Ludmila Chistoserdova

Summary

Affiliation: University of Washington
Country: USA

Publications

  1. pmc Methylotrophy in Methylobacterium extorquens AM1 from a genomic point of view
    Ludmila Chistoserdova
    Department of Chemical Engineering, University of Washington, Seattle, Washington 98195 2125, USA
    J Bacteriol 185:2980-7. 2003
  2. ncbi request reprint Functional metagenomics: recent advances and future challenges
    Ludmila Chistoserdovai
    Department of Chemical Engineering, University of Washington, Seattle WA 98195, USA
    Biotechnol Genet Eng Rev 26:335-52. 2010
  3. pmc Novel dephosphotetrahydromethanopterin biosynthesis genes discovered via mutagenesis in Methylobacterium extorquens AM1
    Ludmila Chistoserdova
    231 Wilcox Hall, Box 352125, Department of Chemical Engineering, University of Washington, Seattle, WA 98195, USA
    J Bacteriol 187:2508-12. 2005
  4. pmc Genome of Methylobacillus flagellatus, molecular basis for obligate methylotrophy, and polyphyletic origin of methylotrophy
    Ludmila Chistoserdova
    University of Washington, Seattle, USA
    J Bacteriol 189:4020-7. 2007
  5. pmc Identification of a fourth formate dehydrogenase in Methylobacterium extorquens AM1 and confirmation of the essential role of formate oxidation in methylotrophy
    Ludmila Chistoserdova
    Department of Chemical Engineering, University of Washington, Seattle, Washington 98195, USA
    J Bacteriol 189:9076-81. 2007
  6. doi request reprint Recent progress and new challenges in metagenomics for biotechnology
    Ludmila Chistoserdova
    Department of Chemical Engineering, University of Washington, Box 355014, Seattle, WA 98195, USA
    Biotechnol Lett 32:1351-9. 2010
  7. pmc A genomic view of methane oxidation by aerobic bacteria and anaerobic archaea
    Ludmila Chistoserdova
    Department of Chemical Engineering, University of Washington, Seattle, WA 98195, USA
    Genome Biol 6:208. 2005
  8. pmc Highly divergent genes for methanopterin-linked C1 transfer reactions in Lake Washington, assessed via metagenomic analysis and mRNA detection
    Marina G Kalyuzhnaya
    231 Wilcox Hall, Box 352125, University of Washington, Seattle, WA 98195
    Appl Environ Microbiol 71:8846-54. 2005
  9. pmc Methylotrophy in a lake: from metagenomics to single-organism physiology
    Ludmila Chistoserdova
    Department of Chemical Engineering, University of Washington, Seattle, Washington 98195, USA
    Appl Environ Microbiol 77:4705-11. 2011
  10. doi request reprint Modularity of methylotrophy, revisited
    Ludmila Chistoserdova
    Department of Chemical Engineering, University of Washington, Seattle, WA 98195, USA
    Environ Microbiol 13:2603-22. 2011

Collaborators

Detail Information

Publications45

  1. pmc Methylotrophy in Methylobacterium extorquens AM1 from a genomic point of view
    Ludmila Chistoserdova
    Department of Chemical Engineering, University of Washington, Seattle, Washington 98195 2125, USA
    J Bacteriol 185:2980-7. 2003
  2. ncbi request reprint Functional metagenomics: recent advances and future challenges
    Ludmila 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...
  3. pmc Novel dephosphotetrahydromethanopterin biosynthesis genes discovered via mutagenesis in Methylobacterium extorquens AM1
    Ludmila 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...
  4. pmc Genome of Methylobacillus flagellatus, molecular basis for obligate methylotrophy, and polyphyletic origin of methylotrophy
    Ludmila 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...
  5. pmc Identification of a fourth formate dehydrogenase in Methylobacterium extorquens AM1 and confirmation of the essential role of formate oxidation in methylotrophy
    Ludmila 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...
  6. doi request reprint Recent progress and new challenges in metagenomics for biotechnology
    Ludmila Chistoserdova
    Department of Chemical Engineering, University of Washington, Box 355014, Seattle, WA 98195, USA
    Biotechnol Lett 32:1351-9. 2010
    ....
  7. pmc A genomic view of methane oxidation by aerobic bacteria and anaerobic archaea
    Ludmila 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...
  8. pmc Highly divergent genes for methanopterin-linked C1 transfer reactions in Lake Washington, assessed via metagenomic analysis and mRNA detection
    Marina 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...
  9. pmc Methylotrophy in a lake: from metagenomics to single-organism physiology
    Ludmila 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...
  10. doi request reprint Modularity of methylotrophy, revisited
    Ludmila 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...
  11. pmc Bacterial populations active in metabolism of C1 compounds in the sediment of Lake Washington, a freshwater lake
    Olivier 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...
  12. ncbi request reprint Methylotenera mobilis gen. nov., sp. nov., an obligately methylamine-utilizing bacterium within the family Methylophilaceae
    Marina 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...
  13. ncbi request reprint Methyloversatilis universalis gen. nov., sp. nov., a novel taxon within the Betaproteobacteria represented by three methylotrophic isolates
    Marina 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)...
  14. pmc Multiple formate dehydrogenase enzymes in the facultative methylotroph Methylobacterium extorquens AM1 are dispensable for growth on methanol
    Ludmila Chistoserdova
    Department of Chemical Engineering, University of Washington, Seattle, Washington 98195 2180, USA
    J Bacteriol 186:22-8. 2004
    ....
  15. doi request reprint Novel methylotrophic isolates from lake sediment, description of Methylotenera versatilis sp. nov. and emended description of the genus Methylotenera
    Marina 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...
  16. pmc An integrated proteomics/transcriptomics approach points to oxygen as the main electron sink for methanol metabolism in Methylotenera mobilis
    David 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...
  17. ncbi request reprint Methylosarcina lacus sp. nov., a methanotroph from Lake Washington, Seattle, USA, and emended description of the genus Methylosarcina
    Marina 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...
  18. doi request reprint High-resolution metagenomics targets specific functional types in complex microbial communities
    Marina 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...
  19. pmc Expressed genome of Methylobacillus flagellatus as defined through comprehensive proteomics and new insights into methylotrophy
    Erik 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...
  20. ncbi request reprint Fishing for biodiversity: novel methanopterin-linked C transfer genes deduced from the Sargasso Sea metagenome
    Marina 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...
  21. ncbi request reprint The enigmatic planctomycetes may hold a key to the origins of methanogenesis and methylotrophy
    Ludmila 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...
  22. pmc Alternative route for glyoxylate consumption during growth on two-carbon compounds by Methylobacterium extorquens AM1
    Yoko Okubo
    Department of Chemical Engineering, University of Washington, Seattle, WA 98195 2180, USA
    J Bacteriol 192:1813-23. 2010
    ....
  23. pmc Analysis of gene islands involved in methanopterin-linked C1 transfer reactions reveals new functions and provides evolutionary insights
    Marina G Kalyuzhnaya
    Department of Chemical Engineering, University of Washington, Seattle, Washington 98195, USA
    J Bacteriol 187:4607-14. 2005
    ....
  24. ncbi request reprint Development and application of polymerase chain reaction primers based on fhcD for environmental detection of methanopterin-linked C1-metabolism in bacteria
    Marina 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...
  25. pmc Fluorescence in situ hybridization-flow cytometry-cell sorting-based method for separation and enrichment of type I and type II methanotroph populations
    Marina 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...
  26. pmc Analysis of fae and fhcD genes in Mono Lake, California
    Olivier 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)...
  27. doi request reprint Real-time detection of actively metabolizing microbes by redox sensing as applied to methylotroph populations in Lake Washington
    Marina G Kalyuzhnaya
    Department of Microbiology, University of Washington, Seattle, WA 98195, USA
    ISME J 2:696-706. 2008
    ....
  28. ncbi request reprint Labrys methylaminiphilus sp. nov., a novel facultatively methylotrophic bacterium from a freshwater lake sediment
    Jonathan 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))...
  29. pmc Characterization of a novel methanol dehydrogenase in representatives of Burkholderiales: implications for environmental detection of methylotrophy and evidence for convergent evolution
    Marina 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...
  30. doi request reprint Functional metagenomics of methylotrophs
    Marina 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...
  31. doi request reprint Insights into the physiology of Methylotenera mobilis as revealed by metagenome-based shotgun proteomic analysis
    Gundula 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...
  32. doi request reprint Functioning in situ: gene expression in Methylotenera mobilis in its native environment as assessed through transcriptomics
    Marina 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...
  33. ncbi request reprint Community-level analysis: genes encoding methanopterin-dependent enzymes
    Marina G Kalyuzhnaya
    University of Washington, Seattle 98195, USA
    Methods Enzymol 397:443-54. 2005
    ....
  34. pmc Formaldehyde-detoxifying role of the tetrahydromethanopterin-linked pathway in Methylobacterium extorquens AM1
    Christopher 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...
  35. pmc Insights into Denitrification in Methylotenera mobilis from Denitrification Pathway and Methanol Metabolism Mutants
    Ildar Mustakhimov
    Departments of Chemical Engineering
    J Bacteriol 195:2207-11. 2013
    ..mobilis JLW8. Reduced levels of nitrous oxide accumulated by the XoxF mutants compared to the wild type suggest that these enzymes must be capable of donating electrons for denitrification...
  36. pmc Poly-beta-hydroxybutyrate biosynthesis in the facultative methylotroph methylobacterium extorquens AM1: identification and mutation of gap11, gap20, and phaR
    Natalia 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...
  37. pmc Identification of genes involved in the glyoxylate regeneration cycle in Methylobacterium extorquens AM1, including two new genes, meaC and meaD
    Natalia 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...
  38. pmc The expanding world of methylotrophic metabolism
    Ludmila 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...
  39. doi request reprint Methylophilaceae link methanol oxidation to denitrification in freshwater lake sediment as suggested by stable isotope probing and pure culture analysis
    Marina G Kalyuhznaya
    Departments of Microbiology, Civil and Environmental Engineering and Chemical Engineering, University of Washington, Seattle, WA 98195, USA
    Environ Microbiol Rep 1:385-92. 2009
    ..This study provides new insights into the potential involvement of Methylophilaceae in global nitrogen cycling in natural environments and highlights the connection between global carbon and nitrogen cycles...
  40. pmc A metagenomic insight into freshwater methane-utilizing communities and evidence for cooperation between the Methylococcaceae and the Methylophilaceae
    David A C Beck
    Department of Chemical Engineering and eScience Institute, University of Washington, Seattle, WA, USA
    Peerj 1:e23. 2013
    ..The relevant abundances of the Methylococcaceae and the Methylophilaceae and their coordinated response to methane and nitrate suggest that these species may be engaged in cooperative behavior, the nature of which remains unknown...
  41. pmc Multiple formaldehyde oxidation/detoxification pathways in Burkholderia fungorum LB400
    Christopher 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...
  42. ncbi request reprint Diversity of Bacteria and Archaea associated with a carbonate-rich metalliferous sediment sample from the Rainbow vent field on the Mid-Atlantic Ridge
    Olivier 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...
  43. pmc Glyoxylate regeneration pathway in the methylotroph Methylobacterium extorquens AM1
    Natalia 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...
  44. pmc Plants in the pink: cytokinin production by methylobacterium
    Mary E Lidstrom
    Department of Chemical Engineering, University of Washington, Seattle, Washington 98195 1750, USA
    J Bacteriol 184:1818. 2002
  45. pmc Genomes of three methylotrophs from a single niche reveal the genetic and metabolic divergence of the methylophilaceae
    Alla Lapidus
    DOE Joint Genome Institute, Walnut Creek, California, USA
    J Bacteriol 193:3757-64. 2011
    ....