Journal
JOURNAL OF GENERAL AND APPLIED MICROBIOLOGY
Volume 69, Issue 2, Pages 68-78Publisher
MICROBIOL RES FOUNDATION
DOI: 10.2323/jgam.2023.06.005
Keywords
AlphaFold2; cytochrome c fold; energy transduction; hot spring; respiratory chain; thermophiles; Thermus thermophilus; ThermusQ
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In this study, the confirmation of 19 c-type cytochromes among 27 selected genes in thermophilic microorganisms was described. The analysis of these genes using a bioinformatics approach revealed the presence of unique beta-strands in the c-type cytochrome domains of Thermus, leading to the proposal of new names for these genes.
In thermophilic microorganisms, c-type cytochrome (cyt) proteins mainly function in the respiratory chain as electron carriers. Genome analyses at the beginning of this century revealed a variety of genes harboring the heme c motif. Here, we describe the results of surveying genes with the heme c motif, CxxCH, in a genome database comprising four strains of Thermus thermophilus , including strain HB8, and the confirmation of 19 c-type cytochromes among 27 selected genes. We analyzed the 19 genes, including the expression of four, by a bioinformatics approach to elucidate their individual attributes. One of the approaches included an analysis based on the secondary structure alignment pattern between the heme c motif and the 6th ligand. The predicted structures revealed many cyt c domains with fewer beta-strands, such as mitochondrial cyt c , in addition to the beta-strand unique to Thermus inserted in cyt c domains, as in T. thermophilus cyt c552 and caa3 cyt c oxidase subunit IIc. The surveyed thermophiles harbor potential proteins with a vari-ety of cyt c folds. The gene analyses led to the devel-opment of an index for the classification of cyt c domains. Based on these results, we propose names for T. thermophilus genes harboring the cyt c fold.
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