Abstract
Cytochromes c (Cytc) are widespread electron transfer proteins and important enzymes in the global nitrogen and sulfur cycles. The distribution of Cytc in more than 300 archaeal proteomes deduced from sequence was analyzed with computational methods including pattern and similarity searches, secondary and tertiary structure prediction. Two hundred and fifty-eight predicted Cytc (with single, double, or multiple heme c attachment sites) were found in some but not all species of the Desulfurococcales, Thermoproteales, Archaeoglobales, Methanosarcinales, Halobacteriales, and in two single-cell genome sequences of the Thermoplasmatales, all of them Cren- or Euryarchaeota. Other archaeal phyla including the Thaumarchaeota are so far free of these proteins. The archaeal Cytc sequences were bundled into 54 clusters of mutual similarity, some of which were specific for Archaea while others had homologs in the Bacteria. The cytochrome c maturation system I (CCM) was the only one found. The highest number and variability of Cytc were present in those species with known or predicted metal oxidation and/or reduction capabilities. Paradoxical findings were made in the haloarchaea: several Cytc had been purified biochemically but corresponding proteins were not found in the proteomes. The results are discussed with emphasis on cell morphologies and envelopes and especially for double-membraned Archaea-like Ignicoccus hospitalis. A comparison is made with compartmentalized bacteria such as the Planctomycetes of the Anammox group with a focus on the putative localization and roles of the Cytc and other electron transport proteins.
Highlights
The chemolithotrophic, hyperthermophilic Archaeon Ignicoccus hospitalis is unusual in several aspects (Huber et al, 2012)
Prediction of Cytochromes c and their Maturation Proteins in Archaea Motif and similarity searches and homology modeling were applied to the prediction of Cytc and their distribution in Archaea. 4795 archaeal proteins (Table 1) were found to contain at least one CxxCH amino acid pattern (Table S1)
Among the 229 proteins with an N-terminal transmembrane helices (TMH) and/or signal sequence, only those were considered as Cytc candidates if they were either similar to known Cytc sequences, or if the CxxCH motif was conserved in a significant percentage of the homologs found in BLAST searches, and if the proteins were not bona fide members of other known protein families
Summary
The chemolithotrophic, hyperthermophilic Archaeon Ignicoccus hospitalis is unusual in several aspects (Huber et al, 2012). Abbreviations and explanation: IMC, intermembrane compartment; IM, inner membrane; OCM, outer cellular membrane; V, vesicles; EPS, extracellular polymeric substances; Hami, extracellular long hooked pili (Moissl et al, 2005). The outer cellular membrane (OCM) surrounds the cell and contains regularly arrayed small hydrophobic proteins (Burghardt et al, 2007; Huber et al, 2012). The IMC contains densely contrasted tubes and vesicles directly involved in the interplay between both membranes (Huber et al, 2012; Meyer et al, 2014). The OCM of I. hospitalis is not equivalent to the outer membrane of Gram-negative bacteria (Huber et al, 2012)
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