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Panich J, Toppari E, Tejedor-Sanz S, Fong B, Dugan E, Chen Y, Petzold CJ, Zhao Z, Yoshikuni Y, Savage DF, Singer SW. Functional plasticity of HCO 3- uptake and CO 2 fixation in Cupriavidus necator H16. BIORESOURCE TECHNOLOGY 2024; 410:131214. [PMID: 39127361 DOI: 10.1016/j.biortech.2024.131214] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2024] [Revised: 08/01/2024] [Accepted: 08/01/2024] [Indexed: 08/12/2024]
Abstract
Despite its prominence, the ability to engineer Cupriavidus necator H16 for inorganic carbon uptake and fixation is underexplored. We tested the roles of endogenous and heterologous genes on C. necator inorganic carbon metabolism. Deletion of β-carbonic anhydrase can had the most deleterious effect on C. necator autotrophic growth. Replacement of this native uptake system with several classes of dissolved inorganic carbon (DIC) transporters from Cyanobacteria and chemolithoautotrophic bacteria recovered autotrophic growth and supported higher cell densities compared to wild-type (WT) C. necator in batch culture. Strains expressing Halothiobacillus neopolitanus DAB2 (hnDAB2) and diverse rubisco homologs grew in CO2 similarly to the wild-type strain. Our experiments suggest that the primary role of carbonic anhydrase during autotrophic growth is to support anaplerotic metabolism, and an array of DIC transporters can complement this function. This work demonstrates flexibility in HCO3- uptake and CO2 fixation in C. necator, providing new pathways for CO2-based biomanufacturing.
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Affiliation(s)
- Justin Panich
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
| | - Emili Toppari
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Sara Tejedor-Sanz
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; Advanced Biofuel and Bioproducts Process Development Unit, Lawrence Berkeley NationalLaboratory, Emeryville, CA 94608, USA
| | - Bonnie Fong
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Eli Dugan
- Department of Molecular and Cell Biology, University of California-Berkeley, Berkeley, CA, 94720, USA
| | - Yan Chen
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Christopher J Petzold
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Zhiying Zhao
- The US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, CA 94720, USA
| | - Yasuo Yoshikuni
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; The US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, CA 94720, USA; Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, CA94720, USA
| | - David F Savage
- Department of Molecular and Cell Biology, University of California-Berkeley, Berkeley, CA, 94720, USA; Howard Hughes Medical Institute, University of California, Berkeley, CA 94720, USA
| | - Steven W Singer
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
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Chadwick BJ, Lin X. Effects of CO 2 in fungi. Curr Opin Microbiol 2024; 79:102488. [PMID: 38759247 PMCID: PMC11162916 DOI: 10.1016/j.mib.2024.102488] [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: 02/18/2024] [Revised: 04/21/2024] [Accepted: 04/25/2024] [Indexed: 05/19/2024]
Abstract
Carbon dioxide supplies carbon for photosynthetic species and is a major product of respiration for all life forms. Inside the human body where CO2 is a by-product of the tricarboxylic acid cycle, its level reaches 5% or higher. In the ambient atmosphere, ∼.04% of the air is CO2. Different organisms can tolerate different CO2 levels to various degrees, and experiencing higher CO2 is toxic and can lead to death. The fungal kingdom shows great variations in response to CO2 that has been documented by different researchers at different time periods. This literature review aims to connect these studies, highlight mechanisms underlying tolerance to high levels of CO2, and emphasize the effects of CO2 on fungal metabolism and morphogenesis.
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Affiliation(s)
| | - Xiaorong Lin
- Department of Microbiology, University of Georgia, Athens, GA 30602, USA.
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3
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Capasso C, Supuran CT. Carbonic anhydrase and bacterial metabolism: a chance for antibacterial drug discovery. Expert Opin Ther Pat 2024; 34:465-474. [PMID: 38506448 DOI: 10.1080/13543776.2024.2332663] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Accepted: 03/08/2024] [Indexed: 03/21/2024]
Abstract
INTRODUCTION Carbonic anhydrases (CAs, EC 4.2.1.1) play a pivotal role in the regulation of carbon dioxide , bicarbonate, and hydrogen ions within bacterial cells, ensuring pH homeostasis and facilitating energy production. We conducted a systematic literature search (PubMed, Web of Science, and Google Scholar) to examine the intricate interplay between CAs and bacterial metabolism, revealing the potential of CA inhibitors (CAIs) as innovative therapeutic agents against pathogenic bacteria. AREA COVERED Inhibition of bacterial CAs was explored in various pathogens, emphasizing the CA roles in microbial virulence, survival, and adaptability. Escherichia coli, a valid and convenient model microorganism, was recently used to investigate the effects of acetazolamide (AAZ) on the bacterial life cycle. Furthermore, the effectiveness of CAIs against pathogenic bacteria has been further substantiated for Vancomycin-Resistant Enterococci (VRE) and antibiotic-resistant Neisseria gonorrhoeae strains. EXPERT OPINION CAIs target bacterial metabolic pathways, offering alternatives to conventional therapies. They hold promise against drug-resistant microorganisms such as VRE and N. gonorrhoeae strains. CAIs offer promising avenues for addressing antibiotic resistance and underscore their potential as novel antibacterial agents. Recognizing the central role of CAs in bacterial growth and pathogenicity will pave the way for innovative infection control and treatment strategies possibly also for other antibiotic resistant species.
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Affiliation(s)
- Clemente Capasso
- Department of Biology, Agriculture and Food Sciences, Institute of Biosciences and Bioresources, CNR, Napoli, Italy
| | - Claudiu T Supuran
- NEUROFARBA Department, Section of Pharmaceutical and Nutraceutical Sciences, University of Florence, Florence, Italy
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Scott KM, Payne RR, Gahramanova A. Widespread dissolved inorganic carbon-modifying toolkits in genomes of autotrophic Bacteria and Archaea and how they are likely to bridge supply from the environment to demand by autotrophic pathways. Appl Environ Microbiol 2024; 90:e0155723. [PMID: 38299815 PMCID: PMC10880623 DOI: 10.1128/aem.01557-23] [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] [Indexed: 02/02/2024] Open
Abstract
Using dissolved inorganic carbon (DIC) as a major carbon source, as autotrophs do, is complicated by the bedeviling nature of this substance. Autotrophs using the Calvin-Benson-Bassham cycle (CBB) are known to make use of a toolkit comprised of DIC transporters and carbonic anhydrase enzymes (CA) to facilitate DIC fixation. This minireview provides a brief overview of the current understanding of how toolkit function facilitates DIC fixation in Cyanobacteria and some Proteobacteria using the CBB and continues with a survey of the DIC toolkit gene presence in organisms using different versions of the CBB and other autotrophic pathways (reductive citric acid cycle, Wood-Ljungdahl pathway, hydroxypropionate bicycle, hydroxypropionate-hydroxybutyrate cycle, and dicarboxylate-hydroxybutyrate cycle). The potential function of toolkit gene products in these organisms is discussed in terms of CO2 and HCO3- supply from the environment and demand by the autotrophic pathway. The presence of DIC toolkit genes in autotrophic organisms beyond those using the CBB suggests the relevance of DIC metabolism to these organisms and provides a basis for better engineering of these organisms for industrial and agricultural purposes.
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Affiliation(s)
- Kathleen M. Scott
- Integrative Biology Department, University of South Florida, Tampa, Florida, USA
| | - Ren R. Payne
- Integrative Biology Department, University of South Florida, Tampa, Florida, USA
| | - Arin Gahramanova
- Integrative Biology Department, University of South Florida, Tampa, Florida, USA
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5
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Di Stadio G, Orita I, Nakamura R, Fukui T. Gas fermentation combined with water electrolysis for production of polyhydroxyalkanoate copolymer from carbon dioxide by engineered Ralstonia eutropha. BIORESOURCE TECHNOLOGY 2024; 394:130266. [PMID: 38159815 DOI: 10.1016/j.biortech.2023.130266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Revised: 12/24/2023] [Accepted: 12/25/2023] [Indexed: 01/03/2024]
Abstract
A recycled-gas closed-circuit culture system was developed for safe autotrophic cultivation of a hydrogen-oxidizing, polyhydroxyalkanoate (PHA)-producing Ralstonia eutropha, using a non-combustible gas mixture with low-concentration of H2 supplied by water electrolysis. Automated feedback regulation of gas flow enabled input of H2, CO2, and O2 well balanced with the cellular demands, leading to constant gas composition throughout the cultivation. The engineered strain of R. eutropha produced 1.71 g/L of poly(3-hydroxybutyrate-co-12.5 mol% 3-hydroxyhexanoate) on a gas mixture of H2/CO2/O2/N2 = 4:12:7:77 vol% with a 69.2 wt% cellular content. Overexpression of can encoding cytosolic carbonic anhydrase increased the 3HHx fraction up to 19.6 mol%. The yields of biomass and PHA on input H2 were determined to be 72.9 % and 63.1 %, corresponding to 51.0 % and 44.2 % yield on electricity, respectively. The equivalent solar-to-biomass/PHA efficiencies were estimated to be 2.1-3.8 %, highlighting the high energy conversion capability of R. eutropha.
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Affiliation(s)
- Gabriele Di Stadio
- School of Life Science and Technology, Tokyo Institute of Technology, 4259 Nagatsuta, Midori-ku, Yokohama 226-8501, Japan
| | - Izumi Orita
- School of Life Science and Technology, Tokyo Institute of Technology, 4259 Nagatsuta, Midori-ku, Yokohama 226-8501, Japan
| | - Ryuhei Nakamura
- Earth-Life Science Institute, Tokyo Institute of Technology, 2-12-1-IE-1 Ookayama, Meguro-ku, Tokyo 152-8550, Japan; Biofunctional Catalyst Research Team, RIKEN Center for Sustainable Resource Science (CSRS), 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Toshiaki Fukui
- School of Life Science and Technology, Tokyo Institute of Technology, 4259 Nagatsuta, Midori-ku, Yokohama 226-8501, Japan.
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Clarà Saracho A, Marek EJ. Uncovering the Dynamics of Urease and Carbonic Anhydrase Genes in Ureolysis, Carbon Dioxide Hydration, and Calcium Carbonate Precipitation. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2024; 58:1199-1210. [PMID: 38173390 DOI: 10.1021/acs.est.3c06617] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
The hydration of CO2 suffers from kinetic inefficiencies that make its natural trapping impractically sluggish. However, CO2-fixing carbonic anhydrases (CAs) remarkably accelerate its equilibration by 6 orders of magnitude and are, therefore, "ideal" catalysts. Notably, CA has been detected in ureolytic bacteria, suggesting its potential involvement in microbially induced carbonate precipitation (MICP), yet the dynamics of the urease (Ur) and CA genes remain poorly understood. Here, through the use of the ureolytic bacteriumSporosarcina pasteurii, we investigate the differing role of Ur and CA in ureolysis, CO2 hydration, and CaCO3 precipitation with increasing CO2(g) concentrations. We show that Ur gene up-regulation coincides with an increase in [HCO3-] following the hydration of CO2 to HCO3- by CA. Hence, CA physiologically promotes buffering, which enhances solubility trapping and affects the phase of the CaCO3 mineral formed. Understanding the role of CO2 hydration on the performance of ureolysis and CaCO3 precipitation provides essential new insights, required for the development of next-generation biocatalyzed CO2 trapping technologies.
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Affiliation(s)
- Alexandra Clarà Saracho
- Department of Civil, Architectural and Environmental Engineering, The University of Texas at Austin, 301 E Dean Keeton St C1700, Austin, Texas 78712, United States
| | - Ewa J Marek
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Philippa Fawcett Dr, Cambridge CB3 0AS, United Kingdom
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Morlino MS, Serna García R, Savio F, Zampieri G, Morosinotto T, Treu L, Campanaro S. Cupriavidus necator as a platform for polyhydroxyalkanoate production: An overview of strains, metabolism, and modeling approaches. Biotechnol Adv 2023; 69:108264. [PMID: 37775073 DOI: 10.1016/j.biotechadv.2023.108264] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Revised: 09/18/2023] [Accepted: 09/26/2023] [Indexed: 10/01/2023]
Abstract
Cupriavidus necator is a bacterium with a high phenotypic diversity and versatile metabolic capabilities. It has been extensively studied as a model hydrogen oxidizer, as well as a producer of polyhydroxyalkanoates (PHA), plastic-like biopolymers with a high potential to substitute petroleum-based materials. Thanks to its adaptability to diverse metabolic lifestyles and to the ability to accumulate large amounts of PHA, C. necator is employed in many biotechnological processes, with particular focus on PHA production from waste carbon sources. The large availability of genomic information has enabled a characterization of C. necator's metabolism, leading to the establishment of metabolic models which are used to devise and optimize culture conditions and genetic engineering approaches. In this work, the characteristics of available C. necator strains and genomes are reviewed, underlining how a thorough comprehension of the genetic variability of C. necator is lacking and it could be instrumental for wider application of this microorganism. The metabolic paradigms of C. necator and how they are connected to PHA production and accumulation are described, also recapitulating the variety of carbon substrates used for PHA accumulation, highlighting the most promising strategies to increase the yield. Finally, the review describes and critically analyzes currently available genome-scale metabolic models and reduced metabolic network applications commonly employed in the optimization of PHA production. Overall, it appears that the capacity of C. necator of performing CO2 bioconversion to PHA is still underexplored, both in biotechnological applications and in metabolic modeling. However, the accurate characterization of this organism and the efforts in using it for gas fermentation can help tackle this challenging perspective in the future.
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Affiliation(s)
- Maria Silvia Morlino
- Department of Biology, University of Padua, via U. Bassi 58/b, 35131 Padova, Italy
| | - Rebecca Serna García
- CALAGUA - Unidad Mixta UV-UPV, Departament d'Enginyeria Química, Universitat de València, Avinguda de la Universitat s/n, 46100 Burjassot, Valencia, Spain
| | - Filippo Savio
- Department of Biology, University of Padua, via U. Bassi 58/b, 35131 Padova, Italy
| | - Guido Zampieri
- Department of Biology, University of Padua, via U. Bassi 58/b, 35131 Padova, Italy
| | - Tomas Morosinotto
- Department of Biology, University of Padua, via U. Bassi 58/b, 35131 Padova, Italy
| | - Laura Treu
- Department of Biology, University of Padua, via U. Bassi 58/b, 35131 Padova, Italy.
| | - Stefano Campanaro
- Department of Biology, University of Padua, via U. Bassi 58/b, 35131 Padova, Italy
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8
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Gogoleva N, Chervyatsova O, Balkin A, Kuzmina L, Shagimardanova E, Kiseleva D, Gogolev Y. Microbial tapestry of the Shulgan-Tash cave (Southern Ural, Russia): influences of environmental factors on the taxonomic composition of the cave biofilms. ENVIRONMENTAL MICROBIOME 2023; 18:82. [PMID: 37990336 PMCID: PMC10662634 DOI: 10.1186/s40793-023-00538-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Accepted: 11/09/2023] [Indexed: 11/23/2023]
Abstract
BACKGROUND Cave biotopes are characterized by stable low temperatures, high humidity, and scarcity of organic substrates. Despite the harsh oligotrophic conditions, they are often inhabited by rich microbial communities. Abundant fouling with a wide range of morphology and coloration of colonies covers the walls of the Shulgan-Tash cave in the Southern Urals. This cave is also famous for the unique Paleolithic painting discovered in the middle of the last century. We aimed to investigate the diversity, distribution, and potential impact of these biofilms on the cave's Paleolithic paintings, while exploring how environmental factors influence the microbial communities within the cave. RESULTS The cave's biofilm morphotypes were categorized into three types based on the ultrastructural similarities. Molecular taxonomic analysis identified two main clusters of microbial communities, with Actinobacteria dominating in most of them and a unique "CaveCurd" community with Gammaproteobacteria prevalent in the deepest cave sections. The species composition of these biofilms reflects changes in environmental conditions, such as substrate composition, temperature, humidity, ventilation, and CO2 content. Additionally, it was observed that cave biofilms contribute to biocorrosion on cave wall surfaces. CONCLUSIONS The Shulgan-Tash cave presents an intriguing example of a stable extreme ecosystem with diverse microbiota. However, the intense dissolution and deposition of carbonates caused by Actinobacteria pose a potential threat to the preservation of the cave's ancient rock paintings.
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Affiliation(s)
- Natalia Gogoleva
- Research Department for Limnology, Mondsee, Universität Innsbruck, Mondsee, 5310, Austria.
- Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan, 420111, Russia.
| | | | - Alexander Balkin
- Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan, 420111, Russia
- Institute for Cellular and Intracellular Symbiosis, Ural Branch of the Russian Academy of Sciences, Orenburg, 460000, Russia
| | - Lyudmila Kuzmina
- Ufa Institute of Biology, Ufa Federal Research Center, Russian Academy of Sciences, Ufa, 450054, Russia
| | - Elena Shagimardanova
- Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan, 420111, Russia
- Loginov Moscow Clinical Scientific Center, Moscow, 111123, Russia
| | - Daria Kiseleva
- Institute of Geology and Geochemistry, Ural Branch of the Russian Academy of Sciences, Ekaterinburg, 620016, Russia
- Institute of Fundamental Education, Ural Federal University named after the first President of Russia B.N. Yeltsin, Ekaterinburg, 620002, Russia
| | - Yuri Gogolev
- Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan, 420111, Russia
- Kazan Institute of Biochemistry and Biophysics, Federal Research Center "Kazan Scientific Center of the Russian Academy of Sciences", Kazan, 420111, Russia
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9
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Tang R, Yuan X, Yang J. Problems and corresponding strategies for converting CO 2 into value-added products in Cupriavidus necator H16 cell factories. Biotechnol Adv 2023; 67:108183. [PMID: 37286176 DOI: 10.1016/j.biotechadv.2023.108183] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 04/17/2023] [Accepted: 05/31/2023] [Indexed: 06/09/2023]
Abstract
Elevated CO2 emissions have substantially altered the worldwide climate, while the excessive reliance on fossil fuels has exacerbated the energy crisis. Therefore, the conversion of CO2 into fuel, petroleum-based derivatives, drug precursors, and other value-added products is expected. Cupriavidus necator H16 is the model organism of the "Knallgas" bacterium and is considered to be a microbial cell factory as it can convert CO2 into various value-added products. However, the development and application of C. necator H16 cell factories has several limitations, including low efficiency, high cost, and safety concerns arising from the autotrophic metabolic characteristics of the strains. In this review, we first considered the autotrophic metabolic characteristics of C. necator H16, and then categorized and summarized the resulting problems. We also provided a detailed discussion of some corresponding strategies concerning metabolic engineering, trophic models, and cultivation mode. Finally, we provided several suggestions for improving and combining them. This review might help in the research and application of the conversion of CO2 into value-added products in C. necator H16 cell factories.
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Affiliation(s)
- Ruohao Tang
- Energy-rich Compounds Production by Photosynthetic Carbon Fixation Research Center, Shandong Key Lab of Applied Mycology, College of Life Sciences, Qingdao Agricultural University, Qingdao, 266109, Shandong Province, People's Republic of China; Shandong Key Laboratory of Environmental Processes and Health, School of Environmental Science and Engineering, Shandong University, Qingdao, 266237, Shandong Province, People's Republic of China
| | - Xianzheng Yuan
- Shandong Key Laboratory of Environmental Processes and Health, School of Environmental Science and Engineering, Shandong University, Qingdao, 266237, Shandong Province, People's Republic of China
| | - Jianming Yang
- Energy-rich Compounds Production by Photosynthetic Carbon Fixation Research Center, Shandong Key Lab of Applied Mycology, College of Life Sciences, Qingdao Agricultural University, Qingdao, 266109, Shandong Province, People's Republic of China.
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10
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Ali J, Faridi S, Sardar M. Carbonic anhydrase as a tool to mitigate global warming. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:83093-83112. [PMID: 37336857 DOI: 10.1007/s11356-023-28122-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Accepted: 06/01/2023] [Indexed: 06/21/2023]
Abstract
The global average temperature breaks the record every year, and this unprecedented speed at which it is unfolding is causing serious climate change which in turn impacts the lives of humans and other living organisms. Thus, it is imperative to take immediate action to limit global warming. Increased CO2 emission from the industrial sector that relies on fossil fuels is the major culprit. Mitigating global warming is an uphill battle that involves an integration of technologies such as switching to renewable energy, increasing the carbon sink capacity, and implementing carbon capture and sequestration (CCS) on major sources of CO2 emissions. Among all these methods, CCS is globally accepted as a potential technology to address this climate change. CCS using carbonic anhydrase (CA) is gaining momentum due to its advantages over other conventional CCS technologies. CA is a metalloenzyme that catalyses a fundamental reaction for life, i.e. the interconversion of bicarbonate and protons from carbon dioxide and water. The practical application of CA requires stable CAs operating under harsh operational conditions. CAs from extremophilic microbes are the potential candidates for the sequestration of CO2 and conversion into useful by-products. The soluble free form of CA is expensive, unstable, and non-reusable in an industrial setup. Immobilization of CA on various support materials can provide a better alternative for application in the sequestration of CO2. The present review provides insight into several types of CAs, their distinctive characteristics, sources, and recent developments in CA immobilization strategies for application in CO2 sequestration.
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Affiliation(s)
- Juned Ali
- Enzyme Technology Lab, Department of Biosciences, Jamia Millia Islamia, New Delhi, 110025, India
| | - Shazia Faridi
- Enzyme Technology Lab, Department of Biosciences, Jamia Millia Islamia, New Delhi, 110025, India
| | - Meryam Sardar
- Enzyme Technology Lab, Department of Biosciences, Jamia Millia Islamia, New Delhi, 110025, India.
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11
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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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12
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Abstract
Cyanobacteria rely on CO2-concentrating mechanisms (CCMs) to grow in today's atmosphere (0.04% CO2). These complex physiological adaptations require ≈15 genes to produce two types of protein complexes: inorganic carbon (Ci) transporters and 100+ nm carboxysome compartments that encapsulate rubisco with a carbonic anhydrase (CA) enzyme. Mutations disrupting any of these genes prohibit growth in ambient air. If any plausible ancestral form-i.e., lacking a single gene-cannot grow, how did the CCM evolve? Here, we test the hypothesis that evolution of the bacterial CCM was "catalyzed" by historically high CO2 levels that decreased over geologic time. Using an E. coli reconstitution of a bacterial CCM, we constructed strains lacking one or more CCM components and evaluated their growth across CO2 concentrations. We expected these experiments to demonstrate the importance of the carboxysome. Instead, we found that partial CCMs expressing CA or Ci uptake genes grew better than controls in intermediate CO2 levels (≈1%) and observed similar phenotypes in two autotrophic bacteria, Halothiobacillus neapolitanus and Cupriavidus necator. To understand how CA and Ci uptake improve growth, we model autotrophy as colimited by CO2 and HCO3-, as both are required to produce biomass. Our experiments and model delineated a viable trajectory for CCM evolution where decreasing atmospheric CO2 induces an HCO3- deficiency that is alleviated by acquisition of CA or Ci uptake, thereby enabling the emergence of a modern CCM. This work underscores the importance of considering physiology and environmental context when studying the evolution of biological complexity.
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13
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De Luca V, Carginale V, Supuran CT, Capasso C. The gram-negative bacterium Escherichia coli as a model for testing the effect of carbonic anhydrase inhibition on bacterial growth. J Enzyme Inhib Med Chem 2022; 37:2092-2098. [PMID: 35899716 PMCID: PMC9341340 DOI: 10.1080/14756366.2022.2101644] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022] Open
Abstract
Carbonic anhydrases, catalysing the reversible CO2 hydration reaction, contribute in all living organisms to the maintenance of stable metabolic functions depending on intracellular concentrations of carbon dioxide, bicarbonate, and protons. Recent studies have examined how CAs affect bacterial lifecycle, considering these enzymes druggable targets due to interference with their activities by using inhibitors or activators. Here, we propose Escherichia coli cells as a model for testing the effect of acetazolamide (AZA), a potent CA inhibitor, on bacterial survival by evaluating E. coli growth through its glucose consumption. AZA, at concentrations higher than 31.2 µg/mL, was able to impair E. coli growth and glucose uptake. AZA is a good inhibitor of the two recombinant E. coli CAs, the β-CA CynT2, and the γ-CA EcoCAγ, with KIs of 227 and 248 nM, respectively. This study provides a proof-of-concept, low-cost method for identifying effective CA inhibitors capable of impairing bacterial metabolism.
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Affiliation(s)
- Viviana De Luca
- Institute of Biosciences and Bioresources, National Research Council, Napoli, Italy
| | - Vincenzo Carginale
- Institute of Biosciences and Bioresources, National Research Council, Napoli, Italy
| | - Claudiu T Supuran
- Section of Pharmaceutical and Nutraceutical Sciences, Department of Neurofarba, University of Florence, Florence, Italy
| | - Clemente Capasso
- Institute of Biosciences and Bioresources, National Research Council, Napoli, Italy
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14
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Rasool A, Batool Z, Khan M, Halim SA, Shafiq Z, Temirak A, Salem MA, Ali TE, Khan A, Al-Harrasi A. Bis-pharmacophore of cinnamaldehyde-clubbed thiosemicarbazones as potent carbonic anhydrase-II inhibitors. Sci Rep 2022; 12:16095. [PMID: 36167735 PMCID: PMC9515202 DOI: 10.1038/s41598-022-19975-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2022] [Accepted: 09/07/2022] [Indexed: 11/24/2022] Open
Abstract
Here, we report the synthesis, carbonic anhydrase-II (CA-II) inhibition and structure–activity relationship studies of cinnamaldehyde-clubbed thiosemicarbazones derivatives. The derivatives showed potent activities in the range of 10.3 ± 0.62–46.6 ± 0.62 µM. Among all the synthesized derivatives, compound 3n (IC50 = 10.3 ± 0.62 µM), 3g (IC50 = 12.1 ± 1.01 µM), and 3h (IC50 = 13.4 ± 0.52 µM) showed higher inhibitory activity as compared to the standard inhibitor, acetazolamide. Furthermore, molecular docking of all the active compounds was carried out to predict their behavior of molecular binding. The docking results indicate that the most active hit (3n) specifically mediate ionic interaction with the Zn ion in the active site of CA-II. Furthermore, the The199 and Thr200 support the binding of thiosemicarbazide moiety of 3n, while Gln 92 supports the interactions of all the compounds by hydrogen bonding. In addition to Gln92, few other residues including Asn62, Asn67, The199, and Thr200 play important role in the stabilization of these molecules in the active site by specifically providing H-bonds to the thiosemicarbazide moiety of compounds. The docking score of active hits are found in range of − 6.75 to − 4.42 kcal/mol, which indicates that the computational prediction correlates well with the in vitro results.
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Affiliation(s)
- Asif Rasool
- Institute of Chemical Sciences, Bahauddin Zakariya University, Multan, 60800, Pakistan
| | - Zahra Batool
- Institute of Chemical Sciences, Bahauddin Zakariya University, Multan, 60800, Pakistan
| | - Majid Khan
- Natural and Medical Sciences Research Center, University of Nizwa, Nizwa, Sultanate of Oman
| | - Sobia Ahsan Halim
- Natural and Medical Sciences Research Center, University of Nizwa, Nizwa, Sultanate of Oman
| | - Zahid Shafiq
- Institute of Chemical Sciences, Bahauddin Zakariya University, Multan, 60800, Pakistan. .,Department of Pharmaceutical and Medicinal Chemistry, University of Bonn, An der Immenburg 4, 53121, Bonn, Germany.
| | - Ahmed Temirak
- National Research Centre, Chemistry of Natural and Microbial Products Department, Pharmaceutical and Drug Industries Research Institute, Dokki, P.O. Box 12622, Cairo, Egypt
| | - Mohamed A Salem
- Department of Chemistry, Faculty of Science and Arts, King Khalid University, Muhayil, Assir, Saudi Arabia.,Department of Chemistry, Faculty of Science, Al-Azhar University, 11284 Nasr City, Cairo, Egypt
| | - Tarik E Ali
- Department of Chemistry, Faculty of Science, King Khalid University, Abha, Saudi Arabia.,Department of Chemistry, Faculty of Education, Ain Shams University, Cairo, Egypt
| | - Ajmal Khan
- Natural and Medical Sciences Research Center, University of Nizwa, Nizwa, Sultanate of Oman.
| | - Ahmed Al-Harrasi
- Natural and Medical Sciences Research Center, University of Nizwa, Nizwa, Sultanate of Oman.
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15
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Borrero‐de Acuña JM, Poblete‐Castro I. Rational engineering of natural polyhydroxyalkanoates producing microorganisms for improved synthesis and recovery. Microb Biotechnol 2022; 16:262-285. [PMID: 35792877 PMCID: PMC9871526 DOI: 10.1111/1751-7915.14109] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Accepted: 06/14/2022] [Indexed: 01/27/2023] Open
Abstract
Microbial production of biopolymers derived from renewable substrates and waste streams reduces our heavy reliance on petrochemical plastics. One of the most important biodegradable polymers is the family of polyhydroxyalkanoates (PHAs), naturally occurring intracellular polyoxoesters produced for decades by bacterial fermentation of sugars and fatty acids at the industrial scale. Despite the advances, PHA production still suffers from heavy costs associated with carbon substrates and downstream processing to recover the intracellular product, thus restricting market positioning. In recent years, model-aided metabolic engineering and novel synthetic biology approaches have spurred our understanding of carbon flux partitioning through competing pathways and cellular resource allocation during PHA synthesis, enabling the rational design of superior biopolymer producers and programmable cellular lytic systems. This review describes these attempts to rationally engineering the cellular operation of several microbes to elevate PHA production on specific substrates and waste products. We also delve into genome reduction, morphology, and redox cofactor engineering to boost PHA biosynthesis. Besides, we critically evaluate engineered bacterial strains in various fermentation modes in terms of PHA productivity and the period required for product recovery.
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Affiliation(s)
| | - Ignacio Poblete‐Castro
- Biosystems Engineering LaboratoryDepartment of Chemical and Bioprocess EngineeringUniversidad de Santiago de Chile (USACH)SantiagoChile
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16
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Di Fiore A, De Luca V, Langella E, Nocentini A, Buonanno M, Maria Monti S, Supuran CT, Capasso C, De Simone G. Biochemical, structural, and computational studies of a γ-carbonic anhydrase from the pathogenic bacterium Burkholderia pseudomallei. Comput Struct Biotechnol J 2022; 20:4185-4194. [PMID: 36016712 PMCID: PMC9389205 DOI: 10.1016/j.csbj.2022.07.033] [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: 05/20/2022] [Revised: 07/18/2022] [Accepted: 07/19/2022] [Indexed: 11/09/2022] Open
Abstract
Melioidosis is a severe disease caused
Burkholderia pseudomallei. γ-carbonic anhydrases (γ-CAs) have been recently
introduced as novel antibacterial drug targets. A new γ-CA from B.
pseudomallei has been investigated by a
multidisciplinary approach. Obtained results provide an important starting point
for developing new anti-melioidosis drugs.
Melioidosis is a severe disease caused by the highly
pathogenic gram-negative bacterium Burkholderia
pseudomallei. Several studies have highlighted the broad
resistance of this pathogen to many antibiotics and pointed out the pivotal
importance of improving the pharmacological arsenal against it. Since γ-carbonic
anhydrases (γ-CAs) have been recently introduced as potential and novel
antibacterial drug targets, in this paper, we report a detailed characterization
of BpsγCA, a γ-CA from B.
pseudomallei by a multidisciplinary approach. In
particular, the enzyme was recombinantly produced and biochemically
characterized. Its catalytic activity at different pH values was measured, the
crystal structure was determined and theoretical pKa calculations were carried
out. Results provided a snapshot of the enzyme active site and dissected the
role of residues involved in the catalytic mechanism and ligand recognition.
These findings are an important starting point for developing new
anti-melioidosis drugs targeting BpsγCA.
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17
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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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18
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Sangeetha M, Sivarajan A, Radhakrishnan M, Siddharthan N, Balagurunathan R. Biosequestration of carbon dioxide using carbonic anhydrase from novel Streptomyces kunmingensis. Arch Microbiol 2022; 204:270. [PMID: 35441896 DOI: 10.1007/s00203-022-02887-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Revised: 03/28/2022] [Accepted: 03/30/2022] [Indexed: 12/01/2022]
Abstract
The increase in the atmospheric concentrations of carbon dioxide due to anthropogenic interventions has led to several undesirable consequences, notably global warming and related changes. Avoidance of and/or removal of carbon dioxide will result in the reduction of global warming. Biosequestration of carbon by using carbonic anhydrase (CA) as biocatalyst is one of most effective approaches. In the present study, actinobacterial cultures isolated from bamboo (Bambusa vulgaris) rhizosphere were screened for the production of carbonic anhydrase enzyme. The strain BS19 which showed promising CA production was selected as the potential strain. Strain BS19 was identified as Streptomyces kunmingensis based on the phenotypic and molecular characteristics. In submerged fermentation, strain BS19 produced 214.21 IU/ml of CA enzyme. The molecular mass of the CA was determined as 45 ± 2 kDa. The production of CA was found to be optimal at pH 7.0 and at temperature of 28 °C. The full length periplasmic CA gene was successfully amplified from S. kunmingensis BS19. Biomimetic sequestration of carbon was detected and quantified through CaCO3 precipitation method. Further, the CA of BS 19 was successfully used to mineralize CO2 present in motorbike exhaust, which has a similar composition to that of flue gas. The well-defined rhombohedral calcite crystals formed in the mineral carbonation reaction was observed through SEM analysis. The findings of this study clearly indicated that Streptomyces kunmingensis BS19 isolated from bamboo rhizosphere is a promising candidate for the production of carbonic anhydrase which deserves the potential for CO2 sequestration.
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Affiliation(s)
- Murthy Sangeetha
- Actinobacterial Research Laboratory, Department of Microbiology, Periyar University, Salem, Tamil Nadu, India
| | - Anbalmani Sivarajan
- Actinobacterial Research Laboratory, Department of Microbiology, Periyar University, Salem, Tamil Nadu, India
| | - Manikkam Radhakrishnan
- Centre for Drug Discovery and Development, Sathyabama Institute of Science and Technology, Chennai, Tamil Nadu, India
| | - Nagarajan Siddharthan
- Actinobacterial Research Laboratory, Department of Microbiology, Periyar University, Salem, Tamil Nadu, India
| | - Ramasamy Balagurunathan
- Actinobacterial Research Laboratory, Department of Microbiology, Periyar University, Salem, Tamil Nadu, India.
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19
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Orhan F, Senturk M, Genisel M. A new carbonic anhydrase identified in the Gram-negative bacterium (Chromohalobacter sp.) and the interaction of anions with the enzyme. Comp Biochem Physiol C Toxicol Pharmacol 2022; 254:109290. [PMID: 35114393 DOI: 10.1016/j.cbpc.2022.109290] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/16/2021] [Revised: 01/20/2022] [Accepted: 01/26/2022] [Indexed: 11/19/2022]
Abstract
In this study, the characterization and inhibition characteristic of α-class carbonic anhydrase from Chromohalobacter (ChCA) was documented for the first time. The carbonic anhydrase enzyme had 47.77% yield and 54.45-fold purity. The specific activity of the enzyme was determined as 318.52 U/mg proteins. Alternative substrate (4-nitrophenyl trifluoroacetate, 4-nitrophenyl phosphate, 4-nitrophenyl sulphate and 4-nitrophenyl acetate) were tested for the enzyme. KM and Vmax values for 4-nitrophenyl acetate were 4.57 mM and 4.29 EU/mL and for 4-nitrophenyl trifluoroacetate were 2.39 mM and 2.41 EU/mL. The anions, Cl-, NO2-, NO3-, Br-, ClO3-, ClO4-, I-, CO32- and SO42-, inhibited the ChCA hydratase activity. Among nine anions, the strongest inhibitor activities were obtained with micro molar concentrations of NO2-, NO3-, Br-, I-, CO32- (KI values of 160-255 μM). Other four anions tested (Cl-, ClO3-, ClO4- and SO42-) showed moderate inhibitory activities (KI values of 680-813.5 μM). The results obtained demonstrate that the anions we tested inhibit the Chromohalobacter CA (ChCA) enzyme as in other α-CAs in mammals; however, the susceptibility of ChCA resulted from anions differed significantly from that of other organism CAs.
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Affiliation(s)
- Furkan Orhan
- Agri Ibrahim Cecen University, Art and Science Faculty, Molecular Biology Department, 4100 Agri, Turkey; Agri Ibrahim Cecen University, Central Research and Application Laboratory, 4100 Agri, Turkey.
| | - Murat Senturk
- Agri Ibrahim Cecen University, Pharmacy Faculty, Department of Biochemistry, 4100 Agri, Turkey
| | - Mucip Genisel
- Agri Ibrahim Cecen University, Central Research and Application Laboratory, 4100 Agri, Turkey; Agri Ibrahim Cecen University, Pharmacy Faculty, Department of Pharmaceutical Botany, 04100 Agri, Turkey
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20
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Strittmatter CS, Eggers J, Biesgen V, Pauels I, Becker F, Steinbüchel A. The reliance of glycerol utilization by Cupriavidus necator on CO 2 fixation and improved glycerol catabolism. Appl Microbiol Biotechnol 2022; 106:2541-2555. [PMID: 35325274 DOI: 10.1007/s00253-022-11842-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 02/15/2022] [Accepted: 02/17/2022] [Indexed: 11/29/2022]
Abstract
While crude glycerol is a cheap carbon source for industrial-scale cultivation of microorganisms, its application relies on fast growth and conversion. The biopolymer producing Cupriavidus necator H16 (synonym: Ralstonia eutropha H16) grows poorly on glycerol. The heterologous expression of glycerol facilitator glpF, glycerol kinase glpK, and glycerol dehydrogenase glpD from E. coli accelerated the growth considerably. The naturally occurring glycerol utilization is inhibited by low glycerol kinase activity. A limited heterotrophic growth promotes the dependency on autotrophic growth by carbon dioxide (CO2) fixation and refixation. As mixotrophic growth occurs in the wildtype due to low consumption rates of glycerol, CO2 fixation by the Calvin-Benson-Bassham (CBB) cycle is essential. The deletion of both cbbX copies encoding putative RuBisCO-activases (AAA + ATPase) resulted in a sharp slowdown of growth and glycerol consumption. Activase activity is necessary for functioning carboxylation by RuBisCO. Each of the two copies compensates for the loss of the other, as suggested by observed expression levels. The strong tendency towards autotrophy supports previous investigations of glycerol growth and emphasizes the versatility of the metabolism of C. necator H16. Mixotrophy with glycerol-utilization and CO2 fixation with a high dependence on the CBB is automatically occurring unless transportation and degradation of glycerol are optimized. Parallel engineering of CO2 fixation and glycerol degradation is suggested towards application for value-added production from crude glycerol. KEY POINTS: • Growth on glycerol is highly dependent on efficient carbon fixation via CBB cycle. • CbbX is essential for the efficiency of RuBisCO in C. necator H16. • Expression of glycerol degradation pathway enzymes accelerates glycerol utilization.
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Affiliation(s)
- Carl Simon Strittmatter
- Insitut für Molekulare Mikrobiologie und Biotechnologie, Westfälische Wilhelms-Universtität Münster, Münster, Germany
| | - Jessica Eggers
- Insitut für Molekulare Mikrobiologie und Biotechnologie, Westfälische Wilhelms-Universtität Münster, Münster, Germany
| | - Vanessa Biesgen
- Insitut für Molekulare Mikrobiologie und Biotechnologie, Westfälische Wilhelms-Universtität Münster, Münster, Germany
| | - Inga Pauels
- Insitut für Molekulare Mikrobiologie und Biotechnologie, Westfälische Wilhelms-Universtität Münster, Münster, Germany
| | - Florian Becker
- Insitut für Molekulare Mikrobiologie und Biotechnologie, Westfälische Wilhelms-Universtität Münster, Münster, Germany
| | - Alexander Steinbüchel
- Insitut für Molekulare Mikrobiologie und Biotechnologie, Westfälische Wilhelms-Universtität Münster, Münster, Germany. .,Environmental Science Department, King Abdulaziz University, Jeddah, Saudi Arabia.
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21
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Pavan M, Reinmets K, Garg S, Mueller AP, Marcellin E, Köpke M, Valgepea K. Advances in systems metabolic engineering of autotrophic carbon oxide-fixing biocatalysts towards a circular economy. Metab Eng 2022; 71:117-141. [DOI: 10.1016/j.ymben.2022.01.015] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 01/24/2022] [Accepted: 01/25/2022] [Indexed: 12/16/2022]
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22
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Sohn YJ, Son J, Jo SY, Park SY, Yoo JI, Baritugo KA, Na JG, Choi JI, Kim HT, Joo JC, Park SJ. Chemoautotroph Cupriavidus necator as a potential game-changer for global warming and plastic waste problem: A review. BIORESOURCE TECHNOLOGY 2021; 340:125693. [PMID: 34365298 DOI: 10.1016/j.biortech.2021.125693] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Revised: 07/26/2021] [Accepted: 07/27/2021] [Indexed: 06/13/2023]
Abstract
Cupriavidus necator, a versatile microorganism found in both soil and water, can have both heterotrophic and lithoautotrophic metabolisms depending on environmental conditions. C. necator has been extensively examined for producing Polyhydroxyalkanoates (PHAs), the promising polyester alternatives to petroleum-based synthetic polymers because it has a superior ability for accumulating a considerable amount of PHAs from renewable resources. The development of metabolically engineered C. necator strains has led to their application for synthesizing biopolymers, biofuels and biochemicals such as ethanol, isobutanol and higher alcohols. Bio-based processes of recombinant C. necator have made much progress in production of these high-value products from biomass wastes, plastic wastes and even waste gases. In this review, we discuss the potential of C. necator as promising platform host strains that provide a great opportunity for developing a waste-based circular bioeconomy.
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Affiliation(s)
- Yu Jung Sohn
- Department of Chemical Engineering and Materials Science, Graduate Program in System Health Science and Engineering, Ewha Womans University, Seoul 03760, Republic of Korea
| | - Jina Son
- Department of Chemical Engineering and Materials Science, Graduate Program in System Health Science and Engineering, Ewha Womans University, Seoul 03760, Republic of Korea
| | - Seo Young Jo
- Department of Chemical Engineering and Materials Science, Graduate Program in System Health Science and Engineering, Ewha Womans University, Seoul 03760, Republic of Korea
| | - Se Young Park
- Department of Chemical Engineering and Materials Science, Graduate Program in System Health Science and Engineering, Ewha Womans University, Seoul 03760, Republic of Korea
| | - Jee In Yoo
- Department of Chemical Engineering and Materials Science, Graduate Program in System Health Science and Engineering, Ewha Womans University, Seoul 03760, Republic of Korea
| | - Kei-Anne Baritugo
- Department of Chemical Engineering and Materials Science, Graduate Program in System Health Science and Engineering, Ewha Womans University, Seoul 03760, Republic of Korea
| | - Jeong Geol Na
- Department of Chemical and Biomolecular Engineering, Sogang University, Seoul, Republic of Korea.
| | - Jong-Il Choi
- Department of Biotechnology and Bioengineering, Chonnam National University, Gwangju 61186, Korea.
| | - Hee Taek Kim
- Department of Food Science and Technology, College of Agriculture and Life Sciences, Chungnam National University, Daejeon 34134, Republic of Korea.
| | - Jeong Chan Joo
- Department of Biotechnology, The Catholic University of Korea, Gyeonggi-do, Republic of Korea.
| | - Si Jae Park
- Department of Chemical Engineering and Materials Science, Graduate Program in System Health Science and Engineering, Ewha Womans University, Seoul 03760, Republic of Korea.
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23
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Del Prete S, Bua S, Supuran CT, Capasso C. Escherichia coli γ-carbonic anhydrase: characterisation and effects of simple aromatic/heterocyclic sulphonamide inhibitors. J Enzyme Inhib Med Chem 2021; 35:1545-1554. [PMID: 32746656 PMCID: PMC7470111 DOI: 10.1080/14756366.2020.1800670] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Carbonic anhydrases (CAs, EC 4.2.1.1) are ubiquitous metalloenzymes involved in biosynthetic processes, transport, supply, and balance of CO2/HCO3- into the cell. In Bacteria, CAs avoid the depletion of the dissolved CO2/HCO3- from the cell, providing them to the central metabolism that is compromised without the CA activity. The involvement of CAs in the survival, pathogenicity, and virulence of several bacterial pathogenic species is recent. Here, we report the kinetic properties of the recombinant γ-CA (EcoCAγ) encoded in the genome of Escherichia coli. EcoCAγ is an excellent catalyst for the physiological CO2 hydration reaction to bicarbonate and protons, with a kcat of 5.7 × 105 s−1 and kcat/KM of 6.9 × 106 M−1 s−1. The EcoCAγ inhibition profile with a broad series of known CA inhibitors, the substituted benzene-sulphonamides, and clinically licenced drugs was explored. Benzolamide showed a KI lower than 100 nM. Our study reinforces the hypothesis that the synthesis of new drugs capable of interfering selectively with the bacterial CA activity, avoiding the inhibition of the human α -CAs, is achievable and may lead to novel antibacterials.
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Affiliation(s)
- Sonia Del Prete
- Department of Biology, Agriculture and Food Sciences, CNR, Institute of Biosciences and Bioresources, Napoli, Italy
| | - Silvia Bua
- Section of Pharmaceutical and Nutraceutical Sciences, Department of NEUROFARBA, University of Florence, Firenze, Italy
| | - Claudiu T Supuran
- Section of Pharmaceutical and Nutraceutical Sciences, Department of NEUROFARBA, University of Florence, Firenze, Italy
| | - Clemente Capasso
- Department of Biology, Agriculture and Food Sciences, CNR, Institute of Biosciences and Bioresources, Napoli, Italy
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24
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Campestre C, De Luca V, Carradori S, Grande R, Carginale V, Scaloni A, Supuran CT, Capasso C. Carbonic Anhydrases: New Perspectives on Protein Functional Role and Inhibition in Helicobacter pylori. Front Microbiol 2021; 12:629163. [PMID: 33815311 PMCID: PMC8017301 DOI: 10.3389/fmicb.2021.629163] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Accepted: 02/22/2021] [Indexed: 12/12/2022] Open
Abstract
Our understanding of the function of bacterial carbonic anhydrases (CAs, EC 4.2.1.1) has increased significantly in the last years. CAs are metalloenzymes able to modulate CO2, HCO3 - and H+ concentration through their crucial role in catalysis of reversible CO2 hydration (CO2 + H2O ⇄ HCO3 - + H+). In all living organisms, CA activity is linked to physiological processes, such as those related to the transport and supply of CO2 or HCO3 -, pH homeostasis, secretion of electrolytes, biosynthetic processes and photosynthesis. These important processes cannot be ensured by the very low rate of the non-catalyzed reaction of CO2 hydration. It has been recently shown that CAs are important biomolecules for many bacteria involved in human infections, such as Vibrio cholerae, Brucella suis, Salmonella enterica, Pseudomonas aeruginosa, and Helicobacter pylori. In these species, CA activity promotes microorganism growth and adaptation in the host, or modulates bacterial toxin production and virulence. In this review, recent literature in this research field and some of the above-mentioned issues are discussed, namely: (i) the implication of CAs from bacterial pathogens in determining the microorganism growth and virulence; (ii) the druggability of these enzymes using classical CA inhibitors (CAIs) of the sulfonamide-type as examples; (iii) the role played by Helicobacter pylori CAs in the acid tolerance/adaptation of the microbe within the human abdomen; (iv) the role of CAs played in the outer membrane vesicles spawned by H. pylori in its planktonic and biofilm phenotypes; (v) the possibility of using H. pylori CAIs in combination with probiotic strains as a novel anti-ulcer treatment approach. The latter approach may represent an innovative and successful strategy to fight gastric infections in the era of increasing resistance of pathogenic bacteria to classical antibiotics.
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Affiliation(s)
- Cristina Campestre
- Department of Pharmacy, "G. d'Annunzio" University of Chieti-Pescara, Chieti, Italy
| | - Viviana De Luca
- Department of Biology, Agriculture and Food Sciences, National Research Council (CNR), Institute of Biosciences and Bioresources, Naples, Italy.,Proteomics and Mass Spectrometry Laboratory, Institute for the Animal Production System in the Mediterranean Environment, National Research Council (ISPAAM-CNR), Naples, Italy
| | - Simone Carradori
- Department of Pharmacy, "G. d'Annunzio" University of Chieti-Pescara, Chieti, Italy
| | - Rossella Grande
- Department of Pharmacy, "G. d'Annunzio" University of Chieti-Pescara, Chieti, Italy
| | - Vincenzo Carginale
- Department of Biology, Agriculture and Food Sciences, National Research Council (CNR), Institute of Biosciences and Bioresources, Naples, Italy
| | - Andrea Scaloni
- Proteomics and Mass Spectrometry Laboratory, Institute for the Animal Production System in the Mediterranean Environment, National Research Council (ISPAAM-CNR), Naples, Italy
| | - Claudiu T Supuran
- Section of Pharmaceutical and Nutraceutical Sciences, Polo Scientifico, Department of NEUROFARBA, University of Florence, Sesto Fiorentino, Italy
| | - Clemente Capasso
- Department of Biology, Agriculture and Food Sciences, National Research Council (CNR), Institute of Biosciences and Bioresources, Naples, Italy
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25
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Panich J, Fong B, Singer SW. Metabolic Engineering of Cupriavidus necator H16 for Sustainable Biofuels from CO 2. Trends Biotechnol 2021; 39:412-424. [PMID: 33518389 DOI: 10.1016/j.tibtech.2021.01.001] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Revised: 01/05/2021] [Accepted: 01/06/2021] [Indexed: 02/08/2023]
Abstract
Decelerating global warming is one of the predominant challenges of our time and will require conversion of CO2 to usable products and commodity chemicals. Of particular interest is the production of fuels, because the transportation sector is a major source of CO2 emissions. Here, we review recent technological advances in metabolic engineering of the hydrogen-oxidizing bacterium Cupriavidus necator H16, a chemolithotroph that naturally consumes CO2 to generate biomass. We discuss recent successes in biofuel production using this organism, and the implementation of electrolysis/artificial photosynthesis approaches that enable growth of C. necator using renewable electricity and CO2. Last, we discuss prospects of improving the nonoptimal growth of C. necator in ambient concentrations of CO2.
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Affiliation(s)
- Justin Panich
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
| | - Bonnie Fong
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Steven W Singer
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
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Del Prete S, Nocentini A, Supuran CT, Capasso C. Bacterial ι-carbonic anhydrase: a new active class of carbonic anhydrase identified in the genome of the Gram-negative bacterium Burkholderia territorii. J Enzyme Inhib Med Chem 2020; 35:1060-1068. [PMID: 32314608 PMCID: PMC7191908 DOI: 10.1080/14756366.2020.1755852] [Citation(s) in RCA: 63] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Accepted: 04/05/2020] [Indexed: 01/30/2023] Open
Abstract
The carbonic anhydrases (CAs, EC 4.2.1.1) catalyse a simple but physiologically crucial reversible reaction, the carbon dioxide hydration with the production of bicarbonate and protons. In the last years, and especially, to the rapid emergence of the bacterial antibiotic resistance that is occurring worldwide, the understanding of the function of bacterial CAs has increased significantly. Recently, a new CA-class (ι-CA) was discovered in the marine diatom T. pseudonana. It has been reported that bacterial genomes may contain genes with relevant homology to the diatom ι-class CA. Still, the catalytic activity of the enzyme encoded by the gene was not investigated. Thus, herein, for the first time, we cloned, expressed, and purified the recombinant bacterial ι-CA (acronym BteCAι) identified in the genome of Burkholderia territorii. The recombinant BteCAι resulted in a good catalyst for the hydration of CO2 to bicarbonate and protons, with a kcat of 3.0 × 105 s -1 and kcat/KM of 3.9 × 107 M -1 s -1, and is also sensitive to inhibition by the sulphonamide acetazolamide. Furthermore, with the aid of the protonography, it has been demonstrated that BteCAι can be present as a dimer. This result is corroborated by the construction of a molecular model of BteCAι, which showed that the enzyme is formed by two equivalent monomers having a structure similar to a butterfly.
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Affiliation(s)
- Sonia Del Prete
- Department of Biology, Agriculture and Food Sciences, Institute of Biosciences and Bioresources, CNR, Napoli, Italy
| | - Alessio Nocentini
- Department of NEUROFARBA, University of Florence, Section of Pharmaceutical and Nutraceutical Sciences, Firenze, Italy
| | - Claudiu T. Supuran
- Department of NEUROFARBA, University of Florence, Section of Pharmaceutical and Nutraceutical Sciences, Firenze, Italy
| | - Clemente Capasso
- Department of Biology, Agriculture and Food Sciences, Institute of Biosciences and Bioresources, CNR, Napoli, Italy
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The gene dosage effect of carbonic anhydrase on the biosynthesis of poly(3-hydroxybutyrate) under autotrophic and mixotrophic culture conditions. Polym J 2020. [DOI: 10.1038/s41428-020-00409-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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28
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Fujitani H, Momiuchi K, Ishii K, Nomachi M, Kikuchi S, Ushiki N, Sekiguchi Y, Tsuneda S. Genomic and Physiological Characteristics of a Novel Nitrite-Oxidizing Nitrospira Strain Isolated From a Drinking Water Treatment Plant. Front Microbiol 2020; 11:545190. [PMID: 33042056 PMCID: PMC7522533 DOI: 10.3389/fmicb.2020.545190] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Accepted: 08/24/2020] [Indexed: 11/13/2022] Open
Abstract
Nitrite-oxidizing bacteria (NOB) catalyze the second step of nitrification, which is an important process of the biogeochemical nitrogen cycle and is exploited extensively as a biological nitrogen removal process. Members of the genus Nitrospira are often identified as the dominant NOB in a diverse range of natural and artificial environments. Additionally, a number of studies examining the distribution, abundance, and characterization of complete ammonia oxidation (comammox) Nitrospira support the ecological importance of the genus Nitrospira. However, niche differentiation between nitrite-oxidizing Nitrospira and comammox Nitrospira remains unknown due to a lack of pure cultures. In this study, we report the isolation, physiology, and genome of a novel nitrite-oxidizing Nitrospira strain isolated from a fixed-bed column at a drinking water treatment plant. Continuous feeding of ammonia led to the enrichment of Nitrospira-like cells, as well as members of ammonia-oxidizing genus Nitrosomonas. Subsequently, a microcolony sorting technique was used to isolate a novel nitrite-oxidizing Nitrospira strain. Sequences of strains showing the growth of microcolonies in microtiter plates were checked. Consequently, the most abundant operational taxonomic unit (OTU) exhibited high sequence similarity with Nitrospira japonica (98%) at the 16S rRNA gene level. The two other Nitrospira OTUs shared over 99% sequence similarities with N. japonica and Nitrospira sp. strain GC86. Only one strain identified as Nitrospira was successfully subcultivated and designated as Nitrospira sp. strain KM1 with high sequence similarity with N. japonica (98%). The half saturation constant for nitrite and the maximum nitrite oxidation rate of strain KM1 were orders of magnitude lower than the published data of other known Nitrospira strains; moreover, strain KM1 was more sensitive to free ammonia compared with previously isolated Nitrospira strains. Therefore, the new Nitrospira strain appears to be better adapted to oligotrophic environments compared with other known non-marine nitrite oxidizers. The complete genome of strain KM1 was 4,509,223 bp in length and contained 4,318 predicted coding sequences. Average nucleotide identities between strain KM1 and known cultured Nitrospira genome sequences are 76.7-78.4%, suggesting at least species-level novelty of the strain in the Nitrospira lineage II. These findings broaden knowledge of the ecophysiological diversity of nitrite-oxidizing Nitrospira.
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Affiliation(s)
- Hirotsugu Fujitani
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology, Tsukuba, Japan.,Research Organization for Nano & Life Innovation, Waseda University, Tokyo, Japan
| | - Kengo Momiuchi
- Department of Life Science and Medical Bioscience, Waseda University, Tokyo, Japan
| | - Kento Ishii
- Department of Life Science and Medical Bioscience, Waseda University, Tokyo, Japan
| | - Manami Nomachi
- Department of Life Science and Medical Bioscience, Waseda University, Tokyo, Japan
| | - Shuta Kikuchi
- Department of Life Science and Medical Bioscience, Waseda University, Tokyo, Japan
| | - Norisuke Ushiki
- Department of Life Science and Medical Bioscience, Waseda University, Tokyo, Japan
| | - Yuji Sekiguchi
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology, Tsukuba, Japan
| | - Satoshi Tsuneda
- Research Organization for Nano & Life Innovation, Waseda University, Tokyo, Japan.,Department of Life Science and Medical Bioscience, Waseda University, Tokyo, Japan
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29
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Supuran CT, Capasso C. Antibacterial carbonic anhydrase inhibitors: an update on the recent literature. Expert Opin Ther Pat 2020; 30:963-982. [PMID: 32806966 DOI: 10.1080/13543776.2020.1811853] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
INTRODUCTION The clinically licensed drugs used as antibiotics prevent the microbial growth interfering with the biosynthesis of proteins, nucleic acids, microorganism wall biosynthesis or wall permeability, and microbial metabolic pathways. A serious, emerging problem is the arisen of extensive drug resistance afflicting most countries worldwide. AREAS COVERED An exciting approach to fight drug resistance is the identification of essential enzymes encoded by pathogen genomes. Inhibition of such enzymes may impair microbial growth or virulence due to interference with crucial metabolic processes. Genome exploration of pathogenic and nonpathogenic microorganisms has revealed carbonic anhydrases (CAs, EC 4.2.1.1) as possible antibacterial targets. EXPERT OPINION Balancing the equilibrium between CO2 and HCO3 - is essential for microbial metabolism and is regulated by at least four classes of CAs. Classical CA inhibitors (CAIs) such as ethoxzolamide were shown to kill the gastric pathogen Helicobacter pylori in vitro, whereas acetazolamide and some of its more lipophilic derivatives were shown to be effective against vancomycin-resistant Enterococcus spp., with MICs in the range of 0.007-2 µg/mL, better than linezolid, the only clinically used agent available to date. Such results reinforce the rationale of considering existing and newly designed CAIs as antibacterials with an alternative mechanism of action.
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García Lobo JM, Ortiz Y, Gonzalez-Riancho C, Seoane A, Arellano-Reynoso B, Sangari FJ. Polymorphisms in Brucella Carbonic Anhydrase II Mediate CO 2 Dependence and Fitness in vivo. Front Microbiol 2020; 10:2751. [PMID: 31921002 PMCID: PMC6915039 DOI: 10.3389/fmicb.2019.02751] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Accepted: 11/12/2019] [Indexed: 11/27/2022] Open
Abstract
Some Brucella isolates are known to require an increased concentration of CO2 for growth, especially in the case of primary cultures obtained directly from infected animals. Moreover, the different Brucella species and biovars show a characteristic pattern of CO2 requirement, and this trait has been included among the routine typing tests used for species and biovar differentiation. By comparing the differences in gene content among different CO2-dependent and CO2-independent Brucella strains, we have confirmed that carbonic anhydrase (CA) II is the enzyme responsible for this phenotype in all the Brucella strains tested. Brucella species contain two CAs of the β family, CA I and CA II; genetic polymorphisms exist for both of them in different isolates, but only those putatively affecting the activity of CA II correlate with the CO2 requirement of the corresponding isolate. Analysis of these polymorphisms does not allow the determination of CA I functionality, while the polymorphisms in CA II consist of small deletions that cause a frameshift that changes the C-terminus of the protein, probably affecting its dimerization status, essential for the activity. CO2-independent mutants arise easily in vitro, although with a low frequency ranging from 10–6 to 10–10 depending on the strain. These mutants carry compensatory mutations that produce a full-length CA II. At the same time, no change was observed in the sequence coding for CA I. A competitive index assay designed to evaluate the fitness of a CO2-dependent strain compared to its corresponding CO2-independent strain revealed that while there is no significant difference when the bacteria are grown in culture plates, growth in vivo in a mouse model of infection provides a significant advantage to the CO2-dependent strain. This could explain why some Brucella isolates are CO2 dependent in primary isolation. The polymorphism described here also allows the in silico determination of the CO2 requirement status of any Brucella strain.
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Affiliation(s)
- Juan M García Lobo
- Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC), CSIC - Universidad de Cantabria, Santander, Spain.,Departamento de Biología Molecular, Universidad de Cantabria, Santander, Spain
| | - Yelina Ortiz
- Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC), CSIC - Universidad de Cantabria, Santander, Spain.,Departamento de Biología Molecular, Universidad de Cantabria, Santander, Spain
| | - Candela Gonzalez-Riancho
- Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC), CSIC - Universidad de Cantabria, Santander, Spain.,Departamento de Biología Molecular, Universidad de Cantabria, Santander, Spain
| | - Asunción Seoane
- Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC), CSIC - Universidad de Cantabria, Santander, Spain.,Departamento de Biología Molecular, Universidad de Cantabria, Santander, Spain
| | - Beatriz Arellano-Reynoso
- Departamento de Microbiología, Delegación Coyoacán, Facultad de Medicina Veterinaria y Zootecnia, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Félix J Sangari
- Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC), CSIC - Universidad de Cantabria, Santander, Spain.,Departamento de Biología Molecular, Universidad de Cantabria, Santander, Spain
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31
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Pander B, Harris G, Scott DJ, Winzer K, Köpke M, Simpson SD, Minton NP, Henstra AM. The carbonic anhydrase of Clostridium autoethanogenum represents a new subclass of β-carbonic anhydrases. Appl Microbiol Biotechnol 2019; 103:7275-7286. [PMID: 31346685 PMCID: PMC6690855 DOI: 10.1007/s00253-019-10015-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Revised: 07/05/2019] [Accepted: 07/08/2019] [Indexed: 02/04/2023]
Abstract
Carbonic anhydrase catalyses the interconversion of carbon dioxide and water to bicarbonate and protons. It was unknown if the industrial-relevant acetogen Clostridium autoethanogenum possesses these enzymes. We identified two putative carbonic anhydrase genes in its genome, one of the β class and one of the γ class. Carbonic anhydrase activity was found for the purified β class enzyme, but not the γ class candidate. Functional complementation of an Escherichia coli carbonic anhydrase knock-out mutant showed that the β class carbonic anhydrase could complement this activity, but not the γ class candidate gene. Phylogenetic analysis showed that the β class carbonic anhydrase of Clostridium autoethanogenum represents a novel sub-class of β class carbonic anhydrases that form the F-clade. The members of this clade have the shortest primary structure of any known carbonic anhydrase.
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Affiliation(s)
- Bart Pander
- Clostridia Research Group, BBSRC/EPSRC Synthetic Biology Research Centre, School of Life Sciences, University of Nottingham, Nottingham, NG7 2RD, UK
| | - Gemma Harris
- Research Complex at Harwell, Rutherford Appleton Laboratory, Harwell Science and Innovation Campus, Didcot, OX11 0FA, UK
| | - David J Scott
- Research Complex at Harwell, Rutherford Appleton Laboratory, Harwell Science and Innovation Campus, Didcot, OX11 0FA, UK.,ISIS Spallation Neutron and Muon Source, Rutherford Appleton Laboratory, Harwell Science and Innovation Campus, Didcot, OX11 0QX, UK.,School of Biosciences, University of Nottingham, Sutton Bonington Campus, Sutton Bonington, LE12 5RD, UK
| | - Klaus Winzer
- Clostridia Research Group, BBSRC/EPSRC Synthetic Biology Research Centre, School of Life Sciences, University of Nottingham, Nottingham, NG7 2RD, UK
| | - Michael Köpke
- LanzaTech Inc., 8045 Lamon Avenue, Suite 400, Skokie, IL, USA
| | - Sean D Simpson
- LanzaTech Inc., 8045 Lamon Avenue, Suite 400, Skokie, IL, USA
| | - Nigel P Minton
- Clostridia Research Group, BBSRC/EPSRC Synthetic Biology Research Centre, School of Life Sciences, University of Nottingham, Nottingham, NG7 2RD, UK
| | - Anne M Henstra
- Clostridia Research Group, BBSRC/EPSRC Synthetic Biology Research Centre, School of Life Sciences, University of Nottingham, Nottingham, NG7 2RD, UK.
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32
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Windhorst C, Gescher J. Efficient biochemical production of acetoin from carbon dioxide using Cupriavidus necator H16. BIOTECHNOLOGY FOR BIOFUELS 2019; 12:163. [PMID: 31297151 PMCID: PMC6598341 DOI: 10.1186/s13068-019-1512-x] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2019] [Accepted: 06/21/2019] [Indexed: 05/26/2023]
Abstract
BACKGROUND Cupriavidus necator is the best-studied knallgas (also termed hydrogen oxidizing) bacterium and provides a model organism for studying the production of the storage polymer polyhydroxybutyrate (PHB). Genetically engineered strains could be applied for the autotrophic production of valuable chemicals. Nevertheless, the efficiency of the catalyzed processes is generally believed to be lower than with acetogenic bacteria. Experimental data on the potential efficiency of autotrophic production with C. necator are sparse. Hence, this study aimed at developing a strain for the production of the bulk chemical acetoin from carbon dioxide and to analyze the carbon and electron yield in detail. RESULTS We developed a constitutive promoter system based on the natural PHB promoter of this organism. Codon-optimized versions of the acetolactate dehydrogenase (alsS) and acetolactate decarboxylase (alsD) from Bacillus subtilis were cloned under control of the PHB promoter in order to produce acetoin from pyruvate. The production process's efficiency could be significantly increased by deleting the PHB synthase phaC2. Further deletion of the other PHB synthase encoded in the genome (phaC1) led to a strain that produced acetoin with > 100% carbon efficiency. This increase in efficiency is most probably due to a minor amount of cell lysis. Using a variation in hydrogen and oxygen gas mixtures, we observed that the optimal oxygen concentration for the process was between 15 and 20%. CONCLUSION To the best of our knowledge, this study describes for the first time a highly efficient process for the chemolithoautotrophic production of the platform chemical acetoin.
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Affiliation(s)
- Carina Windhorst
- Department of Applied Biology, Institute for Applied Biosciences, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Johannes Gescher
- Department of Applied Biology, Institute for Applied Biosciences, Karlsruhe Institute of Technology, Karlsruhe, Germany
- Institute for Biological Interfaces, Karlsruhe Institute of Technology, Eggenstein-Leopoldshafen, Germany
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33
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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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Rogato A, Del Prete S, Nocentini A, Carginale V, Supuran CT, Capasso C. Phaeodactylum tricornutum as a model organism for testing the membrane penetrability of sulphonamide carbonic anhydrase inhibitors. J Enzyme Inhib Med Chem 2019; 34:510-518. [PMID: 30688123 PMCID: PMC6352938 DOI: 10.1080/14756366.2018.1559840] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Carbonic anhydrases (CAs) are ubiquitous metalloenzymes, which started to be investigated in detail in pathogenic, as well as non-pathogenic species since their pivotal role is to accelerate the physiological CO2 hydration/dehydration reaction significantly. Here, we propose the marine unicellular diatom Phaeodactylum tricornutum as a model organism for testing the membrane penetrability of CA inhibitors (CAIs). Seven inhibitors belonging to the sulphonamide type and possessing a diverse scaffold have been explored for their in vitro inhibition of the whole diatom CAs and the in vivo inhibitory effect on the growth of P. tricornutum. Interesting, inhibition of growth was observed, in vivo, demonstrating that this diatom is a good model for testing the cell wall penetrability of this class of pharmacological agents. Considering that many pathogens are difficult and dangerous to grow in the laboratory, the growth inhibition of P. tricornutum with different such CAIs may be subsequently used to design inhibition studies of CAs from pathogenic organisms.
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Affiliation(s)
- Alessandra Rogato
- a Institute of Bioscience and BioResources, CNR , Naples , Italy.,b Department of Integrative Marine Ecology , Stazione Zoologica Anton Dohrn , Naples , Italy
| | - Sonia Del Prete
- a Institute of Bioscience and BioResources, CNR , Naples , Italy
| | - Alessio Nocentini
- c Neurofarba Department, University of Florence, Polo Scientifico , Sesto Fiorentino , Florence , Italy
| | | | - Claudiu T Supuran
- c Neurofarba Department, University of Florence, Polo Scientifico , Sesto Fiorentino , Florence , Italy
| | - Clemente Capasso
- a Institute of Bioscience and BioResources, CNR , Naples , Italy
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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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36
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Siozios S, Pilgrim J, Darby AC, Baylis M, Hurst GD. The draft genome of strain cCpun from biting midges confirms insect Cardinium are not a monophyletic group and reveals a novel gene family expansion in a symbiont. PeerJ 2019; 7:e6448. [PMID: 30809447 PMCID: PMC6387759 DOI: 10.7717/peerj.6448] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Accepted: 01/15/2019] [Indexed: 01/02/2023] Open
Abstract
BACKGROUND It is estimated that 13% of arthropod species carry the heritable symbiont Cardinium hertigii. 16S rRNA and gyrB sequence divides this species into at least four groups (A-D), with the A group infecting a range of arthropods, the B group infecting nematode worms, the C group infecting Culicoides biting midges, and the D group associated with the marine copepod Nitocra spinipes. To date, genome sequence has only been available for strains from groups A and B, impeding general understanding of the evolutionary history of the radiation. We present a draft genome sequence for a C group Cardinium, motivated both by the paucity of genomic information outside of the A and B group, and the importance of Culicoides biting midge hosts as arbovirus vectors. METHODS We reconstructed the genome of cCpun, a Cardinium strain from group C that naturally infects Culicoides punctatus, through Illumina sequencing of infected host specimens. RESULTS The draft genome presented has high completeness, with BUSCO scores comparable to closed group A Cardinium genomes. Phylogenomic analysis based on concatenated single copy core proteins do not support Cardinium from arthropod hosts as a monophyletic group, with nematode Cardinium strains nested within the two groups infecting arthropod hosts. Analysis of the genome of cCpun revealed expansion of a variety of gene families classically considered important in symbiosis (e.g., ankyrin domain containing genes), and one set-characterized by DUF1703 domains-not previously associated with symbiotic lifestyle. This protein group encodes putative secreted nucleases, and the cCpun genome carried at least 25 widely divergent paralogs, 24 of which shared a common ancestor in the C group. The genome revealed no evidence in support of B vitamin provisioning to its haematophagous host, and indeed suggests Cardinium may be a net importer of biotin. DISCUSSION These data indicate strains of Cardinium within nematodes cluster within Cardinium strains found in insects. The draft genome of cCpun further produces new hypotheses as to the interaction of the symbiont with the midge host, in particular the biological role of DUF1703 nuclease proteins that are predicted as being secreted by cCpun. In contrast, the coding content of this genome provides no support for a role for the symbiont in provisioning the host with B vitamins.
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Affiliation(s)
- Stefanos Siozios
- Institute of Integrative Biology, Faculty of Health and Life Sciences, University of Liverpool, Liverpool, UK
| | - Jack Pilgrim
- Institute of Infection and Global Health, Faculty of Health and Life Sciences, University of Liverpool, Liverpool, UK
| | - Alistair C. Darby
- Institute of Integrative Biology, Faculty of Health and Life Sciences, University of Liverpool, Liverpool, UK
| | - Matthew Baylis
- Institute of Infection and Global Health, Faculty of Health and Life Sciences, University of Liverpool, Liverpool, UK
- NIHR Health Protection Research Unit in Emerging and Zoonotic Infections (HPRU-EZI), University of Liverpool, Liverpool, UK
| | - Gregory D.D. Hurst
- Institute of Integrative Biology, Faculty of Health and Life Sciences, University of Liverpool, Liverpool, UK
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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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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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Abstract
INTRODUCTION The hydration/dehydration of CO2 catalyzed by carbonic anhydrases (CAs, EC 4.2.1.1) is a crucial physiological reaction for the survival of all living organisms because it is connected with numerous biosynthetic and biochemical pathways requiring CO2 or HCO3-, such as respiration, photosynthesis, carboxylation reactions, pH homeostasis, secretion of electrolytes, transport of CO2, bicarbonate, etc. AREAS COVERED The bacterial genome encodes CAs belonging to the α-, β-, and γ-CA classes able to ensure the survival and/or satisfying the metabolic needs of the bacteria, as demonstrated by in vivo and in vitro experiments. The discovery of new anti-infectives that target new bacterial pathways, such as those involving CAs, may lead to effective therapies against diseases subject to the antibiotic resistance. This aspect is important in pharmaceutical and biomedical research but received little attention till recently. EXPERT OPINION An overview of the potential use of CAs in biomedical applications, as drug targets, bioindicators, and within artificial organs is presented. The discovery of thermostable bacterial CAs allowed the use of CAs in biotechnological applications, but patents related to the use of bacterial CAs in the development of pharmacological agents are scarce.
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Affiliation(s)
- Claudiu T Supuran
- a Dipartimento Neurofarba, Sezione di Scienze Farmaceutiche, and Laboratorio di Chimica Bioinorganica, Polo Scientifico , Università degli Studi di Firenze , Florence , Italy
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Yu J. Fixation of carbon dioxide by a hydrogen-oxidizing bacterium for value-added products. World J Microbiol Biotechnol 2018; 34:89. [PMID: 29886519 DOI: 10.1007/s11274-018-2473-0] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Accepted: 06/04/2018] [Indexed: 01/03/2023]
Abstract
With rapid technology progress and cost reduction, clean hydrogen from water electrolysis driven by renewable powers becomes a potential feedstock for CO2 fixation by hydrogen-oxidizing bacteria. Cupriavidus necator (formally Ralstonia eutropha), a representative member of the lithoautotrophic prokaryotes, is a promising producer of polyhydroxyalkanoates and single cell proteins. This paper reviews the fundamental properties of the hydrogen-oxidizing bacterium, the metabolic activities under limitation of individual gases and nutrients, and the value-added products from CO2, including the products with large potential markets. Gas fermentation and bioreactor safety are discussed for achieving high cell density and high productivity of desired products under chemolithotrophic conditions. The review also updates the recent research activities in metabolic engineering of C. necator to produce novel metabolites from CO2.
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Affiliation(s)
- Jian Yu
- Hawaii Natural Energy Institute, University of Hawaii at Manoa, Honolulu, USA.
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Solvent production by engineered Ralstonia eutropha: channeling carbon to biofuel. Appl Microbiol Biotechnol 2018; 102:5021-5031. [DOI: 10.1007/s00253-018-9026-1] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Revised: 04/12/2018] [Accepted: 04/14/2018] [Indexed: 12/11/2022]
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DiMario RJ, Machingura MC, Waldrop GL, Moroney JV. The many types of carbonic anhydrases in photosynthetic organisms. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2018; 268:11-17. [PMID: 29362079 DOI: 10.1016/j.plantsci.2017.12.002] [Citation(s) in RCA: 73] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2017] [Revised: 11/22/2017] [Accepted: 12/02/2017] [Indexed: 05/24/2023]
Abstract
Carbonic anhydrases (CAs) are enzymes that catalyze the interconversion of CO2 and HCO3-. In nature, there are multiple families of CA, designated with the Greek letters α through θ. CAs are ubiquitous in plants, algae and photosynthetic bacteria, often playing essential roles in the CO2 concentrating mechanisms (CCMs) which enhance the delivery of CO2 to Rubisco. As algal CCMs become better characterized, it is clear that different types of CAs are playing the same role in different algae. For example, an α-CA catalyzes the conversion of accumulated HCO3- to CO2 in the green alga Chlamydomonas reinhardtii, while a θ-CA performs the same function in the diatom Phaeodactylum tricornutum. In this review we argue that, in addition to its role of delivering CO2 for photosynthesis, other metabolic roles of CA have likely changed as the Earth's atmospheric CO2 level decreased. Since the algal and plant lineages diverged well before the decrease in atmospheric CO2, it is likely that plant, algae and photosynthetic bacteria all adapted independently to the drop in atmospheric CO2. In light of this, we will discuss how the roles of CAs may have changed over time, focusing on the role of CA in pH regulation, how CAs affect CO2 supply for photosynthesis and how CAs may help in the delivery of HCO3- for other metabolic reactions.
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Affiliation(s)
- Robert J DiMario
- School of Biological Sciences, Molecular Plant Sciences, Washington State University, Pullman, WA 99164, United States.
| | - Marylou C Machingura
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, United States.
| | - Grover L Waldrop
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, United States.
| | - James V Moroney
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, United States.
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An Overview of the Bacterial Carbonic Anhydrases. Metabolites 2017; 7:metabo7040056. [PMID: 29137134 PMCID: PMC5746736 DOI: 10.3390/metabo7040056] [Citation(s) in RCA: 133] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2017] [Revised: 11/08/2017] [Accepted: 11/08/2017] [Indexed: 12/12/2022] Open
Abstract
Bacteria encode carbonic anhydrases (CAs, EC 4.2.1.1) belonging to three different genetic families, the α-, β-, and γ-classes. By equilibrating CO2 and bicarbonate, these metalloenzymes interfere with pH regulation and other crucial physiological processes of these organisms. The detailed investigations of many such enzymes from pathogenic and non-pathogenic bacteria afford the opportunity to design both novel therapeutic agents, as well as biomimetic processes, for example, for CO2 capture. Investigation of bacterial CA inhibitors and activators may be relevant for finding antibiotics with a new mechanism of action.
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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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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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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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48
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Hosono T, Alvarez K, Lin IT, Shimada J. Nitrogen, carbon, and sulfur isotopic change during heterotrophic (Pseudomonas aureofaciens) and autotrophic (Thiobacillus denitrificans) denitrification reactions. JOURNAL OF CONTAMINANT HYDROLOGY 2015; 183:72-81. [PMID: 26529303 DOI: 10.1016/j.jconhyd.2015.10.009] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2015] [Revised: 10/22/2015] [Accepted: 10/25/2015] [Indexed: 06/05/2023]
Abstract
In batch culture experiments, we examined the isotopic change of nitrogen in nitrate (δ(15)NNO3), carbon in dissolved inorganic carbon (δ(13)CDIC), and sulfur in sulfate (δ(34)SSO4) during heterotrophic and autotrophic denitrification of two bacterial strains (Pseudomonas aureofaciens and Thiobacillus denitrificans). Heterotrophic denitrification (HD) experiments were conducted with trisodium citrate as electron donor, and autotrophic denitrification (AD) experiments were carried out with iron disulfide (FeS2) as electron donor. For heterotrophic denitrification experiments, a complete nitrate reduction was accomplished, however bacterial denitrification with T. denitrificans is a slow process in which, after seventy days nitrate was reduced to 40% of the initial concentration by denitrification. In the HD experiment, systematic change of δ(13)CDIC (from -7.7‰ to -12.2‰) with increase of DIC was observed during denitrification (enrichment factor εN was -4.7‰), suggesting the contribution of C of trisodium citrate (δ(13)C=-12.4‰). No SO4(2-) and δ(34)SSO4 changes were observed. In the AD experiment, clear fractionation of δ(13)CDIC during DIC consumption (εC=-7.8‰) and δ(34)SSO4 during sulfur use of FeS2-S (around 2‰), were confirmed through denitrification (εN=-12.5‰). Different pattern in isotopic change between HD and AD obtained on laboratory-scale are useful to recognize the type of denitrification occurring in the field.
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Affiliation(s)
- Takahiro Hosono
- Priority Organization for Innovation and Excellence, Kumamoto University, 2-39-1 Kurokami, Kumamoto 860-8555, Japan.
| | - Kelly Alvarez
- Priority Organization for Innovation and Excellence, Kumamoto University, 2-39-1 Kurokami, Kumamoto 860-8555, Japan
| | - In-Tian Lin
- Graduate School of Science and Technology, Kumamoto University, 2-39-1, Kurokami, Kumamoto 860-8555, Japan
| | - Jun Shimada
- Graduate School of Science and Technology, Kumamoto University, 2-39-1, Kurokami, Kumamoto 860-8555, Japan
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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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50
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Blombach B, Takors R. CO2 - Intrinsic Product, Essential Substrate, and Regulatory Trigger of Microbial and Mammalian Production Processes. Front Bioeng Biotechnol 2015; 3:108. [PMID: 26284242 PMCID: PMC4522908 DOI: 10.3389/fbioe.2015.00108] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2015] [Accepted: 07/13/2015] [Indexed: 11/22/2022] Open
Abstract
Carbon dioxide formation mirrors the final carbon oxidation steps of aerobic metabolism in microbial and mammalian cells. As a consequence, CO2/HCO3− dissociation equilibria arise in fermenters by the growing culture. Anaplerotic reactions make use of the abundant CO2/HCO3− levels for refueling citric acid cycle demands and for enabling oxaloacetate-derived products. At the same time, CO2 is released manifold in metabolic reactions via decarboxylation activity. The levels of extracellular CO2/HCO3− depend on cellular activities and physical constraints such as hydrostatic pressures, aeration, and the efficiency of mixing in large-scale bioreactors. Besides, local CO2/HCO3− levels might also act as metabolic inhibitors or transcriptional effectors triggering regulatory events inside the cells. This review gives an overview about fundamental physicochemical properties of CO2/HCO3− in microbial and mammalian cultures effecting cellular physiology, production processes, metabolic activity, and transcriptional regulation.
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Affiliation(s)
- Bastian Blombach
- Institute of Biochemical Engineering, University of Stuttgart , Stuttgart , Germany
| | - Ralf Takors
- Institute of Biochemical Engineering, University of Stuttgart , Stuttgart , Germany
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