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Li X, Bei Q, Rabiei Nematabad M, Peng J, Liesack W. Time-shifted expression of acetoclastic and methylotrophic methanogenesis by a single Methanosarcina genomospecies predominates the methanogen dynamics in Philippine rice field soil. Microbiome 2024; 12:39. [PMID: 38409166 PMCID: PMC10895765 DOI: 10.1186/s40168-023-01739-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Accepted: 12/18/2023] [Indexed: 02/28/2024]
Abstract
BACKGROUND The final step in the anaerobic decomposition of biopolymers is methanogenesis. Rice field soils are a major anthropogenic source of methane, with straw commonly used as a fertilizer in rice farming. Here, we aimed to decipher the structural and functional responses of the methanogenic community to rice straw addition during an extended anoxic incubation (120 days) of Philippine paddy soil. The research combined process measurements, quantitative real-time PCR and RT-PCR of particular biomarkers (16S rRNA, mcrA), and meta-omics (environmental genomics and transcriptomics). RESULTS The analysis methods collectively revealed two major bacterial and methanogenic activity phases: early (days 7 to 21) and late (days 28 to 60) community responses, separated by a significant transient decline in microbial gene and transcript abundances and CH4 production rate. The two methanogenic activity phases corresponded to the greatest rRNA and mRNA abundances of the Methanosarcinaceae but differed in the methanogenic pathways expressed. While three genetically distinct Methanosarcina populations contributed to acetoclastic methanogenesis during the early activity phase, the late activity phase was defined by methylotrophic methanogenesis performed by a single Methanosarcina genomospecies. Closely related to Methanosarcina sp. MSH10X1, mapping of environmental transcripts onto metagenome-assembled genomes (MAGs) and population-specific reference genomes revealed this genomospecies as the key player in acetoclastic and methylotrophic methanogenesis. The anaerobic food web was driven by a complex bacterial community, with Geobacteraceae and Peptococcaceae being putative candidates for a functional interplay with Methanosarcina. Members of the Methanocellaceae were the key players in hydrogenotrophic methanogenesis, while the acetoclastic activity of Methanotrichaceae members was detectable only during the very late community response. CONCLUSIONS The predominant but time-shifted expression of acetoclastic and methylotrophic methanogenesis by a single Methanosarcina genomospecies represents a novel finding that expands our hitherto knowledge of the methanogenic pathways being highly expressed in paddy soils. Video Abstract.
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Affiliation(s)
- Xin Li
- Research group "Methanotrophic Bacteria and Environmental Genomics/Transcriptomics", Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Str. 10, D-35043, Marburg, Germany
- Present address: Institute of Agricultural and Nutritional Sciences, Martin-Luther-Universität Halle-Wittenberg, Betty-Heimann-Strasse 5, Halle (Saale), Germany
| | - Qicheng Bei
- Research group "Methanotrophic Bacteria and Environmental Genomics/Transcriptomics", Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Str. 10, D-35043, Marburg, Germany
- Present address: Department of Soil Ecology, Helmholtz Centre for Environmental Research - UFZ, Theodor-Lieser-Strasse 4, Halle (Saale), Germany
| | - Mehrdad Rabiei Nematabad
- Research group "Methanotrophic Bacteria and Environmental Genomics/Transcriptomics", Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Str. 10, D-35043, Marburg, Germany
| | - Jingjing Peng
- State Key Laboratory of Nutrient Use and Management, College of Resources and Environmental Sciences, Key Laboratory of Plant-Soil Interactions, National Academy of Agriculture Green Development, China Agricultural University, Beijing, 100193, China.
| | - Werner Liesack
- Research group "Methanotrophic Bacteria and Environmental Genomics/Transcriptomics", Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Str. 10, D-35043, Marburg, Germany.
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Richter M, Sattler C, Schöne C, Rother M. Pyruvate-dependent growth of Methanosarcina acetivorans. J Bacteriol 2024; 206:e0036323. [PMID: 38305193 PMCID: PMC10882976 DOI: 10.1128/jb.00363-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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: 11/02/2023] [Accepted: 01/11/2024] [Indexed: 02/03/2024] Open
Abstract
Methanogenesis is a key step during anaerobic biomass degradation. Methanogenic archaea (methanogens) are the only organisms coupling methanogenic substrate conversion to energy conservation. The range of substrates utilized by methanogens is limited, with acetate and H2+CO2 being the ecologically most relevant. The only single methanogenic energy substrate containing more carbon-carbon bonds than acetate is pyruvate. Only the aggregate-forming, freshwater methanogen Methanosarcina barkeri Fusaro was shown to grow on this compound. Here, the pyruvate-utilizing capabilities of the single-celled, marine Methanosarcina acetivorans were addressed. Robust pyruvate-dependent, methanogenic, growth could be established by omitting CO2 from the growth medium. Growth rates which were independent of the pyruvate concentration indicated that M. acetivorans actively translocates pyruvate across the cytoplasmic membrane. When 2-bromoethanesulfonate (BES) inhibited methanogenesis to more than 99%, pyruvate-dependent growth was acetogenic and sustained. However, when methanogenesis was completely inhibited M. acetivorans did not grow on pyruvate. Analysis of metabolites showed that acetogenesis is used by BES-inhibited M. acetivorans as a sink for electrons derived from pyruvate oxidation and that other, thus far unidentified, metabolites are produced.IMPORTANCEThe known range of methanogenic growth substrates is very limited and M. acetivorans is only the second methanogenic species for which growth on pyruvate is demonstrated. Besides some commonalities, analysis of M. acetivorans highlights differences in pyruvate metabolism among Methanosarcina species. The observation that M. acetivorans probably imports pyruvate actively indicates that the capabilities for heterotrophic catabolism in methanogens may be underestimated. The mostly acetogenic growth of M. acetivorans on pyruvate with concomitant inhibition of methanogenesis confirms that energy conservation of methanogenic archaea can be independent of methane formation.
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Affiliation(s)
- Marcus Richter
- Fakultät Biologie, Technische Universität Dresden, Dresden, Germany
| | | | - Christian Schöne
- Fakultät Biologie, Technische Universität Dresden, Dresden, Germany
| | - Michael Rother
- Fakultät Biologie, Technische Universität Dresden, Dresden, Germany
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Habenicht T, Weidenbach K, Velazquez-Campoy A, Buey RM, Balsera M, Schmitz RA. Small protein mediates inhibition of ammonium transport in Methanosarcina mazei-an ancient mechanism? Microbiol Spectr 2023; 11:e0281123. [PMID: 37909787 PMCID: PMC10714827 DOI: 10.1128/spectrum.02811-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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: 07/10/2023] [Accepted: 09/29/2023] [Indexed: 11/03/2023] Open
Abstract
IMPORTANCE Small proteins containing fewer than 70 amino acids, which were previously disregarded due to computational prediction and biochemical detection challenges, have gained increased attention in the scientific community in recent years. However, the number of functionally characterized small proteins, especially in archaea, is still limited. Here, by using biochemical and genetic approaches, we demonstrate a crucial role of the small protein sP36 in the nitrogen metabolism of M. mazei, which modulates the ammonium transporter AmtB1 according to nitrogen availability. This modulation might represent an ancient archaeal mechanism of AmtB1 inhibition, in contrast to the well-studied uridylylation-dependent regulation in bacteria.
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Affiliation(s)
- Tim Habenicht
- Institut für allgemeine Mikrobiologie, Christian-Albrechts-Universität zu Kiel, Kiel, Germany
| | - Katrin Weidenbach
- Institut für allgemeine Mikrobiologie, Christian-Albrechts-Universität zu Kiel, Kiel, Germany
| | - Adrian Velazquez-Campoy
- Institute of Biocomputation and Physics of Complex Systems (BIFI), Universidad de Zaragoza, Zaragoza, Spain
- Departamento de Bioquímica y Biología Molecular y Celular, Universidad de Zaragoza, Zaragoza, Spain
- Instituto de Investigaciones Sanitarias de Aragón (IIS Aragón), Zaragoza, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Madrid, Spain
| | - Ruben M. Buey
- Departamento de Microbiología y Genética, Universidad de Salamanca, Salamanca, Spain
| | - Monica Balsera
- Instituto de Recursos Naturales y Agrobiología de Salamanca, Spanish National Research Council (IRNASA-CSIC), Salamanca, Spain
| | - Ruth A. Schmitz
- Institut für allgemeine Mikrobiologie, Christian-Albrechts-Universität zu Kiel, Kiel, Germany
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Huang R, Tang C, Zhao Y, Liu L, Chen J, Shi Z, Yan Z. Unveiling the Biochar-Respiratory Growth of Methanosarcina acetivorans Involving Extracellular Polymeric Substances. Microb Ecol 2023; 86:2970-2980. [PMID: 37684545 DOI: 10.1007/s00248-023-02294-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Accepted: 08/27/2023] [Indexed: 09/10/2023]
Abstract
Biochar can be applied to diverse natural and engineered anaerobic systems. Biochar plays biogeochemical roles during its production, storage, and environmental dynamics, one of which is related to the global methane flux governed by methanotrophs and methanogens. Our understanding of relevant mechanisms is currently limited to the roles of biochar in methanotrophic growth, but less is known about the roles of biochar in methanogenic growth. Here, we demonstrated that biochar enhanced the methanogenic growth of a model methanogen, Methanosarcina acetivorans, and the role of biochar as an electron acceptor during methanogenic growth was confirmed, which is referred to as biochar-respiratory growth. The biochar-respiratory growth of M. acetivorans promoted the secretion of extracellular polymeric substances (EPS) with augmented electron transfer capabilities, and the removal of EPS significantly attenuated extracellular electron transfer. Identification and quantification of prosthetic cofactors for EPS suggest an important role of flavin and F420 in extracellular electron transfer. Transcriptomic analysis provided additional insights into the biochar-respiratory growth of M. acetivorans, showing that there was a positive response in transcriptional regulation to the favorable growth environment provided by biochar, which stimulated global methanogenesis. Our results shed more light on the in situ roles of biochar in the ecophysiology of methanogens in diverse anaerobic environments.
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Affiliation(s)
- Rui Huang
- Shandong Key Laboratory of Water Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Shandong University, Qingdao, 266237, Shandong, China
| | - Chuyan Tang
- Shandong Key Laboratory of Water Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Shandong University, Qingdao, 266237, Shandong, China
| | - Yameng Zhao
- Shandong Key Laboratory of Water Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Shandong University, Qingdao, 266237, Shandong, China
| | - Lina Liu
- Shandong Key Laboratory of Water Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Shandong University, Qingdao, 266237, Shandong, China
| | - Jiazhe Chen
- Shandong Key Laboratory of Water Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Shandong University, Qingdao, 266237, Shandong, China
| | - Zhirui Shi
- Shandong Key Laboratory of Water Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Shandong University, Qingdao, 266237, Shandong, China
| | - Zhen Yan
- Shandong Key Laboratory of Water Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Shandong University, Qingdao, 266237, Shandong, China.
- Suzhou Research Institute, Shandong University, Suzhou, 215123, Jiangsu, China.
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Williams AM, Jolley EA, Santiago-Martínez MG, Chan CX, Gutell RR, Ferry JG, Bevilacqua PC. In vivo structure probing of RNA in Archaea: novel insights into the ribosome structure of Methanosarcina acetivorans. RNA 2023; 29:1610-1620. [PMID: 37491319 PMCID: PMC10578495 DOI: 10.1261/rna.079687.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Accepted: 06/24/2023] [Indexed: 07/27/2023]
Abstract
Structure probing combined with next-generation sequencing (NGS) has provided novel insights into RNA structure-function relationships. To date, such studies have focused largely on bacteria and eukaryotes, with little attention given to the third domain of life, archaea. Furthermore, functional RNAs have not been extensively studied in archaea, leaving open questions about RNA structure and function within this domain of life. With archaeal species being diverse and having many similarities to both bacteria and eukaryotes, the archaea domain has the potential to be an evolutionary bridge. In this study, we introduce a method for probing RNA structure in vivo in the archaea domain of life. We investigated the structure of ribosomal RNA (rRNA) from Methanosarcina acetivorans, a well-studied anaerobic archaeal species, grown with either methanol or acetate. After probing the RNA in vivo with dimethyl sulfate (DMS), Structure-seq2 libraries were generated, sequenced, and analyzed. We mapped the reactivity of DMS onto the secondary structure of the ribosome, which we determined independently with comparative analysis, and confirmed the accuracy of DMS probing in M. acetivorans Accessibility of the rRNA to DMS in the two carbon sources was found to be quite similar, although some differences were found. Overall, this study establishes the Structure-seq2 pipeline in the archaea domain of life and informs about ribosomal structure within M. acetivorans.
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Affiliation(s)
- Allison M Williams
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania 16802, USA
- Center for RNA Molecular Biology, Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Elizabeth A Jolley
- Center for RNA Molecular Biology, Pennsylvania State University, University Park, Pennsylvania 16802, USA
- Department of Chemistry, Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | | | - Cheong Xin Chan
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane QLD 4072, Australia
| | - Robin R Gutell
- Department of Integrative Biology, The University of Texas at Austin, Austin, Texas 78712, USA
| | - James G Ferry
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Philip C Bevilacqua
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania 16802, USA
- Center for RNA Molecular Biology, Pennsylvania State University, University Park, Pennsylvania 16802, USA
- Department of Chemistry, Pennsylvania State University, University Park, Pennsylvania 16802, USA
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Chanderban M, Hill CA, Dhamad AE, Lessner DJ. Expression of V-nitrogenase and Fe-nitrogenase in Methanosarcina acetivorans is controlled by molybdenum, fixed nitrogen, and the expression of Mo-nitrogenase. Appl Environ Microbiol 2023; 89:e0103323. [PMID: 37695043 PMCID: PMC10537573 DOI: 10.1128/aem.01033-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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: 06/20/2023] [Accepted: 07/07/2023] [Indexed: 09/12/2023] Open
Abstract
All nitrogen-fixing bacteria and archaea (diazotrophs) use molybdenum (Mo) nitrogenase to reduce dinitrogen (N2) to ammonia, with some also containing vanadium (V) and iron-only (Fe) nitrogenases that lack Mo. Among diazotrophs, the regulation and usage of the alternative V-nitrogenase and Fe-nitrogenase in methanogens are largely unknown. Methanosarcina acetivorans contains nif, vnf, and anf gene clusters encoding putative Mo-nitrogenase, V-nitrogenase, and Fe-nitrogenase, respectively. This study investigated nitrogenase expression and growth by M. acetivorans in response to fixed nitrogen, Mo/V availability, and CRISPRi repression of the nif, vnf, and/or anf gene clusters. The availability of Mo and V significantly affected growth of M. acetivorans with N2 but not with NH4Cl. M. acetivorans exhibited the fastest growth rate and highest cell yield during growth with N2 in medium containing Mo, and the slowest growth in medium lacking Mo and V. qPCR analysis revealed the transcription of the nif operon is only moderately affected by depletion of fixed nitrogen and Mo, whereas vnf and anf transcription increased significantly when fixed nitrogen and Mo were depleted, with removal of Mo being key. Immunoblot analysis revealed Mo-nitrogenase is detected when fixed nitrogen is depleted regardless of Mo availability, while V-nitrogenase and Fe-nitrogenase are detected only in the absence of fixed nitrogen and Mo. CRISPRi repression studies revealed that V-nitrogenase and/or Fe-nitrogenase are required for Mo-independent diazotrophy, and unexpectedly that the expression of Mo-nitrogenase is also required. These results reveal that alternative nitrogenase production in M. acetivorans is tightly controlled and dependent on Mo-nitrogenase expression. IMPORTANCE Methanogens and closely related methanotrophs are the only archaea known or predicted to possess nitrogenase. Methanogens play critical roles in both the global biological nitrogen and carbon cycles. Moreover, methanogens are an ancient microbial lineage and nitrogenase likely originated in methanogens. An understanding of the usage and properties of nitrogenases in methanogens can provide new insight into the evolution of nitrogen fixation and aid in the development nitrogenase-based biotechnology. This study provides the first evidence that a methanogen can produce all three forms of nitrogenases, including simultaneously. The results reveal components of Mo-nitrogenase regulate or are needed to produce V-nitrogenase and Fe-nitrogenase in methanogens, a result not seen in bacteria. Overall, this study provides a foundation to understand the assembly, regulation, and activity of the alternative nitrogenases in methanogens.
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Affiliation(s)
- Melissa Chanderban
- Department of Biological Sciences, University of Arkansas-Fayetteville, Fayetteville, Arkansas, USA
| | - Christopher A. Hill
- Department of Biological Sciences, University of Arkansas-Fayetteville, Fayetteville, Arkansas, USA
| | - Ahmed E. Dhamad
- Department of Biological Sciences, University of Arkansas-Fayetteville, Fayetteville, Arkansas, USA
- Department of Biological Sciences, Wasit University, Wasit, Iraq
| | - Daniel J. Lessner
- Department of Biological Sciences, University of Arkansas-Fayetteville, Fayetteville, Arkansas, USA
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Saini J, Deere TM, Lessner DJ. The minimal SUF system is not required for Fe-S cluster biogenesis in the methanogenic archaeon Methanosarcina acetivorans. Sci Rep 2023; 13:15120. [PMID: 37704679 PMCID: PMC10500019 DOI: 10.1038/s41598-023-42400-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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: 08/03/2023] [Accepted: 09/09/2023] [Indexed: 09/15/2023] Open
Abstract
Iron-sulfur (Fe-S) proteins are essential for the ability of methanogens to carry out methanogenesis and biological nitrogen fixation (diazotrophy). Nonetheless, the factors involved in Fe-S cluster biogenesis in methanogens remain largely unknown. The minimal SUF Fe-S cluster biogenesis system (i.e., SufBC) is postulated to serve as the primary system in methanogens. Here, the role of SufBC in Methanosarcina acetivorans, which contains two sufCB gene clusters, was investigated. The CRISPRi-dCas9 and CRISPR-Cas9 systems were utilized to repress or delete sufC1B1 and sufC2B2, respectively. Neither the dual repression of sufC1B1 and sufC2B2 nor the deletion of both sufC1B1 and sufC2B2 affected the growth of M. acetivorans under any conditions tested, including diazotrophy. Interestingly, deletion of only sufC1B1 led to a delayed-growth phenotype under all growth conditions, suggesting that the deletion of sufC2B2 acts as a suppressor mutation in the absence of sufC1B1. In addition, the deletion of sufC1B1 and/or sufC2B2 did not affect the total Fe-S cluster content in M. acetivorans cells. Overall, these results reveal that the minimal SUF system is not required for Fe-S cluster biogenesis in M. acetivorans and challenge the universal role of SufBC in Fe-S cluster biogenesis in methanogens.
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Affiliation(s)
- Jasleen Saini
- Department of Biological Sciences, University of Arkansas-Fayetteville, Fayetteville, AR, USA
| | - Thomas M Deere
- Department of Biological Sciences, University of Arkansas-Fayetteville, Fayetteville, AR, USA
| | - Daniel J Lessner
- Department of Biological Sciences, University of Arkansas-Fayetteville, Fayetteville, AR, USA.
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Schöne C, Poehlein A, Rother M. Genetic and Physiological Probing of Cytoplasmic Bypasses for the Energy-Converting Methyltransferase Mtr in Methanosarcina acetivorans. Appl Environ Microbiol 2023; 89:e0216122. [PMID: 37347168 PMCID: PMC10370330 DOI: 10.1128/aem.02161-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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: 12/21/2022] [Accepted: 06/01/2023] [Indexed: 06/23/2023] Open
Abstract
Methanogenesis is a unique energy metabolism carried out by members of the domain Archaea. Unlike most other methanogens, which reduce CO2 to methane with hydrogen as the electron donor, Methanosarcina acetivorans is able to grow on methylated compounds, on acetate, and on carbon monoxide (CO). These substrates are metabolized via distinct yet overlapping pathways. For the use of any single methanogenic substrate, the membrane-integral, energy-converting N5-methyl-tetrahydrosarcinapterin (H4SPT):coenzyme M (HS-CoM) methyltransferase (Mtr) is required. It was proposed that M. acetivorans can bypass the methyl transfer catalyzed by Mtr via cytoplasmic activities. To address this issue, conversion of different energy substrates by an mtr deletion mutant was analyzed. No significant methyl transfer from H4SPT to HS-CoM could be detected with CO as the electron donor. In contrast, formation of methane and CO2 in the presence of methanol or trimethylamine was indicative of an Mtr bypass in the oxidative direction. As methane thiol and dimethyl sulfide were transiently produced during methylotrophic methanogenesis in the mtr mutant, involvement in this process of methyl sulfide-dependent methyltransferases (Mts) was analyzed in a strain lacking both the Mts system and Mtr. It could be unequivocally demonstrated that the Mts system is not involved in bypassing Mtr, thereby ruling out previous proposals. Conversion of [13C]methanol indicated that in the absence of Mtr M. acetivorans provides the reducing equivalents for methyl-S-CoM reduction to methane by oxidizing (an) intracellular compound(s) to CO2 rather than disproportioning the source of methyl groups. Thus, no in vivo Mtr bypass appears to exist in M. acetivorans. IMPORTANCE Methanogenic archaea possess only a limited number of chemiosmotic coupling sites in their respiratory chains. Among them, N5-methyl-H4SPT:HS-CoM methyltransferase (Mtr) is the most widely distributed. Previous observations led to the conclusion that Methanosarcina acetivorans is able to bypass this reaction via methyl sulfide-dependent methyltransferases (Mts). However, strains lacking Mtr are not able to produce methane from CO. Also, these strains are unable to oxidize methylated substrates to CO2, in contrast to observations in the close relative Methanosarcina barkeri. The results also highlight the sole function of the Mts system in methyl sulfide metabolism. Thus, no in vivo Mtr bypass appears to exist in M. acetivorans.
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Affiliation(s)
- Christian Schöne
- Fakultät Biologie, Technische Universität Dresden, Dresden, Germany
| | - Anja Poehlein
- Department of Genomic and Applied Microbiology, Georg-August-Universität Göttingen, Göttingen, Germany
| | - Michael Rother
- Fakultät Biologie, Technische Universität Dresden, Dresden, Germany
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Taylor CJ, Hardy FJ, Burke AJ, Bednar RM, Mehl RA, Green AP, Lovelock SL. Engineering mutually orthogonal PylRS/tRNA pairs for dual encoding of functional histidine analogues. Protein Sci 2023; 32:e4640. [PMID: 37051694 PMCID: PMC10127257 DOI: 10.1002/pro.4640] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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: 01/31/2023] [Revised: 04/06/2023] [Accepted: 04/09/2023] [Indexed: 04/14/2023]
Abstract
The availability of an expanded genetic code opens exciting new opportunities in enzyme design and engineering. In this regard histidine analogues have proven particularly versatile, serving as ligands to augment metalloenzyme function and as catalytic nucleophiles in designed enzymes. The ability to genetically encode multiple functional residues could greatly expand the range of chemistry accessible within enzyme active sites. Here, we develop mutually orthogonal translation components to selectively encode two structurally similar histidine analogues. Transplanting known mutations from a promiscuous Methanosarcina mazei pyrrolysyl-tRNA synthetase (MmPylRSIFGFF ) into a single domain PylRS from Methanomethylophilus alvus (MaPylRSIFGFF ) provided a variant with improved efficiency and specificity for 3-methyl-L-histidine (MeHis) incorporation. The MaPylRSIFGFF clone was further characterized using in vitro biochemical assays and x-ray crystallography. We subsequently engineered the orthogonal MmPylRS for activity and selectivity for 3-(3-pyridyl)-L-alanine (3-Pyr), which was used in combination with MaPylRSIFGFF to produce proteins containing both 3-Pyr and MeHis. Given the versatile roles played by histidine in enzyme mechanisms, we anticipate that the tools developed within this study will underpin the development of enzymes with new and enhanced functions.
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Affiliation(s)
- Christopher J. Taylor
- Manchester Institute of Biotechnology, School of Chemistry, University of ManchesterManchesterUK
| | - Florence J. Hardy
- Manchester Institute of Biotechnology, School of Chemistry, University of ManchesterManchesterUK
| | - Ashleigh J. Burke
- Manchester Institute of Biotechnology, School of Chemistry, University of ManchesterManchesterUK
| | - Riley M. Bednar
- Department of Biochemistry and BiophysicsOregon State UniversityCorvallisOregonUSA
| | - Ryan A. Mehl
- Department of Biochemistry and BiophysicsOregon State UniversityCorvallisOregonUSA
| | - Anthony P. Green
- Manchester Institute of Biotechnology, School of Chemistry, University of ManchesterManchesterUK
| | - Sarah L. Lovelock
- Manchester Institute of Biotechnology, School of Chemistry, University of ManchesterManchesterUK
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Yanagisawa T, Seki E, Tanabe H, Fujii Y, Sakamoto K, Yokoyama S. Crystal Structure of Pyrrolysyl-tRNA Synthetase from a Methanogenic Archaeon ISO4-G1 and Its Structure-Based Engineering for Highly-Productive Cell-Free Genetic Code Expansion with Non-Canonical Amino Acids. Int J Mol Sci 2023; 24:ijms24076256. [PMID: 37047230 PMCID: PMC10094482 DOI: 10.3390/ijms24076256] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Revised: 03/22/2023] [Accepted: 03/24/2023] [Indexed: 03/29/2023] Open
Abstract
Pairs of pyrrolysyl-tRNA synthetase (PylRS) and tRNAPyl from Methanosarcina mazei and Methanosarcina barkeri are widely used for site-specific incorporations of non-canonical amino acids into proteins (genetic code expansion). Previously, we achieved full productivity of cell-free protein synthesis for bulky non-canonical amino acids, including Nε-((((E)-cyclooct-2-en-1-yl)oxy)carbonyl)-L-lysine (TCO*Lys), by using Methanomethylophilus alvus PylRS with structure-based mutations in and around the amino acid binding pocket (first-layer and second-layer mutations, respectively). Recently, the PylRS·tRNAPyl pair from a methanogenic archaeon ISO4-G1 was used for genetic code expansion. In the present study, we determined the crystal structure of the methanogenic archaeon ISO4-G1 PylRS (ISO4-G1 PylRS) and compared it with those of structure-known PylRSs. Based on the ISO4-G1 PylRS structure, we attempted the site-specific incorporation of Nε-(p-ethynylbenzyloxycarbonyl)-L-lysine (pEtZLys) into proteins, but it was much less efficient than that of TCO*Lys with M. alvus PylRS mutants. Thus, the first-layer mutations (Y125A and M128L) of ISO4-G1 PylRS, with no additional second-layer mutations, increased the protein productivity with pEtZLys up to 57 ± 8% of that with TCO*Lys at high enzyme concentrations in the cell-free protein synthesis.
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Affiliation(s)
- Tatsuo Yanagisawa
- RIKEN Center for Biosystems Dynamics Research, 1-7-22 Suehiro-Cho, Tsurumi, Yokohama 230-0045, Japan;
- RIKEN Cluster for Science, Technology and Innovation Hub, 1-7-22 Suehiro-Cho, Tsurumi, Yokohama 230-0045, Japan; (E.S.); (H.T.)
- Correspondence: (T.Y.); (S.Y.); Tel.: +81-45-503-9196 (S.Y.)
| | - Eiko Seki
- RIKEN Cluster for Science, Technology and Innovation Hub, 1-7-22 Suehiro-Cho, Tsurumi, Yokohama 230-0045, Japan; (E.S.); (H.T.)
| | - Hiroaki Tanabe
- RIKEN Cluster for Science, Technology and Innovation Hub, 1-7-22 Suehiro-Cho, Tsurumi, Yokohama 230-0045, Japan; (E.S.); (H.T.)
| | - Yoshifumi Fujii
- RIKEN Cluster for Science, Technology and Innovation Hub, 1-7-22 Suehiro-Cho, Tsurumi, Yokohama 230-0045, Japan; (E.S.); (H.T.)
| | - Kensaku Sakamoto
- RIKEN Center for Biosystems Dynamics Research, 1-7-22 Suehiro-Cho, Tsurumi, Yokohama 230-0045, Japan;
| | - Shigeyuki Yokoyama
- RIKEN Cluster for Science, Technology and Innovation Hub, 1-7-22 Suehiro-Cho, Tsurumi, Yokohama 230-0045, Japan; (E.S.); (H.T.)
- Correspondence: (T.Y.); (S.Y.); Tel.: +81-45-503-9196 (S.Y.)
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11
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Gottfried-Lee I, Perona JJ, Karplus PA, Mehl RA, Cooley RB. Structures of Methanomethylophilus alvus Pyrrolysine tRNA-Synthetases Support the Need for De Novo Selections When Altering the Substrate Specificity. ACS Chem Biol 2022; 17:3470-3477. [PMID: 36395426 PMCID: PMC9833844 DOI: 10.1021/acschembio.2c00640] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [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] [Indexed: 11/19/2022]
Abstract
A recently developed genetic code expansion (GCE) platform based on the pyrrolysine amino-acyl tRNA synthetase (PylRS)/tRNAPyl pair from Methanomethylophilus alvus (Ma) has improved solubility and lower susceptibility to proteolysis compared with the homologous and commonly used Methanosarcina barkeri (Mb) and M. mazei (Mm) PylRS GCE platforms. We recently created two new Ma PylRS variants for the incorporation of the fluorescent amino acid, acridonyl-alanine (Acd), into proteins at amber codons: one based on "transplanting" active site mutations from an established high-efficiency Mb PylRS and one that was de novo selected from a library of mutants. Here, we present the crystal structures of these two Ma PylRS variants with Acd/ATP bound to understand why the "active site transplant" variant (Acd-AST) displayed 6-fold worse Acd incorporation efficiency than the de novo selected PylRS (called Acd-RS1). The structures reveal that the Acd-AST binding pocket is too small and binds the three-ring aromatic Acd in a distorted conformation, whereas the more spacious Acd-RS1 active site binds Acd in a relaxed, planar conformation stabilized by a network of solvent-mediated hydrogen bonds. The poor performance of the AST enzyme is ascribed to a shift in the Ma PylRS β-sheet framework relative to that of the Mb enzyme. This illustrates a general reason why "active site transplantation" may not succeed in creating efficient Ma PylRSs for other noncanonical amino acids. This work also provides structural details that will help guide the development of future Ma PylRS/tRNAPyl GCE systems via de novo selection or directed evolution methods.
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Affiliation(s)
- Ilana Gottfried-Lee
- Oregon State University, Department of Biochemistry and Biophysics, 2011 Agricultural and Life Sciences, Corvallis, OR 97331, USA
| | - John J. Perona
- Department of Chemistry, Portland State University, P.O. Box 751, Portland, Oregon 97207, USA
| | - P. Andrew Karplus
- Oregon State University, Department of Biochemistry and Biophysics, 2011 Agricultural and Life Sciences, Corvallis, OR 97331, USA
| | - Ryan A. Mehl
- Oregon State University, Department of Biochemistry and Biophysics, 2011 Agricultural and Life Sciences, Corvallis, OR 97331, USA
| | - Richard B. Cooley
- Oregon State University, Department of Biochemistry and Biophysics, 2011 Agricultural and Life Sciences, Corvallis, OR 97331, USA
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Avila-Crump S, Hemshorn ML, Jones CM, Mbengi L, Meyer K, Griffis JA, Jana S, Petrina GE, Pagar VV, Karplus PA, Petersson EJ, Perona JJ, Mehl RA, Cooley RB. Generating Efficient Methanomethylophilus alvus Pyrrolysyl-tRNA Synthetases for Structurally Diverse Non-Canonical Amino Acids. ACS Chem Biol 2022; 17:3458-3469. [PMID: 36383641 PMCID: PMC9833845 DOI: 10.1021/acschembio.2c00639] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [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] [Indexed: 11/17/2022]
Abstract
Genetic code expansion (GCE) technologies commonly use the pyrrolysyl-tRNA synthetase (PylRS)/tRNAPyl pairs from Methanosarcina mazei (Mm) and Methanosarcina barkeri (Mb) for site-specific incorporation of non-canonical amino acids (ncAAs) into proteins. Recently a homologous PylRS/tRNAPyl pair from Candidatus Methanomethylophilus alvus Mx1201 (Ma) was developed that, lacking the N-terminal tRNA-recognition domain of most PylRSs, overcomes insolubility, instability, and proteolysis issues seen with Mb/Mm PylRSs. An open question is how to alter Ma PylRS specificity to encode specific ncAAs with high efficiency. Prior work focused on "transplanting" ncAA substrate specificity by reconstructing the same active site mutations found in functional Mm/Mb PylRSs in Ma PylRS. Here, we found that this strategy produced low-efficiency Ma PylRSs for encoding three structurally diverse ncAAs: acridonyl-alanine (Acd), 3-nitro-tyrosine, and m-methyl-tetrazinyl-phenylalanine (Tet3.0-Me). On the other hand, efficient Ma PylRS variants were generated by a conventional life/death selection process from a large library of active site mutants: for Acd encoding, one variant was highly functional in HEK293T cells at just 10 μM Acd; for nitroY encoding, two variants also encoded 3-chloro, 3-bromo-, and 3-iodo-tyrosine at high efficiency; and for Tet-3.0-Me, all variants were more functional at lower ncAA concentrations. All Ma PylRS variants identified through selection had at least two different active site residues when compared with their Mb PylRS counterparts. We conclude that Ma and Mm/Mb PylRSs are sufficiently different that "active site transplantation" yields suboptimal Ma GCE systems. This work establishes a paradigm for expanding the utility of the promising Ma PylRS/tRNAPyl GCE platform.
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Affiliation(s)
- Savanna Avila-Crump
- Oregon State University, Department of Biochemistry and Biophysics, 2011 Agricultural and Life Sciences, Corvallis, OR 97331, USA
| | - Marcus L. Hemshorn
- Oregon State University, Department of Biochemistry and Biophysics, 2011 Agricultural and Life Sciences, Corvallis, OR 97331, USA
| | - Chloe M. Jones
- Biochemistry and Molecular Biophysics Graduate Group; University of Pennsylvania; 3700 Hamilton Walk, Philadelphia, PA 19104, USA
| | - Lea Mbengi
- Department of Chemistry, Portland State University, P.O. Box 751, Portland, Oregon 97207, USA
| | - Kyle Meyer
- Department of Chemistry, Portland State University, P.O. Box 751, Portland, Oregon 97207, USA
| | - Joshua A. Griffis
- Oregon State University, Department of Biochemistry and Biophysics, 2011 Agricultural and Life Sciences, Corvallis, OR 97331, USA
| | - Subhashis Jana
- Oregon State University, Department of Biochemistry and Biophysics, 2011 Agricultural and Life Sciences, Corvallis, OR 97331, USA
| | - Grace E. Petrina
- Oregon State University, Department of Biochemistry and Biophysics, 2011 Agricultural and Life Sciences, Corvallis, OR 97331, USA
| | - Vinayak V. Pagar
- Department of Chemistry; University of Pennsylvania; 231 South 34th Street; Philadelphia, PA 19104, USA
| | - P. Andrew Karplus
- Oregon State University, Department of Biochemistry and Biophysics, 2011 Agricultural and Life Sciences, Corvallis, OR 97331, USA
| | - E. James Petersson
- Department of Chemistry; University of Pennsylvania; 231 South 34th Street; Philadelphia, PA 19104, USA
| | - John J. Perona
- Department of Chemistry, Portland State University, P.O. Box 751, Portland, Oregon 97207, USA
| | - Ryan A. Mehl
- Oregon State University, Department of Biochemistry and Biophysics, 2011 Agricultural and Life Sciences, Corvallis, OR 97331, USA
| | - Richard B. Cooley
- Oregon State University, Department of Biochemistry and Biophysics, 2011 Agricultural and Life Sciences, Corvallis, OR 97331, USA
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Yan G, Sun X, Dong Y, Gao W, Gao P, Li B, Yan W, Zhang H, Soleimani M, Yan B, Häggblom MM, Sun W. Vanadate reducing bacteria and archaea may use different mechanisms to reduce vanadate in vanadium contaminated riverine ecosystems as revealed by the combination of DNA-SIP and metagenomic-binning. Water Res 2022; 226:119247. [PMID: 36270146 DOI: 10.1016/j.watres.2022.119247] [Citation(s) in RCA: 4] [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: 06/12/2022] [Revised: 10/09/2022] [Accepted: 10/12/2022] [Indexed: 06/16/2023]
Abstract
Vanadium (V) is a transitional metal that poses health risks to exposed humans. Microorganisms play an important role in remediating V contamination by reducing more toxic and mobile vanadate (V(V)) to less toxic and mobile V(IV). In this study, DNA-stable isotope probing (SIP) coupled with metagenomic-binning was used to identify microorganisms responsible for V(V) reduction and determine potential metabolic mechanisms in cultures inoculated with a V-contaminated river sediment. Anaeromyxobacter and Geobacter spp. were identified as putative V(V)-reducing bacteria, while Methanosarcina spp. were identified as putative V(V)-reducing archaea. The bacteria may use the two nitrate reductases NarG and NapA for respiratory V(V) reduction, as has been demonstrated previously for other species. It is proposed that Methanosarcina spp. may reduce V(V) via anaerobic methane oxidation pathways (AOM-V) rather than via respiratory V(V) reduction performed by their bacterial counterparts, as indicated by the presence of genes associated with anaerobic methane oxidation coupled with metal reduction in the metagenome assembled genome (MAG) of Methanosarcina. Briefly, methane may be oxidized through the "reverse methanogenesis" pathway to produce electrons, which may be further captured by V(V) to promote V(V) reduction. More specially, V(V) reduction by members of Methanosarcina may be driven by electron transport (CoMS-SCoB heterodisulfide reductase (HdrDE), F420H2 dehydrogenases (Fpo), and multi-heme c-type cytochrome (MHC)). The identification of putative V(V)-reducing bacteria and archaea and the prediction of their different pathways for V(V) reduction expand current knowledge regarding the potential fate of V(V) in contaminated sites.
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Affiliation(s)
- Geng Yan
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China; Guangdong-Hong Kong-Macao Joint Laboratory for Environmental Pollution and Control, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China
| | - Xiaoxu Sun
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China; Guangdong-Hong Kong-Macao Joint Laboratory for Environmental Pollution and Control, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China
| | - Yiran Dong
- School of Environmental Studies, China University of Geosciences (Wuhan), Wuhan 430074, China
| | - Wenlong Gao
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China; Guangdong-Hong Kong-Macao Joint Laboratory for Environmental Pollution and Control, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China
| | - Pin Gao
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China; College of Environmental Science and Engineering, Donghua University, Shanghai 201620, China
| | - Baoqin Li
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China; Guangdong-Hong Kong-Macao Joint Laboratory for Environmental Pollution and Control, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China
| | - Wangwang Yan
- State Key Laboratory of Biocontrol, School of Ecology, Sun Yat-Sen University, Shenzhen, Guangdong, 518107, China
| | - Haihan Zhang
- Shaanxi Key Laboratory of Environmental Engineering, School of Environmental and Municipal Engineering, Xi'an University of Architecture and Technology, Xi'an 710055, China
| | - Mohsen Soleimani
- Department of Natural Resources, Isfahan University of Technology, 8415683111, Isfahan, Iran
| | - Bei Yan
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China; Guangdong-Hong Kong-Macao Joint Laboratory for Environmental Pollution and Control, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China
| | - Max M Häggblom
- Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, NJ 08901, United States
| | - Weimin Sun
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China; Guangdong-Hong Kong-Macao Joint Laboratory for Environmental Pollution and Control, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China.
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14
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Thomsen J, Schmitz RA. Generating a Small Shuttle Vector for Effective Genetic Engineering of Methanosarcina mazei Allowed First Insights in Plasmid Replication Mechanism in the Methanoarchaeon. Int J Mol Sci 2022; 23:ijms231911910. [PMID: 36233214 PMCID: PMC9569500 DOI: 10.3390/ijms231911910] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Revised: 10/04/2022] [Accepted: 10/05/2022] [Indexed: 11/16/2022] Open
Abstract
Due to their role in methane production, methanoarchaea are of high ecological relevance and genetic systems have been ever more established in the last two decades. The system for protein expression in Methanosarcina using a comprehensive shuttle vector is established; however, details about its replication mechanism in methanoarchaea remain unknown. Here, we report on a significant optimisation of the rather large shuttle vector pWM321 (8.9 kbp) generated by Metcalf through a decrease in its size by about 35% by means of the deletion of several non-coding regions and the ssrA gene. The resulting plasmid (pRS1595) still stably replicates in M. mazei and—most likely due to its reduced size—shows a significantly higher transformation efficiency compared to pWM321. In addition, we investigate the essential gene repA, coding for a rep type protein. RepA was heterologously expressed in Escherichia coli, purified and characterised, demonstrating the significant binding and nicking activity of supercoiled plasmid DNA. Based on our findings we propose that the optimised shuttle vector replicates via a rolling circle mechanism with RepA as the initial replication protein in Methanosarcina. On the basis of bioinformatic comparisons, we propose the presence and location of a double-strand and a single-strand origin, which need to be further verified.
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Liu XY, Ma JY, Duan JL, Sun XD, Feng LJ, Li XH, Han Y, Zhang KX, Zhang M, Wang Y, Liu MY, Sun YC, Yuan XZ. The surface groups of polystyrene nanoparticles control their interaction with the methanogenic archaeon Methanosarcina acetivorans. Water Res 2022; 223:118993. [PMID: 36007401 DOI: 10.1016/j.watres.2022.118993] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [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: 05/13/2022] [Revised: 07/31/2022] [Accepted: 08/16/2022] [Indexed: 06/15/2023]
Abstract
A better understanding of the interaction between nanoplastics and archaea is crucial to fill the knowledge gaps regarding the ecological safety of nanoplastics. As a vital source for global methane emissions, methanogenic archaea have unique cell membranes that are distinctly different from those in all other forms of life, little is known about their interaction with nanoplastics. Here, we show that polystyrene nanoparticles functionalized with sulfonic acid (PS-SO3H) and amino (PS-NH2) interact with this methanogenic archaeon in distinct ways. Although both of them have no significant phenotype effects on Methanosarcina acetivorans C2A, these nanoparticles could affect DNA-mediated transposition of this methanogenic archaeon, and PS-SO3H also downregulated nitrogen fixation, nitrogen cycle metabolic process, oxidoreductase activity, etc. In addition, both nanoplastics decreased the protein contents in the extracellular polymer substances (EPS), with distinct binding sequences to the functional groups of the EPS. The single particle atomic force microscopy revealed that the force between the amino group and the M. acetivorans C2A was greater than that of sulfonic acid group. Our results exhibit that the surface groups of polystyrene nanoparticles control their risk on the methanogenic archaea, and these effects might influence their contribution on global methane emission.
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Affiliation(s)
- Xiao-Yu Liu
- Shandong Key Laboratory of Environmental Processes and Health, School of Environmental Science and Engineering, Shandong University, 72 Rd. Binhai, Qingdao, Shandong 266237, PR China
| | - Jing-Ya Ma
- Shandong Key Laboratory of Environmental Processes and Health, School of Environmental Science and Engineering, Shandong University, 72 Rd. Binhai, Qingdao, Shandong 266237, PR China
| | - Jian-Lu Duan
- Shandong Key Laboratory of Environmental Processes and Health, School of Environmental Science and Engineering, Shandong University, 72 Rd. Binhai, Qingdao, Shandong 266237, PR China
| | - Xiao-Dong Sun
- Shandong Key Laboratory of Environmental Processes and Health, School of Environmental Science and Engineering, Shandong University, 72 Rd. Binhai, Qingdao, Shandong 266237, PR China
| | - Li-Juan Feng
- Shandong Key Laboratory of Environmental Processes and Health, School of Environmental Science and Engineering, Shandong University, 72 Rd. Binhai, Qingdao, Shandong 266237, PR China; College of Geography and Environment, Shandong Normal University, Jinan, Shandong 250014, PR China
| | - Xiao-Hua Li
- Shandong Key Laboratory of Environmental Processes and Health, School of Environmental Science and Engineering, Shandong University, 72 Rd. Binhai, Qingdao, Shandong 266237, PR China
| | - Yi Han
- Shandong Key Laboratory of Environmental Processes and Health, School of Environmental Science and Engineering, Shandong University, 72 Rd. Binhai, Qingdao, Shandong 266237, PR China
| | - Ke-Xin Zhang
- Shandong Key Laboratory of Environmental Processes and Health, School of Environmental Science and Engineering, Shandong University, 72 Rd. Binhai, Qingdao, Shandong 266237, PR China
| | - Mou Zhang
- Shandong Key Laboratory of Environmental Processes and Health, School of Environmental Science and Engineering, Shandong University, 72 Rd. Binhai, Qingdao, Shandong 266237, PR China
| | - Yue Wang
- Shandong Key Laboratory of Environmental Processes and Health, School of Environmental Science and Engineering, Shandong University, 72 Rd. Binhai, Qingdao, Shandong 266237, PR China
| | - Mei-Yan Liu
- Shandong Key Laboratory of Environmental Processes and Health, School of Environmental Science and Engineering, Shandong University, 72 Rd. Binhai, Qingdao, Shandong 266237, PR China
| | - Yu-Chen Sun
- Shandong Key Laboratory of Environmental Processes and Health, School of Environmental Science and Engineering, Shandong University, 72 Rd. Binhai, Qingdao, Shandong 266237, PR China
| | - Xian-Zheng Yuan
- Shandong Key Laboratory of Environmental Processes and Health, School of Environmental Science and Engineering, Shandong University, 72 Rd. Binhai, Qingdao, Shandong 266237, PR China; Sino-French Research Institute for Ecology and Environment (ISFREE), Shandong University, Qingdao, Shandong 266237, PR China.
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Abstract
Undesirable ammonium concentrations can lead to unstable anaerobic digestion processes, and Methanosarcina spp. are the representative methanogens under inhibition. However, no known work seems to exist for directly exploring the detailed metabolic regulation of pure cultured representative Methanosarcina spp. to ammonium inhibition. We used transcriptomics and proteomics to profile the metabolic regulation of Methanosarcina barkeri to 1, 4, and 7 g N/L of total ammoniacal nitrogen (TAN), where free ammonia concentrations were between 1.5 and 36.1 mg N/L. At the initial stages of ammonium inhibition, the genes participating in the acquisition and assimilation of reduced nitrogen sources showed significant upregulation where the minimal fold change of gene transcription was about 2. Apart from nitrogen metabolism, the transcription of some genes in methanogenesis also significantly increased at the initial stages. For example, the genes encoding alternative heterodisulfide reductase subunits (HdrAB), energy-converting hydrogenase subunit (EchC), and methanophenazine-dependent hydrogenase subunits (VhtAC) were significantly upregulated by at least 2.05 times. For the element translocation at the initial stages, the genes participating in the uptake of ferrous iron, potassium ion, and molybdate were significantly upregulated with a minimal fold change of 2.10. As the cultivation proceeded, the gene encoding the cell division protein subunit (FtsH) was significantly upregulated by 13.0 times at 7 g N/L of TAN; meanwhile, an increment in OD600 was observed at the terminal sampling point of 7 g N/L of TAN. The present study explored the metabolic regulation of M. barkeri in stress response, protein synthesis, signal transduction, nitrogen metabolism, methanogenesis, and element translocation. The results would contribute to the understanding of the metabolic effects of ammonium inhibition on methanogens and have significant practical implication in inhibited anaerobic digestion.
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Affiliation(s)
- Haowen Duan
- State Key Laboratory of Pollution Control and Resource Reuse, Tongji University, Shanghai 200092, China
| | - Pinjing He
- Institute of Waste Treatment and Reclamation, Tongji University, Shanghai 200092, China
- Shanghai Multi-Source Solid Waste Collaborative Treatment and Energy Engineering Technology Research Center, Shanghai 200092, China
| | - Hua Zhang
- State Key Laboratory of Pollution Control and Resource Reuse, Tongji University, Shanghai 200092, China
- Shanghai Institute of Pollution Control and Ecological Security, Shanghai 200092, China
| | - Liming Shao
- Institute of Waste Treatment and Reclamation, Tongji University, Shanghai 200092, China
| | - Fan Lü
- State Key Laboratory of Pollution Control and Resource Reuse, Tongji University, Shanghai 200092, China
- Shanghai Institute of Pollution Control and Ecological Security, Shanghai 200092, China
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17
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Holmes DE, Zhou J, Ueki T, Woodard T, Lovley DR. Mechanisms for Electron Uptake by Methanosarcina acetivorans during Direct Interspecies Electron Transfer. mBio 2021; 12:e0234421. [PMID: 34607451 PMCID: PMC8546582 DOI: 10.1128/mbio.02344-21] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Accepted: 08/31/2021] [Indexed: 12/13/2022] Open
Abstract
Direct interspecies electron transfer (DIET) between bacteria and methanogenic archaea appears to be an important syntrophy in both natural and engineered methanogenic environments. However, the electrical connections on the outer surface of methanogens and the subsequent processing of electrons for carbon dioxide reduction to methane are poorly understood. Here, we report that the genetically tractable methanogen Methanosarcina acetivorans can grow via DIET in coculture with Geobacter metallireducens serving as the electron-donating partner. Comparison of gene expression patterns in M. acetivorans grown in coculture versus pure-culture growth on acetate revealed that transcripts for the outer-surface multiheme c-type cytochrome MmcA were higher during DIET-based growth. Deletion of mmcA inhibited DIET. The high aromatic amino acid content of M. acetivorans archaellins suggests that they might assemble into electrically conductive archaella. A mutant that could not express archaella was deficient in DIET. However, this mutant grew in DIET-based coculture as well as the archaellum-expressing parental strain in the presence of granular activated carbon, which was previously shown to serve as a substitute for electrically conductive pili as a conduit for long-range interspecies electron transfer in other DIET-based cocultures. Transcriptomic data suggesting that the membrane-bound Rnf, Fpo, and HdrED complexes also play a role in DIET were incorporated into a charge-balanced model illustrating how electrons entering the cell through MmcA can yield energy to support growth from carbon dioxide reduction. The results are the first genetics-based functional demonstration of likely outer-surface electrical contacts for DIET in a methanogen. IMPORTANCE The conversion of organic matter to methane plays an important role in the global carbon cycle and is an effective strategy for converting wastes to a useful biofuel. The reduction of carbon dioxide to methane accounts for approximately a third of the methane produced in anaerobic soils and sediments as well as waste digesters. Potential electron donors for carbon dioxide reduction are H2 or electrons derived from direct interspecies electron transfer (DIET) between bacteria and methanogens. Elucidating the relative importance of these electron donors has been difficult due to a lack of information on the electrical connections on the outer surfaces of methanogens and how they process the electrons received from DIET. Transcriptomic patterns and gene deletion phenotypes reported here provide insight into how a group of Methanosarcina organisms that play an important role in methane production in soils and sediments participate in DIET.
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Affiliation(s)
- Dawn E. Holmes
- Department of Microbiology, University of Massachusetts—Amherst, Amherst, Massachusetts, USA
- Department of Physical and Biological Science, Western New England University, Springfield, Massachusetts, USA
| | - Jinjie Zhou
- Department of Microbiology, University of Massachusetts—Amherst, Amherst, Massachusetts, USA
- Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong, China
| | - Toshiyuki Ueki
- Department of Microbiology, University of Massachusetts—Amherst, Amherst, Massachusetts, USA
| | - Trevor Woodard
- Department of Microbiology, University of Massachusetts—Amherst, Amherst, Massachusetts, USA
| | - Derek R. Lovley
- Department of Microbiology, University of Massachusetts—Amherst, Amherst, Massachusetts, USA
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Kakuk B, Wirth R, Maróti G, Szuhaj M, Rakhely G, Laczi K, Kovács KL, Bagi Z. Early response of methanogenic archaea to H 2 as evaluated by metagenomics and metatranscriptomics. Microb Cell Fact 2021; 20:127. [PMID: 34217274 PMCID: PMC8254922 DOI: 10.1186/s12934-021-01618-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2021] [Accepted: 06/24/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The molecular machinery of the complex microbiological cell factory of biomethane production is not fully understood. One of the process control elements is the regulatory role of hydrogen (H2). Reduction of carbon dioxide (CO2) by H2 is rate limiting factor in methanogenesis, but the community intends to keep H2 concentration low in order to maintain the redox balance of the overall system. H2 metabolism in methanogens becomes increasingly important in the Power-to-Gas renewable energy conversion and storage technologies. RESULTS The early response of the mixed mesophilic microbial community to H2 gas injection was investigated with the goal of uncovering the first responses of the microbial community in the CH4 formation and CO2 mitigation Power-to-Gas process. The overall microbial composition changes, following a 10 min excessive bubbling of H2 through the reactor, was investigated via metagenome and metatranscriptome sequencing. The overall composition and taxonomic abundance of the biogas producing anaerobic community did not change appreciably 2 hours after the H2 treatment, indicating that this time period was too short to display differences in the proliferation of the members of the microbial community. There was, however, a substantial increase in the expression of genes related to hydrogenotrophic methanogenesis of certain groups of Archaea. As an early response to H2 exposure the activity of the hydrogenotrophic methanogenesis in the genus Methanoculleus was upregulated but the hydrogenotrophic pathway in genus Methanosarcina was downregulated. The RT-qPCR data corroborated the metatranscriptomic RESULTS: H2 injection also altered the metabolism of a number of microbes belonging in the kingdom Bacteria. Many Bacteria possess the enzyme sets for the Wood-Ljungdahl pathway. These and the homoacetogens are partners for syntrophic community interactions between the distinct kingdoms of Archaea and Bacteria. CONCLUSIONS External H2 regulates the functional activity of certain Bacteria and Archaea. The syntrophic cross-kingdom interactions in H2 metabolism are important for the efficient operation of the Power-to-Gas process. Therefore, mixed communities are recommended for the large scale Power-to-Gas process rather than single hydrogenotrophic methanogen strains. Fast and reproducible response from the microbial community can be exploited in turn-off and turn-on of the Power-to-Gas microbial cell factories.
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Affiliation(s)
- Balázs Kakuk
- Institute of Medical Biology, University of Szeged, Szeged, Hungary
- Department of Biotechnology, University of Szeged, Szeged, Hungary
| | - Roland Wirth
- Department of Biotechnology, University of Szeged, Szeged, Hungary
- Institute of Plant Biology, Biological Research Center, Szeged, Hungary
| | - Gergely Maróti
- Institute of Plant Biology, Biological Research Center, Szeged, Hungary
| | - Márk Szuhaj
- Department of Biotechnology, University of Szeged, Szeged, Hungary
| | - Gábor Rakhely
- Department of Biotechnology, University of Szeged, Szeged, Hungary
- Institute of Biophysics, Biological Research Center, Szeged, Hungary
| | - Krisztián Laczi
- Department of Biotechnology, University of Szeged, Szeged, Hungary
| | - Kornél L Kovács
- Department of Biotechnology, University of Szeged, Szeged, Hungary.
- Department of Oral Biology and Experimental Dental Research, University of Szeged, Szeged, Hungary.
| | - Zoltán Bagi
- Department of Biotechnology, University of Szeged, Szeged, Hungary.
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19
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Nayak DD, Liu A, Agrawal N, Rodriguez-Carerro R, Dong SH, Mitchell DA, Nair SK, Metcalf WW. Functional interactions between posttranslationally modified amino acids of methyl-coenzyme M reductase in Methanosarcina acetivorans. PLoS Biol 2020; 18:e3000507. [PMID: 32092071 PMCID: PMC7058361 DOI: 10.1371/journal.pbio.3000507] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Revised: 03/05/2020] [Accepted: 02/04/2020] [Indexed: 01/27/2023] Open
Abstract
The enzyme methyl-coenzyme M reductase (MCR) plays an important role in mediating global levels of methane by catalyzing a reversible reaction that leads to the production or consumption of this potent greenhouse gas in methanogenic and methanotrophic archaea. In methanogenic archaea, the alpha subunit of MCR (McrA) typically contains four to six posttranslationally modified amino acids near the active site. Recent studies have identified enzymes performing two of these modifications (thioglycine and 5-[S]-methylarginine), yet little is known about the formation and function of the remaining posttranslationally modified residues. Here, we provide in vivo evidence that a dedicated S-adenosylmethionine-dependent methyltransferase encoded by a gene we designated methylcysteine modification (mcmA) is responsible for formation of S-methylcysteine in Methanosarcina acetivorans McrA. Phenotypic analysis of mutants incapable of cysteine methylation suggests that the S-methylcysteine residue might play a role in adaption to mesophilic conditions. To examine the interactions between the S-methylcysteine residue and the previously characterized thioglycine, 5-(S)-methylarginine modifications, we generated M. acetivorans mutants lacking the three known modification genes in all possible combinations. Phenotypic analyses revealed complex, physiologically relevant interactions between the modified residues, which alter the thermal stability of MCR in a combinatorial fashion that is not readily predictable from the phenotypes of single mutants. High-resolution crystal structures of inactive MCR lacking the modified amino acids were indistinguishable from the fully modified enzyme, suggesting that interactions between the posttranslationally modified residues do not exert a major influence on the static structure of the enzyme but rather serve to fine-tune the activity and efficiency of MCR.
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Affiliation(s)
- Dipti D. Nayak
- Carl R. Woese Institute of Genomic Biology, University of Illinois, Urbana, Illinois, United States of America
- Department of Microbiology, University of Illinois, Urbana, Illinois, United States of America
| | - Andi Liu
- Department of Microbiology, University of Illinois, Urbana, Illinois, United States of America
| | - Neha Agrawal
- Department of Biochemistry, University of Illinois, Urbana, Illinois, United States of America
| | - Roy Rodriguez-Carerro
- Department of Microbiology, University of Illinois, Urbana, Illinois, United States of America
| | - Shi-Hui Dong
- Department of Biochemistry, University of Illinois, Urbana, Illinois, United States of America
| | - Douglas A. Mitchell
- Carl R. Woese Institute of Genomic Biology, University of Illinois, Urbana, Illinois, United States of America
- Department of Microbiology, University of Illinois, Urbana, Illinois, United States of America
- Department of Chemistry, University of Illinois, Urbana, Illinois, United States of America
| | - Satish K. Nair
- Department of Biochemistry, University of Illinois, Urbana, Illinois, United States of America
- Center for Biophysics & Quantitative Biology, University of Illinois, Urbana, Illinois, United States of America
| | - William W. Metcalf
- Carl R. Woese Institute of Genomic Biology, University of Illinois, Urbana, Illinois, United States of America
- Department of Microbiology, University of Illinois, Urbana, Illinois, United States of America
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20
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Nayak DD, Metcalf WW. Methylamine-specific methyltransferase paralogs in Methanosarcina are functionally distinct despite frequent gene conversion. ISME J 2019; 13:2173-2182. [PMID: 31053830 PMCID: PMC6776008 DOI: 10.1038/s41396-019-0428-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Revised: 03/28/2019] [Accepted: 04/03/2019] [Indexed: 11/09/2022]
Abstract
Sequenced archaeal genomes are mostly smaller and more streamlined than typical bacterial genomes; however, members of the Methanosarcina genus within the Euryarchaeaota are a significant exception, with M. acetivorans being the largest archaeal genome (5.8 Mbp) sequenced thus far. This finding is partially explained by extensive gene duplication within Methanosarcina spp. Significantly, the evolutionary pressures leading to gene duplication and subsequent genome expansion have not been well investigated, especially with respect to biological methane production (methanogenesis), which is the key biological trait of these environmentally important organisms. In this study, we address this question by specifically probing the functional evolution of two methylamine-specific methyltransferase paralogs in members of the Methanosarcina genus. Using the genetically tractable strain, M. acetivorans, we first show that the two paralogs have distinct cellular functions: one being required for methanogenesis from methylamine, the other for use of methylamine as a nitrogen source. Subsequently, through comparative sequence analyses, we show that functional divergence of paralogs is primarily mediated by divergent evolution of the 5' regulatory region, despite frequent gene conversion within the coding sequence. This unique evolutionary paradigm for functional divergence of genes post-duplication underscores a divergent role for an enzyme singularly associated with methanogenic metabolism in other aspects of cell physiology.
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Affiliation(s)
- Dipti D Nayak
- Carl R. Woese Institute for Genomic Biology, University of Illinois, 1206 W. Gregory Drive, Urbana, IL, 61801, USA.
| | - William W Metcalf
- Department of Microbiology, University of Illinois, 601 S. Goodwin Avenue, Urbana, IL, 61801, USA
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21
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Tavares NK, Stracey N, Brunold TC, Escalante-Semerena JC. The l-Thr Kinase/l-Thr-Phosphate Decarboxylase (CobD) Enzyme from Methanosarcina mazei Gö1 Contains Metallocenters Needed for Optimal Activity. Biochemistry 2019; 58:3260-3279. [PMID: 31268299 PMCID: PMC6667302 DOI: 10.1021/acs.biochem.9b00268] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [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] [Indexed: 11/30/2022]
Abstract
The MM2060 (cobD) gene from Methanosarcina mazei strain Gö1 encodes a protein (MmCobD) with l-threonine kinase (PduX) and l-threonine-O-3-phosphate decarboxylase (CobD) activities. In addition to the unexpected l-Thr kinase activity, MmCobD has an extended carboxy-terminal (C-terminal) region annotated as a putative metal-binding zinc finger-like domain. Here, we demonstrate that the C-terminus of MmCobD is a ferroprotein containing ∼25 non-heme iron atoms per monomer of protein. The absence of the C-terminus substantially reduces, but does not abolish, enzymatic activities in vitro and in vivo. Single-residue substitutions of C-terminal putative Fe-binding cysteinyl and histidinyl residues resulted in the loss of Fe and changes in enzyme activity levels. Salmonella enterica ΔpduX and ΔcobD strains were used as heterologous hosts to assess coenzyme B12 biosynthesis as a function of 17 MmCobD variants tested. Some of the latter displayed 5-fold higher enzymatic activity in vitro and enhanced the growth rate of the S. enterica strains that synthesized them. Most of the MmCobD variants tested were up to 6-fold less active in vitro and supported slow growth rates of the S. enterica strains that synthesized them; some substitutions abolished enzyme activity. MmCobD exhibited an ultraviolet-visible absorption spectrum consistent with [4Fe-4S] clusters that appeared to be susceptible to oxidation by H2O2 and reduction by sodium dithionite. The presence of FeS clusters in MmCobD was corroborated by electron paramagnetic resonance and magnetic circular dichroism studies. Collectively, our results suggest that MmCobD contains one or more diamagnetic [4Fe-4S]2+ center(s) that may play a structural or regulatory role.
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Affiliation(s)
- Norbert K. Tavares
- Department of Microbiology, University of Georgia, Athens, Georgia 30602, USA
| | - Nuru Stracey
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706 USA
| | - Thomas C Brunold
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706 USA
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22
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Zhang J, Zhao M, Xiao W, Chang L, Wang F, Xu P. Recombinant expression, purification and characterization of acetylated LysargiNase from Escherichia coli with high activity and stability. Rapid Commun Mass Spectrom 2019; 33:1067-1075. [PMID: 30900783 DOI: 10.1002/rcm.8440] [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] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2019] [Revised: 03/14/2019] [Accepted: 03/15/2019] [Indexed: 06/09/2023]
Abstract
RATIONALE LysargiNase is a novel characterized metalloprotease that can cleave the N-terminii of lysine or arginine residues. The peptides generated by LysargiNase are just mirrors to those generated by trypsin. These characteristics of LysargiNase provide a powerful tool for mass spectrometry (MS)-based proteomics research. A highly active and stable LysargiNase produced by an easy and inexpensive method could greatly benefit proteomics research. Here, we report the soluble recombinant expression, purification and acetyl modification of LysargiNase in Escherichia coli. METHODS The coding sequence of LysargiNase with an enterokinase cleavage site at the N-terminus was inserted into plasmid pGEX-4 T-2 and transformed into E. coli BL21 (DE3). The strain was cultured in a 14-L fermenter with a working volume of 5 L. The protein expression was induced by adding isopropyl-β-D-thiogalactoside (IPTG) to a final concentration of 1 mM. The recombinant LysargiNase was loaded onto a GSTrap and an on-column digestion was performed to remove the GST tag and was subsequently purified by chromatographic purification. In vitro acetylation of LysargiNase was performed by using acetic anhydride. The digestion efficiency and specificity of recombinant LysargiNase and acetylated LysargiNase were compared with simple protein substrate, human serum albumin (HSA), and a complex proteomic sample, yeast lysate, by sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) and liquid chromatography/tandem mass spectrometry (LC/MS/MS). RESULTS Highly soluble expression of recombinant LysargiNase was achieved by plasmid pGEX-4 T-2 in E. coli BL21 (DE3). In addition, acetylation of purified LysargiNase significantly increased its resistance to autolysis, which resulted in a more complete digestion of proteomics samples and more identified peptides and proteins by LC/MS/MS. CONCLUSIONS In this study, we constructed a highly soluble expression system for producing recombinant LysargiNase in E. coli, which gave tremendous advantages in the downstream purification process. We also confirmed that acetyl modification can increase the stability and activity of recombinant LysargiNase. The study provided a superior way to produce this powerful tool for proteomics research.
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Affiliation(s)
- Junling Zhang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing) and Beijing Institute of Lifeomics, Beijing, 102206, P. R. China
| | - Mingzhi Zhao
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing) and Beijing Institute of Lifeomics, Beijing, 102206, P. R. China
| | - Weidi Xiao
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing) and Beijing Institute of Lifeomics, Beijing, 102206, P. R. China
| | - Lei Chang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing) and Beijing Institute of Lifeomics, Beijing, 102206, P. R. China
| | - Fuqiang Wang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing) and Beijing Institute of Lifeomics, Beijing, 102206, P. R. China
| | - Ping Xu
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing) and Beijing Institute of Lifeomics, Beijing, 102206, P. R. China
- Guizhou University School of Medicine, Guiyang, 550025, China
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery of Ministry of Education, School of Pharmaceutical Sciences, School of Medicine, Wuhan University, Wuhan, 430072, China
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23
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Garcia A, Roy G, Kiefer C, Wilson S, Marelli M. qPCR assays to quantitate tRNApyl and pylRS expression in engineered cell lines. PLoS One 2019; 14:e0216356. [PMID: 31071154 PMCID: PMC6508675 DOI: 10.1371/journal.pone.0216356] [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] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Accepted: 04/18/2019] [Indexed: 11/18/2022] Open
Abstract
Non-natural amino acids (nnAA) contain unique functional moieties that greatly expand the available tool set for protein engineering. But incorporation of nnAAs requires the function of an orthogonal aminoacyl tRNA synthetase/tRNA pair. Stable cell lines expressing these components have been shown capable of producing gram per liter levels of antibodies with nnAAs. However, little has been reported on the genetic makeup of these cells. To gain a better understanding of the minimal requirements for efficient nnAA incorporation we developed qPCR methods for the quantitation of the key components. Here we describe the development of qPCR assays for the quantification of tRNApyl and pylRS. qPCR was chosen because it provides a large dynamic range, has high specificity for its target, and is a non-radioactive method used routinely for cell line characterization. Designing assays for tRNAs present challenges due to their short length (~72 nucleotides) and high secondary structure. These tRNA assays have a ≥ 5 log dynamic range with the tRNApyl assays being able to discern the mature and unprocessed forms of the tRNApyl. Cell line analysis showed tRNApyl was expressed at higher levels than the CHO-K1 endogenous Met and Phe tRNAs and that >88% of tRNApyl was the mature form.
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Affiliation(s)
- Andrew Garcia
- Department of Antibody Discovery and Protein Engineering, AstraZeneca, Gaithersburg, MD, United States of America
| | - Gargi Roy
- Department of Antibody Discovery and Protein Engineering, AstraZeneca, Gaithersburg, MD, United States of America
| | - Christine Kiefer
- Department of Antibody Discovery and Protein Engineering, AstraZeneca, Gaithersburg, MD, United States of America
| | - Susan Wilson
- Department of Antibody Discovery and Protein Engineering, AstraZeneca, Gaithersburg, MD, United States of America
| | - Marcello Marelli
- Department of Antibody Discovery and Protein Engineering, AstraZeneca, Gaithersburg, MD, United States of America
- * E-mail:
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24
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Sakamoto K, Hayashi A. Synthetic Tyrosine tRNA Molecules with Noncanonical Secondary Structures. Int J Mol Sci 2018; 20:ijms20010092. [PMID: 30587834 PMCID: PMC6337575 DOI: 10.3390/ijms20010092] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Revised: 12/19/2018] [Accepted: 12/22/2018] [Indexed: 12/17/2022] Open
Abstract
The L-shape form of tRNA is maintained by tertiary interactions occurring in the core. Base changes in this domain can cause structural defects and impair tRNA activity. Here, we report on a method to safely engineer structural variations in this domain utilizing the noncanonical scaffold of tRNAPyl. First, we constructed a naïve hybrid between archaeal tRNAPyl and tRNATyr, which consisted of the acceptor and T stems of tRNATyr and the other parts of tRNAPyl. This hybrid tRNA efficiently translated the UAG codon to 3-iodotyrosine in Escherichia coli cells, when paired with a variant of the archaeal tyrosyl-tRNA synthetase. The amber suppression efficiency was slightly lower than that of the “bench-mark” archaeal tRNATyr suppressor assuming the canonical structure. After a series of modifications to this hybrid tRNA, we obtained two artificial types of tRNATyr: ZtRNA had an augmented D (auD) helix in a noncanonical form and the D and T loops bound by the standard tertiary base pairs, and YtRNA had a canonical auD helix and non-standard interloop interactions. It was then suggested that the ZtRNA scaffold could also support the glycylation and glutaminylation of tRNA. The synthetic diversity of tRNA would help create new tRNA–aminoacyl-tRNA synthetase pairs for reprogramming the genetic code.
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Affiliation(s)
- Kensaku Sakamoto
- Laboratory for Nonnatural Amino Acid Technology, RIKEN Center for Biosystems Dynamics Research (BDR), 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan.
| | - Akiko Hayashi
- Laboratory for Nonnatural Amino Acid Technology, RIKEN Center for Biosystems Dynamics Research (BDR), 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan.
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25
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Abstract
Mevalonate kinase (MK) is a key enzyme of the mevalonate pathway, which produces the biosynthetic precursors for steroids, including cholesterol, and isoprenoids, the largest class of natural products. Currently available crystal structures of MK from different organisms depict the enzyme in its unbound, substrate-bound, and inhibitor-bound forms; however, until now no structure has yet been determined of MK bound to its product, 5-phosphomevalonate. Here, we present crystal structures of mevalonate-bound and 5-phosphomevalonate-bound MK from Methanosarcina mazei (MmMK), a methanogenic archaeon. In contrast to the prior structure of a eukaryotic MK bound with mevalonate, we find a striking lack of direct interactions between this archaeal MK and its substrate. Further, these two MmMK structures join the prior structure of the apoenzyme to complete the first suite of structural snapshots that depict unbound, substrate-bound, and product-bound forms of the same MK. With this collection of structures, we now provide additional insight into the catalytic mechanism of this biologically essential enzyme.
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Affiliation(s)
- Bradley R. Miller
- Department of Chemistry, Bryn Mawr College, Bryn Mawr, PA, United States of America
| | - Yan Kung
- Department of Chemistry, Bryn Mawr College, Bryn Mawr, PA, United States of America
- * E-mail:
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26
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Abstract
A methodology to cluster proteins based on their dynamics’ similarity is presented. For each pair of proteins from a dataset, the structures are superimposed, and the Anisotropic Network Model modes of motions are calculated. The twelve slowest modes from each protein are matched using a local mode alignment algorithm based on the local sequence alignment algorithm of Smith–Waterman. The dynamical similarity distance matrix is calculated based on the top scoring matches of each pair and the proteins are clustered using a hierarchical clustering algorithm. The utility of this method is exemplified on a dataset of protein chains from the globin family and a dataset of tetrameric hemoglobins. The results demonstrate the effect of the quaternary structure of globin members on their intrinsic dynamics and show good ability to distinguish between different states of hemoglobin, revealing the dynamical relations between them.
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Affiliation(s)
- Dror Tobi
- Department of Molecular Biology, Ariel University, Ariel, Israel
- Department of Computer Sciences, Ariel University, Ariel, Israel
- * E-mail:
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27
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Holmes DE, Orelana R, Giloteaux L, Wang LY, Shrestha P, Williams K, Lovley DR, Rotaru AE. Potential for Methanosarcina to Contribute to Uranium Reduction during Acetate-Promoted Groundwater Bioremediation. Microb Ecol 2018; 76:660-667. [PMID: 29500492 PMCID: PMC6132540 DOI: 10.1007/s00248-018-1165-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Accepted: 02/16/2018] [Indexed: 05/06/2023]
Abstract
Previous studies of acetate-promoted bioremediation of uranium-contaminated aquifers focused on Geobacter because no other microorganisms that can couple the oxidation of acetate with U(VI) reduction had been detected in situ. Monitoring the levels of methyl CoM reductase subunit A (mcrA) transcripts during an acetate-injection field experiment demonstrated that acetoclastic methanogens from the genus Methanosarcina were enriched after 40 days of acetate amendment. The increased abundance of Methanosarcina corresponded with an accumulation of methane in the groundwater. In order to determine whether Methanosarcina species could be participating in U(VI) reduction in the subsurface, cell suspensions of Methanosarcina barkeri were incubated in the presence of U(VI) with acetate provided as the electron donor. U(VI) was reduced by metabolically active M. barkeri cells; however, no U(VI) reduction was observed in inactive controls. These results demonstrate that Methanosarcina species could play an important role in the long-term bioremediation of uranium-contaminated aquifers after depletion of Fe(III) oxides limits the growth of Geobacter species. The results also suggest that Methanosarcina have the potential to influence uranium geochemistry in a diversity of anaerobic sedimentary environments.
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Affiliation(s)
- Dawn E Holmes
- Department of Physical and Biological Science, Western New England University, Springfield, MA, USA.
- Department of Microbiology, University of Massachusetts Amherst, Amherst, MA, USA.
| | - Roberto Orelana
- Department of Microbiology, University of Massachusetts Amherst, Amherst, MA, USA
| | - Ludovic Giloteaux
- Department of Molecular Biology and Genetics, College of Agriculture and Life Sciences, Cornell University, Ithaca, NY, USA
| | - Li-Ying Wang
- Department of Microbiology, University of Massachusetts Amherst, Amherst, MA, USA
| | - Pravin Shrestha
- Energy Biosciences Institute, University of California Berkeley, Berkeley, CA, USA
| | | | - Derek R Lovley
- Department of Microbiology, University of Massachusetts Amherst, Amherst, MA, USA
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28
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Poirier S, Déjean S, Chapleur O. Support media can steer methanogenesis in the presence of phenol through biotic and abiotic effects. Water Res 2018; 140:24-33. [PMID: 29684699 DOI: 10.1016/j.watres.2018.04.029] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [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: 08/25/2017] [Revised: 04/11/2018] [Accepted: 04/13/2018] [Indexed: 06/08/2023]
Abstract
A wide variety of inhibitors can induce anaerobic digester disruption. To avoid performance losses, support media can be used to mitigate inhibitions. However, distinguishing the physico-chemical from the biological mechanisms of such strategies remains delicate. In this framework, the impact of 10 g/L of different types of zeolites and activated carbons (AC) on microbial community dynamics during anaerobic digestion of biowaste in the presence of 1.3 g/L of phenol was evaluated with 16 S rRNA gene sequencing. In the presence of AC, methanogenesis inhibition was rapidly removed due to a decrease of phenol concentration. This abiotic effect related to the physico-chemical properties of AC led to increased final CH4 and CO2 productions by 29-31% compared to digesters incubated without support. Interestingly, although zeolite did not adsorb phenol, final CH4 and CO2 production reached comparable levels as with AC. Nevertheless, compared to digesters incubated without support, methanogenesis lag phase duration was less reduced in the presence of zeolites (5 ± 1 days) than in the presence of activated carbons (12 ± 2 days). Both types of support induced biotic effects. AC and zeolite both allowed the preservation of the major representative archaeal genus of the non-inhibited ecosystem, Methanosarcina. By contrast, they distinctly shaped bacterial populations. OTUs belonging to class W5 became dominant at the expense of OTUs assigned to orders Clostridiales, Bacteroidales and Anaerolinales in the presence of AC. Zeolite enhanced the implantation of OTUs assigned to bacterial phylum Cloacimonetes. This study highlighted that supports can induce biotic and abiotic effects within digesters inhibited with phenol, showing potentialities to enhance anaerobic digestion stability under disrupting conditions.
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Affiliation(s)
- Simon Poirier
- Hydrosystems and Bioprocesses Research Unit, Irstea, France.
| | - Sébastien Déjean
- Toulouse Mathematics Institute, UMR 5219 CNRS, Toulouse University, Toulouse, France.
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29
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Tavares NK, Zayas CL, Escalante-Semerena JC. The Methanosarcina mazei MM2060 Gene Encodes a Bifunctional Kinase/Decarboxylase Enzyme Involved in Cobamide Biosynthesis. Biochemistry 2018; 57:4478-4495. [PMID: 29950091 PMCID: PMC6143143 DOI: 10.1021/acs.biochem.8b00546] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [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] [Indexed: 01/12/2023]
Abstract
Cobamides (Cbas) are synthesized by many archaea, but some aspects of Cba biosynthesis in these microorganisms remain unclear. Here, we demonstrate that open reading frame MM2060 in the archaeum Methanosarcina mazei strain Gö1 encodes a bifunctional enzyme with l-threonine- O-3-phosphate (l-Thr-P) decarboxylase (EC 4.1.1.81) and l-Thr kinase activities (EC 2.7.1.177). In Salmonella enterica, where Cba biosynthesis has been extensively studied, the activities mentioned above are encoded by separate genes, namely, cobD and pduX, respectively. The activities associated with the MM2060 protein ( MmCobD) were validated in vitro and in vivo. In vitro, MmCobD used ATP and l-Thr as substrates and generated ADP, l-Thr-P, and ( R)-1-aminopropan-2-ol O-phosphate as products. Notably, MmCobD has a 111-amino acid C-terminal extension of unknown function, which contains a putative metal-binding motif. This C-terminal domain alone did not display activity either in vivo or in vitro. Although the C-terminal MmCobD domain was not required for l-Thr-P decarboxylase or l-Thr kinase activities in vivo, its absence negatively affected both activities. In vitro results suggested that this domain may have a regulatory or substrate-gating role. When purified under anoxic conditions, MmCobD displayed Michaelis-Menten kinetics and had a 1000-fold higher affinity for ATP and a catalytic efficiency 1300-fold higher than that of MmCobD purified under oxic conditions. To the best of our knowledge, MmCobD is the first example of a new class of l-Thr-P decarboxylases that also have l-Thr kinase activity. An archaeal protein with l-Thr kinase activity had not been identified prior to this work.
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Affiliation(s)
- Norbert K. Tavares
- Department of Microbiology, University of Georgia, Athens, GA 30602, USA
| | - Carmen L. Zayas
- Department of Bacteriology, University of Wisconsin, Madison, 53706, USA
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Abstract
The majority of archaea encode CRISPR-Cas systems but only a few CRISPR-Cas-based genetic tools have been developed for organisms from this domain. Nayak and Metcalf have harnessed a bacterial Cas9 protein for genome editing in Methanosarcina acetivorans, enabling efficient gene deletion and replacement.
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Affiliation(s)
- Uri Gophna
- Department of Molecular Microbiology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978-01, Israel
| | - Thorsten Allers
- School of Life Sciences, University of Nottingham, Nottingham NG7 2UH, UK
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Abstract
Although Cas9-mediated genome editing has proven to be a powerful genetic tool in eukaryotes, its application in Bacteria has been limited because of inefficient targeting or repair; and its application to Archaea has yet to be reported. Here we describe the development of a Cas9-mediated genome-editing tool that allows facile genetic manipulation of the slow-growing methanogenic archaeon Methanosarcina acetivorans Introduction of both insertions and deletions by homology-directed repair was remarkably efficient and precise, occurring at a frequency of approximately 20% relative to the transformation efficiency, with the desired mutation being found in essentially all transformants examined. Off-target activity was not observed. We also observed that multiple single-guide RNAs could be expressed in the same transcript, reducing the size of mutagenic plasmids and simultaneously simplifying their design. Cas9-mediated genome editing reduces the time needed to construct mutants by more than half (3 vs. 8 wk) and allows simultaneous construction of double mutants with high efficiency, exponentially decreasing the time needed for complex strain constructions. Furthermore, coexpression the nonhomologous end-joining (NHEJ) machinery from the closely related archaeon, Methanocella paludicola, allowed efficient Cas9-mediated genome editing without the need for a repair template. The NHEJ-dependent mutations included deletions ranging from 75 to 2.7 kb in length, most of which appear to have occurred at regions of naturally occurring microhomology. The combination of homology-directed repair-dependent and NHEJ-dependent genome-editing tools comprises a powerful genetic system that enables facile insertion and deletion of genes, rational modification of gene expression, and testing of gene essentiality.
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Affiliation(s)
- Dipti D Nayak
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801
| | - William W Metcalf
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, IL 61801
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Di Maria F, Barratta M, Bianconi F, Placidi P, Passeri D. Solid anaerobic digestion batch with liquid digestate recirculation and wet anaerobic digestion of organic waste: Comparison of system performances and identification of microbial guilds. Waste Manag 2017; 59:172-180. [PMID: 27816470 DOI: 10.1016/j.wasman.2016.10.039] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [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: 08/26/2016] [Revised: 10/24/2016] [Accepted: 10/25/2016] [Indexed: 06/06/2023]
Abstract
Solid anaerobic digestion batch (SADB) with liquid digestate recirculation and wet anaerobic digestion of organic waste were experimentally investigated. SADB was operated at an organic loading rate (OLR) of 4.55kgVS/m3day, generating about 252NL CH4/kgVS, whereas the wet digester was operated at an OLR of 0.9kgVS/m3day, generating about 320NL CH4/kgVS. The initial total volatile fatty acids concentrations for SADB and wet digestion were about 12,500mg/L and 4500mg/L, respectively. There were higher concentrations of ammonium and COD for the SADB compared to the wet one. The genomic analysis performed by high throughput sequencing returned a number of sequences for each sample ranging from 110,619 to 373,307. More than 93% were assigned to the Bacteria domain. Seven and nine major phyla were sequenced for the SADB and wet digestion, respectively, with Bacteroidetes, Firmicutes and Proteobacteria being the dominant phyla in both digesters. Taxonomic profiles suggested a methanogenic pathway characterized by a relevant syntrophic acetate-oxidizing metabolism mainly in the liquid digestate of the SADB. This result also confirms the benefits of liquid digestate recirculation for improving the efficiency of AD performed with high solids (>30%w/w) content.
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Affiliation(s)
- Francesco Di Maria
- LAR Laboratory - Dipartimento di Ingegneria, Via G. Duranti 93, 06125 Perugia, Italy; CIMIS, Via G. Duranti 67, 06125 Perugia, Italy.
| | - Martino Barratta
- LAR Laboratory - Dipartimento di Ingegneria, Via G. Duranti 93, 06125 Perugia, Italy
| | - Francesco Bianconi
- LAR Laboratory - Dipartimento di Ingegneria, Via G. Duranti 93, 06125 Perugia, Italy
| | - Pisana Placidi
- LAR Laboratory - Dipartimento di Ingegneria, Via G. Duranti 93, 06125 Perugia, Italy
| | - Daniele Passeri
- LAR Laboratory - Dipartimento di Ingegneria, Via G. Duranti 93, 06125 Perugia, Italy
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Ahlert S, Zimmermann R, Ebling J, König H. Analysis of propionate-degrading consortia from agricultural biogas plants. Microbiologyopen 2016; 5:1027-1037. [PMID: 27364538 PMCID: PMC5221444 DOI: 10.1002/mbo3.386] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2016] [Revised: 05/24/2016] [Accepted: 05/25/2016] [Indexed: 02/02/2023] Open
Abstract
In order to investigate the propionate-degrading community of agricultural biogas plants, four propionate-degrading consortia (Ap1a, N12, G12, and Wp2a) were established from different biogas plants which were fed with renewable resources. The consortia were cultivated in a batch for a period of 2-4 years and then analyzed in an 8-week batch experiment for microbial succession during propionate degradation. Community shifts showed considerable propagation of Syntrophobacter sulfatireducens, Cryptanaerobacter sp./Pelotomaculum sp., and "Candidatus Cloacamonas sp." in the course of decreasing propionate concentration. Methanogenic species belonged mainly to the genera Methanosarcina, Methanosaeta, and Methanoculleus. Due to the prevalent presence of the syntrophic acetate-oxidizing species Tepidanaerobacter acetatoxydans and potentially autotrophic homoacetogenic bacteria (Moorella sp., Thermacetogenium sp.), a theoretical involvement of syntrophic acetate oxidation and autotrophic homoacetogenesis in stable and efficient propionate degradation was indicated. Considering theoretical Gibbs free energy values at different hydrogen partial pressures, it is noticeable that syntrophic acetate oxidation and autotrophic homoacetogenesis have the potential to counterbalance adverse hydrogen partial pressure fluctuations, stabilizing most probably continuous and stable propionate degradation.
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Affiliation(s)
- Stephan Ahlert
- Institute of Microbiology and Wine ResearchJohannes Gutenberg UniversityMainzGermany
| | - Rita Zimmermann
- Institute of Microbiology and Wine ResearchJohannes Gutenberg UniversityMainzGermany
| | - Johannes Ebling
- Institute of Microbiology and Wine ResearchJohannes Gutenberg UniversityMainzGermany
| | - Helmut König
- Institute of Microbiology and Wine ResearchJohannes Gutenberg UniversityMainzGermany
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Zhou J, Zhang R, Liu F, Yong X, Wu X, Zheng T, Jiang M, Jia H. Biogas production and microbial community shift through neutral pH control during the anaerobic digestion of pig manure. Bioresour Technol 2016; 217:44-49. [PMID: 26944458 DOI: 10.1016/j.biortech.2016.02.077] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [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: 12/30/2015] [Revised: 02/17/2016] [Accepted: 02/19/2016] [Indexed: 06/05/2023]
Abstract
Laboratory-scale reactors, in which the pH could be auto-adjusted, were employed to investigate the mesophilic methane fermentation with pig manure (7.8% total solids) at pH 6.0, 7.0, and 8.0. Results showed that the performance of anaerobic digestion was strongly dependent on pH value. Biogas production and methane content at neutral pH 7.0 were significantly higher (16,607mL, 51.81%) than those at pH 6.0 (6916mL, 42.9%) and 8.0 (9739mL, 35.6%). Denaturing gradient gel electrophoresis fingerprinting and Shannon's index indicated that the samples contained highly diverse microbial communities. The major genus at pH 7.0 was Methanocorpusculum, compared with that was Methanosarcina at both pH 6.0 and 8.0. Our research revealed that cultures maintained at pH 7.0 could support increased biogas production, which has significant implications for the scale-up biogas engineering.
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Affiliation(s)
- Jun Zhou
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211816, China
| | - Rui Zhang
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211816, China
| | - Fenwu Liu
- Environmental Engineering Laboratory, College of Resource and Environment, Shanxi Agricultural University, Taigu 030801, China
| | - Xiaoyu Yong
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211816, China
| | - Xiayuan Wu
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211816, China
| | - Tao Zheng
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211816, China
| | - Min Jiang
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211816, China
| | - Honghua Jia
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211816, China.
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Ernst RJ, Krogager TP, Maywood ES, Zanchi R, Beránek V, Elliott TS, Barry NP, Hastings MH, Chin JW. Genetic code expansion in the mouse brain. Nat Chem Biol 2016; 12:776-778. [PMID: 27571478 PMCID: PMC5215917 DOI: 10.1038/nchembio.2160] [Citation(s) in RCA: 90] [Impact Index Per Article: 11.3] [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] [Received: 04/01/2016] [Accepted: 07/15/2016] [Indexed: 11/08/2022]
Abstract
Site-specific incorporation of non-natural amino acids into proteins, via genetic code expansion with pyrrolysyl tRNA synthetase (PylRS) and tRNA(Pyl)CUA pairs (and their evolved derivatives) from Methanosarcina sp., forms the basis of powerful approaches to probe and control protein function in cells and invertebrate organisms. Here we demonstrate that adeno-associated viral delivery of these pairs enables efficient genetic code expansion in primary neuronal culture, organotypic brain slices and the brains of live mice.
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Affiliation(s)
- Russell J Ernst
- Medical Research Council Laboratory of Molecular Biology, Cambridge, England, UK
| | - Toke P Krogager
- Medical Research Council Laboratory of Molecular Biology, Cambridge, England, UK
| | - Elizabeth S Maywood
- Medical Research Council Laboratory of Molecular Biology, Cambridge, England, UK
| | - Roberto Zanchi
- Medical Research Council Laboratory of Molecular Biology, Cambridge, England, UK
| | - Václav Beránek
- Medical Research Council Laboratory of Molecular Biology, Cambridge, England, UK
| | - Thomas S Elliott
- Medical Research Council Laboratory of Molecular Biology, Cambridge, England, UK
| | - Nicholas P Barry
- Medical Research Council Laboratory of Molecular Biology, Cambridge, England, UK
| | - Michael H Hastings
- Medical Research Council Laboratory of Molecular Biology, Cambridge, England, UK
| | - Jason W Chin
- Medical Research Council Laboratory of Molecular Biology, Cambridge, England, UK
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Ziganshin AM, Schmidt T, Lv Z, Liebetrau J, Richnow HH, Kleinsteuber S, Nikolausz M. Reduction of the hydraulic retention time at constant high organic loading rate to reach the microbial limits of anaerobic digestion in various reactor systems. Bioresour Technol 2016; 217:62-71. [PMID: 26853042 DOI: 10.1016/j.biortech.2016.01.096] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [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: 12/06/2015] [Revised: 01/22/2016] [Accepted: 01/25/2016] [Indexed: 05/27/2023]
Abstract
The effects of hydraulic retention time (HRT) reduction at constant high organic loading rate on the activity of hydrogen-producing bacteria and methanogens were investigated in reactors digesting thin stillage. Stable isotope fingerprinting was additionally applied to assess methanogenic pathways. Based on hydA gene transcripts, Clostridiales was the most active hydrogen-producing order in continuous stirred tank reactor (CSTR), fixed-bed reactor (FBR) and anaerobic sequencing batch reactor (ASBR), but shorter HRT stimulated the activity of Spirochaetales. Further decreasing HRT diminished Spirochaetales activity in systems with biomass retention. Based on mcrA gene transcripts, Methanoculleus and Methanosarcina were the predominantly active in CSTR and ASBR, whereas Methanosaeta and Methanospirillum activity was more significant in stably performing FBR. Isotope values indicated the predominance of aceticlastic pathway in FBR. Interestingly, an increased activity of Methanosaeta was observed during shortening HRT in CSTR and ASBR despite high organic acids concentrations, what was supported by stable isotope data.
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Affiliation(s)
- Ayrat M Ziganshin
- Department of Microbiology, Kazan (Volga Region) Federal University, Kazan 420008, The Republic of Tatarstan, Russia
| | - Thomas Schmidt
- Department of Biochemical Conversion, Deutsches Biomasseforschungszentrum gGmbH, 04347 Leipzig, Germany; Faculty of Agricultural and Environmental Sciences, University of Rostock, 18059 Rostock, Germany
| | - Zuopeng Lv
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research - UFZ, 04318 Leipzig, Germany
| | - Jan Liebetrau
- Department of Biochemical Conversion, Deutsches Biomasseforschungszentrum gGmbH, 04347 Leipzig, Germany
| | - Hans Hermann Richnow
- Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research - UFZ, 04318 Leipzig, Germany
| | - Sabine Kleinsteuber
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research - UFZ, 04318 Leipzig, Germany
| | - Marcell Nikolausz
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research - UFZ, 04318 Leipzig, Germany.
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Ho D, Jensen P, Gutierrez-Zamora ML, Beckmann S, Manefield M, Batstone D. High-rate, High Temperature Acetotrophic Methanogenesis Governed by a Three Population Consortium in Anaerobic Bioreactors. PLoS One 2016; 11:e0159760. [PMID: 27490246 PMCID: PMC4973872 DOI: 10.1371/journal.pone.0159760] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2016] [Accepted: 07/07/2016] [Indexed: 11/18/2022] Open
Abstract
A combination of acetate oxidation and acetoclastic methanogenesis has been previously identified to enable high-rate methanogenesis at high temperatures (55 to 65°C), but this capability had not been linked to any key organisms. This study combined RNA–stable isotope probing on 13C-labelled acetate and 16S amplicon sequencing to identify the active micro-organisms involved in high-rate methanogenesis. Active biomass was harvested from three bench-scale thermophilic bioreactors treating waste activated sludge at 55, 60 and 65°C, and fed with 13-C labelled and 12C-unlabelled acetate. Acetate uptake and cumulative methane production were determined and kinetic parameters were estimated using model-based analysis. Pyrosequencing performed on 13C- enriched samples indicated that organisms accumulating labelled carbon were Coprothermobacter (all temperatures between 55 and 65°C), acetoclastic Methanosarcina (55 to 60°C) and hydrogenotrophic Methanothermobacter (60 to 65°C). The increased relative abundance of Coprothermobacter with increased temperature corresponding with a shift to syntrophic acetate oxidation identified this as a potentially key oxidiser. Methanosarcina likely acts as both a hydrogen utilising and acetoclastic methanogen at 55°C, and is replaced by Methanothermobacter as a hydrogen utiliser at higher temperatures.
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MESH Headings
- Acetates/chemistry
- Acetates/metabolism
- Biomass
- Bioreactors
- Carbon Isotopes
- DNA, Bacterial/chemistry
- DNA, Bacterial/isolation & purification
- DNA, Bacterial/metabolism
- Euryarchaeota/classification
- Euryarchaeota/genetics
- Euryarchaeota/growth & development
- Isotope Labeling
- Kinetics
- Methane/biosynthesis
- Methanosarcina/classification
- Methanosarcina/genetics
- Methanosarcina/growth & development
- Oxidation-Reduction
- Phylogeny
- RNA, Ribosomal, 16S/chemistry
- RNA, Ribosomal, 16S/genetics
- RNA, Ribosomal, 16S/metabolism
- Sequence Analysis, DNA
- Sewage/microbiology
- Temperature
- Thermoanaerobacter/classification
- Thermoanaerobacter/genetics
- Thermoanaerobacter/growth & development
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Affiliation(s)
- Dang Ho
- Advanced Water Management Centre, The University of Queensland, St Lucia, Queensland, Australia
| | - Paul Jensen
- Advanced Water Management Centre, The University of Queensland, St Lucia, Queensland, Australia
| | - Maria-Luisa Gutierrez-Zamora
- Centre for Marine BioInnovation, School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Kensington, New South Wales, Australia
| | - Sabrina Beckmann
- Centre for Marine BioInnovation, School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Kensington, New South Wales, Australia
| | - Mike Manefield
- Centre for Marine BioInnovation, School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Kensington, New South Wales, Australia
| | - Damien Batstone
- Advanced Water Management Centre, The University of Queensland, St Lucia, Queensland, Australia
- * E-mail:
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Poirier S, Desmond-Le Quéméner E, Madigou C, Bouchez T, Chapleur O. Anaerobic digestion of biowaste under extreme ammonia concentration: Identification of key microbial phylotypes. Bioresour Technol 2016; 207:92-101. [PMID: 26874221 DOI: 10.1016/j.biortech.2016.01.124] [Citation(s) in RCA: 93] [Impact Index Per Article: 11.6] [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: 12/22/2015] [Revised: 01/26/2016] [Accepted: 01/31/2016] [Indexed: 06/05/2023]
Abstract
Ammonia inhibition represents a major operational issue for anaerobic digestion (AD). In order to get more insights into AD microbiota resistance, anaerobic batch reactors performances were investigated under a wide range of Total Ammonia Nitrogen (TAN) concentrations up to 50.0g/L at 35°C. The half maximal inhibitory concentration (IC50) value was determined to be 19.0g/L. Microbial community dynamics revealed that above a TAN concentration of 10.0g/L, remarkable modifications within archaeal and bacterial communities occurred. 16S rRNA gene sequencing analysis showed a gradual methanogenic shift between two OTUs from genus Methanosarcina when TAN concentration increased up to 25.0g/L. Proportion of potential syntrophic microorganisms such as Methanoculleus and Treponema progressively raised with increasing TAN up to 10.0 and 25.0g/L respectively, while Syntrophomonas and Ruminococcus groups declined. In 25.0g/L assays, Caldicoprobacter were dominant. This study highlights the emergence of AD key phylotypes at extreme ammonia concentrations.
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Affiliation(s)
- Simon Poirier
- Hydrosystems and Bioprocesses Research Unit, Irstea, 1 rue Pierre-Gilles de Gennes, CS 10030, 92761 Antony Cedex, France.
| | - Elie Desmond-Le Quéméner
- Hydrosystems and Bioprocesses Research Unit, Irstea, 1 rue Pierre-Gilles de Gennes, CS 10030, 92761 Antony Cedex, France
| | - Céline Madigou
- Hydrosystems and Bioprocesses Research Unit, Irstea, 1 rue Pierre-Gilles de Gennes, CS 10030, 92761 Antony Cedex, France
| | - Théodore Bouchez
- Hydrosystems and Bioprocesses Research Unit, Irstea, 1 rue Pierre-Gilles de Gennes, CS 10030, 92761 Antony Cedex, France
| | - Olivier Chapleur
- Hydrosystems and Bioprocesses Research Unit, Irstea, 1 rue Pierre-Gilles de Gennes, CS 10030, 92761 Antony Cedex, France
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Town JR, Dumonceaux TJ. Laboratory-scale bioaugmentation relieves acetate accumulation and stimulates methane production in stalled anaerobic digesters. Appl Microbiol Biotechnol 2015; 100:1009-17. [PMID: 26481626 PMCID: PMC4703610 DOI: 10.1007/s00253-015-7058-3] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2015] [Revised: 09/27/2015] [Accepted: 10/02/2015] [Indexed: 11/26/2022]
Abstract
An imbalance between acidogenic and methanogenic organisms during anaerobic digestion can result in increased accumulation of volatile fatty acids, decreased reactor pH, and inhibition of methane-producing Archaea. Most commonly the result of organic input overload or poor inoculum selection, these microbiological and biochemical changes severely hamper reactor performance, and there are a few tools available to facilitate reactor recovery. A small, stable consortium capable of catabolizing acetate and producing methane was propagated in vitro and evaluated as a potential bioaugmentation tool for stimulating methanogenesis in acidified reactors. Replicate laboratory-scale batch digesters were seeded with a combination of bioethanol stillage waste and a dairy manure inoculum previously observed to result in high volatile fatty acid accumulation and reactor failure. Experimental reactors were then amended with the acetoclastic consortium, and control reactors were amended with sterile culture media. Within 7 days, bioaugmented reactors had significantly reduced acetate accumulation and the proportion of methane in the biogas increased from 0.2 ± 0 to 74.4 ± 9.9 % while control reactors showed no significant reduction in acetate accumulation or increase in methane production. Organisms from the consortium were enumerated using specific quantitative PCR assays to evaluate their growth in the experimental reactors. While the abundance of hydrogenotrophic microorganisms remained stable during the recovery period, an acetoclastic methanogen phylogenetically similar to Methanosarcina sp. increased more than 100-fold and is hypothesized to be the primary contributor to reactor recovery. Genomic sequencing of this organism revealed genes related to the production of methane from acetate, hydrogen, and methanol.
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Affiliation(s)
- Jennifer R Town
- Agriculture and Agri-Food Canada, 107 Science P1, Saskatoon, SK, Canada
- Department of Veterinary Microbiology, WCVM, University of Saskatchewan, Saskatoon, SK, Canada
| | - Tim J Dumonceaux
- Agriculture and Agri-Food Canada, 107 Science P1, Saskatoon, SK, Canada.
- Department of Veterinary Microbiology, WCVM, University of Saskatchewan, Saskatoon, SK, Canada.
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Guo J, Peng Y, Ni BJ, Han X, Fan L, Yuan Z. Dissecting microbial community structure and methane-producing pathways of a full-scale anaerobic reactor digesting activated sludge from wastewater treatment by metagenomic sequencing. Microb Cell Fact 2015; 14:33. [PMID: 25880314 PMCID: PMC4381419 DOI: 10.1186/s12934-015-0218-4] [Citation(s) in RCA: 265] [Impact Index Per Article: 29.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2014] [Accepted: 02/24/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Anaerobic digestion has been widely applied to treat the waste activated sludge from biological wastewater treatment and produce methane for biofuel, which has been one of the most efficient solutions to both energy crisis and environmental pollution challenges. Anaerobic digestion sludge contains highly complex microbial communities, which play crucial roles in sludge treatment. However, traditional approaches based on 16S rRNA amplification or fluorescent in situ hybridization cannot completely reveal the whole microbial community structure due to the extremely high complexity of the involved communities. In this sense, the next-generation high-throughput sequencing provides a powerful tool for dissecting microbial community structure and methane-producing pathways in anaerobic digestion. RESULTS In this work, the metagenomic sequencing was used to characterize microbial community structure of the anaerobic digestion sludge from a full-scale municipal wastewater treatment plant. Over 3.0 gigabases of metagenomic sequence data were generated with the Illumina HiSeq 2000 platform. Taxonomic analysis by MG-RAST server indicated that overall bacteria were dominant (~93%) whereas a considerable abundance of archaea (~6%) were also detected in the anaerobic digestion sludge. The most abundant bacterial populations were found to be Proteobacteria, Firmicutes, Bacteroidetes, and Actinobacteria. Key microorganisms and related pathways involved in methanogenesis were further revealed. The dominant proliferation of Methanosaeta and Methanosarcina, together with the functional affiliation of enzymes-encoding genes (acetate kinase (AckA), phosphate acetyltransferase (PTA), and acetyl-CoA synthetase (ACSS)), suggested that the acetoclastic methanogenesis is the dominant methanogenesis pathway in the full-scale anaerobic digester. CONCLUSIONS In short, the metagenomic sequencing study of this work successfully dissected the detail microbial community structure and the dominated methane-producing pathways of a full-scale anaerobic digester. The knowledge garnered would facilitate to develop more efficient full-scale anaerobic digestion systems to achieve high-rate waste sludge treatment and methane production.
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Affiliation(s)
- Jianhua Guo
- Key Laboratory of Beijing for Water Quality Science and Water Environmental Recovery Engineering, Engineering Research Center of Beijing, Beijing University of Technology, Beijing, 100124, Peoples' Republic of China.
- Advanced Water Management Centre (AWMC), The University of Queensland, St Lucia, Brisbane, QLD, 4072, Australia.
| | - Yongzhen Peng
- Key Laboratory of Beijing for Water Quality Science and Water Environmental Recovery Engineering, Engineering Research Center of Beijing, Beijing University of Technology, Beijing, 100124, Peoples' Republic of China.
| | - Bing-Jie Ni
- Advanced Water Management Centre (AWMC), The University of Queensland, St Lucia, Brisbane, QLD, 4072, Australia.
| | - Xiaoyu Han
- Key Laboratory of Beijing for Water Quality Science and Water Environmental Recovery Engineering, Engineering Research Center of Beijing, Beijing University of Technology, Beijing, 100124, Peoples' Republic of China.
- Beijing Drainage Group Co., Ltd, Beijing, 100022, Peoples' Republic of China.
| | - Lu Fan
- Advanced Water Management Centre (AWMC), The University of Queensland, St Lucia, Brisbane, QLD, 4072, Australia.
| | - Zhiguo Yuan
- Advanced Water Management Centre (AWMC), The University of Queensland, St Lucia, Brisbane, QLD, 4072, Australia.
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Jasso-Chávez R, Santiago-Martínez MG, Lira-Silva E, Pineda E, Zepeda-Rodríguez A, Belmont-Díaz J, Encalada R, Saavedra E, Moreno-Sánchez R. Air-adapted Methanosarcina acetivorans shows high methane production and develops resistance against oxygen stress. PLoS One 2015; 10:e0117331. [PMID: 25706146 PMCID: PMC4338226 DOI: 10.1371/journal.pone.0117331] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2014] [Accepted: 12/22/2014] [Indexed: 12/27/2022] Open
Abstract
Methanosarcina acetivorans, considered a strict anaerobic archaeon, was cultured in the presence of 0.4–1% O2 (atmospheric) for at least 6 months to generate air-adapted cells; further, the biochemical mechanisms developed to deal with O2 were characterized. Methane production and protein content, as indicators of cell growth, did not change in air-adapted cells respect to cells cultured under anoxia (control cells). In contrast, growth and methane production significantly decreased in control cells exposed for the first time to O2. Production of reactive oxygen species was 50 times lower in air-adapted cells versus control cells, suggesting enhanced anti-oxidant mechanisms that attenuated the O2 toxicity. In this regard, (i) the transcripts and activities of superoxide dismutase, catalase and peroxidase significantly increased; and (ii) the thiol-molecules (cysteine + coenzyme M-SH + sulfide) and polyphosphate contents were respectively 2 and 5 times higher in air-adapted cells versus anaerobic-control cells. Long-term cultures (18 days) of air-adapted cells exposed to 2% O2 exhibited the ability to form biofilms. These data indicate that M. acetivorans develops multiple mechanisms to contend with O2 and the associated oxidative stress, as also suggested by genome analyses for some methanogens.
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Affiliation(s)
- Ricardo Jasso-Chávez
- Departamento de Bioquímica, Instituto Nacional de Cardiología Ignacio Chávez, Mexico City, Mexico
- * E-mail:
| | | | - Elizabeth Lira-Silva
- Departamento de Bioquímica, Instituto Nacional de Cardiología Ignacio Chávez, Mexico City, Mexico
| | - Erika Pineda
- Departamento de Bioquímica, Instituto Nacional de Cardiología Ignacio Chávez, Mexico City, Mexico
| | | | - Javier Belmont-Díaz
- Departamento de Bioquímica, Instituto Nacional de Cardiología Ignacio Chávez, Mexico City, Mexico
| | - Rusely Encalada
- Departamento de Bioquímica, Instituto Nacional de Cardiología Ignacio Chávez, Mexico City, Mexico
| | - Emma Saavedra
- Departamento de Bioquímica, Instituto Nacional de Cardiología Ignacio Chávez, Mexico City, Mexico
| | - Rafael Moreno-Sánchez
- Departamento de Bioquímica, Instituto Nacional de Cardiología Ignacio Chávez, Mexico City, Mexico
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Walter A, Franke-Whittle IH, Wagner AO, Insam H. Methane yields and methanogenic community changes during co-fermentation of cattle slurry with empty fruit bunches of oil palm. Bioresour Technol 2015; 175:619-23. [PMID: 25453442 DOI: 10.1016/j.biortech.2014.10.085] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [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: 09/10/2014] [Revised: 10/16/2014] [Accepted: 10/17/2014] [Indexed: 05/28/2023]
Abstract
The biomethane potential and structural changes of the methanogenic community in a solid-state anaerobic digestion process co-digesting cattle slurry and empty fruit bunches were investigated under mesophilic (37°C) and thermophilic (55°C) conditions. Phylogenetic microarrays revealed the presence of two hydrogenotrophic genera (Methanoculleus and Methanobrevibacter) and one acetoclastic genus (Methanosarcina). Methanosarcina numbers were found to increase in both mesophilic and thermophilic treatments of empty fruit bunches. Methanobrevibacter, which dominated in the cattle slurry, remained constant during anaerobic digestion (AD) at 37°C and decreased in numbers during digestion at 55°C. Numbers of Methanoculleus remained constant at 37°C and increased during the thermophilic digestion. Physicochemical data revealed non-critical concentrations for important monitoring parameters such as total ammonia nitrogen, free ammonia nitrogen and volatile fatty acids in all treatments after AD. The biomethane potential of empty fruit bunches was higher under thermophilic conditions than under mesophilic conditions.
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Affiliation(s)
- Andreas Walter
- Institut für Mikrobiologie, Universität Innsbruck, Technikerstraße 25d, 6020 Innsbruck, Austria; Hochschule Hamm-Lippstadt, Biotechnologie, Marker Allee 76-78, 59063 Hamm, Germany
| | - Ingrid H Franke-Whittle
- Institut für Mikrobiologie, Universität Innsbruck, Technikerstraße 25d, 6020 Innsbruck, Austria
| | - Andreas O Wagner
- Institut für Mikrobiologie, Universität Innsbruck, Technikerstraße 25d, 6020 Innsbruck, Austria
| | - Heribert Insam
- Institut für Mikrobiologie, Universität Innsbruck, Technikerstraße 25d, 6020 Innsbruck, Austria
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Wang PP, Sun GX, Zhu YG. Identification and characterization of arsenite methyltransferase from an archaeon, Methanosarcina acetivorans C2A. Environ Sci Technol 2014; 48:12706-12713. [PMID: 25295694 DOI: 10.1021/es503869k] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Arsenic is a ubiquitous toxic contaminant in the environment. The methylation of arsenic can affect its toxicity and is primarily mediated by biological processes. Few studies have focused on the mechanism of arsenic methylation in archaea although archaea are widespread in the environment. Here, an arsenite [As(III)] methyltransferase (ArsM) was identified and characterized from an archaeon Methanosarcina acetivorans C2A. Heterologous expression of MaarsM was shown to confer As(III) resistance to an arsenic-sensitive strain of E. coli through arsenic methylation and subsequent volatilization. Purified MaArsM protein was further identified the function in catalyzing the formation of various methylated products from As(III) in vitro. Methylation of As(III) by MaArsM is highly dependent on the characteristics of the thiol cofactors used, with some of them (coenzyme M, homocysteine, and dithiothreitol) more efficient than GSH. Site-directed mutagenesis demonstrated that three conserved cysteine (Cys) residues (Cys62, Cys150, and Cys200) in MaArsM were necessary for As(III) methylation, of which only Cys150 and Cys200 were required for the methylation of monomethylarsenic. These results present a molecular pathway for arsenic methylation in archaea and provide some insight into the role of archaea in As biogeochemistry.
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Affiliation(s)
- Pei-Pei Wang
- State Key Lab of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences , Beijing 100085, People's Republic of China
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Lieber DJ, Catlett J, Madayiputhiya N, Nandakumar R, Lopez MM, Metcalf WW, Buan NR. A multienzyme complex channels substrates and electrons through acetyl-CoA and methane biosynthesis pathways in Methanosarcina. PLoS One 2014; 9:e107563. [PMID: 25232733 PMCID: PMC4169405 DOI: 10.1371/journal.pone.0107563] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2013] [Accepted: 08/20/2014] [Indexed: 11/25/2022] Open
Abstract
Multienzyme complexes catalyze important metabolic reactions in many organisms, but little is known about the complexes involved in biological methane production (methanogenesis). A crosslinking-mass spectrometry (XL-MS) strategy was employed to identify proteins associated with coenzyme M-coenzyme B heterodisulfide reductase (Hdr), an essential enzyme in all methane-producing archaea (methanogens). In Methanosarcina acetivorans, Hdr forms a multienzyme complex with acetyl-CoA decarbonylase synthase (ACDS), and F420-dependent methylene-H4MPT reductase (Mer). ACDS is essential for production of acetyl-CoA during growth on methanol, or for methanogenesis from acetate, whereas Mer is essential for methanogenesis from all substrates. Existence of a Hdr:ACDS:Mer complex is consistent with growth phenotypes of ACDS and Mer mutant strains in which the complex samples the redox status of electron carriers and directs carbon flux to acetyl-CoA or methanogenesis. We propose the Hdr:ACDS:Mer complex comprises a special class of multienzyme redox complex which functions as a "biological router" that physically links methanogenesis and acetyl-CoA biosynthesis pathways.
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Affiliation(s)
- Dillon J. Lieber
- Department of Biochemistry and Redox Biology Center, University of Nebraska-Lincoln, Lincoln, Nebraska, United States of America
| | - Jennifer Catlett
- Department of Biochemistry and Redox Biology Center, University of Nebraska-Lincoln, Lincoln, Nebraska, United States of America
| | - Nandu Madayiputhiya
- Redox Biology Center Metabolomics Core Facility, University of Nebraska-Lincoln, Lincoln, Nebraska, United States of America
| | - Renu Nandakumar
- Redox Biology Center Metabolomics Core Facility, University of Nebraska-Lincoln, Lincoln, Nebraska, United States of America
| | - Madeline M. Lopez
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
| | - William W. Metcalf
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
| | - Nicole R. Buan
- Department of Biochemistry and Redox Biology Center, University of Nebraska-Lincoln, Lincoln, Nebraska, United States of America
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Yamada C, Kato S, Ueno Y, Ishii M, Igarashi Y. Inhibitory effects of ferrihydrite on a thermophilic methanogenic community. Microbes Environ 2014; 29:227-30. [PMID: 24859310 PMCID: PMC4103531 DOI: 10.1264/jsme2.me14026] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2014] [Accepted: 03/08/2014] [Indexed: 11/12/2022] Open
Abstract
The addition of ferrihydrite to methanogenic microbial communities obtained from a thermophilic anaerobic digester suppressed methanogenesis in a dose-dependent manner. The amount of reducing equivalents consumed by the reduction of iron was significantly smaller than that expected from the decrease in the production of CH4, which suggested that competition between iron-reducing microorganisms and methanogens was not the most significant cause for the suppression of methanogenesis. Microbial community analyses revealed that the presence of ferrihydrite markedly affected the bacterial composition, but not the archaeal composition. These results indicate that the presence of ferrihydrite directly and indirectly suppresses thermophilic methanogenesis.
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MESH Headings
- Anaerobiosis
- Archaea/drug effects
- Archaea/genetics
- Bacteria/drug effects
- Bacteria/genetics
- Bacteria/metabolism
- Base Sequence
- DNA, Archaeal/chemistry
- DNA, Archaeal/genetics
- DNA, Bacterial/chemistry
- DNA, Bacterial/genetics
- Ferric Compounds/pharmacology
- Hot Temperature
- Iron/metabolism
- Methane/metabolism
- Methanobacteriaceae/drug effects
- Methanobacteriaceae/genetics
- Methanobacteriaceae/metabolism
- Methanosarcina/drug effects
- Methanosarcina/genetics
- Methanosarcina/metabolism
- Polymorphism, Restriction Fragment Length
- RNA, Archaeal/chemistry
- RNA, Archaeal/genetics
- RNA, Bacterial/chemistry
- RNA, Bacterial/genetics
- RNA, Ribosomal, 16S/genetics
- Sequence Analysis, DNA
- Sewage/microbiology
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Affiliation(s)
- Chihaya Yamada
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Yayoi 1–1–1, Bunkyo-ku, Tokyo 113–8657, Japan
| | - Souichiro Kato
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, Tsukisamu-Higashi 2–17–2–1, Toyohira, Sapporo, Hokkaido 062–8517, Japan
- Division of Applied Bioscience, Graduate School of Agriculture, Hokkaido University, Kita-9 Nishi-9, Kita-ku, Sapporo, Hokkaido 060–8589, Japan
- Research Center for Advanced Science and Technology, The University of Tokyo, Komaba 4–6–1, Meguro-ku, Tokyo 153–8904, Japan
| | - Yoshiyuki Ueno
- Kajima Technical Research Institute, Tobitakyu 2–19–1, Chofu-shi, Tokyo 182–0036, Japan
| | - Masaharu Ishii
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Yayoi 1–1–1, Bunkyo-ku, Tokyo 113–8657, Japan
| | - Yasuo Igarashi
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Yayoi 1–1–1, Bunkyo-ku, Tokyo 113–8657, Japan
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Cao Y, Li J, Jiang N, Dong X. Mechanism for stabilizing mRNAs involved in methanol-dependent methanogenesis of cold-adaptive Methanosarcina mazei zm-15. Appl Environ Microbiol 2014; 80:1291-8. [PMID: 24317083 PMCID: PMC3911069 DOI: 10.1128/aem.03495-13] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2013] [Accepted: 12/02/2013] [Indexed: 11/20/2022] Open
Abstract
Methylotrophic methanogenesis predominates at low temperatures in the cold Zoige wetland in Tibet. To elucidate the basis of cold-adapted methanogenesis in these habitats, Methanosarcina mazei zm-15 was isolated, and the molecular basis of its cold activity was studied. For this strain, aceticlastic methanogenesis was reduced 7.7-fold during growth at 15°C versus 30°C. Methanol-derived methanogenesis decreased only 3-fold under the same conditions, suggesting that it is more cold adaptive. Reverse transcription-quantitative PCR (RT-qPCR) detected <2-fold difference in the transcript abundances of mtaA1, mtaB1, and mtaC1, the methanol methyltransferase (Mta) genes, in 30°C versus 15°C culture, while ackA and pta mRNAs, encoding acetate kinase (Ack) and phosphotransacetylase (Pta) in aceticlastic methanogenesis, were 4.5- and 6.8-fold higher in 30°C culture than in 15°C culture. The in vivo half-lives of mtaA1 and mtaC1B1 mRNAs were similar in 30°C and 15°C cultures. However, the pta-ackA mRNA half-life was significantly reduced in 15°C culture compared to 30°C culture. Using circularized RNA RT-PCR, large 5' untranslated regions (UTRs) (270 nucleotides [nt] and 238 nt) were identified for mtaA1 and mtaC1B1 mRNAs, while only a 27-nt 5' UTR was present in the pta-ackA transcript. Removal of the 5' UTRs significantly reduced the in vitro half-lives of mtaA1 and mtaC1B1 mRNAs. Remarkably, fusion of the mtaA1 or mtaC1B1 5' UTRs to pta-ackA mRNA increased its in vitro half-life at both 30°C and 15°C. These results demonstrate that the large 5' UTRs significantly enhance the stability of the mRNAs involved in methanol-derived methanogenesis in the cold-adaptive M. mazei zm-15.
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Affiliation(s)
- Yi Cao
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, People's Republic of China
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Lira-Silva E, Santiago-Martínez MG, García-Contreras R, Zepeda-Rodríguez A, Marín-Hernández A, Moreno-Sánchez R, Jasso-Chávez R. Cd2+ resistance mechanisms in Methanosarcina acetivorans involve the increase in the coenzyme M content and induction of biofilm synthesis. Environ Microbiol Rep 2013; 5:799-808. [PMID: 24249288 DOI: 10.1111/1758-2229.12080] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2013] [Accepted: 06/22/2013] [Indexed: 06/02/2023]
Abstract
To assess what defence mechanisms are triggered by Cd(2+) stress in Methanosarcina acetivorans, cells were cultured at different cadmium concentrations. In the presence of 100 μM CdCl2, the intracellular contents of cysteine, sulfide and coenzyme M increased, respectively, 8, 27 and 7 times versus control. Cells incubated for 24 h in medium with less cysteine and sulfide removed up to 80% of Cd(2+) added, whereas their cysteine and coenzyme M contents increased 160 and 84 times respectively. Cadmium accumulation (5.2 μmol/10-15 mg protein) resulted in an increase in methane synthesis of 4.5 times in cells grown on acetate. Total phosphate also increased under high (0.5 mM) Cd(2+) stress. On the other hand, cells preadapted to 54 μM CdCl2 and further exposed to > 0.63 mM CdCl2 developed the formation of a biofilm with an extracellular matrix constituted by carbohydrates, DNA and proteins. Biofilm cells were able to synthesize methane. The data suggested that increased intracellular contents of thiol molecules and total phosphate, and biofilm formation, are all involved in the cadmium resistance mechanisms in this marine archaeon.
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Affiliation(s)
- Elizabeth Lira-Silva
- Departamento de Bioquímica, Instituto Nacional de Cardiología, Mexico City, Mexico
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Novak D, Franke-Whittle IH, Pirc ET, Jerman V, Insam H, Logar RM, Stres B. Biotic and abiotic processes contribute to successful anaerobic degradation of cyanide by UASB reactor biomass treating brewery waste water. Water Res 2013; 47:3644-3653. [PMID: 23726700 DOI: 10.1016/j.watres.2013.04.027] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2012] [Revised: 03/02/2013] [Accepted: 04/08/2013] [Indexed: 06/02/2023]
Abstract
In contrast to the general aerobic detoxification of industrial effluents containing cyanide, anaerobic cyanide degradation is not well understood, including the microbial communities involved. To address this knowledge gap, this study measured anaerobic cyanide degradation and the rearrangements in bacterial and archaeal microbial communities in an upflow anaerobic sludge blanket (UASB) reactor biomass treating brewery waste water using bio-methane potential assays, molecular profiling, sequencing and microarray approaches. Successful biogas formation and cyanide removal without inhibition were observed at cyanide concentrations up to 5 mg l(-1). At 8.5 mg l(-1) cyanide, there was a 22 day lag phase in microbial activity, but subsequent methane production rates were equivalent to when 5 mg l(-1) was used. The higher cumulative methane production in cyanide-amended samples indicated that part of the biogas was derived from cyanide degradation. Anaerobic degradation of cyanide using autoclaved UASB biomass proceeded at a rate more than two times lower than when UASB biomass was not autoclaved, indicating that anaerobic cyanide degradation was in fact a combination of simultaneous abiotic and biotic processes. Phylogenetic analyses of bacterial and archaeal 16S rRNA genes for the first time identified and linked the bacterial phylum Firmicutes and the archaeal genus Methanosarcina sp. as important microbial groups involved in cyanide degradation. Methanogenic activity of unadapted granulated biomass was detected at higher cyanide concentrations than reported previously for the unadapted suspended biomass, making the aggregated structure and predominantly hydrogenotrophic nature of methanogenic community important features in cyanide degradation. The combination of brewery waste water and cyanide substrate was thus shown to be of high interest for industrial level anaerobic cyanide degradation.
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Affiliation(s)
- Domen Novak
- E-Net Okolje, doo, Linhartova 13, SI-1000 Ljubljana, Slovenia
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49
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Xu A, Desai AM, Brenner SE, Kirsch JF. A continuous fluorescence assay for the characterization of Nudix hydrolases. Anal Biochem 2013; 437:178-84. [PMID: 23481913 PMCID: PMC3744803 DOI: 10.1016/j.ab.2013.02.023] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2012] [Revised: 02/16/2013] [Accepted: 02/22/2013] [Indexed: 11/28/2022]
Abstract
The common substrate structure for the functionally diverse Nudix protein superfamily is nucleotide-diphosphate-X, where X is a large variety of leaving groups. The substrate specificity is known for less than 1% of the 29,400 known members. Most activities result in the release of an inorganic phosphate ion or of a product bearing a terminal phosphate moiety. Reactions have typically been monitored by a modification of the discontinuous Fiske-SubbaRow assay, which is relatively insensitive and slow. We report here the development of a continuous fluorescence assay that enables the rapid and accurate determination of substrate specificities in a 96-well format. We used this novel assay to confirm the reported substrate characterizations of MutT and NudD of Escherichia coli and to characterize DR_1025 of Deinococcus radiodurans and MM_0920 of Methanosarcina mazei. Novel findings enabled by the new assay include the following. First, in addition to the well-characterized hydrolysis of 8-oxo-dGTP at the α-β position, MutT cleaves at the β-γ phosphate bond at a rate of 3% of that recorded for hydrolysis at the α-β position. Second, MutT also catalyzes the hydrolysis of 5-methyl-dCTP. Third, 8-oxo-dGTP was observed to be the best substrate for DR_1025 of the 41 compounds screened.
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Affiliation(s)
- Anting Xu
- Department of Comparative Biochemistry, University of California, Berkeley, CA 94720, USA
| | - Anna M. Desai
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA
| | - Steven E. Brenner
- Department of Comparative Biochemistry, University of California, Berkeley, CA 94720, USA
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA
| | - Jack F. Kirsch
- QB3 Institute, University of California, Berkeley, CA 94720, USA
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50
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Pesce A, Tilleman L, Donné J, Aste E, Ascenzi P, Ciaccio C, Coletta M, Moens L, Viappiani C, Dewilde S, Bolognesi M, Nardini M. Structure and haem-distal site plasticity in Methanosarcina acetivorans protoglobin. PLoS One 2013; 8:e66144. [PMID: 23776624 PMCID: PMC3680402 DOI: 10.1371/journal.pone.0066144] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2013] [Accepted: 05/01/2013] [Indexed: 12/04/2022] Open
Abstract
Protoglobin from Methanosarcina acetivorans C2A (MaPgb), a strictly anaerobic methanogenic Archaea, is a dimeric haem-protein whose biological role is still unknown. As other globins, protoglobin can bind O2, CO and NO reversibly in vitro, but it displays specific functional and structural properties within members of the hemoglobin superfamily. CO binding to and dissociation from the haem occurs through biphasic kinetics, which arise from binding to (and dissociation from) two distinct tertiary states in a ligation-dependent equilibrium. From the structural viewpoint, protoglobin-specific loops and a N-terminal extension of 20 residues completely bury the haem within the protein matrix. Thus, access of small ligand molecules to the haem is granted by two apolar tunnels, not common to other globins, which reach the haem distal site from locations at the B/G and B/E helix interfaces. Here, the roles played by residues Trp(60)B9, Tyr(61)B10 and Phe(93)E11 in ligand recognition and stabilization are analyzed, through crystallographic investigations on the ferric protein and on selected mutants. Specifically, protein structures are reported for protoglobin complexes with cyanide, with azide (also in the presence of Xenon), and with more bulky ligands, such as imidazole and nicotinamide. Values of the rate constant for cyanide dissociation from ferric MaPgb-cyanide complexes have been correlated to hydrogen bonds provided by Trp(60)B9 and Tyr(61)B10 that stabilize the haem-Fe(III)-bound cyanide. We show that protoglobin can strikingly reshape, in a ligand-dependent way, the haem distal site, where Phe(93)E11 acts as ligand sensor and controls accessibility to the haem through the tunnel system by modifying the conformation of Trp(60)B9.
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Affiliation(s)
| | - Lesley Tilleman
- Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
| | - Joke Donné
- Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
| | - Elisa Aste
- Department of Physics, University of Genova, Genova, Italy
| | - Paolo Ascenzi
- Interdepartmental Laboratory for Electron Microscopy, University Roma Tre, Roma, Italy
- Institute of Protein Biochemistry, National Research Council (CNR), Napoli, Italy
| | - Chiara Ciaccio
- Department of Clinical Sciences and Translational Medicine, University of Roma “Tor Vergata”, Roma, Italy
- Interuniversity Consortium for the Research on Chemistry of Metals in Biological Systems, Bari, Italy
| | - Massimo Coletta
- Department of Clinical Sciences and Translational Medicine, University of Roma “Tor Vergata”, Roma, Italy
- Interuniversity Consortium for the Research on Chemistry of Metals in Biological Systems, Bari, Italy
| | - Luc Moens
- Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
| | | | - Sylvia Dewilde
- Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
| | - Martino Bolognesi
- Department of Bioscience, University of Milano, Milano, Italy
- National Research Council-Biophysical Institute (CNR-IBF) and Interdisciplinary Centre for Nanostructured Materials and Interfaces (CIMaINa), University of Milano, Milano, Italy
| | - Marco Nardini
- Department of Bioscience, University of Milano, Milano, Italy
- * E-mail:
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