New perspectives for biotechnological applications of methanogens
Tài liệu tham khảo
Aldridge, 2021, Anaerobic production of isoprene by engineered Methanosarcina spp. archaea, Appl. Environ. Microbiol., 87, 10.1128/AEM.02417-20
Angenent, 2004, Production of bioenergy and biochemicals from industrial and agricultural wastewater, Trends Biotechnol., 22, 477, 10.1016/j.tibtech.2004.07.001
Angenent, 2022, Upgrading anaerobic digestion within the energy economy – the methane platform
Bai, 2020, Bioelectrochemical methane production from CO2 by Methanosarcina barkeri via direct and H2-mediated indirect electron transfer, Energy, 210, 10.1016/j.energy.2020.118445
Bang, 2014, The intestinal archaea Methanosphaera stadtmanae and Methanobrevibacter smithii activate human dendritic cells, PLoS ONE, 9, e99411, 10.1371/journal.pone.0099411
Bao, 2022, Efficient CRISPR/Cas12a-based genome-editing toolbox for metabolic engineering in Methanococcus maripaludis, ACS Synth. Biol., 11, 2496, 10.1021/acssynbio.2c00137
Bervoets, 2019, Diversity, versatility and complexity of bacterial gene regulation mechanisms: Opportunities and drawbacks for applications in synthetic biology, FEMS Microbiol. Rev., 43, 304, 10.1093/femsre/fuz001
Blasco-Gómez, 2017, On the edge of research and technological application: A critical review of electromethanogenesis, Int. J. Mol. Sci., 18, 874, 10.3390/ijms18040874
Boone, 2015, Methanothermobacter, Bergey's Manual of Systematics of Archaea and Bacteria, 1
Born, 2021, A synthetic riboswitch to regulate haloarchaeal gene expression, Front. Microbiol., 12, 1566, 10.3389/fmicb.2021.696181
Borrel, 2020, The host-associated archaeome, Nat. Rev. Microbiol., 18, 622, 10.1038/s41579-020-0407-y
Breaker, 2022, The biochemical landscape of riboswitch ligands, Biochemistry, 10.1021/acs.biochem.1c00765
Brugère, 2014
Cheng, 2009, Direct biological conversion of electrical current into methane by electromethanogenesis, Environ. Sci. Technol., 43, 3953, 10.1021/es803531g
Chibani, 2022, A catalogue of 1,167 genomes from the human gut archaeome, Nat. Microbiol., 7, 48, 10.1038/s41564-021-01020-9
Choi, 2016, Extracellular electron transfer from cathode to microbes: Application for biofuel production, Biotechnol. Biofuels, 9, 11, 10.1186/s13068-016-0426-0
De Buck, 2018, Energy transition in europe: the case for gas and gas infrastructure, 23
Demolli, 2014, Development of β- lactamase as a tool for monitoring conditional gene expression by a tetracycline-riboswitch in Methanosarcina acetivorans, Archaea, 2014, 10.1155/2014/725610
Deutzmann, 2017, Enhanced microbial electrosynthesis by using defined co-cultures, The ISME J., 11, 704, 10.1038/ismej.2016.149
Dhamad, A.E., Lessner, D.J., 2020. A CRISPRi-dCas9 system for archaea and its use to examine gene function during nitrogen fixation by Methanosarcina acetivorans. Appl. Environ. Microbiol. 86:e01402-01420.
Enzmann, 2019, Rational Scale-Up of a methane producing bioelectrochemical reactor to 50 L pilot scale, Chem. Eng. Sci., 207, 1148, 10.1016/j.ces.2019.07.051
Enzmann, 2018, Methanogens: Biochemical background and biotechnological applications, AMB Express, 8, 1, 10.1186/s13568-017-0531-x
Enzmann, 2019, Process parameters influence the extracellular electron transfer mechanism in bioelectromethanogenesis, Int. J. Hydrogen Energy, 44, 24450, 10.1016/j.ijhydene.2019.07.039
Fink, 2021, A shuttle-vector system allows heterologous gene expression in the thermophilic methanogen Methanothermobacter thermautotrophicus ΔH, mBio, 12, e02766, 10.1128/mBio.02766-21
Fonseca, 2020, Type IV-like pili facilitate transformation in naturally competent archaea, J. Bacteriol., 202, 10.1128/JB.00355-20
Gernhardt, 1990, Construction of an integration vector for use in the archaebacterium Methanococcus voltae and expression of a eubacterial resistance gene, Mol. Gen. Genet., 221, 273, 10.1007/BF00261731
Goodrich, 2017, The relationship between the human genome and microbiome comes into view, Annu. Rev. Genet., 51, 413, 10.1146/annurev-genet-110711-155532
Gupta, 2019, Riboswitches in archaea, Comb. Chem. High Throughput Screening, 22, 135, 10.2174/1386207322666190425143301
Guss, 2008, New methods for tightly regulated gene expression and highly efficient chromosomal integration of cloned genes for Methanosarcina species, Archaea, 2, 193, 10.1155/2008/534081
Klähn, 2018, A glutamine riboswitch is a key element for the regulation of glutamine synthetase in cyanobacteria, Nucleic Acids Res., 46, 10082
Koeth, 2013, Intestinal microbiota metabolism of L-carnitine, a nutrient in red meat, promotes atherosclerosis, Nat. Med., 19, 576, 10.1038/nm.3145
Kohler, 2012, Genetic manipulation of Methanosarcina spp, Front. Microbiol., 3, 259, 10.3389/fmicb.2012.00259
Kracke, 2020, In situ electrochemical H2 production for efficient and stable power-to-gas electromethanogenesis, Green Chem., 22, 6194, 10.1039/D0GC01894E
Lie, 2002, Regulatory response of Methanococcus maripaludis to alanine, an intermediate nitrogen source, J. Bacteriol., 184, 5301, 10.1128/JB.184.19.5301-5306.2002
Liu, 2008, Metabolic, phylogenetic, and ecological diversity of the methanogenic archaea, Ann. N. Y. Acad. Sci., 1125, 171, 10.1196/annals.1419.019
Logan, 2019, Electroactive microorganisms in bioelectrochemical systems, Nat. Rev. Microbiol., 17, 307, 10.1038/s41579-019-0173-x
Lohner, 2014, Hydrogenase-independent uptake and metabolism of electrons by the archaeon Methanococcus maripaludis, The ISME J., 8, 1673, 10.1038/ismej.2014.82
Lovley, 2017, Happy together: Microbial communities that hook up to swap electrons, The ISME J., 11, 327, 10.1038/ismej.2016.136
Lyu, 2016, Engineering the autotroph Methanococcus maripaludis for geraniol production, ACS Synth. Biol., 5, 577, 10.1021/acssynbio.5b00267
Marshall, 2012, Electrosynthesis of Commodity Chemicals by an Autotrophic Microbial Community, Appl. Environ. Microbiol., 78, 8412, 10.1128/AEM.02401-12
Martin, 2013, A single-culture bioprocess of Methanothermobacter thermautotrophicus to upgrade digester biogas by CO2-to-CH4 conversion with H2, Archaea, 2013, 10.1155/2013/157529
Mayer, 2019, Performance of different methanogenic species for the microbial electrosynthesis of methane from carbon dioxide, Bioresour. Technol., 289, 10.1016/j.biortech.2019.121706
Mondorf, 2012, A novel inducible protein production system and neomycin resistance as selection marker for Methanosarcina mazei, Archaea, 2012
Nayak, D.D., Metcalf, W.W., 2017. Cas9-mediated genome editing in the methanogenic archaeon Methanosarcina acetivorans. Proc. Natl. Acad. Sci., U.S.A. 114:2976–2981.
Pfeifer, K., Ergal, İ., Koller, M., Basen, M., Schuster, B., Rittmann, S.K.M.R., 2020. Archaea biotechnology. Biotechnol. Adv. 107668.
Roßmanith, 2016, Exploring the modular nature of riboswitches and RNA thermometers, Nucleic Acids Res., 44, 5410, 10.1093/nar/gkw232
Rother, 2005, Methanol-dependent gene expression demonstrates that methyl-coenzyme M reductase is essential in Methanosarcina acetivorans C2A and allows isolation of mutants with defects in regulation of the methanol utilization pathway, J. Bacteriol., 187, 5552, 10.1128/JB.187.16.5552-5559.2005
Sarmiento, 2011, Genetic systems for hydrogenotrophic methanogens, Methods Enzymol., 494, 43, 10.1016/B978-0-12-385112-3.00003-2
Schill, 1996, Continuous cultures limited by a gaseous substrate: Development of a simple, unstructured mathematical model and experimental verification with Methanobacterium thermoautotrophicum, Biotechnol. Bioeng., 51, 645, 10.1002/(SICI)1097-0290(19960920)51:6<645::AID-BIT4>3.0.CO;2-H
Schmidt, 2020, Treatments of trimethylaminuria: where we are and where we might be heading, Drug Discovery Today, 25, 1710, 10.1016/j.drudis.2020.06.026
Schöne, C., Poehlein, A., Jehmlich, N., Adlung, N., Daniel, R., von Bergen, M., Scheller, S., Rother, M., 2022. Deconstructing Methanosarcina acetivorans into an acetogenic archaeon. Proc. Natl. Acad. Sci., U.S.A. 119:e2113853119.
Söllinger, 2019, Methylotrophic methanogens everywhere—physiology and ecology of novel players in global methane cycling, Biochem. Soc. Trans., 47, 1895, 10.1042/BST20180565
Speed, M.C., Burkhart, B.W., Picking, J.W., Santangelo, T.J., 2018. An archaeal fluoride-responsive riboswitch provides an inducible expression system for hyperthermophiles. Appl. Environ. Microbiol., 84:e02306-02317.
Sprott, 2011, Archaeal membrane lipids and applications, eLS, 10.1002/9780470015902.a0000385.pub3
Stöckl, 2022, Coupling electrochemical CO2 reduction to microbial product generation – identification of the gaps and opportunities, Curr. Opin. Biotechnol., 74, 154, 10.1016/j.copbio.2021.11.007
Susanti, 2019, A genetic system for Methanocaldococcus jannaschii: An evolutionary deeply rooted hyperthermophilic methanarchaeon, Front. Microbiol., 10, 10.3389/fmicb.2019.01256
Thauer, 1998, Biochemistry of methanogenesis: A tribute to Marjory Stephenson: 1998 Marjory Stephenson Prize Lecture, Microbiology, 144, 2377, 10.1099/00221287-144-9-2377
Thauer, 2008, Methanogenic archaea: Ecologically relevant differences in energy conservation, Nat. Rev. Microbiol., 6, 579, 10.1038/nrmicro1931
Thema, 2019, Power-to-Gas: electrolysis and methanation status review, Renew. Sustain. Energy Rev., 112, 775, 10.1016/j.rser.2019.06.030
Vierbuchen, 2017, The human-associated archaeon Methanosphaera stadtmanae is recognized through its RNA and induces TLR8-dependent NLRP3 inflammasome activation, Front. Immunol., 8, 1535, 10.3389/fimmu.2017.01535
Vinokur, 2014, Evidence of a novel mevalonate pathway in archaea, Biochemistry, 53, 4161, 10.1021/bi500566q
Wagner, 2015, Small RNAs in bacteria and archaea: who they are, what they do, and how they do it, Adv. Genetics, 90, 133, 10.1016/bs.adgen.2015.05.001
Wulf, 2020, Review of power-to-x demonstration projects in Europe, Front. Energy Res., 8, 191, 10.3389/fenrg.2020.00191
Xie, 2021, Synthetic small regulatory RNAs in microbial metabolic engineering, Appl. Microbiol. Biotechnol., 105, 1, 10.1007/s00253-020-10971-8
Zhang, Y., Zhang, Z., Zhang, H., Zhao, Y., Zhang, Z., Xiao, J., 2020. PADS Arsenal: A database of prokaryotic defense systems related genes. Nucleic Acids Res. 48:D590-D598.
