Towards understanding nitrate-reducing Fe(II) oxidation in Ferrigenium straubiae: spotlight on old and new key protein candidates

Autotrophic Fe(II) oxidation is a key microbial process linking iron cycling to global carbon and nitrogen turnover in anoxic and low-oxygen environments. While Fe(II) oxidation, and electron utilization by canonical denitrification or oxygen-reducing pathways have been proposed, the whole electron transport chain via the periplasm is unknown. To address this gap, we compared the transcriptome of Ferrigenium straubiae strain KS (= KCTC 25982; = DSM 118991) cultivated under autotrophic conditions using Fe(II) as the electron donor and either nitrate or oxygen as the terminal electron acceptor. Additionally, we reanalyzed the genome using bioinformatic tools (FeGenie, MHCScan, Foldseek, AlphaFold, COFACTOR, and InterProScan) to classify known, putative, and previously uncharacterized proteins. Using these analyses, we (i) identified a form II RubisCO-mediated, sedoheptulose-7-phosphate-forming transaldolase variant of the Calvin-Benson-Bassham cycle, (ii) revealed the metabolic possibility of a reversed oxidative TCA cycle and an alternative CO2 fixation route via 10-formyl-tetrahydrofolate, (iii) found novel structural features of the proposed Fe(II) oxidases (Cyc2 and MtoA/B: {beta}-barrel outer membrane cytochromes), (iv) observed two previously unrecognized redox-complexes specifically upregulated under nitrate-reducing Fe(II)-oxidizing conditions and (v) uncovered two sphaeroides heme protein homologues and one homologue of the closely related cytochrome c. RepositoriesGenBank whole genome sequence of strain KS: JAGRPI00000000 IMG Taxon ID of strain KS: 2878407288 NCBI BioProject ID of RNA-Seq data: PRJNA1399691 Strain availability: KCTC 25982 and DSM 118991 Normalized transcripts and Log2FoldChanges (Excel file), and supplementary information are available with the online version of this article. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=111 SRC="FIGDIR/small/701106v1_ufig1.gif" ALT="Figure 1000"> View larger version (30K): org.highwire.dtl.DTLVardef@1d467bdorg.highwire.dtl.DTLVardef@1e6b270org.highwire.dtl.DTLVardef@ccdf37org.highwire.dtl.DTLVardef@52cec2_HPS_FORMAT_FIGEXP M_FIG C_FIG