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Eckert P, Johs A, Semrau JD, DiSpirito AA, Richardson J, Sarangi R, Herndon E, Gu B, Pierce EM. Spectroscopic and computational investigations of organometallic complexation of group 12 transition metals by methanobactins from Methylocystis sp. SB2. J Inorg Biochem 2021; 223:111496. [PMID: 34271330 PMCID: PMC10569158 DOI: 10.1016/j.jinorgbio.2021.111496] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Revised: 05/17/2021] [Accepted: 05/26/2021] [Indexed: 12/30/2022]
Abstract
Methanotrophic bacteria catalyze the aerobic oxidation of methane to methanol using Cu-containing enzymes, thereby exerting a modulating influence on the global methane cycle. To facilitate the acquisition of Cu ions, some methanotrophic bacteria secrete small modified peptides known as "methanobactins," which strongly bind Cu and function as an extracellular Cu recruitment relay, analogous to siderophores and Fe. In addition to Cu, methanobactins form complexes with other late transition metals, including the Group 12 transition metals Zn, Cd, and Hg, although the interplay among solution-phase configurations, metal interactions, and the spectroscopic signatures of methanobactin-metal complexes remains ambiguous. In this study, the complexation of Zn, Cd, and Hg by methanobactin from Methylocystis sp. strain SB2 was studied using a combination of absorbance, fluorescence, extended x-ray absorption fine structure (EXAFS) spectroscopy, and time-dependent density functional theory (TD-DFT) calculations. We report changes in sample absorbance and fluorescence spectral dynamics, which occur on a wide range of experimental timescales and characterize a clear stoichiometric complexation dependence. Mercury L3-edge EXAFS and TD-DFT calculations suggest a linear model for HgS coordination, and TD-DFT suggests a tetrahedral model for Zn2+ and Cd2+. We observed an enhancement in the fluorescence of methanobactin upon interaction with transition metals and propose a mechanism of complexation-hindered isomerization drawing inspiration from the wild-type Green Fluorescent Protein active site. Collectively, our results represent the first combined computational and experimental spectroscopy study of methanobactins and shed new light on molecular interactions and dynamics that characterize complexes of methanobactins with Group 12 transition metals.
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Affiliation(s)
- Peter Eckert
- Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37830, USA.
| | - Alexander Johs
- Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37830, USA
| | - Jeremy D Semrau
- Civil & Environmental Engineering, The University of Michigan, Ann Arbor, MI 48109, USA
| | - Alan A DiSpirito
- Roy J. Carver Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames, IA 50011, USA
| | - Jocelyn Richardson
- Structural Molecular Biology Division, SLAC National Accelerator Laboratory, Menlo Park, CA 94306, USA
| | - Ritimukta Sarangi
- Structural Molecular Biology Division, SLAC National Accelerator Laboratory, Menlo Park, CA 94306, USA
| | - Elizabeth Herndon
- Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37830, USA
| | - Baohua Gu
- Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37830, USA
| | - Eric M Pierce
- Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37830, USA.
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Kuźniar A, Furtak K, Włodarczyk K, Stępniewska Z, Wolińska A. Methanotrophic Bacterial Biomass as Potential Mineral Feed Ingredients for Animals. Int J Environ Res Public Health 2019; 16:ijerph16152674. [PMID: 31357395 PMCID: PMC6696423 DOI: 10.3390/ijerph16152674] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Revised: 07/16/2019] [Accepted: 07/23/2019] [Indexed: 11/16/2022]
Abstract
Microorganisms play an important role in animal nutrition, as they can be used as a source of food or feed. The aim of the study was to determine the nutritional elements and fatty acids contained in the biomass of methanotrophic bacteria. Four bacterial consortia composed of Methylocystis and Methylosinus originating from Sphagnum flexuosum (Sp1), S. magellanicum (Sp2), S. fallax II (Sp3), S. magellanicum IV (Sp4), and one composed of Methylocaldum, Methylosinus, and Methylocystis that originated from coalbed rock (Sk108) were studied. Nutritional elements were determined using the flame atomic absorption spectroscopy technique after a biomass mineralization stage, whereas the fatty acid content was analyzed with the GC technique. Additionally, the growth of biomass and dynamics of methane consumption were monitored. It was found that the methanotrophic biomass contained high concentrations of K, Mg, and Fe, i.e., approx. 9.6–19.1, 2.2–7.6, and 2.4–6.6 g kg−1, respectively. Consequently, the biomass can be viewed as an appropriate feed and/or feed additive for supplementation with macroelements and certain microelements. Moreover, all consortia demonstrated higher content of unsaturated acids than saturated ones. Thus, methanotrophic bacteria seem to be a good solution, in natural supplementation of animal diets.
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Affiliation(s)
- Agnieszka Kuźniar
- Department of Biochemistry and Environmental Chemistry, The John Paul II Catholic University of Lublin, Konstantynów St. 1 I, 20-708 Lublin, Poland.
| | - Karolina Furtak
- Department of Agriculture Microbiology, Institute of Soil Sciences and Plant Cultivation State Research Institute, Czartoryskich St. 8, 24-100 Puławy, Poland
| | - Kinga Włodarczyk
- Department of Biochemistry and Environmental Chemistry, The John Paul II Catholic University of Lublin, Konstantynów St. 1 I, 20-708 Lublin, Poland
| | - Zofia Stępniewska
- Department of Biochemistry and Environmental Chemistry, The John Paul II Catholic University of Lublin, Konstantynów St. 1 I, 20-708 Lublin, Poland
| | - Agnieszka Wolińska
- Department of Biochemistry and Environmental Chemistry, The John Paul II Catholic University of Lublin, Konstantynów St. 1 I, 20-708 Lublin, Poland
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Liu B, Peng Q, Sheng M, Hu S, Qian M, Fan B, He J. Directed Evolution of Sulfonylurea Esterase and Characterization of a Variant with Improved Activity. J Agric Food Chem 2019; 67:836-843. [PMID: 30585487 DOI: 10.1021/acs.jafc.8b06198] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Esterase SulE detoxicates a variety of sulfonylurea herbicides through de-esterification. SulE exhibits high activity against thifensulfuron-methyl but low activity against other sulfonylureas. In this study, two variants, m2311 (P80R) and m0569 (P80R and G176A), with improved activity were screened from a mutation library constructed by error-prone PCR. Variant m2311 showed a higher activity against sulfonylureas in comparison variant m0569 and was further investigated. The kcat/ Km value of variant m2311 for metsulfuron-methyl, sulfometuron-methyl, chlorimuron-ethyl, tribenuron-methyl, and ethametsulfuron-methyl increased by 3.20-, 1.72-, 2.94-, 2.26- and 2.96-fold, respectively, in comparison with the wild type. Molecular modeling suggested that the activity improvement of variant m2311 is due to the substitution of Pro80 by arginine, leading to the formation of new hydrogen bonds between the enzyme and substrate. This study facilitates further elucidation of the structure and function of SulE and provides an improved gene resource for the detoxification of sulfonylurea residues and the genetic engineering of sulfonylurea-resistant crops.
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Affiliation(s)
- Bin Liu
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences , Nanjing Agricultural University , Nanjing 210095 , Jiangsu , People's Republic of China
| | - Qian Peng
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences , Nanjing Agricultural University , Nanjing 210095 , Jiangsu , People's Republic of China
| | - Mengyao Sheng
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences , Nanjing Agricultural University , Nanjing 210095 , Jiangsu , People's Republic of China
| | - Shishan Hu
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences , Nanjing Agricultural University , Nanjing 210095 , Jiangsu , People's Republic of China
| | - Meng Qian
- Laboratory Centre of Life Science, College of Life Sciences , Nanjing Agricultural University , Nanjing 210095 , Jiangsu , People's Republic of China
| | - Ben Fan
- College of Forest Resources and Environment , Nanjing Forestry University , Nanjing , Jiangsu , People's Republic of China
| | - Jian He
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences , Nanjing Agricultural University , Nanjing 210095 , Jiangsu , People's Republic of China
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Karthikeyan OP, Chidambarampadmavathy K, Nadarajan S, Lee PKH, Heimann K. Effect of CH4/O2 ratio on fatty acid profile and polyhydroxybutyrate content in a heterotrophic-methanotrophic consortium. Chemosphere 2015; 141:235-42. [PMID: 26247542 DOI: 10.1016/j.chemosphere.2015.07.054] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2015] [Revised: 06/14/2015] [Accepted: 07/19/2015] [Indexed: 05/22/2023]
Abstract
Understanding the role of heterotrophic-methanotrophic (H-Meth) communities is important for improvement of methane (CH4) oxidation capacities (MOC) particularly in conjunction with bio-product development in industrial bio-filters. Initially, a H-Meth consortium was established and enriched from marine sediments and characterized by next generation sequencing of the 16s rDNA gene. The enriched consortium was subjected to 10-50% CH4 (i.e., 0.20-1.6 CH4/O2 ratios) to study the effects on MOCs, biomass growth, fatty acid profiles and biopolymer (e.g. polyhydroxybutyrate; PHB) content. Methylocystis, Methylophaga and Pseudoxanthomonas dominated the H-Meth consortium. Culture enrichment of the H-Meth consortium resulted in 15-20-folds higher MOC compared to seed sediments. Increasing CH4 concentration (and decreased O2 levels) yielded higher MOCs, but did not improve total fatty acid contents. PHB contents varied between 2.5% and 8.5% independently of CH4/O2 ratios. The results suggest that H-Meth consortia could potentially be used in industrial bio-filters for production of biopolymer/biofuel precursors from CH4.
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Affiliation(s)
- Obulisamy P Karthikeyan
- College of Marine and Environmental Sciences, James Cook University, Townsville 4811, Queensland, Australia; Centre for Sustainable Fisheries and Aquaculture, James Cook University, Townsville 4811, Queensland, Australia; Comparative Genomics Centre, James Cook University, Townsville 4811, Queensland, Australia
| | - Karthigeyan Chidambarampadmavathy
- College of Marine and Environmental Sciences, James Cook University, Townsville 4811, Queensland, Australia; Centre for Sustainable Fisheries and Aquaculture, James Cook University, Townsville 4811, Queensland, Australia
| | - Saravanan Nadarajan
- College of Marine and Environmental Sciences, James Cook University, Townsville 4811, Queensland, Australia; Centre for Sustainable Fisheries and Aquaculture, James Cook University, Townsville 4811, Queensland, Australia
| | - Patrick K H Lee
- School of Energy and Environment, City University of Hong Kong, Hong Kong
| | - Kirsten Heimann
- College of Marine and Environmental Sciences, James Cook University, Townsville 4811, Queensland, Australia; Centre for Sustainable Fisheries and Aquaculture, James Cook University, Townsville 4811, Queensland, Australia; Comparative Genomics Centre, James Cook University, Townsville 4811, Queensland, Australia; Centre for Bio-discovery and Molecular Development of Therapeutics, James Cook University, Townsville 4811, Queensland, Australia.
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Smith SM, Rawat S, Telser J, Hoffman BM, Stemmler TL, Rosenzweig AC. Crystal structure and characterization of particulate methane monooxygenase from Methylocystis species strain M. Biochemistry 2011; 50:10231-40. [PMID: 22013879 PMCID: PMC3364217 DOI: 10.1021/bi200801z] [Citation(s) in RCA: 111] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Particulate methane monooxygenase (pMMO) is an integral membrane metalloenzyme that oxidizes methane to methanol in methanotrophic bacteria. Previous biochemical and structural studies of pMMO have focused on preparations from Methylococcus capsulatus (Bath) and Methylosinus trichosporium OB3b. A pMMO from a third organism, Methylocystis species strain M, has been isolated and characterized. Both membrane-bound and solubilized Methylocystis sp. strain M pMMO contain ~2 copper ions per 100 kDa protomer and exhibit copper-dependent propylene epoxidation activity. Spectroscopic data indicate that Methylocystis sp. strain M pMMO contains a mixture of Cu(I) and Cu(II), of which the latter exhibits two distinct type 2 Cu(II) electron paramagnetic resonance (EPR) signals. Extended X-ray absorption fine structure (EXAFS) data are best fit with a mixture of Cu-O/N and Cu-Cu ligand environments with a Cu-Cu interaction at 2.52-2.64 Å. The crystal structure of Methylocystis sp. strain M pMMO was determined to 2.68 Å resolution and is the best quality pMMO structure obtained to date. It provides a revised model for the pmoA and pmoC subunits and has led to an improved model of M. capsulatus (Bath) pMMO. In these new structures, the intramembrane zinc/copper binding site has a different coordination environment from that in previous models.
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Affiliation(s)
- Stephen M. Smith
- Departments of Molecular Biosciences and of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
| | - Swati Rawat
- Department of Biochemistry and Molecular Biology, Wayne State University, School of Medicine, Detroit, Michigan 48201, United States
| | - Joshua Telser
- Departments of Molecular Biosciences and of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
| | - Brian M. Hoffman
- Departments of Molecular Biosciences and of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
| | - Timothy L. Stemmler
- Department of Biochemistry and Molecular Biology, Wayne State University, School of Medicine, Detroit, Michigan 48201, United States
| | - Amy C. Rosenzweig
- Departments of Molecular Biosciences and of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
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Dedysh SN, Belova SE, Bodelier PLE, Smirnova KV, Khmelenina VN, Chidthaisong A, Trotsenko YA, Liesack W, Dunfield PF. Methylocystis heyeri sp. nov., a novel type II methanotrophic bacterium possessing 'signature' fatty acids of type I methanotrophs. Int J Syst Evol Microbiol 2007; 57:472-479. [PMID: 17329771 DOI: 10.1099/ijs.0.64623-0] [Citation(s) in RCA: 82] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel species is proposed for two strains of methanotrophic bacteria (H2(T) and Sakb1) isolated from an acidic (pH 4.3) Sphagnum peat bog lake (Teufelssee, Germany) and an acidic (pH 4.2) tropical forest soil (Thailand), respectively. Cells of strains H2(T) and Sakb1 were aerobic, Gram-negative, non-motile, straight or curved rods that were covered by large polysaccharide capsules and contained an intracytoplasmic membrane system typical of type II methanotrophs. They possessed both a particulate and a soluble methane monooxygenase and utilized the serine pathway for carbon assimilation. They were moderately acidophilic organisms capable of growth between pH 4.4 and 7.5 (optimum 5.8-6.2). The most unique characteristic of these strains was the phospholipid fatty acid profile. In addition to the signature fatty acid of type II methanotrophs (18 : 1omega8c), the cells also contained large amounts of what was previously considered to be a signature fatty acid of type I methanotrophs, 16 : 1omega8c. The DNA G+C contents of strains H2(T) and Sakb1 were 61.5 and 62.1 mol%, respectively. The 16S rRNA gene sequences possessed 96-98 % similarity to sequences of other type II methanotrophs in the genera Methylosinus and Methylocystis. 16S rRNA gene sequence and pmoA phylogeny demonstrated that the strains form a novel lineage within the genus Methylocystis. DNA-DNA hybridization values of strain H2(T) with Methylocystis parvus OBBP(T) and Methylocystis echinoides IMET 10491(T) were 18 and 25 %, respectively. Thus, it is proposed that these two strains represent a novel species, Methylocystis heyeri sp. nov. Strain H2(T) (=DSM 16984(T)=VKM B-2426(T)) is the type strain.
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Affiliation(s)
- Svetlana N Dedysh
- S. N. Winogradsky Institute of Microbiology, Russian Academy of Sciences, Moscow 117312, Russia
| | - Svetlana E Belova
- S. N. Winogradsky Institute of Microbiology, Russian Academy of Sciences, Moscow 117312, Russia
| | - Paul L E Bodelier
- Netherlands Institute of Ecology, NL3631 AC Nieuwersluis, The Netherlands
| | - Ksenia V Smirnova
- G. K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Pushchino, Moscow Region 142292, Russia
| | - Valentina N Khmelenina
- G. K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Pushchino, Moscow Region 142292, Russia
| | - Amnat Chidthaisong
- Joint Graduate School of Energy and Environment, King Mongkut's University of Technology, Bangkok 10140, Thailand
| | - Yuri A Trotsenko
- G. K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Pushchino, Moscow Region 142292, Russia
| | - Werner Liesack
- Max-Planck-Institut für terrestrische Mikrobiologie, D-35043 Marburg, Germany
| | - Peter F Dunfield
- Institute of Geological and Nuclear Sciences, Wairakei Research Centre, Taupo, New Zealand
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Helm J, Wendlandt KD, Rogge G, Kappelmeyer U. Characterizing a stable methane-utilizing mixed culture used in the synthesis of a high-quality biopolymer in an open system. J Appl Microbiol 2006; 101:387-95. [PMID: 16882146 DOI: 10.1111/j.1365-2672.2006.02960.x] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
AIMS To characterize a methane-utilizing poly-beta-hydroxybutyrate (PHB)-producing microbial community. METHODS AND RESULTS Three different approaches based on microbiology, analytical chemistry and molecular biology were used to determine the composition of the mixed culture. The dominant species, Methylocystis sp. GB25, represents more than 86% of the total biomass. Seven accompanying bacterial species are present in the mixed culture of which two are methylotrophic bacteria and five are utilizers of complex carbon sources. Both these groups were found to be present at the same ratio with respect to each other. Results of fatty acid analysis and PCR-DGGE fingerprints reflect the stability of the mixed-culture composition in the open system during multiple continuous growth and polymer formation processes throughout a period of 29 months. The consistently high quality of the accumulated polymer further corroborates this finding. CONCLUSION The methane-utilizing mixed culture has the potential of self-regulation resulting in a stable composition even under non-aseptic conditions. SIGNIFICANCE AND IMPACT OF THE STUDY Avoiding the necessity of sterile conditions, as demonstrated in this paper, is an important step towards the development of a viable large-scale process for the production of PHB using cheap substrates like methane from natural or renewable sources. This is the first report characterizing a bacterial mixed culture being used for the biotechnological production of a high-value product in an open system.
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Affiliation(s)
- J Helm
- Department of Environmental Biotechnology, UFZ Centre for Environmental Research, Leipzig-Halle P.O. Box 2, D-04301 Leipzig, Germany.
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