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Krueger LA, Koester LR, Jones DF, Spangler DA. Carbon dioxide equivalent emissions from corn silage fermentation. Front Microbiol 2023; 13:1092315. [PMID: 36699579 PMCID: PMC9869070 DOI: 10.3389/fmicb.2022.1092315] [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: 11/07/2022] [Accepted: 12/06/2022] [Indexed: 01/12/2023] Open
Abstract
The European Climate Law recently codified the goal for European climate neutrality by 2050, highlighting the need for sustainable farming practices within a robust and transparent carbon dioxide equivalent (CO2e) accounting system. In the present study, a series of equations were proposed for the estimation of CO2e emissions from corn silage fermentation. Systematic review of previous meta-analyses of corn silage fermentation identified the mean and standard deviation statistics for key model inputs of acetic acid, ethanol, lactic acid, ammonia, and volatile-corrected dry matter loss. Estimates of CO2e emissions were determined for a mock dataset comprising 1,000 iterations of randomly-generated values for each metric in accordance with mean and variance statistics of the source data. Estimates for CO2e emissions of corn silage based on meta-analysis review of laboratory experiments were 1.9 ± 5.6% (GWP20) and 0.2 ± 5.5% (GWP100) of silage dry matter. Furthermore, model results demonstrated a precedent for CO2 recycling by silage microorganisms, which was supported by genome annotation of strains belonging to common silage species. Linear model equations for GWP20 and GWP100 with inputs and outputs in mg kg-1 silage dry matter were developed, where inputs are acetic acid (A), ethanol (E), lactic acid (L), and volatile corrected dry matter loss (DV). Linear equations are (for GWP20; Eq. 11): GWP 20 = - 3626.1 - 0.04343 A + 0.8011 E - 0.03173 L + 1.46573 D V and for GWP100; Eq. 12: GWP 100 = - 8526.10 - 0.22403 A - 0.11963 E - 0.03173 L + 1.46573 D V . .
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Affiliation(s)
- Lucas A Krueger
- Department of Research, Development, and Biotechnology, Agri-King, Inc., Fulton, IL, United States
| | - Lucas R Koester
- Department of Research, Development, and Biotechnology, Agri-King, Inc., Fulton, IL, United States
| | - David F Jones
- Department of Research, Development, and Biotechnology, Agri-King, Inc., Fulton, IL, United States
| | - David A Spangler
- Department of Research, Development, and Biotechnology, Agri-King, Inc., Fulton, IL, United States
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2
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Han Z, Li D, Zhao Y, Wang J, Guo N, Yan H, Han C, Li Q, Tucker ME. Mineralogy of Bioprecipitate Evolution over Induction Times Mediated by Halophilic Bacteria under Various Mg/Ca Molar Ratios. ACS OMEGA 2022; 7:29755-29772. [PMID: 36061657 PMCID: PMC9435042 DOI: 10.1021/acsomega.2c02443] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Accepted: 08/10/2022] [Indexed: 06/15/2023]
Abstract
In microbial mineralization experiments, the induction time of mineral precipitation is ambiguous, and this may lead to difficulties in reproducing and confirming the test results. To explore the link between induction time and microbially mediated carbonate precipitation, we report here the mineralogy and morphology of carbonate precipitates induced by the halophilic Halomonas utahensis WMS2 bacterium in media with various Mg/Ca molar ratios over a range of induction times. The results show that the biominerals are formed in an alkaline environment affected by ammonia secreted by H. utahensis WMS2 bacteria. The content of dissolved inorganic carbon increased as a result of carbonic anhydrase catalyzing the hydration of carbon dioxide to release bicarbonate and carbonate ions. The X-ray diffraction (XRD) results show that the phase of mineral precipitated gradually changes from an unstable Mg-rich calcite to metastable monohydrocalcite and then to stable hydromagnesite with an increase in the Mg2+ ion concentration and induction time. The scanning electron microscopy (SEM), energy-dispersive X-ray spectroscopy (EDS), and Fourier transform infrared spectroscopy (FTIR) results show that minerals mostly change from single particles/crystallites to aggregations under the action of the microorganisms at different Mg2+ ion concentrations and induction times. Our experiments demonstrate that the carbonate minerals produced in the presence of microbes change significantly with the induction time, in addition to the influence of the hydrochemical factors; this indicates that the induction time is significant in determining the mineralogy of biominerals.
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Affiliation(s)
- Zuozhen Han
- College
of Earth Science and Engineering, Shandong Provincial Key Laboratory
of Depositional Mineralization and Sedimentary Minerals, Shandong University of Science and Technology, Qingdao 266590, China
- Laboratory
for Marine Mineral Resources, Qingdao National
Laboratory for Marine Science and Technology, Qingdao 266237, China
| | - Dan Li
- College
of Earth Science and Engineering, Shandong Provincial Key Laboratory
of Depositional Mineralization and Sedimentary Minerals, Shandong University of Science and Technology, Qingdao 266590, China
| | - Yanyang Zhao
- College
of Earth Science and Engineering, Shandong Provincial Key Laboratory
of Depositional Mineralization and Sedimentary Minerals, Shandong University of Science and Technology, Qingdao 266590, China
| | - Jiajia Wang
- College
of Earth Science and Engineering, Shandong Provincial Key Laboratory
of Depositional Mineralization and Sedimentary Minerals, Shandong University of Science and Technology, Qingdao 266590, China
| | - Na Guo
- College
of Earth Science and Engineering, Shandong Provincial Key Laboratory
of Depositional Mineralization and Sedimentary Minerals, Shandong University of Science and Technology, Qingdao 266590, China
| | - Huaxiao Yan
- College
of Chemical and Biological Engineering, Shandong University of Science and Technology, Qingdao 266590, China
| | - Chao Han
- College
of Earth Science and Engineering, Shandong Provincial Key Laboratory
of Depositional Mineralization and Sedimentary Minerals, Shandong University of Science and Technology, Qingdao 266590, China
| | - Qiang Li
- College
of Earth Science and Engineering, Shandong Provincial Key Laboratory
of Depositional Mineralization and Sedimentary Minerals, Shandong University of Science and Technology, Qingdao 266590, China
| | - Maurice E. Tucker
- School
of Earth Sciences, University of Bristol, Bristol BS8 1RJ, U.K.
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3
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Steger F, Reich J, Fuchs W, Rittmann SKMR, Gübitz GM, Ribitsch D, Bochmann G. Comparison of Carbonic Anhydrases for CO 2 Sequestration. Int J Mol Sci 2022; 23:957. [PMID: 35055147 PMCID: PMC8777876 DOI: 10.3390/ijms23020957] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Revised: 01/13/2022] [Accepted: 01/13/2022] [Indexed: 02/07/2023] Open
Abstract
Strategies for depleting carbon dioxide (CO2) from flue gases are urgently needed and carbonic anhydrases (CAs) can contribute to solving this problem. They catalyze the hydration of CO2 in aqueous solutions and therefore capture the CO2. However, the harsh conditions due to varying process temperatures are limiting factors for the application of enzymes. The current study aims to examine four recombinantly produced CAs from different organisms, namely CAs from Acetobacterium woodii (AwCA or CynT), Persephonella marina (PmCA), Methanobacterium thermoautotrophicum (MtaCA or Cab) and Sulphurihydrogenibium yellowstonense (SspCA). The highest expression yields and activities were found for AwCA (1814 WAU mg-1 AwCA) and PmCA (1748 WAU mg-1 PmCA). AwCA was highly stable in a mesophilic temperature range, whereas PmCA proved to be exceptionally thermostable. Our results indicate the potential to utilize CAs from anaerobic microorganisms to develop CO2 sequestration applications.
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Affiliation(s)
- Franziska Steger
- Institute of Environmental Biotechnology, Department for Agrobiotechnology, University of Natural Resources and Life Sciences Vienna, Konrad Lorenz Str. 20, A-3430 Tulln, Austria
| | - Johanna Reich
- Institute of Environmental Biotechnology, Department for Agrobiotechnology, University of Natural Resources and Life Sciences Vienna, Konrad Lorenz Str. 20, A-3430 Tulln, Austria
- ACIB-Austrian Centre of Industrial Biotechnology, Krenngasse 37, 8010 Graz, Austria
| | - Werner Fuchs
- Institute of Environmental Biotechnology, Department for Agrobiotechnology, University of Natural Resources and Life Sciences Vienna, Konrad Lorenz Str. 20, A-3430 Tulln, Austria
| | - Simon K-M R Rittmann
- Archaea Physiology & Biotechnology Group, Department of Functional and Evolutionary Ecology, University of Vienna, Djerassiplatz 1, 1030 Vienna, Austria
| | - Georg M Gübitz
- Institute of Environmental Biotechnology, Department for Agrobiotechnology, University of Natural Resources and Life Sciences Vienna, Konrad Lorenz Str. 20, A-3430 Tulln, Austria
| | - Doris Ribitsch
- ACIB-Austrian Centre of Industrial Biotechnology, Krenngasse 37, 8010 Graz, Austria
| | - Günther Bochmann
- Institute of Environmental Biotechnology, Department for Agrobiotechnology, University of Natural Resources and Life Sciences Vienna, Konrad Lorenz Str. 20, A-3430 Tulln, Austria
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Park M, Park S, Yoo JY, Kim Y, Lee KM, Hwang DY, Son HJ. Enzyme-mediated biocalcification by a novel alkaliphilic Bacillus psychrodurans LC40 and its eco-friendly application as a biosealant for crack healing. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 802:149841. [PMID: 34455282 DOI: 10.1016/j.scitotenv.2021.149841] [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: 05/19/2021] [Revised: 08/18/2021] [Accepted: 08/18/2021] [Indexed: 06/13/2023]
Abstract
Biocalcification is a natural biochemical process, which has been regarded as a promising method for sequestering heavy metals or carbon dioxide in the environment, healing cracks in concrete structures, and stabilizing soil. One of the key factors in this process is calcium carbonate-producing bacteria. The purpose of this study was to maximize the production of calcium carbonate by alkaliphilic Bacillus psychrodurans LC40 isolated from a limestone cave, by manipulating the medium composition for fast and non-detrimental crack healing, and to investigate the mechanism of its production. Strain LC40 could grow well in the strongly alkaline region (pH 9.5-11), indicating its alkaliphilic nature. The optimal medium for calcium carbonate production contained 2% tryptone, 1.5% urea, 0.15% NaHCO3, and 150 mM calcium formate (pH 6). Using this medium, the yield of calcium carbonate at 72 h was approximately 8.6-fold higher than that obtained through Urea-CaCl2 medium. In this culture, the urease and carbonic anhydrase activities were observed simultaneously, and the pH of the medium was found to have increased to 9.4, leading to maximum calcium carbonate production. This suggests that this pH value is achieved by the synergistic action of the two enzymes, resulting in a high calcium carbonate yield. The crystals were characterized by FESEM, EDS and XRD, which confirmed the production of rhombohedral and spherical calcium carbonate crystals containing vaterite and calcite. Strain LC40 completely healed a 0.75 mm wide crack in a very short time of 3 days using the optimized medium as a cementation solution. Our findings indicate that B. psychrodurans LC40 could be a promising candidate for the development of eco-friendly biosealant applicable to environmentally stressed concrete structures.
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Affiliation(s)
- Minjoo Park
- Department of Life Science and Environmental Biochemistry/Life and Industry Convergence Research Institute, Pusan National University, Miryang 50463, Republic of Korea
| | - Sungjin Park
- Department of Life Science and Environmental Biochemistry/Life and Industry Convergence Research Institute, Pusan National University, Miryang 50463, Republic of Korea
| | - Ji-Yeon Yoo
- Department of Life Science and Environmental Biochemistry/Life and Industry Convergence Research Institute, Pusan National University, Miryang 50463, Republic of Korea
| | - Yerin Kim
- Department of Life Science and Environmental Biochemistry/Life and Industry Convergence Research Institute, Pusan National University, Miryang 50463, Republic of Korea
| | - Kwang Min Lee
- Department of Life Science and Environmental Biochemistry/Life and Industry Convergence Research Institute, Pusan National University, Miryang 50463, Republic of Korea
| | - Dae-Youn Hwang
- Department of Biomaterials Science, Pusan National University, Miryang 50463, Republic of Korea
| | - Hong-Joo Son
- Department of Life Science and Environmental Biochemistry/Life and Industry Convergence Research Institute, Pusan National University, Miryang 50463, Republic of Korea.
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Balch WE, Ferry JG. The Wolfe cycle of carbon dioxide reduction to methane revisited and the Ralph Stoner Wolfe legacy at 100 years. Adv Microb Physiol 2021; 79:1-23. [PMID: 34836609 DOI: 10.1016/bs.ampbs.2021.07.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Methanogens are a component of anaerobic microbial consortia decomposing biomass to CO2 and CH4 that is an essential link in the global carbon cycle. One of two major pathways of methanogenesis involves reduction of the methyl group of acetate to CH4 with electrons from oxidation of the carbonyl group while the other involves reduction of CO2 to CH4 with electrons from H2 or formate. Pioneering investigations of the CO2 reduction pathway by Ralph S. Wolfe in the 70s and 80s contributed findings impacting the broader fields of biochemistry and microbiology that directed discovery of the domain Archaea and expanded research on anaerobic microbes for decades that continues to the present. This review presents an historical overview of the CO2 reduction pathway (Wolfe cycle) with recent developments, and an account of Wolfe's larger and enduring impact on the broad field of biology 100 years after his birth.
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Affiliation(s)
- William E Balch
- Department of Molecular Medicine, Scripps Research, La Jolla, CA, United States
| | - James G Ferry
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA, United States.
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6
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Zhao Y, Han Z, Yan H, Zhao H, Tucker ME, Gao X, Guo N, Meng R, Owusu DC. Selective Adsorption of Amino Acids in Crystals of Monohydrocalcite Induced by the Facultative Anaerobic Enterobacter ludwigii SYB1. Front Microbiol 2021; 12:696557. [PMID: 34394038 PMCID: PMC8358455 DOI: 10.3389/fmicb.2021.696557] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2021] [Accepted: 06/23/2021] [Indexed: 12/05/2022] Open
Abstract
The morphology, crystal structure, and elemental composition of biominerals are commonly different from chemically synthesized minerals, but the reasons for these are not fully understood. A facultative anaerobic bacterium, Enterobacter ludwigii SYB1, is used in experiments to document the hydrochemistry, mineral crystallization, and cell surface characteristics of biomineralization. It was found that carbonate anhydrase and ammonia production were major factors influencing the alkalinity and saturation of the closed biosystem. X-ray diffraction (XRD) spectra showed that calcite, monohydrocalcite (MHC), and dypingite formed in samples with bacterial cells. It was also found that the (222) plane of MHC was the preferred orientation compared to standard data. Scanning transmission electron microscopy (STEM) analysis of cell slices provides direct evidence of concentrated calcium and magnesium ions on the surface of extracellular polymeric substances (EPS). In addition, high-resolution transmission electron microscopy (HRTEM) showed that crystallized nanoparticles were formed within the EPS. Thus, the mechanism of the biomineralization induced by E. ludwigii SYB1 can be divided into three stages: (i) the production of carbonate anhydrase and ammonia increases the alkalinity and saturation state of the milieu, (ii) free calcium and magnesium ions are adsorbed and chelated onto EPS, and (iii) nanominerals crystallize and grow within the EPS. Seventeen kinds of amino acids were identified within both biotic MHC and the EPS of SYB1, while the percentages of glutamic and aspartic acid in MHC increased significantly (p < 0.05). Furthermore, the adsorption energy was calculated for various amino acids on seven diffracted crystal faces, with preferential adsorption demonstrated on (111) and (222) faces. At the same time, the lowest adsorption energy was always that of glutamic and aspartic acid for the same crystal plane. These results suggest that aspartic and glutamic acid always mix preferentially in the crystal lattice of MHC and that differential adsorption of amino acids on crystal planes can lead to their preferred orientation. Moreover, the mixing of amino acids in the mineral structure may also have a certain influence on the mineral lattice dislocations, thus enhancing the thermodynamic characteristics.
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Affiliation(s)
- Yanyang Zhao
- Shandong Provincial Key Laboratory of Depositional Mineralization and Sedimentary Minerals, College of Earth Science and Engineering, Shandong University of Science and Technology, Qingdao, China.,Laboratory for Marine Mineral Resources, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Zuozhen Han
- Shandong Provincial Key Laboratory of Depositional Mineralization and Sedimentary Minerals, College of Earth Science and Engineering, Shandong University of Science and Technology, Qingdao, China.,Laboratory for Marine Mineral Resources, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Huaxiao Yan
- Department of Bioengineering, College of Chemical and Biological Engineering, Shandong University of Science and Technology, Qingdao, China
| | - Hui Zhao
- Department of Bioengineering, College of Chemical and Biological Engineering, Shandong University of Science and Technology, Qingdao, China
| | - Maurice E Tucker
- School of Earth Sciences, University of Bristol, Bristol, United Kingdom.,Cabot Institute, University of Bristol, Bristol, United Kingdom
| | - Xiao Gao
- Shandong Provincial Key Laboratory of Depositional Mineralization and Sedimentary Minerals, College of Earth Science and Engineering, Shandong University of Science and Technology, Qingdao, China
| | - Na Guo
- Shandong Provincial Key Laboratory of Depositional Mineralization and Sedimentary Minerals, College of Earth Science and Engineering, Shandong University of Science and Technology, Qingdao, China
| | - Ruirui Meng
- Shandong Provincial Key Laboratory of Depositional Mineralization and Sedimentary Minerals, College of Earth Science and Engineering, Shandong University of Science and Technology, Qingdao, China
| | - Daniel Cosmos Owusu
- Department of Bioengineering, College of Chemical and Biological Engineering, Shandong University of Science and Technology, Qingdao, China
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7
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Yadav PR, Hussain Basha S, Satyanarayana SDV, Pindi PK. Microsecond simulation analysis of carbonic anhydrase - II in complex with (+)-cathechin revealed molecular interactions responsible for its amelioration effect on fluoride toxicity. J Biomol Struct Dyn 2021; 40:7469-7482. [PMID: 33719850 DOI: 10.1080/07391102.2021.1898471] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Fluorosis is a chronic condition caused by overexposure to fluoride, marked by impaired dental, skeletal, and non-skeletal health. In presence of excess fluoride ions, in severe cases calcification of the ligaments observed. Earlier studies have suggested that the disruption of carbonic anhydrase activity via ionic homeostasis change was associated with F toxicity. In a recent study, it was demonstrated that Tamarind fruit extract was effective in increasing the urinary F excretion in male Wistar rats via studying the mRNA expression of carbonic anhydrase II (CA II) in kidney homogenates using western blotting, immunohistochemistry and quantitative Realtime PCR based studies. We have carried out this study to understand the detailed molecular level interactions responsible for this tamarind extract based (+)-cathechin compound towards lowering the F toxicity via targeting CA-II. From our study, it was revealed that due to the ability of (+)-cathechin compound to bind tightly filling complete available space at the catalytically important site forming metal coordinated ionic bonds with His94, His96 and His119 residues helps in restricting F ions to interact with Zn ion located at the core of catalytic site responsible for its functionality. On the other hand, interaction of (+)-cathechin compound with Gln92 was observed to be critically important towards inducing conformational changes in CA-II, thus allowing (+)-cathechin compound to burry even deeply inside the catalytic site.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Pulala Raghuveer Yadav
- Department of Biotechnology, Indian Institute of Technology Hyderabad, Hyderabad, Telangana, India
| | | | | | - Pavan Kumar Pindi
- Department of Microbiology, Palamuru University, Mahabubnagar, Telangana, India
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8
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Kim S, Yeon J, Sung J, Kim NJ, Hong S, Jin MS. Structural insights into novel mechanisms of inhibition of the major β-carbonic anhydrase CafB from the pathogenic fungus Aspergillus fumigatus. J Struct Biol 2021; 213:107700. [PMID: 33545350 DOI: 10.1016/j.jsb.2021.107700] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Revised: 01/22/2021] [Accepted: 01/23/2021] [Indexed: 01/04/2023]
Abstract
In fungi the β-class of carbonic anhydrases (β-CAs) are zinc metalloenzymes that are essential for growth, survival, differentiation, and virulence. Aspergillus fumigatus is the most important pathogen responsible for invasive aspergillosis and possesses two major β-CAs, CafA and CafB. Recently we reported the biochemical characterization and 1.8 Å crystal structure of CafA. Here, we report a crystallographic analysis of CafB revealing the mechanism of enzyme catalysis and establish the relationship of this enzyme to other β-CAs. While CafA has a typical open conformation, CafB, when exposed to acidic pH and/or an oxidative environment, has a novel type of active site in which a disulfide bond is formed between two zinc-ligating cysteines, expelling the zinc ion and stabilizing the inactive form of the enzyme. Based on the structural data, we generated an oxidation-resistant mutant (Y159A) of CafB. The crystal structure of the mutant under reducing conditions retains a catalytic zinc at the expected position, tetrahedrally coordinated by three residues (C57, H113 and C116) and an aspartic acid (D59), and replacing the zinc-bound water molecule in the closed form. Furthermore, the active site of CafB crystals grown under zinc-limiting conditions has a novel conformation in which the solvent-exposed catalytic cysteine (C116) is flipped out of the metal coordination sphere, facilitating release of the zinc ion. Taken together, our results suggest that A. fumigatus use sophisticated activity-inhibiting strategies to enhance its survival during infection.
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Affiliation(s)
- Subin Kim
- School of Life Sciences, GIST, 123 Cheomdan-gwagiro, Buk-gu, Gwangju 61005, Republic of Korea
| | - Jungyoon Yeon
- School of Life Sciences, GIST, 123 Cheomdan-gwagiro, Buk-gu, Gwangju 61005, Republic of Korea
| | - Jongmin Sung
- School of Life Sciences, GIST, 123 Cheomdan-gwagiro, Buk-gu, Gwangju 61005, Republic of Korea
| | - Na Jin Kim
- School of Life Sciences, GIST, 123 Cheomdan-gwagiro, Buk-gu, Gwangju 61005, Republic of Korea
| | - Semi Hong
- School of Life Sciences, GIST, 123 Cheomdan-gwagiro, Buk-gu, Gwangju 61005, Republic of Korea
| | - Mi Sun Jin
- School of Life Sciences, GIST, 123 Cheomdan-gwagiro, Buk-gu, Gwangju 61005, Republic of Korea.
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Molecular Evidence for an Active Microbial Methane Cycle in Subsurface Serpentinite-Hosted Groundwaters in the Samail Ophiolite, Oman. Appl Environ Microbiol 2021; 87:AEM.02068-20. [PMID: 33127818 DOI: 10.1128/aem.02068-20] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Accepted: 10/20/2020] [Indexed: 01/04/2023] Open
Abstract
Serpentinization can generate highly reduced fluids replete with hydrogen (H2) and methane (CH4), potent reductants capable of driving microbial methanogenesis and methanotrophy, respectively. However, CH4 in serpentinized waters is thought to be primarily abiogenic, raising key questions about the relative importance of methanogens and methanotrophs in the production and consumption of CH4 in these systems. Herein, we apply molecular approaches to examine the functional capability and activity of microbial CH4 cycling in serpentinization-impacted subsurface waters intersecting multiple rock and water types within the Samail Ophiolite of Oman. Abundant 16S rRNA genes and transcripts affiliated with the methanogenic genus Methanobacterium were recovered from the most alkaline (pH, >10), H2- and CH4-rich subsurface waters. Additionally, 16S rRNA genes and transcripts associated with the aerobic methanotrophic genus Methylococcus were detected in wells that spanned varied fluid geochemistry. Metagenomic sequencing yielded genes encoding homologs of proteins involved in the hydrogenotrophic pathway of microbial CH4 production and in microbial CH4 oxidation. Transcripts of several key genes encoding methanogenesis/methanotrophy enzymes were identified, predominantly in communities from the most hyperalkaline waters. These results indicate active methanogenic and methanotrophic populations in waters with hyperalkaline pH in the Samail Ophiolite, thereby supporting a role for biological CH4 cycling in aquifers that undergo low-temperature serpentinization.IMPORTANCE Serpentinization of ultramafic rock can generate conditions favorable for microbial methane (CH4) cycling, including the abiotic production of hydrogen (H2) and possibly CH4 Systems of low-temperature serpentinization are geobiological targets due to their potential to harbor microbial life and ubiquity throughout Earth's history. Biomass in fracture waters collected from the Samail Ophiolite of Oman, a system undergoing modern serpentinization, yielded DNA and RNA signatures indicative of active microbial methanogenesis and methanotrophy. Intriguingly, transcripts for proteins involved in methanogenesis were most abundant in the most highly reacted waters that have hyperalkaline pH and elevated concentrations of H2 and CH4 These findings suggest active biological methane cycling in serpentinite-hosted aquifers, even under extreme conditions of high pH and carbon limitation. These observations underscore the potential for microbial activity to influence the isotopic composition of CH4 in these systems, which is information that could help in identifying biosignatures of microbial activity on other planets.
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Verma M, Deshpande PA. Mechanistic insights into biomimetic CO2hydration activity of titania nanoclusters. INT J CHEM KINET 2020. [DOI: 10.1002/kin.21440] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Manju Verma
- Quantum and Molecular Engineering Laboratory Department of Chemical Engineering Indian Institute of Technology Kharagpur Kharagpur India
- Department of Chemical Engineering Motilal Nehru National Institute of Technology Allahabad Prayagraj India
| | - Parag A. Deshpande
- Quantum and Molecular Engineering Laboratory Department of Chemical Engineering Indian Institute of Technology Kharagpur Kharagpur India
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11
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Kumari M, Lee J, Lee DW, Hwang I. High-level production in a plant system of a thermostable carbonic anhydrase and its immobilization on microcrystalline cellulose beads for CO 2 capture. PLANT CELL REPORTS 2020; 39:1317-1329. [PMID: 32651706 DOI: 10.1007/s00299-020-02566-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Accepted: 07/03/2020] [Indexed: 05/22/2023]
Abstract
KEY MESSAGE Plant-produced SazCA and its application to CO2 capture. Technologies that rely on chemical absorption or physical adsorption have been developed to capture CO2 from industrial flue gases and sequester it at storage sites. Carbonic anhydrases (CAs), metalloenzymes, that catalyze the reversible hydration of CO2 have recently received attention as biocatalysts in the capture of CO2 from flue gases, but their cost presents a major obstacle for use at an industrial scale. This cost, however, can be reduced either by producing a long-lasting enzyme suitable for CO2 capture or by lowering production costs. High-level expression, easy purification, and immobilization of CAs from Sulfurihydrogenibium azorense (SazCA) were investigated in a plant system. Fusion of the 60-amino acid-long ectodomain (M-domain) of the human receptor-type tyrosine-protein phosphatase C increased the levels of SazCA accumulation. Fusion of the cellulose-binding module (CBM3) from Clostridium thermocellum resulted in tight binding of recombinant protein to microcrystalline cellulose beads, enabling easy purification. The chimeric fusion protein, BMC-SazCA, which consisted of SazCA with the M and CBM3 domains, was expressed in tobacco (Nicotiana benthamiana), giving a recombinant protein yield in leaf extracts of 350 mg/kg fresh weight. BMC-SazCA produced in planta was active in the presence of various chemicals used in CO2 capture. Immobilization of BMC-SazCA on the surface of microcrystalline cellulose beads extended its heat stability, allowing its reuse in multiple rounds of the CO2 hydration reaction. These results suggest that production of SazCA in plants has great potential for CA-based CO2 sequestration and mineralization.
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Affiliation(s)
- Madhu Kumari
- Division of Integrative Biosciences and Biotechnology, Pohang University of Science and Technology, Pohang, 37673, South Korea
| | - Junho Lee
- Division of Integrative Biosciences and Biotechnology, Pohang University of Science and Technology, Pohang, 37673, South Korea
| | - Dong Wook Lee
- Division of Integrative Biosciences and Biotechnology, Pohang University of Science and Technology, Pohang, 37673, South Korea
- Department of Bioenergy Science and Technology, Chonnam National University, Gwangju, 61186, South Korea
| | - Inhwan Hwang
- Division of Integrative Biosciences and Biotechnology, Pohang University of Science and Technology, Pohang, 37673, South Korea.
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, 37673, South Korea.
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12
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Kim S, Yeon J, Sung J, Jin MS. Crystal Structure of β-Carbonic Anhydrase CafA from the Fungal Pathogen Aspergillus fumigatus. Mol Cells 2020; 43:831-840. [PMID: 32975213 PMCID: PMC7528686 DOI: 10.14348/molcells.2020.0168] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Revised: 09/03/2020] [Accepted: 09/03/2020] [Indexed: 01/07/2023] Open
Abstract
The β-class of carbonic anhydrases (β-CAs) are zinc metalloenzymes widely distributed in the fungal kingdom that play essential roles in growth, survival, differentiation, and virulence by catalyzing the reversible interconversion of carbon dioxide (CO2) and bicarbonate (HCO3-). Herein, we report the biochemical and crystallographic characterization of the β-CA CafA from the fungal pathogen Aspergillus fumigatus, the main causative agent of invasive aspergillosis. CafA exhibited apparent in vitro CO2 hydration activity in neutral to weak alkaline conditions, but little activity at acidic pH. The high-resolution crystal structure of CafA revealed a tetramer comprising a dimer of dimers, in which the catalytic zinc ion is tetrahedrally coordinated by three conserved residues (C119, H175, C178) and an acetate anion presumably acquired from the crystallization solution, indicating a freely accessible ″open″ conformation. Furthermore, knowledge of the structure of CafA in complex with the potent inhibitor acetazolamide, together with its functional intolerance of nitrate (NO3-) ions, could be exploited to develop new antifungal agents for the treatment of invasive aspergillosis.
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Affiliation(s)
- Subin Kim
- School of Life Sciences, Gwangju Institute of Science and Technology (GIST), Gwangju 61005, Korea
| | - Jungyoon Yeon
- School of Life Sciences, Gwangju Institute of Science and Technology (GIST), Gwangju 61005, Korea
| | - Jongmin Sung
- School of Life Sciences, Gwangju Institute of Science and Technology (GIST), Gwangju 61005, Korea
| | - Mi Sun Jin
- School of Life Sciences, Gwangju Institute of Science and Technology (GIST), Gwangju 61005, Korea
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13
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Design of carbonic anhydrase with improved thermostability for CO2 capture via molecular simulations. J CO2 UTIL 2020. [DOI: 10.1016/j.jcou.2020.01.017] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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14
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Giri A, Pant D. Carbonic anhydrase modification for carbon management. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2020; 27:1294-1318. [PMID: 31797268 DOI: 10.1007/s11356-019-06667-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2019] [Accepted: 10/01/2019] [Indexed: 06/10/2023]
Abstract
Carbonic anhydrase modification (chemical and biological) is an attractive strategy for its diverse application to accelerate the absorption of CO2 from a flue gas with improved activity and stability. This article reports various possibilities of CA modification using metal-ligand homologous chemistry, cross-linking agents, and residue- and group-specific and genetic modifications, and assesses their role in carbon management. Chemically modified carbonic anhydrase is able to improve the absorption of carbon dioxide from a gas stream into mediation compounds with enhanced sequestration and mineral formation. Genetically modified CA polypeptide can also increase carbon dioxide conversion. Chemical modification of CA can be categorized in terms of (i) residue-specific modification (involves protein-ligand interaction in terms of substitution/addition) and group-specific modifications (based on the functional groups of the target CA). For every sustainable change, there should be no/limited toxic or immunological response. In this review, several CA modification pathways and biocompatibility rules are proposed as a theoretical support for emerging research in this area.
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Affiliation(s)
- Anand Giri
- Department of Environmental Sciences, Central University of Himachal Pradesh, Kangra, India
| | - Deepak Pant
- School of Chemical Sciences, Central University of Haryana, Mahendragarh, Haryana, 123029, India.
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15
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16
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Dutta A, Sar P, Sarkar J, Dutta Gupta S, Gupta A, Bose H, Mukherjee A, Roy S. Archaeal Communities in Deep Terrestrial Subsurface Underneath the Deccan Traps, India. Front Microbiol 2019; 10:1362. [PMID: 31379755 PMCID: PMC6646420 DOI: 10.3389/fmicb.2019.01362] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Accepted: 05/31/2019] [Indexed: 11/13/2022] Open
Abstract
Archaeal community structure and potential functions within the deep, aphotic, oligotrophic, hot, igneous provinces of ∼65 Myr old basalt and its Archean granitic basement was explored through archaeal 16S rRNA gene amplicon sequencing from extracted environmental DNA of rocks. Rock core samples from three distinct horizons, basaltic (BS), transition (weathered granites) (TZ) and granitic (GR) showed limited organic carbon (4–48 mg/kg) and varied concentrations (<1.0–5000 mg/kg) of sulfate, nitrate, nitrite, iron and metal oxides. Quantitative PCR estimated the presence of nearly 103–104 archaeal cells per gram of rock. Archaeal communities within BS and GR horizons were distinct. The absence of any common OTU across the samples indicated restricted dispersal of archaeal cells. Younger, relatively organic carbon- and Fe2O3-rich BS rocks harbor Euryarchaeota, along with varied proportions of Thaumarchaeota and Crenarchaeota. Extreme acid loving, thermotolerant sulfur respiring Thermoplasmataceae, heterotrophic, ferrous-/H-sulfide oxidizing Ferroplasmaceae and Halobacteriaceae were more abundant and closely interrelated within BS rocks. Samples from the GR horizon represent a unique composition with higher proportions of Thaumarchaeota and uneven distribution of Euryarchaeota and Bathyarchaeota affiliated to Methanomicrobia, SAGMCG-1, FHMa11 terrestrial group, AK59 and unclassified taxa. Acetoclastic methanogenic Methanomicrobia, autotrophic SAGMCG-1 and MCG of Thaumarcheaota could be identified as the signature groups within the organic carbon lean GR horizon. Sulfur-oxidizing Sulfolobaceae was relatively more abundant in sulfate-rich amygdaloidal basalt and migmatitic gneiss samples. Methane-oxidizing ANME-3 populations were found to be ubiquitous, but their abundance varied greatly between the analyzed samples. Changes in diversity pattern among the BS and GR horizons highlighted the significance of local rock geochemistry, particularly the availability of organic carbon, Fe2O3 and other nutrients as well as physical constraints (temperature and pressure) in a niche-specific colonization of extremophilic archaeal communities. The study provided the first deep sequencing-based illustration of an intricate association between diverse extremophilic groups (acidophile-halophile-methanogenic), capable of sulfur/iron/methane metabolism and thus shed new light on their potential role in biogeochemical cycles and energy flow in deep biosphere hosted by hot, oligotrophic igneous crust.
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Affiliation(s)
- Avishek Dutta
- Environmental Microbiology and Genomics Laboratory, Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, India.,School of Bioscience, Indian Institute of Technology Kharagpur, Kharagpur, India
| | - Pinaki Sar
- Environmental Microbiology and Genomics Laboratory, Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, India
| | - Jayeeta Sarkar
- Environmental Microbiology and Genomics Laboratory, Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, India
| | - Srimanti Dutta Gupta
- School of Environmental Science and Engineering, Indian Institute of Technology Kharagpur, Kharagpur, India
| | - Abhishek Gupta
- Environmental Microbiology and Genomics Laboratory, Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, India
| | - Himadri Bose
- Environmental Microbiology and Genomics Laboratory, Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, India
| | - Abhijit Mukherjee
- School of Environmental Science and Engineering, Indian Institute of Technology Kharagpur, Kharagpur, India.,Department of Geology and Geophysics, Indian Institute of Technology Kharagpur, Kharagpur, India
| | - Sukanta Roy
- Ministry of Earth Sciences, Borehole Geophysics Research Laboratory, Karad, India.,CSIR-National Geophysical Research Institute, Hyderabad, India
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17
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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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18
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Bhagat C, Dudhagara P, Tank S. Trends, application and future prospectives of microbial carbonic anhydrase mediated carbonation process for CCUS. J Appl Microbiol 2017; 124:316-335. [PMID: 28921830 DOI: 10.1111/jam.13589] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2017] [Revised: 06/17/2017] [Accepted: 09/06/2017] [Indexed: 12/21/2022]
Abstract
Growing industrialization and the desire for a better economy in countries has accelerated the emission of greenhouse gases (GHGs), by more than the buffering capacity of the earth's atmosphere. Among the various GHGs, carbon dioxide occupies the first position in the anthroposphere and has detrimental effects on the ecosystem. For decarbonization, several non-biological methods of carbon capture, utilization and storage (CCUS) have been in use for the past few decades, but they are suffering from narrow applicability. Recently, CO2 emission and its disposal related problems have encouraged the implementation of bioprocessing to achieve a zero waste economy for a sustainable environment. Microbial carbonic anhydrase (CA) catalyses reversible CO2 hydration and forms metal carbonates that mimic the natural phenomenon of weathering/carbonation and is gaining merit for CCUS. Thus, the diversity and specificity of CAs from different micro-organisms could be explored for CCUS. In the literature, more than 50 different microbial CAs have been explored for mineral carbonation. Further, microbial CAs can be engineered for the mineral carbonation process to develop new technology. CA driven carbonation is encouraging due to its large storage capacity and favourable chemistry, allowing site-specific sequestration and reusable product formation for other industries. Moreover, carbonation based CCUS holds five-fold more sequestration capacity over the next 100 years. Thus, it is an eco-friendly, feasible, viable option and believed to be the impending technology for CCUS. Here, we attempt to examine the distribution of various types of microbial CAs with their potential applications and future direction for carbon capture. Although there are few key challenges in bio-based technology, they need to be addressed in order to commercialize the technology.
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Affiliation(s)
- C Bhagat
- Department of Biosciences (UGC-SAP-DRS-II), Veer Narmad South Gujarat University, Surat, Gujarat, India
| | - P Dudhagara
- Department of Biosciences (UGC-SAP-DRS-II), Veer Narmad South Gujarat University, Surat, Gujarat, India
| | - S Tank
- Department of Biosciences (UGC-SAP-DRS-II), Veer Narmad South Gujarat University, Surat, Gujarat, India
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19
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Dhami NK, Alsubhi WR, Watkin E, Mukherjee A. Bacterial Community Dynamics and Biocement Formation during Stimulation and Augmentation: Implications for Soil Consolidation. Front Microbiol 2017; 8:1267. [PMID: 28744265 PMCID: PMC5504299 DOI: 10.3389/fmicb.2017.01267] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2016] [Accepted: 06/23/2017] [Indexed: 11/23/2022] Open
Abstract
Microbially-induced CaCO3 precipitation (MICP) is a naturally occurring process wherein durable carbonates are formed as a result of microbial metabolic activities. In recent years, MICP technology has been widely harnessed for applications in civil engineering wherein synthesis of calcium carbonate crystals occurs at ambient temperature paving way for low energy biocement. MICP using pure urease (UA) and carbonic anhydrase (CA) producing bacteria has been promising in laboratory conditions. In the current study we enriched ureolytic and carbonic anhydrase communities in calcareous soil under biostimulation and bioaugmentation conditions and investigated the effect of microbial dynamics on carbonate precipitation, calcium carbonate polymorph selection and consolidation of biological sand column under nutrient limited and rich conditions. All treatments for stimulation and augmentation led to significant changes in the composition of indigenous bacterial population. Biostimulation as well as augmentation through the UA route was found to be faster and more effective compared to the CA route in terms of extracellular enzyme production and carbonate precipitation. Synergistic role of augmented cultures along with indigenous communities was recorded via both the routes of UA and CA as more effective calcification was seen in case of augmentation compared to stimulation. The survival of supplemented isolates in presence of indigenous bacterial communities was confirmed through sequencing of total diversity and it was seen that both UA and CA isolate had the potential to survive along with native communities under high nutrient conditions. Nutrient conditions played significant role in determining calcium carbonate polymorph fate as calcitic crystals dominated under high carbon supplementation. Finally, the consolidation of sand columns via stimulation and augmentation was successfully achieved through both UA and CA route under high nutrient conditions but higher consolidation in short time period was noticed in UA route. The study reports that based upon the organic carbon content in native soils, stimulation can be favored at sites with high organic carbon content while augmentation with repeated injections of nutrients can be applied on poor nutrient soils via different enrichment routes of microbial metabolism.
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Affiliation(s)
- Navdeep K Dhami
- Biologically Activated Materials Laboratory, Department of Civil Engineering, Curtin UniversityPerth, WA, Australia
| | - Walaa R Alsubhi
- School of Biomedical Sciences, Curtin Health Innovation Research Institute-Biosciences, Curtin UniversityPerth, WA, Australia
| | - Elizabeth Watkin
- School of Biomedical Sciences, Curtin Health Innovation Research Institute-Biosciences, Curtin UniversityPerth, WA, Australia
| | - Abhijit Mukherjee
- Biologically Activated Materials Laboratory, Department of Civil Engineering, Curtin UniversityPerth, WA, Australia
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20
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Precipitation of Carbonate Minerals Induced by the Halophilic Chromohalobacter Israelensis under High Salt Concentrations: Implications for Natural Environments. MINERALS 2017. [DOI: 10.3390/min7060095] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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21
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Dhami NK, Mukherjee A, Reddy MS. Applicability of bacterial biocementation in sustainable construction materials. ASIA-PAC J CHEM ENG 2016. [DOI: 10.1002/apj.2014] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Navdeep Kaur Dhami
- Department of Civil Engineering; Curtin University; GPO Box U1987 Perth Western Australia Australia
| | - Abhijit Mukherjee
- Department of Civil Engineering; Curtin University; GPO Box U1987 Perth Western Australia Australia
| | - M. Sudhakara Reddy
- Department of Biotechnology; Thapar University; Patiala 147004 Punjab India
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22
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Rudenko NN, Ignatova LK, Fedorchuk TP, Ivanov BN. Carbonic anhydrases in photosynthetic cells of higher plants. BIOCHEMISTRY (MOSCOW) 2016; 80:674-87. [PMID: 26531014 DOI: 10.1134/s0006297915060048] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
This review presents information about carbonic anhydrases, enzymes catalyzing the reversible hydration of carbon dioxide in aqueous solutions. The families of carbonic anhydrases are described, and data concerning the presence of their representatives in organisms of different classes, and especially in the higher plants, are considered. Proven and hypothetical functions of carbonic anhydrases in living organisms are listed. Particular attention is given to those functions of the enzyme that are relevant to photosynthetic reactions. These functions in algae are briefly described. Data about probable functions of carbonic anhydrases in plasma membrane, mitochondria, and chloroplast stroma of higher plants are discussed. Update concerning carbonic anhydrases in chloroplast thylakoids of higher plants, i.e. their quantity and possible participation in photosynthetic reactions, is given in detail.
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Affiliation(s)
- N N Rudenko
- Institute of Basic Biological Problems, Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia.
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23
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Engineering de novo disulfide bond in bacterial α-type carbonic anhydrase for thermostable carbon sequestration. Sci Rep 2016; 6:29322. [PMID: 27385052 PMCID: PMC4935852 DOI: 10.1038/srep29322] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2016] [Accepted: 06/16/2016] [Indexed: 11/29/2022] Open
Abstract
Exploiting carbonic anhydrase (CA), an enzyme that rapidly catalyzes carbon dioxide hydration, is an attractive biomimetic route for carbon sequestration due to its environmental compatibility and potential economic viability. However, the industrial applications of CA are strongly hampered by the unstable nature of enzymes. In this work, we introduced in silico designed, de novo disulfide bond in a bacterial α-type CA to enhance thermostability. Three variants were selected and expressed in Escherichia coli with an additional disulfide bridge. One of the variants showed great enhancement in terms of both kinetic and thermodynamic stabilities. This improvement could be attributed to the loss of conformational entropy of the unfolded state, showing increased rigidity. The variant showed an upward-shifted optimal temperature and appeared to be thermoactivated, which compensated for the lowered activity at 25 °C. Collectively, the variant constructed by the rapid and effective de novo disulfide engineering can be used as an efficient biocatalyst for carbon sequestration under high temperature conditions.
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Suitability of the alkalistable carbonic anhydrase from a polyextremophilic bacterium Aeribacillus pallidus TSHB1 in biomimetic carbon sequestration. Bioprocess Biosyst Eng 2016; 39:1515-25. [PMID: 27215773 DOI: 10.1007/s00449-016-1627-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2016] [Accepted: 05/15/2016] [Indexed: 10/21/2022]
Abstract
Carbonic anhydrase (CA) was produced from the polyextremophilic (halotolerant, moderately thermophilic and alkaliphilic) bacterium Aeribacillus pallidus TSHB1 isolated from water and sediment samples of Choti Anhoni hot spring of Pipariya, Madhya Pradesh (India), is being reported to be suitable for carbon sequestration. Growth and CA production were inhibited at higher CO2 concentration (5-10 %). Under optimized culture variables (tryptone 0.8 %, yeast extract 0.08 %, glucose 1 %, micronutrient solution 1 %, inoculums size 1.10 %, agitation 200 at pH 8, and temperature 55 °C), 3.7-fold higher CA production was attained than that under unoptimized conditions. The zymogram analysis of the partially purified CA revealed an activity band corresponding to 32 kDa. The enzyme is stable in the pH range between 8.0 and 11.0 with T 1/2 of 40, 15, and 8 min at 60, 70, and 80 °C, respectively. The CA of A. pallidus displayed a marked enhancement in the rate of CaCO3 precipitation from aqueous CO2. The CA-aided formation of CaCO3 was 42.5 mg mg(-1) protein. Scanning electron microscopy revealed the formation of rhomboid calcite crystals. This is the first report on the production and applicability of CA from the polyextremophilic A. pallidus in carbon sequestration.
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25
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Li CX, Jiang XC, Qiu YJ, Xu JH. Identification of a new thermostable and alkali-tolerant α-carbonic anhydrase from Lactobacillus delbrueckii as a biocatalyst for CO2 biomineralization. BIORESOUR BIOPROCESS 2015. [DOI: 10.1186/s40643-015-0074-4] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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26
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Butterfield CN, Tao L, Chacón KN, Spiro TG, Blackburn NJ, Casey WH, Britt RD, Tebo BM. Multicopper manganese oxidase accessory proteins bind Cu and heme. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2015; 1854:1853-1859. [PMID: 26327317 DOI: 10.1016/j.bbapap.2015.08.012] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2015] [Revised: 08/24/2015] [Accepted: 08/27/2015] [Indexed: 10/23/2022]
Abstract
Multicopper oxidases (MCOs) catalyze the oxidation of a diverse group of metal ions and organic substrates by successive single-electron transfers to O2 via four bound Cu ions. MnxG, which catalyzes MnO2 mineralization by oxidizing both Mn(II) and Mn(III), is unique among multicopper oxidases in that it carries out two energetically distinct electron transfers and is tightly bound to accessory proteins. There are two of these, MnxE and MnxF, both approximately 12kDa. Although their sequences are similar to those found in the genomes of several Mn-oxidizing Bacillus species, they are dissimilar to those of proteins with known function. Here, MnxE and MnxF are co-expressed independent of MnxG and are found to oligomerize into a higher order stoichiometry, likely a hexamer. They bind copper and heme, which have been characterized by electron paramagnetic resonance (EPR), X-ray absorption spectroscopy (XAS), and UV-visible (UV-vis) spectrophotometry. Cu is found in two distinct type 2 (T2) copper centers, one of which appears to be novel; heme is bound as a low-spin species, implying coordination by two axial ligands. MnxE and MnxF do not oxidize Mn in the absence of MnxG and are the first accessory proteins to be required by an MCO. This may indicate that Cu and heme play roles in electron transfer and/or Cu trafficking.
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Affiliation(s)
- Cristina N Butterfield
- Division of Environmental and Biomolecular Systems, Institute of Environmental Health, Oregon Health & Science University, Portland, OR 97239, United States
| | - Lizhi Tao
- Department of Chemistry, University of California, Davis, CA 95616, United States
| | - Kelly N Chacón
- Division of Environmental and Biomolecular Systems, Institute of Environmental Health, Oregon Health & Science University, Portland, OR 97239, United States
| | - Thomas G Spiro
- Department of Chemistry, University of Washington, Seattle, WA 98195, United States
| | - Ninian J Blackburn
- Division of Environmental and Biomolecular Systems, Institute of Environmental Health, Oregon Health & Science University, Portland, OR 97239, United States
| | - William H Casey
- Department of Geology, University of California, Davis, CA 95616, United States
| | - R David Britt
- Department of Chemistry, University of California, Davis, CA 95616, United States
| | - Bradley M Tebo
- Division of Environmental and Biomolecular Systems, Institute of Environmental Health, Oregon Health & Science University, Portland, OR 97239, United States.
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27
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Thermostable Carbonic Anhydrases in Biotechnological Applications. Int J Mol Sci 2015; 16:15456-80. [PMID: 26184158 PMCID: PMC4519908 DOI: 10.3390/ijms160715456] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2015] [Revised: 07/01/2015] [Accepted: 07/02/2015] [Indexed: 01/10/2023] Open
Abstract
Carbonic anhydrases are ubiquitous metallo-enzymes which catalyze the reversible hydration of carbon dioxide in bicarbonate ions and protons. Recent years have seen an increasing interest in the utilization of these enzymes in CO2 capture and storage processes. However, since this use is greatly limited by the harsh conditions required in these processes, the employment of thermostable enzymes, both those isolated by thermophilic organisms and those obtained by protein engineering techniques, represents an interesting possibility. In this review we will provide an extensive description of the thermostable carbonic anhydrases so far reported and the main processes in which these enzymes have found an application.
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28
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Pinard MA, Lotlikar SR, Boone CD, Vullo D, Supuran CT, Patrauchan MA, McKenna R. Structure and inhibition studies of a type II beta-carbonic anhydrase psCA3 from Pseudomonas aeruginosa. Bioorg Med Chem 2015; 23:4831-4838. [PMID: 26068018 DOI: 10.1016/j.bmc.2015.05.029] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Revised: 05/10/2015] [Accepted: 05/19/2015] [Indexed: 10/23/2022]
Abstract
Carbonic anhydrases (CAs) are metallo-enzymes that catalyze the reversible hydration of carbon dioxide into bicarbonate and a proton. The β-class CAs (β-CAs) are expressed in prokaryotes, fungi, plants, and more recently have been isolated in some animals. The β-CA class is divided into two subclasses, termed type I and II, defined by pH catalytic activity profile and active site structural configuration. Type I β-CAs display catalytic activity over a broad pH range (6.5-9.0) with the active site zinc tetrahedrally coordinated by three amino acids and a hydroxide/water. In contrast, type II β-CAs are catalytically active only at a pH 8 and higher where they adopt a functional active site configuration like that of type I. However, below pH 8 they are conformationally self-inactivated by the addition of a fourth amino acid coordinating the zinc and thereby displacing the zinc bound solvent. We have determined the structure of psCA3, a type II β-CA, isolated from Pseudomonas aeruginosa (P. aeruginosa) PAO1 at pH 8.3, in its open active state to a resolution of 1.9 Å. The active site zinc is coordinated by Cys42, His98, Cys101 and a water/hydroxide molecule. P. aeruginosa is a multi-drug resistant bacterium and displays intrinsic resistance to most of the currently used antibiotics; therefore, there is a need for new antibacterial targets. Kinetic data confirm that psCA3 belongs to the type II subclass and that sulfamide, sulfamic acid, phenylboronic acid and phenylarsonic acid are micromolar inhibitors. In vivo studies identified that among six tested inhibitors representing sulfonamides, inorganic anions, and small molecules, acetazolamide has the most significant dose-dependent inhibitory effect on P. aeruginosa growth.
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Affiliation(s)
- Melissa A Pinard
- Department of Biochemistry and Molecular Biology, College of Medicine, University of Florida, Gainesville, FL 32610, USA
| | - Shalaka R Lotlikar
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK 74078, USA
| | - Christopher D Boone
- Department of Biochemistry and Molecular Biology, College of Medicine, University of Florida, Gainesville, FL 32610, USA
| | - Daniela Vullo
- Università degli Studi di Firenze, Laboratorio di Chimica Bioinorganica, Rm. 188, Via della Lastruccia 3, I-50019 Sesto Fiorentino (Firenze), Italy; Università degli Studi di Firenze, Polo Scientifico, Dipartimento Neurofaba, Sezione di Scienze Farmaceutiche e Nutraceutiche, Via Ugo Schiff 6, 50019 Sesto Fiorentino (Firenze), Italy
| | - Claudiu T Supuran
- Università degli Studi di Firenze, Laboratorio di Chimica Bioinorganica, Rm. 188, Via della Lastruccia 3, I-50019 Sesto Fiorentino (Firenze), Italy; 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 A Patrauchan
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK 74078, USA
| | - Robert McKenna
- Department of Biochemistry and Molecular Biology, College of Medicine, University of Florida, Gainesville, FL 32610, USA.
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Bracht F, de Alencastro RB. Dynamical study, hydrogen bond analysis, and constant pH simulations of the beta carbonic anhydrase ofMethanobacterium thermoautotrophicum. J Biomol Struct Dyn 2015; 34:259-71. [DOI: 10.1080/07391102.2015.1025100] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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30
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Influence of Exopolymeric Materials on Bacterially Induced Mineralization of Carbonates. Appl Biochem Biotechnol 2015; 175:3531-41. [DOI: 10.1007/s12010-015-1524-3] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2014] [Accepted: 01/21/2015] [Indexed: 10/24/2022]
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Srivastava S, Bharti RK, Verma PK, Thakur IS. Cloning and expression of gamma carbonic anhydrase from Serratia sp. ISTD04 for sequestration of carbon dioxide and formation of calcite. BIORESOURCE TECHNOLOGY 2015; 188:209-213. [PMID: 25686723 DOI: 10.1016/j.biortech.2015.01.108] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2014] [Revised: 01/24/2015] [Accepted: 01/27/2015] [Indexed: 06/04/2023]
Abstract
Bacterial strains isolated from marble mines rock and enriched in the chemostat culture with different concentrations of sodium bicarbonate. The enriched consortium had six bacterial isolates. One of bacterium isolate showed carbonic anhydrase (CA) activity by catalyzing the reversible hydration reaction of carbon dioxide to bicarbonate. The bacterium was identified as Serratia sp. by 16S rRNA sequence analysis. The carbonic anhydrase gene from Serratia sp. was found to be homologous with gamma carbonic anhydrase. The carbonic anhydrase gene was cloned in PET21b(+) and expressed it in recombinant Escherichia coli BL21 (DE3) with His-tag at the C-terminus. The recombinant protein was purified efficiently by using one-step nickel affinity chromatography. Expected size of carbonic anhydrase was approximately 29 kDa in SDS-PAGE gel. Recombinant carbonic anhydrase enzyme was used for biomineralization-based conversion of atmospheric CO2 into valuable calcite minerals. The calcification was confirmed by using XRD, FTIR, EDX and SEM analysis.
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Affiliation(s)
- Shaili Srivastava
- School of Environmental Sciences, Jawaharlal Nehru University, New Delhi 110067, India; Amity School of Earth and Environmental Science, Amity University Gurgaon, India
| | - Randhir Kumar Bharti
- School of Environmental Sciences, Jawaharlal Nehru University, New Delhi 110067, India
| | - Praveen Kumar Verma
- National Institute of Plant Genome Research, Aruna Asaf Ali Road, New Delhi, India
| | - Indu Shekhar Thakur
- School of Environmental Sciences, Jawaharlal Nehru University, New Delhi 110067, India.
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Patel TN, Park AHA, Banta S. Genetic manipulation of outer membrane permeability: generating porous heterogeneous catalyst analogs in Escherichia coli. ACS Synth Biol 2014; 3:848-54. [PMID: 24932924 DOI: 10.1021/sb400202s] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The limited permeability of the E. coli outer membrane can significantly hinder whole-cell biocatalyst performance. In this study, the SARS coronavirus small envelope protein (SCVE) was expressed in E. coli cells previously engineered for periplasmic expression of carbonic anhydrase (CA) activity. This maneuver increased small molecule uptake by the cells, resulting in increased apparent CA activity of the biocatalysts. The enhancements in activity were quantified using methods developed for traditional heterogeneous catalysis. The expression of the SCVE protein was found to significantly reduce the Thiele moduli (ϕ), as well as increase the effectiveness factors (η), effective diffusivities (De), and permeabilities (P) of the biocatalysts. These catalytic improvements translated into superior performance of the biocatalysts for the precipitation of calcium carbonate from solution which is an attractive strategy for long-term sequestration of captured carbon dioxide. Overall, these results demonstrate that synthetic biology approaches can be used to enhance heterogeneous catalysts incorporated into microbial whole-cell scaffolds.
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Affiliation(s)
- Tushar N Patel
- Department
of Chemical Engineering, Columbia University, New York, New York 10027, United States
| | - Ah-Hyung Alissa Park
- Department
of Earth and Environmental Engineering, Columbia University, New York, New York 10027, United States
| | - Scott Banta
- Department
of Chemical Engineering, Columbia University, New York, New York 10027, United States
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Bacterial extremo-α-carbonic anhydrases from deep-sea hydrothermal vents as potential biocatalysts for CO2 sequestration. ACTA ACUST UNITED AC 2014. [DOI: 10.1016/j.molcatb.2014.08.002] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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34
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Le Roy N, Jackson DJ, Marie B, Ramos-Silva P, Marin F. The evolution of metazoan α-carbonic anhydrases and their roles in calcium carbonate biomineralization. Front Zool 2014. [DOI: 10.1186/s12983-014-0075-8] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
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35
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Lehneck R, Pöggeler S. A matter of structure: structural comparison of fungal carbonic anhydrases. Appl Microbiol Biotechnol 2014; 98:8433-41. [DOI: 10.1007/s00253-014-5993-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2014] [Revised: 07/24/2014] [Accepted: 07/25/2014] [Indexed: 01/10/2023]
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36
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Lehneck R, Elleuche S, Pöggeler S. The filamentous ascomyceteSordaria macrosporacan survive in ambient air without carbonic anhydrases. Mol Microbiol 2014; 92:931-44. [DOI: 10.1111/mmi.12607] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/02/2014] [Indexed: 10/25/2022]
Affiliation(s)
- Ronny Lehneck
- Institute of Microbiology and Genetics; Department of Genetics of Eukaryotic Microorganisms; Georg-August-University Göttingen; Göttingen Germany
| | - Skander Elleuche
- Institute of Technical Microbiology; Hamburg University of Technology; Hamburg Germany
| | - Stefanie Pöggeler
- Institute of Microbiology and Genetics; Department of Genetics of Eukaryotic Microorganisms; Georg-August-University Göttingen; Göttingen Germany
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Yadav RR, Krishnamurthi K, Mudliar SN, Devi SS, Naoghare PK, Bafana A, Chakrabarti T. Carbonic anhydrase mediated carbon dioxide sequestration: promises, challenges and future prospects. J Basic Microbiol 2014; 54:472-81. [PMID: 24740638 DOI: 10.1002/jobm.201300849] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2013] [Accepted: 03/12/2014] [Indexed: 11/07/2022]
Abstract
Anthropogenic activities have substantially increased the level of greenhouse gases (GHGs) in the atmosphere and are contributing significantly to the global warming. Carbon dioxide (CO2 ) is one of the major GHGs which plays a key role in the climate change. Various approaches and methodologies are under investigation to address CO2 capture and sequestration worldwide. Carbonic anhydrase (CA) mediated CO2 sequestration is one of the promising options. Therefore, the present review elaborates recent developments in CA, its immobilization and bioreactor methodologies towards CO2 sequestration using the CA enzyme. The promises and challenges associated with the efficient utilization of CA for CO2 sequestration and scale up from flask to lab-scale bioreactor are critically discussed. Finally, the current review also recommends the possible future needs and directions to utilize CA for CO2 sequestration.
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Affiliation(s)
- Raju R Yadav
- Environmental Health Division, CSIR-National Environmental Engineering Research Institute (NEERI), Nagpur, India
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38
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Patel TN, Park AHA, Banta S. Surface Display of Small Peptides on Escherichia coli for Enhanced Calcite Precipitation Rates. Biopolymers 2014; 102:191-6. [PMID: 26820015 DOI: 10.1002/bip.22466] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Mineralization has emerged as a promising strategy for long-term carbon sequestration. These processes involve carbon dioxide hydration followed by mineral precipitation. We have explored the production of whole-cell biocatalysts engineered with carbonic anhydrase (CA) activity to accelerate the CO₂ hydration reaction. In this study, short polypeptides were displayed on the surface of E. coli cells and whole-cell biocatalysts containing periplasmically expressed CAs in an attempt to enhance calcite mineral formation. It was found that cells coexpressing recombinant periplasmic CA and surface-displayed GPA peptide (PEVPEGAFDTAI) outperformed other peptide-expressing biocatalysts evaluated in terms of the amount of precipitate formed, as well as the overall formation rate of solids. Cells expressing the Cab CA isoform (BLR-pCab) and Cam isoform (BLR-pCam) with the surface-displayed GPA peptide exhibited 36 and 59% improvements in precipitation amounts, as well as 18 and 60% improvements in overall formation rates, respectively, over similar biocatalysts without GPA expression. The biocatalyst with the best performance was BLR-pCam/GPA, which generated 0.15 g of CaCO₃, while BLR cells generated only 0.08 g of CaCO₃ under the same small batch reaction conditions. The BLR-pCam/GPA cells also exhibited the fastest formation rates, achieving the maximum change in solution turbidity after only 2.2 min, as opposed to 6.3 min for BLR cells. These results demonstrate that synthetic biology approaches can be used to create novel biocatalysts with the ability to enhance both catalysis and precipitation activities.
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Lehneck R, Neumann P, Vullo D, Elleuche S, Supuran CT, Ficner R, Pöggeler S. Crystal structures of two tetrameric β-carbonic anhydrases from the filamentous ascomycete Sordaria macrospora. FEBS J 2014; 281:1759-72. [PMID: 24506675 DOI: 10.1111/febs.12738] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2013] [Revised: 01/30/2014] [Accepted: 01/31/2014] [Indexed: 01/11/2023]
Abstract
UNLABELLED Carbonic anhydrases (CAs) are metalloenzymes catalyzing the reversible hydration of carbon dioxide to bicarbonate (hydrogen carbonate) and protons. CAs have been identified in archaea, bacteria and eukaryotes and can be classified into five groups (α, β, γ, δ, ζ) that are unrelated in sequence and structure. The fungal β-class has only recently attracted attention. In the present study, we investigated the structure and function of the plant-like β-CA proteins CAS1 and CAS2 from the filamentous ascomycete Sordaria macrospora. We demonstrated that both proteins can substitute for the Saccharomyces cerevisiae β-CA Nce103 and exhibit an in vitro CO2 hydration activity (kcat /Km of CAS1: 1.30 × 10(6) m(-1) ·s(-1) ; CAS2: 1.21 × 10(6 ) m(-1) ·s(-1) ). To further investigate the structural properties of CAS1 and CAS2, we determined their crystal structures to a resolution of 2.7 Å and 1.8 Å, respectively. The oligomeric state of both proteins is tetrameric. With the exception of the active site composition, no further major differences have been found. In both enzymes, the Zn(2) (+) -ion is tetrahedrally coordinated; in CAS1 by Cys45, His101 and Cys104 and a water molecule and in CAS2 by the side chains of four residues (Cys56, His112, Cys115 and Asp58). Both CAs are only weakly inhibited by anions, making them good candidates for industrial applications. STRUCTURED DIGITAL ABSTRACT CAS1 and CAS2 bind by x-ray crystallography (View interaction) DATABASE Structural data have been deposited in the Protein Data Bank database under accession numbers 4O1J for CAS1 and 4O1K for CAS2.
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Affiliation(s)
- Ronny Lehneck
- Institute of Microbiology and Genetics, Department of Genetics of Eukaryotic Microorganisms, Georg-August-University Göttingen, Germany
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40
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Zolfaghari Emameh R, Barker H, Tolvanen MEE, Ortutay C, Parkkila S. Bioinformatic analysis of beta carbonic anhydrase sequences from protozoans and metazoans. Parasit Vectors 2014; 7:38. [PMID: 24447594 PMCID: PMC3907363 DOI: 10.1186/1756-3305-7-38] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2013] [Accepted: 01/10/2014] [Indexed: 12/02/2022] Open
Abstract
Background Despite the high prevalence of parasitic infections, and their impact on global health and economy, the number of drugs available to treat them is extremely limited. As a result, the potential consequences of large-scale resistance to any existing drugs are a major concern. A number of recent investigations have focused on the effects of potential chemical inhibitors on bacterial and fungal carbonic anhydrases. Among the five classes of carbonic anhydrases (alpha, beta, gamma, delta and zeta), beta carbonic anhydrases have been reported in most species of bacteria, yeasts, algae, plants, and particular invertebrates (nematodes and insects). To date, there has been a lack of knowledge on the expression and molecular structure of beta carbonic anhydrases in metazoan (nematodes and arthropods) and protozoan species. Methods Here, the identification of novel beta carbonic anhydrases was based on the presence of the highly-conserved amino acid sequence patterns of the active site. A phylogenetic tree was constructed based on codon-aligned DNA sequences. Subcellular localization prediction for each identified invertebrate beta carbonic anhydrase was performed using the TargetP webserver. Results We verified a total of 75 beta carbonic anhydrase sequences in metazoan and protozoan species by proteome-wide searches and multiple sequence alignment. Of these, 52 were novel, and contained highly conserved amino acid residues, which are inferred to form the active site in beta carbonic anhydrases. Mitochondrial targeting peptide analysis revealed that 31 enzymes are predicted with mitochondrial localization; one was predicted to be a secretory enzyme, and the other 43 were predicted to have other undefined cellular localizations. Conclusions These investigations identified 75 beta carbonic anhydrases in metazoan and protozoan species, and among them there were 52 novel sequences that were not previously annotated as beta carbonic anhydrases. Our results will not only change the current information in proteomics and genomics databases, but will also suggest novel targets for drugs against parasites.
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41
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Synergistic Role of Bacterial Urease and Carbonic Anhydrase in Carbonate Mineralization. Appl Biochem Biotechnol 2014; 172:2552-61. [DOI: 10.1007/s12010-013-0694-0] [Citation(s) in RCA: 63] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2013] [Accepted: 12/25/2013] [Indexed: 10/25/2022]
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42
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Patel TN, Swanson EJ, Park AHA, Banta S. An automated method for measuring the operational stability of biocatalysts with carbonic anhydrase activity. Biochem Eng J 2014. [DOI: 10.1016/j.bej.2013.11.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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43
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Abstract
The potential of carbonic anhydrase (CA) family as target for the drug design of inhibitors with various medicinal chemistry applications has been recognized from long time, whereas the industrial interest in using these enzymes as biocatalysts for carbon dioxide sequestration and biofuel production is only recently emerging. However, an efficient utilization in these processes often requires stable enzymes, able to work in the harsh conditions typical of the CO2 capture process. In this context CAs active at very high temperatures are of extreme interest. In this chapter we have summarized in a comparative manner all existing data on thermostable CAs both isolated by extremophiles and obtained by protein engineering studies. Among the five CA-classes, the biochemical and structural features of thermostable α-, β- and γ-CAs have been discussed. Data show that so far α-CAs isolated from thermophilic organisms are the best candidates to be used in biotechnological processes, even if plenty of work can be still done in this field also with help of protein engineering.
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Abstract
The β-carbonic anhydrases (β-CAs) are a structurally distinct family of carbonic anhydrase that is widely distributed in microorganisms, algae, plants, and invertebrates. Like all carbonic anhydrases, β-CAs catalyze the reaction CO2 + H2O ⇆ HCO3 (-) + H(+), and is typically associated with other enzymes that produce or utilize CO2 or HCO3 (-). β-CA is required for normal growth for many organisms. Unique among the five different families of carbonic anhydrases, β-CA is the only family of carbonic anhydrase to exhibit allostery. This chapter summarizes the structure, catalytic mechanism, and allosteric regulation of β-CA.
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Affiliation(s)
- Roger S Rowlett
- Department of Chemistry, Colgate University, Hamilton, NY, USA,
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45
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Abstract
Carbonic anhydrase is a metalloenzyme catalyzing the reversible hydration of carbon dioxide to bicarbonate. Five independently evolved classes have been described for which one or more are found in nearly every cell type underscoring the general importance of this ubiquitous enzyme in Nature. The bulk of research to date has centered on the enzymes from mammals and plants with less emphasis on prokaryotes. Prokaryotic carbonic anhydrases play important roles in the ecology of Earth's biosphere including acquisition of CO2 for photosynthesis and the physiology of aerobic and anaerobic prokaryotes decomposing the photosynthate back to CO2 thereby closing the global carbon cycle. This review focuses on the physiology and biochemistry of carbonic anhydrases from prokaryotes belonging to the domains Bacteria and Archaea that play key roles in the ecology of Earth's biosphere.
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Affiliation(s)
- R Siva Sai Kumar
- Department of Biochemistry and Molecular Biology, Ebery College of Science, The Pennsylvania State University, University Park, PA, USA,
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46
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Kanth BK, Lee J, Pack SP. Carbonic anhydrase: Its biocatalytic mechanisms and functional properties for efficient CO2capture process development. Eng Life Sci 2013. [DOI: 10.1002/elsc.201200157] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Affiliation(s)
| | - Jinwon Lee
- Department of Chemical and Biomolecular Engineering; Sogang University; Seoul Korea
| | - Seung Pil Pack
- Department of Biotechnology and Bioinformatics; Korea University; Sejong Korea
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47
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Pinard M, Lotlikar S, Patrauchan MA, McKenna R. Preliminary X-ray crystallographic analysis of β-carbonic anhydrase psCA3 from Pseudomonas aeruginosa. Acta Crystallogr Sect F Struct Biol Cryst Commun 2013; 69:891-4. [PMID: 23908036 PMCID: PMC3729167 DOI: 10.1107/s1744309113017594] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2013] [Accepted: 06/26/2013] [Indexed: 11/10/2022]
Abstract
Pseudomonas aeruginosa is a Gram-negative bacterium that causes life-threatening infections in susceptible individuals and is resistant to most clinically available antimicrobials. Genomic and proteomic studies have identified three genes, pa0102, pa2053 and pa4676, in P. aeruginosa PAO1 encoding three functional β-carbonic anhydrases (β-CAs): psCA1, psCA2 and psCA3, respectively. These β-CAs could serve as novel antimicrobial drug targets for this pathogen. X-ray crystallographic structural studies have been initiated to characterize the structure and function of these proteins. This communication describes the production of two crystal forms (A and B) of β-CA psCA3. Form A diffracted to a resolution of 2.9 Å; it belonged to space group P212121, with unit-cell parameters a = 81.9, b = 84.9, c = 124.2 Å, and had a calculated Matthews coefficient of 2.23 ų Da⁻¹ assuming four molecules in the crystallographic asymmetric unit. Form B diffracted to a resolution of 3.0 Å; it belonged to space group P21212, with unit-cell parameters a = 69.9, b = 77.7, c = 88.5 Å, and had a calculated Matthews coefficient of 2.48 ų Da⁻¹ assuming two molecules in the crystallographic asymmetric unit. Preliminary molecular-replacement solutions have been determined with the PHENIX AutoMR wizard and refinement of both crystal forms is currently in progress.
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Affiliation(s)
- Melissa Pinard
- Department of Biochemistry and Molecular Biology, University of Florida, PO Box 100245, Gainesville, FL 32610, USA
| | - Shalaka Lotlikar
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK 74078, USA
| | - Marianna A. Patrauchan
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK 74078, USA
| | - Robert McKenna
- Department of Biochemistry and Molecular Biology, University of Florida, PO Box 100245, Gainesville, FL 32610, USA
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Bacterial CS2 hydrolases from Acidithiobacillus thiooxidans strains are homologous to the archaeal catenane CS2 hydrolase. J Bacteriol 2013; 195:4046-56. [PMID: 23836868 DOI: 10.1128/jb.00627-13] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Carbon disulfide (CS(2)) and carbonyl sulfide (COS) are important in the global sulfur cycle, and CS(2) is used as a solvent in the viscose industry. These compounds can be converted by sulfur-oxidizing bacteria, such as Acidithiobacillus thiooxidans species, to carbon dioxide (CO(2)) and hydrogen sulfide (H2S), a property used in industrial biofiltration of CS(2)-polluted airstreams. We report on the mechanism of bacterial CS(2) conversion in the extremely acidophilic A. thiooxidans strains S1p and G8. The bacterial CS(2) hydrolases were highly abundant. They were purified and found to be homologous to the only other described (archaeal) CS(2) hydrolase from Acidianus strain A1-3, which forms a catenane of two interlocked rings. The enzymes cluster in a group of β-carbonic anhydrase (β-CA) homologues that may comprise a subclass of CS(2) hydrolases within the β-CA family. Unlike CAs, the CS(2) hydrolases did not hydrate CO(2) but converted CS(2) and COS with H(2)O to H(2)S and CO(2). The CS(2) hydrolases of A. thiooxidans strains G8, 2Bp, Sts 4-3, and BBW1, like the CS(2) hydrolase of Acidianus strain A1-3, exist as both octamers and hexadecamers in solution. The CS(2) hydrolase of A. thiooxidans strain S1p forms only octamers. Structure models of the A. thiooxidans CS(2) hydrolases based on the structure of Acidianus strain A1-3 CS(2) hydrolase suggest that the A. thiooxidans strain G8 CS(2) hydrolase may also form a catenane. In the A. thiooxidans strain S1p enzyme, two insertions (positions 26 and 27 [PD] and positions 56 to 61 [TPAGGG]) and a nine-amino-acid-longer C-terminal tail may prevent catenane formation.
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Dhami NK, Reddy MS, Mukherjee A. Bacillus megaterium mediated mineralization of calcium carbonate as biogenic surface treatment of green building materials. World J Microbiol Biotechnol 2013; 29:2397-406. [PMID: 23793943 DOI: 10.1007/s11274-013-1408-z] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2013] [Accepted: 06/17/2013] [Indexed: 11/30/2022]
Abstract
Microbially induced calcium carbonate precipitation is a biomineralization process that has various applications in remediation and restoration of range of building materials. In the present study, calcifying bacteria, Bacillus megaterium SS3 isolated from calcareous soil was applied as biosealant to enhance the durability of low energy, green building materials (soil-cement blocks). This bacterial isolate produced high amounts of urease, carbonic anhydrase, extra polymeric substances and biofilm. The calcium carbonate polymorphs produced by B. megaterium SS3 were analyzed by scanning electron microscopy, confocal laser scanning microscopy, X-ray diffraction and Fourier transmission infra red spectroscopy. These results suggested that calcite is the most predominant carbonate formed by this bacteria followed by vaterite. Application of B. megaterium SS3 as biogenic surface treatment led to 40 % decrease in water absorption, 31 % decrease in porosity and 18 % increase in compressive strength of low energy building materials. From the present investigation, it is clear that surface treatment of building materials by B. megaterium SS3 is very effective and eco friendly way of biodeposition of coherent carbonates that enhances the durability of building materials.
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Affiliation(s)
- Navdeep Kaur Dhami
- Department of Biotechnology, Thapar University, Patiala, 147004, Punjab, India
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50
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Lotlikar SR, Hnatusko S, Dickenson NE, Choudhari SP, Picking WL, Patrauchan MA. Three functional β-carbonic anhydrases in Pseudomonas aeruginosa PAO1: role in survival in ambient air. MICROBIOLOGY-SGM 2013; 159:1748-1759. [PMID: 23728627 DOI: 10.1099/mic.0.066357-0] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Bacterial β-class carbonic anhydrases (CAs) are zinc metalloenzymes catalysing reversible hydration of CO2. They maintain the intracellular balance of CO2/bicarbonate required for biosynthetic reactions and represent a new group of antimicrobial drug targets. Genome sequence analysis of Pseudomonas aeruginosa PAO1, an opportunistic human pathogen causing life threatening infections, identified three genes, PAO102, PA2053 and PA4676, encoding putative β-CAs that share 28-45 % amino acid sequence identity and belong to clades A and B. The genes are conserved among all sequenced pseudomonads. The CAs were cloned, heterologously expressed and purified. Metal and enzymic analyses confirmed that the proteins contain Zn(2+) and catalyse hydration of CO2 to bicarbonate. PAO102 (psCA1) was 19-26-fold more active, and together with PA2053 (psCA2) showed CA activity at both pH 7.5 and 8.3, whereas PA4676 (psCA3) was active only at pH 8.3. Circular dichroism spectroscopy suggested that psCA2 and psCA3 undergo pH-dependent structural changes. Taken together, the data suggest that psCA1 may belong to type I and psCA3 to type II β-CAs. Immunoblot analysis showed that all three CAs are expressed in PAO1 cells when grown in ambient air and at 5 % CO2; psCA1 appeared more abundant under both conditions. Growth studies of transposon mutants showed that the disruption of psCA1 impaired PAO1 growth in ambient air and caused a minor defect at high CO2. Thus, psCA1 contributes to the adaptation of P. aeruginosa to low CO2 conditions and will be further studied for its role in virulence and as a potential antimicrobial drug target in this organism.
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Affiliation(s)
- Shalaka R Lotlikar
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK 74078, USA
| | - Shane Hnatusko
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK 74078, USA
| | - Nicholas E Dickenson
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK 74078, USA
| | - Shyamal P Choudhari
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK 74078, USA
| | - Wendy L Picking
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK 74078, USA
| | - Marianna A Patrauchan
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK 74078, USA
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