title: Multiphyletic origins of methylotrophy in Alphaproteobacteria, exemplified by comparative genomics of Lake Washington isolates.
abstract: We sequenced the genomes of 19 methylotrophic isolates from Lake Washington, which belong to nine genera within eight families of the Alphaproteobacteria, two of the families being the newly proposed families. Comparative genomic analysis with a focus on methylotrophy metabolism classifies these strains into heterotrophic and obligately or facultatively autotrophic methylotrophs. The most persistent metabolic modules enabling methylotrophy within this group are the N-methylglutamate pathway, the two types of methanol dehydrogenase (MxaFI and XoxF), the tetrahydromethanopterin pathway for formaldehyde oxidation, the serine cycle and the ethylmalonyl-CoA pathway. At the same time, a great potential for metabolic flexibility within this group is uncovered, with different combinations of these modules present. Phylogenetic analysis of key methylotrophy functions reveals that the serine cycle must have evolved independently in at least four lineages of Alphaproteobacteria and that all methylotrophy modules seem to be prone to lateral transfers as well as deletions.
authors: Department of Chemical Engineering, University of Washington, Seattle, WA, USA; eScience Institute, University of Washington, Seattle, WA, USA.
authors: David A C
authors: DA
authors: Beck
authors: Tami L
authors: TL
authors: McTaggart
authors: Usanisa
authors: U
authors: Setboonsarng
authors: Alexey
authors: A
authors: Vorobev
authors: Lynne
authors: L
authors: Goodwin
authors: Nicole
authors: N
authors: Shapiro
authors: Tanja
authors: T
authors: Woyke
authors: Marina G
authors: MG
authors: Kalyuzhnaya
authors: Mary E
authors: ME
authors: Lidstrom
authors: Ludmila
authors: L
authors: Chistoserdova
mesh_terms: D000214:Acyl Coenzyme A / Q000378:metabolism*; D000429:Alcohol Oxidoreductases / Q000235:genetics / Q000378:metabolism*; D020561:Alphaproteobacteria / Q000145:classification / Q000235:genetics / Q000378:metabolism*; D001483:Base Sequence; D005557:Formaldehyde / Q000378:metabolism; D023281:Genomics; D019015:Geologic Sediments / Q000382:microbiology; D005971:Glutamates / Q000378:metabolism*; D060106:Lakes / Q000382:microbiology*; D008780:Methyltransferases / Q000378:metabolism; D010802:Phylogeny; D017422:Sequence Analysis, DNA; D012694:Serine / Q000378:metabolism*; D014861:Washington
chemical_list: D000214:Acyl Coenzyme A; D005971:Glutamates; C476559:N-methylglutamate; C102829:ethylmalonyl-coenzyme A; D005557:Formaldehyde; D012694:Serine; D000429:Alcohol Oxidoreductases; C019641:alcohol dehydrogenase (acceptor); D008780:Methyltransferases; C048755:tetrahydromethanopterin S-methyltransferase