Sequence similarity network and protein structure prediction offer insights into the evolution of microbial pathways for ferrous iron oxidation

Abstract

Dissimilatory ferrous iron [Fe(II)] oxidation is a well-established microbial energy generation strategy. This study aims to comprehensively investigate the distribution and evolution of recognized Fe(II) oxidation pathways through comparative analysis. Interestingly, we have discovered a wide range of taxonomic groups that harbor homologs to known Fe(II) oxidation proteins. The presence of these homologs among phylogenetically distant lineages and their frequent association with mobile genetic elements strongly suggest horizontal gene transfer events involving Fe(II) oxidation proteins, such as the rus operon of Acidithiobacillus and Cyc572 from Leptospirillum lineages belonging to classes Gammaproteobacteria and Betaproteobacteria often present at the hub positions of the protein sequence similarity networks from which homologs of other taxa are derived. In addition, RoseTTAFold predictions have provided valuable insights into the structural characteristics of previously unknown Fe(II) oxidation components. Despite having limited sequence identity, a significant number of acknowledged proteins involved in different Fe(II) oxidation pathways exhibit close structural similarities, including Cyc2 and Cyc572. Collectively, this study significantly enhances our understanding of the distribution and evolution of microbial ferrous iron oxidation pathways. IMPORTANCE Microbial Fe(II) oxidation is a crucial process that harnesses and converts the energy available in Fe, contributing significantly to global element cycling. However, there are still many aspects of this process that remain unexplored. In this study, we utilized a combination of comparative genomics, sequence similarity network analysis, and artificial intelligence-driven structure modeling methods to address the lack of structural information on Fe(II) oxidation proteins and offer a comprehensive perspective on the evolution of Fe(II) oxidation pathways. Our findings suggest that several microbial Fe(II) oxidation pathways currently known may have originated within classes Gammaproteobacteria and Betaproteobacteria .

Characterize the Growth and Metabolism of Acidithiobacillus ferrooxidans under Electroautotrophic and Chemoautotrophic Conditions

“…We looked up genes known to be involved in Fe 2+ oxidation [ 15 , 16 , 56 ] in the set of DEGs. Interestingly, the genes that are essential for chemoautotrophic electron transfer are down-regulated in electroautotrophic (Fe 2+ -free) cells ( Table 1 ).…”

“…Together with pilin proteins, porins form an electron channel [ 63 ]. By utilizing pore proteins, A. ferrooxidans establishes a direct connection between its cellular machinery and an external iron source, facilitating the transfer of extracellular electrons from the Fe 2+ substrate to subsequent components of the iron respiratory chain [ 56 ]. Up-regulation of type IV pili and porin proteins detected in our study indicated that they are critical for the phenomenon of electron consumption by electroautotrophic cells of A. ferrooxidans , as described in Section 3.3 .…”