Research Topics
| Ludmila ChistoserdovaSummaryAffiliation: University of Washington Country: USA Publications
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Detail Information
Publications
Methylotrophy in Methylobacterium extorquens AM1 from a genomic point of viewLudmila Chistoserdova
Department of Chemical Engineering, University of Washington, Seattle, Washington 98195-2125, USA
J Bacteriol 185:2980-7. 2003
Functional metagenomics: recent advances and future challengesLudmila Chistoserdovai
Department of Chemical Engineering, University of Washington, Seattle WA 98195, USA
Biotechnol Genet Eng Rev 26:335-52. 2010..At this time the sequencing effort will be taken to a new level to allow addressing new, previously unattainable biological questions as well as accelerating genome-based discovery for medical and biotechnological applications...- Novel dephosphotetrahydromethanopterin biosynthesis genes discovered via mutagenesis in Methylobacterium extorquens AM1Ludmila Chistoserdova
231 Wilcox Hall, Box 352125, Department of Chemical Engineering, University of Washington, Seattle, WA 98195, USA
J Bacteriol 187:2508-12. 2005..extorquens AM1 were analyzed for the ability to synthesize dH(4)MPT, and six were found to be dH(4)MPT negative. Putative functions of these genes in dH(4)MPT biosynthesis are discussed... - Genome of Methylobacillus flagellatus, molecular basis for obligate methylotrophy, and polyphyletic origin of methylotrophyLudmila Chistoserdova
University of Washington, Seattle, USA
J Bacteriol 189:4020-7. 2007..capsulatus and M. extorquens than to the ones in the more closely related M. petroleiphilum species, providing the first genomic evidence for the polyphyletic origin of methylotrophy in Betaproteobacteria... - Identification of a fourth formate dehydrogenase in Methylobacterium extorquens AM1 and confirmation of the essential role of formate oxidation in methylotrophyLudmila Chistoserdova
Department of Chemical Engineering, University of Washington, Seattle, Washington 98195, USA
J Bacteriol 189:9076-81. 2007..Mutation of a small open reading frame (fdh4B) downstream of fdh4A resulted in mutant phenotypes similar to the phenotypes of fdh4A mutants, suggesting that fdh4B is also involved in formate oxidation... 
A genomic view of methane oxidation by aerobic bacteria and anaerobic archaeaLudmila Chistoserdova
Department of Chemical Engineering, University of Washington, Seattle, WA 98195, USA
Genome Biol 6:208. 2005..In parallel, environmental genomics has provided glimpses into anaerobic methane oxidation by certain archaea, further supporting the hypothesis of reverse methanogenesis...
Recent progress and new challenges in metagenomics for biotechnologyLudmila Chistoserdova
Department of Chemical Engineering, University of Washington, Box 355014, Seattle, WA 98195, USA
Biotechnol Lett 32:1351-9. 2010....- Highly divergent genes for methanopterin-linked C1 transfer reactions in Lake Washington, assessed via metagenomic analysis and mRNA detectionMarina G Kalyuzhnaya
231 Wilcox Hall, Box 352125, University of Washington, Seattle, WA 98195
Appl Environ Microbiol 71:8846-54. 2005..We also demonstrate, via specific mRNA detection, that these divergent genes are expressed in the environment, pointing toward their potential role in local carbon cycling... - Methylotrophy in a lake: from metagenomics to single-organism physiologyLudmila Chistoserdova
Department of Chemical Engineering, University of Washington, Seattle, Washington 98195, USA
Appl Environ Microbiol 77:4705-11. 2011..Comparative analyses of individual genomes of Methylophilaceae from Lake Washington provide insights into their genomic divergence and suggest significant metabolic flexibility... - Modularity of methylotrophy, revisitedLudmila Chistoserdova
Department of Chemical Engineering, University of Washington, Seattle, WA 98195, USA
Environ Microbiol 13:2603-22. 2011..This review integrates the new findings with the previously developed concept of modularity of methylotrophy... - Methylotenera mobilis gen. nov., sp. nov., an obligately methylamine-utilizing bacterium within the family MethylophilaceaeMarina G Kalyuzhnaya
Department of Chemical Engineering, University of Washington, Seattle, WA 98195, USA
Int J Syst Evol Microbiol 56:2819-23. 2006..Strain JLW8(T) (=ATCC BAA-1282(T)=DSM 17540(T)) is proposed as the type strain of a novel species in a new genus within the family Methylophilaceae, Methylotenera mobilis gen. nov., sp. nov... - Bacterial populations active in metabolism of C1 compounds in the sediment of Lake Washington, a freshwater lakeOlivier Nercessian
Department of Chemical Engineering, University of Washington, Seattle, WA 98195, USA
Appl Environ Microbiol 71:6885-99. 2005..Overall, these data point toward the presence of a diverse population of active methylotrophs in Lake Washington sediments and toward the existence of yet-uncultivated organisms... - Methyloversatilis universalis gen. nov., sp. nov., a novel taxon within the Betaproteobacteria represented by three methylotrophic isolatesMarina G Kalyuzhnaya
Department of Chemical Engineering, University of Washington, Seattle, WA 98195, USA
Int J Syst Evol Microbiol 56:2517-22. 2006..nov., is proposed within the family Rhodocyclaceae. The type strain of Methyloversatilis universalis gen. nov., sp. nov. is FAM5T (=CCUG 52030T=JCM 13912T)... - Multiple formate dehydrogenase enzymes in the facultative methylotroph Methylobacterium extorquens AM1 are dispensable for growth on methanolLudmila Chistoserdova
Department of Chemical Engineering, University of Washington, Seattle, Washington 98195-2180, USA
J Bacteriol 186:22-8. 2004.... - Novel methylotrophic isolates from lake sediment, description of Methylotenera versatilis sp. nov. and emended description of the genus MethyloteneraMarina G Kalyuzhnaya
Department of Microbiology, University of Washington, Seattle, WA, USA
Int J Syst Evol Microbiol 62:106-11. 2012..nov. is proposed; the type strain is 301(T) (=VKM B-2679(T)=JCM 17579(T)). An emended description of the genus Methylotenera is provided... - High-resolution metagenomics targets specific functional types in complex microbial communitiesMarina G Kalyuzhnaya
Department of Microbiology, University of Washington, Benjamin Hall IRB, 616 NE Northlake Place, Seattle, Washington 98105, USA
Nat Biotechnol 26:1029-34. 2008..This high-resolution, targeted metagenomics approach may be applicable to a wide variety of ecosystems... - An integrated proteomics/transcriptomics approach points to oxygen as the main electron sink for methanol metabolism in Methylotenera mobilisDavid A C Beck
Department of Chemical Engineering, University of Washington, Box 355014, Seattle, Washington 98195, USA
J Bacteriol 193:4758-65. 2011..This study identifies initial targets for future focused physiological studies, including mutant analysis, which will provide further details into this novel process... - Expressed genome of Methylobacillus flagellatus as defined through comprehensive proteomics and new insights into methylotrophyErik L Hendrickson
Department of Chemical Engineering, University of Washington, Box 355014, Seattle, WA 98195, USA
J Bacteriol 192:4859-67. 2010..Mutant analysis revealed that GndA and FDH4 are crucial for the organism's fitness, while GndB and FDH1 are auxiliary... - Fishing for biodiversity: novel methanopterin-linked C transfer genes deduced from the Sargasso Sea metagenomeMarina G Kalyuzhnaya
Department of Chemical Engineering, University of Washington, Seattle WA 98195, USA
Environ Microbiol 7:1909-16. 2005..These data imply a broader distribution of methanopterin-linked functions in the microbial world than has been previously known... - Methylosarcina lacus sp. nov., a methanotroph from Lake Washington, Seattle, USA, and emended description of the genus MethylosarcinaMarina G Kalyuzhnaya
Department of Chemical Engineering, University of Washington, Seattle, WA 98195, USA
Int J Syst Evol Microbiol 55:2345-50. 2005..nov. is proposed, with LW14T (=ATCC BAA-1047T=JCM 13284T) as the type strain... - The enigmatic planctomycetes may hold a key to the origins of methanogenesis and methylotrophyLudmila Chistoserdova
Departments of Chemical Engineering, University of Washington, Seattle, WA, USA
Mol Biol Evol 21:1234-41. 2004..This finding suggests a possible role for Planctomycetes in the evolution of the methane cycle on Earth... - Alternative route for glyoxylate consumption during growth on two-carbon compounds by Methylobacterium extorquens AM1Yoko Okubo
Department of Chemical Engineering, University of Washington, Seattle, WA 98195 2180, USA
J Bacteriol 192:1813-23. 2010.... - Analysis of gene islands involved in methanopterin-linked C1 transfer reactions reveals new functions and provides evolutionary insightsMarina G Kalyuzhnaya
Department of Chemical Engineering, University of Washington, Seattle, Washington 98195, USA
J Bacteriol 187:4607-14. 2005.... - Development and application of polymerase chain reaction primers based on fhcD for environmental detection of methanopterin-linked C1-metabolism in bacteriaMarina G Kalyuzhnaya
Department of Chemical Engineering, University of Washington, Seattle, WA, USA
Environ Microbiol 7:1269-74. 2005..Overall, our data suggest that C1 oxidation reactions linked to H4MPT are much more widespread in natural environments than previously thought... - Labrys methylaminiphilus sp. nov., a novel facultatively methylotrophic bacterium from a freshwater lake sedimentJonathan A Miller
Department of Microbiology, University of Washington, Seattle, 98195, USA
Int J Syst Evol Microbiol 55:1247-53. 2005..monachus is less than 3 %, justifying the placement of this isolate into a novel species of the genus Labrys. The name Labrys methylaminiphilus sp. nov. is proposed (type strain JLW10(T) = ATCC BAA-1080(T) = DSM 16812(T))... - Real-time detection of actively metabolizing microbes by redox sensing as applied to methylotroph populations in Lake WashingtonMarina G Kalyuzhnaya
Department of Microbiology, University of Washington, Seattle, WA 98195, USA
ISME J 2:696-706. 2008.... - Analysis of fae and fhcD genes in Mono Lake, CaliforniaOlivier Nercessian
Department of Chemical Engineering, University of Washington, Seattle, WA 98195, USA
Appl Environ Microbiol 71:8949-53. 2005..Low diversity for fae and fhcD was noted, in contrast to the diversity previously detected in a freshwater lake, Lake Washington (Washington)... - Fluorescence in situ hybridization-flow cytometry-cell sorting-based method for separation and enrichment of type I and type II methanotroph populationsMarina G Kalyuzhnaya
Department of Chemical Engineering, University of Washington, Seattle, WA 98195, USA
Appl Environ Microbiol 72:4293-301. 2006..We demonstrated that efficient WGA can be achieved using 10(4) or more cells separated by 16S rRNA-specific FISH/FC/FACS, while fewer cells resulted in less specific WGA... - Functional metagenomics of methylotrophsMarina G Kalyuzhnaya
Department of Microbiology, University of Washington, Seattle, Washington, USA
Methods Enzymol 495:81-98. 2011..The methodologies described in this chapter can be applied in a wide variety of ecosystems for targeting methylotrophs as well as other functional guilds of microbes... - Characterization of a novel methanol dehydrogenase in representatives of Burkholderiales: implications for environmental detection of methylotrophy and evidence for convergent evolutionMarina G Kalyuzhnaya
Department of Microbiology, University of Washington, Box 355014, Seattle, WA 98195, USA
J Bacteriol 190:3817-23. 2008..Our findings also have implications for understanding the evolution of methanol oxidation, suggesting a convergence toward the enzymatic function for methanol oxidation in MxaF and Mdh2-type proteins... - Insights into the physiology of Methylotenera mobilis as revealed by metagenome-based shotgun proteomic analysisGundula Bosch
Department of Chemical Engineering, University of Washington, Seattle, WA 98195, USA
Microbiology 155:1103-10. 2009..20 %) could be identified with high confidence (three or more peptide sequences), thus gaining insights into the physiology of this bacterium, which represents a new genus within the family Methylophilaceae... - Formaldehyde-detoxifying role of the tetrahydromethanopterin-linked pathway in Methylobacterium extorquens AM1Christopher J Marx
Department of Microbiology, University of Washington, Seattle, Washington 98195, USA
J Bacteriol 185:7160-8. 2003..These results define the role of the H(4)MPT pathway as the primary formaldehyde oxidation and detoxification pathway in M. extorquens AM1... - Community-level analysis: genes encoding methanopterin-dependent enzymesMarina G Kalyuzhnaya
University of Washington, Seattle 98195, USA
Methods Enzymol 397:443-54. 2005.... - Functioning in situ: gene expression in Methylotenera mobilis in its native environment as assessed through transcriptomicsMarina G Kalyuzhnaya
Department of Microbiology, University of Washington, Seattle, WA 98195, USA
ISME J 4:388-98. 2010..Overall, this study offers a novel approach for gaining insights into the lifestyle of individual microbes in their native environments... - Poly-beta-hydroxybutyrate biosynthesis in the facultative methylotroph methylobacterium extorquens AM1: identification and mutation of gap11, gap20, and phaRNatalia Korotkova
Department of Chemical Engineering, University of Washington, Seattle 98195-1750, USA
J Bacteriol 184:6174-81. 2002..extorquens AM1, as well as the entry metabolite for the PHB cycle. Therefore, it seems likely that PhaR acts to control acetyl-CoA flux to PHB in this methylotrophic bacterium... - Identification of genes involved in the glyoxylate regeneration cycle in Methylobacterium extorquens AM1, including two new genes, meaC and meaDNatalia Korotkova
Department of Chemical Engineering, University of Washington, Seattle, WA 98195, USA
J Bacteriol 187:1523-6. 2005..Mutants have been generated in several genes involved in the GRC, and phenotypic analysis has been carried out to clarify their role in this cycle... - The expanding world of methylotrophic metabolismLudmila Chistoserdova
Departments of Chemical Engineering, University of Washington, Seattle, Washington 98195, USA
Annu Rev Microbiol 63:477-99. 2009..We also review new directions in methylotroph ecology that improve our understanding of the role of methylotrophy in global biogeochemical processes, along with an outlook for the future challenges in the field... - Multiple formaldehyde oxidation/detoxification pathways in Burkholderia fungorum LB400Christopher J Marx
Department of Microbiology, University of Washington, Seattle, Washington 98195-2180, USA
J Bacteriol 186:2173-8. 2004..Our data suggest that all three pathways are involved in formaldehyde detoxification and are functionally redundant under the tested conditions... - Diversity of Bacteria and Archaea associated with a carbonate-rich metalliferous sediment sample from the Rainbow vent field on the Mid-Atlantic RidgeOlivier Nercessian
Laboratoire des Sciences de l Environnement Marin, UMR 6539, Centre National de la Recherche Scientifique and Université de Bretagne Occidentale, Institut Universitaire Europeen de la Mer, 29280 Plouzane, France
Environ Microbiol 7:698-714. 2005..Together with chemical and microbiological data, this suggested that hydrothermal fluids may have circulated through this sediment... - Glyoxylate regeneration pathway in the methylotroph Methylobacterium extorquens AM1Natalia Korotkova
Department of Chemical Engineering, University of Washington, Seattle, Washington 98195-1750, USA
J Bacteriol 184:1750-8. 2002..A new scheme for the pathway is proposed based on these data... - Plants in the pink: cytokinin production by methylobacteriumMary E Lidstrom
Department of Chemical Engineering, University of Washington, Seattle, Washington 98195-1750, USA
J Bacteriol 184:1818. 2002 - Genomes of three methylotrophs from a single niche reveal the genetic and metabolic divergence of the methylophilaceaeAlla Lapidus
DOE Joint Genome Institute, Walnut Creek, California, USA
J Bacteriol 193:3757-64. 2011....