Increased mutation rates and diversity are dominant features of Geobacter multiheme cytochromes

Abstract

Multi-heme cytochromes are the central catalysts of extracellular electron transfer and are uniquely abundant in the genomes of model organisms like Geobacter sulfurreducens. While specific functions for some multiheme cytochromes are known, the complex repertoire present in any genome makes annotation and prediction of electron transfer circuitry challenging. Here we examine patterns of conservation and rates of evolutionary change among Geobacter cytochromes that help explain these difficulties. Using the Ppc and OmcS cytochromes as test cases we find that sequence based methods of determining protein homology can be inadequate for distinguishing between cytochromes known to have differing functions. Importantly, using mutation rate analysis, we find that multi-heme cytochromes in Geobacter and Shewanella exhibit increased mutation rates, which may account for inaccurate homolog identification even between closely related organisms. Finally, an analysis of multi-heme cytochrome diversity reveals that each Geobacter genome contains a high proportion of cytochromes that are unique to that individual species, suggesting a high rate of horizontal acquisition and gene loss. These increased mutational and genetic exchange rates will need to be properly accounted for in annotation tools before we can accurately ascribe function and catalog the complex repertoire of cytochromes essential to extracellular electron transfer. ImportanceDissimilatory metal reducing bacteria are found worldwide and encode diverse multi-heme cytochromes with properties suitable for applications in bioremediation, bioenergy, and bioelectronics. We find that multi-heme cytochromes involved in extracellular electron transfer show poor conservation, with significantly higher mutation rates than other elements of the proteome. This previously undescribed characteristic will limit the efficacy of standard methods of homolog annotation and database mining currently used to identify specific multi-heme cytochromes. Our findings also suggest a vast pool of undiscovered multi-heme cytochromes exists that is constantly being acquired or exchanged.