Combining metagenomics with metaproteomics and stable isotope probing reveals metabolic pathways used by a naturally occurring marine methylotroph.
暂无分享,去创建一个
Martin Taubert | Martin von Bergen | Nico Jehmlich | Alexandra M Howat | N. Jehmlich | M. von Bergen | J. Murrell | H. Richnow | Yin Chen | C. Grob | M. Bergen | M. Taubert | Carolina Grob | Oliver J Burns | Joanna L Dixon | Hans H Richnow | Yin Chen | J Colin Murrell | J. Dixon | Alexandra M. Howat | Oliver J. Burns | M. Bergen
[1] Natalia Ivanova,et al. The Expanded Diversity of Methylophilaceae from Lake Washington through Cultivation and Genomic Sequencing of Novel Ecotypes , 2014, PloS one.
[2] J. Murrell,et al. Oxidation of dimethylsulfide to tetrathionate by Methylophaga thiooxidans sp. nov.: a new link in the sulfur cycle. , 2010, Environmental microbiology.
[3] M. Lidstrom,et al. Comparative transcriptomics in three Methylophilaceae species uncover different strategies for environmental adaptation , 2013, PeerJ.
[4] M. Lidstrom,et al. Molecular and mutational analysis of a DNA region separating two methylotrophy gene clusters in Methylobacterium extorquens AM1. , 1997, Microbiology.
[5] P. Steudler,et al. The Methanol Dehydrogenase Gene, mxaF, as a Functional and Phylogenetic Marker for Proteobacterial Methanotrophs in Natural Environments , 2013, PloS one.
[6] Victor Markowitz,et al. High-resolution metagenomics targets specific functional types in complex microbial communities , 2008, Nature Biotechnology.
[7] Steffen Kolb,et al. Prerequisites for amplicon pyrosequencing of microbial methanol utilizers in the environment , 2013, Front. Microbiol..
[8] Martin Taubert,et al. Insights from quantitative metaproteomics and protein-stable isotope probing into microbial ecology , 2013, The ISME Journal.
[9] M. Lidstrom,et al. Construction of insertion and deletion mxa mutants of Methylobacterium extorquens AM1 by electroporation. , 1998, FEMS microbiology letters.
[10] C. Blake,et al. The structure and function of methanol dehydrogenase and related quinoproteins containing pyrrolo-quinoline quinone. , 1994, The Biochemical journal.
[11] Advanced MudPIT as a next step toward high proteome coverage , 2011, Proteomics.
[12] J. Murrell,et al. Bacterial metabolism of methylated amines and identification of novel methylotrophs in Movile Cave , 2014, The ISME Journal.
[13] Knut Reinert,et al. TOPP - the OpenMS proteomics pipeline , 2007, Bioinform..
[14] S. Bryant,et al. Open mass spectrometry search algorithm. , 2004, Journal of proteome research.
[15] Martin Hartmann,et al. Introducing mothur: Open-Source, Platform-Independent, Community-Supported Software for Describing and Comparing Microbial Communities , 2009, Applied and Environmental Microbiology.
[16] S. Kleinsteuber,et al. Protein-SIP enables time-resolved analysis of the carbon flux in a sulfate-reducing, benzene-degrading microbial consortium , 2012, The ISME Journal.
[17] R. Villemur,et al. Methylophaga nitratireducenticrescens sp. nov. and Methylophaga frappieri sp. nov., isolated from the biofilm of the methanol-fed denitrification system treating the seawater at the Montreal Biodome. , 2013, International journal of systematic and evolutionary microbiology.
[18] Daniel Patrick Smith,et al. One Carbon Metabolism in SAR11 Pelagic Marine Bacteria , 2011, PloS one.
[19] Knut Reinert,et al. OpenMS – An open-source software framework for mass spectrometry , 2008, BMC Bioinformatics.
[20] Josh D Neufeld,et al. Marine methylotrophs revealed by stable-isotope probing, multiple displacement amplification and metagenomics. , 2008, Environmental microbiology.
[21] Philip Ineson,et al. Stable-isotope probing as a tool in microbial ecology , 2000, Nature.
[22] V. Davidson. Pyrroloquinoline quinone (PQQ) from methanol dehydrogenase and tryptophan tryptophylquinone (TTQ) from methylamine dehydrogenase. , 2001, Advances in protein chemistry.
[23] J. Murrell,et al. XoxF encoding an alternative methanol dehydrogenase is widespread in coastal marine environments. , 2015, Environmental microbiology.
[24] Sergey I. Nikolenko,et al. SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing , 2012, J. Comput. Biol..
[25] M. Lidstrom,et al. A new cofactor in a prokaryotic enzyme: tryptophan tryptophylquinone as the redox prosthetic group in methylamine dehydrogenase , 1991, Science.
[26] Josh D Neufeld,et al. DNA stable-isotope probing , 2007, Nature Protocols.
[27] Ludmila Chistoserdova,et al. Modularity of methylotrophy, revisited. , 2011, Environmental microbiology.
[28] Lynne A. Goodwin,et al. Genome of Methylobacillus flagellatus, Molecular Basis for Obligate Methylotrophy, and Polyphyletic Origin of Methylotrophy , 2007, Journal of bacteriology.
[29] M. Lidstrom,et al. Analysis of two formaldehyde oxidation pathways in Methylobacillus flagellatus KT, a ribulose monophosphate cycle methylotroph. , 2000, Microbiology.
[30] Sergey I. Nikolenko,et al. BayesHammer: Bayesian clustering for error correction in single-cell sequencing , 2012, BMC Genomics.
[31] Role of EctR as transcriptional regulator of ectoine biosynthesis genes in Methylophaga thalassica , 2012, Biochemistry (Moscow).
[32] Dawn Field,et al. The seasonal structure of microbial communities in the Western English Channel. , 2009, Environmental microbiology.
[33] J. Murrell,et al. The methanol dehydrogenase structural gene mxaF and its use as a functional gene probe for methanotrophs and methylotrophs , 1997, Applied and environmental microbiology.
[34] Ludmila Chistoserdova,et al. The expanding world of methylotrophic metabolism. , 2009, Annual review of microbiology.
[35] Eoin L. Brodie,et al. Greengenes, a Chimera-Checked 16S rRNA Gene Database and Workbench Compatible with ARB , 2006, Applied and Environmental Microbiology.
[36] S. Dowd,et al. Survey of fungi and yeast in polymicrobial infections in chronic wounds. , 2011, Journal of wound care.
[37] Manesh Shah,et al. Environmental proteomics of microbial plankton in a highly productive coastal upwelling system , 2011, The ISME Journal.
[38] Huub J. M. Op den Camp,et al. PQQ-dependent methanol dehydrogenases: rare-earth elements make a difference , 2014, Applied Microbiology and Biotechnology.
[39] F. Grimont,et al. Methylophaga marina gen. nov., sp. nov. and Methylophaga thalassica sp. nov., marine methylotrophs , 1985 .
[40] T. Smyth,et al. Annual study of oxygenated volatile organic compounds in UK shelf waters , 2015 .
[41] Rick L. Stevens,et al. The RAST Server: Rapid Annotations using Subsystems Technology , 2008, BMC Genomics.
[42] Matthew Z. DeMaere,et al. Metaproteogenomic analysis of a dominant green sulfur bacterium from Ace Lake, Antarctica , 2010, The ISME Journal.
[43] V. Davidson,et al. MauG, a diheme enzyme that catalyzes tryptophan tryptophylquinone biosynthesis by remote catalysis. , 2014, Archives of biochemistry and biophysics.
[44] S. Ferriera,et al. Draft Genome Sequence of the Chemolithoheterotrophic, Halophilic Methylotroph Methylophaga thiooxydans DMS010 , 2011, Journal of bacteriology.
[45] P. Nightingale,et al. Microbial methanol uptake in northeast Atlantic waters , 2011, The ISME Journal.
[46] J. Murrell,et al. γ-Glutamylmethylamide Is an Essential Intermediate in the Metabolism of Methylamine by Methylocella silvestris , 2010, Applied and Environmental Microbiology.
[47] J. Tiedje,et al. Naïve Bayesian Classifier for Rapid Assignment of rRNA Sequences into the New Bacterial Taxonomy , 2007, Applied and Environmental Microbiology.
[48] C. Anthony,et al. The methanol oxidation genes mxaFJGIR (S) ACKLD in Methylobacterium extorquens. , 1997, FEMS microbiology letters.
[49] J. Murrell,et al. Metabolic aspects of aerobic obligate methanotrophy. , 2008, Advances in applied microbiology.
[50] M. Dumont,et al. Community-level analysis: key genes of aerobic methane oxidation. , 2005, Methods in enzymology.
[51] T. Barends,et al. Rare earth metals are essential for methanotrophic life in volcanic mudpots. , 2014, Environmental microbiology.
[52] J. R. Quayle,et al. MICROBIAL GROWTH ON C1 COMPOUNDS. SYNTHESIS OF CELL CONSTITUENTS BY METHANE- AND METHANOL-GROWN PSEUDOMONAS METHANICA. , 1965, The Biochemical journal.
[53] H. Schäfer. Isolation of Methylophaga spp. from Marine Dimethylsulfide-Degrading Enrichment Cultures and Identification of Polypeptides Induced during Growth on Dimethylsulfide , 2007, Applied and Environmental Microbiology.
[54] J. Neufeld,et al. Stable-isotope probing implicates Methylophaga spp and novel Gammaproteobacteria in marine methanol and methylamine metabolism , 2007, The ISME Journal.
[55] M. Lidstrom,et al. Novel Formaldehyde-Activating Enzyme inMethylobacterium extorquens AM1 Required for Growth on Methanol , 2000, Journal of bacteriology.
[56] M. Kalyuzhnaya,et al. Genetics of the glutamate‐mediated methylamine utilization pathway in the facultative methylotrophic beta‐proteobacterium Methyloversatilis universalis FAM5 , 2010, Molecular microbiology.
[57] Robert C. Edgar,et al. UPARSE: highly accurate OTU sequences from microbial amplicon reads , 2013, Nature Methods.
[58] N. Shapiro,et al. Multiphyletic origins of methylotrophy in Alphaproteobacteria, exemplified by comparative genomics of Lake Washington isolates. , 2015, Environmental microbiology.
[59] Andreas Wilke,et al. phylogenetic and functional analysis of metagenomes , 2022 .
[60] C. Anthony,et al. The Biochemistry of Methylotrophs , 1982 .
[61] J. Gilbert,et al. Metagenomes and metatranscriptomes from the L4 long-term coastal monitoring station in the Western English Channel , 2010, Standards in genomic sciences.
[62] R. Villemur,et al. Complete Genome Sequences of Methylophaga sp. Strain JAM1 and Methylophaga sp. Strain JAM7 , 2012, Journal of bacteriology.
[63] J. Neufeld,et al. Substrate-Specific Clades of Active Marine Methylotrophs Associated with a Phytoplankton Bloom in a Temperate Coastal Environment , 2008, Applied and Environmental Microbiology.
[64] U. Völker,et al. Protein-based stable isotope probing (protein-SIP) in functional metaproteomics. , 2012, Mass spectrometry reviews.