; 39:96-119. [PMID: 25227915 DOI: 10.1111/1574-6976.12089] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
In this review, we examine how bacterial metabolism is shaped by chemical constraints acting on the material and dynamic layout of enzymatic networks and beyond. These are moulded not only for optimisation of given metabolic objectives (e.g. synthesis of a particular amino acid or nucleotide) but also for curbing the detrimental reactivity of chemical intermediates. Besides substrate channelling, toxicity is avoided by barriers to free diffusion (i.e. compartments) that separate otherwise incompatible reactions, along with ways for distinguishing damaging vs. harmless molecules. On the other hand, enzymes age and their operating lifetime must be tuned to upstream and downstream reactions. This time dependence of metabolic pathways creates time-linked information, learning and memory. These features suggest that the physical structure of existing biosystems, from operon assemblies to multicellular development may ultimately stem from the need to restrain chemical damage and limit the waste inherent to basic metabolic functions. This provides a new twist of our comprehension of fundamental biological processes in live systems as well as practical take-home lessons for the forward DNA-based engineering of novel biological objects.
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Affiliation(s)
- Víctor de Lorenzo
- Systems Biology Program, Centro Nacional de Biotecnología CSIC, Cantoblanco-Madrid, Spain
| | - Agnieszka Sekowska
- AMAbiotics SAS, Institut du Cerveau et de la Moëlle Épinière, Hôpital de la Pitié-Salpêtrière, Paris, France
| | - Antoine Danchin
- AMAbiotics SAS, Institut du Cerveau et de la Moëlle Épinière, Hôpital de la Pitié-Salpêtrière, Paris, France
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26
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Cummins EP, Selfridge AC, Sporn PH, Sznajder JI, Taylor CT. Carbon dioxide-sensing in organisms and its implications for human disease. Cell Mol Life Sci 2013; 71:831-45. [PMID: 24045706 DOI: 10.1007/s00018-013-1470-6] [Citation(s) in RCA: 87] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2013] [Revised: 08/22/2013] [Accepted: 08/30/2013] [Indexed: 12/29/2022]
Abstract
The capacity of organisms to sense changes in the levels of internal and external gases and to respond accordingly is central to a range of physiologic and pathophysiologic processes. Carbon dioxide, a primary product of oxidative metabolism is one such gas that can be sensed by both prokaryotic and eukaryotic cells and in response to altered levels, elicit the activation of multiple adaptive pathways. The outcomes of activating CO2-sensitive pathways in various species include increased virulence of fungal and bacterial pathogens, prey-seeking behavior in insects as well as taste perception, lung function, and the control of immunity in mammals. In this review, we discuss what is known about the mechanisms underpinning CO2 sensing across a range of species and consider the implications of this for physiology, disease progression, and the possibility of developing new therapeutics for inflammatory and infectious disease.
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Affiliation(s)
- Eoin P Cummins
- School of Medicine and Medical Science, UCD Conway Institute, University College Dublin, Belfield, Dublin 4, Ireland
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