Extended Data Fig. 1: Proteomic analysis of Methanothermobacter marburgensis cells under limiting conditions.

a. Change of the expression under 250 nM, 125 nM, and 50 nM Ni²⁺ concentrations. The control culture contained 5 µM Ni²⁺. Means of the proteome intensity of distinct samples (n = 3) are shown and error bars indicate standard error (SE). Membrane-associated [NiFe]-hydrogenases (Eha and Ehb). CO dehydrogenase (Cdh), 30S ribosomal protein (Rps), 50S ribosomal protein (Rpl). For other abbreviations, see Fig. 1 of the main text. The up-regulation of production of “Transporter” and “ABC transporter” suggests that these proteins could be transporters involved in Ni transport. b. In this figure, proteins that are not involved in the CO₂-reducing hydrogenotrophic methanogenic pathway but exhibited changes in protein intensity are shown. The concentration (Conc) of Ni²⁺ and Fe²⁺, the total intensity of the mass spectrometry-based proteomic analysis (Intensity) and the proteome intensity of the individual proteins are shown as a percentage of the values obtained under the standard culture condition (Control), in which the concentration of Ni²⁺ and Fe²⁺ in the control are 5 μM and 50 μM, respectively. Means of three distinct samples are shown. The specific growth rate (μ) was calculated from the dilution rate of the continuous flow rate of the cultures used for the proteomic analysis. The product of the genes up-regulated under the Ni²⁺ and Fe²⁺-limited condition might be involved in transport of the respective metal ion.

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