Figure 4 link
The majority of ORFs represented in the C1 domain tree contain the C1
domain homolog either as a free cytochrome, or as one of multiple
cytochrome-type or cytochrome superfamily domains. In rare or isolated
cases, C1 homologs co-occur in ORFs with membrane or structural protein
domains (Table S1). The ORF containing the C1 homolog was annotated as a
nitric oxide reductase in several members of the Nitrospirae and one
Geobacteraceae genome (Table S1); domain analysis of these genes yielded
limited additional data, but representative sequences showed detectable
sequence similarity to Pseudomonas norC genes.
The occurrence of C1 domain homologs within predicted nitrite reductase
genes is restricted to the Chloroflexi. The majority of these
C1-containing nir genes have the cytochrome-type NirS domain;
however, a small number of Chloroflexi MAGs contain an ORF pairing the
C1 cytochrome with the copper-type NirK domain instead. This NirK ORF
also included an N-terminal cupredoxin/plastocyanin domain. As this
fusion is only apparent within a small number of MAGs, which are
identical across the length of the analyzed ORF, this may represent an
assembly artifact. However, several of the nir genes that
contained a C1 homolog and a cytochrome-type NirS (not copper-type NirK)
also contained cupredoxins or other copper-containing domains (Fig. S1).
The distinct phylogeny and taxonomic distribution of C1, as compared
with C2 and NirS domains, strongly suggest that the C1-C2-NirS domain
structure observed in Chloroflexi is the result of fusion of the C1
domain with a horizontally-acquired Proteobacterial nir gene.
Though topology and extant taxon sampling of these gene trees does not
allow us to reliably infer the donor lineage, the C2-NirS
architecture—or similar arrangements of functional domains—is
widespread among members of the Alpha-, Beta-, and Gammaproteobacteria.
Additionally, it appears that Chloroflexi may have been the source for
an independent transfer of the free C1 domain into Nitrospirae and
Nitrospinae.