cyt c  (Proteintech)

Journal: bioRxiv

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

doi: 10.64898/2026.01.22.701106

Figure Lengend Snippet: AlphaFold computational protein models of Cyc2 of F. straubiae KS (A-F, H) and other Fe(II)-oxidizing bacteria (G). (A) Structural features of Cyc2 KS . The amino acids of the protein are colored by conservation (high conservation: dark blue; not-conserved: white). Scale bar represents 50 Å in the front layer of the image. (B) Cytochrome c domain colored by conservation. The barrel in the background is transparent, thus not colored by conservation. (C) Potential structure of Cyc2 as homotrimer. (D) The aromatic girdle, interacting with the head groups of the lipids of the membrane bilayer. (F) Potential binding surface which has less aromatic amino acids than the barrel surface shown in (D). (E) β-sheets differ in length forming a truncated cylinder/barrel. On the right (D) is the surface with long sheets displayed and, on the left, (F) the surface with the short sheets. All aromatic amino acids are shown in the structure (D-F) which is colored by hydrophobicity (hydrophobic surface: brown; hydrophilic surface: blue). (G) AlphaFold models of Cyc2 of different species showing a negatively charged surface at the tunnel entrance towards the heme c molecule. (H) negatively charged tunnel towards the heme c of Cyc2 KS . The barrels are similarly tilted as the displayed cylinder, which serves as an orientation reference in the 3D space. (G) and (H) are colored by polarity (positively charged: blue, no charge: white; negatively charged: red).

Article Snippet: We therefore compared the SHP-like proteins of F. straubiae with the three best-studied SHP/SHP-like representatives: cytochrome c ’’ of Methylophilus methylotrophus ATCC 53528 (Taxon ID: 2518645588), the SHP-like protein of Shewanella baltica OS117 (a metal oxide-reducing bacterium; Taxon ID: 651053066), and the original SHP of Rhodobacter sphaeroides 2.4.1 (Taxon ID: 8067927082).

Techniques: Bacteria, Membrane, Binding Assay

Journal: bioRxiv

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

doi: 10.64898/2026.01.22.701106

Figure Lengend Snippet: Cytochrome c rich gene neighborhood of unknown function. (A) Gene regions identical or similar to those in other bacteria identified by a clinker search using the NCBI database. The black line indicates matching gene patterns in a selection of taxa. The neighborhood was only partially present in the nitrate-reducing Fe(II)-oxidizing bacterial strains BP and AG. (B) Gene neighborhood of scaffold Ga0439409_04, 174669 bp – 185529 bp, of IMG data base. All IMG gene IDs have the format 287840XXXX; the corresponding last four digits are shown above each gene. (C) Gene product descriptions and the corresponding fold changes of normalized counts (Log2FoldChange) of transcripts is shown as colored dots. The labels follow the structure: gene name, last four numbers of IMG Gene ID. The four conditions were: autotrophic denitrifying Fe(II) oxidation at 28°C (A_denit_28°C, n=3), heterotrophic denitrification at 28°C (H_denit, n=1), autotrophic denitrifying Fe(II) oxidation at 20°C (A_denit_20°C, n=2) and autotrophic microaerophilic Fe(II) oxidation at 20°C (A_microox, n=2). F. straubiae was grown as community member of culture KS in all nitrate-containing conditions. 1 no transcript detected in H_denit. *no signal peptide was identified by SignalP 6.0, however note that cytochrome c biogenesis takes place in the periplasm, thus the cytochromes are expected to be located in the periplasm anyway.

Article Snippet: We therefore compared the SHP-like proteins of F. straubiae with the three best-studied SHP/SHP-like representatives: cytochrome c ’’ of Methylophilus methylotrophus ATCC 53528 (Taxon ID: 2518645588), the SHP-like protein of Shewanella baltica OS117 (a metal oxide-reducing bacterium; Taxon ID: 651053066), and the original SHP of Rhodobacter sphaeroides 2.4.1 (Taxon ID: 8067927082).

Techniques: Bacteria, Selection

Journal: bioRxiv

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

doi: 10.64898/2026.01.22.701106

Figure Lengend Snippet: (B) Sphaeroides heme protein (SHP) hypothetical complex with soluble diheme cytochrome c (sDHC) and either cytochrome b (CytB) or cytochrome b extended by chimera of the diheme cytochrome c . (B) The log₂ fold changes of normalized transcript count (Log2FoldChange) are shown as colored dots. The labels follow the structure: gene name, last four numbers of IMG Gene ID. All IMG Gene IDs share the prefix 287840XXXX. The four conditions were: autotrophic denitrifying Fe(II) oxidation at 28°C (A_denit_28°C, n=3), heterotrophic denitrification at 28°C (H_denit, n=1), autotrophic denitrifying Fe(II) oxidation at 20°C (A_denit_20°C, n=2) and autotrophic microaerophilic Fe(II) oxidation at 20°C (A_microox, n=2). F. straubiae was grown as community member of culture KS in all nitrate-containing conditions. Gene abbreviation in table S6.

Article Snippet: We therefore compared the SHP-like proteins of F. straubiae with the three best-studied SHP/SHP-like representatives: cytochrome c ’’ of Methylophilus methylotrophus ATCC 53528 (Taxon ID: 2518645588), the SHP-like protein of Shewanella baltica OS117 (a metal oxide-reducing bacterium; Taxon ID: 651053066), and the original SHP of Rhodobacter sphaeroides 2.4.1 (Taxon ID: 8067927082).

Techniques:

Journal: bioRxiv

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

doi: 10.64898/2026.01.22.701106

Figure Lengend Snippet: Phylogenetic tree of SHP (blue) ( Leys et al . 2000 ), cytochrome c ″ (green) ( Enguita et al . 2006 ), and SHP-like proteins identified in iron-metabolizing bacteria. The three SHP paralogs of F. straubiae (SHP1–3) are highlighted in red. SHP-like protein from Sideroxydans lithotrophicus ES-1 has been found in an iron-responsive gene cluster ( Zhou et al . 2022a ).

Article Snippet: We therefore compared the SHP-like proteins of F. straubiae with the three best-studied SHP/SHP-like representatives: cytochrome c ’’ of Methylophilus methylotrophus ATCC 53528 (Taxon ID: 2518645588), the SHP-like protein of Shewanella baltica OS117 (a metal oxide-reducing bacterium; Taxon ID: 651053066), and the original SHP of Rhodobacter sphaeroides 2.4.1 (Taxon ID: 8067927082).

Techniques: Bacteria

Journal: bioRxiv

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

doi: 10.64898/2026.01.22.701106

Figure Lengend Snippet: Sequence alignment of SHP-like proteins, with secondary structure motifs indicated based on the protein crystal structures of SHP (pdb – 1DW1) and cytochrome c ’’(pdb – 1OAE). The yellow box indicates two distinct clusters where the SHP-like protein of strain KS, BP and AG share the same genomic neighborhood.

Article Snippet: We therefore compared the SHP-like proteins of F. straubiae with the three best-studied SHP/SHP-like representatives: cytochrome c ’’ of Methylophilus methylotrophus ATCC 53528 (Taxon ID: 2518645588), the SHP-like protein of Shewanella baltica OS117 (a metal oxide-reducing bacterium; Taxon ID: 651053066), and the original SHP of Rhodobacter sphaeroides 2.4.1 (Taxon ID: 8067927082).

Techniques: Sequencing