Fig. 2 in Isolation of an archaeon at the prokaryote eukaryote interface

Fig. 2 | Syntrophic amino acid utilization of MK-D1. a, Genome-based metabolic reconstruction of MK-D1.Metabolic pathways identified (coloured or black) and not identified (grey) are shown.For identified pathways,each step (solid line) or process (dotted) is marked by whether it is oxidative (red),...

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Hauptverfasser: Imachi, Hiroyuki, Nobu, Masaru K., Nakahara, Nozomi, Morono, Yuki, Ogawara, Miyuki, Takaki, Yoshihiro, Takano, Yoshinori, Uematsu, Katsuyuki, Ikuta, Tetsuro, Ito, Motoo, Matsui, Yohei, Miyazaki, Masayuki, Murata, Kazuyoshi, Saito, Yumi, Sakai, Sanae, Song, Chihong, Tasumi, Eiji, Yamanaka, Yuko, Yamaguchi, Takashi, Kamagata, Yoichi, Tamaki, Hideyuki, Takai, Ken
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Zusammenfassung:Fig. 2 | Syntrophic amino acid utilization of MK-D1. a, Genome-based metabolic reconstruction of MK-D1.Metabolic pathways identified (coloured or black) and not identified (grey) are shown.For identified pathways,each step (solid line) or process (dotted) is marked by whether it is oxidative (red), reductive (blue),ATP-yielding (orange) or ATP-consuming (purple).Wavy arrows indicate exchange of compounds:formate,H2, amino acids,vitamin B12, biotin, lipoate and thiamine pyrophosphate (TPP),which are predicted to be metabolized or synthesized by the partnering Halodesulfovibrio and/or Methanogenium. Biosynthetic pathways are indicated with a yellow background.Metatranscriptomics-detected amino-acid-catabolizing pathways are indicated (black dots above amino acids).DHDH,4,5-dihydroxy- 2,6-dioxohexanoate;DHDG,2-dehydro-3-deoxy-d-gluconate;DHDG6P, 3-dehydro-3-deoxy-d-gluconate 6-phosphate;Ac-CoA,acetyl-CoA;uro, urocanate;Fo-Glu,formyl glutamate;CH3=H4F,methylene-tetrahydrofolate; CH≡H4F,methenyl-tetrahydrofolate;Fo-H4F,formyl-tetrahydrofolate;2OB, 2-oxobutyrate;Prop-CoA,propionyl-CoA;ACAC,acetoacetate; GB-CoA, γ-amino-butyryl-CoA;But-CoA,butyryl-CoA;Fd,ferredoxin;XSH/X-S-S-X, thiol/disulfide pair; TCA,tricarboxylic acid cycle;PPP,pentose-phosphate pathway.b–e, NanoSIMS analysis of a highly purified MK-D1 culture incubated with a mixture of 13C- and 15N-labelled amino acids.b, Green fluorescent micrograph of SYBR Green I-stained cells.Aggregates are MK-D1,and filamentous cells are Methanobacterium sp. strain MO-MB1 (fluorescence can be weak owing to the high rigidity and low permeability of the cell membrane (Extended Data Fig.2m,n; see also ref.49). c, NanoSIMS ion image of 12C (cyan). d, NanoSIMS ion image of 12C15N/12C14N (magenta).e, Overlay image of b–d. d, The colour bar indicates the relative abundance of 15N expressed as 15N/14N. Scale bars 5 µm.The NanoSIMS analysis was performed without replicates due to its slow growth rate and low cell density.However,to ensure the reproducibility,we used two different types of highly purified cultures of MK-D1 (see Methods).Representative of n = 8 recorded images.The iTAG analysis of the imaged culture is shown in Supplementary Table 1.
DOI:10.5281/zenodo.3609903